Protein fold recognition score functions: Unusual construction strategies

We describe two ways of optimizing score functions for protein sequence to structure threading. The first method adjusts parameters to improve sequence to structure alignment. The second adjusts parameters so as to improve a score function's ability to rank alignments calculated in the first score function. Unlike those functions known as knowledge-based force fields, the resulting parameter sets do not rely on Boltzmann statistics, have no claim to representing free energies and are purely constructions for recognizing protein folds. The methods give a small improvement, but suggest that functions can be profitably optimized for very specific aspects of protein fold recognition, Proteins 1999;36:454-461. (C) 1999 Wiley-Liss, Inc.

The crack tip strain field of AISI 4340 - Part I - Measurement technique

This is the first paper in a study on the influence of the environment on the crack tip strain field for AISI 4340. A stressing stage for the environmental scanning electron microscope (ESEM) was constructed which was capable of applying loads up to 60 kN to fracture-mechanics samples. The measurement of the crack tip strain field required preparation (by electron lithography or chemical etching) of a system of reference points spaced at similar to 5 mu m intervals on the sample surface, loading the sample inside an electron microscope, image processing procedures to measure the displacement at each reference point and calculation of the strain field. Two algorithms to calculate strain were evaluated. Possible sources of errors were calculation errors due to the algorithm, errors inherent in the image processing procedure and errors due to the limited precision of the displacement measurements. Estimation of the contribution of each source of error was performed. The technique allows measurement of the crack tip strain field over an area of 50 x 40 mu m with a strain precision better than +/- 0.02 at distances larger than 5 mu m from the crack tip. (C) 1999 Kluwer Academic Publishers.

The crack tip strain field of AISI 4340 - Part II - Experimental measurements

Crack tip strain maps have been measured for AISI 4340 high strength steel. No significant creep was observed. The measured values of CTOD were greater than expected from the HRR model. Crack tip branching was observed in every experiment. The direction of crack branching was in the same direction as a major ridge'' of epsilon(yy) strain, which in turn was in the same direction as predicted by the HRR model. Furthermore, the measured magnitudes of the epsilon(y)y strain in this same direction were in general greater than the values predicted by the HRR model. This indicates more plasticity in the crack tip region than expected from the HRR model. This greater plasticity could be related to the larger than expected CTOD values. The following discrepancies between the measured strain fields for AISI 4340 and the HRR predictions are noteworthy: (1) The crack branching. (2) Values of CTOD significantly higher than predicted by HRR. (3) The major ridge'' of epsilon(yy) strain an angle of about 60 degrees with the direction of overall propagation of the fatigue precrack, in which the measured magnitudes of the epsilon(yy) strain were greater than the values predicted by the HRR model. (4) Asymmetric shape of the plastic zone as measured by the epsilon(yy) strain. (5) Values of shear strain gamma(xy) significantly higher than predicted by the HRR model. (C) 1999 Kluwer Academic Publishers.

The crack tip strain field of AISI 4340 - Part III - Hydrogen influence

This paper studied the influence of hydrogen and water vapour environments on the plastic behaviour in the vicinity of the crack tip for AISI 4340. Hydrogen and water vapour (at a pressure of 15 Torr) significantly increased the crack tip opening displacement. The crack tip strain distribution in 15 Torr hydrogen was significantly different to that measured in vacuum. In the presence of sufficient hydrogen, the plastic zone was larger, was elongated in the direction of crack propagation and moreover there was significant creep. These observations support the hydrogen enhanced localised plasticity model for hydrogen embrittlement in this steel. The strain distribution in the presence of water vapour also suggests that SCC in AISI 4340 occurs via the hydrogen enhanced localised plasticity mechanism. (C) 1999 Kluwer Academic Publishers.

Paramagnetic limiting of the upper critical field of the layered organic superconductor kappa-(BEDT-TTF)(2)Cu(SCN)(2)

We report detailed measurements of the interlayer magnetoresistance of the layered organic superconductor kappa-(BEDT-TTF)(2)Cu(SCN)(2) for temperatures down to 0.5 K and fields up to 30 T. The upper critical field is determined from the resistive transition for a wide range of temperatures and field directions. For magnetic fields parallel to the layers, the upper critical field increases approximately linearly with decreasing temperature. The upper critical field at low temperatures is compared to the Pauli paramagnetic limit, at which singlet superconductivity should be destroyed by the Zeeman splitting of the electron spins. The measured value is comparable to a value for the paramagnetic limit calculated from thermodynamic quantities but exceeds the limit calculated from BCS theory. The angular dependence of the upper critical field shows a cusplike feature for fields close to the layers, consistent with decoupled layers.

Intraspecific co-variation between egg and body size affects fertilisation kinetics of free-spawning marine invertebrates

Fertilisation of eggs of free-spawning marine invertebrates depends on factors affecting sperm concentration in the field and also on gamete characteristics such as egg size. In the free-spawning intertidal ascidian Pyura stolonifera mean egg size increased with maternal size in 2 separate populations. The largest ascidian produced eggs that were, on average, 50% greater in volume than the eggs produced by the smallest individual studied. There was no evidence to suggest that egg density varied with adult size and egg dry organic weight increased with maternal size. The fertilisation kinetics of this species were strongly affected by the variation in egg size, with the eggs of large individuals requiring much less concentrated sperm to achieve maximal levels of fertilisation success than the eggs of small individuals. We suggest that variation in egg size between individuals of different sizes and ages may be an important factor in determining fertilisation success for ascidians of this species.

The Fornax spectroscopic survey I. Survey strategy and preliminary results on the redshift distribution of a complete sample of stars and galaxies

The Fornax Spectroscopic Survey will use the Two degree Field spectrograph (2dF) of the Angle-Australian Telescope to obtain spectra for a complete sample of all 14000 objects with 16.5 less than or equal to b(j) less than or equal to 19.7 in a 12 square degree area centred on the Fornax Cluster. The aims of this project include the study of dwarf galaxies in the cluster (both known low surface brightness objects and putative normal surface brightness dwarfs) and a comparison sample of background field galaxies. We will also measure quasars and other active galaxies, any previously unrecognised compact galaxies and a large sample of Galactic stars. By selecting all objects-both stars and galaxies-independent of morphology, we cover a much larger range of surface brightness and scale size than previous surveys. In this paper we first describe the design of the survey. Our targets are selected from UK Schmidt Telescope sky survey plates digitised by the Automated Plate Measuring (APM) facility. We then describe the photometric and astrometric calibration of these data and show that the APM astrometry is accurate enough for use with the 2dF. We also describe a general approach to object identification using cross-correlations which allows us to identify and classify both stellar and galaxy spectra. We present results from the first 2dF field. Redshift distributions and velocity structures are shown for all observed objects in the direction of Fornax, including Galactic stars? galaxies in and around the Fornax Cluster, and for the background galaxy population. The velocity data for the stars show the contributions from the different Galactic components, plus a small tail to high velocities. We find no galaxies in the foreground to the cluster in our 2dF field. The Fornax Cluster is clearly defined kinematically. The mean velocity from the 26 cluster members having reliable redshifts is 1560 +/- 80 km s(-1). They show a velocity dispersion of 380 +/- 50 km s(-1). Large-scale structure can be traced behind the cluster to a redshift beyond z = 0.3. Background compact galaxies and low surface brightness galaxies are found to follow the general galaxy distribution.

Toxicity of biorational insecticides to Helicoverpa spp. (Lepidoptera : Noctuidae) and predators in cotton field

Field trials on upland cotton (Gossypium hirstum L.) during its reproductive phase were used to assess the toxicity of several biorational pesticides and chemicals to Helicoverpa armigera (Hubner) and H. puntigera Wallengren, as well as major predators at Dalby, Queensland, Australia. Moderate rate-dependent control was obtained in plots treated with neem (Azadirachta indica A. Juss) seed extract-azadirachtin (Aza) at rates of 30, 60 and 90 g/ha. Plots treated with Talstar EC (bifenthrin) applications achieved the best results, followed by treatment with alternation of chemicals (methomyl, bifenthrin, thiodicarb and endosulfan) and biorational insecticides (neem oil, azadirachtin and Bacillus thuringiensis kurstaki var. Berliner). Predators, including lady beetles, lacewings, spiders and predatory bugs, were insensitive to Aza, tooseendanin (Tsdn) and BT applications. In contrast, chemicals were very destructive of predators. All treatments provided some protection from infestation of H. armigera and H. puntigera. The effect of Aza on Helicoverpa spp. was reflected in a relatively higher yield of seed cotton harvested from Aza-treated plots compared with the control, but chemical control achieved significantly higher yields than any other treatment.

Heat flow for the Yang-Mills-Higgs field and the Hermitian Yang-Mills-Higgs metric

For a parameter lambda > 0, we study a type of vortex equations, which generalize the well-known Hermitian-Einstein equation, for a connection A and a section phi of a holomorphic vector bundle E over a Kahler manifold X. We establish a global existence of smooth solutions to heat flow for a self-dual Yang-Mills-Higgs field on E. Assuming the lambda -stability of (E, phi), we prove the existence of the Hermitian Yang-Mills-Higgs metric on the holomorphic bundle E by studying the limiting behaviour of the gauge flow.

The neutral hydrogen content of Fornax cluster galaxies

We present a new set of deep H I observations of member galaxies of the Fornax cluster. We detected 35 cluster galaxies in H I. The resulting sample, the most comprehensive to date, is used to investigate the distribution of neutral hydrogen in the cluster galaxies. We compare the H I content of the detected cluster galaxies with that of field galaxies by measuring H I mass-to-light ratios and the H I deficiency parameter of Solanes et al. (1996). The mean H I mass-to-light ratio of the cluster galaxies is 0.68 +/- 0.15, significantly lower than for a sample of H I-selected field galaxies (1.15 +/- 0.10), although not as low as in the Virgo cluster (0.45 +/- 0.03). In addition, the H I content of two cluster galaxies (NGC1316C and NGC1326B) appears to have been affected by interactions. The mean H I deficiency for the cluster is 0.38 +/- 0.09 (for galaxy types T = 1-6), significantly greater than for the field sample (0.05 +/- 0.03). Both these tests show that Fornax cluster galaxies are H I-deficient compared to field galaxies. The kinematics of the cluster galaxies suggests that the H I deficiency may be caused by ram-pressure stripping of galaxies on orbits that pass close to the cluster core. We also derive the most complete B-band Tully-Fisher relation of inclined spiral galaxies in Fornax. A subcluster in the South-West of the main cluster contributes considerably to the scatter. The scatter for galaxies in the main cluster alone is 0.50 mag, which is slightly larger than the intrinsic scatter of 0.4 mag. We use the Tully-Fisher relation to derive a distance modulus of Fornax relative to the Virgo cluster of -0.38 +/- 0.14 mag. The galaxies in the subcluster are (1.0 +/- 0.5) mag brighter than the galaxies of the main cluster, indicating that they are situated in the foreground. With their mean velocity 95 km s(-1) higher than that of the main cluster we conclude that the subcluster is falling into the main Fornax cluster.

Field-swept pulsed electron paramagnetic resonance of Cr3+-doped ZBLAN fluoride glass

Field-swept pulsed electron paramagnetic resonance (EPR) spectra of a ZBLAN fluoride glass doped with a low concentration of Cr3+ are obtained using echo-detected EPR and hole-burning free induction decay detection. We review the utility of the pulsed EPR technique in generating field-swept EPR spectra, as well as some of the distorting effects that are peculiar to the pulsed detection method. The application of this technique to Cr3+-doped ZBLAN reveals that much of the broad resonance extending from g(eff) = 5.1 to g(eff) = 1.97, characteristic of X-band continuous wave EPR of Cr3+ in glasses, is absent. We attribute this largely to the variation in nutation frequencies across the spectrum that result from sites possessing large fine structure interactions. The description of the spin dynamics of such sites is complicated and we discuss some possible approaches to the simulation of the pulsed EPR spectra.

Determining complicated winding patterns for shim coils using stream functions and the target-field method

In a magnetic resonance imaging equipment, gradient and shim coils are needed to produce a spatially varying magnetic field throughout the sample being imaged. Such coils consist of turns of wire wound on the surface of a cylindrical tube. Shim coils in particular, must sometimes be designed to produce complicated magnetic fields to correct for impurities. Streamline patterns for shim coils are much more complicated than those for gradient coils, In this work we present a detailed analysis of streamline methods and their application to shim coil design, A method is presented for determining the winding patterns to generate these complicated fields. (C) 2002 John Wiley & Sons, Inc.

Progress in high field MRI at the University of Florida

In this article we report on progress in high magnetic field MRI at the University of Florida in support of our new 750MHz wide bore and 11.7T/40cm MR instruments. The primary emphasis is on the associated rf technology required, particularly high frequency volume and phased array coils. Preliminary imaging results at 750MHz are presented. Our results imply that the pursuit of even higher fields seems warranted. (C) 2002 Elsevier Science B.V. All rights reserved.

Semiochemicals and social signaling in the wild European rabbit in Australia: I. Scent profiles of chin gland secretion from the field

The European rabbit (Oryctolagus cuniculus) uses the secretion of the chin gland in the maintenance of social status. Previous work has concentrated on secretion collected directly from the animal. In this study, the analysis was conducted by collecting scent marks made by free-ranging animals. Scent marks were found to be concentrated at the center of the area controlled by a social group, and at the boundaries between two adjacent social groups. Only the mark from dominant animals could be identified. Marks were also collected from the skin of rabbits, where they had been placed by the dominant individual. The mark found on the head of a subordinate animal may, in the future, be used to identify the dominant animal of the social group, who placed the mark.

Magnetic-field-induced superconductivity in layered organic molecular crystals with localized magnetic moments

The synthetic organic compound λ(BETS)2FeCl4 undergoes successive transitions from an antiferromagnetic insulator to a metal and then to a superconductor as a magnetic field is increased. We use a Hubbard-Kondo model to clarify the role of the Fe3+ magnetic ions in these phase transition. In the high-field regime, the magnetic field acting on the electron spins is compensated by the exchange field He due to the magnetic ions. This suggests that the field-induced superconducting state is the same as the zero-field superconducting state which occurs under pressure or when the Fe3+ ions are replaced by non-magnetic Ga3+ ions. We show how Hc can be extracted from the observed splitting of the Shybnikov-de Haas frequencies. Furthermore, we use this method of extracting He to predict the field range for field-induced superconductivity in other materials. We also show that at high fields the spin fluctuations of the localized spins are not important.