bluuebunny/crossref_metadata_2025 huggingface dataset:
Approximate treatment of higher excitations in coupled-cluster theory
Authors: Kállay Mihály , Gauss Jürgen
Published: December 2005

The possibilities for the approximate treatment of higher excitations in coupled-cluster (CC) theory are discussed. Potential routes for the generalization of corresponding approximations to lower-level CC methods are analyzed for higher excitations. A general string-based algorithm is presented for the evaluation of the special contractions appearing in the equations specific to those approximate CC models. It is demonstrated that several iterative and noniterative approximations to higher excitations can be efficiently implemented with the aid of our algorithm and that the coding effort is mostly reduced to the generation of the corresponding formulas. The performance of the proposed and implemented methods for total energies is assessed with special regard to quadruple and pentuple excitations. The applicability of our approach is illustrated by benchmark calculations for the butadiene molecule. Our results demonstrate that the proposed algorithm enables us to consider the effect of quadruple excitations for molecular systems consisting of up to 10–12 atoms.
Effects of varying the step particle distribution on a probabilistic transport model
Authors: Bouzat S. , Farengo R.
Published: December 2005

The consequences of varying the step particle distribution on a probabilistic transport model, which captures the basic features of transport in plasmas and was recently introduced in Ref. 1 [B. Ph. van Milligen et al., Phys. Plasmas 11, 2272 (2004)], are studied. Different superdiffusive transport mechanisms generated by a family of distributions with algebraic decays (Tsallis distributions) are considered. It is observed that the possibility of changing the superdiffusive transport mechanism improves the flexibility of the model for describing different situations. The use of the model to describe the low (L) and high (H) confinement modes is also analyzed.
Ab initio and direct quasiclassical-trajectory study of the F+CH4→HF+CH3 reaction
Authors: Troya Diego
Published: December 2005

We present an electronic structure and dynamics study of the F+CH4→HF+CH3 reaction. CCSD(T)/aug-cc-pVDZ geometry optimizations, harmonic-frequency, and energy calculations indicate that the potential-energy surface is remarkably isotropic near the transition state. In addition, while the saddle-point F–H–C angle is 180° using MP2 methods, CCSD(T) geometry optimizations predict a bent transition state, with a 153° F–H–C angle. We use these high-quality ab initio data to reparametrize the parameter-model 3 (PM3) semiempirical Hamiltonian so that calculations with the improved Hamiltonian and employing restricted open-shell wave functions agree with the higher accuracy data. Using this specific-reaction-parameter PM3 semiempirical Hamiltonian (SRP-PM3), we investigate the reaction dynamics by propagating quasiclassical trajectories. The results of our calculations using the SRP-PM3 Hamiltonian are compared with experiments and with the estimates of two recently reported potential-energy surfaces. The trajectory calculations using the SRP-PM3 Hamiltonian reproduce quantitatively the measured HF vibrational distributions. The calculations also agree with the experimental HF rotational distributions and capture the essential features of the excitation function. The results of the SRP semiempirical Hamiltonian developed here clearly improve over those using the two prior potential-energy surfaces and suggest that reparametrization of semiempirical Hamiltonians is a promising strategy to develop accurate potential-energy surfaces for reaction dynamics studies of polyatomic systems.
Hidden ferrimagnetism in pniktides (Fe–Mn)1.95As
Authors: Val’kov V. I. , Gribanov I. F. , Golovchan A. V. , Todris B. M.
Published: November 2005

The results of experimental investigations of the magnetic properties of the antiferromagnetic alloy Fe0.765Mn1.185As are presented. They show that at atmospheric pressure and temperatures below 65 K the antiferromagnetic state is not the only stable state, since the imposition of a magnetic field in this temperature range makes it possible to observe irreversible induced transitions into a state with a canted ferrimagnetic structure. This is a second stable state for the experimental sample. As the temperature increases, this state vanishes via a first-order phase transformation at 65 K. Above 65 K reversible induced first-order transitions from the antiferromagnetic into a canted ferrimagnetic structure are observed. The results are discussed on the basis of a phenomenological expression for the free energy of a system with two interacting magnetic-order parameters. It is shown that a simple phenomenological model qualitatively describes the behavior of the system investigated. A single-band Hubbard model is used to give a microscopic substantiation of the phenomenological approach.
Isotopic effects in the heat capacity of concentrated orientationally disordered solid solutions of methane and deuteromethane in krypton
Authors: Bagatskiĭ M. I. , Dudkin V. V. , Mashchenko D. A. , Manzheliĭ V. G. , Manzheliĭ E. V.
Published: November 2005

The heat capacity of orientationally disordered solid solutions (CH4)nKr1−n (n=75 and 78 mole% CH4 in the temperature interval ΔT=0.8–20 K) and (CD4)nKr1−n (n=50, 60, and 70 mole% CD4, ΔT=0.6–30 K) is investigated. At liquid-helium temperatures the temperature dependences of the molar heat capacities of the rotational subsystems of the solutions are qualitatively and quantitatively very different. One of the main reasons for the effect is that in the concentrated solutions investigated the CD4 molecules are in a substantially stronger molecular field than the CH4 molecules. This is because in low-energy states the effective octupole electric moment of CD4 molecules, which determines the molecular field, is larger than the effective octupole moment of the more quantum molecules CH4. The weak concentration dependences of the heat capacity of the solutions studied are due to the influence of frustration, which weakens the molecular fields produced at the lattice sites by the surrounding molecules. No evidence of the formation of orientational octupole glasses in the experimental systems was found.
Pressure tuning of the Fermi resonance in liquid methanol: Implications for the analysis of high-pressure vibrational spectroscopy experiments
Authors: Arencibia A. , Taravillo M. , Cáceres M. , Núñez J. , Baonza V. G.
Published: November 2005

It has been argued that pressure tuning allows for unambiguous assignment of the nonperturbed bands involved in the Fermi coupling of molecular systems in the condensed phase. Here we study the pressure evolution of the Fermi resonance occurring in liquid methanol between the symmetric methyl-stretch fundamental and the methyl-bending overtones. Our analysis is based on Raman experiments in both stretching and bending fundamental regions, which are used to evaluate the effect of pressure on accidental degeneracies occurring in the vibrational spectra of liquid methanol. We emphasize that the difference in frequency of the Fermi doublet constitutes the governing quantity to determine the condition at which the exact degeneracy of the unperturbed modes occurs. Analysis based on the intensity ratio of the Fermi doublet must be disregarded. We confirm the necessity of measuring the full vibrational spectrum under pressure in order to obtain the Fermi coupling parameters unambiguously and to give a correct assignment of the bands involved in the resonance phenomenon. We also analyze the possible occurrence of several simultaneous resonance effects using a multilevel perturbation model. This model provides an appropriate description of the frequencies observed in the experiments over the whole pressure range if we consider that the main resonance occurs between ν3 and 2ν10, in contrast to previous assignments. Our global analysis leads to some general rules concerning measurement and interpretation of high-pressure vibrational spectroscopy experiments.
Assessment of a new approach for the two-electron cumulant in natural-orbital-functional theory
Authors: Leiva P. , Piris M.
Published: November 2005

The Piris natural orbital functional (PNOF) based on a new approach for the two-electron cumulant has been used to predict adiabatic ionization potentials, equilibrium bond distances, and harmonic vibrational frequencies of 18 diatomic molecules. Vertical ionization potentials have been calculated for the same set of diatomic molecules and another set of 20 polyatomic molecules using energy-difference methods as well as the extended Koopman theorem. The PNOF properties compare favorably with the coupled-cluster-doubles results. The calculated PNOF values are in good agreement with the corresponding experimental data, considering the basis sets used (6-31G**).
Thermal stability of sputter-deposited 330 austenitic stainless-steel thin films with nanoscale growth twins
Authors: Zhang X. , Misra A. , Wang H. , Swadener J. G. , Lima A. L. , Hundley M. F. , Hoagland R. G.
Published: December 2005

We have explored the thermal stability of nanoscale growth twins in sputter-deposited 330 stainless-steel (SS) films by vacuum annealing up to 500°C. In spite of an average twin spacing of only 4nm in the as-deposited films, no detectable variation in the twin spacing or orientation of twin interfaces was observed after annealing. An increase in the average columnar grain size was observed after annealing. The hardness of 330 SS films increases after annealing, from 7GPa for as-deposited films to around 8GPa for annealed films, while the electrical resistivity decreases slightly after annealing. The changes in mechanical and electrical properties after annealing are interpreted in terms of the corresponding changes in the residual stress and microstructure of the films.
Optical properties of δ-Bi2O3 thin films grown by reactive sputtering
Authors: Fan H. T. , Teng X. M. , Pan S. S. , Ye C. , Li G. H. , Zhang L. D.
Published: December 2005

The optical properties of δ-Bi2O3 thin films were investigated using spectroscopic ellipsometry and optical absorption spectrum. δ-Bi2O3 thin films were grown on Si and quartz substrates under different oxygen flow ratios (OFR) by radio frequency reactive magnetron sputtering. The Tauc-Lorentz dispersion method was adopted to model the optical dispersion functions of the thin films. The optical bandgap was obtained by three different methods. It was found that refractive index and extinction coefficient decrease, and the optical bandgap has a slight blue shift with increasing the OFR. Factors influencing the optical constants and optical bandgap are discussed.
Sheared flow effects on ballooning instabilities in three-dimensional equilibria
Authors: Hegna C. C.
Published: December 2005

The stability of ideal magnetohydrodynamic ballooning modes in the presence of sheared flow is investigated for three-dimensional equilibria. Application of ballooning formalism reduces the problem to a partial differential equation in three dimensions that can be solved in the limit of small flow. Analytic calculations demonstrate the stabilizing effect of shear flow. The derived stability criterion generalizes prior work related to axisymmetric equilibrium with sheared toroidal flow.
Direct resistance profile for an electrical pulse induced resistance change device
Authors: Chen X. , Wu N. J. , Strozier J. , Ignatiev A.
Published: December 2005

We report the direct microscale resistance profile measurements on a symmetric thin-film electrical pulse induced resistance change (EPIR) device composed of a Pa0.7Ca0.3MnO3 (PCMO) active layer, using surface scanning Kelvin probe microscopy. The resistance switching is found to be an integration of the resistance changes from three parts of the device: the two interface regions within ∼1–3μm of the electrical contacts, and the bulk PCMO material. Such a symmetric EPIR device showed a “table leg” resistance switching hysteresis loop under electric pulsing at room temperature. The symmetric EPIR device may be used as a resistive random access memory nonvolatile memory device with different operation modes by controlling electric pulse voltage.
Carbon nanotube based nonvolatile memory
Authors: Hollingsworth J. P. , Bandaru P. R.
Published: December 2005

We propose the use of carbon-nanotube based vacuum microelectronics for a nonvolatile memory core. A design that can be implemented with state-of-the art nanotube fabrication techniques is presented and nonvolatile memory operation, up to 0.25 GHz, is shown to be feasible through circuit simulations. When integrated with flip-chip technology, this type of memory offers a possible solution to the problem of flash memory scaling coupled with the advantages of high density integrated circuitry and a faster speed of operation.
Copper(I) complex employed in organic light-emitting electrochemical cells: Device and spectra shift
Authors: Wang Yuan-Min , Teng Feng , Hou Yan-Bing , Xu Zheng , Wang Yong-Sheng , Fu Wen-Fu
Published: December 2005

Copper(I) complex employed in organic light-emitting electrochemical cells (OLECs) are reported. During the study we found that the electroluminescence (EL) spectra under forward voltage redshifted compared with the photoluminescence spectra of the film. Moreover, the EL spectra under reverse voltage also redshifted compared with the forward EL spectra. Based on the electric-field theory and the device mechanism of OLECs, we suggest that the spectra shift is ascribed to the polarization effect of molecular orbitals under high electric field in the device. The polarization and radiation models under electric field have been proposed.
Magnetically steered liquid crystal-nanotube switch
Authors: Dierking Ingo , San S. Eren
Published: December 2005

A magnetically steered electric switch based on nematic liquid crystal-single-wall carbon nanotube dispersions is demonstrated. The device exploits the conductivity anisotropy of nanotubes in combination with the magnetic Freedericksz transition of a nematic liquid crystal. The performance is characterized with respect to the electric measuring field amplitude, frequency and sample cell gap. The dynamic behavior indicates a response time of approximately 4s, and possible applications for magnetic field sensors are discussed.
Low-temperature crystallized pyrochlore bismuth zinc niobate thin films by excimer laser annealing
Authors: Cheng Jian-Gong , Wang Junling , Dechakupt Tanawadee , Trolier-McKinstry Susan
Published: November 2005

The crystallization temperature of Bi1.5Zn0.5Nb1.5O6.5 (BZN) films was reduced by a combination of conventional heating and irradiation with a pulsed KrF excimer laser. Both the energy density and substrate temperature affect the properties of laser-annealed BZN films. It was found that the crystallinity and dielectric properties improved after a postannealing at 400°C for 2h in an oxygen atmosphere. BZN films crystallized with an energy density of 27mJ∕cm2 at a substrate temperature of 400°C with postannealing showed dielectric properties comparable to those of rapid thermal annealed BZN films. Laser crystallization at substrate temperatures ⩽400°C makes integration with polymeric substrates possible.
Optical gain at 650 nm from a polymer waveguide with dye-doped cladding
Authors: Reilly M. A. , Coleman B. , Pun E. Y. B. , Penty R. V. , White I. H. , Ramon M. , Xia R. , Bradley D. D. C.
Published: November 2005

Signal amplification at the polymer optical fiber low-loss window of 650 nm is reported in an SU8 rib waveguide coated with Rhodamine-640 doped poly(methyl methacrylate). A signal beam is end-fired into the facet of a 7×100μm waveguide and amplified by top pumping of the 2-μm-thick cladding region with a pulsed pump source focused into a 9-mm-long stripe. A gain of 14dB and a minimum signal-to-noise ratio of around 2 dB are achieved in a 15-mm-long device with a low threshold pump intensity of 0.25μJ∕mm2, which is an order of magnitude lower than previously reported.
Device structure for electronic transport through individual molecules using nanoelectrodes
Authors: Ghosh Subhasis , Halimun Henny , Mahapatro Ajit Kumar , Choi Jaewon , Lodha Saurabh , Janes David
Published: December 2005

We present a simple and reliable method for making electrical contacts to small organic molecules with thiol endgroups. Nanometer-scale gaps between metallic electrodes have been fabricated by passing a large current through a lithographically-patterned Au-line with appropriate thickness. Under appropriate conditions, the passage of current breaks the Au-line, creating two opposite facing electrodes separated by a gap comparable to the length of small organic molecules. Current-voltage characteristics have been measured both before and after deposition of short organic molecules. The resistance of single 1,4-benzenedithiol and 1,4-bezenedimethanedithiol molecules were found to be 9MΩ and 26MΩ, respectively. The experimental results indicate strong electronic coupling to the contacts and are discussed using a relatively simple model of mesoscopic transport. The use of electrodes formed on an insulating surface by lithography and electromigration provides a stable structure suitable for integrated circuit applications.
Realization of 10Tbit∕in.2 memory density and subnanosecond domain switching time in ferroelectric data storage
Authors: Cho Yasuo , Hashimoto Sunao , Odagawa Nozomi , Tanaka Kenkou , Hiranaga Yoshiomi
Published: December 2005

Nanosized inverted domain dots in ferroelectric materials have potential application in ultrahigh-density rewritable data storage systems. Herein, a data storage system is presented based on scanning nonlinear dielectric microscopy and a thin film of ferroelectric single-crystal lithium tantalite. Through domain engineering, nanosized inverted domain dots have been successfully formed at a data density above 10.1Tbit∕in.2 and subnanosecond (500ps) domain switching speed has been achieved. Moreover, actual information storage is demonstrated at a density of 1Tbit∕in.2
Assessment of vegetation change and landscape variability by using stable carbon isotopes of soil organic matter
Authors: Krull Evelyn G. , Bray Steven S.
Published: December 2005

Stable carbon isotopic (δ13C) analyses of soil organic matter (SOM) have been used in the past to characterise C3–C4 vegetation changes. However, the temporal and spatial resolution of these isotopic data are not well established. Here, we present data from δ13C analyses of whole and size-separated SOM, which are discussed in conjunction with organic (total organic carbon (TOC) content) and inorganic (%clay) soil data. These data are put into context with the current vegetation state (assessed from tree size-class distribution) and the 50-year vegetation history (assessed from aerial photographs). By linking below- and above-ground datasets, we show that δ13C analyses of SOM can accurately record vegetation-change histories over short- (10 and 50years) and longer-term (hundreds of years) time scales. Our data also show that spatial variability was relatively small for the clay TOC content but was much larger for δ13C data, indicating that the number of soil cores required for statistical significance is highly dependent on the kind of measurements intended. Finally, interpretation of δ13C data from SOM to assess the history of C3–C4 vegetation change is complicated by the inherent 13C-enrichment of SOM, owing to decomposition processes, which occurs regardless of vegetation change. We suggest a method for distinguishing 13C-enrichment of SOM that is due to soil-inherent (decomposition-related) processes from 13C-enrichment that is due to increased inputs of C4 organic matter.
Prospects for improving savanna biophysical models by using multiple-constraints model-data assimilation methods
Authors: Barrett Damian J. , Hill Michael J. , Hutley Lindsay B. , Beringer Jason , Xu Johnny H. , Cook Garry D. , Carter John O. , Williams Richard J.
Published: December 2005

A ‘multiple-constraints’ model-data assimilation scheme using a diverse range of data types offers the prospect of improved predictions of carbon and water budgets at regional scales. Global savannas, occupying more than 12% of total land area, are an economically and ecologically important biome but are relatively poorly covered by observations. In Australia, savannas are particularly poorly sampled across their extent, despite their amenity to ground-based measurement (largely intact vegetation, low relief and accessible canopies). In this paper, we describe the theoretical and practical requirements of integrating three types of data (ground-based observations, measurements of CO2/H2O fluxes and remote-sensing data) into a terrestrial carbon, water and energy budget model by using simulated observations for a hypothetical site of given climatic and vegetation conditions. The simulated data mimic specific errors, biases and uncertainties inherent in real data. Retrieval of model parameters and initial conditions by the assimilation scheme, using only one data type, led to poor representation of modelled plant-canopy production and ecosystem respiration fluxes because of errors and bias inherent in the underlying data. By combining two or more types of data, parameter retrieval was improved; however, the full compliment of data types was necessary before all measurement errors and biases in data were minimised. This demonstration illustrates the potential of these techniques to improve the performance of ecosystem biophysical models by examining consistency among datasets and thereby reducing uncertainty in model parameters and predictions. Furthermore, by using existing available data, it is possible to design field campaigns with a specified network design for sampling to maximise uncertainty reduction, given available funding. Application of these techniques will not only help fill knowledge gaps in the carbon and water dynamics of savannas but will result in better information for decision support systems to solve natural-resource management problems in this biome worldwide.
OzFACE: the Australian savanna free air CO2 enrichment facility and its relevance to carbon-cycling issues in a tropical savanna
Authors: Stokes Chris , Ash Andrew , Tibbett Mark , Holtum Joe
Published: December 2005

A free air CO2 enrichment (FACE) facility has recently been constructed in a tropical savanna in north-eastern Queensland, Australia. The system has a novel and cost-effective design and uses an industrial source of pure CO2 piped directly to the site. We describe the design details of this facility and assess the likely contribution it will make towards advancing our understanding of the direct impacts of rising atmospheric CO2 on savannas. These include addressing uncertainties about future shifts in the tree–grass balance and associated changes in carbon stocks, responses of C4 grasses in dry tropical environments, potential sequestration of soil carbon, and the modifications of CO2 responses by moisture and nutrient interactions. Tropical regions have been poorly represented in climate change research, and the work at the OzFACE facility will complement existing and ongoing FACE studies at temperate latitudes.
Inositol Deacylation by Bst1p Is Required for the Quality Control of Glycosylphosphatidylinositol-anchored Proteins
Authors: Fujita Morihisa , Yoko-o Takehiko , Jigami Yoshifumi
Published: December 2005

Misfolded proteins are recognized in the endoplasmic reticulum (ER), transported back to the cytosol, and degraded by the proteasome. A number of proteins are processed and modified by a glycosylphosphatidylinositol (GPI) anchor in the ER, but the quality control mechanisms of GPI-anchored proteins remain unclear. Here, we report on the quality control mechanism of misfolded GPI-anchored proteins. We have constructed a mutant form of the β-1,3-glucanosyltransferase Gas1p (Gas1*p) as a model misfolded GPI-anchored protein. Gas1*p was modified with a GPI anchor but retained in the ER and was degraded rapidly via the proteasome. Disruption of BST1, which encodes GPI inositol deacylase, caused a delay in the degradation of Gas1*p. This delay was because of an effect on the deacylation activity of Bst1p. Disruption of genes involved in GPI-anchored protein concentration and N-glycan processing caused different effects on the degradation of Gas1*p and a soluble misfolded version of carboxypeptidase Y. Furthermore, Gas1*p associated with both Bst1p and BiP/Kar2p, a molecular chaperone, in vivo. Our data suggest that GPI inositol deacylation plays important roles in the quality control and ER-associated degradation of GPI-anchored proteins.
Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology
Authors: Schmidt Henning , Jirstrand Mats
Published: November 2005

Summary: We present a Systems Biology Toolbox for the widely used general purpose mathematical software MATLAB. The toolbox offers systems biologists an open and extensible environment, in which to explore ideas, prototype and share new algorithms, and build applications for the analysis and simulation of biological and biochemical systems. Additionally it is well suited for educational purposes. The toolbox supports the Systems Biology Markup Language (SBML) by providing an interface for import and export of SBML models. In this way the toolbox connects nicely to other SBML-enabled modelling packages. Models are represented in an internal model format and can be described either by entering ordinary differential equations or, more intuitively, by entering biochemical reaction equations. The toolbox contains a large number of analysis methods, such as deterministic and stochastic simulation, parameter estimation, network identification, parameter sensitivity analysis and bifurcation analysis.

Availability: The Systems Biology Toolbox for MATLAB is open source and freely available from . The website also contains a tutorial, extensive documentation and examples.

Contact:  henning@fcc.chalmers.se
Loss of function of def selectively up-regulates Δ113p53 expression to arrest expansion growth of digestive organs in zebrafish
Authors: Chen Jun , Ruan Hua , Ng Sok Meng , Gao Chuan , Soo Hui Meng , Wu Wei , Zhang Zhenhai , Wen Zilong , Lane David P. , Peng Jinrong
Published: December 2005

Transcription factor p53 forms a network with associated factors to regulate the cell cycle and apoptosis in response to environmental stresses. However, there is currently no direct genetic evidence to show if or how the p53 pathway functions during organogenesis. Here we present evidence to show that the zebrafish def (digestive-organ expansion factor) gene encodes a novel pan-endoderm-specific factor. A loss-of-function mutation in def confers hypoplastic digestive organs and selectively up-regulates the expression of Δ113p53, counterpart to a newly identified isoform of p53 produced by an alternative internal promoter in intron 4 of the p53 gene in human. The increased Δ113p53 expression is limited to within the mutant digestive organs, and this increase selectively induces the expression of p53-responsive genes to trigger the arrest of the cell cycle but not apoptosis, resulting in compromised organ growth in the mutant. Our data demonstrate that, while induction of expression of p53 and/or its isoforms is crucial to suppress abnormal cell growth, Δ113p53 is tightly regulated by an organ/tissue-specific factor Def, especially during organogenesis, to prevent adverse inhibition of organ/tissue growth.
Reconsolidation of a context long-term memory in the terrestrial snail requires protein synthesis
Authors: Gainutdinova Tatiana H. , Tagirova Rosa R. , Ismailova Asja I. , Muranova Lyudmila N. , Samarova Elena I. , Gainutdinov Khalil L. , Balaban Pavel M.
Published: December 2005

We investigated the influence of the protein synthesis blocker anisomycin
on contextual memory in the terrestrial snail Helix. Prior to the
training session, the behavioral responses in two contexts were similar. Two
days after a session of electric shocks (5 d) in one context only, the context
conditioning was observed as the significant difference of behavioral response
amplitudes in two contexts. On the day following testing of context learning,
a session of “reminding” was performed, immediately after which
the snails were injected with anisomycin or vehicle. Testing of long-term
context memory has shown that only anisomycin injections impaired the context
conditioning. In control series, the snails were injected after the training
session with anisomycin/saline without reminding, and no impairment of the
long-term context memory was observed, while injection of anisomycin during
the training session completely abolished the long-term memory. No effects of
anisomycin on the short-term memory were observed. Surprisingly, injection of
anisomycin after the reminding combined with reinforcing stimuli elicited no
effect on the context memory. Differences between single-trial and
multisession learning are discussed.
Engineering covalent oligomers of the mechanosensitive channel of large conductance from Escherichia coli with native conductance and gating characteristics
Authors: Folgering Joost H.A. , Wolters Justina C. , Poolman Bert
Published: December 2005

To obtain a gene construct for making single substitutions per channel and to determine the quaternary structure of the mechanosensitive channel MscL from Escherichia coli, covalent oligomers (monomer to hexamer) were engineered by gene fusion; up to six copies of the mscL gene were fused in tandem. All the multimeric tandem constructs yielded functional channels with wild‐type conductance and dwell times. Importantly, only the covalent pentamer opened at the same relative pressure (compared to the pressure required to open MscS) as the wild‐type MscL channel. The in vivo data strongly suggest that pentameric MscL represents the functional state of the channel.
A potential role for invasive sunbleak in the further dissemination of a non‐native parasite
Authors: Beyer K. , Kochanowska D. , Longshaw M. , Feist S. W. , Gozlan R. E.
Published: December 2005

Since its first introduction to English waters in the mid 1980s, sunbleak Leucaspius delineatus has spread widely and it is shown in the present study that this non‐native cyprinid is a new host for Neoergasilus japonicus. This copepod parasite from South East Asia has a limited host range and distribution in the U.K. Rapid dispersal of sunbleak in the U.K. raises concerns for further dispersal of this introduced parasite.
First observations of the burrows of Anguilla japonica
Authors: Aoyama J. , Shinoda A. , Sasai S. , Miller M. J. , Tsukamoto K.
Published: December 2005

The burrow morphology of the Japanese eel Anguilla japonica was studied using in situ resin‐casting in a mud bottomed tidal drainage channel adjacent to the Fukui River in Tokushima, Japan. Two eels (62·5 and 56·3 cm total length) were initially fished from the burrows to verify that they were being used by A. japonica. Casts were made of 10 burrows that were found to have from one to three openings and main tunnels that were parallel to the axis of water flow in the channel. The maximum depths of the tunnels in the mud were 17·8–30·0 cm. The diameters of main tunnels ranged from 1·2 to 7·9 cm, were almost always wider than the bodies of the Japanese eels examined, and were more variable in the horizontal axis than in the vertical axis. There were no other animals capable of constructing a long and thin burrow in this channel, so these observations indicate that anguillids are able to construct their own burrows in soft mud sediments that may be used for extended periods of time.
Intersex in feral brown trout from Swiss midland rivers
Authors: Körner O. , Vermeirssen E. L. M. , Burkhardt‐Holm P.
Published: December 2005

The incidence of intersex in feral populations of brown trout Salmo trutta in Switzerland is reported. The affected brown trout showed spermatogenic activity in ovarian tissue.
Seasonal growth of wild Atlantic salmon juveniles and implications on age at smoltification
Authors: Strothotte E. , Chaput G. J. , Rosenthal H.
Published: December 2005

The seasonal growth trajectories of wild Atlantic salmon Salmo salar juveniles by age group within the Margaree River, Canada, are described. Circuli counts from scales were used to infer growth rates at different ages and these were used to predict the proportions of age 2‐ and 3‐year old smolts from different portions of the watershed. In the wild Atlantic salmon juveniles from the Margaree River, there was no bimodality in fork length frequencies and no 1 year old smolts were produced. Water temperature differences during the growing season were insufficient to explain the differences in growth rates and size at age among the sites sampled. There was a positive association between the growth rate in the first year and the subsequent age at smoltification. In the Margaree River, differences in tributary specific growth rates and size at age were expected to produce important differences in the relative ages at smoltification.
A pilot clinical trial comparing an acid‐buffering formulation (ACIDFORM gel) with metronidazole gel for the treatment of symptomatic bacterial vaginosis
Authors: Simoes Jose A. , Bahamondes Luis G. , Camargo Rodrigo P. S. , Alves Valeria M. N. , Zaneveld Lourens J. D. , Waller Donald P. , Schwartz Jill , Callahan Marianne M. , Mauck Christine K.
Published: December 2005

Aim

To compare the effectiveness of an acid‐buffering formulation gel (ACIDFORM) with metronidazole gel in the treatment of symptomatic bacterial vaginosis (BV).

Methods

After a confirmed diagnosis of BV according to the criteria established by Nugent and Amsel, 30 nonpregnant women were enrolled in a randomized, double‐blind clinical study. The women were randomly assigned to receive either 5 g ACIDFORM gel (n = 13) or 10% metronidazole gel (n = 17) intravaginally once daily for five consecutive days. Participants were evaluated in two follow‐up visits (7–12 days and 28–35 days after treatment). Therapeutic success was defined as the presence of less than three of Amsel's criteria. If three or more criteria were present at first or second follow‐up visit, the woman was excluded from the study and treated orally with metronidazole. Nugent scores were recorded at each visit but these were not used to define cure.

Results

At the first follow‐up visit, 15 (88%) of the women in the metronidazole group were cured compared with only three (23%) in the ACIDFORM group (P < 0.001). The remaining 12 women (10 of the ACIDFORM group and two of the metronidazole group) were considered as failure and were treated orally with metronidazole. At the second follow‐up visit, two of the ACIDFORM‐treated women and six of the metronidazole‐treated women presented recurrent BV. Four women in the ACIDFORM group and one in the metronidazole group reported occasional burning and itching during product use.

Conclusion

ACIDFORM gel was significantly less effective than high‐dose metronidazole gel for the treatment of symptomatic BV.
Congenital adrenal hyperplasia in adults: a review of medical, surgical and psychological issues
Authors: Ogilvie Cara Megan , Crouch Naomi S. , Rumsby Gill , Creighton Sarah M. , Liao Lih‐Mei , Con Way Gerard S.
Published: December 2005

Our knowledge of the experience of adults with congenital adrenal hyperplasia (CAH) as they pass through life is only now emerging. In this review we gather medical, surgical and psychological literature pertaining to adults with CAH and consider this alongside practical experience gained from a dedicated adult CAH clinic. There is increasing awareness for the need for multidisciplinary teams who have knowledge of CAH particularly with respect to gynaecological surgery and clinical psychology for women and testicular function in men.

Routine management of CAH comprises adjustment of glucocorticoid and mineralocorticoid treatment according to individual needs balancing biochemical markers, compliance and long term risks. Bone density is one such long term concern and is not greatly reduced in most individuals with CAH. More recently, attention has turned to cardiovascular risk factors and catecholamine deficiency in adults with CAH.

Women with CAH require access to an experienced gynaecologist, specialised pregnancy care and psychosexual support. The very low fertility rates for women with CAH previously reported appear to be improving with time. Men with CAH are often lost to follow up and therefore miss out on surveillance for hypogonadism either through the effect of adrenal rests of from suppression of gonadotrophins resulting in a high prevalence of oligospermia.
Selecting discriminant function models for predicting the expected richness of aquatic macroinvertebrates
Authors: SICKLE JOHN VAN , HUFF DAVID D. , HAWKINS CHARLES P.
Published: November 2005

1. The predictive modelling approach to bioassessment estimates the macroinvertebrate assemblage expected at a stream site if it were in a minimally disturbed reference condition. The difference between expected and observed assemblages then measures the departure of the site from reference condition.

2. Most predictive models employ site classification, followed by discriminant function (DF) modelling, to predict the expected assemblage from a suite of environmental variables. Stepwise DF analysis is normally used to choose a single subset of DF predictor variables with a high accuracy for classifying sites. An alternative is to screen all possible combinations of predictor variables, in order to identify several ‘best’ subsets that yield good overall performance of the predictive model.

3. We applied best‐subsets DF analysis to assemblage and environmental data from 199 reference sites in Oregon, U.S.A. Two sets of 66 best DF models containing between one and 14 predictor variables (that is, having model orders from one to 14) were developed, for five‐group and 11‐group site classifications.

4. Resubstitution classification accuracy of the DF models increased consistently with model order, but cross‐validated classification accuracy did not improve beyond seventh or eighth‐order models, suggesting that the larger models were overfitted.

5. Overall predictive model performance at model training sites, measured by the root‐mean‐squared error of the observed/expected species richness ratio, also improved steadily with DF model order. But high‐order DF models usually performed poorly at an independent set of validation sites, another sign of model overfitting.

6. Models selected by stepwise DF analysis showed evidence of overfitting and were outperformed by several of the best‐subsets models.

7. The group separation strength of a DF model, as measured by Wilks’Λ, was more strongly correlated with overall predictive model performance at training sites than was DF classification accuracy.

8. Our results suggest improved strategies for developing reliable, parsimonious predictive models. We emphasise the value of independent validation data for obtaining a realistic picture of model performance. We also recommend assessing not just one or two, but several, candidate models based on their overall performance as well as the performance of their DF component.

9. We provide links to our free software for stepwise and best‐subsets DF analysis.
Spatial heterogeneity of tundra vegetation response to recent temperature changes
Authors: JIA GENSUO J. , EPSTEIN HOWARD E. , WALKER DONALD A.
Published: December 2005

The spatial heterogeneity of recent decadal dynamics in vegetation greenness and biomass in response to changes in summer warmth index (SWI) was investigated along spatial gradients on the Arctic Slope of Alaska. Image spatial analysis was used to examine the spatial pattern of greenness dynamics from 1991 to 2000 as indicated by variations of the maximum normalized difference vegetation index (Peak NDVI) and time‐integrated NDVI (TI‐NDVI) along latitudinal gradients. Spatial gradients for both the means and temporal variances of the NDVI indices for 0.1° latitude intervals crossing three bioclimate subzones were analyzed along two north–south Arctic transects. NDVI indices were generally highly variable over the decade, with great heterogeneity across the transects. The greatest variance in TI‐NDVI was found in low shrub vegetation to the south (68.7–68.8°N) and corresponded to high fractional cover of shrub tundra and moist acidic tundra (MAT), while the greatest variance in Peak‐NDVI predominately occurred in areas dominated by wet tundra (WT) and moist nonacidic tundra (MNT). Relatively high NDVI temporal variances were also related to specific transitional areas between dominant vegetation types. The regional temporal variances of NDVI from 1991 to 2000 were largely driven by meso‐scale climate dynamics. The spatial heterogeneity of the NDVI variance was mostly explained by the fractional land cover composition, different responses of each vegetation type to climate change, and patterned ground features. Aboveground plant biomass exhibited similar spatial heterogeneity as TI‐NDVI; however, spatial patterns are slightly different from NDVI because of their nonlinear relationship.
Effects of elevated CO2 on fine root dynamics in a Mojave Desert community: a FACE study
Authors: PHILLIPS DONALD L. , JOHNSON MARK G. , TINGEY DAVID T. , CATRICALA CHRISTINA E. , HOYMAN TONI L. , NOWAK ROBERT S.
Published: December 2005

Fine roots (≤1 mm diameter) are critical in plant water and nutrient absorption, and it is important to understand how rising atmospheric CO2 will affect them as part of terrestrial ecosystem responses to global change. This study's objective was to determine the effects of elevated CO2 on production, mortality, and standing crops of fine root length over 2 years in a free‐air CO2 enrichment (FACE) facility in the Mojave Desert of southern Nevada, USA. Three replicate 25 m diameter FACE rings were maintained at ambient (∼370 μmol mol−1) and elevated CO2 (∼550 μmol mol−1) atmospheric concentrations. Twenty‐eight minirhizotron tubes were placed in each ring to sample three microsite locations: evergreen Larrea shrubs, drought‐deciduous Ambrosia shrubs, and along systematic community transects (primarily in shrub interspaces which account for ∼85% of the area). Seasonal dynamics were similar for ambient and elevated CO2: fine root production peaked in April–June, with peak standing crop occurring about 1 month later, and peak mortality occurring during the hot summer months, with higher values for all three measures in a wet year compared with a dry year. Fine root standing crop, production, and mortality were not significantly different between treatments except standing crop along community transects, where fine root length was significantly lower in elevated CO2. Fine root turnover (annual cumulative mortality/mean standing crop) ranged from 2.33 to 3.17 year−1, and was not significantly different among CO2 treatments, except for community transect tubes where it was significantly lower for elevated CO2. There were no differences in fine root responses to CO2 between evergreen (Larrea) and drought‐deciduous (Ambrosia) shrubs. Combined with observations of increased leaf‐level water‐use efficiency and lack of soil moisture differences, these results suggest that under elevated CO2 conditions, reduced root systems (compared with ambient CO2) appear sufficient to provide resources for modest aboveground production increases across the community, but in more fertile shrub microsites, fine root systems of comparable size with those in ambient CO2 were required to support the greater aboveground production increases. For community transects, development of the difference in fine root standing crops occurred primarily through lower stimulation of fine root production in the elevated CO2 treatment during periods of high water availability.
Mineral nitrogen cycling through earthworm casts in a grazed pasture under elevated atmospheric CO2
Authors: CHEVALLIER ALEXIS J. T. , LIEFFERING MARK , CARRAN R. A. , NEWTON P. C. D.
Published: December 2005

We used the New Zealand grazed pasture free air CO2 enrichment experiment to determine the effects of elevated CO2 on earthworm (Aporrectodea caliginosa and Lumbricus rubellus) cast production and mineral nitrogen (N) concentration over a 5‐week period in the spring. Elevated CO2 did not affect earthworm biomass or the amount of cast material produced. However, cast mineral N concentrations were 18% lower, resulting in 27% less mineral N being deposited on the soil surface under elevated CO2. An analysis of the earthworms' potential diet showed that a reduction in the N content of sheep dung at elevated CO2 was the most likely cause of the lower cast N concentrations. Earthworm casts made only a small contribution to mineral N cycling in our system; however, their quality may act as a sensitive indicator of reduced N availability under elevated CO2 which is consistent with the hypothesised process of progressive N limitation.
Interprofessional education in undergraduate healthcare programmes: the reaction of student dietitians
Authors: Whelan K. , Thomas J. E. , Cooper S. , Hilton R. , Jones S. C. , Newton T. , O'Neill B. , Gill E. E.
Published: December 2005

Background  Interprofessional education (IPE) is a novel teaching and learning initiative where students of more than one health profession learn interactively together. However, despite its potential for improving interprofessional relationships, there is little information regarding the participation of student dietitians in IPE. The aim of this paper was to consider the reaction of student dietitians to an IPE course in order to stimulate debate between dietitians regarding the issues relating to IPE.

Methods  Student dietitians participated in an IPE course consisting of seven sessions on communication and ethics in health care together with students of medicine and nursing. Student dietitians completed an evaluation questionnaire following each session that surveyed their reaction to the session using both a Likert scale and free‐text comments.

Results  Twenty‐six student dietitians completed the IPE course. All sessions were rated positively for interest value (P ≤ 0.14), learning experience (P ≤ 0.036) and value for clinical practice (P ≤ 0.05). The limited number of free‐text comments indicated some positive experiences regarding interprofessional learning, teaching content and teaching strategy.

Conclusions  This is one of very few evaluations to describe the reaction of student dietitians to IPE. Student dietitians had largely positive reactions to the IPE course. Further research is required to evaluate whether these positive reactions were a direct consequence of the inclusion of students from other health professions and whether these translate into positive effects on learning, behaviour and results. The opportunities for the dietetic profession posed by students’ involvement in IPE are discussed.