DockoMatic - Automated Ligand Creation and Docking

Background: The application of computational modeling to rationally design drugs and characterize macro biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results. This paper presents DockoMatic, a user friendly Graphical User Interface (GUI) application that eases and automates the creation and management of AutoDock jobs for high throughput screening of ligand to receptor interactions. Results: DockoMatic allows the user to invoke and manage AutoDock jobs on a single computer or cluster, including jobs for evaluating secondary ligand interactions. It also automates the process of collecting, summarizing, and viewing results. In addition, DockoMatic automates creation of peptide ligand .pdb files from strings of single-letter amino acid abbreviations. Conclusions: DockoMatic significantly reduces the complexity of managing multiple AutoDock jobs by facilitating ligand and AutoDock job creation and management

Regional Development: An Econometric Study of the Role of Water Development in Effectuating Population and Income Changes

Twelve measures of regional economic growth, including populations and three measures of income were compared for areas with and without water investment in 246 counties and 42 water resources subareas in the states of Utah, Colorado, New Mexico, Montana, Wyoming, Idaho, and Nevada. Simple mean omparisons for these measures compiled for the decades of 1940-1950, 1950-1960, and 1960-1970 failed to support the hypothesis that economic growth of those counties and subareas receiving water investment was significantly highter than in those areas which did not, with the possible exception of the 1940-1950 decade. This result is obciously tempered by the fact that with-without comparisons taken on a cross-sectional basis may be inaccurage to the extent that spatial units used in the analysis are not homogenous in all respects but the presence or absence of water investment. Population, farm income, median family income, and per acre agricultural land values as measures of economic growth were regressed on various classes of water investment (Total, M&1, Recreation, and Irrigation investment, and other related variables) for the spatial units. Results obtained from this analysis were inconclusive with respect to the hypothesized role of water investment in effectuating economic growth. For small areas in New Mexico where more detailed records of water investment were available, a nine equation econometric model was estimated using a three-stage least squares analysis. As specified, this model facilitated an examination of the interactive effect of water development as a causal variable and as an endogenous variable which responds to other growth inducements. Test statistics for multi-equation systems are only indicative, and the statistical results were nonconclusive, although expected signs on the coefficients were obtained in most instances. Input-output and economic base-models were used to examine two case studies of water investment in Western Coloado. The objective was to demonstrate the methodology and the magnitudes of change in regional economic activity (gross regional output, exports, income, and employment) which could be associated with major irrigation-type water developments. In this analysis it was found that total gross output attributable to the projects ranged from zero in the petroleum and mining sectors to a high of 260,302 in the dairy industry. Multiplicative effects on employment income and gross economic activity ranged from 1.06 to 2.30 times their initial magnitude. Income and employment multipliers were of similar magnitude. it should be recognized that these estimates cannot e viewed in the same manner as similar growth increments at the national level, as would typically be done, because of the strong possibility of regional offsets occurring in other regions not participating in water development. To the extent that growth in other areas is reduced by the growth of a particular region, these reductions should be subtracted from the growth measured in the latter set of regions. In all tests conducted no conclusive evidence was found taht water development causes regions to grow faster than those regions which did not receive water investment. This is not to say that growth in those regions receiving water investment was not higher than it would have been had the investment not been made. However, it does provide evidence that, an average among the regions included within this analysis, that those areas which did not receive major water investments grow at a faster rate than those which did. Thus, the input-output approach shows potential inpacts from water investment in a general equilibrium context, but rest son the assumption that other concurrent events which could produce similar or offsetting effects in the region are held constant. The cross-section analysis measures total changes in a regional economy overtime, but the multiplicity of events, other than water investment, may obscure the effects of water investment

Is thirty-seven years sufficient for full return of the ant biota following restoration?

Introduction: An assessment of whether rehabilitated mine sites have resulted in natural or novel ecosystems requires monitoring over considerable periods of time or the use of space-for-time substitution (chronosequence) approaches. Methods: To provide an assessment of ecosystem recovery in areas mined for bauxite in 1975, the ant fauna of one area planted with Eucalyptus resinifera, one seeded with mixed native species, one topsoiled but unrestored, and a forest reference was subjected to a ‘long-term’ study by sampling monthly and latterly annually between 1976 and 1989 using pitfall traps. These plots were resampled in 2012. A companion ‘short-term’ chronosequence study was performed in 1979 in 28 bauxite mines of various ages and restored by a range of different methods, plus three forest references. In order to examine the assertion that the observed differences between restored areas and forest references will lessen with time, sampling using comparable methods was repeated in 2012 in seven of the original plots, representing progressive advances in rehabilitation technology: planted pines; planted eastern states eucalypts; planted native eucalypts; planted eucalypts over seeded understorey; and planted eucalypts on fresh, double-stripped topsoil, plus two forest reference sites. Results: Ant and other invertebrate richness in the long-term study was initially superior in the seeded plot, with little difference between the planted and unplanted plots. It was concluded that although composition of the ant fauna had converged on that of the forest over the 14-year period, differences still persisted.The 2012 resampling revealed that ant species richness and composition had deteriorated in the seeded plot, while values in the unplanted plot, which now supported naturally colonised trees and an understorey, had increased. Differences between all rehabilitated plots and forest still persisted. As with the long-term study, the rate of fauna return and the type of ants present in the short-term study plots differed with the method of rehabilitation used, and, in 1979, no plots had converged on the forest in terms of the ant assemblage. By 2012 ant richness increased, and more so with each advance in rehabilitation technology, except for seeding, in which the understorey had collapsed. Double-stripping of topsoil resulted in the greatest improvements in ant species richness, although none of the areas had converged on the forest reference areas in terms of assemblage composition or ant functional group profiles. Furthermore, assemblage composition in the forest had changed over time, possibly due to reductions in rainfall, which further complicates rehabilitation objectives. Conclusions: It is concluded that although rehabilitation can achieve its objective of restoring diversity, the original assemblage has still not been achieved after 37 years, suggesting that a degree of novelty has been introduced into these older-style rehabilitated areas. The company’s current rehabilitation practices reflect multiple advances in their approach, lending optimism that current restoration may achieve something close to the original ecosystem, an outcome that can only be verified by extended studies like the one described here

First-Principles Based Matrix-Green's Function Approach to Molecular Electronic Devices: General Formalism

Transport in molecular electronic devices is different from that in semiconductor mesoscopic devices in two important aspects: (1) the effect of the electronic structure and (2) the effect of the interface to the external contact. A rigorous treatment of molecular electronic devices will require the inclusion of these effects in the context of an open system exchanging particle and energy with the external environment. This calls for combining the theory of quantum transport with the theory of electronic structure starting from the first-principles. We present a rigorous yet tractable matrix Green's function approach for studying transport in molecular electronic devices, based on the Non-Equilibrium Green's Function Formalism of quantum transport and the density-functional theory of electronic structure using local orbital basis sets. By separating the device rigorously into the molecular region and the contact region, we can take full advantage of the natural spatial locality associated with the metallic screening in the electrodes and focus on the physical processes in the finite molecular region. This not only opens up the possibility of using the existing well-established technique of molecular electronic structure theory in transport calculations with little change, but also allows us to use the language of qualitative molecular orbital theory to interpret and rationalize the results of the computation. For the device at equilibrium, our method provides an alternative approach for solving the molecular chemisorption problem. For the device out of equilibrium, we show that the calculation of elastic current transport through molecules, both conceptually and computationally, is no more difficult than solving the chemisorption problem.Comment: To appear in Chemical Physic

Influence of hand position on the near-effect in 3D attention

Voluntary reorienting of attention in real depth situations is characterized by an attentional bias to locations near the viewer once attention is deployed to a spatially cued object in depth. Previously this effect (initially referred to as the ‘near-effect’) was attributed to access of a 3D viewer-centred spatial representation for guiding attention in 3D space. The aim of this study was to investigate whether the near-bias could have been associated with the position of the response-hand, always near the viewer in previous studies investigating endogenous attentional shifts in real depth. In Experiment 1, the response-hand was placed at either the near or far target depth in a depth cueing task. Placing the response-hand at the far target depth abolished the near-effect, but failed to bias spatial attention to the far location. Experiment 2 showed that the response-hand effect was not modulated by the presence of an additional passive hand, whereas Experiment 3 confirmed that attentional prioritization of the passive hand was not masked by the influence of the responding hand on spatial attention in Experiment 2. The pattern of results is most consistent with the idea that response preparation can modulate spatial attention within a 3D viewer-centred spatial representation

Gamma-ray emission from Cassiopeia A produced by accelerated cosmic rays

The nonlinear kinetic model of cosmic ray (CR) acceleration in supernova remnants (SNRs) is used to describe the relevant properties of Cassiopeia A (Cas A). In order to reproduce the SNR's observed size, expansion rate and thermal X-ray emission we employ a piecewise homogeneous model for the progenitor's circumstellar medium developed by Borkowski et al. (1996). It consists of a tenuous inner wind bubble, a dense shell of swept-up red supergiant wind material, and a subsequent red supergiant wind region. A quite large SNR interior magnetic field B_d approx 1 mG is required to give a good fit for the radio and X-ray synchrotron emission. The steep radio spectrum is consistent with efficient proton acceleration which produces a significant shock modification and leads to a steep electron spectrum at energies E_e < 1 GeV. The calculated integral gamma-ray flux from Cas A, F propto E_gamma^-1, is dominated by pi^0-decay gamma-rays due to relativistic protons. It extends up to roughly 30 TeV if CR diffusion is as strong as the Bohm limit. At TeV energies it satisfactorily agrees with the value 5.8 x 10^-13 cm^-2 s^-1 detected by the HEGRA collaboration.Comment: 11 pages, 5 figures. Accepted in Astronomy and Astrophyics. Version 2 contains one typo correction (sect.3.6 par.2

Protocol for Work place adjusted Intelligent physical exercise reducing Musculoskeletal pain in Shoulder and neck (VIMS): a cluster randomized controlled trial

<p>Abstract</p> <p>Background</p> <p>Neck and shoulder complaints are common among employees in sedentary occupations characterized by intensive computer use. Specific strength training is a promising type of physical exercise for relieving neck and shoulder pain in office workers. However, the optimal combination of frequency and exercise duration, as well as the importance of exercise supervision, is unknown. The VIMS study investigates in a cluster randomized controlled design the effectiveness of different time wise combinations of specific strength training with identical accumulated volume, and the relevance of training supervision for safe and effective training.</p> <p>Methods/design</p> <p>A cluster randomized controlled trial of 20 weeks duration where employed office workers are randomized to 1 × 60 min, 3 × 20 min, 9 × 7 min per week of specific strength training with training supervision, to 3 × 20 min per week of specific strength training with a minimal amount of training supervision, or to a reference group without training. A questionnaire will be sent to 2000 employees in jobs characterized by intensive computer work. Employees with cardiovascular disease, trauma, hypertension, or serious chronic disease will be excluded. The main outcome measure is pain in the neck and shoulders at week 20.</p> <p>Trial Registration</p> <p>The trial is registered at ClinicalTrials.gov, number NCT01027390.</p

Birth weight and stuttering:Evidence from three birth cohorts

Purpose Previous studies have produced conflicting results with regard to the association between birth weight and developmental stuttering. This study sought to determine whether birth weight was associated with childhood and/or adolescent stuttering in three British birth cohort samples. Methods Logistic regression analyses were carried out on data from the Millenium Cohort Study (MCS), British Cohort Study (BCS70) and National Child Development Study (NCDS), whose initial cohorts comprised over 56,000 individuals. The outcome variables were parent-reported stuttering in childhood or in adolescence; the predictors, based on prior research, were birth weight, sex, multiple birth status, vocabulary score and mother's level of education. Birth weight was analysed both as a categorical variable (low birth weight, <2500 g; normal range; high birth weight, ≥ 4000 g) and as a continuous variable. Separate analyses were carried out to determine the impact of birth weight and the other predictors on stuttering during childhood (age 3, 5 and 7 and MCS, BCS70 and NCDS, respectively) or at age 16, when developmental stuttering is likely to be persistent. Results None of the multivariate analyses revealed an association between birth weight and parent-reported stuttering. Sex was a significant predictor of stuttering in all the analyses, with males 1.6 to 3.6 times more likely than females to stutter. Conclusion Our results suggest that birth weight is not a clinically useful predictor of childhood or persistent stuttering