bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling microbial reactions at the plume fringe subject to transverse mixing in porous media: When can the rates of microbial reaction be assumed to be instantaneous?
Authors: Chu M. , Kitanidis P. K. , McCarty P. L.
Published: June 2005

In this research, we investigate the large‐time solution behavior of a representative bioreactive transport model under the conditions that the mixing of two required substrates occurs only in the directions transverse to groundwater flow. The transport physics is governed by the commonly used advection‐dispersion equations at a steady uniform flow field. The microbial population dynamics are described by double Monod kinetics and a linear decay term. Through mathematical analyses we developed useful formulations to estimate the size of reaction zones and the level of microbial concentrations with the model parameters. The results show that microbial reaction rates are always limited by the transverse transport of the substrates at steady state, providing the substrate concentrations far away from the reaction zone are much larger than a characteristic concentration determined only by microbial kinetic parameters. Thus the reaction rates can be considered to be instantaneous. This greatly simplifies the governing equations and allows us to efficiently solve the steady state solutions for large‐scale problems. The method was applied to a large‐scale steady contaminant source problem, in which a dissolved contaminant was assumed to be biodegraded only at its plume fringe because of transverse mixing but not inside the plume. The results indicate that the transverse mixing at the plume fringe may successfully constrain the spread of a plume of high total organic carbon (TOC) concentrations (TOC = 500 mg/L) generated from a passive bioreactive barrier. However, the TOC reduction along the plume center line is insignificant even after the plume has traveled 10 km.
Rapid estimation of rupture extent for large earthquakes: Application to the 2004, M9 Sumatra‐Andaman mega‐thrust
Authors: Lomax Anthony
Published: May 2005

Rapid estimation of the rupture extent of large earthquakes is critical for tsunami warning and emergency response. The hypocenter of a distant earthquake is determined from the first seismic P waves within about 15 minutes after the event. However, methods for determining the size and rupture extent of very large earthquakes rely on long period recordings and aftershock locations, which are not available until several hours or more after the event. Here we introduce a method for rapid estimation of the rupture termination location for large earthquakes based on short period, P‐wave recordings, available about 30 minutes after an event. The hypocenter and the rupture termination location provide estimates of the extent of rupture and the event size. Application to the 2004, M9 Sumatra‐Andaman earthquake gives a rupture termination location near the Andaman Islands, about 1100 km north of the hypocenter, and a rupture duration of about 8 minutes.
“Missing” cloud condensation nuclei in peat smoke
Authors: Dusek U. , Frank G. P. , Helas G. , Iinuma Y. , Zeromskiene K. , Gwaze P. , Hennig T. , Massling A. , Schmid O. , Herrmann H. , Wiedensohler A. , Andreae M. O.
Published: June 2005

We characterized particulate emissions from vegetation fires by burning Indonesian and German peat and other biomass fuels in a controlled laboratory setting. By measuring cloud condensation nuclei (CCN) both as a function of particle diameter (dp) and supersaturation (S), we discovered particles in peat smoke that were not activated to cloud droplets at high S (1.6%). These hydrophobic particles were present predominantly in the size range of dp > 200 nm, where typical wood burning particles are activated at S < 0.3%. Ambient measurements during the 1997 Indonesian peat fires suggested that peat smoke particles are highly soluble and therefore efficient CCN. Our CCN measurements performed on fresh smoke from peat samples of the same area suggest that these Indonesian smoke particles probably acquired soluble material through chemical processing in the atmosphere. Freshly emitted peat smoke particles are at least partially not very efficient CCN.
The use of interstation P wave arrival time differences to account for regional path variability
Authors: Phillips W. S. , Rowe C. A. , Steck L. K.
Published: June 2005

The difference between arrival times from one seismic event to a pair of receivers is largely insensitive to source location error when certain geometric conditions are met. Using catalog data from a Chinese regional network, we illustrate the use of arrival time differences to control data quality and to derive a two‐dimensional map of Pn velocity and relative site terms. The resulting velocity patterns follow regional geology closely, site terms reflect variations in crustal thickness, and both are consistent with previous work based on single ray methods. The model fits the time difference data to better than 1 s and we obtain a variance reduction of 75%. We believe that the continued development of time‐difference techniques will lead to improved location accuracy and precision using regional network data.
On contrail climate sensitivity
Authors: Ponater M. , Marquart S. , Sausen R. , Schumann U.
Published: May 2005

In equilibrium climate change simulations with a global climate model we estimate the climate sensitivity parameter to contrail cirrus to be 0.43 K/(Wm−2), only about 60% of the corresponding value for a CO2 forcing. The spatial pattern of the surface temperature response is much smoother than the forcing pattern of contrails with little correlation between both. As the thermal inertia of the climate system causes a marked delay of the transient response, only about 30% of the equilibrium surface warming to be expected from some aircraft induced radiative forcing is actually realised for aviation increase rates typical for the 1990s. Our findings do not confirm recent results of a dominating influence of contrail cirrus on temperature change over the United States between 1975 and 1994.
Evidence for excess pore‐water pressure generated in subglacial sediment: Implications for clast ploughing
Authors: Rousselot M. , Fischer U. H.
Published: June 2005

Pore water pressure in front of an object pulled through subglacial sediment and water pressure at the base of a borehole were simultaneously recorded at Unteraargletscher, Switzerland, to investigate the generation of excess pore pressures downglacier from ploughing clasts. Analysis of the strongly correlated pressure records revealed that the amplitude of the pore‐pressure fluctuations was larger than that of the corresponding borehole pressure fluctuations. Guided by high temporal resolution measurements of glacier surface motion from a different year, this finding suggests that temporal changes in glacier speed lead to changes in the degree of excess pore‐pressure in front of the ploughing object. The generation of excess pore water pressure has the potential to weaken the sediment downglacier from ploughing clasts. Instead of these clasts providing the roughness at the ice–bed interface to resist glacier motion, the ploughing process may in fact help to decouple the ice from the bed reducing basal resistance.
Shock‐induced isotope evolution of hydrogen and carbon in meteorites
Authors: Mimura Koichi , Okamoto Michioki , Nakatsuka Takeshi , Sugitani Kenichiro , Abe Osamu
Published: June 2005

Single‐ and multiple‐shock recovery experiments on Murchison meteorite samples were performed, to examine the shock‐induced isotope behavior of their hydrogen and carbon contents. δD values of the shocked Murchison showed an initial increase from +10.6‰ to +59.1‰ before declining to −87.6‰, as the dehydrogenation progressed. Isotope behavior of δD can be controlled by dehydrogenation involving extremely large isotope fractionation and is attributed to the composition of organic matter in the Murchison. On the other hand, the behavior of δ13C simply decreased from −5.15‰ to −17.65‰ and is explainable by decarbonization only. The plot of those isotope data collected along devolatilization shows a variation curve that suggests the evolution of those isotopes in the meteorites. Shock is one of the processes effectively controlling the isotope features of the solar system.
Sensitization to Brain Antigens after Stroke is Augmented by Lipopolysaccharide
Authors: Becker Kyra J , Kindrick Darin L , Lester Mark P , Shea Connor , Ye Zu-Cheng
Published: June 2005

After stroke, the blood–brain barrier is transiently disrupted, allowing leukocytes to enter the brain and brain antigens to enter the peripheral circulation. This encounter of normally sequestered brain antigens by the systemic immune system could therefore present an opportunity for an autoimmune response to brain to occur after stroke. In this study, we assessed the immune response to myelin basic protein (MBP) in animals subjected to middle cerebral artery occlusion (MCAO). Some animals received an intraperitoneal injection of lipopolysaccharide (LPS; 1 mg/kg) at reperfusion to stimulate a systemic inflammatory response. At 1 month after MCAO, animals exposed to LPS were more likely to be sensitized to MBP (66.7% versus 22.2%; P = 0.007) and had more profound and persistent neurologic deficits than non-LPS-treated animals. Exposure to LPS was associated with increased expression of the costimulatory molecule B7.1 early after stroke onset ( P = 0.009) and increased brain atrophy 1 month after MCAO ( P = 0.03). These data suggest that animals subjected to a systemic inflammatory insult at the time of stroke are predisposed to develop an autoimmune response to brain, and that this response is associated with worse outcome. These data may partially explain why patients who become infected after stroke experience increased morbidity.
Planar (x,z) mixtures discrete Boltzmann equations with species either in odd or even ∣x∣+∣z∣ values
Authors: Cornille Henri
Published: June 2005

We present large size “physical” discrete Boltzmann equations or discrete velocity models results for binary mixtures of gas (light mass 1 and heavy mass M) in a half-plane (coordinates x,z, interface at z=0 without velocities except the rest-particle) where the sums ∣x∣+∣z∣ are either odd or even for heavy or light species. The models fill all integer coordinates z≠0 of the plane with only a z spatial dependence [densities with (±x, z) are equal]. Here, to previous results, we generalize with new mathematical tools, to any binary mixture with M ratio of any even to odd values, M=2p∕(2q+1) and ratio of odd to odd values M=(2p+1)∕(2q+1), p,q arbitrary integers. With only binary collisions, we construct large size “physical” discrete models (only mass, energy, and momentum along the z-axis invariants, without other invariants which are called spurious). We prove the existence of a “physical” square (diagonals along the x and z axes) grid where for the first component all ∣x∣+∣z∣⩽ a sufficient value (function of p and q) while for the other “physical” components we add 2, 4, etc., to the sufficient value. The numerical “physical” applications, with only binary collisions, could be done with this grid. The heavy species Hausdorff’ dimension has the limit 2 when the number of velocities →∞.
Free vibration of multiwall carbon nanotubes
Authors: Wang C. Y. , Ru C. Q. , Mioduchowski A.
Published: June 2005

A multiple-elastic shell model is applied to systematically study free vibration of multiwall carbon nanotubes (MWNTs). Using Flugge [Stresses in Shells (Springer, Berlin, 1960)] equations of elastic shells, vibrational frequencies and associated modes are calculated for MWNTs of innermost radii 5 and 0.65 nm, respectively. The emphasis is placed on the effect of interlayer van der Waals (vdW) interaction on free vibration of MWNTs. Our results show that the interlayer vdW interaction has a crucial effect on radial (R) modes of large-radius MWNTs (e.g., of the innermost radius 5 nm), but is less pronounced for R modes of small-radius MWNTs (e.g., of the innermost radius 0.65 nm), and usually negligible for torsional (T) and longitudinal (L) modes of MWNTs. This is attributed to the fact that the interlayer vdW interaction, characterized by a radius-independent vdW interaction coefficient, depends on radial deflections only, and is dominant only for large-radius MWNTs of lower radial rigidity but less pronounced for small-radius MWNTs of much higher radial rigidity. As a result, the R modes of large-radius MWNTs are typically collective motions of almost all nested tubes, and the R modes of small-radius MWNTs, as well as the T and L modes of MWNTs, are basically vibrations of individual tubes. In particular, an approximate single-shell model is suggested to replace the multiple-shell model in calculating the lowest frequency of R mode of thin MWNTs (defined by the innermost radius-to-thickness ratio not less than 4) with relative errors less than 10%. In addition, the simplified Flugge single equation is adopted to substitute the exact Flugge equations in determining the R-mode frequencies of MWNTs with relative errors less than 10%.
Gas dynamical approach to study dust acoustic solitary waves
Authors: Maitra Sarit , Roychoudhury Rajkumar
Published: June 2005

Dust acoustic nonlinear waves are studied using gas dynamical approach. The structure equation for dust fluid has been obtained using the conservation laws for mass flux and momentum. The role of dust sonic point for the formation of soliton has been discussed. Conditions for the existence of soliton have been derived in terms of collective Mach number, taking into account the dust charge variation.
Thick-film permanent magnets by membrane electrodeposition
Authors: Rhen F. M. F. , Backen E. , Coey J. M. D.
Published: June 2005

Thick films of nearly equiatomic Co–Pt produced by electrodeposition into nanoporous membranes exhibit an isotropic magnetic phase with square hysteresis loops (Mr∕Ms=0.95) and coercivity of up to 1.3 T. The initial magnetization curve is characteristic of pinning-type magnets. The coercivity can be controlled by the choice of annealing temperature or alloy composition, which depends on the chemical composition of the plating bath, properties which can be exploited to produce fine-pitch pole patterns.
Parametric mechanism of the rotation energy pumping by a relativistic plasma
Authors: Machabeli G. Z. , Osmanov Z. N. , Mahajan Swadesh M.
Published: June 2005

An investigation of the kinematics of a plasma stream rotating in the pulsar magnetosphere is presented. On the basis of an exact set of equations describing the behavior of the plasma stream, the increment of the instability is obtained, and the possible relevance of this approach for the understanding of the pulsar rotation energy pumping mechanism is discussed.
Analytic calculation of first-order molecular properties at the explicitly correlated second-order Møller–Plesset level: Basis-set limits for the molecular quadrupole moments of BH and HF
Authors: Kordel Elena , Villani Cristian , Klopper Wim
Published: June 2005

The analytic calculation of first-order properties has been implemented in the DALTON program at the level of explicitly correlated second-order Møller-Plesset perturbation theory (MP2-R12). The implementation has been accomplished for MP2-R12 theory based on standard approximations A, A′, and B, using an auxiliary basis for the resolution-of-the-identity approximation, with and without a frozen core. MP2-R12 first-order molecular properties have been calculated analytically for a few small test molecules. For BH and HF, the MP2-R12 results were supplemented with explicitly correlated coupled-cluster calculations (but at this level from numerical derivatives) including vibrational and relativistic corrections.
Nonlinear instability of density-independent orbital-free kinetic-energy functionals
Authors: Blanc X. , Cancès E.
Published: June 2005

We study in this article the mathematical properties of a class of orbital-free kinetic-energy functionals. We prove that these models are linearly stable but nonlinearly unstable, in the sense that the corresponding kinetic-energy functionals are not bounded from below. As a matter of illustration, we provide an example of an electronic density of simple shape, the kinetic energy of which is negative.
Nematic-nematic demixing in polydisperse thermotropic liquid crystals
Authors: Sollich Peter
Published: June 2005

We consider the effects of polydispersity on isotropic-nematic phase equilibria in thermotropic liquid crystals, using a Maier–Saupe theory [Z. Naturforsch. A 13A, 564 (1958)] with factorized interactions. A sufficient spread (≈50%) in the interaction strengths of the particles leads to phase separation into two or more nematic phases, which can in addition coexist with an isotropic phase. The isotropic–nematic coexistence region widens dramatically as polydispersity is increased, leading to reentrant isotropic–nematic phase separation in some regions of the phase diagram. We show that similar phenomena will occur also for nonfactorized interactions as long as the interaction strength between any two particle species is lower than the mean of the intraspecies interactions.
Real-time study of domain dynamics in ferroelectric Sr0.61Ba0.39Nb2O6
Authors: Tian L. , Scrymgeour David A. , Gopalan Venkatraman
Published: June 2005

Systematic studies of ferroelectric domain reversal of strontium barium niobate (Sr0.61Ba0.4Nb2O6 or SBN:61) single crystals by electric-field poling using liquid electrodes are reported. In contrast with previous studies using metal electrodes, it is shown that repeated domain reversal does not lead to polarization fatigue. Real-time optical imaging of domain nucleation and growth is reported in SBN:61 using electro-optic imaging microscopy. Measurements of hysteresis loops, switching times, and domain-wall mobility as a function of applied field are reported. The domain backswitching phenomenon was absent in SBN:61 crystals.
Anomalous resistivity due to nonlinear lower-hybrid drift waves
Authors: Silin I. , Büchner J. , Vaivads A.
Published: June 2005

The generation of anomalous collision rate and resistivity by lower-hybrid drift waves is investigated. A general expression involving particle density and current perturbations and electromagnetic field fluctuations is used to estimate the effective collision frequency. Results of Vlasov-code simulations and Cluster spacecraft measurements suggest that electrostatic and electromagnetic fluctuations provide approximately equal contributions to the electron collision rate, which is of the order of the lower-hybrid frequency. The anomalous resistivity based on such collision rate could be significant for the large-scale plasma dynamics in Earth’s magnetosphere, such as magnetic reconnection.
Manipulating the electronic structures of silicon carbide nanotubes by selected hydrogenation
Authors: Zhao Mingwen , Xia Yueyuan , Zhang R. Q. , Lee S.-T.
Published: June 2005

We show that the electronic and atomic structures of silicon carbide nanotubes (SiCNTs) undergo dramatic changes with hydrogenation from first-principles calculations based on density-functional theory. The exo-hydrogenation of a single C atom results in acceptor states close to the highest occupied valence band of pristine SiCNT, whereas donor states close to the lowest unoccupied conduction band appear as a Si atom being hydrogenated. Upon fully hydrogenating Si atoms, (8,0) and (6,6) SiCNTs become metallic with very high density of states at the Fermi level. The full hydrogenation of C atoms, on the other hand, increases the band gap to 2.6eV for (8,0) SiCNT and decreases the band gap to 1.47eV for (6,6) SiCNT, respectively. The band gap of SiCNTs can also be greatly increased through the hydrogenation of all the atoms.
Effect of point defect injection on diffusion of boron in silicon and silicon–germanium in the presence of carbon
Authors: Karunaratne M. S. A. , Willoughby A. F. W. , Bonar J. M. , Zhang J. , Ashburn P.
Published: June 2005

Boron diffusion in Si and strained SiGe with and without C was studied using point defect injection. Interstitial-, vacancy- and noninjection conditions were achieved by annealing Si capping layers which were either bare, with Si3N4 film or with Si3N4+SiO2 bilayers, respectively. Concentration profiles of B, Ge, and C were obtained using secondary-ion-mass spectrometry and diffusion coefficients of B in each type of matrix were extracted by computer simulation. Under inert annealing, we find that C strongly suppresses B diffusion in SiGe:C, but the effect of C is less strong in Si:C, particularly at high temperatures. In contrast, C only weakly suppresses B diffusion in both Si:C and SiGe:C under interstitial injection. For inert anneal conditions, C reduces the B diffusion coefficient in Si:C by factors of 4.2, 5.9, and 1.9 at 940, 1000, and 1050 °C respectively, whereas for interstitial injection the factors are 2.1, 1.3, and 1.1, respectively. The equivalent factors for SiGe:C are 8.4, 5.9, and 8.0 for inert anneal conditions and 2.2, 3.4, and 1.6 for interstitial injection conditions. The degree of B diffusion suppression achieved in both Si:C and SiGe:C is dependent on the level of C retained during annealing. Diffusion of C is shown to be faster in Si:C and hence less C is retained there after annealing than in SiGe:C. Interstitial injection is shown to strongly enhance C diffusion in both Si:C and SiGe:C and hence decreases the effectiveness of C for B diffusion suppression. These findings illustrate that the retarding effect of C on B diffusion in both Si:C and SiGe:C is strongly reduced when the anneal is carried out under conditions where interstitials are injected from the surface.
Measurement of preheat due to fast electrons in laser implosions of cryogenic deuterium targets
Authors: Yaakobi B. , Stoeckl C. , Seka W. , Delettrez J. A. , Sangster T. C. , Meyerhofer D. D.
Published: June 2005

Preheat due to fast electrons generated by nonlinear laser-plasma interactions can reduce the gain in laser-imploded fusion targets. The first measurements of electron preheat in directly driven, imploding cryogenic-deuterium targets are reported. The preheat level is derived directly from the measured hard-x-ray spectrum. The hard-x-ray detectors were calibrated in situ with a parylene-coated molybdenum solid-sphere target where both the hard x rays and the Mo Kα line were measured. Using electron and radiation transport calculations to relate the measurements to preheat, the fraction of the incident laser energy that preheats the cryogenic deuterium fuel is found to be less than 0.1%, suggesting that preheat will have a negligible impact on target performance. The results are encouraging for the success of planned high-gain direct-drive-ignition experiments on the National Ignition Facility [W. J. Hogan, E. I. Moses, B. E. Warner, M. S. Sorem, and J. M. Soures, Nucl. Fusion 41, 567 (2001)].
A super-integrable discretization of the Calogero model
Authors: Ujino Hideaki , Vinet Luc , Yoshida Haruo
Published: June 2005

A time discretization that preserves the super-integrability of the Calogero model is obtained by application of the integrable time discretization of the harmonic oscillator to the projection method for the Calogero model with continuous time. In particular, the difference equations of motion, which provide an explicit scheme for time integration, are explicitly presented for the two-body case. Numerical results exhibit that the scheme conserves all the (=3) conserved quantities of the (two-body) Calogero model with a precision of the machine epsilon times the number of iterations.
Thermal convection in superposed fluid and porous layers subjected to a horizontal plane Couette flow
Authors: Chang Min-Hsing
Published: June 2005

Thermal convection in a two-layer system with the presence of a plane Couette flow is investigated. The system comprises a fluid layer overlying a porous layer saturated with the same fluid and the lower plate is maintained warmer than the upper. A shear is generated by moving the upper wall horizontally at a constant speed. Both convection modes including longitudinal and transverse rolls are considered. Numerical results show that the neutral curves of both modes may be bimodal which depends on the depth ratio (i.e., the ratio of the depth of fluid layer to that of porous layer). The longitudinal rolls are always preferred at the onset of convection and the stability of this mode is independent of Reynolds and Prandtl numbers. But the transverse rolls may have the same stability as the longitudinal rolls when Reynolds number or Prandtl number approaches zero. Either increase of Reynolds number or Prandtl number raises its stability, and both produce the same effects on the stability behaviors of transverse rolls and the critical convection mode of transverse rolls tends to be within the porous layer with long wavelength.
Large tunnel magnetoresistance at room temperature with a Co2FeAl full-Heusler alloy electrode
Authors: Okamura S. , Miyazaki A. , Sugimoto S. , Tezuka N. , Inomata K.
Published: June 2005

Magnetic tunnel junctions (MTJs) with a Co2FeAl Heusler alloy electrode are fabricated by the deposition of the film using an ultrahigh vacuum sputtering system followed by photolithography and Ar ion etching. A tunnel magnetoresistance (TMR) of 47% at room temperature (RT) are obtained in a stack of Co2FeAl∕Al–Ox∕Co75Fe25 magnetic tunnel junction (MTJ) fabricated on a thermally oxidized Si substrate despite the A2 type atomic site disorder for Co2FeAl. There is no increase of TMR in MTJs with the B2 type Co2FeAl, which is prepared by the deposition on a heated substrate. X-ray photoelectron spectroscopy (XPS) depth profiles in Co2FeAl single layer films reveal that Al atoms in Co2FeAl are oxidized preferentially at the surfaces. On the other hand, at the interfaces in Co2FeAl∕Al–Ox∕Co75Fe25 MTJs, the ferromagnetic layers are hardly oxidized during plasma oxidation for a formation of Al oxide barriers.
Colorless transparent fluorescence material: Sintered porous glass containing rare-earth and transition-metal ions
Authors: Chen Danping , Miyoshi Hiroshi , Akai Tomoko , Yazawa Tetsuo
Published: June 2005

Transparent fluorescence oxide glass with high emission yields has been prepared. Porous glass was impregnated with rare-earth and transition-metal ions and consequently sintered at 1100°C into a compact nonporous glass. Reduction sintering is indispensable for obtaining fluorescence glass with high emission yield. Sintering of glass impregnated with Eu ions in a reducing atmosphere enhances the emission intensity by about 15 times than that sintered in air. The Eu2+ and Ce3+ ions and Sn2+ and Cu+ ions incorporated in SiO2 glass obtained by reduction sintering exhibit intense fluorescence in the near-ultraviolet and visible ranges, their emission yields are 97%, 70%, 100%, and 90%, respectively.
Observation of low-temperature specific-heat anomaly in CuZrAl bulk metallic glasses
Authors: Li Yong , Yu Peng , Bai Hai Yang
Published: June 2005

Low-temperature specific heat and ultrasonic experiments on CuZrAl bulk metallic glass (BMG) are performed. The low-temperature specific-heat anomaly arising from the low-frequency vibrations responsible for the boson peak, which is correlated with the nature and physical properties of the glasses, is clearly observed in the BMG. The ratio of the excess specific heat to the Debye contribution around the maximum is 1.93 for the BMG.
Water and nutrient availabilities do not affect lignotuber growth and sprouting ability of three eucalypt species of south-eastern Queensland
Authors: Walters Judi R. , House Alan P. N. , Doley David
Published: May 2005

Shoot biomass and lignotuber size of seedlings of three eucalypt species, Eucalyptus acmenoides Schauer, E. siderophloia Benth. and Corymbia variegata [syn. E. maculata (F.Muell.) K.D.Hill and L.A.S.Johnson], were measured for glasshouse-grown seedlings established under two water and nutrient regimes. Seedlings were subjected to shoot removal (clipping) at ages from 9 to 19 weeks, and transferred to the high water treatment for a further 8 weeks to assess shoot emergence from lignotubers. Seedling shoot biomass was greater in both the high than the low nutrient and water treatments, but lignotuber diameter was not affected significantly. C. variegata seedlings had the largest lignotuber diameters, followed by E. siderophloia and E. acmenoides, respectively. Although growth of shoots was influenced by nutrient availability, results suggest that species differences in the growth of lignotubers was less affected. It is suggested that lignotuber growth was strongly influenced by genotype. More than 70% of C. variegata seedlings clipped at 9 weeks sprouted, compared with only 5 and 10% of seedlings of E. siderophloia and E. acmenoides, respectively. All C. variegata seedlings sprouted after being clipped at 19 weeks, but <80% of E. siderophloia and <60% of E. acmenoides sprouted when clipped at the same age. It was concluded that seedlings forming part of the regeneration stratum in dry sclerophyll forests need to be protected from damage for at least 4 months (for C. variegata) or at least 6 months (for E. siderophloia and E. acmenoides) if they are to survive by sprouting from lignotubers.
Comparison of the genetic diversity in two species of cycads
Authors: Xiao Longqian , Gong Xun , Hao Gang , Ge Xuejun , Tian Bo , Zheng Sixiang
Published: May 2005

Inter-simple sequence repeat (ISSR) markers were used to examine the level and distribution of genetic diversity in two cycad species: Cycas parvula S.L.Yang and C. balansae Warburg. The former is found in only two adjacent populations and the latter in a relatively wider distribution. Although genetic diversity in C. balansae (He = 0.1301) is higher than that in C. parvula (He = 0.0538), both are still low in comparison with the mean value (He = 0.169) in gymnosperms. This confirms the general opinion that cycads are genetic relics. The genetic differentiation in both species, however, presents a striking contrast: Gst is 0.0978 in C. parvula, but 0.4003 in C. balansae, which may be ascribed to the difference in distances between their populations.
Corrigendum to: A novel in vitro rooting method employing an aerobic medium
Authors: Newell Chris , McComb Jen A. , Growns Digby J.
Published: May 2005

The beneficial influence of an aerobic propagation medium for in vitro cultures during the rooting phase was found for 28 Australian species and genotypes from the families Liliaceae, Haemodoraceae, Myrtaceae, Thymelaeaceae, Proteaceae, Goodeniaceae and Rutaceae. Microcuttings from established shoot cultures were pulsed for 7 days in the dark on a high-auxin (40 µM indole-3-butyric acid, IBA), agar-solidified medium. The microcuttings were then transferred either to an agar-solidified medium without plant-growth regulators (M1) or a sterile propagation mix. The protocol utilising propagation mix used is referred to as IVS (in vitro soil-less medium). The pulsed cuttings in agar or IVS were placed in the culture room under standard light and temperature regimes and allowed to root. When compared over two harvest times, the use of IVS as a rooting medium gave consistent improvements over the use of M1 medium for percentage rooting, average total root length and root number per microcutting. In total, 27 of the 28 species tested rooted in IVS medium at equal or better rates than in M1. In three cases, Actinodium cunninghamii, one of the genotypes of Pimelea physodes and one of the genotypes of Eriostemon australasis shoots did not root in M1 but showed good root development in IVS medium. With few exceptions, average root length and root number in microcuttings rooted in IVS were superior to the lengths and numbers recorded in agar medium. The materials handing advantages and the application of IVS are discussed.
Taxonomic patterns in the distribution of polyols within the Proteaceae
Authors: Bieleski R. L. , Briggs B. G.
Published: May 2005

More than 120 leaf samples from 82 species of Proteaceae, representative of floras in South Africa, Australia, New Zealand and South America, were studied for sugar composition. Generally, sucrose was dominant, with one or another polyol being second in importance. Presence of polygalatol (1,5-anhydrosorbitol), bornesitol (O-methyl-myo-inositol) and quebrachitol (O-methyl-D-chiro-inositol) was confirmed, pinitol (O-methyl-L-chiro-inositol) was identified and high levels of myo-inositol were sometimes encountered. Only four species, including Placospermum lacked any polyol other than inositol. High concentrations of polygalatol were characteristic of two South African genera, Protea and Faurea. Pinitol was characteristic of three genera in the Persoonieae and was also found in Petrophile (Australian) and Aulax (African). Most other genera were characterised by bornesitol alone, or by quebrachitol plus smaller amounts of bornesitol and inositol. Other unidentified compounds in the sugar fraction (possibly inositol isomers and glycosides) have potential to provide additional information on relationships. With only two exceptions, the pattern was consistent within a genus as currently defined; however, there was only partial concordance between the polyols and the phylogenetic relationships of genera. The findings support relatively close affinity between Buckinghamia and Grevillea, and between Aulax and Petrophile, as concluded from DNA sequencing. We suggest that the ability to produce the various inositol-based polyols in Proteaceae evolved early in the evolution of this ancient family, and has been retained in a wide range of habitats. Polygalatol has to be synthesised through a different biochemical pathway, which appears to have evolved later.
The sources of Schwinger's Green's functions
Authors: Schweber Silvan S.
Published: June 2005

Julian Schwinger's development of his Green's functions methods in quantum field theory is placed in historical context. The relation of Schwinger's quantum action principle to Richard Feynman's path-integral formulation of quantum mechanics is reviewed. The nonperturbative character of Schwinger's approach is stressed as well as the ease with which it can be extended to finite temperature situations.
Holliday junction dynamics and branch migration: Single-molecule analysis
Authors: Karymov Mikhail , Daniel Douglas , Sankey Otto F. , Lyubchenko Yuri L.
Published: May 2005

The Holliday junction (HJ) is a central intermediate in various genetic processes including homologous and site-specific recombination and DNA replication. Branch migration allows the exchange between homologous DNA regions, but the detailed mechanism for this key step of DNA recombination is unidentified. Here, we report direct real-time detection of branch migration in individual molecules. Using appropriately designed HJ constructs we were able to follow junction branch migration at the single-molecule level. Branch migration is detected as a stepwise random process with the overall kinetics dependent on Mg
2+
concentration. We developed a theoretical approach to analyze the mechanism of HJ branch migration. The data show steps in which the junction flips between conformations favorable to branch migration and conformations unfavorable to it. In the favorable conformation (the extended HJ geometry), the branch can migrate over several base pairs detected, usually as a single large step. Mg
2+
cations stabilize folded conformations and stall branch migration for a period considerably longer than the hopping step. The conformational flip and the variable base pair hopping step provide insights into the regulatory mechanism of genetic processes involving HJs.
HIV dynamics with multiple infections of target cells
Authors: Dixit Narendra M. , Perelson Alan S.
Published: June 2005

The high incidence of multiple infections of cells by HIV sets the stage for rapid HIV evolution by means of recombination. Yet how HIV dynamics proceeds with multiple infections remains poorly understood. Here, we present a mathematical model that describes the dynamics of viral, target cell, and multiply infected cell subpopulations during HIV infection. Model calculations reproduce several experimental observations and provide key insights into the influence of multiple infections on HIV dynamics. We find that the experimentally observed scaling law, that the number of cells coinfected with two distinctly labeled viruses is proportional to the square of the total number of infected cells, can be generalized so that the number of triply infected cells is proportional to the cube of the number of infected cells, etc. Despite the expectation from Poisson statistics, we find that this scaling relationship only holds under certain conditions, which we predict. We also find that multiple infections do not influence viral dynamics when the rate of viral production from infected cells is independent of the number of times the cells are infected, a regime expected when viral production is limited by cellular rather than viral factors. This result may explain why extant models, which ignore multiple infections, successfully describe viral dynamics in HIV patients. Inhibiting CD4 down-modulation increases the average number of infections per cell. Consequently, altering CD4 down-modulation may allow for an experimental determination of whether viral or cellular factors limit viral production.
Prolonged coexistence of humans and megafauna in Pleistocene Australia
Authors: Trueman Clive N. G. , Field Judith H. , Dortch Joe , Charles Bethan , Wroe Stephen
Published: June 2005

Recent claims for continent wide disappearance of megafauna at 46.5 thousand calendar years ago (ka) in Australia have been used to support a “blitzkrieg” model, which explains extinctions as the result of rapid overkill by human colonizers. A number of key sites with megafauna remains that significantly postdate 46.5 ka have been excluded from consideration because of questions regarding their stratigraphic integrity. Of these sites, Cuddie Springs is the only locality in Australia where megafauna and cultural remains are found together in sequential stratigraphic horizons, dated from 36-30 ka. Verifying the stratigraphic associations found here would effectively refute the rapid-overkill model and necessitate reconsideration of the regional impacts of global climatic change on megafauna and humans in the lead up to the last glacial maximum. Here, we present geochemical evidence that demonstrates the coexistence of humans and now-extinct megafaunal species on the Australian continent for a minimum of 15 ka.
Dynamic positioning of the fission yeast cell division plane
Authors: Daga Rafael R. , Chang Fred
Published: June 2005

A key question in cytokinesis is how the cell division plane is positioned. Whereas microtubules of the mitotic apparatus specify the division site in animal cells, we show here that the nucleus plays this role in the fission yeast
Schizosaccharomyces pombe
. By centrifuging cells to move the nucleus, we find that the nucleus (or a nuclear-associated structure) actively influences the position of contractile ring assembly during early mitosis. Displacement of the nucleus during this induction period can lead to formation of multiple rings. The nucleus signals its position in a microtubule-independent manner by emitting the protein mid1p. Furthermore, movement of ring fragments together minimizes formation of multiple division sites. These dynamic mechanisms of ring positioning provide a robust coordination of nuclear and cell division.
Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA: The giant moas of New Zealand
Authors: Baker Allan J. , Huynen Leon J. , Haddrath Oliver , Millar Craig D. , Lambert David M.
Published: June 2005

The tempo and mode of evolution of the extinct giant moas of New Zealand remain obscure because the number of lineages and their divergence times cannot be estimated reliably by using fossil bone characters only. We therefore extracted ancient DNA from 125 specimens and genetically typed them for a 658-bp mtDNA control region sequence. The sequences detected 14 monophyletic lineages, 9 of which correspond to currently recognized species. One of the newly detected lineages was a genetically divergent form ofMegalapteryxoriginally described as a separate species, two more were lineages ofPachyornisin southern and northeastern New Zealand, and two were basal lineages of South IslandDinornis. When results from genetic typing and previous molecular sexing were combined, at least 33.6% of the specimens were incorrectly classified. We used longer sequences of the control region and nine other mtDNA genes totaling 2,814 base pairs to derive a strongly supported phylogeny of the 14 moa lineages. Molecular dating estimated the most recent common ancestor of moas existed after the Oligocene drowning of New Zealand. However, a cycle of lineage-splitting occurred ≈4–10 million years ago, when the landmass was fragmented by tectonic and mountain-building events and general cooling of the climate. These events resulted in the geographic isolation of lineages and ecological specialization. The spectacular radiation of moa lineages involved significant changes in body size, shape, and mass and provides another example of the general influence of large-scale paleoenvironmental changes on vertebrate evolutionary history.
The target of ezetimibe is Niemann-Pick C1-Like 1 (NPC1L1)
Authors: Garcia-Calvo Margarita , Lisnock JeanMarie , Bull Herbert G. , Hawes Brian E. , Burnett Duane A. , Braun Matthew P. , Crona James H. , Davis Harry R. , Dean Dennis C. , Detmers Patricia A. , Graziano Michael P. , Hughes Meredith , MacIntyre D. Euan , Ogawa Anthony , O'Neill Kim A. , Iyer Sai Prasad N. , Shevell Diane E. , Smith Marsha M. , Tang Yui S. , Makarewicz Amanda M. , Ujjainwalla Feroze , Altmann Scott W. , Chapman Kevin T. , Thornberry Nancy A.
Published: June 2005

Ezetimibe is a potent inhibitor of cholesterol absorption that has been approved for the treatment of hypercholesterolemia, but its molecular target has been elusive. Using a genetic approach, we recently identified Niemann-Pick C1-Like 1 (NPC1L1) as a critical mediator of cholesterol absorption and an essential component of the ezetimibe-sensitive pathway. To determine whether NPC1L1 is the direct molecular target of ezetimibe, we have developed a binding assay and shown that labeled ezetimibe glucuronide binds specifically to a single site in brush border membranes and to human embryonic kidney 293 cells expressing NPC1L1. Moreover, the binding affinities of ezetimibe and several key analogs to recombinant NPC1L1 are virtually identical to those observed for native enterocyte membranes.
K
D
values of ezetimibe glucuronide for mouse, rat, rhesus monkey, and human NPC1L1 are 12,000, 540, 40, and 220 nM, respectively. Last, ezetimibe no longer binds to membranes from NPC1L1 knockout mice. These results unequivocally establish NPC1L1 as the direct target of ezetimibe and should facilitate efforts to identify the molecular mechanism of cholesterol transport.
Characterization of human glutaredoxin 2 as iron–sulfur protein: A possible role as redox sensor
Authors: Lillig Christopher Horst , Berndt Carsten , Vergnolle Olivia , Lönn Maria Elisabet , Hudemann Christoph , Bill Eckhard , Holmgren Arne
Published: May 2005

Human mitochondrial glutaredoxin 2 (Grx2) is a glutathione-dependent oxidoreductase (active site: Cys-Ser-Tyr-Cys) that facilitates the maintenance of mitochondrial redox homeostasis upon induction of apoptosis by oxidative stress. Here, we have characterized Grx2 as an iron–sulfur center-containing member of the thioredoxin fold protein family. Mössbauer spectroscopy revealed the presence of a four cysteine-coordinated nonoxidizable [2Fe-2S]
2+
cluster that bridges two Grx2 molecules via two structural Cys residues to form dimeric holo Grx2. Coimmunoprecipitation of radiolabeled iron with Grx2 from human cell lines indicated the presence of the cluster
in vivo
. The [2Fe-2S]-bridged dimer was enzymatically inactive, but degradation of the cluster and the resulting monomerization of Grx2 activated the protein. Slow degradation under aerobic conditions was prevented by the presence of glutathione, whereas glutathione disulfide as well as one-electron oxidants or reductants promoted monomerization of Grx2. We propose that the iron–sulfur cluster serves as a redox sensor for the activation of Grx2 during conditions of oxidative stress when free radicals are formed and the glutathione pool becomes oxidized.
Zebrafish
bandoneon
mutants display behavioral defects due to a mutation in the glycine receptor β-subunit
Authors: Hirata Hiromi , Saint-Amant Louis , Downes Gerald B. , Cui Wilson W. , Zhou Weibin , Granato Michael , Kuwada John Y.
Published: June 2005

Bilateral alternation of muscle contractions requires reciprocal inhibition between the two sides of the hindbrain and spinal cord, and disruption of this inhibition should lead to simultaneous activation of bilateral muscles. At 1 day after fertilization, wild-type zebrafish respond to mechanosensory stimulation with multiple fast alternating trunk contractions, whereas
bandoneon
(
beo
) mutants contract trunk muscles on both sides simultaneously. Similar simultaneous contractions are observed in wild-type embryos treated with strychnine, a blocker of the inhibitory glycine receptor (GlyR). This result suggests that glycinergic synaptic transmission is defective in
beo
mutants. Muscle voltage recordings confirmed that muscles on both sides of the trunk in
beo
are likely to receive simultaneous synaptic input from the CNS. Recordings from motor neurons revealed that glycinergic synaptic transmission was missing in
beo
mutants. Furthermore, immunostaining with an antibody against GlyR showed clusters in wild-type neurons but not in
beo
neurons. These data suggest that the failure of GlyRs to aggregate at synaptic sites causes impairment of glycinergic transmission and abnormal behavior in
beo
mutants. Indeed, mutations in the GlyR β-subunit, which are thought to be required for proper localization of GlyRs, were identified as the basis for the
beo
mutation. These data demonstrate that GlyRβ is essential for physiologically relevant clustering of GlyRs
in vivo
. Because GlyR mutations in humans lead to hyperekplexia, a motor disorder characterized by startle responses, the zebrafish
beo
mutant should be a useful animal model for this condition.
Competence-programmed predation of noncompetent cells in the human pathogen
Streptococcus pneumoniae
: Genetic requirements
Authors: Guiral Sébastien , Mitchell Tim J. , Martin Bernard , Claverys Jean-Pierre
Published: June 2005

Natural competence for genetic transformation is the best-characterized feature of the major human pathogen
Streptococcus pneumoniae
. Recent studies have shown the virulence of competence-deficient mutants to be attenuated, but the nature of the connection between competence and virulence remained unknown. Here we document the release, triggered by competent cells, of virulence factors (e.g., the cytolytic toxin pneumolysin) from noncompetent cells. This phenomenon, which we name allolysis, involves a previously undescribed bacteriocin system consisting of a two-peptide bacteriocin, CibAB, and its immunity factor, CibC; the major autolysin, LytA, and lysozyme, LytC; and a proposed new amidase, CbpD. We show that CibAB are absolutely required for allolysis, whereas LytA and LytC can be supplied either by the competent cells or by the targeted cells. We propose that allolysis constitutes a competence-programmed mechanism of predation of noncompetent cells, which benefits to the competent cells and contributes to virulence by coordinating the release of virulence factors.