HepForge: A lightweight development environment for HEP software

Setting up the infrastructure to manage a software project can become a task as significant writing the software itself. A variety of useful open source tools are available, such as Web-based viewers for version control systems, "wikis" for collaborative discussions and bug-tracking systems, but their use in high-energy physics, outside large collaborations, is insubstantial. Understandably, physicists would rather do physics than configure project management tools. We introduce the CEDAR HepForge system, which provides a lightweight development environment for HEP software. Services available as part of HepForge include the above-mentioned tools as well as mailing lists, shell accounts, archiving of releases and low-maintenance Web space. HepForge also exists to promote best-practice software development methods and to provide a central repository for re-usable HEP software and phenomenology codes.Comment: 3 pages, 0 figures. To be published in proceedings of CHEP06. Refers to the HepForge facility at http://hepforge.cedar.ac.u

HepData and JetWeb: HEP data archiving and model validation

The CEDAR collaboration is extending and combining the JetWeb and HepData systems to provide a single service for tuning and validating models of high-energy physics processes. The centrepiece of this activity is the fitting by JetWeb of observables computed from Monte Carlo event generator events against their experimentally determined distributions, as stored in HepData. Caching the results of the JetWeb simulation and comparison stages provides a single cumulative database of event generator tunings, fitted against a wide range of experimental quantities. An important feature of this integration is a family of XML data formats, called HepML.Comment: 4 pages, 0 figures. To be published in proceedings of CHEP0

Paraoxonase gene polymorphisms and haplotype analysis in a stroke population

Peer reviewedPublisher PD

Formation and Evolution of Single Molecule Junctions

We analyze the formation and evolution statistics of single molecule junctions bonded to gold electrodes using amine, methyl sulfide and dimethyl phosphine link groups by measuring conductance as a function of junction elongation. For each link, maximum elongation and formation probability increase with molecular length, strongly suggesting that processes other than just metal-molecule bond breakage play a key role in junction evolution under stress. Density functional theory calculations of adiabatic trajectories show sequences of atomic-scale changes in junction structure, including shifts in attachment point, that account for the long conductance plateau lengths observed.Comment: 10 pages, 4 figures, submitte

A More Accurate Generalized Gradient Approximation for Solids

We present a new nonempirical density functional generalized gradient approximation (GGA) that gives significant improvements for lattice constants, crystal structures, and metal surface energies over the most popular Perdew-Burke-Ernzerhof (PBE) GGA. The new functional is based on a diffuse radial cutoff for the exchange-hole in real space, and the analytic gradient expansion of the exchange energy for small gradients. There are no adjustable parameters, the constraining conditions of PBE are maintained, and the functional is easily implemented in existing codes.Comment: 5 pages, corrected the errors of the sublimation energy of Ih ic

Cannabinol and cannabidiol exert opposing effects on rat feeding patterns

Rationale: Increased food consumption following Δ9- tetrahydrocannabinol-induced cannabinoid type 1 receptor agonism is well documented. However, possible non-Δ9- tetrahydrocannabinol phytocannabinoid-induced feeding effects have yet to be fully investigated. Therefore, we have assessed the effects of the individual phytocannabinoids, cannabigerol, cannabidiol and cannabinol, upon feeding behaviors. Methods: Adult male rats were treated (p.o.) with cannabigerol, cannabidiol, cannabinol or cannabinol plus the CB1R antagonist, SR141716A. Prior to treatment, rats were satiated and food intake recorded following drug administration. Data were analyzed for hourly intake and meal microstructure. Results: Cannabinol induced a CB1R-mediated increase in appetitive behaviors via significant reductions in the latency to feed and increases in consummatory behaviors via increases in meal 1 size and duration. Cannabinol also significantly increased the intake during hour 1 and total chow consumed during the test. Conversely, cannabidiol significantly reduced total chow consumption over the test period. Cannabigerol administration induced no changes to feeding behavior. Conclusion: This is the first time cannabinol has been shown to increase feeding. Therefore, cannabinol could, in the future, provide an alternative to the currently used and psychotropic Δ9-tetrahydrocannabinol-based medicines since cannabinol is currently considered to be non-psychotropic. Furthermore, cannabidiol reduced food intake in line with some existing reports, supporting the need for further mechanistic and behavioral work examining possible anti-obesity effects of cannabidiol

The Effect of Forest Management Options on Forest Resilience to Pathogens

Invasive pathogens threaten the ability of forests globally to produce a range of valuable ecosystem services over time. However, the ability to detect such pathogen invasions—and thus to produce appropriate and timely management responses—is relatively low. We argue that a promising approach is to plan and manage forests in a way that increases their resilience to invasive pathogens not yet present or ubiquitous in the forest. This paper is based on a systematic search and critical review of empirical evidence of the effect of a wide range of forest management options on the primary and secondary infection rates of forest pathogens, and on subsequent forest recovery. Our goals are to inform forest management decision making to increase forest resilience, and to identify the most important evidence gaps for future research. The management options for which there is the strongest evidence that they increase forest resilience to pathogens are: reduced forest connectivity, removal or treatment of inoculum sources such as cut stumps, reduced tree density, removal of diseased trees and increased tree species diversity. In all cases the effect of these options on infection dynamics differs greatly amongst tree and pathogen species and between forest environments. However, the lack of consistent effects of silvicultural systems or of thinning, pruning or coppicing treatments is notable. There is also a lack of evidence of how the effects of treatments are influenced by the scale at which they are applied, e.g., the mixture of tree species. An overall conclusion is that forest managers often need to trade-off increased resilience to tree pathogens against other benefits obtained from forests

Optimisation and analysis of streamwise-varying wall-normal blowing in a turbulent boundary layer

Skin-friction drag is a major engineering concern, with wide-ranging consequences across many industries. Active flow-control techniques targeted at minimising skin friction have the potential to significantly enhance aerodynamic efficiency, reduce operating costs, and assist in meeting emission targets. However, they are difficult to design and optimise. Furthermore, any performance benefits must be balanced against the input power required to drive the control. Bayesian optimisation is a technique that is ideally suited to problems with a moderate number of input dimensions and where the objective function is expensive to evaluate, such as with high-fidelity computational fluid dynamics simulations. In light of this, this work investigates the potential of low-intensity wall-normal blowing as a skin-friction drag reduction strategy for turbulent boundary layers by combining a high-order flow solver (Incompact3d) with a Bayesian optimisation framework. The optimisation campaign focuses on streamwise-varying wall-normal blowing, parameterised by a cubic spline. The inputs to be optimised are the amplitudes of the spline control points, whereas the objective function is the net-energy saving (NES), which accounts for both the skin-friction drag reduction and the input power required to drive the control (with the input power estimated from real-world data). The results of the optimisation campaign are mixed, with significant drag reduction reported but no improvement over the canonical case in terms of NES. Selected cases are chosen for further analysis and the drag reduction mechanisms and flow physics are highlighted. The results demonstrate that low-intensity wall-normal blowing is an effective strategy for skin-friction drag reduction and that Bayesian optimisation is an effective tool for optimising such strategies. Furthermore, the results show that even a minor improvement in the blowing efficiency of the device used in the present work will lead to meaningful NES

Preventing weed spread: a survey of lifestyle and commercial landholders about Nassella trichotoma in the Northern Tablelands of New South Wales, Australia

Nassella trichotoma (Nees) Hack. ex Arechav. (common name, serrated tussock) occupies large areas of south-eastern Australia and has considerable scope for expansion in the Northern Tablelands of New South Wales. This highly invasive grass reduces pasture productivity and has the potential to severely affect the region’s economy by decreasing the livestock carrying capacity of grazing land. Other potential consequences of this invasion include increased fuel loads and displacement of native plants, thereby threatening biodiversity. Rural property owners in the Northern Tablelands were sent a mail questionnaire that examined use of measures to prevent new outbreaks of the weed. The questionnaire was sent to professional farmers as well as lifestyle farmers (owners of rural residential blocks and hobby farms) and 271 responses were obtained (a response rate of 18%). Key findings were respondents’ limited capacity to detect N. trichotoma, and low adoption of precautions to control seed spread by livestock, vehicles and machinery. This was particularly the case among lifestyle farmers. There have been considerable recent changes to biosecurity governance arrangements in New South Wales, and now is an ideal time for regulators and information providers to consider how to foster regional communities’ engagement in biosecurity, including the adoption of measures that have the capacity to curtail the spread of N. trichotoma