Why higher resolution graphics cards are needed in colour vision research

The colour resolution of a 14‐bit and an 8‐bit per channel graphics card were evaluated and compared with the just noticeable difference between colours (varying only in luminance) for: (1) a standard observer (based on the CIE 1976 L*u*v* colour space) and (2) real observers in a colour discrimination task. The results of this study show that an 8‐bit per channel graphics card seems adequate for colour discrimination experiments where stimuli only vary in luminance. However, considering that the resolution of the graphics card should be equal to the Nyquist rate, an 8‐bit per channel card turns out to be inadequate. For colour discrimination experiments where stimuli only vary in chromaticity, there is an undersampling of the colour space with respect to MacAdam ellipses when using 8‐bit per channel graphics cards. The extremely fine colour resolution of a 14‐bit per channel graphics card overcomes these problems. Its use allows more accurate measurements of achromatic and chromatic discrimination thresholds and avoids experimental (spatial or luminance) artefacts, such as bandings that can occur on achromatic or chromatic gradients. © 2010 Wiley Periodicals, Inc. Col Res Appl, 2011     

Phosphorus dynamics in permanent pastures: differential fertilizing and the animal effect

The general objective of this study was to evaluate the deviation between measured and estimated soil phosphorus (P) content, over 3 years, in a permanent bio-diverse pasture system in Southern Portugal with grazing sheep, and subjected to annual, differential P fertilization. The results can be a contribution to the development of practical and effective site-specific management strategies to minimize pasture yield variation. The soil and pasture samples were taken from a 6 ha field and were geo-referenced with RTK GPS. This procedure was carried out, each year, from March to May, according to the vegetative growth of the pasture. In October of each year the field was fertilized in a differential manner, as a function of soil P concentration measured at the end of the pasture growth cycle (May–June). Maps were developed in ARCGIS 9.3 considering: (1) the soil P concentration and pH; (2) the average P plant uptake; (3) the differential P application; and (4) the extractable P. The significant temporal variability of soil P concentration and pasture dry matter yield confirm the complexity of soil P dynamics in pastures involving two biological systems: plant and animal, under Mediterranean conditions and the consequent difficulties in implementing precision agriculture techniques. The results of this work indicate that 3 years of P variable-rate application rate were not sufficient to obtain homogeneous and adequate levels of P in the whole field for crop production. Despite differential P fertilization with the objective of obtaining homogenous values of soil P content in experimental field, the undulating topography of the experimental field associated with the presence of grazing animals adds a notable short-range spatial variation in nutrients that generally arises from heterogeneous excreta depositions. The small and positive final deviation between measured and estimated P levels suggests the irregular and gradual release of P by the fertilizer over years, contributing to an increase in soil P concentration. P input in fertilizer and removal in the crop greatly exceed all other inputs and outputs. However, the pH effect on extractable P, the estimation of amounts of export/import by livestock, atmospheric deposition or erosion/leaching losses are complex and justify more experiments to evaluate the confidence of long-term estimated P dynamic balance before sustained decision making is possible for differential pasture fertilization and site-specific management strategy implementation.     

Towards Automated Binding Affinity Prediction Using an Iterative Linear Interaction Energy Approach

Binding affinity prediction of potential drugs to target and off-target proteins is an essential asset in drug development. These predictions require the calculation of binding free energies. In such calculations, it is a major challenge to properly account for both the dynamic nature of the protein and the possible variety of ligand-binding orientations, while keeping computational costs tractable. Recently, an iterative Linear Interaction Energy (LIE) approach was introduced, in which results from multiple simulations of a protein-ligand complex are combined into a single binding free energy using a Boltzmann weighting-based scheme. This method was shown to reach experimental accuracy for flexible proteins while retaining the computational efficiency of the general LIE approach. Here, we show that the iterative LIE approach can be used to predict binding affinities in an automated way. A workflow was designed using preselected protein conformations, automated ligand docking and clustering, and a (semi-)automated molecular dynamics simulation setup. We show that using this workflow, binding affinities of aryloxypropanolamines to the malleable Cytochrome P450 2D6 enzyme can be predicted without a priori knowledge of dominant protein-ligand conformations. In addition, we provide an outlook for an approach to assess the quality of the LIE predictions, based on simulation outcomes only.     

Recovery of platinum, tin and indium from spent catalysts in chloride medium using strong basic anion exchange resins

This work describes a route for platinum recovery from spent commercial Pt and PtSnIn/Al₂O₃ catalysts using strong basic mesoporous and macroporous anion exchange resins (Cl⁻ form). The catalysts were leached with aqua regia (75 °C, 20-25 min). Platinum adsorption was influenced by the presence of other metals which form chlorocomplexes (tin, indium) and also base metals (aluminum). However, it was possible to overcome this fact by a sequential desorption procedure. Aluminum was selectively removed from the resins by elution with 3 mol L⁻¹ HCl. Platinum was desorbed passing 1 mol L⁻¹ Na₂S₂O₃ (pH 9). Tin was removed by elution with 0.1 mol L⁻¹ ascorbic acid. Indium was removed using 0.1 mol L⁻¹ EDTA as eluent. Desorption efficiency exceeded 99% for all metals. Metals were recovered in high yields (>98 wt%).     

Verification of cardiac tissue electrophysiology simulators using an N-version benchmark

Ongoing developments in cardiac modelling have resulted, in particular, in the development of advanced and increasingly complex computational frameworks for simulating cardiac tissue electrophysiology. The goal of these simulations is often to represent the detailed physiology and pathologies of the heart using codes that exploit the computational potential of high-performance computing architectures. These developments have rapidly progressed the simulation capacity of cardiac virtual physiological human style models; however, they have also made it increasingly challenging to verify that a given code provides a faithful representation of the purported governing equations and corresponding solution techniques. This study provides the first cardiac tissue electrophysiology simulation benchmark to allow these codes to be verified. The benchmark was successfully evaluated on 11 simulation platforms to generate a consensus gold-standard converged solution. The benchmark definition in combination with the gold-standard solution can now be used to verify new simulation codes and numerical methods in the future.