Kinetic energy conserving integrators for Gaussian thermostatted SLLOD

A new integration scheme is developed for nonequilibrium molecular dynamics simulations where the temperature is constrained by a Gaussian thermostat. The utility of the scheme is demonstrated by its application to the SLLOD algorithm which is the standard nonequilibrium molecular dynamics algorithm for studying shear flow. Unlike conventional integrators, the new integrators are constructed using operator-splitting techniques to ensure stability and that little or no drift in the kinetic energy occurs. Moreover, they require minimum computer memory and are straightforward to program. Numerical experiments show that the efficiency and stability of the new integrators compare favorably with conventional integrators such as the Runge-Kutta and Gear predictor-corrector methods. (C) 1999 American Institute of Physics. [S0021-9606(99)50125-6].

Chemical treatment of Escherichia coli: 3. Selective extraction of a recombinant protein from cytoplasmic inclusion bodies in intact cells

In previous parts of this study we developed procedures for the high-efficiency chemical extraction of soluble and insoluble protein from intact Escherichia coli cells. Although high yields were obtained, extraction of recombinant protein directly from cytoplasmic inclusion bodies led to low product purity due to coextraction of soluble contaminants. In this work, a two-stage procedure for the selective extraction of recombinant protein at high efficiency and high purity is reported. In the first stage, inclusion-body stability is promoted by the addition of 15 mM 2-hydroxyethyldisulfide (2-HEDS), also known as oxidized P-mercaptoethanol, to the permeabil ization buffer (6 M urea + 3 mM ethylenediaminetetra-acetate [EDTA]). 2-HEDS is an oxidizing agent believed to promote disulfide bond formation, rendering the inclusion body resistant to solubilization in 6 M urea. Contaminating proteins are separated from the inclusion-body fraction by centrifugation. in the second stage, disulfide bonds are readily eliminated by including reducing agent (20 mM dithiothreitol [DTT]) into the permeabilization buffer. Extraction using this selective two-stage process yielded an 81% (w/w) recovery of the recombinant protein Long-R-3-IGF-I from inclusion bodies located in the cytoplasm of intact E. coli, at a purity of 46% (w/w). This was comparable to that achieved by conventional extraction (mechanical disruption followed by centrifugation and solubilization). A pilot-scale procedure was also demonstrated using a stirred reactor and diafiltration. This is the first reported study that achieves both high extraction efficiency and selectivity by the chemical treatment of cytoplasmic inclusion bodies in intact bacterial cells. (C) 1999 John Wiley & Sons, Inc.

Single amino acid substitutions in alpha-conotoxin PnIA shift selectivity for subtypes of the mammalian neuronal nicotinic acetylcholine receptor

The alpha-conotoxins, a class of nicotinic acetylcholine receptor (nAChR) antagonists, are emerging as important probes of the role played by different nAChR subtypes in cell function and communication, In this study, the native alpha-conotoxins PnIA and PnIB were found to cause concentration-dependent inhibition of the ACh-induced current in all rat parasympathetic neurons examined, with IC50 values of 14 and 33 nM, and a maximal reduction in current amplitude of 87% and 71%, respectively. The modified alpha-conotoxin [N11S]PnIA reduced the ACh-induced current with an IC50 value of 375 nM and a maximally effective concentration caused 91% block, [A10L]PnIA was the most potent inhibitor, reducing the ACh-induced current in similar to 80% of neurons, with an IC50 value of 1.4 nM and 46% maximal block of the total current, The residual current was not inhibited further by alpha-bungarotoxin, but was further reduced by the cu-conotoxins PnIA or PnIB, and by mecamylamine. H-1 NMR studies indicate that PnIA, PnIB, and the analogues, [A10L]PnIA and [N11S]PnIA, have identical backbone structures. We propose that positions 10 and II of PnIA and PnIB influence potency and determine selectivity among alpha 7 and other nAChR subtypes, including alpha 3 beta 2 and alpha 3 beta 4, Four distinct components of the nicotinic ACh-induced current in mammalian parasympathetic neurons have been dissected with these conopeptides.

Increasing the efficiency of solute leaching: impacts of flow interruption with drainage of the "preferential flow paths"

Most soils contain preferential flow paths that can impact on solute mobility. Solutes can move rapidly down the preferential flow paths with high pore-water velocities, but can be held in the less permeable region of the soil matrix with low pore-water velocities, thereby reducing the efficiency of leaching. In this study, we conducted leaching experiments with interruption of the flow and drainage of the main flow paths to assess the efficiency of this type of leaching. We compared our experimental results to a simple analytical model, which predicts the influence of the variations in concentration gradients within a single spherical aggregate (SSA) surrounded by preferential flow paths on leaching. We used large (length: 300 mm, diameter: 216 mm) undisturbed field soil cores from two contrasting soil types. To carry out intermittent leaching experiments, the field soil cores were first saturated with tracer solution (CaBr2), and background solution (CaCl2) was applied to mimic a leaching event. The cores were then drained at 25- to 30-cm suction to empty the main flow paths to mimic a dry period during which solutes could redistribute within the undrained region. We also conducted continuous leaching experiments to assess the impact of the dry periods on the efficiency of leaching. The flow interruptions with drainage enhanced leaching by 10-20% for our soils, which was consistent with the model's prediction, given an optimised equivalent aggregate radius for each soil. This parameter quantifies the time scales that characterise diffusion within the undrained region of the soil, and allows us to calculate the duration of the leaching events and interruption periods that would lead to more efficient leaching. Application of these methodologies will aid development of strategies for improving management of chemicals in soils, needed in managing salts in soils, in improving fertiliser efficiency, and in reclaiming contaminated soils. (C) 2000 Elsevier Science B.V. All rights reserved.

Stochastic structure and individual-tree growth models

The majority of past and current individual-tree growth modelling methodologies have failed to characterise and incorporate structured stochastic components. Rather, they have relied on deterministic predictions or have added an unstructured random component to predictions. In particular, spatial stochastic structure has been neglected, despite being present in most applications of individual-tree growth models. Spatial stochastic structure (also called spatial dependence or spatial autocorrelation) eventuates when spatial influences such as competition and micro-site effects are not fully captured in models. Temporal stochastic structure (also called temporal dependence or temporal autocorrelation) eventuates when a sequence of measurements is taken on an individual-tree over time, and variables explaining temporal variation in these measurements are not included in the model. Nested stochastic structure eventuates when measurements are combined across sampling units and differences among the sampling units are not fully captured in the model. This review examines spatial, temporal, and nested stochastic structure and instances where each has been characterised in the forest biometry and statistical literature. Methodologies for incorporating stochastic structure in growth model estimation and prediction are described. Benefits from incorporation of stochastic structure include valid statistical inference, improved estimation efficiency, and more realistic and theoretically sound predictions. It is proposed in this review that individual-tree modelling methodologies need to characterise and include structured stochasticity. Possibilities for future research are discussed. (C) 2001 Elsevier Science B.V. All rights reserved.

Corruption and auctions

We investigate how corruption affects the outcome of a first-price auction (bidding behavior, efficiency and the seller's expected revenue). The auctioneer approaches the winner to offer the possibility of a reduction in his bid in exchange for a bribe. The bribe can be a percentage of the difference between the winning and the second-highest bid or a fixed amount. We show that there exists a symmetric bidding strategy equilibrium that is monotone, i.e., higher valuation buyers bid higher. Corruption does not affect efficiency but both the auctioneer's expected bribe and the seller's expected revenue depend on the format of the bribe payments. We also find the optimal bribe scheme.

New gene technologies and their potential value for sugarcane

An efficient system is now in place for improving diverse sugarcane cultivars by genetic transformation, that is, the insertion of useful new genes into single cells followed by the regeneration of genetically modified (transgenic) plants. The method has already been used to introduce genes for resistance to several major diseases, insect pests and a herbicide, Field testing has begun, and research is underway to identify other genes for increased environmental stress resistance, agronomic efficiency and yield of sucrose or other valuable products. Experience in other crops has shown that genetically improved varieties which provide genuine environmental and consumer benefits are welcomed by producers and consumers. Substantial research is still needed, but these new gene technologies will reshape the sugar industry and determine the international competitive efficiency of producers.

Impairments of movement kinematics in patients with Huntington's disease: A comparison with and without a concurrent task

This study aimed to quantify the efficiency and smoothness of voluntary movement in Huntington's disease (HD) by the use of a graphics tablet that permits analysis of movement profiles. In particular, we aimed to ascertain whether a concurrent task (digit span) would affect the kinematics of goal-directed movements. Twelve patients with HD and their matched controls performed 12 vertical zig-zag movements, with both left and right hands (with and without the concurrent task), to large or small circular targets over long or short extents. The concurrent task was associated with shorter movement times and reduced right-hand superiority. Patients with HD were overall slower, especially with long strokes, and had similar peak velocities for both small and large targets, so that controls could better accommodate differences in target size. Patients with HD spent more time decelerating, especially with small targets, whereas controls allocated more nearly equal proportions of time to the acceleration and deceleration phases of movement, especially with large targets. Short strokes were generally less force inefficient than were long strokes, especially so for either hand in either group in the absence of the concurrent task, and for the right hand in its presence. With the concurrent task, however, the left hand's behavior changed differentially for the two groups; for patients with HD, it became more force efficient with short strokes and even less efficient with long strokes, whereas for controls, it became more efficient with long strokes. Controls may be able to divert attention away from the inferior left hand, increasing its automaticity, whereas patients with HD, because of disease, may be forced to engage even further online visual control under the demands of a concurrent task. Patients with HD may perhaps become increasingly reliant on terminal visual guidance, which indicates an impairment in constructing and refining an internal representation of the movement necessary for its. effective execution. Basal ganglia dysfunction may impair the ability to use internally generated cues to guide movement.

The effects of information request ambiguity and construct incongruence on query development

This paper examines the effects of information request ambiguity and construct incongruence on end user's ability to develop SQL queries with an interactive relational database query language. In this experiment, ambiguity in information requests adversely affected accuracy and efficiency. Incongruities among the information request, the query syntax, and the data representation adversely affected accuracy, efficiency, and confidence. The results for ambiguity suggest that organizations might elicit better query development if end users were sensitized to the nature of ambiguities that could arise in their business contexts. End users could translate natural language queries into pseudo-SQL that could be examined for precision before the queries were developed. The results for incongruence suggest that better query development might ensue if semantic distances could be reduced by giving users data representations and database views that maximize construct congruence for the kinds of queries in typical domains. (C) 2001 Elsevier Science B.V. All rights reserved.

Least-Cost Planning and electricity industry reform in Australia

Least-Cost Planning played a key role in the development of the energy efficiency and renewable energy industries in the USA, It has not been widely used elsewhere, largely due to differences in other nations' regulatory environments and the emergence of competitive markets as the dominant paradigm for electricity planning, Least-Cost Planning, however may over valuable insights for creating regulatory framework for competitive electricity markers. This paper examines some lessons which may be extracted from an analysis of the Least-Cost Planning experience in the USA and suggests how these lessons might prove beneficial in guiding Australia's electricity industry reform, This analysis demonstrates how market-based reforms may be flawed if they ignore the history of previous reform processes.

Development and implementation of the population Fisher information matrix for the evaluation of population pharmacokinetic designs.

In population pharmacokinetic studies, the precision of parameter estimates is dependent on the population design. Methods based on the Fisher information matrix have been developed and extended to population studies to evaluate and optimize designs. In this paper we propose simple programming tools to evaluate population pharmacokinetic designs. This involved the development of an expression for the Fisher information matrix for nonlinear mixed-effects models, including estimation of the variance of the residual error. We implemented this expression as a generic function for two software applications: S-PLUS and MATLAB. The evaluation of population designs based on two pharmacokinetic examples from the literature is shown to illustrate the efficiency and the simplicity of this theoretic approach. Although no optimization method of the design is provided, these functions can be used to select and compare population designs among a large set of possible designs, avoiding a lot of simulations.

Stay-green: A consequence of the balance between supply and demand for nitrogen during grain filling?

Retention of green leaf area in grain sorghum under post-anthesis drought, known as stay-green, is associated with greater biomass production, lodging resistance and yield. The stay-green phenomenon can be examined at a cell, leaf, or whole plant level. At a cell level, the retention of chloroplast proteins such as LHCP2, OEC33 and Rubisco until late in senescence has been reported in sorghum containing the KS19 source of stay-green, indicating that photosynthesis may be maintained for longer during senescence in these genotypes. At a leaf level, longevity of photosynthetic apparatus is intimately related to nitrogen (N) status. At a whole plant level, stay-green can be viewed as a consequence of the balance between N demand by the grain and N supply during grain filling. To examine some of these concepts, nine hybrids varying in the B35 and KS19 sources of stay-green were grown under a postanthesis water deficit. Genotypic variation in delayed onset and reduced rate of leaf senescence were explained by differences in specific leaf nitrogen (SLN) and N uptake during grain filling. Matching N supply from age-related senescence and N uptake during grain tilling with grain N demand found that the shortfall in N supply for grain filling was greater in the senescent than stay-green hybrids, resulting in more accelerated leaf senescence in the former. We hypothesise that increased N uptake by stay-green hybrids is a result of greater biomass accumulation during grain filling in response to increased sink demand (higher grain numbers) which, in turn, is the result of increased radiation use efficiency and transpiration efficiency due to higher SLN. Delayed leaf senescence resulting from higher SLN should, in turn, allow snore carbon and nitrogen to be allocated to the roots of stay-green hybrids during grain filling, thereby maintaining a greater capacity to extract N from the soil compared with senescent hybrids.

Supply chain management as beyond operational efficiency

The orthodoxy of supply chain management (SCM) emphasises competitive advantage through increased operational efficiency and market responsiveness from production and distribution processes into the hands of consumers. It anticipates that future competition will be between chains rather than between firms. While well established in other industry sectors, the SCM concept is newly developed in the Australian agri-food sector. Critical review of the concept has identified key issues of power among channel members, processes of chain initiation and innovation, and the inability of SCM to offer a viable business strategy for some firms. Building on those insights, this paper examines the supply chain concept for horticulture. Horticultural products are characterised by perishability, heterogeneity and lags in production response to market signals. Producers’ profits are vulnerable to quantity, timing of supply and product specification. Many supply chains in smaller industries are loose, fragmented, interwoven, unstable and unique! Firms operating within these environments need an astute understanding of the chains, the hierarchy of channel members and their relative position. Effective business strategies – for individual firms and supply chains - need to be developed and redeveloped to accommodate the dynamic nature of horticulture. Two case studies are discussed as contributions to this early stage of the theoretical development of supply chain management. The SCM concept also has implications for horticultural researchers, involving a wider range of industry stakeholders, technical problems and research skills. As for business management, the usefulness of the concept will depend on its capacity to increase responsiveness to customers’ preferences and customer value.

The influence of key chemical constituents in activated sludge on surface and flocculating properties

This paper examines the influence of the chemical constituents of activated sludge and extracted extracellular polymeric substances (EPS) on the surface properties, hydrophobicity, surface charge (SC) and flocculating ability (FA) of activated sludge floes. Activated sludge samples from 7 different full-scale wastewater treatment plants were examined. Protein and humic substances were found to be the dominant polymeric compounds in the activated sludges and the extracted EPS, and they significantly affected the FA and surface properties, hydrophobicity and SC, of the sludge floes. The polymeric compounds proteins, humic substances and carbohydrates in the sludge floes and the extracted EPS contributed to the negative SC, but correlated negatively to the hydrophobicity of sludge floes. The quantity of protein and carbohydrate within the sludge and the extracted EPS was correlated positively to the FA of the sludge floes, while increased amounts of humic substances resulted in lower FA. In contrast, increased amounts of total extracted EPS had a negative correlation to FA. The results reveal that the quality and quantity of the polymeric compounds within the sludge floes is more informative, with respect to understanding the mechanisms involved in flocculation, than if only the extracted EPS are considered. This is an important finding as it indicates that extracting EPS may be insufficient to characterise the EPS. This is due to the low extraction efficiency and difficulties involved in the separation of EPS from other organic compounds. Correlations were observed between the surface properties and FA of the sludge floes., This confirms that the surface properties of the, sludge flocs play an important role in the bioflocculation process but that also other interactions like polymer entanglement are important. (C) 2002 Elsevier Science Ltd. All rights reserved.

Evaluating plant breeding strategies by simulating gene action and dryland environment effects

Functional genomics is the systematic study of genome-wide effects of gene expression on organism growth and development with the ultimate aim of understanding how networks of genes influence traits. Here, we use a dynamic biophysical cropping systems model (APSIM-Sorg) to generate a state space of genotype performance based on 15 genes controlling four adaptive traits and then search this spice using a quantitative genetics model of a plant breeding program (QU-GENE) to simulate recurrent selection. Complex epistatic and gene X environment effects were generated for yield even though gene action at the trait level had been defined as simple additive effects. Given alternative breeding strategies that restricted either the cultivar maturity type or the drought environment type, the positive (+) alleles for 15 genes associated with the four adaptive traits were accumulated at different rates over cycles of selection. While early maturing genotypes were favored in the Severe-Terminal drought environment type, late genotypes were favored in the Mild-Terminal and Midseason drought environment types. In the Severe-Terminal environment, there was an interaction of the stay-green (SG) trait with other traits: Selection for + alleles of the SG genes was delayed until + alleles for genes associated with the transpiration efficiency and osmotic adjustment traits had been fixed. Given limitations in our current understanding of trait interaction and genetic control, the results are not conclusive. However, they demonstrate how the per se complexity of gene X gene X environment interactions will challenge the application of genomics and marker-assisted selection in crop improvement for dryland adaptation.