Delivering alcohol IBA: broadening the base from health to non-health contexts: review of the literature and scoping

A review of the literature and scoping on alcohol brief interventions. The review considers the evidence base on the delivery of identification and brief advice in a wide range of settings. It concludes that broader delivery of IBA is feasible, but requires strong organisational support, effective training and financial investment

Constraints, Histones, and the 30 Nanometer Spiral

We investigate the mechanical stability of a segment of DNA wrapped around a histone in the nucleosome configuration. The assumption underlying this investigation is that the proper model for this packaging arrangement is that of an elastic rod that is free to twist and that writhes subject to mechanical constraints. We find that the number of constraints required to stabilize the nuclesome configuration is determined by the length of the segment, the number of times the DNA wraps around the histone spool, and the specific constraints utilized. While it can be shown that four constraints suffice, in principle, to insure stability of the nucleosome, a proper choice must be made to guarantee the effectiveness of this minimal number. The optimal choice of constraints appears to bear a relation to the existence of a spiral ridge on the surface of the histone octamer. The particular configuration that we investigate is related to the 30 nanometer spiral, a higher-order organization of DNA in chromatin.Comment: ReVTeX, 15 pages, 18 figure

Sequence Effects on DNA Entropic Elasticity

DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by this method is a combination of bend stiffness and intrinsic bend effects reflecting sequence information, just as at zero stretching force. This observation resolves the discrepancy between the value of A measured in these experiments and the larger ``dynamic persistence length'' measured by other means. On the other hand, the twist persistence length deduced from torsionally-constrained stretching experiments suffers no such correction. Our calculation is very simple and analytic; it applies to DNA and other polymers with weak intrinsic disorder.Comment: LaTeX; postscript available at http://dept.physics.upenn.edu/~nelson/index.shtm

VPLanet: The Virtual Planet Simulator

We describe a software package called VPLanet that simulates fundamental aspects of planetary system evolution over Gyr timescales, with a focus on investigating habitable worlds. In this initial release, eleven physics modules are included that model internal, atmospheric, rotational, orbital, stellar, and galactic processes. Many of these modules can be coupled simultaneously to simulate the evolution of terrestrial planets, gaseous planets, and stars. The code is validated by reproducing a selection of observations and past results. VPLanet is written in C and designed so that the user can choose the physics modules to apply to an individual object at runtime without recompiling, i.e., a single executable can simulate the diverse phenomena that are relevant to a wide range of planetary and stellar systems. This feature is enabled by matrices and vectors of function pointers that are dynamically allocated and populated based on user input. The speed and modularity of VPLanet enables large parameter sweeps and the versatility to add/remove physical phenomena to assess their importance. VPLanet is publicly available from a repository that contains extensive documentation, numerous examples, Python scripts for plotting and data management, and infrastructure for community input and future development.Comment: 75 pages, 34 figures, 10 tables, accepted to the Proceedings of the Astronomical Society of the Pacific. Source code, documentation, and examples available at https://github.com/VirtualPlanetaryLaboratory/vplane

Statistical Algorithms for Ontology-based Annotation of Scientific Literature

Background: Ontologies encode relationships within a domain in robust data structures that can be used to annotate data objects, including scientific papers, in ways that ease tasks such as search and meta-analysis. However, the annotation process requires significant time and effort when performed by humans. Text mining algorithms can facilitate this process, but they render an analysis mainly based upon keyword, synonym and semantic matching. They do not leverage information embedded in an ontology’s structure. Methods: We present a probabilistic framework that facilitates the automatic annotation of literature by indirectly modeling the restrictions among the different classes in the ontology. Our research focuses on annotating human functional neuroimaging literature within the Cognitive Paradigm Ontology (CogPO). We use an approach that combines the stochastic simplicity of naïve Bayes with the formal transparency of decision trees. Our data structure is easily modifiable to reflect changing domain knowledge. Results: We compare our results across naïve Bayes, Bayesian Decision Trees, and Constrained Decision Tree classifiers that keep a human expert in the loop, in terms of the quality measure of the F1-mirco score. Conclusions: Unlike traditional text mining algorithms, our framework can model the knowledge encoded by the dependencies in an ontology, albeit indirectly. We successfully exploit the fact that CogPO has explicitly stated restrictions, and implicit dependencies in the form of patterns in the expert curated annotations

Refraction in exoplanet atmospheres: Photometric signatures, implications for transmission spectroscopy, and search in Kepler data

Refraction deflects photons that pass through atmospheres, which affects transit light curves. Refraction thus provides an avenue to probe physical properties of exoplanet atmospheres and to constrain the presence of clouds and hazes. In addition, an effective surface can be imposed by refraction, thereby limiting the pressure levels probed by transmission spectroscopy. The main objective of the paper is to model the effects of refraction on photometric light curves for realistic planets and to explore the dependencies on atmospheric physical parameters. We also explore under which circumstances transmission spectra are significantly affected by refraction. Finally, we search for refraction signatures in photometric residuals in Kepler data. We use the model of Hui & Seager (2002) to compute deflection angles and refraction transit light curves, allowing us to explore the parameter space of atmospheric properties. The observational search is performed by stacking large samples of transit light curves from Kepler. We find that out-of-transit refraction shoulders are the most easily observable features, which can reach peak amplitudes of ~10 parts per million (ppm) for planets around Sun-like stars. More typical amplitudes are a few ppm or less for Jovians and at the sub-ppm level for super-Earths. Interestingly, the signal-to-noise ratio of any refraction residuals for planets orbiting Sun-like hosts are expected to be similar for planets orbiting red dwarfs. We also find that the maximum depth probed by transmission spectroscopy is not limited by refraction for weakly lensing planets, but that the incidence of refraction can vary significantly for strongly lensing planets. We find no signs of refraction features in the stacked Kepler light curves, which is in agreement with our model predictions.Comment: Accepted for publication in A&