bluuebunny/crossref_metadata_2025 huggingface dataset:
Two-color pump-probe system broadly tunable over the visible and the near infrared with sub-30fs temporal resolution
Authors: Manzoni Cristian , Polli Dario , Cerullo Giulio
Published: February 2006

We describe an ultrafast spectroscopy system based on two synchronized noncollinear optical parametric amplifiers (NOPAs). Each NOPA can be independently configured to generate ultrabroadband sub-10fs visible pulses, tunable 15fs visible pulses (500–720nm), tunable 15–30fs near-infrared pulses (900–1500nm), and 15–20fs blue pulses (430–480nm). This system enables to perform pump-probe experiments over nearly two octaves of spectrum with unprecedented temporal resolution. We present application examples highlighting the capability of this instrument to track excited-state dynamics occurring on the sub-100fs time scale: electron transfer in polymer-fullerene blends, intersubband energy relaxation in carbon nanotubes, and internal conversion in carotenoids.
The water exchange process of tetraaquaplatinum(II): Density-functional theory and ab initio computational study
Authors: Sengupta Partha Sarathi
Published: February 2006

The water exchange process of square planar tetraaquaplatinum(II) was computationally investigated at the Hartree-Fock, density-functional theory (B3LYP, PW91PW91, and mPW1PW91) and the second-order Møller-Plesset perturbation theory of levels of calculation. The stationary points on the gas phase and on the reaction field potential-energy surface were fully optimized and characterized. The self-consistent reaction field (SCRF) methods were also applied on the same system. The structures and energetic processes of all the species involved were investigated. The kinetic and thermodynamic properties for the gas phase and SCRF model data were compared with the available experimental data. The rate constants in MP2 level of theory and B3LYP isodensity polarized continuum model reaction field are in good agreement with the experimental data.
Radial distribution function of freely jointed hard-sphere chains in the solid phase
Authors: Cochran T. W. , Chiew Y. C.
Published: February 2006

Monte Carlo simulation is used to generate the radial distribution function of freely jointed tangent-bonded hard-sphere chains in the disordered solid phase for chain lengths of three, four, six, and eight segments. The data are used to create an accurate analytical expression of the total radial distribution function of the hard-sphere chains that covers a density range from the solidification point up to a packing fraction of 0.71. It is envisioned that the correlation will help further progress toward molecular thermodynamic treatment of the solid phase in general and toward perturbed chain theories for the solid phase, in particular.
Classical and quantum-mechanical plane switching in CO2
Authors: Sanrey Michaël , Joyeux Marc , Sadovskii Dmitrii A.
Published: February 2006

Classical plane switching takes place in systems with a pronounced 1:2 resonance, where the degree of freedom with the lowest frequency is doubly degenerate. Under appropriate conditions, one observes a periodic and abrupt precession of the plane in which the doubly degenerate motion takes place. In this article, we show that quantum plane switching exists in CO2. Based on our analytical solutions of classical Hamilton’s equations of motion, we describe the dependence on vibrational angular momentum and energy of the frequency of switches and the plane switching angle. Using these results, we find optimal initial wave-packet conditions for CO2 and show, through quantum-mechanical propagation, that such a wave packet indeed displays plane switching at energies around 10000cm−1 above the ground state on time scales of about 100fs.
Absolute rate coefficients for the reactions of O2−+N(S3∕24) and O2−+O(P3) at 298 K in a selected-ion flow tube instrument
Authors: Poutsma John C. , Midey Anthony J. , Viggiano Albert A.
Published: February 2006

The absolute rate coefficients at 298 K for the reactions of O2−+N(S3∕24) and O2−+O(P3) have been determined in a selected-ion flow tube instrument. O atoms are generated by the quantitative titration of N atoms with NO, where the N atoms are produced by microwave discharge on N2. The experimental procedure allows for the determination of rate constants for the reaction of the reactant ion with N(S3∕24) and O(P3). The rate coefficient for O2−+N is found to be 2.3×10−10±40%cm3molecule−1s−1, a factor of 2 slower than previously determined. In addition, it was found that the reaction proceeds by two different reaction channels to give (1) NO2+e− and (2) O−+NO. The second channel was not reported in the previous study and accounts for ca. 35% of the reaction. An overall rate coefficient of 3.9×10−10cm3molecule−1s−1 was determined for O2−+O, which is slightly faster than previously reported. Branching ratios for this reaction were determined to be <55%O3+e− and >45%O−+O2.
Beam dynamics in a spectrometer for the polarized positron production experiment
Authors: Batygin Yuri K.
Published: February 2006

The proposed experiment E-166 at SLAC is designed to demonstrate the possibility of producing longitudinally polarized positrons from circularly polarized photons to be used in future linear collider. The experimental setup utilizes a low emittance 50GeV electron beam passing through a helical undulator in the final focus test beam line of the SLAC accelerator. Circularly polarized photons generated by the electron beam in the undulator hit a target and produce electron-positron pairs. The purpose of the post-target spectrometer is to select the positron beam and to deliver it to a polarimeter while keeping the positron beam polarization as high as possible. This article analyzes positron transmission and polarization in the E-166 spectrometer experiment. The positron transmission has a maximum value of 7% for a positron beam energy of 5.5MeV, while positron polarization is approximately 60%.
Demonstration of low-temperature atomic force microscope with atomic resolution using piezoresistive cantilevers
Authors: Shiraki Ichiro , Miyatake Yutaka , Nagamura Toshihiko , Miki Kazushi
Published: February 2006

Compared to current optical-lever methods adopted in atomic force microscopes, nonoptical methods such as piezoresistive methods and quartz fork methods can be more advantageous due to their smaller installation size and the lack of electromagnetic effects from laser light during electrical conductivity experiments. As a technological demonstration of nonoptical methods, a low-temperature atomic force microscope using piezoresistive cantilevers was developed and operated at liquid-He4 temperatures (5K). The cantilever and sample can be transferred from atmosphere to the microscope head operating at low temperatures. Both contact mode and noncontact mode were used for testing the system while carrying out atomic resolution studies on clean Si(111) and clean Si(100) surfaces.
Converting the nanodomains of a diblock-copolymer thin film from spheres to cylinders with an external electric field
Authors: Matsen M. W.
Published: February 2006

We investigate the ability of an applied electric field to convert the morphology of a diblock-copolymer thin film from a monolayer of spherical domains embedded in the matrix to cylindrical domains that penetrate through the matrix. As expected, the applied field increases the relative stability of cylindrical domains, while simultaneously reducing the energy barrier that impedes the transition to cylinders. The effectiveness of the field is enhanced by a large dielectric contrast between the two block-copolymer components, particularly when the low-dielectric contrast component forms the matrix. Furthermore, the energy barrier is minimized by selecting sphere-forming diblock copolymers that are as compositionally symmetric as possible. Our calculations, which are the most quantitatively reliable to date, are performed using a numerically precise spectral algorithm based on self-consistent-field theory supplemented with an exact treatment for linear dielectric materials.
Electromechanical properties of calcium bismuth titanate films: A potential candidate for lead-free thin-film piezoelectrics
Authors: Simões A. Z. , Ramírez M. A. , Ries A. , Varela J. A. , Longo E. , Ramesh R.
Published: February 2006

Ca Bi 4 Ti 4 O 15 (CBTi144) thin films were evaluated for use as lead-free thin-film piezoelectrics in microelectromechanical systems. The films were grown by the polymeric precursor method on (100)Pt∕Ti∕SiO2∕Si substrates. The a∕b-axis orientation of the ferroelectric film is considered to be associated with the preferred orientation of the Pt bottom electrode. The Pr and Ec were 14μC∕cm2 and 64kV∕cm, respectively, for a maximum applied field of 400kV∕cm. The domain structure was investigated by piezoresponse force microscopy. The film has a piezoelectric coefficient, d33, equal to 60pm∕V and a current density of 0.7mA∕cm2.
Surface enhanced Raman scattering of p-aminothiophenol self-assembled monolayers in sandwich structure fabricated on glass
Authors: Wang Yuling , Chen Hongjun , Dong Shaojun , Wang Erkang
Published: February 2006

A sandwich structure consisting of Ag nanoparticles (NPs), p-aminothiophenol (p-ATP) self-assembled monolayers (SAMs), and Ag NPs was fabricated on glass and characterized by surface enhanced Raman scattering (SERS). The SERS spectrum of a p-ATP SAM in such sandwich structure shows that the electromagnetic enhancement is greater than that on Ag NPs assembled on glass. The obtained enhancement factors (EF) on solely one sandwich structure were as large as 6.0±0.62×104 and 1.2±0.62×107 for the 7a and 3b(b2) vibration modes, respectively. The large enhancement effect of p-ATP SAMs is likely a result of plasmon coupling between the two layers of Ag NP (localized surface plasmon) resonance, creating a large localized electromagnetic field at their interface, where p-ATP resides. Moreover, the fact that large EF values (∼1.9±0.7×104 and 9.4±0.7×106 for the 7a- and b2-type vibration modes, respectively) were also obtained on a single sandwich structure of Au NPs∕p-ATPSAMs∕Ag NPs in the visible demonstrates that the electromagnetic coupling does not exist only between Ag NPs but also between Au and Ag NPs. The lower EF values on Au-to-Ag NPs compared to those on Ag-to-Ag NPs demonstrate that the Au-to-Ag coupling must be less effective than the Ag-to-Ag coupling for the induction of SERS in the visible.
Enhancing the charge ordering temperature in thin films of Pr0.5Ca0.5MnO3 by strain
Authors: Yang Z. Q. , Zhang Y. Q. , Aarts J. , Wu M.-Y. , Zandbergen H. W.
Published: February 2006

We report the effects of biaxial strain on the charge ordering temperature Tco of the mixed-valent manganite perovskite oxide Pr0.5Ca0.5MnO3. Thin films were grown on SrTiO3, which has a 1.3% larger in-plane lattice parameter. Other substrates were used for comparison. Transport measurements combined with data from electron microscopy show that Tco is considerably enhanced. At thicknesses of the order of 10nm, where the films are fully strained, Tco is above 320K, more than 70K above the bulk value of 250K, while around 50nm, where relaxation has set in, the enhancement is around 40K. The bulk value is only reached at a thickness of about 150nm.
High-efficiency microcavity top-emitting organic light-emitting diodes using silver anode
Authors: Peng Huajun , Sun Jiaxin , Zhu Xiuling , Yu Xiaoming , Wong Man , Kwok Hoi-Sing
Published: February 2006

Top-emitting organic light-emitting diodes (TOLEDs) employing highly reflective Ag as anode and semitransparent LiF∕Al∕Ag as cathode were fabricated. The hole injection efficiency of Ag anode can be significantly improved with surface modification using a CF4 plasma. With C545T-doped Alq3 emitter, the top-emitting device shows a low turn-on voltage of 2.65V. The optimized microcavity TOLED shows a current efficiency enhancement of 65% and a total outcoupling efficiency enhancement of 35%, compared with a conventional OLED. No color variation was observed in the forward 140° forward viewing cone. Strong dependence of efficiency on Ag cathode thickness was observed, in good agreement with numerical simulations.
Dissociation energy of ekaplutonium fluoride E126F: The first diatomic with molecular spinors consisting of g atomic spinors
Authors: Malli Gulzari L.
Published: February 2006

Our ab initio all-electron fully relativistic Dirac-Fock (DF) and nonrelativistic (NR) Hartree-Fock (HF) self-consistent field (SCF) calculations predict the superheavy diatomic ekaplutonium fluoride E126F to be bound with the calculated dissociation energy of 7.44 and 10.46eV at the predicted E126-F bond lengths of 2.03 and 2.18Å, respectively. The antibinding effects of relativity to the dissociation energy of E126F are ∼3eV. The predicted dissociation energy with both our NR HF and relativistic DF SCF wave functions is fairly large and is comparable to that for very stable diatomics. This is the first case, where in a diatomic, an atom has g orbital (l=4) occupied in its ground state electronic configuration and such superheavy diatomics would have occupied molecular spinors (orbitals) consisting of g atomic spinors (orbitals). This opens up a whole new field of chemistry where g atomic spinors (orbitals) may be involved in electronic structure and chemical bonding of systems of superheavy elements with Z⩾122.
Dipole and quadrupole moments of molecules in crystals: A novel approach based on integration over Hirshfeld surfaces
Authors: Whitten Andrew E. , Radford Christopher J. , McKinnon Joshua J. , Spackman Mark A.
Published: February 2006

Elegant expressions are derived for the computation of dipole and quadrupole moments of molecules using the electrostatic potential and electric field evaluated on an oriented molecular surface. These expressions are implemented for Hirshfeld surfaces, applied to various molecular crystals, and compared with the results from the quantum theory of atoms in molecules. The effect of intermolecular interactions is also explored by examining the differences between electrostatic moments derived from a periodic Hartree-Fock electron density and an electron density resulting from a superposition of noninteracting molecules. The enhancement of the dipole moment for hydrogen bonded molecular crystals is typically 30%–40% and shown to be largely independent of the partitioning scheme. Dipole moments calculated from Hirshfeld surfaces systematically underestimate those from zero-flux surfaces, a result attributed to the translation of the Hirshfeld surface relative to the zero-flux surfaces for these molecules. For acetylene and benzene, the differences between a crystal calculation and the sum of noninteracting molecules are small, and both partitioning schemes yield quadrupole and second moment results in close agreement.
Chemical identification using an impedance sensor based on dispersive charge transport
Authors: Yang Richard D. , Fruhberger Bernd , Park Jeongwon , Kummel Andrew C.
Published: February 2006

Impedance spectroscopy has been used to identify analytes in semiconducting metallophthalocyanine thin films. Above a critical concentration, the magnitudes of the high frequency conductivity changes are invariant with concentration but distinct for different analytes and can be used for analyte identification. The analyte-induced ac conductivity changes above 5kHz have been converted to frequency shifts in a circuit resonance and used to differentiate methanol, ethanol, and isopropanol vapors in a nitrogen carrier gas. The analyte-induced changes in the conductivity are consistent with analyte-induced changes in the charge relaxation times.
Effect of perforated transparent electrodes on light transmittance and light scattering in substrates used for microcrystalline silicon thin-film solar cells
Authors: Nasuno Yoshiyuki , Kohama Noriyoshi , Nishimura Kazuhito , Hayakawa Takashi , Taniguchi Hiroshi , Shimizu Masafumi
Published: February 2006

The effect of a perforated transparent electrode, which is an electrode punctuated with holes, on light transmittance and light scattering was studied using textured ZnO:Ga formed by wet etching. The perforations were found to play a role not only in improving transmittance but also in maintaining high haze factor. The influence of the surface morphology of textured ZnO:Ga on the growth of hydrogenated microcrystalline silicon and on solar cell performance was also studied. It was found that, while the ZnO:Ga surface is not steep, a height difference is present on the substrate surface at the edge of the perforations. To resolve this problem, an additional thin ZnO:Ga layer was deposited on a substrate which already had a perforated transparent electrode. Improvements in solar cell performance were obtained while high open circuit voltage and high fill factor were maintained.
Effects of polymer gate dielectrics roughness on pentacene field-effect transistors
Authors: Shin Kwonwoo , Yang Chanwoo , Yang Sang Yoon , Jeon Hayoung , Park Chan Eon
Published: February 2006

The effects of the surface roughness of the polymer gate dielectrics on pentacene field-effect transistors were investigated. Using a poly(methylmethacrylate)/anodized Al2O3 dual-layer gate dielectric, the root-mean-square roughness of the gate dielectrics varied from 0.45 to 1.51nm, independently of other gate dielectric properties such as the capacitance and surface energy. This range of root-mean-square roughnesses had little effect on the carrier mobility. X-ray diffraction analyses further revealed that the roughness of poly(methylmethacrylate) neither decreased the degree of crystallinity nor distorted the crystalline structure of pentacene.
Structural changes and catalytic activity of platinum nanoparticles supported on C60 and carbon nanotube films during the operation of direct methanol fuel cells
Authors: Robel István , Girishkumar G. , Bunker Bruce A. , Kamat Prashant V. , Vinodgopal K.
Published: February 2006

Comparison of the structure and activity of Pt nanoparticles anchored on two nanostructured carbon supports, C60 and carbon nanotubes (CNTs) provides insight into their electrocatalytic activity in direct methanol fuel cells. The local structure of platinum atoms during the initial stages of the catalytic oxidation of methanol was probed using x-ray absorption spectroscopy. A large fraction of the Pt atoms in the Pt–C60 nanocomposite continuously undergoes structural changes during the initial stages of methanol oxidation. The Pt-CNT system, however, proves to be more robust in maintaining its initial morphology and higher electrocatalytic activity. These observations reflect the importance of the carbon support in controlling the catalyst morphology and activity during methanol oxidation.
Optical characterizations of iodine molecular wires formed inside the one-dimensional channels of an AlPO4-5 single crystal
Authors: Ye J. T. , Tang Z. K. , Siu G. G.
Published: February 2006

A uniform array of one-dimensional molecular iodine wires is fabricated by introducing iodine molecules into the channels of AFI zeolite crystals through the vapor phase. The only possible wire structures are formed by linking individual iodine molecules along intramolecular bond axis into a single line. Polarization dependence of Raman intensity at modes of iodine species indicates that the wires are aligned perfectly along the c axis of AFI crystal. Polarized optical absorption as well as resonant Raman scattering reveal two wire species inside the channels of AFI zeolite: In− and (I2)n wires.
Current-voltage characteristics and parameter retrieval of semiconducting nanowires
Authors: Zhang Z. Y. , Jin C. H. , Liang X. L. , Chen Q. , Peng L.-M.
Published: February 2006

Electrical transport measurements were conducted on semiconducting nanowires and three distinct current-voltage (I-V) characteristics were observed, i.e., almost symmetric, almost rectifying, and almost linear. These I-V characteristics were modeled by treating the transport in the nanowire as in a metal-semiconductor-metal structure involving two Schottky barriers and a resistor in between these barriers, and the transport is shown to be dominated by the reverse-biased Schottky barrier under low bias and by the semiconducting nanowire at large bias. In contrast to the conventional Schottky diode, the reverse current in the nano-Schottky barrier structure is not negligible and the current is largely tunneling rather than thermionic. Experimental I-V curves are reproduced very well using our model, and a method for extracting nanowire resistance, electron density, and mobility is proposed and applied to ZnO, CdS, and Bi2S3 nanowires.
Growth of internal melt figures in superheated ice
Authors: Takeya Satoshi
Published: February 2006

The use of light radiation to superheat the interior of an ice crystal and the transparency of ice allows one to observe internal melt figures, also called Tyndall figures, in an ice crystal. In this study, the growth process and growth rates of the melt figures were compared with those of ice crystals in supercooled water and also to the universal law of dendrite growth theory. The results suggest that growth of dendritic melt figures can be explained by the same factors as the growth process of dendritic ice crystals from the melt; that is, transport of latent heat, interfacial tension, and the anisotropic interfacial kinetics of ice.
Efficient generation of Cherenkov-type terahertz radiation from a lithium niobate crystal with a silicon prism output coupler
Authors: Theuer M. , Torosyan G. , Rau C. , Beigang R. , Maki K. , Otani C. , Kawase K.
Published: February 2006

We report on the generation of broadband terahertz (THz) pulses using Cherenkov-type generation in magnesium oxide-doped lithium niobate (MgO:LN). The efficiency of the output coupling process of THz radiation at higher frequencies into free space is considerably increased by the use of a properly cut silicon prism. The achieved spectrum is broader compared to the normal Cherenkov-cut geometry. Due to a considerably reduced propagation length in the absorbing MgO:LN, the effective application of longer crystals is possible. Thus, the measured spectral intensity is much higher and the spectrum broader.
Fabrication and characterization of metal-ferroelectric (PbZr0.53Ti0.47O3)-insulator (Dy2O3)-semiconductor capacitors for nonvolatile memory applications
Authors: Chang Chung-Yuan , Juan Trevor Pi-chun , Lee Joseph Ya-min
Published: February 2006

Metal-ferroelectric-insulator-semiconductor capacitors with Pb(Zr0.53,Ti0.47)O3 (PZT) ferroelectric layer and dysprosium oxide (Dy2O3) insulator layer were fabricated and characterized. The measured memory window of 0.86V was close to the theoretical value ΔW≈2dfEc≈0.78V at a sweep voltage of 8V. The size of the memory window as a function of PZT film thickness was discussed. The C-V flatband voltage shift (ΔVFB) as function of charge injection was also studied. An energy band diagram of the Al∕PZT∕Dy2O3∕p-Si system was proposed to explain the memory window and flatband voltage shift. The charge injection is mainly due to electrons.
Electronic conduction in GaN nanowires
Authors: Simpkins B. S. , Pehrsson P. E. , Laracuente A. R.
Published: February 2006

Conductivity mechanisms in unintentionally doped GaN nanowires (NWs) are studied. Gated current-voltage measurements and threshold voltage modeling demonstrate the unique impact of device parameters on NW field-effect transistors as compared to conventional systems. Temperature-dependent resistivity results, acquired with a scanning tunneling microscope equipped with multiple tips, reveal only mild temperature dependence at higher temperatures, with temperature-independent resistivity observed below ∼100K indicating impurity band conduction. The likely origins and implications of these results are discussed.
Optical channel waveguides in Nd:YVO4 crystal produced by O+ ion implantation
Authors: Chen Feng , Wang Lei , Jiang Yi , Wang Xue-Lin , Wang Ke-Ming , Fu Gang , Lu Qing-Ming , Rüter Christian E. , Kip Detlef
Published: February 2006

In this letter, we report on optical channel waveguides in Nd:YVO4 crystals produced by photographic masking and following direct O+ ion implantation at 3.0MeV. Annealing treatments of the samples are performed to improve the waveguide stability and to reduce losses. An increase of the ordinary refractive index induced by the implantation is believed to be responsible for waveguide formation. Quasi-TM guided modes are observed, while no quasi-TE ones are detected. The optical damping coefficients are of 0.43, 0.63, and 0.54cm−1 for channel waveguides with widths of 4, 5, and 6μm, respectively. The result of modal analysis is in agreement with the experimental data.
Open circuit voltage of stacked bulk heterojunction organic solar cells
Authors: Kawano Kenji , Ito Norihiro , Nishimori Taisuke , Sakai Jun
Published: February 2006

We investigate the open circuit voltage (VOC) of stacked bulk heterojunction (BHJ) organic solar cells based on conjugated polymer and fullerene derivative by spin-coating method. Poly[2-methoxy-5-(3′,7′-dimethyloctyloxy)-1,4-phenylene vinylene] (MDMO-PPV) blended with [6, 6]-phenyl C61-butyric acid methyl ester (PCBM) is used as a photoactive layer. The structure is ITO(lower BHJ cell)PEDOT:PSS/MDMO-PPV:PCBM/ITO/(upper BHJ cell)PEDOT:PSS/MDMO-PPV:PCBM/Al. VOC of the stacked cell is 1.34V and is about 1.6 times as large as that of single BHJ organic solar cell. VOC of the stacked cell is not proportional to the number of photoactive layers, but is the sum of the VOC values of the upper and the lower BHJ cells.
Photoconductivity and highly selective ultraviolet sensing features of amorphous silicon carbon nitride thin films
Authors: Chen Chun-Wei , Huang Cheng-Chia , Lin Yun-Yue , Su Wei-Fang , Chen Li-Chyong , Chen Kuei-Hsien
Published: February 2006

Photoconductivity of amorphous silicon carbon nitride (a-SiCN) as a function of incident photon energies has been studied. A metal-semiconductor-metal photodetector device based on the a-SiCN thin film demonstrates excellent selective ultraviolet sensing features. A large photo-to-dark current ratio about 5000 and a relative quantum efficiency about ∼105 under illumination of the 250nm light source and a bias voltage of 5V were observed. A model based on the heterogeneous structure in the a-SiCN thin film which consists of π−π* bands and σ−σ* bands was introduced to account for the observed photoconductive transport properties.
Properties of iron oxides in red Oxisols and red Ultisols as affected by rainfall and soil parent material
Authors: Trakoonyingcharoen P. , Kheoruenromne I. , Suddhiprakarn A. , Gilkes R.J.
Published: February 2006

Tropical soils developed from various parent materials and under various rainfalls were analysed to identify whether these environmental factors influence the properties of the iron oxides.
Iron contents of the soils range from 5 to 134 g/kg, with hematite and goethite being the major secondary iron minerals. Hematite is the dominant iron oxide in all soils developed on limestone irrespective of rainfall, whereas for other parent materials the relative abundance of goethite tends to increase with rainfall. Aluminum substitution in goethite and hematite ranges from 13 to 21 mol% and 7 to 15 mol%, respectively. The mole% Al substitution in hematite is about half the level for goethite in the same soil. Crystal size estimated from X-ray diffraction line broadening ranges from 12 to 47 nm for goethite and from 15 to 44 nm for hematite. Similar sizes were obtained by electron microscopy. The properties of the iron oxides did not vary systematically with parent material or rainfall and are similar to those described by other workers for red tropical soils on diverse parent materials.
Palæochannels in Northern New South Wales: Inversion of electromagnetic induction data to infer hydrologically relevant stratigraphy
Authors: Vervoort R. W. , Annen Y. L.
Published: February 2006

Palæochannels, or prior streams, are strings of sandier sediments that occur frequently in the irrigated alluvial plains of Northern New South Wales, Australia. These landscape features have been recognised as locations of substantial deep drainage losses, and are therefore target areas for water use efficiency. Electromagnetic induction (EM) measurements were used to identify the width and the depth of the palæochannel sediments in a 2-dimensional transect. Three different inversion techniques, Tikhonov regularisation, the McNeill layered earth model, and an optimal linear combination of EM measurements, were applied to a combination of EM-38 and EM-34 data. Using various kriging techniques, the resulting conductivity profiles were interpolated to soil property data and transformed to saturated hydraulic conductivities using pedotransfer functions. There were distinct differences in the resulting stratigraphies depending on the inversion and interpolation method employed. Trend kriging of the sampled soil property data using the Cook and Walker and Tikhonov inversion data as a trend surface gave the most consistent hydraulic conductivity values compared to the sampled soil property data. However, differences between inversion and interpolation methods were negated by uncertainties in the pedotransfer functions.
Emerging infectious disease and the loss of biodiversity in a Neotropical amphibian community
Authors: Lips Karen R. , Brem Forrest , Brenes Roberto , Reeve John D. , Alford Ross A. , Voyles Jamie , Carey Cynthia , Livo Lauren , Pessier Allan P. , Collins James P.
Published: February 2006

Pathogens rarely cause extinctions of host species, and there are few examples of a pathogen changing species richness and diversity of an ecological community by causing local extinctions across a wide range of species. We report the link between the rapid appearance of a pathogenic chytrid fungus
Batrachochytrium dendrobatidis
in an amphibian community at El Copé, Panama, and subsequent mass mortality and loss of amphibian biodiversity across eight families of frogs and salamanders. We describe an outbreak of chytridiomycosis in Panama and argue that this infectious disease has played an important role in amphibian population declines. The high virulence and large number of potential hosts of this emerging infectious disease threaten global amphibian diversity.
Impact of behavior on central and peripheral circadian clocks in the common vole
Microtus arvalis
, a mammal with ultradian rhythms
Authors: van der Veen Daan R. , Minh Nguyet Le , Gos Pascal , Arneric Milica , Gerkema Menno P. , Schibler Ueli
Published: February 2006

In most mammals, daily rhythms in physiology are driven by a circadian timing system composed of a master pacemaker in the suprachiasmatic nucleus (SCN) and peripheral oscillators in most body cells. The SCN clock, which is phase-entrained by light–dark cycles, is thought to synchronize subsidiary oscillators in peripheral tissues, mainly by driving cyclic feeding behavior. Here, we examined the expression of circadian clock genes in the SCN and the liver of the common vole
Microtus arvalis
, a rodent with ultradian activity and feeding rhythms. In these animals, clock-gene mRNAs accumulate with high circadian amplitudes in the SCN but are present at nearly constant levels in the liver. Interestingly, high-amplitude circadian liver gene expression can be elicited by subjecting voles to a circadian feeding regimen. Moreover, voles with access to a running wheel display a composite pattern of circadian and ultradian behavior, which correlates with low-amplitude circadian gene expression in the liver. Our data indicate that, in
M. arvalis
, the amplitude of circadian liver gene expression depends on the contribution of circadian and ultradian components in activity and feeding rhythms.
Assessment of cystic fibrosis transmembrane conductance regulator (CFTR) activity in CFTR-null mice after bone marrow transplantation
Authors: Bruscia Emanuela M. , Price Joanna E. , Cheng Ee-Chun , Weiner Scott , Caputo Christina , Ferreira Elisa C. , Egan Marie E. , Krause Diane S.
Published: February 2006

Several studies have demonstrated that bone marrow (BM)-derived cells give rise to rare epithelial cells in the gastrointestinal (GI) and respiratory tracts after BM transplantation into myeloablated recipients. We investigate whether, after transplantation of cystic fibrosis transmembrane conductance regulator (CFTR)-positive BM-derived cells, BM-derived GI and airway epithelial cells can provide CFTR activity in the GI tract and nasal epithelium of recipient cystic fibrosis mice. CFTR−/− mice were transplanted with wild-type BM after receiving different doses of irradiation, and CFTR activity was assessed
in vivo
in individual mice over time by using rectal and nasal potential difference analyses and
in vitro
by Ussing chamber analysis. The data suggest that rare BM-derived epithelial cells in the GI and nasal epithelium detected in CFTR−/− transplanted mice provide a modest level of CFTR-dependent chloride secretion. Detection of CFTR mRNA and protein in tissues of transplanted CFTR−/− mice supports these data.
The antioxidant protein alkylhydroperoxide reductase of
Helicobacter pylori
switches from a peroxide reductase to a molecular chaperone function
Authors: Chuang Ming-Hong , Wu Ming-Shiang , Lo Wan-Lin , Lin Jaw-Town , Wong Chi-Huey , Chiou Shyh-Horng
Published: February 2006

Helicobacter pylori
, an oxygen-sensitive microaerophilic bacterium, contains many antioxidant proteins, among which alkylhydroperoxide reductase (AhpC) is the most abundant. The function of AhpC is to protect
H. pylori
from a hyperoxidative environment by reduction of toxic organic hydroperoxides. We have found that the sequence of AhpC from
H. pylori
is more homologous to mammalian peroxiredoxins than to eubacterial AhpC. We have also found that the protein structure of AhpC could shift from low-molecular-weight oligomers with peroxide-reductase activity to high-molecular-weight complexes with molecular-chaperone function under oxidative stresses. Time-course study by following the quaternary structural change of AhpC
in vivo
revealed that this enzyme changes from low-molecular-weight oligomers under normal microaerobic conditions or short-term oxidative shock to high-molecular-weight complexes after severe long-term oxidative stress. This study revealed that AhpC of
H. pylori
acts as a peroxide reductase in reducing organic hydroperoxides and as a molecular chaperone for prevention of protein misfolding under oxidative stress.
Fishing through marine food webs
Authors: Essington Timothy E. , Beaudreau Anne H. , Wiedenmann John
Published: February 2006

A recurring pattern of declining mean trophic level of fisheries landings, termed “fishing down the food web,” is thought to be indicative of the serial replacement of high-trophic-level fisheries with less valuable, low-trophic-level fisheries as the former become depleted to economic extinction. An alternative to this view, that declining mean trophic levels indicate the serial addition of low-trophic-level fisheries (“fishing through the food web”), may be equally severe because it ultimately leads to conflicting demands for ecosystem services. By analyzing trends in fishery landings in 48 large marine ecosystems worldwide, we find that fishing down the food web was pervasive (present in 30 ecosystems) but that the sequential addition mechanism was by far the most common one underlying declines in the mean trophic level of landings. Specifically, only 9 ecosystems showed declining catches of upper-trophic-level species, compared with 21 ecosystems that exhibited either no significant change (
n
= 6) or significant increases (
n
= 15) in upper-trophic-level catches when fishing down the food web was occurring. Only in the North Atlantic were ecosystems regularly subjected to sequential collapse and replacement of fisheries. We suggest that efforts to promote sustainable use of marine resources will benefit from a fuller consideration of all processes giving rise to fishing down the food web.
Vacuolar invertase regulates elongation of
Arabidopsis thaliana
roots as revealed by QTL and mutant analysis
Authors: Sergeeva Lidiya I. , Keurentjes Joost J. B. , Bentsink Leónie , Vonk Jenneke , van der Plas Linus H. W. , Koornneef Maarten , Vreugdenhil Dick
Published: February 2006

The possible role of the sucrose-splitting enzymes sucrose synthase and invertase in elongating roots and hypocotyls of
Arabidopsis
was tested by using a combination of histochemical methods and quantitative trait locus (QTL) analysis. Lengths of roots and hypocotyls correlated better with invertase activities than with sucrose synthase activities. The highest correlations were observed with activities in the elongating zones of roots. The genetic basis of these correlations was studied by using QTL analysis. Several loci, affecting invertase activity, colocated with loci that had an effect on root or hypocotyl length. Further fine mapping of a major locus for root length, but not for hypocotyl length (top chromosome 1), consistently showed colocation with the locus for invertase activity containing a gene coding for a vacuolar invertase. The analysis of a functional knockout line confirmed the role of this invertase in root elongation, whereas other invertase genes might play a role in hypocotyl elongation. Thus, we show the power of QTL analysis, combined for morphological and biochemical traits, followed by fine-mapping and mutant analysis, in unraveling the function of genes and their role in growth and development.
A pneumococcal pilus influences virulence and host inflammatory responses
Authors: Barocchi M. A. , Ries J. , Zogaj X. , Hemsley C. , Albiger B. , Kanth A. , Dahlberg S. , Fernebro J. , Moschioni M. , Masignani V. , Hultenby K. , Taddei A. R. , Beiter K. , Wartha F. , von Euler A. , Covacci A. , Holden D. W. , Normark S. , Rappuoli R. , Henriques-Normark B.
Published: February 2006

Streptococcus pneumoniae
(pneumococcus) is a major cause of morbidity and mortality world-wide. The initial event in invasive pneumococcal disease is the attachment of encapsulated pneumococci to epithelial cells in the upper respiratory tract. This work provides evidence that initial bacterial adhesion and subsequent ability to cause invasive disease is enhanced by pili, long organelles able to extend beyond the polysaccharide capsule, previously unknown to exist in pneumococci. These adhesive pili-like appendages are encoded by the pneumococcal
rlrA
islet, present in some, but not all, clinical isolates. Introduction of the
rlrA
islet into an encapsulated
rlrA
-negative isolate allowed pilus expression, enhanced adherence to lung epithelial cells, and provided a competitive advantage upon mixed intranasal challenge of mice. Furthermore, a pilus-expressing
rlrA
islet-positive clinical isolate was more virulent than a nonpiliated deletion mutant, and it out-competed the mutant in murine models of colonization, pneumonia, and bacteremia. Additionally, piliated pneumococci evoked a higher TNF response during systemic infection, compared with nonpiliated derivatives, suggesting that pneumococcal pili not only contribute to adherence and virulence but also stimulate the host inflammatory response.
A complete ferredoxin/thioredoxin system regulates fundamental processes in amyloplasts
Authors: Balmer Yves , Vensel William H. , Cai Nick , Manieri Wanda , Schürmann Peter , Hurkman William J. , Buchanan Bob B.
Published: February 2006

A growing number of processes throughout biology are regulated by redox via thiol–disulfide exchange. This mechanism is particularly widespread in plants, where almost 200 proteins have been linked to thioredoxin (Trx), a widely distributed small regulatory disulfide protein. The current study extends regulation by Trx to amyloplasts, organelles prevalent in heterotrophic plant tissues that, among other biosynthetic activities, catalyze the synthesis and storage of copious amounts of starch. Using proteomics and immunological methods, we identified the components of the ferredoxin/Trx system (ferredoxin, ferredoxin–Trx reductase, and Trx), originally described for chloroplasts, in amyloplasts isolated from wheat starchy endosperm. Ferredoxin is reduced not by light, as in chloroplasts, but by metabolically generated NADPH via ferredoxin–NADP reductase. However, once reduced, ferredoxin appears to act as established for chloroplasts, i.e., via ferredoxin–Trx reductase and a Trx (
m
-type). A proteomics approach in combination with affinity chromatography and a fluorescent thiol probe led to the identification of 42 potential Trx target proteins, 13 not previously recognized, including a major membrane transporter (Brittle-1 or ADP-glucose transporter). The proteins function in a range of processes in addition to starch metabolism: biosynthesis of lipids, amino acids, and nucleotides; protein folding; and several miscellaneous reactions. The results suggest a mechanism whereby light is initially recognized as a thiol signal in chloroplasts, then as a sugar during transit to the sink, where it is converted again to a thiol signal. In this way, amyloplast reactions in the grain can be coordinated with photosynthesis taking place in leaves.
Agrobacterium tumefaciens
VirB8 structure reveals potential protein–protein interaction sites
Authors: Bailey Susan , Ward Doyle , Middleton Rebecca , Grossmann J. Gunter , Zambryski Patricia C.
Published: February 2006

Bacterial type IV secretion systems (T4SS) translocate DNA and/or proteins to recipient cells, thus providing a mechanism for conjugative transfer of genetic material and bacterial pathogenesis. Here we describe the first structure of a core component from the archetypal
Agrobacterium tumefaciens
T4SS: the 2.2-Å resolution crystal structure of the VirB8 periplasmic domain (pVirB8
AT
). VirB8 forms a dimer in the crystal, and we identify residues likely important for stabilization of the dimer interface. Structural comparison of pVirB8
AT
with
Brucella suis
VirB8 confirms that the monomers have a similar fold. In addition, the pVirB8
AT
dimer superimposes very closely on the
B. suis
VirB8 dimer, supporting the proposal that dimer formation in the crystal reflects self-interactions that are biologically significant. The evolutionary conservation level for each residue was obtained from a data set of 84 VirB8 homologs and projected onto the protein structure to indicate conserved surface patches that likely contact other T4SS proteins.
Analysis of calstabin2 (FKBP12.6)–ryanodine receptor interactions: Rescue of heart failure by calstabin2 in mice
Authors: Huang Fannie , Shan Jian , Reiken Steven , Wehrens Xander H. T. , Marks Andrew R.
Published: February 2006

The ryanodine receptor (RyR)/calcium-release channel on the sarcoplasmic reticulum mediates intracellular calcium release required for striated muscle contraction. RyR2, the predominant isoform in cardiac myocytes, comprises a macromolecular complex that includes calstabin2 (FKBP12.6). Calstabin2, an 11.8-kDa cis-trans peptidyl-prolyl isomerase (apparent molecular mass 12.6 kDa), stabilizes the closed state of the RyR2 channel, but the mechanism by which it achieves this regulation is not fully understood. Protein kinase A (PKA) phosphorylation of RyR2 decreases the affinity of calstabin2 for the RyR2 channel complex. In the present study we identified key aspartic acid residues on calstabin2 that are involved in binding to RyR2 and likely play a role in PKA phosphorylation-induced dissociation of calstabin2 from RyR2. We show that a mutant calstabin2 in which a key negatively charged residue (Asp-37) has been neutralized binds to a mutant RyR2 channel that mimics constitutively PKA-phosphorylated RyR2 (RyR2–S2808D). Furthermore, using wild-type and genetically altered murine models of heart failure induced by myocardial infarction, we show that manipulating the stoichiometry between calstabin2 and RyR2 can restore normal cardiac function
in vivo
.
Changes in food supply in Mediterranean countries from 1961 to 2001
Authors: Garcia-Closas Reina , Berenguer Antoni , González Carlos A
Published: February 2006

Objective

To describe geographical differences and time trends in the supply of the most important food components of the traditional Mediterranean diet.

Design

Food supply data collected from national food balance sheets for the period 1961–2001.

Setting

Selected Mediterranean countries: Spain, Italy, France, Greece, Algeria, Morocco, Tunisia and Turkey.

Results

Differences of almost 30-fold and five-fold were found in the supply of olive oil and fruits and vegetables, respectively, among the Mediterranean countries studied during the 1960s. A favourable increasing trend for the supply of fruit and vegetables was observed in most Mediterranean countries. However, an increase in the supply of meats and dairy products and a decrease in the supply of cereals and wine were observed in European Mediterranean countries from 1961 until 2001. Only in African and Asiatic Mediterranean countries were cereals the base of food supply. During the 1990s, Greece's food supply pattern was closest to the traditional Mediterranean diet, while Italy and Spain maintained a high availability of fruits, vegetables and olive oil, but were losing the other typical components. Among African and Asiatic Mediterranean countries, only Turkey presented a traditional Mediterranean dietary pattern except with respect to olive oil, the supply of which was very low. France showed a Western dietary pattern, with a high supply of animal products and a low supply of olive oil.

Conclusions

Dietary supplies in the Mediterranean area were quite heterogeneous in the 1960s and have experienced a process of Westernization, especially in European Mediterranean countries.
A multilevel study of socio-economic inequalities in food choice behaviour and dietary intake among the Dutch population: the GLOBE study
Authors: Giskes Katrina , Turrell Gavin , van Lenthe Frank J , Brug Johannes , Mackenbach Johan P
Published: February 2006

Objective

To examine the influence of individual- and area-level socio-economic characteristics on food choice behaviour and dietary intake.

Setting

The city of Eindhoven in the south-east Netherlands.

Design

A total of 1339 men and women aged 25–79 years were sampled from 85 areas (mean number of participants per area = 18.4, range 2–49). Information on socio-economic position (SEP) and diet was collected by structured face-to-face interviews (response rate 80.9%). Individual-level SEP was measured by education and household income, and area-level deprivation was measured using a composite index that included residents' education, occupation and employment status. Diet was measured on the basis of (1) a grocery food index that captured compliance with dietary guidelines, (2) breakfast consumption and (3) intakes of fruit, total fat and saturated fat. Multilevel analyses were performed to examine the independent effects of individual- and area-level socio-economic characteristics on the dietary outcome variables.

Results

After adjusting for individual-level SEP, few trends or significant effects of area deprivation were found for the dietary outcomes. Significant associations were found between individual-level SEP and food choice, breakfast consumption and fruit intake, with participants from disadvantaged backgrounds being less likely to report food behaviours or nutrient intakes consistent with dietary recommendations.

Conclusions

The findings suggest that an individual's socio-economic characteristics play a more important role in shaping diet than the socio-economic characteristics of the area in which they live. In this Dutch study, no independent influence of area-level socio-economic characteristics on diet was detected, which contrasts with findings from the USA, the UK and Finland.