bluuebunny/crossref_metadata_2025 huggingface dataset:
Broadband hydroseismograms observed by closed borehole wells in the Kamioka mine, central Japan: Response of pore pressure to seismic waves from 0.05 to 2 Hz
Authors: Kano Yasuyuki , Yanagidani Takashi
Published: March 2006

We obtained broadband hydroseismograms by monitoring the pore pressure changes of a rock mass in the Kamioka mine, using borehole wells. The wellhead was sealed to maintain an undrained condition, under which there is no flow of water through the interface between the well and the rock mass. This reduces the wellbore storage effect, which can cause a high‐frequency cutoff response for systems of conventional open wells and rock mass. Using these closed borehole wells, 16 hydroseismograms were recorded for earthquakes in a range of magnitudes of 4.5–7.9 and epicentral distances of 1.0°–71.6°. Direct P waves, SV waves converted to P, and Rayleigh phases are clearly observed on the hydroseismograms. The similarity between hydroseismograms and seismograms reveals a clear relationship between radial ground velocity and pore pressure. The relationship is expressed as a zero‐order system, which is characterized by no distortion or time lag between the input and output, and the pore pressure has no coupling with shear deformation. These results are consistent with an undrained constitutive relation of linear poroelastic theory and confirm that the relation is valid for the seismic frequency range. We determined in situ values of pore pressure sensitivity to volumetric change of the rock mass, which were then used to estimate in situ Skempton coefficients with values of 0.70–0.85.
Plankton are not passive tracers: Plankton in a turbulent environment
Authors: Currie Warren J. S. , Roff John C.
Published: March 2006

Spectral analysis was performed on a series of oceanographic transects collected using an optical plankton counter and conductivity‐temperature‐depth probe. The “physical” time series (i.e., temperature) power spectra showed a single passive scaling relationship across the entire range of sampling scales (1–8192 s) that was expected from turbulence. However, the “biological” time series possessed more than one scaling region. The Chl a fluorescence had three scaling regions, a flattened (whitened) intermediate range bound by passive regions at scales approximately <30 and >300 s. Cross‐spectral analysis indicated that the chlorophyll‐temperature spectra were similar at these scales. The zooplankton biomass had a single break in the power spectrum and was passive only at scales >300 s, the zooplankton‐temperature spectra being similar only at these scales. The zooplankton‐chlorophyll cross‐spectra were often negatively coupled at the intermediate (300–30 s) scale giving a strong indication that zooplankton grazing was affecting the phytoplankton distributions.
Secondary craters of Tycho: Size‐frequency distributions and estimated fragment size–velocity relationships
Authors: Hirata Naru , Nakamura Akiko M.
Published: March 2006

We examined the size‐frequency distribution and the spatial distribution of secondary craters around the lunar crater Tycho. Secondary crater diameters were found to range from 0.55 to 4.0 km, and their distance from Tycho to range from 130 to 370 km. The diameter and ejection velocity of the secondary‐forming fragments were also estimated from the crater size and the distance from the primary using the scaling relationships for cratering. The power law index of the size‐frequency distribution of the Tycho secondary craters ranges from 3.3 to 4.0, the same as the steep slope of the typical size‐frequency distribution for lunar craters of less than 4 km diameter. The decay index of secondary crater densities with distance from the primary craters is not constant and is small at large distances (less than 2.5 for r > 2.5R). The total number of secondaries forming ejecta fragments is more than twice larger than for other lunar primaries previously studied. These results imply that there are many small secondary craters in fields far from the primary crater. A dominant contribution of secondaries to the size‐frequency distribution of all lunar craters is thus strongly suggested. The index range of 2.6 to 3.0 for estimated fragment size distributions is not only close to other natural and experimental craters, but also to those of blocks on asteroids. The relative fragment size distributions are independent of the ejection velocity. This result is the first observational confirmation of the theoretical assumption, and agrees with a recent result from laboratory experiments.
Anisotropic texture of ice sheet surfaces
Authors: Smith Benjamin E. , Raymond Charles F. , Scambos Theodore
Published: March 2006

In this paper we analyze the magnitude and spatial organization of small‐scale surface features (the surface texture) of the Greenland and Antarctic ice sheets. The texture is revealed in shaded relief maps of digital elevation models because surface slopes emphasize short‐wavelength topography. We show that the surface slope components parallel to and perpendicular to the ice flow direction of ice sheets are both qualitatively and quantitatively different from one another. The parallel component variations are larger in magnitude than the perpendicular component variations, and features in maps of the parallel component are elongated perpendicular to the ice flow direction, while features in maps of the perpendicular component are elongated at a diagonal to the ice flow direction. These properties may be explained by a simple model of glacier dynamics in which a linearly viscous slab of ice flows over a random, isotropic, red noise bed. In this model an anisotropic surface results from an isotropic bed because the surface anisotropy derives from the anisotropic transfer of bed topography to the surface by viscous flow dynamics. The modeling results suggest that analysis of surface texture magnitude and anisotropy can be used to identify areas of sliding ice from surface topography data alone and can be used to roughly estimate sliding rates where bed topography is known.
The Relationship between Diffusion Anisotropy and Time of Onset after Stroke
Authors: Bhagat Yusuf A , Emery Derek J , Shuaib Ashfaq , Sher Faiz , Rizvi Nasir H , Akhtar Naveed , Clare Tracey L , Leatherdale Tammy , Beaulieu Christian
Published: March 2006

Diffusion anisotropy changes in stroke lesions less than 24 h after onset have been reported to be elevated, decreased, or both. To address these mixed findings, we sought to characterize temporal changes of diffusion anisotropy by analyzing anatomically distinct ischemic white matter (WM) regions at 3 time phases within the first 34 h of ischemic stroke onset in 26 stroke patients (2 to 5 h, N = 7; 7 to 14 h, N = 11; 18 to 34 h, N = 8). Mean diffusivity (Trace/3 apparent diffusion coefficient (ADC)), fractional anisotropy (FA), and T2-weighted signal intensity were measured for major and subcortical WM in lesions defined by a > 30% drop in Trace/3 ADC. Major WM tract lesions with mean decreases of ~40% in relative (r) Trace/3 ADC showed an increased rFA of 1.11 ± 0.18 ( P < 0.01) during the hyperacute phase (2 to 5h), whereas rFA declined to 0.90 ± 0.20 ( P < 0.01) and 0.88 ± 0.12 ( P < 0.01) in the acute (7 to 14 h) and subacute (18 to 34h) phases, respectively. Of those patients with lesions in major WM, 4 of 8 patients ≤ 7 h showed elevated rFA as opposed to none of the remaining 13 patients after 7 h. A greater proportion of the evaluated WM regions-of-interest (ROI) in the hyperacute phase revealed increases in rFA (60%), whereas conversely large proportions of ROIs (55% and 59%) in the acute and subacute phases showed reduced rFA. Similar anisotropy changes were noted in subcortical WM regions in the gyri.
Combined target-ion source unit for production of rare nuclides
Authors: Panteleev V. N. , Barzakh A. E. , Fedorov D. V. , Ionan A. M. , Mezilev K. A. , Moroz F. V. , Orlov S. Yu. , Volkov Yu. M. , Andrighetto A. , Lhersonneau G. , Rizzi V. , Tecchio L. B. , Dubois M. , Gaubert G. , Jardin P. , Lecesne N. , Leroy R. , Pacquet J. Y. , Saint Laurent M. G. , Villari A. C. C. , Bajeat O. , Essabaa S. , Lau C. , Menna M.
Published: March 2006

A combined target-ion source unit (ionizing target) has been developed for the on-line production of radioactive single-charged ions. The target is able to withstand temperatures of up to 2500 °C and also acts as an ion source of surface, electron-beam, and laser ionizations. Using tantalum foil as a target material, the on-line combined target-ion source unit efficiency, which is the product of the ionization and release efficiencies, has been obtained for neutron-deficient isotopes of Eu, Gd, and Yb. These nuclides were ionized by the surface ionization inside a hot tungsten target container, holding tantalum foils as a target material. The results of the combined target-ion source unit use for on-line laser resonant ionization spectroscopy investigation of neutron-deficient Gd isotopes have been also presented. For neutron-rich isotopes produced from a high-density UC target, which were ionized by the surface ionization inside the target container, the ionization efficiency values have been obtained close to 100% for Rb and Cs and 10% for In. For Ag and Sn neutron-richisotopes, the values of the electron-beam ionization efficiency in the volume of the targetcontainer, correspondingly equal to 4% and 2%, have been obtained.
Enhancement of ion current from the TRIPS source by means of different electron donors
Authors: Gammino S. , Ciavola G. , Celona L. , Torrisi L. , Mascali D. , Passarello S. , Galatà A.
Published: March 2006

A series of measurements were carried out with the TRasco Intense Proton Source (TRIPS) to determine the effectiveness of different materials as electron donors. It is well known that the use of boron nitride (BN) disks inside the plasma chamber increases the current extracted from microwave discharge ion sources, generating additional electrons. In the past, one of the two disks was replaced by a 40μm Al2O3 coating over the extraction electrode, which gave some increase of current, but after less than 200h was heavily damaged. The tests here reported concern three different options: (a) thicker Al2O3 layer (100μm) deposited over the extraction electrode; a 1-mm-thick aluminium foil over which an alumina layer is deposited, inserted in the plasma chamber; a 5-mm-thick Al2O3 tube embedded in the plasma chamber of the TRIPS source (the outer diameter of the tube being slightly smaller than the inner diameter of the chamber). The tests were carried out in the same conditions as for magnetic field topology and only rf power and gas input were variable. Special attention was paid to the proton fraction. In fact, a higher proton fraction can be considered as a signature of the higher availability of electrons in the plasma. With the thick alumina tube not only was a better current and proton fraction observed but also a lower beam ripple and better stability.
Ion source with LaB6 hollow cathode for a diagnostic neutral beam injector
Authors: Deichuli P. P. , Abdrashitov G. F. , Ivanov A. A. , Kolmogorov V. V. , Mishagin V. V. , Shul’zhenko G. I. , Stupishin N. V. , Beals D. , Granetz R.
Published: March 2006

In this article ion source capable of providing 8 A, 54 keV proton beam in maximum 3 s pulses is described. A general description of the diagnostic injector based on this ion source is also given. The ion beam is extracted and accelerated by a four-electrode multiaperture ion-optical system. In the ion source, hydrogen (deuterium) plasma is generated by an arc discharge plasma box with a hot LaB6 cathode. The plasma jet diverging from a small anode orifice enters the plasma expansion volume with a peripheral multipole magnetic field and after partial reflection from this field forms a uniform plasma emitter of 160 mm in diameter in the plasma grid plane. The plasma box operates with an arc current of 350–700 A, providing more than 75% of full energy specie in the extracted ion beam. The ion beam is subsequently neutralized in a hydrogen target with ∼50% efficiency and is focused 4 m downstream from the ion source that is provided by a spherical shape of the grids. The beam angular divergence is 0.6°. The ion source is used for plasma diagnostics at Alcator C-mod tokamak.
H
−
ion beam extraction from a transformer coupled plasma source with triode extraction system
Authors: Jeong H. S. , Kim Y. J. , Hong I. S. , Park D. H. , Hwang Y. S.
Published: March 2006

A continuous-mode H− ion source has been developed in SNU by using rf transformer coupled plasma source for long lifetime. Recently, its plasma confinement has been improved by modifying the main cusp magnet system that covers rf antenna and plasma electrode regions. The extraction system has also been upgraded to triode extraction system, where permanent magnets in dipole configuration are embedded in extraction electrode to provide additional magnetic field for filtering out fast electrons. Electrode shape, extraction hole size, and gap distance are optimized for high beam currents with low emittance by using PBGUNS code. With new configuration, H− beam currents of up to 1.67mA with 1.7kW, 13.56MHz rf power are extracted in a continuous mode. Low e∕H− ratios down to 8 are achieved by increasing total filtering field strength up to 190G.
Dynamical response of the Galileo Galilei on the ground rotor to test the equivalence principle: Theory, simulation, and experiment. I. The normal modes
Authors: Comandi G. L. , Chiofalo M. L. , Toncelli R. , Bramanti D. , Polacco E. , Nobili A. M.
Published: March 2006

Recent theoretical work suggests that violation of the equivalence principle might be revealed in a measurement of the fractional differential acceleration η between two test bodies—of different compositions, falling in the gravitational field of a source mass—if the measurement is made to the level of η≃10−13 or better. This being within the reach of ground based experiments gives them a new impetus. However, while slowly rotating torsion balances in ground laboratories are close to reaching this level, only an experiment performed in a low orbit around the Earth is likely to provide a much better accuracy. We report on the progress made with the “Galileo Galilei on the ground” (GGG) experiment, which aims to compete with torsion balances using an instrument design also capable of being converted into a much higher sensitivity space test. In the present and following articles (Part I and Part II), we demonstrate that the dynamical response of the GGG differential accelerometer set into supercritical rotation—in particular, its normal modes (Part I) and rejection of common mode effects (Part II)—can be predicted by means of a simple but effective model that embodies all the relevant physics. Analytical solutions are obtained under special limits, which provide the theoretical understanding. A simulation environment is set up, obtaining a quantitative agreement with the available experimental data on the frequencies of the normal modes and on the whirling behavior. This is a needed and reliable tool for controlling and separating perturbative effects from the expected signal, as well as for planning the optimization of the apparatus.
Aircraft instrument for simultaneous, in situ measurement of NO3 and N2O5 via pulsed cavity ring-down spectroscopy
Authors: Dubé William P. , Brown Steven S. , Osthoff Hans D. , Nunley Maya R. , Ciciora Steven J. , Paris Mark W. , McLaughlin Richard J. , Ravishankara A. R.
Published: March 2006

This article describes a cavity ring-down spectrometer (CaRDS) specifically designed and constructed for installation on the NOAA WP-3D Orion (P-3) aircraft for sensitive, rapid in situ measurement of NO3 and N2O5. While similar to our previously described CaRDS instrument, this instrument has significant improvements in the signal-to-noise ratio, the time resolution, and in overall size and weight. Additionally, the instrument utilizes a custom-built, automated filter changer that was designed and constructed to meet the requirement for removal of particulate matter in the airflow while allowing fully autonomous instrument operation. The CaRDS instrument has a laboratory detection sensitivity of 4×10−11cm−1 in absorbance or 0.1pptv (pptv denotes parts per trillion volume) of NO3 in a 1s average, although the typical detection sensitivities encountered in the field were 0.5pptv for NO3 and 1pptv for N2O5. The instrument accuracy is 25% for NO3 and 20%–40% for N2O5, limited mainly by the uncertainty in the inlet transmission. The instrument has been deployed on the P-3 aircraft as part of a major field campaign in the summer of 2004 and during several ground and tower deployments near Boulder, CO.
Structural changes of an octanethiol monolayer via hyperthermal rare-gas collisions
Authors: Fogarty Daniel P. , Kandel S. Alex
Published: March 2006

In situ scanning tunneling microscopy is used to measure the effect of hyperthermal rare-gas bombardment on octanethiol self-assembled monolayers. Close-packed monolayers remain largely unchanged, even after repeated collisions with 0.4eV argon and 1.3eV xenon atoms. In contrast, gas-surface collisions do induce structural changes in the octanethiol film near defects, domain boundaries, and disordered regions, with relatively larger changes observed for xenon-atom bombardment.
Monolithic polymer microcavity lasers with on-top evaporated dielectric mirrors
Authors: Persano Luana , Carro Pompilio Del , Mele Elisa , Cingolani Roberto , Pisignano Dario , Zavelani-Rossi Margherita , Longhi Stefano , Lanzani Guglielmo
Published: March 2006

We report on a monolithic polymeric microcavity laser with all dielectric mirrors realized by low-temperature electron-beam evaporation. The vertical heterostructure was realized by 9.5 TiOx∕SiOx pairs evaporated onto an active conjugated polymer, that was previously spincast onto the bottom distributed Bragg reflector (DBR). The cavity supports single-mode lasing at 509nm, with a linewidth of 1.8nm, and a lasing threshold of 84μJ∕cm2. We also report on the emission properties of the polymer we used, investigated by a pump-probe technique. These results show that low-temperature electron-beam evaporation is a powerful and straightforward fabrication technique for molecular-based fully integrable microcavity resonators.
Phase change random access memory cell with superlattice-like structure
Authors: Chong T. C. , Shi L. P. , Zhao R. , Tan P. K. , Li J. M. , Lee H. K. , Miao X. S. , Du A. Y. , Tung C. H.
Published: March 2006

A superlattice-like structure (SLL) incorporating two nonpromising phase change materials was applied to phase change random access memory (PCRAM) cell. A properly designed SLL structure could balance both the phase change speed and stability of a PCRAM. Moreover, SLL PCRAM cells exhibited lower programming current and fast working time of 5ns. The main reason for the excellent performances is due to the much lower thermal conductivity of the SLL material compared to that of bulk materials. The thermal conductivity of eight SLL layers cycle was found to be smaller than 30% of that of single layer material.
Conductance-voltage measurements on germanium nanocrystal memory structures and effect of gate electric field coupling
Authors: Ng T. H. , Chim W. K. , Choi W. K.
Published: March 2006

Conductance-voltage (G-V) analyses were performed on trilayer germanium (Ge) nanocrystal memory capacitor structures, consisting of a high dielectric constant (high-κ) layer (5nm thick) grown on silicon, a sputtered Ge middle layer (4nm thick), and a 20nm thick sputtered cap oxide layer (either SiO2 for moderate gate electric field coupling or HfAlOx for better electric field coupling). Comparisons of the G-V characteristics were performed with a control capacitor sample without nanocrystals. The distinctive characteristics due to nanocrystals could be separated and identified from the interface traps provided the memory structure has sufficiently high electric field coupling from the gate applied voltage, resulting in a large electric field across the tunnel dielectric layer. This work attempts to provide an explanation to the G-V characteristics under the following three conditions: (1) interface trap dominated, (2) nanocrystal dominated, and (3) a combination of effects from both interface traps and nanocrystals. A method for estimating the density of nanocrystals based on the G-V data is also described.
Polarization dependent Bragg diffraction and electro-optic switching of three-dimensional assemblies of nematic liquid crystal droplets
Authors: Fernández-Nieves A. , Link D. R. , Weitz D. A.
Published: March 2006

We report the fabrication of three-dimensional lattices of bipolar nematic liquid crystal droplets. The electro-optic properties of these materials consist of transitions between opaque, Bragg diffracting, and transparent states. These occur continuously at moderate electric (E) fields through bipolar axis rotation of the nematic droplets. An E field applied normal to the hexagonally close packed planes results in a Bragg diffraction pattern that is polarization independent. Application of in-plane fields allows switching between diffracting and transmitting states that depends on the polarization of the incident light.
Production of low-density plasma by coaxially segmented rf discharge for void-free dusty cloud in microgravity experiments
Authors: Suzukawa Wataru , Ikada Reijiro , Tanaka Yasuhiro , Iizuka Satoru
Published: March 2006

A technique is presented for producing a low density plasma by introducing a coaxially segmented parallel-plate radio-frequency discharge for void-free dusty-cloud formation. Main plasma for the dusty plasma experiment is produced in a central core part of the parallel-plate discharge, while a plasma for igniting the core plasma discharge is produced in the periphery region surrounding the core plasma. The core plasma density can be markedly decreased to reduce the ion drag force, which is important for a formation of void-free dusty cloud under microgravity.
Fabrication of genuine single-quantum-dot light-emitting diodes
Authors: Schmidt R. , Scholz U. , Vitzethum M. , Fix R. , Metzner C. , Kailuweit P. , Reuter D. , Wieck A. , Hübner M. C. , Stufler S. , Zrenner A. , Malzer S. , Döhler G. H.
Published: March 2006

We present a simple approach for the fabrication of genuine single quantum-dot light-emitting diodes. A submicron wide bottom contact stripe is formed by focused ion beam implantation doping into a GaAs buffer layer. Successive overgrowth with a thin intrinsic layer incorporating self-assembled InAs quantum dots, followed by a top contact layer of complementary doping type and standard photolithographic processing, allows for electrical cross sections in the sub-μm2 range. In devices with sufficiently low dot densities, only one single dot is expected to be electrically addressed. Both the observed current versus voltage characteristics and the evolution of the electroluminescence spectra as a function of applied voltage clearly demonstrate that this goal has been achieved.
Excitation energy transfer between tris-(8-hydroxyquinoline) aluminum and a red dye
Authors: Wu Y. , Wu H. R. , Zhou Y. C. , Zhan Y. Q. , Zhou J. , Ding X. M. , Hou X. Y.
Published: March 2006

Excitation energy transfer between tris-(8-hydroxyquinoline) aluminum (Alq3) and a red dye 4-(dicyanomethylene)-2-methyl-6-(p-dimethylaminostyryl)-4H-pyran (DCM) has been investigated by means of in situ measurements of photoluminescence (PL) of bilayer Alq3∕DCM films with various Alq3 thicknesses. It is found that exciton diffusion in Alq3 and Förster energy transfer from Alq3 to DCM are contributive to the PL spectra measured. A rate equation model based on these two processes is derived and used to fit experimental results. The Förster energy transfer radius obtained for the system is R0=3.3±0.1nm. Energy transfer in the blend system is also analyzed based on the model.
Spatiotemporal quantum manipulation of traveling light: Quantum transport
Authors: Ham B. S.
Published: March 2006

A method of quantum transport between quantum nodes using stationary lights is presented. The quantum transport of a single photon or a quantum state from one node to another is performed by a slow light phenomenon, where the transport time and path between nodes are classically determined. With both no-mirror-cavity characteristics of the stationary light and propagation velocity control of the slow light, the quantum transport has potential applications in quantum information sciences such as type-II quantum computing and quantum communications.
Near-field scanning optical microscopy with an active probe
Authors: Gan Qiaoqiang , Song Guofeng , Yang Guohua , Xu Yun , Gao Jianxia , Li Yuzhang , Cao Qing , Chen Lianghui , Lu Haiwei , Chen Zhonghao , Zeng Wei , Yan Rongjin
Published: March 2006

A near-field scanning optical microscopy (NSOM) system employing a very-small-aperture laser (VSAL) as an active probe is reported in this Letter. The VSAL in our experiment has an aperture size of 300nm×300nm and a near-field spot size of about 600nm. The resolution of the NSOM system with the VSAL can reach about 600nm, and even 400nm. Considering the high output power of the VSAL, such a NSOM system is a potentially useful tool for nanodetection, data storage, nanolithography, and nanobiology.
Analysis of protein solvent interactions in glucose dehydrogenase from the extreme halophile
Haloferax mediterranei
Authors: Britton K. Linda , Baker Patrick J. , Fisher Martin , Ruzheinikov Sergey , Gilmour D. James , Bonete María-José , Ferrer Juan , Pire Carmen , Esclapez Julia , Rice David W.
Published: March 2006

The structure of glucose dehydrogenase from the extreme halophile
Haloferax mediterranei
has been solved at 1.6-Å resolution under crystallization conditions which closely mimic the “
in vivo
” intracellular environment. The decoration of the enzyme’s surface with acidic residues is only partially neutralized by bound potassium counterions, which also appear to play a role in substrate binding. The surface shows the expected reduction in hydrophobic character, surprisingly not from changes associated with the loss of exposed hydrophobic residues but rather arising from a loss of lysines consistent with the genome wide-reduction of this residue in extreme halophiles. The structure reveals a highly ordered, multilayered solvation shell that can be seen to be organized into one dominant network covering much of the exposed surface accessible area to an extent not seen in almost any other protein structure solved. This finding is consistent with the requirement of the enzyme to form a protective shell in a dehydrating environment.
Dynamic behavior of fully solvated β2-adrenergic receptor, embedded in the membrane with bound agonist or antagonist
Authors: Spijker Peter , Vaidehi Nagarajan , Freddolino Peter L. , Hilbers Peter A. J. , Goddard William A.
Published: March 2006

Recently we predicted the 3D structure of the human β2-adrenergic receptor (β2AR) and of the binding site of several agonists and antagonists to β2AR. These predictions (MembStruk and HierDock) included no explicit water and only a few lipid molecules. Here we include explicit H
2
O and an infinite lipid bilayer membrane in molecular dynamics (MD) simulations of three systems: apo-β2AR, epinephrine-bound β2AR, and butoxamine-bound β2AR (epinephrine is an endogenous agonist, and butoxamine is a β2AR selective antagonist). The predicted structures for apo-β2AR and butoxamine-β2AR are stable in MD, but in epinephrine-β2AR, extracellular water trickles into the binding pocket to mediate hydrogen bonding between the catechol of epinephrine and Ser-204 on helix 5. The epinephrine-β2AR structure shows dynamic flexibility with small, piston-like movements of helices 3 and 6 and transient interhelical hydrogen bonding between Ser-165 on transmembrane 4 and Ser-207 on transmembrane 5. These couplings and motions may play a role in protein activation. The apo-β2AR shows less dynamic flexibility, whereas the antagonist-β2AR structure is quite rigid. This MD validation of the structure predictions for G protein-coupled receptors in explicit lipid and water suggests that these methods can be trusted for studying the mechanism of activation and the design of subtype-specific agonists and antagonists.
High-pressure polymorphism in L-cysteine: the crystal structures of L-cysteine-III and L-cysteine-IV
Authors: Moggach Stephen A. , Allan David R. , Clark Stewart J. , Gutmann Matthias J. , Parsons Simon , Pulham Colin R. , Sawyer Lindsay
Published: March 2006

The crystal structure of the orthorhombic phase of L-cysteine (hereafter L-cysteine-I) consists of chains of molecules linked via NH...O hydrogen bonds. The chains are linked into a layer by other NH...O hydrogen bonds, forming R_4^4(16) ring motifs. The layers are linked by further NH...O and disordered SH...S/SH...O interactions. The main effects of compression to 1.8 GPa are to contract voids in the middle of the R_4^4(16) rings and to reduce S...S distances from 3.8457 (10) to 3.450 (4) Å. The latter is at the lower limit for S...S distances and we suggest that strain about the S atom is responsible for the formation of a new phase of L-cysteine, L-cysteine-III, above 1.8 GPa. The phase transition is accompanied by a change in the NCCS torsion angle from ca 60 to ca −60° and small positional displacements, but with no major changes in the orientations of the molecules. The structure of L-cysteine-III contains similar R-type ring motifs to L-cysteine-I, but there are no S...S contacts within 3.6 Å. L-Cysteine-III was found to be stable to at least 4.2 GPa. On decompression to 1.7 GPa, another single-crystal to single-crystal phase transition formed another previously uncharacterized phase, L-cysteine-IV. This phase is not observed on increasing pressure. The structure consists of two crystallographically independent cysteine molecules in the same conformations as those found in L-cysteine-I and L-cysteine-III. The structure separates into zones with are alternately phase I-like and phase III-like. L-Cysteine-IV can therefore be thought of as an unusual example of an intermediate phase. Further decompression to ambient pressure generates L-cysteine-I.
Effect of pressure on the crystal structure of α-glycylglycine to 4.7 GPa; application of Hirshfeld surfaces to analyse contacts on increasing pressure
Authors: Moggach Stephen A. , Allan David R. , Parsons Simon , Sawyer Lindsay
Published: March 2006

The crystal structure of α-glycylglycine (α-GLYGLY) has been determined at room temperature at pressures between 1.4 and 4.7 GPa. The structure can be considered to consist of layers. The arrangement of molecules within each layer resembles the antiparallel β-sheet motif observed in proteins, except that in α-GLYGLY the motif is constructed through NH...O hydrogen bonds rather than covalent amide links. Compression of α-GLYGLY proceeds via the reduction in void sizes. Voids close in such a way as to decrease the distances of stabilizing interactions such as hydrogen bonds and dipolar contacts. The largest reductions in interaction distances tend to occur for those contacts which are longest at ambient pressure. These longer interactions are formed between the β-sheet-like layers, and the largest component of the strain tensor lies in the same direction. The N...O distance in one NH...O hydrogen bond measures 2.624 (9) Å at 4.7 GPa. This is very short for this kind of interaction and the crystal begins to break up above 5.4 GPa, presumably as the result of a phase transition. The changes that occur have been analysed using Hirshfeld surfaces. Changes in the appearance of these surfaces enable rapid assessment of the structural changes that occur on compression.
Modulated structure of potassium sodium strontium barium niobates (KNSBN): harmonic solution
Authors: Surmin Audrey , Fertey Pierre , Schaniel Dominik , Woike Theo
Published: March 2006

The structures of two specimens of the (K1 − y
Na
y
)2F − 2(Sr
x
Ba1 − x
)2 − F
Nb2O6 family (KNSBN) have been solved and refined (x
I = 0.6, y
I = 0.45, F
I = 1.07 and x
II = 0.72, y
II = 0.45, F
II = 1.08). The KNSBN compounds appear to be incommensurately modulated, as described in a five-dimensional superspace approach with the tetragonal P4bm (pp1/2, p − p1/2) superspace group. Their modulation wavevectors are almost independent of the composition. The description of the modulation is restricted to first-order harmonics in order to limit the number of refined parameters. The modulation mainly affects the positions of the O atoms and their displacements depend on the Sr/Ba ratio. The structural models for the two compounds are not only almost identical, but also analoguous to the structural model of the Sr
x
Ba1 − x
Nb2O6 parent compound: doping with K+ and Na+ cations has no significant influence on the incommensurate modulation, contrary to the strong dependence observed for the physical properties.
Personal view: the management of chronic hepatitis B infection
Authors: SHERMAN M.
Published: March 2006

There are two new nucleoside analogues available for the management of chronic hepatitis B, adefovir and entecavir, and several more in development. In addition, pegylated interferon has become available. Large‐scale population studies have re‐emphasized the significance of viral load in predicting a poor outcome over the longer term. These new developments have prompted a reassessment of the indications and objectives of therapy for chronic hepatitis B.

Hepatitis B virus deoxyribonucleic acid, rather than alanine aminotransferase should be the prime indication for therapy. Hepatitis B e antigen seroconversion can be achieved in 30–40% of treated patients whatever agent is used. However, it takes longer for nucleoside analogues to achieve the same seroconversion rates as interferon. In anti‐HBe‐positive disease long‐term therapy is required for most patients because the relapse rate after withdrawal of therapy is very high, irrespective of the agent used.

Viral resistance limits the use of lamivudine, and to a lesser extent adefovir. Resistance to entecavir has so far only been described in pre‐existing lamivudine resistance. Although therapy with combinations of nucleoside analogues has not been investigated to any extent, this is the only way to reduce the emergence or resistance, and studies are urgently needed.
The pseudo‐receiver domain of CikA regulates the cyanobacterial circadian input pathway
Authors: Zhang Xiaofan , Dong Guogang , Golden Susan S.
Published: March 2006

CikA (circadian input kinase) is a component of the cyanobacterial circadian clock that aids in synchronizing the endogenous oscillator with the external environment. cikA mutants of the prokaryotic circadian model organism Synechococcus elongatus PCC 7942 fail to reset the phase of the circadian rhythm of gene expression after an environmental time cue, and also exhibit reduced amplitude and shortened period of circadian oscillation. CikA has histidine protein kinase (HPK) activity that is modulated in vitro by GAF and pseudo‐receiver (PsR) domains. Here we show that the PsR domain negatively regulates HPK activity in vivo and also serves as an interaction module to dock CikA at a specific subcellular location. Phenotypes conferred by alleles that encode CikA variants showed that all domains except the featureless N‐terminus are required for CikA function. Overexpression of all alleles that encode the PsR domain, whether or not the HPK is functional, caused a dominant arrhythmic phenotype, whereas overexpressed variants that lack PsR did not. Subcellular localization of intact CikA identified a polar focus whereas a variant without PsR showed uniform distribution in the cell, consistent with a model in which PsR mediates interaction with other input pathway components.
A novel dnaC mutation that suppresses priB rep mutant phenotypes in Escherichia coli K‐12
Authors: Boonsombat Ruethairat , Yeh Su‐Ping , Milne Amy , Sandler Steven J.
Published: March 2006

The loading of a replisome in prokaryotic and eukaryotic cells at an origin of DNA replication and during replication restart is a highly ordered and regulated process. During replication restart in Escherichia coli, the PriA, PriB, PriC, DnaT and Rep proteins form multiple pathways that bind to repaired replication forks. These complexes are then recognized by DnaC as sites to load DnaB, the replicative helicase. Several dnaC mutations have been isolated that suppress phenotypes of some replication restart mutants. A new dnaC mutation (dnaC824) is reported here that efficiently suppresses priB rep mutant phenotypes. Furthermore, it is shown that dnaC824 will suppress phenotypes of priB priA300, rep priA300 and priB priC strains. Unlike other dnaC suppressors, it can only weakly suppress the absence of priA. Others have reported a different type of dnaC mutation, dnaC1331, is able to mimic priB mutant phenotypes. This is supported herein by showing that like dnaC1331, a priB mutation is synthetically lethal with a dam mutation and this can be rescued by a mutH mutation. Furthermore, priB dam lethality can also be suppressed by dnaC824. Like a priB mutation, a dnaC1331 mutation causes a priA2::kan‐like phenotype when combined with priA300. Lastly, we show that dnaC824 is dominant to wild type and that dnaC1331 is recessive to wild type. Several models are discussed for the action of these mutant dnaC proteins in replication restart.
Inhibition of dissolution within shallow water carbonate sediments: impacts of terrigenous sediment input on syn‐depositional carbonate diagenesis
Authors: PERRY CHRISTOPHER T. , TAYLOR KEVIN G.
Published: March 2006

The early diagenetic chemical dissolution of skeletal carbonates has previously been documented as taking place within bioturbated, shallow water, tropical carbonate sediments. The diagenetic reactions operating within carbonate sediments that fall under the influence of iron‐rich (terrigenous) sediment input are less clearly understood. Such inputs should modify carbonate diagenetic reactions both by minimizing bacterial sulphate reduction in favour of bacterial iron reduction, and by the reaction of any pore‐water sulphide with iron oxides, thereby minimizing sulphide oxidation and associated acidity. To test this hypothesis sediment cores were taken from sites within Discovery Bay (north Jamaica), which exhibit varying levels of Fe‐rich bauxite sediment contamination. At non‐impacted sites sediments are dominated by CaCO3 (up to 99% by weight). Pore waters from the upper few centimetres of cores show evidence for active sulphate reduction (reduced SO4/Cl− ratios) and minor CaCO3 dissolution (increased Ca2+/Cl− ratios). Petrographic observations of carbonate grains (specifically Halimeda and Amphiroa) show clear morphological evidence for dissolution throughout the sediment column. In contrast, at bauxite‐impacted sites, the sediment is composed of up to 15% non‐carbonate and contains up to 6000 μg g−1 Fe. Pore waters show no evidence for sulphate reduction, but marked levels of Fe(II), suggesting that bacterial Fe(III) reduction is active. Carbonate grains show little evidence for dissolution, often exhibiting pristine surface morphologies. Samples from the deeper sections of these cores, which pre‐date bauxite influence, commonly exhibit morphological evidence for dissolution implying that this was a significant process prior to bauxite input. Previous studies have suggested that dissolution, driven by sulphate reduction and sulphide oxidation, can account for the loss of as much as 50% of primary carbonate production in localized platform environments. The finding that chemical dissolution is minor in a terrigenous‐impacted carbonate environment, therefore, has significant implications for carbonate budgets and cycling, and the preservation of carbonate grains in such sediment systems.
The influence of an Enhanced Recovery Programme on clinical outcomes, costs and quality of life after surgery for colorectal cancer
Authors: King P. M. , Blazeby J. M. , Ewings P. , Longman R. J. , Kipling R. M. , Franks P. J. , Sheffield J. P. , Evans L. B. , Soulsby M. , Bulley S. H. , Kennedy R. H.
Published: March 2006

Objective  Optimizing peri‐operative care using an enhanced recovery programme improves short‐term outcomes following colonic resection. This study compared a prospective group of patients undergoing resection of colorectal cancer within an enhanced recovery programme, with a prospectively studied historic cohort receiving conventional care.

Patients and methods  Sixty patients underwent elective resection within an enhanced recovery programme (ERP). This incorporated pre‐operative counselling, epidural analgesia, early feeding and mobilization. Clinical outcomes were compared with 86 prospectively studied historic control patients receiving conventional care (CC). All patients completed EORTC QLQ‐C30, QLQ‐CR38 and health economics questionnaires up to three months after surgery.

Results  Baseline clinical data were similar in both groups. Postoperative hospital stay was significantly reduced in the ERP, with patients staying 49% as long as those in the CC group including convalescent hospital stay (95% CI 39% to 61%P < 0.001). There were no differences in the number of complications, readmissions or re‐operations. There were no significant differences in quality of life or health economic outcomes.

Conclusion  Patients undergoing colorectal resection within an ERP stay in hospital half as long as those receiving conventional care, with no increased morbidity, deterioration in quality of life or increased cost.
The rectal pocket syndrome after stapled mucosectomy
Authors: Pescatori M. , Spyrou M. , Cobellis L. , Bottini C. , Tessera G.
Published: March 2006

Objective  Stapled rectal mucosectomy (SM) is less painful than manual haemorrhoidectomy but may be followed by unusual complications which may require reinterventions. The aim of the present study was to report on a particular postoperative complication, the rectal pocket syndrome (RPS).

Methods  Six patients, four females and two males, five with severe proctalgia and signs of intermittent sepsis and one with faecal soiling following SM, underwent clinical examination, proctoscopy (n = 5) anal manometry and ultrasound (n = 4) revealing a painful rectal intramucosal pocket with an endoluminal orifice at the level of the suture line. Four of them underwent a reintervention.

Results  At surgery, a faecolyth was found to be entrapped in the rectal pocket with an underlying chronic abscess in four patients. The cavity was laid open and curetted in all cases. One of the females needed a fistulotomy of a low intersphincteric track after one year. In none of the others did endorectal pocketing and abscess or prostatitis recur after a mean follow up of 25 months (range 2–60 months). The male patient still had moderate postevacuation pain and prostatitis possibly via a bacterial translocation after two months. Overall, the incidence of the post mucosectomy RPS at our Units was 2.5%.

Conclusions  The RPS can occur after SM, is likely to be due to a failure of either the purse‐string or of the staples causing a suture defect leading to an intramural sinus, and may be successfully treated by a transanal lay‐open in most cases.
Development of microsatellite markers in ginkgo (Ginkgo biloba L.)
Authors: YAN X. F. , LIAN C. L. , HOGETSU T.
Published: March 2006

Ginkgo biloba L. is one of the oldest unevolved tree species on Earth. We isolated five polymorphic microsatellite loci from G. biloba using a dual‐suppression polymerase chain reaction technique. These loci provided microsatellite markers with high polymorphism ranging from three to 13 alleles per locus. The observed and expected heterozygosities ranged from 0.667 to 0.952 and from 0.640 to 0.897, respectively. The markers will contribute to research on the conservation, genetic diversity and mating patterns of G. biloba.
Isolation and characterization of five microsatellite loci in an ectomycorrhizal fungus Laccaria laccata
Authors: WADUD M. A. , LIAN C. L. , NARA K. , HOGETSU T.
Published: March 2006

Laccaria laccata is an early successional ectomycorrhizal fungus. We isolated five polymorphic microsatellite loci from L. laccata using a dual‐suppression polymerase chain reaction technique. The number of alleles per locus ranged from three to six. The observed and expected heterozygosities ranged from 0.269 to 0.462, and 0.249 to 0.775, respectively. These microsatellite markers would be valuable molecular tools for population genetic studies of L. laccata.
Free radical generation by skeletal muscle of adult and old mice: effect of contractile activity
Authors: Vasilaki A. , Mansouri A. , Van Remmen H. , Van Der Meulen J. H. , Larkin L. , Richardson A. G. , McArdle A. , Faulkner J. A. , Jackson M. J.
Published: March 2006

Oxidative modification of cellular components may contribute to tissue dysfunction during aging. In skeletal muscle, contractile activity increases the generation of reactive oxygen and nitrogen species (ROS). The question of whether contraction‐induced ROS generation is further increased in skeletal muscle of the elderly is important since this influences recommendations on their exercise participation. Three different approaches were used to examine whether aging influences contraction‐induced ROS generation. Hind limb muscles of adult and old mice underwent a 15‐min period of isometric contractions and we examined ROS generation by isolated skeletal muscle mitochondria, ROS release into the muscle extracellular fluid using microdialysis techniques, and the muscle glutathione and protein thiol contents. Resting skeletal muscle of old mice compared with adult mice showed increased ROS release from isolated mitochondria, but no changes in the extracellular levels of superoxide, nitric oxide, hydrogen peroxide, hydroxyl radical activity or muscle glutathione and protein thiol contents. Skeletal muscle mitochondria isolated from both adult and old mice after contractile activity showed significant increases in hydrogen peroxide release compared with pre‐contraction values. Contractions increased extracellular hydroxyl radical activity in adult and old mice, but had no significant effect on extracellular hydrogen peroxide or nitric oxide in either group. In adult mice only, contractile activity increased the skeletal muscle release of superoxide. A similar decrease in muscle glutathione and protein thiol contents was seen in adult and old mice following contractions. Thus, contractile activity increased skeletal muscle ROS generation in both adult and old mice with no evidence for an age‐related exacerbation of ROS generation.