Emergence of Chenopodium album and Stellaria media of different origins under different climatic conditions

The emergence behaviour of weed species in relation to cultural and meteorological events was studied. Dissimilarities between populations in dormancy and germination ecology, between-year maturation conditions and seed quality and burial site climate all contribute to potentially unpredictable variability. Therefore, a weed emergence data set was produced for weed seeds of Stellaria media and Chenopodium album matured and collected from three populations (Italy, Sweden and UK). The seeds were collected in two consecutive seasons (1999 and 2000) and subsequently buried in the autumn of the same year of maturation in eight contrasting climatic locations throughout Europe and the USA. The experiment sought to explore and explain differences between the three populations in their emergence behaviour. Evidence was demonstrated of synchrony in the timing of the emergence of different populations of a species at a given burial site. The relative magnitudes of emergence from the three populations at a given burial site in a given year were generally similar across all the burial sites in the study. The resulting data set was also used to construct a simple weed emergence model, which was tested for its application to the range of different burial environments and populations. The study demonstrated the possibility of using a simple thermal time-based model to describe part of the emergence behaviour across different burial sites, seed populations and seasons, and a simple winter chilling relationship to adjust for the magnitude of the flush of emergence at a given burial site. This study demonstrates the possibility of developing robust generic models for simple predictions of emergence timing across populations.

Effects of grazing management on beetle and plant assemblages during the re-creation of a flood-plain meadow

Flood-plain meadows (Alopecurus-Sanguisorba grassland) are a floristically rich community of conservation importance throughout Europe. Declines in their distribution due in part to modern farming practices mean they now cover less than 1500 ha in the UK. To investigate the effect of grazing regime during the re-creation of this grassland type, target plant species were sown onto ex-arable land during 1985. Traditional management, based on a July hay cut followed by aftermath grazing was subsequently instigated, and the site was divided into replicated grazing regimes of cattle, sheep and an un-grazed control. Plant and beetle assemblages were sampled and compared to those of target flood-plain meadows and improved grassland communities. Within the re-creation treatments the absence of aftermath grazing reduced beetle abundances and species richness. Assemblages of plants were closest to that of the target flood-plain meadow under sheep grazing, although this differed little from cattle grazing. Beetle species assemblages and functional group structure were, however, closest to the target grassland under cattle grazing. For all taxa the greatest resilience to succession to the target flood-plain meadow occurred when grazing was not part of the management prescription. Although successful re-creation had not been achieved for either the plants or beetles, cutting followed by aftermath cattle grazing has provided the best management to date. (c) 2006 Elsevier B.V. All rights reserved.

The economic viability and potential of a novel poultry agroforestry system

Investigating agroforestry systems that incorporate poultry is warranted in Northern Europe as they may offer benefits including: improved welfare and use of range; reduced feed costs; price premia on products; reduced payback periods for forests; and, greater returns on investment. Free-range egg production accounts for 27% of the United Kingdom egg market and demand for outdoor broilers is increasing. No research has been conducted recently on the economic viability of agroforestry systems with poultry. An economic model was constructed to: assess economic viability of a broiler agroforestry system; and, investigate the sensitivity of economic performance to key factors and interactions, and identify those which warrant attention in research and management. The system modelled is a commercial trial established in Southern England in 2002 where deciduous trees were planted and broilers reared in six- or nine-week periods. The model uses Monte Carlo simulation and financial performance analyses run for a 120-year period. An Internal Rate of Return (IRR) of 15.5% is predicted for the six-week system which remains viable under a 'worst case' scenario (IRR of 12.6%). Factors which affect financial performance most (decreasing in magnitude) are prices achieved for broilers, costs of brooding houses, chicks, arks, feed and timber prices. The main anticipated effects of biological interactions on financial performance (increased ranging on feed conversion and excess nutrient supply on tree health) were not supported by analysis. Further research is particularly warranted on the welfare benefits offered by the tree component and its relation to price premia.

Multivariate relationships between groundwater chemistry and toxicity in an urban aquifer

Multivariate statistical methods were used to investigate file Causes of toxicity and controls on groundwater chemistry from 274 boreholes in an Urban area (London) of the United Kingdom. The groundwater was alkaline to neutral, and chemistry was dominated by calcium, sodium, and Sulfate. Contaminants included fuels, solvents, and organic compounds derived from landfill material. The presence of organic material in the aquifer caused decreases in dissolved oxygen, sulfate and nitrate concentrations. and increases in ferrous iron and ammoniacal nitrogen concentrations. Pearson correlations between toxicity results and the concentration of individual analytes indicated that concentrations of ammoinacal nitrogen, dissolved oxygen, ferrous iron, and hydrocarbons were important where present. However, principal component and regression analysis suggested no significant correlation between toxicity and chemistry over the whole area. Multidimensional Scaling was used to investigate differences in sites caused by historical use, landfill gas status, or position within the sample area. Significant differences were observed between sites with different historical land use and those with different gas status. Examination of the principal component matrix revealed that these differences are related to changes in the importance of reduced chemical species.

Synergetic effects of the Cu/Pt{110} surface alloy: enhanced reactivity of water and carbon monoxide

We have used synchrotron-based high-resolution X-ray photoelectron spectroscopy in combination with ab initio density functional theory calculations to investigate the characteristics of water and CO adsorption on the bimetallic Cu/Pt{110}-(2 x 1) surface at a Cu coverage near 0.5 ML. Cu fills the troughs of the reconstructed clean surface forming nanowires, which are stable up to 830 K. Their presence dramatically influences the adsorption of water and CO. Water adsorption changes from intact to partially dissociated while the desorption temperature of CO on this surface increases by up to 27 K with respect to the clean Pt{110} surface. Ab initio calculations and experimental valence band spectra reveal that the Cu 3d-band is narrowed and shifted upward with respect to bulk Cu surfaces. This and electron donation to surface Pt atoms cause the increase in the bond strength between CO and the Pt surface atoms. The pathway for water dissociation occurs via Cu surface atoms. The heat of adsorption of water bonding to Cu surface atoms was calculated to be 0.82 eV, which is significantly higher than on the clean Pt{110} surface; the activation energy for partial dissociation is 0.53 eV (not corrected for zero point energy).

Anion-templated assembly of pseudorotaxanes: importance of anion template, strength of ion-pair thread association, and macrocycle ring size

A wide range of pseuclorotaxane assemblies containing positively charged pyridinium, pyridinium nicotinamide, imidazolium, benzimidazolium and guanidinium threading components, and macrocyclic isophthalamide polyether ligands have been prepared using a general anion templation procedure. In noncompetitive solvent media, coupling halide anion recognition by a macrocyclic ligand with ion-pairing between the halide anion and a strongly associated cation provides the driving force for interpenetration. Extensive solution H-1 NMR binding studies, thermodynamic investigations, and single-crystal X-ray structure determinations reveal that the nature of the halide anion template, strength of the ion-pairing between the anion template and the cationic threading component, and to a lesser extent favorable second sphere pi-pi aromatic stacking interactions between the positively charged threading component and macrocyclic ligand, together with macrocyclic ring size, affect the efficacy of pseudorotaxane formation.

Development of a liquid chromatographic time-of-flight mass spectrometric method for the determination of unlabelled and deuterium-labelled alpha-tocopherol in blood components

A method is described for the analysis of deuterated and undeuterated alpha-tocopherol in blood components using liquid chromatography coupled to an orthogonal acceleration time-of-flight (TOF) mass spectrometer. Optimal ionisation conditions for undeuterated (d0) and tri- and hexadeuterated (d3 or d6) alpha-tocopherol standards were found with negative ion mode electrospray ionisation. Each species produced an isotopically resolved single ion of exact mass. Calibration curves of pure standards were linear in the range tested (0-1.5 muM, 0-15 pmol injected). For quantification of d0 and d6 in blood components following a standard solvent extraction, a stable-isotope-labelled internal standard (d3-alpha-tocopherol) was employed. To counter matrix ion suppression effects, standard response curves were generated following identical solvent extraction procedures to those of the samples. Within-day and between-day precision were determined for quantification of d0- and d6-labelled alpha-tocopherol in each blood component and both averaged 3-10%. Accuracy was assessed by comparison with a standard high-performance liquid chromatography (HPLC) method, achieving good correlation (r(2) = 0.94), and by spiking with known concentrations of alpha-tocopherol (98% accuracy). Limits of detection and quantification were determined to be 5 and 50 fmol injected, respectively. The assay was used to measure the appearance and disappearance of deuterium-labelled alpha-tocopherol in human blood components following deuterium-labelled (d6) RRR-alpha-tocopheryl acetate ingestion. The new LC/TOFMS method was found to be sensitive, required small sample volumes, was reproducible and robust, and was capable of high throughput when large numbers of samples were generated. Copyright (C) 2003 John Wiley Sons, Ltd.

Hydrogen bond-induced pair formation of glycine on the chiral Cu{531} surface

Enantio-specific interactions on intrinsically chiral or chirally modified surfaces can be identified experimentally via comparison of the adsorption geometries of similar nonchiral and chiral molecules. Information about the effects of substrate-related and in interactions on the adsorption geometry of glycine, the only natural nonchiral amino acid, is therefore important for identifying enantio-specific interactions of larger chiral amino acids. We have studied the long- and short-range adsorption geometry and bonding properties of glycine on the intrinsically chiral Cu{531} surface with low-energy electron diffraction, near-edge X-ray absorption One structure spectroscopy, X-ray photoelectron spectroscopy, and temperature-programmed desorption. For coverages between 0.15 and 0.33 ML (saturated chemisorbed layer) and temperatures between 300 and 430 K, glycine molecules adsorb in two different azimuthal orientations, which are associated with adsorption sites on the {110} and {311} microfacets of Cu{531}. Both types of adsorption sites allow a triangular footprint with surface bonds through the two oxygen atoms and the nitrogen atom. The occupation of the two adsorption sites is equal for all coverages, which can be explained by pair formation due to similar site-specific adsorption energies and the possibility of forming hydrogen bonds between molecules on adjacent {110} and {311} sites. This is not the ease for alanine and points toward higher site specificity in the case of alanine, which is eventually responsible for the enantiomeric differences observed for the alanine system.

Global trends and factors associated with the illegal killing of elephants: a hierarchical bayesian analysis of carcass encounter data

Elephant poaching and the ivory trade remain high on the agenda at meetings of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Well-informed debates require robust estimates of trends, the spatial distribution of poaching, and drivers of poaching. We present an analysis of trends and drivers of an indicator of elephant poaching of all elephant species. The site-based monitoring system known as Monitoring the Illegal Killing of Elephants (MIKE), set up by the 10th Conference of the Parties of CITES in 1997, produces carcass encounter data reported mainly by anti-poaching patrols. Data analyzed were site by year totals of 6,337 carcasses from 66 sites in Africa and Asia from 2002–2009. Analysis of these observational data is a serious challenge to traditional statistical methods because of the opportunistic and non-random nature of patrols, and the heterogeneity across sites. Adopting a Bayesian hierarchical modeling approach, we used the proportion of carcasses that were illegally killed (PIKE) as a poaching index, to estimate the trend and the effects of site- and country-level factors associated with poaching. Important drivers of illegal killing that emerged at country level were poor governance and low levels of human development, and at site level, forest cover and area of the site in regions where human population density is low. After a drop from 2002, PIKE remained fairly constant from 2003 until 2006, after which it increased until 2008. The results for 2009 indicate a decline. Sites with PIKE ranging from the lowest to the highest were identified. The results of the analysis provide a sound information base for scientific evidence-based decision making in the CITES process.

Incorporation of water vapour transfer in the JULES Land Surface Model: implications for key soil variables and land surface fluxes

This study focuses on the mechanisms underlying water and heat transfer in upper soil layers, and their effects on soil physical prognostic variables and the individual components of the energy balance. The skill of the JULES (Joint UK Land Environment Simulator) land surface model (LSM) to simulate key soil variables, such as soil moisture content and surface temperature, and fluxes such as evaporation, is investigated. The Richards equation for soil water transfer, as used in most LSMs, was updated by incorporating isothermal and thermal water vapour transfer. The model was tested for three sites representative of semi-arid and temperate arid climates: the Jornada site (New Mexico, USA), Griffith site (Australia) and Audubon site (Arizona, USA). Water vapour flux was found to contribute significantly to the water and heat transfer in the upper soil layers. This was mainly due to isothermal vapour diffusion; thermal vapour flux also played a role at the Jornada site just after rainfall events. Inclusion of water vapour flux had an effect on the diurnal evolution of evaporation, soil moisture content and surface temperature. The incorporation of additional processes, such as water vapour flux among others, into LSMs may improve the coupling between the upper soil layers and the atmosphere, which in turn could increase the reliability of weather and climate predictions.

FunFOLDQA: a quality assessment tool for protein-ligand binding site residue predictions

The estimation of prediction quality is important because without quality measures, it is difficult to determine the usefulness of a prediction. Currently, methods for ligand binding site residue predictions are assessed in the function prediction category of the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment, utilizing the Matthews Correlation Coefficient (MCC) and Binding-site Distance Test (BDT) metrics. However, the assessment of ligand binding site predictions using such metrics requires the availability of solved structures with bound ligands. Thus, we have developed a ligand binding site quality assessment tool, FunFOLDQA, which utilizes protein feature analysis to predict ligand binding site quality prior to the experimental solution of the protein structures and their ligand interactions. The FunFOLDQA feature scores were combined using: simple linear combinations, multiple linear regression and a neural network. The neural network produced significantly better results for correlations to both the MCC and BDT scores, according to Kendall’s τ, Spearman’s ρ and Pearson’s r correlation coefficients, when tested on both the CASP8 and CASP9 datasets. The neural network also produced the largest Area Under the Curve score (AUC) when Receiver Operator Characteristic (ROC) analysis was undertaken for the CASP8 dataset. Furthermore, the FunFOLDQA algorithm incorporating the neural network, is shown to add value to FunFOLD, when both methods are employed in combination. This results in a statistically significant improvement over all of the best server methods, the FunFOLD method (6.43%), and one of the top manual groups (FN293) tested on the CASP8 dataset. The FunFOLDQA method was also found to be competitive with the top server methods when tested on the CASP9 dataset. To the best of our knowledge, FunFOLDQA is the first attempt to develop a method that can be used to assess ligand binding site prediction quality, in the absence of experimental data.

P-found: grid-enabling distributed repositories of protein folding and unfolding simulations for data mining

The P-found protein folding and unfolding simulation repository is designed to allow scientists to perform data mining and other analyses across large, distributed simulation data sets. There are two storage components in P-found: a primary repository of simulation data that is used to populate the second component, and a data warehouse that contains important molecular properties. These properties may be used for data mining studies. Here we demonstrate how grid technologies can support multiple, distributed P-found installations. In particular, we look at two aspects: firstly, how grid data management technologies can be used to access the distributed data warehouses; and secondly, how the grid can be used to transfer analysis programs to the primary repositories — this is an important and challenging aspect of P-found, due to the large data volumes involved and the desire of scientists to maintain control of their own data. The grid technologies we are developing with the P-found system will allow new large data sets of protein folding simulations to be accessed and analysed in novel ways, with significant potential for enabling scientific discovery.

Roll of the rhythmic component in the proactive control of a human hand

In terms of evolution, the strategy of catching prey would have been an important part of survival in a constantly changing environment. A prediction mechanism would have developed to compensate for any delay in the sensory-motor system. In a previous study, “proactive control” was found, in which the motion of the hands preceded the virtual moving target. These results implied that the positive phase shift of the hand motion represents the proactive nature of the visual-motor control system, which attempts to minimize the brief error in the hand motion when the target changes position unexpectedly. In our study, a visual target moves in circle (13 cm diameter) on a computer screen, and each subject is asked to keep track of the target’s motion by the motion of a cursor. As the frequency of the target increases, a rhythmic component was found in the velocity of the cursor in spite of the fact that the velocity of the target was constant. The generation of a rhythmic component cannot be explained simply as a feedback mechanism for the phase shifts of the target and cursor in a sensory-motor system. Therefore, it implies that the rhythmic component was generated to predict the velocity of the target, which is a feed-forward mechanism in the sensory-motor system. Here, we discuss the generation of the rhythmic component and its roll in the feed-forward mechanism.

Displacement of methane by coadsorbed carbon dioxide is facilitated in narrow carbon nanopores

By using simulation methods, we studied the adsorption of binary CO2-CH4 mixtures on various CH4 preadsorbed carbonaceous materials (e.g., triply periodic carbon minimal surfaces, slit-shaped carbon micropores, and Harris's virtual porous carbons) at 293 K. Regardless of the different micropore geometry, two-stage mechanism of CH4 displacement from carbon nanospaces by coadsorbed CO2 has been proposed. In the first stage, the coadsorbed CO2 molecules induced the enhancement of CH4 adsorbed amount. In the second stage, the stronger affinity of CO2 to flat/curved graphitic surfaces as well as CO2-CO2 interactions cause the displacement of CH4 molecules from carbonaceous materials. The operating conditions of CO2-induced cleaning of the adsorbed phase from CH4 mixture component strongly depend on the size of the carbon micropores, but, in general, the enhanced adsorption field in narrow carbon ultramicropores facilitates the nonreactive displacement of CH4 by coadsorbed CO2. This is because in narrow carbon ultramicropores the equilibrium CO2/CH4 selectivity (i.e., preferential adsorption toward CO2) increased significantly. The adsorption field in wider micropores (i.e., the overall surface energy) for both CO2 and CH4 is very similar, which decreases the preferential CO2 adsorption. This suppresses the displacement of CH4 by coadsorbed CO2 and assists further adsorption of CH4 from the bulk mixture (i.e., CO2/CH4 mixing in adsorbed phase).

New age estimates for the Palaeolithic assemblages and Pleistocene succession of Casablanca, Morocco

Marine and aeolian Quaternary sediments from Casablanca, Morocco were dated using the optically stimulated luminescence (OSL) signal of quartz grains. These sediments form part of an extensive succession spanning the Pleistocene, and contain a rich faunal and archaeological record, including an Acheulian lithic assemblage from before the Brunhes–Matayama boundary, and a Homo erectus jaw from younger cave deposits. Sediment samples from the sites of Reddad Ben Ali, Oulad J’mel, Sidi Abderhamane and Thomas Quarries have been dated, in order to assess the upper limits of OSL. The revision of previously measured mammalian tooth enamel electron spin resonance (ESR) dates from the Grotte des Rhinocéros, Oulad Hamida Quarry 1, incorporating updated environmental dose rate measurements and attenuation calculations, also provide chronological constraint for the archaeological material preserved at Thomas Quarries. Several OSL age estimates extend back to around 500,000 years, with a single sample providing an OSL age close to 1 Ma in magnetically reversed sediments. These luminescence dates are some of the oldest determined, and their reliability is assessed using both internal criteria based on stratigraphic consistency, and external lithostratigraphic, morphostratigraphic and independent chronological constraints. For most samples, good internal agreement is observed using single aliquot regenerative-dose OSL measurements, while multiple aliquot additive-dose measurements generally have poorer resolution and consistency. Novel slow-component and component-resolved OSL approaches applied to four samples provide significantly enhanced dating precision, and an examination of the degree of signal zeroing at deposition. A comparison of the OSL age estimates with the updated ESR dates and one U-series date demonstrate that this method has great potential for providing reliable age estimates for sediments of this antiquity. We consider the cause of some slight age inversion observed at Thomas Quarries, and provide recommendations for further luminescence dating within this succession.