Relating traits to diversification: A simple test

We describe a simple comparative method for determining whether rates of diversification are correlated with continuous traits in species-level phylogenies. This involves comparing traits of species with net speciation rate (number of nodes linking extant species with the root divided by the root to tip evolutionary distance), using a phylogenetically corrected correlation. We use simulations to examine the power of this test. We find that the approach has acceptable power to uncover relationships between speciation and a continuous trait and is robust to background random extinction; however, the power of the approach is reduced when the rate of trait evolution is decreased. The test has low power to relate diversification to traits when extinction rate is correlated with the trait. Clearly, there are inherent limitations in using only data on extant species to infer correlates of extinction; however, this approach is potentially a powerful tool in analyzing correlates of speciation.

Simple general method of generating non-oxo, non-amavadine model octacoordinated vanadium(IV) complexes of some tetradentate ONNO chelating ligands from various oxovanadium(IV/V) compounds and structural characterization of one of them

A simple general route of obtaining very stable octacoordinated non-oxovanadium( IV) complexes of the general formula VL2 (where H2L is a tetradentate ONNO donor) is presented. Six such complexes (1-6) are adequately characterized by elemental analysis, mass spectrometry, and various spectroscopic techniques. One of these compounds (1) has been structurally characterized. The molecule has crystallographic 4 symmetry and has a dodecahedral structure existing in a tetragonal space group P4n2. The non-oxo character and VL2 stoichiometry for all of the complexes are established from analytical and mass spectrometric data. In addition, the non-oxo character is clearly indicated by the complete absence of the strong nu(v=o) band in the 925-1025 cm(-1) region, which is a signature of all oxovanadium species. The complexes are quite stable in open air in the solid state and in solution, a phenomenon rarely observed in non-oxovanadium(IV) or bare vanadium(IV) complexes.

A capture–recapture approach for screening using two diagnostic tests with availability of disease status for the test positives only

The article considers screening human populations with two screening tests. If any of the two tests is positive, then full evaluation of the disease status is undertaken; however, if both diagnostic tests are negative, then disease status remains unknown. This procedure leads to a data constellation in which, for each disease status, the 2 × 2 table associated with the two diagnostic tests used in screening has exactly one empty, unknown cell. To estimate the unobserved cell counts, previous approaches assume independence of the two diagnostic tests and use specific models, including the special mixture model of Walter or unconstrained capture–recapture estimates. Often, as is also demonstrated in this article by means of a simple test, the independence of the two screening tests is not supported by the data. Two new estimators are suggested that allow associations of the screening test, although the form of association must be assumed to be homogeneous over disease status. These estimators are modifications of the simple capture–recapture estimator and easy to construct. The estimators are investigated for several screening studies with fully evaluated disease status in which the superior behavior of the new estimators compared to the previous conventional ones can be shown. Finally, the performance of the new estimators is compared with maximum likelihood estimators, which are more difficult to obtain in these models. The results indicate the loss of efficiency as minor.

A capture-recapture approach for screening using two diagnostic tests with availability of disease status for the test positives only

The article considers screening human populations with two screening tests. If any of the two tests is positive, then full evaluation of the disease status is undertaken; however, if both diagnostic tests are negative, then disease status remains unknown. This procedure leads to a data constellation in which, for each disease status, the 2 x 2 table associated with the two diagnostic tests used in screening has exactly one empty, unknown cell. To estimate the unobserved cell counts, previous approaches assume independence of the two diagnostic tests and use specific models, including the special mixture model of Walter or unconstrained capture-recapture estimates. Often, as is also demonstrated in this article by means of a simple test, the independence of the two screening tests is not supported by the data. Two new estimators are suggested that allow associations of the screening test, although the form of association must be assumed to be homogeneous over disease status. These estimators are modifications of the simple capture-recapture estimator and easy to construct. The estimators are investigated for several screening studies with fully evaluated disease status in which the superior behavior of the new estimators compared to the previous conventional ones can be shown. Finally, the performance of the new estimators is compared with maximum likelihood estimators, which are more difficult to obtain in these models. The results indicate the loss of efficiency as minor.

Octanol-water partition coefficients for predicting the effects of tannins in ruminant nutrition

Tannins can cause beneficial or harmful nutritional effects, but their great diversity has until now prevented a rational distinction between tannin structures and their nutritional responses. An attempt has been made to study this problem by examining the octanol-water solubilities of tannins. A relatively simple HPLC method has been developed for screening mixtures of plant tannins for their octanol-water partition coefficients (K-ow coefficients). Tannins were isolated from the fruits and leaves of different Acacia, Calliandra, Dichrostachys, and Piliostigma species, which are known to produce beneficial or harmful effects. The K-ow coefficients of these tannins ranged from 0.061 to 13.9, average coefficients of variation were 9.2% and recoveries were 107%. Acacia nilotica fruits and leaves had the highest K-ow coefficients, that is, 2.0 and 13.9, respectively. These A. nilotica products also have high concentrations of tannins. The combined effects of high octanol solubilities and high tannin concentrations may explain their negative effects on animal nutrition and health. It is known that compounds with high octanol solubilities are more easily absorbed into tissues, and it is, therefore, proposed that such compounds are more likely to cause toxicity problems especially if consumed in large quantities. According to the literature, tannins in human foods tend to have low K-ow coefficients, and this was confirmed for the tannins in Piliostigma thonningii fruits. Therefore, unconventional feeds or browse products should be screened not only for their tannin concentrations but also for low octanol-water partition coefficients in order to identify nutritionally safe feeds and to avoid potentially toxic feeds.

Carbon-decorated FePt nanoparticles

FePt magnetic nanoparticles are an important candidate material for many future magnetic applications. FePt exists as two main phases, that is, a disordered face-centered cubic (fcc) structure, which is generally prepared by chemical methods at low temperatures, and the high-temperature chemically ordered face-centered tetragonal (fct) structure. The fee FePt, with low coercivity but associated with superparamagnetic properties, may find applications as a magnetic fluid or as a nanoscale carrier for chemical or biochemical species in biomedical areas, while fct FePt is proposed for use in ultrahigh-density magnetic recording applications. However, for both of these applications an enhancement of the intrinsically weak magnetic properties, the avoidance of magnetic interferences from neighbor particles, and the improved stability of the small magnetic body remain key practical issues. We report a simple synthetic method for producing FePt nanoparticles that involves hydrothermal treatment of Fe and Pt precursors in glucose followed by calcination at 900 degrees C. This new method produces thermally stable spheroidal graphite nanoparticles (large and fullerene-like) that encapsulate or decorate FePt particles of ca. 5 nm with no severe macroscopic particle coalescence. Also, a low coercivity of the material is recorded; indicative of small magnetic interference from neighboring carbon-coated particles. Thus, this simple synthetic method involves the use of a more environmentally acceptable glucose/aqueous phase to offer a protective coating for FePt nanoparticles. It is also believed that such a synthetic protocol can be readily extended to the preparation of other graphite-coated magnetic iron alloys of controlled size, stoichiometry, and physical properties.

Blood-clotting response tests for resistance to diphacinone and chlorophacinone in the Norway rat (Rattus norvegicus Berk.)

Resistance baselines were obtained for the first generation anticoagulant rodenticides chlorophacinone and diphacinone using laboratory, caesarian-derived Norway rats (Rattus norvegicus) as the susceptible strain and the blood clotting response test method. The ED99 estimates for a quantal response were: chlorophacinone, males 0.86 mg kg−1, females 1.03 mg kg−1; diphacinone, males 1.26 mg kg−1, females 1.60 mg kg−1. The dose-response data also showed that chlorophacinone was significantly (p<0.0001) more potent than diphacinone for both male and female rats, and that male rats were more susceptible than females to both compounds (p<0.002). The ED99 doses were then given to groups of five male and five female rats of the Welsh and Hampshire warfarin-resistant strains. Twenty-four hours later, prothrombin times were slightly elevated in both strains but all the animals were classified as resistant to the two compounds, indicating cross-resistance from warfarin to diphacinone and chlorophacinone. When rats of the two resistant strains were fed for six consecutive days on baits containing either diphacinone or chlorophacinone, many animals survived, indicating that their resistance might enable them to survive treatments with these compounds in the field.

Neurofuzzy design and model construction of nonlinear dynamical processes from data

A common problem in many data based modelling algorithms such as associative memory networks is the problem of the curse of dimensionality. In this paper, a new two-stage neurofuzzy system design and construction algorithm (NeuDeC) for nonlinear dynamical processes is introduced to effectively tackle this problem. A new simple preprocessing method is initially derived and applied to reduce the rule base, followed by a fine model detection process based on the reduced rule set by using forward orthogonal least squares model structure detection. In both stages, new A-optimality experimental design-based criteria we used. In the preprocessing stage, a lower bound of the A-optimality design criterion is derived and applied as a subset selection metric, but in the later stage, the A-optimality design criterion is incorporated into a new composite cost function that minimises model prediction error as well as penalises the model parameter variance. The utilisation of NeuDeC leads to unbiased model parameters with low parameter variance and the additional benefit of a parsimonious model structure. Numerical examples are included to demonstrate the effectiveness of this new modelling approach for high dimensional inputs.

Conditioning model output statistics of regional climate model precipitation on circulation patterns

Dynamical downscaling of Global Climate Models (GCMs) through regional climate models (RCMs) potentially improves the usability of the output for hydrological impact studies. However, a further downscaling or interpolation of precipitation from RCMs is often needed to match the precipitation characteristics at the local scale. This study analysed three Model Output Statistics (MOS) techniques to adjust RCM precipitation; (1) a simple direct method (DM), (2) quantile-quantile mapping (QM) and (3) a distribution-based scaling (DBS) approach. The modelled precipitation was daily means from 16 RCMs driven by ERA40 reanalysis data over the 1961–2000 provided by the ENSEMBLES (ENSEMBLE-based Predictions of Climate Changes and their Impacts) project over a small catchment located in the Midlands, UK. All methods were conditioned on the entire time series, separate months and using an objective classification of Lamb's weather types. The performance of the MOS techniques were assessed regarding temporal and spatial characteristics of the precipitation fields, as well as modelled runoff using the HBV rainfall-runoff model. The results indicate that the DBS conditioned on classification patterns performed better than the other methods, however an ensemble approach in terms of both climate models and downscaling methods is recommended to account for uncertainties in the MOS methods.

A Gaussian-mixture ensemble transform filter

We generalize the popular ensemble Kalman filter to an ensemble transform filter, in which the prior distribution can take the form of a Gaussian mixture or a Gaussian kernel density estimator. The design of the filter is based on a continuous formulation of the Bayesian filter analysis step. We call the new filter algorithm the ensemble Gaussian-mixture filter (EGMF). The EGMF is implemented for three simple test problems (Brownian dynamics in one dimension, Langevin dynamics in two dimensions and the three-dimensional Lorenz-63 model). It is demonstrated that the EGMF is capable of tracking systems with non-Gaussian uni- and multimodal ensemble distributions. Copyright © 2011 Royal Meteorological Society

The binding site distance test score: a robust method for the assessment of predicted protein binding sites

We propose a novel method for scoring the accuracy of protein binding site predictions – the Binding-site Distance Test (BDT) score. Recently, the Matthews Correlation Coefficient (MCC) has been used to evaluate binding site predictions, both by developers of new methods and by the assessors for the community wide prediction experiment – CASP8. Whilst being a rigorous scoring method, the MCC does not take into account the actual 3D location of the predicted residues from the observed binding site. Thus, an incorrectly predicted site that is nevertheless close to the observed binding site will obtain an identical score to the same number of nonbinding residues predicted at random. The MCC is somewhat affected by the subjectivity of determining observed binding residues and the ambiguity of choosing distance cutoffs. By contrast the BDT method produces continuous scores ranging between 0 and 1, relating to the distance between the predicted and observed residues. Residues predicted close to the binding site will score higher than those more distant, providing a better reflection of the true accuracy of predictions. The CASP8 function predictions were evaluated using both the MCC and BDT methods and the scores were compared. The BDT was found to strongly correlate with the MCC scores whilst also being less susceptible to the subjectivity of defining binding residues. We therefore suggest that this new simple score is a potentially more robust method for future evaluations of protein-ligand binding site predictions.

An extension of an over-dispersion test for count data

While over-dispersion in capture–recapture studies is well known to lead to poor estimation of population size, current diagnostic tools to detect the presence of heterogeneity have not been specifically developed for capture–recapture studies. To address this, a simple and efficient method of testing for over-dispersion in zero-truncated count data is developed and evaluated. The proposed method generalizes an over-dispersion test previously suggested for un-truncated count data and may also be used for testing residual over-dispersion in zero-inflation data. Simulations suggest that the asymptotic distribution of the test statistic is standard normal and that this approximation is also reasonable for small sample sizes. The method is also shown to be more efficient than an existing test for over-dispersion adapted for the capture–recapture setting. Studies with zero-truncated and zero-inflated count data are used to illustrate the test procedures.

A simple and rapid method for preserving RNA of aquatic invertebrates for ecotoxicogenomics

Here we describe a novel, inexpensive and simple method for preserving RNA that reduces handling stress in aquatic invertebrates following ecotoxicogenomic experimentation. The application of the method is based on transcriptomic experiments conducted on Daphnia magna, but may easily be applied on a range of other aquatic organisms of a particular size with e.g. amphipod Gammarus pulex representing an upper size limit. We explain in detail how to apply this new method, named the "Cylindrical Sieve (CS) system", and highlight its advantages and disadvantages.