An automatic method for assessing structural importance of amino acid positions

Background: A great deal is known about the qualitative aspects of the sequence-structure relationship, for example that buried residues are usually more conserved between structurally similar homologues, but no attempts have been made to quantitate the relationship between evolutionary conservation at a sequence position and change to global tertiary structure. In this paper we demonstrate that the Spearman correlation between sequence and structural change is suitable for this purpose. Results: Buried residues, bends, cysteines, prolines and leucines were significantly more likely to occupy positions highly correlated with structural change than expected by chance. Some buried residues were found to be less informative than expected, particularly residues involved in active sites and the binding of small molecules. Conclusion: The correlation-based method generates predictions of structural importance for superfamily positions which agree well with previous results of manual analyses, and may be of use in automated residue annotation piplines. A PERL script which implements the method is provided

Statistical modelling of groundwater contamination monitoring data: a comparison of spatial and spatiotemporal methods

Field monitoring of groundwater contamination plumes is an important component of managing risks for downgradient receptors and remedial strategies that rely on monitored natural attenuation. Collection of groundwater quality data can however take a considerable effort and be associated with high cost. Here, we investigated the relative merits of analyzing groundwater quality data using spatial compared to spatiotemporal statistical modelling and assessed the accuracy of both methods and implications for data collection requirements. The aim of this was to determine whether the quantity of data collected can be reduced, while retaining the same level of estimation accuracy, by analyzing groundwater contamination data using a spatiotemporal model which “borrows strength” across time, rather than a spatial model for individual sampling events. To capture the variability encountered under field conditions, we used three hypothetical groundwater contamination plumes with increasing complexity, and site data for a large groundwater gasoline additive plume. The results show that spatiotemporal methods can increase efficiency markedly so that, in comparison with repeated spatial analysis, spatiotemporal methods can achieve the same level of performance but with smaller sample sizes

Logistic regression for simulating damage occurrence on a fruit grading line

Many factors influence the incidence of mechanical damage in fruit handled on a grading line. This makes it difficult to address damage estimation from an analytical point of view. During fruit transfer from one element of a grading line to another, damage occurs as a combined effect of machinery roughness and the intrinsic susceptibility of fruit. This paper describes a method to estimate bruise probability by means of logistic regression, using data yielded by specific laboratory tests. Model accuracy was measured via the statistical significance of its parameters and its classification ability. The prediction model was then linked to a simulation model through which impacts and load levels, similar to those of real grading lines, could be generated. The simulation output sample size was determined to yield reliable estimations. The process makes it possible to derive a suitable line design and the type of fruit that should be handled to maintain bruise levels within European Union (EU) Standards. A real example with peaches was carried out with the aid of the software implementation SIMLIN®, developed by the authors and registered by Madrid Technical University. This kind of tool has been demanded by inter-professional associations and grading lines designers in recent year

Adatoms and nanoengineering of carbon

We present a new and general mechanism for inter-conversion of carbon structures via a catalytic exchange process, which operates under conditions of Frenkel pair generation. The mechanism typically lowers reaction barriers by a factor of four compared to equivilent uncatalysed reactions. We examine the relevance of this mechanism for fullerene growth, carbon onions and nanotubes, and dislocations in irradiated graphite.Comment: 3 Figures, 5 Page letter accepted for publication in Chemical Physics Letter

Merthyr Mawr: a case study for the assessment of nitrate at humid dunes in England and Wales

Humid dunes in the UK are at risk from nutrient pressures from multiple sources. The Water Framework Directive 2000/60/EC (WFD) requires assessment and identification of these pressures with appropriate measures defined to mitigate against further damage. We discuss the application of nitrate threshold values for the WFD classification, illustrating this with a case study at Merthyr Mawr, South Wales, where ephemeral groundwater discharge from a spring (‘Burrows Well’) sourced within the Carboniferous Limestone, creates a large dune slack. Ecological surveys suggest that the vegetation in this slack was in unfavourable condition, due to high levels of nitrate. Applying the source-pathway-receptor model an investigation was undertaken to improve the conceptual model and assess the significance of damage from groundwater derived nutrients. Results show groundwater nitrate concentrations ~ 10 mg/l as NO3-N feeding the main slack waters. The vegetation survey data shows clear evidence of ecological damage, and the hydrogeological data traces the source of this back to the Carboniferous Limestone aquifer and not the overlying blown sands. Discharging groundwater is the source of the enrichment. Isotopic analysis suggests that the N is derived from inorganic fertilizer and/or atmospheric N. During the first cycle WFD characterisation the unfavourable status of the dunes due to chemical groundwater pressure resulted in a failure of the surrounding groundwater body, which was designated as poor status. The site has been re assessed for the 2nd Cycle WFD characterisation where recently developed nitrate ‘threshold’ values have been applied to assess the significance of damage for groundwater derived nutrients. The surrounding Carboniferous Limestone catchment is complex and could not be sufficiently constrained, thus land management changes could not be targeted. The paucity of historical or repeat vegetation surveys limits our ability to measure change within the dune vegetation and causes difficulties in understanding the impact of multiple pressures

Supporting self-management after traumatic brain injury : codesign and evaluation of a new intervention across a trauma pathway

Background Supported self‐management (SSM) is a recognized approach for people with long‐term conditions but, despite the prevalence of unmet needs, little is known about its role for people with traumatic brain injury (TBI). Objectives To codesign an SSM intervention with people with TBI and evaluate feasibility of implementation through multidisciplinary staff across a trauma pathway. Setting and participants People who had previously been admitted to a Major Trauma Centre following TBI and family members participated in a series of codesign activities. Staff attended SSM workshops and used the intervention with patients in acute and rehabilitation settings. Methods We used Normalization Process Theory constructs to guide and interpret implementation. Knowledge, beliefs and confidence of staff in SSM were assessed through pre‐ and post‐training questionnaires, and staff, patients' and families' experiences were explored through semi‐structured interviews. Qualitative data were analysed thematically, and clinical measures were mapped against a matched sample. Results Codesigned resources were created and used within an SSM approach for which 110 staff participated in training. Evaluation demonstrated significant differences in staff SSM confidence and skills, following training. Qualitative evaluation revealed adoption by staff, and patients' and families' experiences of using the resources. Challenges included reaching staff across complex pathways to achieve collective implementation. Conclusion This is the first project to demonstrate feasibility of SSM for people after TBI starting in an acute trauma setting. Through an open approach to codesign with a marginalized group, the SSM resources were valued by them and held meaning and relevance for staff

Charged particle production in the Pb+Pb system at 158 GeV/c per nucleon

Charged particle multiplicities from high multiplicity central interactions of 158 GeV/nucleon Pb ions with Pb target nuclei have been measured in the central and far forward projectile spectator regions using emulsion chambers. Multiplicities are significantly lower than predicted by Monte Carlo simulations. We examine the shape of the pseudorapidity distribution and its dependence on centrality in detail.Comment: 17 pages text plus 12 figures in postscript 12/23/99 -- Add TeX version of sourc

The 6dF galaxy survey: cosmological constraints from the velocity power spectrum

We present scale-dependent measurements of the normalized growth rate of structure fσ8(k, z = 0) using only the peculiar motions of galaxies. We use data from the 6-degree Field Galaxy Survey velocity sample together with a newly compiled sample of low-redshift (z 300 h−1 Mpc, which represents one of the largest scale growth rate measurement to date. We find no evidence for a scale-dependence in the growth rate, or any statistically significant variation from the growth rate as predicted by the Planck cosmology. Bringing all the scales together, we determine the normalized growth rate at z = 0 to ∼15 per cent in a manner independent of galaxy bias and in excellent agreement with the constraint from the measurements of redshift-space distortions from 6-degree Field Galaxy Survey. We pay particular attention to systematic errors. We point out that the intrinsic scatter present in Fundamental Plane and Tully–Fisher relations is only Gaussian in logarithmic distance units; wrongly assuming it is Gaussian in linear (velocity) units can bias cosmological constraints. We also analytically marginalize over zero-point errors in distance indicators, validate the accuracy of all our constraints using numerical simulations, and demonstrate how to combine different (correlated) velocity surveys using a matrix ‘hyperparameter’ analysis. Current and forthcoming peculiar velocity surveys will allow us to understand in detail the growth of structure in the low-redshift universe, providing strong constraints on the nature of dark energy

The geometry of spontaneous spiking in neuronal networks

The mathematical theory of pattern formation in electrically coupled networks of excitable neurons forced by small noise is presented in this work. Using the Freidlin-Wentzell large deviation theory for randomly perturbed dynamical systems and the elements of the algebraic graph theory, we identify and analyze the main regimes in the network dynamics in terms of the key control parameters: excitability, coupling strength, and network topology. The analysis reveals the geometry of spontaneous dynamics in electrically coupled network. Specifically, we show that the location of the minima of a certain continuous function on the surface of the unit n-cube encodes the most likely activity patterns generated by the network. By studying how the minima of this function evolve under the variation of the coupling strength, we describe the principal transformations in the network dynamics. The minimization problem is also used for the quantitative description of the main dynamical regimes and transitions between them. In particular, for the weak and strong coupling regimes, we present asymptotic formulas for the network activity rate as a function of the coupling strength and the degree of the network. The variational analysis is complemented by the stability analysis of the synchronous state in the strong coupling regime. The stability estimates reveal the contribution of the network connectivity and the properties of the cycle subspace associated with the graph of the network to its synchronization properties. This work is motivated by the experimental and modeling studies of the ensemble of neurons in the Locus Coeruleus, a nucleus in the brainstem involved in the regulation of cognitive performance and behavior

Frozen spatial chaos induced by boundaries

We show that rather simple but non-trivial boundary conditions could induce the appearance of spatial chaos (that is stationary, stable, but spatially disordered configurations) in extended dynamical systems with very simple dynamics. We exemplify the phenomenon with a nonlinear reaction-diffusion equation in a two-dimensional undulated domain. Concepts from the theory of dynamical systems, and a transverse-single-mode approximation are used to describe the spatially chaotic structures.Comment: 9 pages, 6 figures, submitted for publication; for related work visit http://www.imedea.uib.es/~victo