bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermal conduction from microcantilever heaters in partial vacuum
Authors: Lee Jungchul , Wright Tanya L. , Abel Mark R. , Sunden Erik O. , Marchenkov Alexei , Graham Samuel , King William P.
Published: January 2007

This paper reports the thermal and electrical characteristics of a heated microcantilever in air and helium over a wide range of pressures. The cantilever heater size modulates thermal conductance between the cantilever and its gaseous surroundings; and the Knudsen number, Kn characterizes this thermal conductance. When Kn<1, thermal transport from the cantilever heater depends on gas pressure, and when Kn>1, thermal transport from the cantilever heater remains constant. This measurement of thermal conductance around Kn=1 could aid the design and analysis of Pirani sensors and other microscale thermal sensors and actuators.
Dispersion and purification of Mo6S3I6 nanowires in organic solvents
Authors: McCarthy Denis N. , Nicolosi Valeria , Vengust Damjan , Mihailovic Dragan , Compagnini Giuseppe , Blau Werner J. , Coleman Jonathan N.
Published: January 2007

Sedimentation measurements have been performed on dispersions of Mo6S3I6 nanowires in a range of common solvents. By far the best solvents were N,N-dimethylformamide (DMF) and acetone. Stable dispersions of purified Mo6S3I6 nanowires in DMF, with concentrations as high as 0.06gl−1, could be produced. Detailed analysis of the sedimentation curves showed that the material consisted of three phases, two insoluble phases and one which could be stably dispersed. We associate the insoluble phases with pseudospherical impurities and insoluble nanowires. The sedimenting nanowires tend to be in the form of large diameter bundles, in contrast to the dispersed phase which consists of nanowires arranged in smaller bundles. The average diameters of the nanowire bundles stably suspended in DMF are 12±14nm. The measured sedimentation time constants of the insoluble nanowires agree very well with theory allowing us to calculate the solid-fluid interaction parameter, β, to be very close to 105Pa. The material could be purified by controlled sedimentation hence the identification of the various phases was confirmed by x-ray photoelectron spectroscopy and scanning electron microscopy.
Trapping motile magnetotactic bacteria with a magnetic recording head
Authors: Krichevsky A. , Smith M. J. , Whitman L. J. , Johnson M. B. , Clinton T. W. , Perry L. L. , Applegate B. M. , O’Connor K. , Csonka L. N.
Published: January 2007

We report reliable, reversible trapping of live magnetotactic bacteria, Magnetospirillum magneticum AMB-1, using a commercial magnetic recording head. The magnetic recording head was modified to generate spatially localized magnetic fields of high magnitude and gradient, and effectively trapped AMB-1, which have a magnetic moment per cell one order of magnitude smaller than cells previously trapped using Amperian fields. We also describe selective trapping of magnetic wild-type AMB-1 with discrimination against a nonmagnetic mutant strain of the same bacteria. Finally, we discuss the prospects of using the built-in spin valve sensor on a recording head for integrated detection of trapped bacteria. Using the chip-based methods we describe, it may be possible to capture, sort, and count magnetic bacteria quickly from samples taken directly from their natural aquatic habitat. More generally, the method may be applicable to the manipulation, spatial control, and integrated detection of magnetically labeled cells and magnetic nanoparticles.
Effects of Al doping on the electromigration performance of damascene Cu interconnects
Authors: Yokogawa Shinji , Tsuchiya Hideaki
Published: January 2007

We report the effects of Al doping on electromigration in damascene Cu interconnects. Al doping was performed by thermal diffusion from a CuAl seed layer positioned underneath the Cu interconnects. To investigate the dependencies of the Al concentration, the seed CuAl layer thickness was increased from 40to90nm on a planar surface. The effects of Al doping on the incubation time, drift velocity, and critical product of electromigration were investigated. The drift velocity of Cu mass transport in CuAl alloys decreases with an increase in the concentration of Al atoms. The observed critical product of electromigration is 1500A∕cm, and it is independent of the Al concentration. The measured activation energies of the normalized drift velocities for CuAl seed layer thicknesses of 40, 60, and 90nm are 1.2, 1.4, and 1.5eV, respectively. The Al concentrations at Cu∕SiCN interface, grain boundary, Ta∕Cu interface, and bulk were investigated along the length of a line by the electron microprobe technique. The time dependent Al concentration at the Cu∕SiCN interface near the cathode end of the line is observed. These characteristics indicate that the doped Al affects the electromigration-induced Cu diffusion and does not affect the driving force.
Effect of Al addition on the microstructure and electronic structure of HfO2 film
Authors: Wang X. F. , Li Quan , Egerton R. F. , Lee P. F. , Dai J. Y. , Hou Z. F. , Gong X. G.
Published: January 2007

We have investigated the microstructures and electronic structures of a series of hafnium aluminate (HfAlO) films with Al concentration ranging from 0% to 100%. When the films evolve from pure HfO2 to pure Al2O3 by increasing the aluminum content, we find changes in their radial distribution functions, which disclose the short-range order of the materials, despite the amorphous nature of all films. The HfAlO films (with Al∕Hf ratio ranging from 0.25 to 5.8) appear to be a single glassy phase of Hf, Al, and O, instead of simple mixtures of HfO2 and Al2O3. The Hf (Al)–O, Hf (Al)–Al, and Hf–Hf bonds are observed to be insensitive to the amount of Al in the film, except when the Al concentration is large (Al∕Hf∼5.8), in which case the bonding is similar to that in pure Al2O3. Although the local symmetry of Hf in amorphous HfO2 is suggested by the electron energy-loss spectrum taken at an oxygen K edge, it is largely disrupted when Al is introduced. The valence electron energy-loss spectroscopy reveals three distinct evolving features as the Al content increases, which we discuss in terms of the electronic structure of HfO2.
Comment on “Ab initio studies of (H2O)14− clusters: Existence of surface and interior-bound extra electrons” [J. Chem. Phys. 125, 024307 (2006)]
Authors: Sommerfeld Thomas
Published: January 2007

In a recent paper Khan [J. Chem. Phys.125, 024307 (2006)] presented ab initio calculations for a surface and a cavity bound isomer of (H2O)14− that turn out to be almost isoenergetic. Khan concluded that this result contradicts earlier studies that found that for small to intermediate size water clusters the most stable surface bound anion states were far more stable than the lowest cavity-type anion states. This conclusion is not warranted by the computational results.
Three-dimensional chaotic mixing inside drops driven by a transient electric field
Authors: Xu Xiumei , Homsy G. M.
Published: January 2007

We numerically study the three-dimensional (3D) chaotic trajectories inside a neutrally buoyant drop driven by periodically switching a uniform electric field through an angle αm. Periodically switching the field is equivalent to periodically alternating the direction of the interfacial electric force; thus, symmetries of the steady Taylor circulation are broken and 3D chaotic advection is generated inside the drop. The extent of the chaotic mixing is related to two parameters: the switching angle αm and modulation period Τ. The parametric dependence of mixing is investigated by tracing trajectories of Lagrangian particles. Analysis shows that depending on the range of αm there are either four or eight center fixed points (CFPs), around which invariant surfaces exist and chaotic mixing is suppressed. Our calculations of the mixed volume fraction and Lyapunov exponents suggest an optimal range of αm for best mixing. For a given αm, by varying modulation period Τ, we find that a resonant phenomena may occur, and global uniform mixing is possible. Therefore, the numerical results suggest optimum operation conditions for our future experiments.
Exploring conformational energy landscape of glassy disaccharides by cross polarization magic angle spinning C13 NMR and numerical simulations. I. Methodological aspects
Authors: Lefort Ronan , Bordat Patrice , Cesaro Attilio , Descamps Marc
Published: January 2007

This article demonstrates the ability of chemical shift surfaces to provide information on distributions of various conformations of disaccharides in the glassy, solid state. The validity of the general method leading to a simulation of inhomogeneous C13 chemical shift distributions is discussed in detail. In particular, a proper consideration of extrema and saddle points of the chemical shift map correctly accounts for the observed discontinuities in the experimental cross polarization magic angle spinning spectra. Provided that these basic requirements are met, density functional theory/gauge-independent atomic orbital chemical shift maps calculated on relaxed conformations lead to a very satisfactory description of the experimental line shapes. Using amorphous trehalose as a model disaccharide, the simulation unambiguously defines the range of most populated conformations in the glass.
Electronic characteristics of fluorene/TiO2 molecular heterojunctions
Authors: Wu Jing , Mobley Ken , McCreery Richard L.
Published: January 2007

The electronic properties of molecular junctions of the general type carbon/molecule/TiO2∕Au were examined as examples of “molecular heterojunctions” consisting of a molecular monolayer and a semiconducting oxide. Junctions containing fluorene bonded to pyrolyzed photoresist film (PPF) were compared to those containing Al2O3 instead of fluorene, and those with only the TiO2 layer. The responses to voltage sweep and pulse stimulation were strongly dependent on junction composition and temperature. A transient current response lasting a few milliseconds results from injection and trapping of electrons in the TiO2 layer, and occurred in all three junction types studied. Conduction in PPF∕TiO2∕Au junctions is consistent with space charge limited conduction at low voltage, then a sharp increase in current once the space charge fills all the traps. With fluorene present, there is a slower, persistent change in junction conductance which may be removed by a reverse polarity pulse. This “memory” effect is attributed to a redox process in the TiO2 which generates TiIII and/or TiII, which have much higher conductance than TiO2 due to the presence of conduction band electrons. The redox process amounts to “dynamic doping” of the TiO2 layer by the imposed electric field. The memory effect arises from a combination of the properties of the molecular and oxide layers, and is a special property of the molecular heterojunction configuration.
The effect of sheared axial flow on the interchange mode in a hard-core Z pinch
Authors: Kouznetsov A. , Freidberg J. P. , Kesner J.
Published: January 2007

It is well known that a static (i.e., v=0) closed field line configuration, such as a levitated dipole, or a hard-core Z pinch, can be stabilized against ideal magnetohydrodynamic (MHD) interchange modes when the edge pressure gradient is sufficiently weak. The stabilizing effect is provided by plasma compressibility. However, many laboratory plasmas exhibit a sheared velocity flow (i.e., n∙∇v≠0), and this flow may affect the marginal stability boundary. The present work addresses this issue by an analysis of the effect of axially sheared flow on interchange stability in a hard-core Z pinch, a cylindrical model for the levitated dipole configuration. Specifically, the goal is to learn whether sheared flow is favorable, unfavorable, or neutral with respect to MHD stability. Analytic calculations of marginal stability for several idealistic velocity profiles show that all three options are possible depending on the shape of the shear profile. This variability reflects the competition between the destabilizing Kelvin-Helmholtz effect and the fact that shear makes it more difficult for interchange perturbations to form. Numerical calculation are also presented for more realistic experimental profiles and compared with the results for the idealized analytic profiles.
Polyion-induced liposomal vesicle aggregation: A radiowave dielectric relaxation study
Authors: Bordi F. , Cametti C. , Sennato S. , Viscomi D.
Published: January 2007

The radiowave dielectric properties of aqueous heterogeneous systems during the complexation of charged polyions and oppositely charged liposomal particles have been measured in a wide frequency range, between 100Hz and 2GHz. The formation of a polyion-liposome complex driven by the correlated polyion adsorption at the particle surface implies two concomitant effects referred to as reentrant condensation and charge inversion. Both of them are governed by electrostatic interactions and there is now strong evidence, based on experiments and simulations, that counterion release is the driving force of the aggregation process. From this point of view, dielectric technique may offer a suitable tool in the investigation of the structural properties of these aggregates. In spite of the fact that interaction of polyions with oppositely charged surfaces was extensively experimentally investigated, there are no papers concerning the dielectric properties during the polyion-induced aggregation. To get an insight into this important topic, the authors present here an extensive set of radiowave dielectric measurements of liposomal vesicle aqueous suspensions where the liposome aggregation was induced by an oppositely charged polyion. The aggregation was followed from the beginning, when most of the isolated liposomes predominate, up to the formation of polyion-coated liposomes of inverted charge, crossing the isoelectric condition, where large, almost neutral, aggregates appear. The authors describe the observed dielectric dispersions as due to counterion polarization in the adjacency of the liposome and liposome aggregate surface, primarily governed by the ζ potential, according to the standard electrokinetic model.
Spatially resolved spectroscopy of detached recombining plasmas in the University of Manchester Linear System divertor simulator
Authors: Mihaljčić B. , Browning P. K. , Gibson K. J.
Published: January 2007

The University of Manchester Linear System (ULS) [M. G. Rusbridge et al., Plasma Phys. Controlled Fusion 42, 588 (2000)] is an experiment in which a steady-state plasma stream is confined along a longitudinal magnetic field. The plasma passes through a tapered orifice into a separate gas target chamber (GTC) where it interacts with neutral gas at pressures of up to 15mTorr. The upstream plasma beam is 6–14mm in diameter with electron temperatures between 2and15eV, and densities in the range of 1017–1019m−3. The primary aim of this study is to investigate physical processes relevant to gas target divertors in tokamaks. Upstream parameters, in terms of electron temperature and density, can be varied in the ULS enabling the investigation of electron-ion recombination (EIR) or molecular-activated recombination (MAR) processes. Detached recombining plasmas have been studied in the GTC using an axially scanning spectroscopic system with a spatial resolution of less than 5mm. We have investigated two distinct plasma regimes having the same electron temperature upstream, but upstream densities that differ by an order of magnitude. Vibrationally excited molecules, which are a necessary prerequisite for MAR, have been detected in both these cases. In the higher density case, which ultimately detaches via EIR processes, these excited molecules are present upstream of the EIR region.
Three-axis acoustic device for levitation of droplets in an open gas stream and its application to examine sulfur dioxide absorption by water droplets
Authors: Stephens Terrance L. , Budwig Ralph S.
Published: January 2007

Two acoustic devices to stabilize a droplet in an open gas stream (single-axis and three-axis levitators) have been designed and tested. The gas stream was provided by a jet apparatus with a 64mm exit diameter and a uniform velocity profile. The acoustic source used was a Langevin vibrator with a concave reflector. The single-axis levitator relied primarily on the radial force from the acoustic field and was shown to be limited because of significant droplet wandering. The three-axis levitator relied on a combination of the axial and radial forces. The three-axis levitator was applied to examine droplet deformation and circulation and to investigate the uptake of SO2 from the gas stream to the droplet. Droplets ranging in diameters from 2to5mm were levitated in gas streams with velocities up to 9m∕s. Droplet wandering was on the order of a half droplet diameter for a 3mm diameter droplet. Droplet circulation ranged from the predicted Hadamard-Rybczynski pattern to a rotating droplet pattern. Droplet pH over a central volume of the droplet was measured by planar laser induced fluorescence. The results for the decay of droplet pH versus time are in general agreement with published theory and experiments.
Second harmonic generation analysis in hydrogenated amorphous silicon nitride thin films
Authors: Lettieri S. , Merola F. , Maddalena P. , Ricciardi C. , Giorgis F.
Published: January 2007

Surface and interface electronic properties of plasma-deposited hydrogenated amorphous silicon nitride films have been investigated by means of optical second harmonic generation (SHG) technique. Polarization analysis shows that the nonlinear field origins from isotropic interfaces (film/substrate interface and film/air interface) whose spectral features are ascribed to surface/interface Si dangling bonds and strained Si–Si bonds. Differences and similarities with SHG spectra of pure amorphous silicon (a-Si:H) are discussed in terms of compositional inhomogeneities of the ternary alloy.
Quantum surface diffusion of vibrationally excited molecular dimers
Authors: Pijper E. , Fasolino A.
Published: January 2007

We consider the thermally activated quantum diffusion of a molecular dimer in a periodic surface potential by means of a time-dependent wave packet method. We show that the potential energy surface resulting from the interplay of intradimer and dimer-surface interactions can lead to resonant states and predict high tunneling probabilities at specific, below barrier, energies that depend also on the initial vibrational state of the dimer. For soft molecular bonds, we show that the chaotic dynamical regime of classical dimers is mirrored, in the quantum case, by the tunneling induced mixing of vibrational states. The knowledge of the transmission coefficient is used to formulate an approximate description of quantum thermal diffusion by defining an effective temperature-dependent activation energy that can be compared to the classical case.
Simulated scaling method for localized enhanced sampling and simultaneous “alchemical” free energy simulations: A general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations
Authors: Li Hongzhi , Fajer Mikolai , Yang Wei
Published: January 2007

A potential scaling version of simulated tempering is presented to efficiently sample configuration space in a localized region. The present “simulated scaling” method is developed with a Wang-Landau type of updating scheme in order to quickly flatten the distributions in the scaling parameter λm space. This proposal is meaningful for a broad range of biophysical problems, in which localized sampling is required. Besides its superior capability and robustness in localized conformational sampling, this simulated scaling method can also naturally lead to efficient “alchemical” free energy predictions when dual-topology alchemical hybrid potential is applied; thereby simultaneously, both of the chemically and conformationally distinct portions of two end point chemical states can be efficiently sampled. As demonstrated in this work, the present method is also feasible for the quantum mechanical and quantum mechanical/molecular mechanical simulations.
Effect of interfacial free energy on hydriding reaction of Mg–Ni thin films
Authors: Ouyang L. Z. , Ye S. Y. , Dong H. W. , Zhu M.
Published: January 2007

The Mg2.9Ni film with preferential orientated nanocrystalline structure was obtained by magnetron sputtering. The hydrogen storage properties and microstructure were investigated by pressure-composition-isotherms measurement, x-ray diffraction and transmission electron microscopy. A reversible hydrogen storage content of about 4.45mass% at 497K has been obtained. The preferential orientation of the deposited film was destroyed after only one hydrogenation/dehydrogenation cycle. Both experiment and simplified calculation results proved that the hydrogenation/dehydrogenation reaction temperature decreases due to the extra interfacial free energy stored in the boundary, which demonstrate that Mg based hydride can be substantially destabilized by inducing nanocrystalline structure.
Nanoscale phase separation in amorphous immiscible copper-niobium alloy thin films
Authors: Banerjee R. , Puthucode A. , Bose S. , Ayyub P.
Published: January 2007

While amorphous phases have been reported in immiscible alloy systems, there is still some controversy regarding the reason for the stabilization of these unusual amorphous phases. In this letter, using three-dimensional atom probe tomography, direct evidence of nanoscale phase separation within the amorphous phase forming in immiscible Cu–Nb alloy thin films has been presented. This evidence clearly indicates that the nanoscale phase separation is responsible for the stabilization of the amorphous phase in such immiscible systems since it substantially reduces the free energy of the undercooled liquid (or amorphous) phase, below that of the competing supersaturated crystalline phases.
Recombination-mechanism dependence of transport and light emission of ambipolar long-channel carbon-nanotube field-effect transistors
Authors: Hsieh Chi-Ti , Citrin D. S. , Ruden P. P.
Published: January 2007

The transport properties of ambipolar long-channel carbon-nanotube field-effect transistors are calculated in the framework of a diffusive-transport model. The effects associated with radiative and nonradiative recombinations of injected electrons and holes in the channel are considered, and the spatial dependence of the recombination profile on the gate and drain voltages is explored. Nonradiative recombination is shown to play a decisive role in the transport characteristics. The emitted light spot size is predicted to exhibit sensitive dependence on the nonradiative recombination mechanism. Moreover, the local electric field reaches a maximum but remains relatively small inside the recombination region.
Reynolds transport theorem for a two-phase flow
Authors: Collado Francisco J.
Published: January 2007

Transport equations for one-dimensional (1d), steady, two-phase flow have been proposed based on the fact that if the phases have different velocities, they cannot cover the same distance (the control volume length) in the same time. Thus, working in the same control volume for the two phases, the time scales of the phases have to be different. From this approach, transport balances for 1D, steady, two-phase flow have been already derived, supplying acceptable correlations for two-phase flow. Here, based on the strict application of the Reynolds transport theorem, general transport balances for two-phase flow are suggested.
Formation of single quantum dot in single-walled carbon nanotube channel using focused-ion-beam technique
Authors: Maehashi Kenzo , Ozaki Hirokazu , Ohno Yasuhide , Inoue Koichi , Matsumoto Kazuhiko , Seki Shu , Tagawa Seiichi
Published: January 2007

The authors fabricated a single quantum dot in a single-walled carbon nanotube (SWCNT) channel using focused-ion-beam techniques. They used this technique to form two tunnel barriers, constituting a single quantum dot, by introducing two damaged regions with a separation of 50nm into a SWCNT channel. Electrical properties revealed that source-drain current oscillation as a function of gate voltage was clearly observed at room temperature, resulting from the Coulomb blockade effect. Charging energy of the single quantum dot in the SWCNT channel was estimated to be 255meV, which is approximately ten times larger than thermal energy at room temperature.
Piezoelectric response hysteresis in the presence of ferroelastic 90° domain walls
Authors: Le Rhun G. , Vrejoiu I. , Alexe M.
Published: January 2007

Piezoelectric response hysteresis curves of Pb(Zr0.2Ti0.8)O3-based capacitors have been measured by piezoresponse force microscopy. The piezoelectric coefficient d33 was found to vary considerably depending on the position of the probing tip on the top electrode for films possessing a c∕a∕c domain structure. d33 values up to 125pm∕V, which is twice the theoretical value for a clamped film, have been measured. The spatial variations of the piezoelectric response amplitude is explained by a local movement of ferroelastic 90° a domains. This work experimentally proves the local enhancement of the polarization near the 90° wall boundaries, as predicted by Ishibashi et al. [Jpn. J. Appl. Phys. 44, 7512 (2005)].
Unconditionally secure one-way quantum key distribution using decoy pulses
Authors: Yuan Z. L. , Sharpe A. W. , Shields A. J.
Published: January 2007

The authors report here a complete experimental realization of one-way decoy pulse quantum key distribution, demonstrating an unconditionally secure key rate of 5.51kbits∕s for a 25.3km fiber length. This is two orders of magnitudes higher than the value that can be obtained with a nondecoy system. They also introduce a simple test for detecting the photon number splitting attack and highlight that it is essential for the security of the technique to fully characterize the source and detectors used.
Room-temperature ferromagnetism in self-assembled (In, Mn)As quantum dots
Authors: Chen Y. F. , Huang J. H. , Lee W. N. , Chin T. S. , Huang R. T. , Chen F. R. , Kai J. J. , Ku H. C.
Published: January 2007

Self-assembled In1−xMnxAs quantum dots (0.19⩽x⩽0.45) have been grown on GaAs (100) substrates by low-temperature molecular beam epitaxy. The microstructure analysis revealed that the uniformly distributed In1−xMnxAs dots have a zinc blende structure as x⩽0.38. Furthermore, all samples exhibit ferromagnetic state at 5K, and their Curie temperatures range from 260to340K varying with x. These (In, Mn)As quantum dots are promising for room-temperature spintronic devices.
Effect of annealing temperature and ambient gas on phosphorus doped p-type ZnO
Authors: Hwang Dae-Kue , Oh Min-Suk , Lim Jae-Hong , Kang Chang-Goo , Park Seong-Ju
Published: January 2007

The authors report on the thermal activation of phosphorus doped p-type ZnO thin films grown by radio frequency magnetron sputtering. The p-type ZnO was produced by activating phosphorus doped ZnO thin films in N2, Ar, or O2 ambients. The hole concentration of the p-type ZnO, prepared in an O2 ambient, showed a lower hole concentration compared to samples annealed in N2 and Ar ambients. The activation energies of the phosphorus dopant in the p-type ZnO under different ambient gases indicate that phosphorus atoms replace oxygen atoms in the ZnO to form PO which acts as an acceptor.
Context-dependent effect of social environment on immune response and sexual signalling in male zebra finches
Authors: Gleeson Deborah J.
Published: January 2007

Variation in avian immune response can be influenced by social environment. This is of particular interest in the context of immunomediated sexual behaviour because social environment may subsequently affect a bird’s relative investment in immunocompetence versus sexual signalling. I tested whether the effect of social environment on immune response and sexual signalling depends on socio-sexual status using male zebra finches (Taeniopygia guttata). To do this, I manipulated social environment (‘same sex’ versus ‘dual sex’) and socio-sexual status (‘high’ versus ‘low’) of the males. I then determined what effect these manipulations had on an index of immunocompetence, namely cell-mediated immune response, and two indices of sexual signalling (bill colour and song rate). I found that social environment influenced cell-mediated immune response and sexual signalling in low-status males. These males had lower immune responses and increased sexual signalling in the dual-sex environment compared with the same-sex environment. In contrast, high-status males had similar immune responses and sexual signalling regardless of social environment. These results suggest that social environment can influence immune response and sexual signalling; however, the nature of this effect was context-dependent, with low-status males more affected than high-status males.
Growth dynamics of freshwater crocodiles (Crocodylus johnstoni) in the Lynd River, Queensland
Authors: Tucker Anton D. , Limpus Colin J. , McDonald Keith R. , McCallum Hamish I.
Published: January 2007

We analysed growth models for a population of Australian freshwater crocodiles (Crocodylus johnstoni). Competing growth models were tested with two data sets: individuals of known-age, and growth interval data from capture-recapture records. A von Bertalanffy function provided the best empirical fit of several growth models. The estimated asymptotic lengths (snout–vent length of males = 125.3 cm; females = 97.4 cm) agreed well with average lengths of the ten largest males and females in the population. Sexual size dimorphism in this species resulted from a combination of smaller mean length at maturity for females and a subsequent decline in female growth rate. Size dimorphism may result from individual trade-offs in age v. length at maturity as a consequence of sexual selection.
Axon guidance genes identified in a large-scale RNAi screen using the RNAi-hypersensitive
Caenorhabditis elegans
strain
nre-1(hd20) lin-15b(hd126
)
Authors: Schmitz Caroline , Kinge Parag , Hutter Harald
Published: January 2007

The navigation of axons toward their targets is a highly dynamic and precisely regulated process during nervous system development. The molecular basis of this navigation process is only partly understood. In
Caenorhabditis elegans
, we isolated the RNAi-hypersensitive strain
nre-1(hd20) lin-15b(hd126)
, which allows us to phenocopy axon guidance defects of known genes by feeding RNAi. We used this mutant strain to systematically screen 4,577 genes on chromosomes I and III for axon guidance phenotypes. We identified 93 genes whose down-regulation led to penetrant ventral cord fasciculation defects or motoneuron commissure outgrowth defects. These genes encode various classes of proteins, ranging from secreted or putative cell surface proteins to transcription factors controlling gene expression. A majority of the genes is evolutionary conserved and previously uncharacterized. In addition, we found axon guidance functions for known genes like
pry-1
, a component of the Wnt-signaling pathway, and
ced-1
, a receptor required for the engulfment of neurons undergoing apoptosis during development. Our screen provides insights into molecular pathways operating during the generation of neuronal circuits and provides a basis for a more detailed analysis of gene networks regulating axon navigation.
Temperature control of larval dispersal and the implications for marine ecology, evolution, and conservation
Authors: O'Connor Mary I. , Bruno John F. , Gaines Steven D. , Halpern Benjamin S. , Lester Sarah E. , Kinlan Brian P. , Weiss Jack M.
Published: January 2007

Temperature controls the rate of fundamental biochemical processes and thereby regulates organismal attributes including development rate and survival. The increase in metabolic rate with temperature explains substantial among-species variation in life-history traits, population dynamics, and ecosystem processes. Temperature can also cause variability in metabolic rate within species. Here, we compare the effect of temperature on a key component of marine life cycles among a geographically and taxonomically diverse group of marine fish and invertebrates. Although innumerable lab studies document the negative effect of temperature on larval development time, little is known about the generality versus taxon-dependence of this relationship. We present a unified, parameterized model for the temperature dependence of larval development in marine animals. Because the duration of the larval period is known to influence larval dispersal distance and survival, changes in ocean temperature could have a direct and predictable influence on population connectivity, community structure, and regional-to-global scale patterns of biodiversity.
Alleviation of 1,
N
6
-ethanoadenine genotoxicity by the
Escherichia coli
adaptive response protein AlkB
Authors: Frick Lauren E. , Delaney James C. , Wong Cintyu , Drennan Catherine L. , Essigmann John M.
Published: January 2007

1,
N
6
-ethanoadenine (EA) forms through the reaction of adenine in DNA with the antitumor agent 1,3-bis(2-chloroethyl)-1-nitrosourea, a chemotherapeutic used to combat various brain, head, and neck tumors. Previous studies of the toxic and mutagenic properties of the DNA adduct EA have been limited to
in vitro
experiments using mammalian polymerases and have revealed the lesion to be both miscoding and genotoxic. This work explores lesion bypass and mutagenicity of EA replicated
in vivo
and demonstrates that EA is neither toxic nor mutagenic in wild-type
Escherichia coli
. Although the base excision repair glycosylase enzymes of both humans and
E. coli
possess a weak ability to act on the lesion
in vitro
, an
in vivo
repair pathway has not yet been demonstrated. Here we show that an enzyme mechanistically unrelated to DNA glycosylases, the adaptive response protein AlkB, is capable of acting on EA via its canonical mechanism of oxidative dealkylation. The reaction alleviates the unrepaired adduct's potent toxicity through metabolism at the C8 position (attached to N1 of adenine), producing a nontoxic and weakly mutagenic
N
6
adduct. AlkB is shown here to be a geno-protective agent that reduces the toxicity of DNA damage by converting the primary adduct to a less toxic secondary product.
Combination angiostatic therapy completely inhibits ocular and tumor angiogenesis
Authors: Dorrell Michael I. , Aguilar Edith , Scheppke Lea , Barnett Faith H. , Friedlander Martin
Published: January 2007

Angiostatic therapies designed to inhibit neovascularization associated with multiple pathological conditions have only been partially successful; complete inhibition has not been achieved. We demonstrate synergistic effects of combining angiostatic molecules that target distinct aspects of the angiogenic process, resulting in the complete inhibition of neovascular growth associated with development, ischemic retinopathy, and tumor growth, with little or no effect on normal, mature tissue vasculature. Tumor vascular obliteration using combination angiostatic therapy was associated with reduced tumor mass and increased survival in a rat 9L gliosarcoma model, whereas individual monotherapies were ineffective. Significant compensatory up-regulation of several proangiogenic factors was observed after treatment with a single angiostatic agent. In contrast, treatment with combination angiostatic therapy significantly reduced compensatory up-regulation. Therapies that combine angiostatic molecules targeting multiple, distinct aspects of the angiogenic process may represent a previously uncharacterized paradigm for the treatment of many devastating diseases with associated pathological neovascularization.
Gas-phase ions of solute species from charged droplets of solutions
Authors: Nguyen Steve , Fenn John B.
Published: January 2007

Charged droplets, produced by electrostatic dispersion of solutions of amino acids and peptides are driven by a potential difference a countercurrent to a flow of heated nitrogen bath gas. Evaporation of solvent from those droplets increases surface charge density, resulting in subdivision into smaller charged droplets. Each smaller droplet repeats that sequence until the ultimate result is a dispersion of solvent-free solute ions in the bath gas. Surprisingly, mass spectrometric analyses of the final ion-bath gas mixtures showed that the relative abundances of the desolvated ions were substantially higher when the nitrogen bath gas contained vapor of a polar solvent species than when no such solvent vapor was present. Adding solvent vapor to the background bath gas can certainly not increase, but must decrease, the net rate of solvent evaporation from the charged droplets. Consequently, the observed enhancement of ion formation by the presence of solvent vapor in the bath gas constitutes persuasive evidence that the observed solute ions cannot have been produced by the charged residue mechanism originally suggested by Dole
et al.
[Dole M,
et al
. (1968)
J Chem Phys
49:2240–2249 and Dole M, Rheude A, Mack LL (1970)
J Chem Phys
52:4977–4986]. It is therefore concluded that electrospray ions are most likely produced by the ion evaporation mechanism of Iribarne and Thomson [Iribarne JV, Thomson BA (1975)
J Chem Phys
64:2287–2294]. Moreover, and probably as important, this observed signal enhancement constitutes a welcome increase in detection sensitivity.
Prospects for the biological control of the groundnut leaf miner,
Aproaerema modicella
, in Africa.
Authors: Kenis M. , Cugala D.
Published: January 2007

The groundnut leaf miner,
Aproaerema modicella
, is a pest of groundnut and soyabean in South and Southeast Asia that has recently invaded Africa. It was first found in Uganda in 1998 and is now recorded in Mozambique, Malawi, Democratic Republic of Congo and South Africa. In all African countries where
A. modicella
has been found, the pest has reached outbreak densities and severe yield losses have been observed on groundnut. In this paper, we review the natural enemies of
A. modicella
in Asia and evaluate their potential for biological control in Africa. The main natural enemies of
A. modicella
in Asia are parasitoids. Over 30 primary parasitoid species have been recorded with mean parasitism rates fluctuating between 20% and 50% and peak parasitism reaching 53-91%. The most often cited parasitoids belong to the genera
Goniozus
(Hym.: Bethylidae),
Apanteles
,
Bracon
,
Chelonus
and
Avga
(Hym.: Braconidae),
Brachymeria
(Hym.: Chalcididae), and
Stenomesius
,
Sympiesis
and
Tetrastichus
(Hym.: Eulophidae). Predators and pathogens have been poorly studied.
A. modicella
is a promising target for classical biological control using natural enemies from Asia. Damage levels are, on average, higher in Africa than in Asia, where parasitoids, and possibly predators and pathogens, probably play an important role in the natural control of the pest. However, surveys are needed in Asia to better study natural enemies of
A. modicella
before selecting the most suitable agents. Until now, most studies on natural enemies were carried out in India, where
A. modicella
is considered a serious pest. New surveys should focus on other regions, where the moth causes little damage and very little is known on its natural enemy complex.
Topology and energy of time-dependent unitons
Authors: Dunajski Maciej , Plansangkate Prim
Published: January 2007

We consider a class of time-dependent finite energy multi-soliton solutions of theU(N) integrable chiral model in (2+1) dimensions. The corresponding extended solutions of the associated linear problem have a pole with arbitrary multiplicity in the complex plane of the spectral parameter. Restrictions of these extended solutions to any space-like plane inhave trivial monodromy and give rise to maps from a three-sphere toU(N). We demonstrate that the total energy of each multi-soliton is quantized at the classical level and given by the third homotopy class of the extended solution. This is the first example of a topological mechanism explaining the classical energy quantization of moving solitons.
Osmosis in semi-permeable pores: an examination of the basic flow equations based on an experimental and molecular dynamics study
Authors: Davis I.S , Shachar-Hill B , Curry M.R , Kim K.S , Pedley T.J , Hill A.E
Published: January 2007

Classically ‘semi-permeable’ pores are generally considered to mediate osmotic flow at a rate dependent upon the hydraulic conductance of the pore and the difference in water potential. The shape or size of the solute molecules is not considered to exert a first-order effect on the flow rate nor is the hydraulic conductance thought to be solute dependent. By the experimental measurement of osmosis in the biological pore AQP (aquaporin) and hard-sphere molecular dynamics simulation of a model pore, we show here that the solute radius can have a profound effect on the osmotic flow rate, causing it to decline steeply with decreasing solute radius.

Using a simple non-equilibrium thermodynamic theory, we propose that an additional ‘osmotic flow coefficient’ is required to describe flows in semi-permeable structures such as AQPs, and that the fall in flow rate with radius represents a conversion from hydraulic to diffusive water flow due to increasing penetration of the pore by the solute. The interaction between the pore geometry and the solute size cannot, therefore, be overlooked, although for every solute the system obeys the criterion for semi-permeability required by basic thermodynamics. The osmotic pore theory therefore reveals a novel and potentially rich structure that remains to be explored in full.
Natural selection acts on Atlantic salmon major histocompatibility (MH) variability in the wild
Authors: de Eyto Elvira , McGinnity Philip , Consuegra Sofia , Coughlan Jamie , Tufto Jarle , Farrell Killian , Megens Hendrik-Jan , Jordan William , Cross Tom , Stet René J.M
Published: January 2007

Pathogen-driven balancing selection is thought to maintain polymorphism in major histocompatibility (MH) genes. However, there have been few empirical demonstrations of selection acting on MH loci in natural populations. To determine whether natural selection on MH genes has fitness consequences for wild Atlantic salmon in natural conditions, we compared observed genotype frequencies of Atlantic salmon (Salmo salar) surviving in a river six months after their introduction as eggs with frequencies expected from parental crosses. We found significant differences between expected and observed genotype frequencies at the MH class II alpha locus, but not at a MH class I-linked microsatellite or at seven non-MH-linked microsatellite loci. We therefore conclude that selection at the MH class II alpha locus was a result of disease-mediated natural selection, rather than any demographic event. We also show that survival was associated with additive allelic effects at the MH class II alpha locus. Our results have implications for both the conservation of wild salmon stocks and the management of disease in hatchery fish. We conclude that natural or hatchery populations have the best chance of dealing with episodic and variable disease challenges if MH genetic variation is preserved both within and among populations.
Correlation versus gradient type motion detectors: the pros and cons
Authors: Borst Alexander
Published: January 2007

Visual motion contains a wealth of information about self-motion as well as the three-dimensional structure of the environment. Therefore, it is of utmost importance for any organism with eyes. However, visual motion information is not explicitly represented at the photoreceptor level, but rather has to be computed by the nervous system from the changing retinal images as one of the first processing steps. Two prominent models have been proposed to account for this neural computation: the Reichardt detector and the gradient detector. While the Reichardt detector correlates the luminance levels derived from two adjacent image points, the gradient detector provides an estimate of the local retinal image velocity by dividing the spatial and the temporal luminance gradient. As a consequence of their different internal processing structure, both the models differ in a number of functional aspects such as their dependence on the spatial-pattern structure as well as their sensitivity to photon noise. These different properties lead to the proposal that an ideal motion detector should be of Reichardt type at low luminance levels, but of gradient type at high luminance levels. However, experiments on the fly visual systems provided unambiguous evidence in favour of the Reichardt detector under all luminance conditions. Does this mean that the fly nervous system uses suboptimal computations, or is there a functional aspect missing in the optimality criterion? In the following, I will argue in favour of the latter, showing that Reichardt detectors have an automatic gain control allowing them to dynamically adjust their input–output relationships to the statistical range of velocities presented, while gradient detectors do not have this property. As a consequence, Reichardt detectors, but not gradient detectors, always provide a maximum amount of information about stimulus velocity over a large range of velocities. This important property might explain why Reichardt type of computations have been demonstrated to underlie the extraction of motion information in the fly visual system under all luminance levels.
Prehistoric human impact on rainforest biodiversity in highland New Guinea
Authors: Haberle Simon G
Published: January 2007

In the highlands of New Guinea, the development of agriculture as an indigenous innovation during the Early Holocene is considered to have resulted in rapid loss of forest cover, a decrease in forest biodiversity and increased land degradation over thousands of years. But how important is human activity in shaping the diversity of vegetation communities over millennial time-scales? An evaluation of the change in biodiversity of forest habitats through the Late Glacial transition to the present in five palaeoecological sites from highland valleys, where intensive agriculture is practised today, is presented. A detailed analysis of the longest and most continuous record from Papua New Guinea is also presented using available biodiversity indices (palynological richness and biodiversity indicator taxa) as a means of identifying changes in diversity. The analysis shows that the collapse of key forest habitats in the highland valleys is evident during the Mid–Late Holocene. These changes are best explained by the adoption of new land management practices and altered disturbance regimes associated with agricultural activity, though climate change may also play a role. The implications of these findings for ecosystem conservation and sustainability of agriculture in New Guinea are discussed.