bluuebunny/crossref_metadata_2025 huggingface dataset:
More water stored along major rivers during El Niño years
Authors: Bhattacharya Atreyee
Published: October 2012

El Niño–Southern Oscillation (ENSO)—the semiperiodic climate event associated with warming sea surface temperatures off the coast of Peru—not only disrupts atmospheric circulations, dramatically altering weather patterns across the globe, but also may be determining the amount of fresh water stored on continents in tropical rainforests, according to a new study. Phillips et al. used more than 7 years of satellite‐based observations of fresh water content of continents from the Gravity Recovery and Climate Experiment (GRACE) to show that between 2003 and 2010 the amount of fresh water stored on land (in terms of rainwater, river water, lake water, groundwater, and snow) between the 15°N and 15°S latitudes depends on El Niño– Southern Oscillation. The authors also found that the effect of ENSO is strongest on land areas adjacent to the Pacific Ocean. The maximum increase in the amount of stored fresh water on land was observed during El Niño years along major river valleys in the Borneo region of southeast Asia, the Amazon, the Congo, and the Yangzte and Met Cong in China.
Seismic evidence for the α‐β quartz transition beneath Taiwan from Vp/Vs tomography
Authors: Kuo‐Chen H. , Wu F. T. , Jenkins D. M. , Mechie J. , Roecker S. W. , Wang C.‐Y. , Huang B.‐S.
Published: October 2012

Knowledge of the rock types and pressure‐temperature conditions at crustal depths in an active orogeny is key to understanding the mechanism of mountain building and its associated modern deformation, erosion and earthquakes. Seismic‐wave velocities by themselves generally do not have the sensitivity to discriminate one rock type from another or to decipher the P‐T conditions at which they exist. But laboratory‐measured ratios of velocities of P to S waves (Vp/Vs) have been shown to be effective. Results of 3‐D Vp and Vp/Vs tomographic imaging based on dense seismic arrays in the highly seismic environment of Taiwan provides the first detailed Vp/Vs structures of the orogen. The sharp reduction in the observed Vp/Vs ratio in the felsic core of the mountain belts implies that theα‐β quartz transition temperature is reached at a mean depth of 24 ± 3 km. The transition temperature is estimated to be 750 ± 25°C at this depth, yielding an average thermal gradient of 30 ± 3°C/km.
Identification of structural controls in an active lava dome with high resolution DEMs: Volcán de Colima, Mexico
Authors: James M. R. , Varley N.
Published: October 2012

Monitoring the topography of active lava domes is critical for detecting changes that may trigger or influence collapse or explosive activity. Internal dome structure and conditions are more difficult to elucidate, but also play vital roles. Here, we describe the exposure (following an explosion) of significant scarps in the active dome at Volcán de Colima, Mexico, that are interpreted as evidence of brittle failure planes and a complex internal dome morphology. In the first use of automated 3D computer vision reconstruction techniques (structure‐from‐motion and multi‐view stereo, SfM‐MVS) on an active volcanic dome, we derive high resolution surface models from oblique and archive photographs taken with a consumer camera. The resulting 3D models were geo‐referenced using features identified in a web‐sourced orthoimage; no ground‐based measurements were required. In December 2010, the dome (2.14 × 106 m3) had a flat upper surface, reflecting an overall ductile emplacement regime. Between then and May 2011, a period of low explosivity was accompanied by a small volume loss (0.4 × 105 m3) and arcuate steps appeared in the dome surface, suggesting the presence of localized planes of weakness. The complex array of summit scarps was exposed following a significant explosion in June 2011, and is interpreted to be the surface expression of fault planes in the dome. The 1‐m resolution DEMs indicated that the region of greatest volume loss was not coincident with the assumed location of the conduit, and that heterogeneity within the dome may have been important during the June explosion.
THEMIS observations of unusual bow shock motion attending a transient magnetospheric event
Authors: Korotova G. I. , Sibeck D. G. , Omidi N. , Angelopoulos V.
Published: October 2012

We present a multipoint case study of solar wind and magnetospheric observations during a transient magnetospheric compression at 23:19 UT on 15 October 2008. We use high time resolution magnetic field and plasma data from the THEMIS and GOES 11/12 spacecraft to show that this transient event corresponded to an abrupt rotation in the IMF orientation, a change in the location of the foreshock, and transient outward bow shock motion. We employ results from a global hybrid code model to reconcile the observations indicating transient inward magnetopause motion with the outward bow shock motion.
Mode water ventilation and subtropical countercurrent over the North Pacific in CMIP5 simulations and future projections
Authors: Xu Lixiao , Xie Shang‐Ping , Liu Qinyu
Published: October 2012

Seventeen coupled general circulation models from the Coupled Model Intercomparison Project Phase 5 (CMIP5) are analyzed to assess the dynamics and variability of the North Pacific Subtropical Countercurrent (STCC). Consistent with observations, the STCC is anchored by mode water to the north. For the present climate, the STCC tends to be stronger in models than in observations because of too strong a low potential vorticity signature of mode water. There are significant variations in mode water simulation among models, i.e., in volume and core layer density. The northeast slanted bands of sea surface height (SSH) anomalies associated with the STCC variability are caused by variability in mode water among models and the Hawaii islands are represented in some models, where the island‐induced wind curls drive the Hawaiian Lee Countercurrent (HLCC) located to the south of STCC. Projected future changes in STCC and mode water under the Representative Concentration Pathways (RCP) 4.5 scenario are also investigated. By combining the historical and RCP 4.5 runs, an empirical orthogonal function analysis for SSH over the central subtropical gyre (160°E–140°W, 15°–30°N) is performed. The dominant mode of SSH change in 17 CMIP5 models is characterized by the weakening of the STCC because of the reduced formation of mode water. The weakened mode water is closely related to the increased stratification of the upper ocean, the latter being one of the most robust changes as climate warms. Thus the weakened STCC and mode water are common to CMIP5 future climate projections.
Density stratification in an estuary with complex geometry: Driving processes and relationship to hypoxia on monthly to inter‐annual timescales
Authors: Codiga Daniel L.
Published: October 2012

The density field in Narragansett Bay (NB), a northeast U.S. estuary with complex geometry that suffers hypoxia, is described and related to driving factors using monthly means from time series observations at 9 sites during late spring to early fall 2001–2009. Stratification (deep‐shallow density difference) is dominated by salinity and strongest (4–7 kg m−3 in late spring) near rivers in the north and east. Shallow horizontal density gradients are about 0.2 kg m−3 km−1; deep densities have minor spatial and seasonal variations. Geographic structure in density, and its inter‐annual anomalies, is weaker than expected based on the complex geometry and large size relative to the internal deformation radius. Inter‐annual variability is primarily driven by river flow and weakly influenced by winds, contrasting nearby systems (Chesapeake Bay, Long Island Sound), likely due to reduced fetch and/or unfavorable alignment with prevailing winds. Stratification response to river flow follows 2/3 power scaling despite that the theory omits important NB attributes (complex geometry, depth‐varying horizontal gradients). Contrasting other systems (Delaware Bay, San Francisco Bay), horizontal gradients are at least as responsive to river forcing as theoretical 1/3 power scaling; depth‐dependent horizontal gradients or finite basin constraint of intrusion length may be responsible. Bay‐wide inter‐annual variations in seasonal hypoxia correlate with late spring stratification, though stratification peaks in the north and east with hypoxia most severe in the north and west. Long‐term response of stratification, and thus its role in hypoxia, to climate‐driven increases in river flow and temperatures will be dominated by the former.
MESSENGER observations of Mercury's magnetic field structure
Authors: Johnson Catherine L. , Purucker Michael E. , Korth Haje , Anderson Brian J. , Winslow Reka M. , Al Asad Manar M. H. , Slavin James A. , Alexeev Igor. I. , Phillips Roger J. , Zuber Maria T. , Solomon Sean C.
Published: October 2012

We present a baseline, time‐averaged model for Mercury's magnetosphere, derived from MESSENGER Magnetometer data from 24 March to 12 December 2011, comprising the spacecraft's first three Mercury years in orbit around the innermost planet. The model, constructed under the approximation that the magnetospheric shape can be represented as a paraboloid of revolution, includes two external (magnetopause and magnetotail) current systems and an internal (dipole) field and allows for reconnection. We take advantage of the geometry of the orbital Magnetometer data to estimate all but one of the model parameters, and their ranges, directly from the observations. These parameters are then used as a priori constraints in the paraboloid magnetospheric model, and the sole remaining parameter, the dipole moment, is estimated as 190 nTRM3from a grid search. We verify that the best fit dipole moment is insensitive to changes in the other parameters within their determined ranges. The model provides an excellent first‐order fit to the MESSENGER observations, with a root‐mean‐square misfit of less than 20 nT globally. The results show that the magnetopause field strength ranges from 10% to 50% of the dipole field strength at observation locations on the dayside and at nightside latitudes north of 60°N. Globally, the residual signatures observed to date are dominated by the results of magnetospheric processes, confirming the dynamic nature of Mercury's magnetosphere.
An iterative semi‐analytical technique solving the boundary value problem of transmission through an anisotropic wedge
Authors: Valagiannopoulos Constantinos A. , Simovski Constantin R.
Published: October 2012

An iterative technique imitating the physical mechanism of transmission through an anisotropic prism is introduced, analyzed and tested. The solution is obtained by treating the boundary value problem along one boundary of the device at a time, as if the other is extended to infinite. This approximation makes the proposed method more suitable for small wedge angles. However, comprehensive numerical checks concerning the accuracy and the convergence speed of the method are performed with satisfying results. Several geometrical configurations with various constituent materials have been considered and certain conclusions for the operational features of the corresponding devices have been obtained.
On the origins of drug polypharmacology
Authors: Jalencas Xavier , Mestres Jordi
Published: October 2012

The ability of many drugs, unintended most often, to interact with multiple proteins is commonly referred to as polypharmacology. Could this be a reminiscent chemical signature of early protein evolution?
GTPase of the immune-associated nucleotide-binding protein 5 (GIMAP5) regulates calcium influx in T-lymphocytes by promoting mitochondrial calcium accumulation
Authors: Chen Xi Lin , Serrano Daniel , Mayhue Marian , Wieden Hans-Joachim , Stankova Jana , Boulay Guylain , Ilangumaran Subburaj , Ramanathan Sheela
Published: October 2012

Mature T-lymphocytes undergo spontaneous apoptosis in the biobreeding diabetes-prone strain of rats due to the loss of the functional GIMAP5 (GTPase of the immune-associated nucleotide-binding protein 5) protein. The mechanisms underlying the pro-survival function of GIMAP5 in T-cells have not yet been elucidated. We have previously shown that GIMAP5 deficiency in T-cells impairs Ca2+ entry via plasma membrane channels following exposure to thapsigargin or stimulation of the T-cell antigen receptor. In the present study we report that this reduced Ca2+ influx in GIMAP5-deficient T-cells is associated with the inability of their mitochondria to sequester Ca2+ following capacitative entry, which is required for sustained Ca2+ influx via the plasma membrane channels. Consistent with a role for GIMAP5 in regulating mitochondrial Ca2+, overexpression of GIMAP5 in HEK (human embryonic kidney)-293 cells resulted in increased Ca2+ accumulation within the mitochondria. Disruption of microtubules, but not the actin cytoskeleton, abrogated mitochondrial Ca2+ sequestration in primary rat T-cells, whereas both microtubules and actin cytoskeleton were needed for the GIMAP5-mediated increase in mitochondrial Ca2+ in HEK-293 cells. Moreover, GIMAP5 showed partial colocalization with tubulin in HEK-293 cells. On the basis of these findings, we propose that the pro-survival function of GIMAP5 in T-lymphocytes may be linked to its requirement to facilitate microtubule-dependent mitochondrial buffering of Ca2+ following capacitative entry.
Adiabatic and nonadiabatic contributions to the energy of a system subject to a time-dependent perturbation: Complete separation and physical interpretation
Authors: Mandal Anirban , Hunt Katharine L. C.
Published: October 2012

When a time-dependent perturbation acts on a quantum system that is initially in the nondegenerate ground state |0⟩ of an unperturbed Hamiltonian H0, the wave function acquires excited-state components |k⟩ with coefficients ck(t) exp(−iEkt/ℏ), where Ek denotes the energy of the unperturbed state |k⟩. It is well known that each coefficient ck(t) separates into an adiabatic term ak(t) that reflects the adjustment of the ground state to the perturbation – without actual transitions – and a nonadiabatic term bk(t) that yields the probability amplitude for a transition to the excited state. In this work, we prove that the energy at any time t also separates completely into adiabatic and nonadiabatic components, after accounting for the secular and normalization terms that appear in the solution of the time-dependent Schrödinger equation via Dirac's method of variation of constants. This result is derived explicitly through third order in the perturbation. We prove that the cross-terms between the adiabatic and nonadiabatic parts of ck(t) vanish, when the energy at time t is determined as an expectation value. The adiabatic term in the energy is identical to the total energy obtained from static perturbation theory, for a system exposed to the instantaneous perturbation λH′(t). The nonadiabatic term is a sum over excited states |k⟩ of the transition probability multiplied by the transition energy. By evaluating the probabilities of transition to the excited eigenstates |k′(t)⟩ of the instantaneous Hamiltonian H(t), we provide a physically transparent explanation of the result for E(t). To lowest order in the perturbation parameter λ, the probability of finding the system in state |k′(t)⟩ is given by λ2 |bk(t)|2. At third order, the transition probability depends on a second-order transition coefficient, derived in this work. We indicate expected differences between the results for transition probabilities obtained from this work and from Fermi's golden rule.
Electronic structure of Co-doped ZnO nanorods
Authors: Neffati Ahmed , Souissi Hajer , Kammoun Souha
Published: October 2012

The optical transmission spectra, the photoluminescence (PL), and the photoluminescence excitation (PLE) spectra of the cobalt doped zinc oxide nanorods Zn1−xCoxO (x = 0.01, 0.10) were measured by Loan et al. [J. Phys. D: Appl. Phys. 42, 065412 (2009)] in the region 1.5-4 eV. These spectra exhibit a group of ultraviolet narrow lines in the region of 3.0-3.4 eV related to the near-band-edge emission of the host ZnO materials and a group of emission lines in the red region of 1.8–1.9 eV assigned to the radiative transitions within the tetrahedral Co2+ ions in the ZnO host crystal. The group of lines in the visible region provides important information about the electronic structure of the cobalt doped zinc oxide nanorods. This work investigates a theoretical crystal-field analysis of the visible lines associated to the Co2+ ion transition occupying a Td site symmetry in ZnO host crystal. A satisfactory correlations were obtained between experimental and calculated energy levels. The electronic structure was compared with the reported for cobalt transition ion doped in ZnO nanoparticles and bulk crystals [Volbers et al., Appl. Phys. A 88, 153 (2007) and H. J. Schulz and M. Thiede, Phys. Rev. B 35, 18 (1987)]. In order to explain the existence of excitation peaks observed near the band edge of the ZnO host, an energy transfer mechanism is proposed.
Optimal filter bandwidth for pulse oximetry
Authors: Stuban Norbert , Niwayama Masatsugu
Published: October 2012

Pulse oximeters contain one or more signal filtering stages between the photodiode and microcontroller. These filters are responsible for removing the noise while retaining the useful frequency components of the signal, thus improving the signal-to-noise ratio. The corner frequencies of these filters affect not only the noise level, but also the shape of the pulse signal. Narrow filter bandwidth effectively suppresses the noise; however, at the same time, it distorts the useful signal components by decreasing the harmonic content. In this paper, we investigated the influence of the filter bandwidth on the accuracy of pulse oximeters. We used a pulse oximeter tester device to produce stable, repetitive pulse waves with digitally adjustable R ratio and heart rate. We built a pulse oximeter and attached it to the tester device. The pulse oximeter digitized the current of its photodiode directly, without any analog signal conditioning. We varied the corner frequency of the low-pass filter in the pulse oximeter in the range of 0.66–15 Hz by software. For the tester device, the R ratio was set to R = 1.00, and the R ratio deviation measured by the pulse oximeter was monitored as a function of the corner frequency of the low-pass filter. The results revealed that lowering the corner frequency of the low-pass filter did not decrease the accuracy of the oxygen level measurements. The lowest possible value of the corner frequency of the low-pass filter is the fundamental frequency of the pulse signal. We concluded that the harmonics of the pulse signal do not contribute to the accuracy of pulse oximetry. The results achieved by the pulse oximeter tester were verified by human experiments, performed on five healthy subjects. The results of the human measurements confirmed that filtering out the harmonics of the pulse signal does not degrade the accuracy of pulse oximetry.
A theoretical study of structure and thermodynamics of fluids with long-range competing interactions exhibiting pattern formation
Authors: Bomont Jean-Marc , Costa Dino
Published: October 2012

We study the structure and phase behavior of a model fluid with competing short-range attraction and long-range repulsion, constituted by hard spheres interacting by means of two opposite Kac potentials. We use, to this purpose, a thermodynamically self-consistent integral equation approach developed by one of the authors [J.-M. Bomont and J.-L. Bretonnet, J. Chem. Phys. 119, 2188 (2003)]10.1063/1.1583675, which proven accurate in predicting the properties of other competing fluids. We choose the potential parameters in such a way that, upon appropriate thermodynamic conditions, the fluid displays microphase separation terminating, at sufficiently low temperatures, with a phase transition into an ordered-pattern fluid. The propensity toward the pattern formation is indicated by long-wavelength, slowly decaying oscillations in the pair correlation function, and by the presence of a sharp peak in the structure factor S(q) at a small but finite wavevector qc. The limits of stability of the micro-separated phase are identified by a drastic, diverging-like, increase of S(qc) as the temperature drops. The behavior of S(q) in the disordered-pattern phase suggests that different morphologies of the ordered patterns should be expected, depending on the ratio between the strengths of competing interactions. The structural predictions are confirmed, at the thermodynamic level, by the change of sign observed in the “residual multi-particle entropy,” according to the one-phase ordering criterion developed by Giaquinta and Giunta [Physica A 187, 145 (1992)]10.1016/0378-4371(92)90415-M, and by the trend shown by the chemical potential. Our self-consistent approach succeeds in describing the thermodynamic regime where the phase transition occurs, whereas, as reported in the literature, other sophisticated schemes within the same theoretical framework generally fail; reasons of this outcome and putative remedies are discussed.
Influence of grain boundary properties on spall strength: Grain boundary energy and excess volume
Authors: Fensin S. J. , Valone S. M. , Cerreta E. K. , Gray G. T.
Published: October 2012

Several factors can affect the spall strength of a grain boundary, such as grain boundary structure, energy, and excess volume (EV), in addition to its interactions with dislocations. In this paper, we focus on the influence of grain boundary energy and excess volume on the spall strength of a grain boundary, in copper from molecular-dynamics simulations. Flyer plate simulations were carried out for five boundary types with different energies and excess volumes. These boundaries were chosen as model systems to represent various boundaries observed in “real” materials. Simulations indicate that there is no direct correlation between the spall strength of a boundary and either its energy and excess volume. This result suggests that average properties of grain boundaries alone are not sufficient indicators of the spall strength of a boundary and perhaps local boundary properties need to be taken into account in order to predict its spall strength for broad ranges of materials.
Two orders of magnitude increase in metal piezoresistor sensitivity through nanoscale inhomogenization
Authors: Mohanasundaram S. M. , Pratap Rudra , Ghosh Arindam
Published: October 2012

Metal-based piezoresistive sensing devices could find a much wider applicability if their sensitivity to mechanical strain could be substantially improved. Here, we report a simple method to enhance the strain sensitivity of metal films by over two orders of magnitude and demonstrate it on specially designed microcantilevers. By locally inhomogenizing thin gold films using controlled electromigration, we have achieved a logarithmic divergence in the strain sensitivity with progressive microstructural modification. The enhancement in strain sensitivity could be explained using non-universal tunneling-percolation transport. We find that the Johnson noise limited signal-to-noise ratio is an order of magnitude better than silicon piezoresistors. This method creates a robust platform for engineering low resistance, high gauge factor metallic piezoresistors that may have profound impact on micro and nanoscale self-sensing technology.
Fourier transform infrared absorption spectroscopy characterization of gaseous atmospheric pressure plasmas with 2 mm spatial resolution
Authors: Laroche G. , Vallade J. , Bazinette R. , van Nijnatten P. , Hernandez E. , Hernandez G. , Massines F.
Published: October 2012

This paper describes an optical setup built to record Fourier transform infrared (FTIR) absorption spectra in an atmospheric pressure plasma with a spatial resolution of 2 mm. The overall system consisted of three basic parts: (1) optical components located within the FTIR sample compartment, making it possible to define the size of the infrared beam (2 mm × 2 mm over a path length of 50 mm) imaged at the site of the plasma by (2) an optical interface positioned between the spectrometer and the plasma reactor. Once through the plasma region, (3) a retro-reflector module, located behind the plasma reactor, redirected the infrared beam coincident to the incident path up to a 45° beamsplitter to reflect the beam toward a narrow-band mercury-cadmium-telluride detector. The antireflective plasma-coating experiments performed with ammonia and silane demonstrated that it was possible to quantify 42 and 2 ppm of these species in argon, respectively. In the case of ammonia, this was approximately three times less than this gas concentration typically used in plasma coating experiments while the silane limit of quantification was 35 times lower. Moreover, 70% of the incoming infrared radiation was focused within a 2 mm width at the site of the plasma, in reasonable agreement with the expected spatial resolution. The possibility of reaching this spatial resolution thus enabled us to measure the gaseous precursor consumption as a function of their residence time in the plasma.
Microstructural and antibacterial properties of zinc-substituted cobalt ferrite nanopowders synthesized by sol-gel methods
Authors: Sanpo Noppakun , Berndt Christopher C. , Wang James
Published: October 2012

Zinc-substituted cobalt ferrite nanopowders were prepared via a sol-gel route using citric acid as a chelating agent. The influence of zinc concentration on the microstructure, crystal structure, surface wettability, surface roughness, and antibacterial property of zinc-substituted cobalt ferrite nanopowders was investigated systematically. The substitution of zinc influences slightly the microstructure, surface wettability, surface roughness, and crystal structure but strongly affects the antibacterial property of the cobalt ferrite nanopowders.
Development of shock waves in traveling-wave field-effect transistors
Authors: Narahara Koichi
Published: October 2012

We investigated shock waves that developed in a traveling-wave field-effect transistor (TWFET) and determine that waves in a TWFET are dynamically governed by the damped nonlinear hyperbolic equation, which is known to have traveling fronts and shock waves as solutions. This paper describes the conditions for shock wave formation in TWFETs and details several results of numerical and experimental investigations for validation. Two different propagation modes developed on a TWFET because of the coupling between the gate and drain lines. A shock wave is generally supported by the slower mode of the above-mentioned two modes and can reflect the faster mode waves originating ahead. Because the shock wave acts as a moving reflection wall, the carrier frequency of reflected waves increases due to the Doppler effect. This mechanism leads to an effective method of frequency conversion.
Thrust performance of a flexible low-aspect-ratio pitching plate
Authors: Dai Hu , Luo Haoxiang , de Sousa Paulo J. S. A. Ferreira , Doyle James F.
Published: October 2012

We numerically investigate the hydrodynamic performance of an elastic plate of aspect ratio 0.54 and mass ratio 0.1 that pitches around its leading edge in a free stream at Reynolds number 640. It is found that for the rigid plate and the flexible plate with the first-mode deformation, the thrust coefficient nearly collapses onto the same curve when plotted against the Strouhal number that is defined using the tail excursion. Exceptions are found when the plate is overly flexible and higher deformation modes take place. On the other hand, the flexible plate has significantly higher power efficiency than the rigid plate at the same Strouhal number. Like the rigid plate, wake transition is observed for the flexible plate as the Strouhal number is varied. Specifically, at low Strouhal numbers (St < 0.28) the wake consists of a chain of interlocked horseshoe-shape vortices; at high Strouhal numbers (St > 0.28), the wake turns into two trains of closed vortex rings with hairpin legs.
Magnetically insulated theory with both electron and ion flows
Authors: Wang Huihui , Meng Lin , Liu Dagang , Liu Laqun , Yang Chao
Published: October 2012

Both the ion emission from anode surface and the electron emission from cathode surface may occur in the magnetically insulated transmission line (MITL) with a very high pulsed power and a very large current density. A model for the MITL with both electron and ion flow is developed. In this model, physical quantities (such as space-charge sheath thicknesses and flow currents) in the MITL are theoretically analyzed, and the specific expression for the voltage on the line by the terms of currents is derived. Furthermore, particle-in-cell simulations are carried out to verify the theoretical results.
Average atom transport properties for pure and mixed species in the hot and warm dense matter regimes
Authors: Starrett C. E. , Clérouin J. , Recoules V. , Kress J. D. , Collins L. A. , Hanson D. E.
Published: October 2012

The Kubo-Greenwood formulation for calculation of optical conductivities with an average atom model is extended to calculate thermal conductivities. The method is applied to species and conditions of interest for inertial confinement fusion. For the mixed species studied, the partial pressure mixing rule is used. Results including pressures, dc, and thermal conductivities are compared to ab initio calculations. Agreement for pressures is good, for both the pure and mixed species. For conductivities, it is found that the ad hoc renormalization method with line broadening, described in the text, gives best agreement with the ab initio results. However, some disagreement is found and the possible reasons for this are discussed.
Topological phase transition and unexpected mass acquisition of Dirac fermion in TlBi(S1−xSex)2
Authors: Niu Chengwang , Dai Ying , Zhu Yingtao , Lu Jibao , Ma Yandong , Huang Baibiao
Published: October 2012

Based on first-principles calculations and effective Hamiltonian analysis, we predict a topological phase transition from normal to topological insulators and the opening of a gap without breaking the time-reversal symmetry in TlBi(S1−xSex)2. The transition can be driven by modulating the Se concentration, and the rescaled spin-orbit coupling and lattice parameters are the key ingredients for the transition. For topological surface states, the Dirac cone evolves differently as the explicit breaking of inversion symmetry and the energy band can be opened under asymmetry surface. Our results present theoretical evidence for experimental observations [Xu et al., Science 332, 560 (2011); Sato et al., Nat. Phys. 7, 840 (2011)].
Probing for the Pharmacophore of the Cytotoxic Neoclerodane Salvileucalin B
Authors: Heinrich Nora , Banwell Martin G. , Willis Anthony C. , Cade Ian A. , Capon Robert J. , Huang Xiao-Cong
Published: October 2012

The novel [4.3.1]propelladiene 2, which embodies the key structural elements of the pentacyclic core of the cytotoxic neoclerodane salvileucalin B (1), has been prepared using a rhodium-catalysed intramolecular Büchner reaction as the key step. Compound 2 and the readily obtained derivatives 12–17 all proved to be essentially inactive when tested against a panel of four human cancer cell lines. Furthermore, not one of these compounds was a P-gp inhibitor.
Oxo-Centred Trimetallic Clusters Supported by Electron-Withdrawing Carboxylates: Highly Inert Character in Ligand Exchange Kinetics of the Dichloroacetate-Bridged Complex [Ru3(µ3-O)(µ-CHCl2COO)6(pyridine)3]
Authors: Inatomi Atsushi , Abe Masaaki , Hisaeda Yoshio
Published: October 2012

Two new oxo-centred trinuclear ruthenium clusters supported by six dichloroacetate ligands, [Ru3(μ3-O)(μ-CHCl2COO)6(CH3OH)3]CHCl2COO (1) and [Ru3(μ3-O)(μ-CHCl2COO)6(pyridine)3] (2), have been synthesised and characterised by spectroscopic methods, electrospray ionisation mass spectrometry, single-crystal X-ray diffraction, and cyclic voltammetry. Due to the strong inductive effect of the dichloroacetate ligands, the redox potential of 2 was shifted to the positive side (~1.0 V or more) relative to the acetate analogue [Ru3(μ3-O)(μ-CH3COO)6(pyridine)3], and also the rate of pyridine/pyridine-d5 exchange reaction of 2 in CD3CN was retarded with the rate constant of kex298 K = 1.9 × 10–8 s–1 which is 105-fold smaller than the value for [Ru3(μ3-O)(μ-CH3COO)6(pyridine)3]. Highly positive activation parameters obtained for 2, ΔH‡ = 138 ± 7 kJ mol–1 and ΔS‡ = 71 ± 20 J K–1 mol–1, illustrate a dissociative activation pathway in which rupture of the Ru–N(pyridine) bond is involved in the rate-determining step.
Stochastic effects are important in intrahost HIV evolution even when viral loads are high
Authors: Read Elizabeth L. , Tovo-Dwyer Allison A. , Chakraborty Arup K.
Published: October 2012

Blood plasma viral loads and the time to progress to AIDS differ widely among untreated HIV-infected humans. Although people with certain HLA (HLA-I) alleles are more likely to control HIV infections without therapy, the majority of such untreated individuals exhibit high viral loads and progress to AIDS. Stochastic effects are considered unimportant for evolutionary dynamics in HIV-infected people when viral load is high or when selective forces strongly drive mutation. We describe a computational study of host–pathogen interaction demonstrating that stochastic effects can have a profound influence on disease dynamics, even in cases of high viral load and strong selective pressure. These stochastic effects are pronounced when the virus must traverse a fitness “barrier” in sequence space to escape the host’s cytotoxic T-lymphocyte (CTL) response, as often occurs when a fitness defect imposed by a CTL-driven mutation must be compensated for by other mutations. These “barrier-crossing” events are infrequent and stochastic, resulting in divergent disease outcomes in genetically identical individuals infected by the same viral strain. Our results reveal how genetic determinants of the CTL response control the probability with which an individual is able to control HIV infection indefinitely, and thus provide clues for vaccine design.
Separation of supercritical slab-fluids to form aqueous fluid and melt components in subduction zone magmatism
Authors: Kawamoto Tatsuhiko , Kanzaki Masami , Mibe Kenji , Matsukage Kyoko N. , Ono Shigeaki
Published: October 2012

Subduction-zone magmatism is triggered by the addition of H2O-rich slab-derived components: aqueous fluid, hydrous partial melts, or supercritical fluids from the subducting slab. Geochemical analyses of island arc basalts suggest two slab-derived signatures of a melt and a fluid. These two liquids unite to a supercritical fluid under pressure and temperature conditions beyond a critical endpoint. We ascertain critical endpoints between aqueous fluids and sediment or high-Mg andesite (HMA) melts located, respectively, at 83-km and 92-km depths by using an in situ observation technique. These depths are within the mantle wedge underlying volcanic fronts, which are formed 90 to 200 km above subducting slabs. These data suggest that sediment-derived supercritical fluids, which are fed to the mantle wedge from the subducting slab, react with mantle peridotite to form HMA supercritical fluids. Such HMA supercritical fluids separate into aqueous fluids and HMA melts at 92 km depth during ascent. The aqueous fluids are fluxed into the asthenospheric mantle to form arc basalts, which are locally associated with HMAs in hot subduction zones. The separated HMA melts retain their composition in limited equilibrium with the surrounding mantle. Alternatively, they equilibrate with the surrounding mantle and change the major element chemistry to basaltic composition. However, trace element signatures of sediment-derived supercritical fluids remain more in the melt-derived magma than in the fluid-induced magma, which inherits only fluid-mobile elements from the sediment-derived supercritical fluids. Separation of slab-derived supercritical fluids into melts and aqueous fluids can elucidate the two slab-derived components observed in subduction zone magma chemistry.
Ion desolvation as a mechanism for kinetic isotope fractionation in aqueous systems
Authors: Hofmann Amy E. , Bourg Ian C. , DePaolo Donald J.
Published: October 2012

Molecular dynamics simulations show that the desolvation rates of isotopes of Li
+
, K
+
, Rb
+
, Ca
2+
, Sr
2+
, and Ba
2+
may have a relatively strong dependence on the metal cation mass. This inference is based on the observation that the exchange rate constant,
k
wex
, for water molecules in the first hydration shell follows an inverse power-law mass dependence (
k
wex
∝
m
−γ
), where the coefficient γ is 0.05 ± 0.01 on average for all cations studied. Simulated water-exchange rates increase with temperature and decrease with increasing isotopic mass for each element. The magnitude of the water-exchange rate is different for simulations run using different water models [i.e., extended simple point charge (SPC/E) vs. four-site transferrable intermolecular potential (TIP4P)]; however, the value of the mass exponent γ is the same. Reaction rate theory calculations predict mass exponents consistent with those determined via molecular dynamics simulations. The simulation-derived mass dependences imply that solids precipitating from aqueous solution under kinetically controlled conditions should be enriched in the light isotopes of the metal cations relative to the solutions, consistent with measured isotopic signatures in natural materials and laboratory experiments. Desolvation effects are large enough that they may be a primary determinant of the observed isotopic fractionation during precipitation.
CDX1 confers intestinal phenotype on gastric epithelial cells via induction of stemness-associated reprogramming factors SALL4 and KLF5
Authors: Fujii Yumiko , Yoshihashi Kyoko , Suzuki Hidekazu , Tsutsumi Shuichi , Mutoh Hiroyuki , Maeda Shin , Yamagata Yukinori , Seto Yasuyuki , Aburatani Hiroyuki , Hatakeyama Masanori
Published: October 2012

Intestinal metaplasia of the stomach, a mucosal change characterized by the conversion of gastric epithelium into an intestinal phenotype, is a precancerous lesion from which intestinal-type gastric adenocarcinoma arises. Chronic infection with
Helicobacter pylori
is a major cause of gastric intestinal metaplasia, and aberrant induction by
H. pylori
of the intestine-specific caudal-related homeobox (CDX) transcription factors, CDX1 and CDX2, plays a key role in this metaplastic change. As such, a critical issue arises as to how these factors govern the cell- and tissue-type switching. In this study, we explored genes directly activated by CDX1 in gastric epithelial cells and identified stemness-associated reprogramming factors
SALL4
and
KLF5
. Indeed,
SALL4
and
KLF5
were aberrantly expressed in the CDX1
+
intestinal metaplasia of the stomach in both humans and mice. In cultured gastric epithelial cells, sustained expression of CDX1 gave rise to the induction of early intestinal-stemness markers, followed by the expression of intestinal-differentiation markers. Furthermore, the induction of these markers was suppressed by inhibiting either SALL4 or KLF5 expression, indicating that CDX1-induced SALL4 and KLF5 converted gastric epithelial cells into tissue stem-like progenitor cells, which then transdifferentiated into intestinal epithelial cells. Our study places the stemness-related reprogramming factors as critical components of CDX1-directed transcriptional circuitries that promote intestinal metaplasia. Requirement of a transit through dedifferentiated stem/progenitor-like cells, which share properties in common with cancer stem cells, may underlie predisposition of intestinal metaplasia to neoplastic transformation.
Precursor of ether phospholipids is synthesized by a flavoenzyme through covalent catalysis
Authors: Nenci Simone , Piano Valentina , Rosati Sara , Aliverti Alessandro , Pandini Vittorio , Fraaije Marco W. , Heck Albert J. R. , Edmondson Dale E. , Mattevi Andrea
Published: October 2012

The precursor of the essential ether phospholipids is synthesized by a peroxisomal enzyme that uses a flavin cofactor to catalyze a reaction that does not alter the redox state of the substrates. The enzyme crystal structure reveals a V-shaped active site with a narrow constriction in front of the prosthetic group. Mutations causing inborn ether phospholipid deficiency, a very severe genetic disease, target residues that are part of the catalytic center. Biochemical analysis using substrate and flavin analogs, absorbance spectroscopy, mutagenesis, and mass spectrometry provide compelling evidence supporting an unusual mechanism of covalent catalysis. The flavin functions as a chemical trap that promotes exchange of an acyl with an alkyl group, generating the characteristic ether bond. Structural comparisons show that the covalent versus noncovalent mechanistic distinction in flavoenzyme catalysis and evolution relies on subtle factors rather than on gross modifications of the cofactor environment.
Stay-at-home transcription factor saves axons
Authors: Leslie Mitch
Published: October 2012

Without departing for the nucleus, STAT3 stabilizes microtubules.
The discovery of natalizumab, a potent therapeutic for multiple sclerosis
Authors: Steinman Lawrence
Published: October 2012

Multiple sclerosis (MS) is the major inflammatory demyelinating disease of the central nervous system. There is strong evidence that an immune response in the brain is a critical component of the disease. In 1992, in a collaboration between academia and biotechnology, my colleagues and I showed that α4 integrin was the critical molecule involved in the homing of immune cells into the inflamed brain. Was it sheer luck that these results led to the development of a drug for MS?
Using force to visualize conformational activation of integrins
Authors: Boettiger David
Published: October 2012

The development of biophysical approaches to analyze integrin–ligand binding allows us to visualize in real time the conformational changes that shift the bond affinity between low- and high-affinity states. In this issue, Chen et al. (2012. J. Cell Biol. http://dx.doi.org/jcb.201201091) use these approaches to validate some aspects of the classical integrin regulation model; however, their data suggest that much of the regulation occurs after ligand binding rather than in preparation for ligand binding to occur.
Mass spectrometric study of discharges produced by a large-area dual-frequency–dual-antenna inductively coupled plasma source
Authors: Mishra Anurag , Kim Tae Hyung , Kim Kyong Nam , Yeom Geun Young
Published: October 2012

An energy-resolved quadrupole mass spectrometer is used to investigate the time-averaged ion energy distribution (IED) of positive ionic species in an Ar/CF4 (90%/10%) discharge produced by dual-frequency–dual-antenna, next-generation large-area inductively coupled plasma source. The operating pressure is 10 mTorr. Two radio frequencies of 2 MHz (low frequency) and 13.56 MHz (high frequency) are used to initiate and sustain the discharge. The orifice of the mass spectrometer was 100 µm in diameter and placed at 30 mm below the ICP source and 20 mm outside the discharge volume.

It is observed that both of the frequencies have significant effect on IEDs of all prominent discharge species. The evolution of IEDs with power shows that the discharge undergoes a mode transition (E to H) as the applied power is increased. At a fixed value of P
13.56 MHz (250 and 500 W), the energy spread and the energy separation between two peaks of IEDs increase illustrating enhanced E-mode. Above P
13.56 MHz = 500 W, the IEDs show opposite trends, i.e. decreasing energy spread and energy separation between two peaks, showing the strengthening of H-mode. Increasing P
13.56 MHz at a fixed value of P
2 MHz has similar effects. A comparison of IEDs sampled at a fixed total power (P
13.56 MHz + P
2 MHz) demonstrates that an IED can be tailored by changing the power ratio (P
13.56 MHz/P
2 MHz).
Living matter—nexus of physics and biology in the 21st century
Authors: Gardel Margaret L.
Published: October 2012

Cells are made up of complex assemblies of cytoskeletal proteins that facilitate force transmission from the molecular to cellular scale to regulate cell shape and force generation. The “living matter” formed by the cytoskeleton facilitates versatile and robust behaviors of cells, including their migration, adhesion, division, and morphology, that ultimately determine tissue architecture and mechanics. Elucidating the underlying physical principles of such living matter provides great opportunities in both biology and physics. For physicists, the cytoskeleton provides an exceptional toolbox to study materials far from equilibrium. For biologists, these studies will provide new understanding of how molecular-scale processes determine cell morphological changes.
An expanding role for cell biologists in drug discovery and pharmacology
Authors: Sorger Peter K. , Schoeberl Birgit
Published: October 2012

The profound challenges facing clinicians, who must prescribe drugs in the face of dramatic variability in response, and the pharmaceutical industry, which must develop new drugs despite ever-rising costs, represent opportunities for cell biologists interested in rethinking the conceptual basis of pharmacology and drug discovery. Much better understanding is required of the quantitative behaviors of networks targeted by drugs in cells, tissues, and organisms. Cell biologists interested in these topics should learn more about the basic structure of drug development campaigns and hone their quantitative and programming skills. A world of conceptual challenges and engaging industry–academic collaborations awaits, all with the promise of delivering real benefit to patients and strained healthcare systems.
Business as a Means of Foreign Policy or Politics as a Means of Production? The German Government and the Creation of Friedrich Flick’s Upper Silesian Industrial Empire (1921–1935)
Authors: Reckendrees Alfred
Published: October 2012

In the 1920s, the German government secretly supported private business activities across the German-Polish border due to revisionist political aims. Based on these aims, the (in-) famous industrialist Friedrich Flick was able to attract financial support for otherwise uneconomical activities in Upper Silesia to which the government provided “insurance.” Not even considering the possibility of moral hazard and holdup, the German government was captured in its secret cooperation with Flick, who could effectively exploit this “insurance.” Until 1931, Flick was able to gain high subsidies and to use them efficiently building up an industrial empire that comprehended the German, Polish, and Austrian iron and steel industry. The interplay of German foreign policy and private business activities in the inter-war years is analyzed as an agency problem in a specific “public-private partnership” that allowed for blackmailing the Government.