CXTANNEAL: an improved program for estimating solute transport parameters

CXTANNEAL is a program for analysing contaminant transport in soils. The code, written in Fortran 77, is a modified version of CXTFIT, a commonly used package for estimating solute transport parameters in soils. The improvement of the present code is that it includes simulated annealing as the optimization technique for curve fitting. Tests with hypothetical data show that CXTANNEAL performs better than the original code in searching for optimal parameter estimates. To reduce the computational time, a parallel version of CXTANNEAL (CXTANNEAL_P) was also developed. (C) 1999 Elsevier Science Ltd. All rights reserved.

MiAMP1, a novel protein from Macadamia integrifolia adopts a Greek key beta-barrel fold unique amongst plant antimicrobial proteins

MiAMP1 is a recently discovered 76 amino acid residue, highly basic protein from the nut kernel of:Macadamia integrifolia which possesses no sequence homology to any known protein and inhibits the growth of several microbial plant pathogens in vitro while having no effect on mammalian or plant cells. It is considered to be a potentially useful tool for the genetic engineering of disease resistance in transgenic crop plants and for the design of new fungicides. The three-dimensional structure of MiAMP1 was determined through homonuclear and heteronuclear (N-15) 2D NMR spectroscopy and subsequent simulated annealing calculations with the ultimate aim of understanding the structure-activity relationships of the protein. MiAMP1 is made up of eight beta-strands which are arranged in two Greek key motifs. These Greek key motifs associate to form a Greek key beta-barrel. This structure is unique amongst plant antimicrobial proteins and forms a new class which we term the beta-barrelins. Interestingly, the structure of MiAMP1 bears remarkable similarity to a yeast killer toxin from Williopsis mrakii. This toxin acts by inhibiting beta-glucan synthesis and thereby cell wall construction in sensitive strains of yeast. The structural similarity of MiAMP1 and WmKT, which originate from plant and fungal phyla respectively, may reflect a similar mode of action. (C) 1999 Academic Press.

Two-dimensional nonlinear dynamics of evanescent-wave guided atoms in a hollow fiber

We describe the classical and quantum two-dimensional nonlinear dynamics of large blue-detuned evanescent-wave guiding cold atoms in hollow fiber. We show that chaotic dynamics exists for classic dynamics, when the intensity of the beam is periodically modulated. The two-dimensional distributions of atoms in (x,y) plane are simulated. We show that the atoms will accumulate on several annular regions when the system enters a regime of global chaos. Our simulation shows that, when the atomic flux is very small, a similar distribution will be obtained if we detect the atomic distribution once each the modulation period and integrate the signals. For quantum dynamics, quantum collapses, and revivals appear. For periodically modulated optical potential, the variance of atomic position will be suppressed compared to the no modulation case. The atomic angular momentum will influence the evolution of wave function in two-dimensional quantum system of hollow fiber.

Experimental examination of solute transport by surface runoff from low-angle slopes

The removal of chemicals in solution, by overland flow from agricultural land has the potential to be a significant source of chemical loss from zero-till and surface mulched farming systems. The objective of this study was to determine the magnitude of solute loss by surface runoff from agricultural systems. Previous experiments have enhanced the understanding of the exchange process, but the initial soil conditions together with the tracer application method in these experiments have meant that in some cases the results have limited applicability to field situations. In this study, two different sets of experiments were carried out to determine the magnitude of solute loss by surface runoff. These experiments entailed the surface application of bromide to (1) field scale plots 18 m long by 2 m wide and (2) repacked soil cores 236 mm in diameter; followed by the application of simulated rainfall in both cases. The most substantial finding of the field experiments was that the quantities of solute in surface runoff varied greatly with soil type and structure (0.07-14.9% of the applied bromide). Also, on some soils, large quantities of tracer were measured in the surface runoff even after several hours of infiltration. The experiments on soil cores showed that soil structure plays an important role in the quantity of chemical that may be transported in the surface runoff. These field results showed that, in certain systems, solute movement by overland flow is an important transport mechanism, which should be considered when budgeting for chemical loss. (C) 2000 Elsevier Science B.V. All rights reserved.

Prediction of rock alteration patterns: a potential tool in mineral exploration

Hydrothermal alteration of a quartz-K-feldspar rock is simulated numerically by coupling fluid flow and chemical reactions. Introduction of CO2 gas generates an acidic fluid and produces secondary quartz, muscovite and/or pyrophyllite at constant temperature and pressure of 300 degrees C and 200 MPa. The precipitation and/or dissolution of the secondary minerals is controlled by either mass-action relations or rate laws. In our simulations the mass of the primary elements are conserved and the mass-balance equations are solved sequentially using an implicit scheme in a finite-element code. The pore-fluid velocity is assumed to be constant. The change of rock volume due to the dissolution or precipitation of the minerals, which is directly related to their molar volume, is taken into account. Feedback into the rock porosity and the reaction rates is included in the model. The model produces zones of pyrophyllite quartz and muscovite due to the dissolution of K-feldspar. Our model simulates, in a simplified way, the acid-induced alteration assemblages observed in various guises in many significant mineral deposits. The particular aluminosilicate minerals produced in these experiments are associated with the gold deposits of the Witwatersrand Basin.

Syndrome packets and health worker training improve sexually transmitted disease case management in rural South Africa: randomized controlled trial

Background: Sexually transmitted diseases (STD) are important co-factors in HIV transmission. We studied the impact of health worker training and STD syndrome packets (containing recommended drugs, condoms, partner notification cards and information leaflets) on the quality of STD case management in primary care clinics in rural South Africa. Methods: A randomized controlled trial of five matched pairs of clinics compared the intervention with routine syndromic management. Outcomes were measured by simulated patients using standardized scripts, and included the proportion given recommended drugs; correctly case managed (given recommended drugs plus condoms and partner cards); adequately counselled; reporting good staff attitude; and consulted in privacy. Results: At baseline, the quality of STD case management was similarly poor in both groups. Only 36 and 46% of simulated patients visiting intervention and control clinics, respectively, were given recommended drugs. After the intervention, intervention clinics provided better case management than controls: 88 versus 50% (P < 0.01) received recommended drugs; 83 versus 12% (P < 0.005) were correctly case managed; 68 versus 46% (P = 0.06) were adequately counselled; 84 versus 58% experienced good staff attitude (P = 0.07); and 92 versus 86% (P = 0.4) were consulted privately. A syndrome packet cost US$1.50; the incremental cost was US$6.80. The total intervention cost equalled 0.3% of annual district health expenditure. Interpretation: A simple and affordable health service intervention achieved substantial improvements in STD case management. Although this is a critical component of STD control and can reduce HIV transmission, community-level interventions to influence health-seeking behaviour are also needed. (C) 2000 Lippincott Williams & Wilkins.

Three-dimensional structure of RK-1: A novel alpha-defensin peptide

NMR spectroscopy and simulated annealing calculations have been used to determine the three-dimensional structure of RK-1, an antimicrobial peptide from rabbit kidney recently discovered from homology screening based on the distinctive physicochemical properties of the corticostatins/defensins. RK-1 consists of 32 residues, including six cysteines arranged into three disulfide bonds. It exhibits antimicrobial activity against Escherichia coli and activates Ca2+ channels in vitro. Through its physicochemical similarity, identical cysteine spacing, and linkage to the corticostatins/defensins, it was presumed to be a member of this family. However, RK-1 lacks both a large number of arginines in the primary sequence and a high overall positive charge, which are characteristic of this family of peptides. The three-dimensional solution structure, determined by NMR, consists of a triple-stranded antiparallel beta -sheet and a series of turns and is similar to the known structures of other alpha -defensins. This has enabled the definitive classification of RK-1 as a member of this family of antimicrobial peptides. Ultracentrifuge measurements confirmed that like rabbit neutrophil defensins, RK-1 is monomeric in solution, in contrast to human neutrophil defensins, which are dimeric.

Galaxy threshing and the formation of ultracompact dwarf galaxies

Recent spectroscopic and morphological observational studies of galaxies around NGC 1399 in the Fornax Cluster have discovered several ultracompact dwarf galaxies with intrinsic sizes of similar to 100 pc and absolute B-band magnitudes ranging from -13 to -11 mag. In order to elucidate the origin of these enigmatic objects, we perform numerical simulations on the dynamical evolution of nucleated dwarf galaxies orbiting NGC 1399 and suffering from its strong tidal gravitational field. Adopting a plausible scaling relation for dwarf galaxies, we find that the outer stellar components of a nucleated dwarf are totally removed. This is due to them being tidally stripped over the course of several passages past the central region of NGC 1399. The nucleus, however, manages to survive. We also find that the size and luminosity of the remnant are similar to those observed for ultracompact dwarf galaxies, if the simulated precursor nucleated dwarf has a mass of similar to 10(8) M.. These results suggest that ultracompact dwarf galaxies could have previously been more luminous dwarf spheroidal or elliptical galaxies with rather compact nuclei.

NMR shim coil design utilising a rapid spherical harmonic calculation method

A rapid spherical harmonic calculation method is used for the design of Nuclear Magnetic Resonance shim coils. The aim is to design each shim such that it generates a field described purely by a single spherical harmonic. By applying simulated annealing techniques, coil arrangements are produced through the optimal positioning of current-carrying circular arc conductors of rectangular cross-section. This involves minimizing the undesirable harmonies in relation to a target harmonic. The design method is flexible enough to be applied for the production of coil arrangements that generate fields consisting significantly of either zonal or tesseral harmonics. Results are presented for several coil designs which generate tesseral harmonics of degree one.

Event-related FMRI analysis with maximum correlation modelling

Functional magnetic resonance imaging (FMRI) analysis methods can be quite generally divided into hypothesis-driven and data-driven approaches. The former are utilised in the majority of FMRI studies, where a specific haemodynamic response is modelled utilising knowledge of event timing during the scan, and is tested against the data using a t test or a correlation analysis. These approaches often lack the flexibility to account for variability in haemodynamic response across subjects and brain regions which is of specific interest in high-temporal resolution event-related studies. Current data-driven approaches attempt to identify components of interest in the data, but currently do not utilise any physiological information for the discrimination of these components. Here we present a hypothesis-driven approach that is an extension of Friman's maximum correlation modelling method (Neurolmage 16, 454-464, 2002) specifically focused on discriminating the temporal characteristics of event-related haemodynamic activity. Test analyses, on both simulated and real event-related FMRI data, will be presented.

Micromorphological study of slumping in a hardsetting seedbed under various wetting conditions

Slumping of hardsetting seedbeds upon wetting has not been extensively studied despite the likelihood that it determines the physical properties after drying. Slumping results from processes similar to those involved in crusting except that overburden pressure can dominate rather than rainfall kinetic energy. Only a few studies have dealt with the morphological description of slumping. To simulate different climatic and management conditions, repacked seedbeds of a hardsetting sandy-loam soil were subjected to a range of wetting conditions, e.g. capillary rise, immersion, and rainfall simulation. Slumping processes were characterized using qualitative and quantitative micromorphological observations of polished blocks and thin sections from resin-impregnated samples. A morphogenetical framework was proposed to help description of the complex associations of processes which can lead to structural collapse (crusting and slumping) on wetting. Three main stages were considered, i.e. aggregate disruption or abrasion, relocation of the released material, and compaction. In the hardsetting material studied here, structural collapse under slow wetting occurred at the bottom of cores due to aggregate coalescence under overburden pressure. Coalescence required aggregate cohesion being reduced by microcracking; therefore, it differed from the coalescence previously described in unstable silty loam soils where microcracking was not necessary for aggregates to coalesce. Macroporosity decreased most strongly under fast wetting due to physical dispersion and aggregate breakdown. Under simulated rainfall, compaction by raindrops could not be distinguish from aggregate breakdown. The role of overburden pressure and of rainfall kinetic energy remains to be stated; new data are required including measurement of total porosity in the initial, wet, and dry states. (C) 2003 Elsevier B.V. All rights reserved.

Evaluating the efficiency of fractional integration parameter estimators

This article deals with the efficiency of fractional integration parameter estimators. This study was based on Monte Carlo experiments involving simulated stochastic processes with integration orders in the range]-1,1[. The evaluated estimation methods were classified into two groups: heuristics and semiparametric/maximum likelihood (ML). The study revealed that the comparative efficiency of the estimators, measured by the lesser mean squared error, depends on the stationary/non-stationary and persistency/anti-persistency conditions of the series. The ML estimator was shown to be superior for stationary persistent processes; the wavelet spectrum-based estimators were better for non-stationary mean reversible and invertible anti-persistent processes; the weighted periodogram-based estimator was shown to be superior for non-invertible anti-persistent processes.

Use of bulk density profiles from X-radiography to examine structural crust models

Exponential and sigmoidal functions have been suggested to describe the bulk density profiles of crusts. The present work aims to evaluate these conceptual models using high resolution X-radiography. Repacked seedbeds from two soil materials, air-dried or prewetted by capillary rise, were subjected to simulated rain, which resulted in three types of structural crusts, namely, slaking, infilling, and coalescing. Bulk density distributions with depth were generated using high-resolution (70 mum), calibrated X-ray images of slices from the resin-impregnated crusted seedbeds. The bulk density decreased progressively with depth, which supports the suggestion that a crust should be considered as a nonuniform layer. For the slaking and the coalescing crusts, the exponential function underestimated the strong change in bulk density across the morphologically defined transition between the crust and the underlying material; the sigmoidal function provided a better description. Neither of these crust models effectively described the shape of the bulk density profiles through the whole seedbed. Below the infilling and slaking crusts, bulk density increased linearly with depth as a result of slumping. In the coalescing crusted seedbed, the whole seedbed uniformly collapsed and most of the bulk density change within the crust could be ascribed to slumping (0.33 g cm(-3)) rather than to crusting (0.12 g cm(-3)). Finally, (i) X-radiography appears as a unique tool to generate high resolution bulk density profiles and (ii) in structural crusts, bulk density profiles could be modeled using the existing exponential and sigmoidal crusting models, provided a slumping model would be coupled.

Thermal Characteristics of Polybia scutellaris Nests (Hymenoptera: Vespidae) Using Computational Fluid Dynamics: A Possible Adaptation to Tropical Climates

Polybia scutellaris constructs huge nests characterized by numerous spinal projections on the surface. We investigated the thermal characteristics of P scutellaris nests in order to determine whether their nest temperature is homeothermically maintained and whether the spines play a role in the thermoregulation of the nests. In order to examine these hypotheses, we measured the nest temperature in a active nest and in an abandoned nest. The temperature in the active nest was almost stable at 27 degrees C, whereas that of the abandoned nest varied with changes in the ambient temperature, suggesting that nest temperature was maintained by the thermogenesis of colony individuals. In order to predict the thermal properties of the spines, a numerical simulation was employed. To construct a 3D-model of a P scutellaris nest, the nest architecture was simplified into an outer envelope and the surface spines, for both of which the initial temperature was set at 27 degrees C. The physical properties of the simulated nest were regarded to be those of wood since the nest of this species is constructed from plant materials. When the model was exposed to cool air (12 degrees C), the temperature was lower in the models with more spines. On the other hand, when the nest was heated (42 degrees C), the temperature increase was smaller in models with more spines. It is suggested that the spines act as a heat radiator, not as an insulator, against the changes in ambient temperature.

Fight versus flight: the interaction of temperature and body size determines antipredator behaviour in tegu lizards

Ectotherm antipredator behaviour might be strongly affected both by body temperature and size: when environmental temperatures do not favour maximal locomotor performance, large individuals may confront predators, whereas small animals may flee, simply because they have no other option. However, integration of body size and temperature effects is rarely approached in the study of antipredator behaviour in vertebrate ectotherms. In the present study we investigated whether temperature affects antipredator responses of tegu lizards, Tupinambis merianae, with distinct body sizes, testing the hypothesis that small tegus (juveniles) run away from predators regardless of the environmental temperature, because defensive aggression may not be an effective predator deterrent, whereas adults, which are larger, use aggressive defence at low temperatures, when running performance might be suboptimal. We recorded responses of juvenile (small) and adult (large) tegu lizards to a simulated predatory attack at five environmental temperatures in the laboratory. Most differences between the two size classes were observed at low temperatures: large tegus were more aggressive overall than were small tegus at all temperatures tested, but at lower temperatures, the small lizards often used escape responses whereas the large ones either adopted a defensive posture or remained inactive. These results provide strong evidence that body size and temperature affect the antipredator responses of vertebrate ectotherms. We discuss the complex and intricate network of evolutionary and ecological parameters that are likely to be involved in the evolution of such interactions. (C) 2009 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.