VINYL: The VIrtual Neutron and x-raY Laboratory and its applications

Experiments conducted in large scientific research infrastructures, such as synchrotrons, free electron lasers and neutron sources become increasingly complex. Such experiments, often investigating complex physical systems, are usually performed under strict time limitations and may depend critically on experimental parameters. To prepare and analyze these complex experiments, a virtual laboratory which provides start-to-end simulation tools can help experimenters predict experimental results under real or close to real instrument conditions. As a part of the PaNOSC (Photon and Neutron Open Science Cloud) project, the VIrtual Neutron and x-raY Laboratory (VINYL) is designed to be a cloud service framework to implement start-to-end simulations for those scientific facilities. In this paper, we present an introduction of the virtual laboratory framework and discuss its applications to the design and optimization of experiment setups as well as the estimation of experimental artifacts in an X-ray experiment

Expected resolution limits of x-ray free-electron laser single-particle imaging for realistic source and detector properties

The unprecedented intensity of x-ray free-electron laser sources has enabled single-particle x-ray diffraction imaging (SPI) of various biological specimens in both two-dimensional projection and three dimensions (3D). The potential of studying protein dynamics in their native conditions, without crystallization or chemical staining, has encouraged researchers to aim for increasingly higher resolutions with this technique. The currently achievable resolution of SPI is limited to the sub-10 nanometer range, mainly due to background effects, such as instrumental noise and parasitic scattering from the carrier gas used for sample delivery. Recent theoretical studies have quantified the effects of x-ray pulse parameters, as well as the required number of diffraction patterns to achieve a certain resolution, in a 3D reconstruction, although the effects of detector noise and the random particle orientation in each diffraction snapshot were not taken into account. In this work, we show these shortcomings and address limitations on achievable image resolution imposed by the adaptive gain integrating pixel detector noise

An advanced Bayesian model for the visual tracking of multiple interacting objects

Visual tracking of multiple objects is a key component of many visual-based systems. While there are reliable algorithms for tracking a single object in constrained scenarios, the object tracking is still a challenge in uncontrolled situations involving multiple interacting objects that have a complex dynamics. In this article, a novel Bayesian model for tracking multiple interacting objects in unrestricted situations is proposed. This is accomplished by means of an advanced object dynamic model that predicts possible interactive behaviors, which in turn depend on the inference of potential events of object occlusion. The proposed tracking model can also handle false and missing detections that are typical from visual object detectors operating in uncontrolled scenarios. On the other hand, a Rao-Blackwellization technique has been used to improve the accuracy of the estimated object trajectories, which is a fundamental aspect in the tracking of multiple objects due to its high dimensionality. Excellent results have been obtained using a publicly available database, proving the efficiency of the proposed approach

Thomson Scattering at FLASH - Status Report

The basic idea is to implement Thomson scattering with free electron laser (FEL) radiation at near-solid density plasmas as a diagnostic method which allows the determination of plasma temperatures and densities in the warm dense matter (WDM) regime (free electron density of n{sub e} = 10{sup 21}-10{sup 26} cm{sup -3} with temperatures of several eV). The WDM regime [1] at near-solid density (n{sub e} = 10{sup 21}-10{sup 22} cm{sup -3}) is of special interest because, it is where the transition from an ideal plasma to a degenerate, strongly coupled plasma occurs. A systematic understanding of this largely unknown WDM domain is crucial for the modeling and understanding of contemporary plasma experiments, like laser shock-wave or Z-pinch experiments as well as for inertial confinement fusion (ICF) experiments as the plasma evolution follows its path through this domain

Dynamic metabolomic data analysis: a tutorial review

In metabolomics, time-resolved, dynamic or temporal data is more and more collected. The number of methods to analyze such data, however, is very limited and in most cases the dynamic nature of the data is not even taken into account. This paper reviews current methods in use for analyzing dynamic metabolomic data. Moreover, some methods from other fields of science that may be of use to analyze such dynamic metabolomics data are described in some detail. The methods are put in a general framework after providing a formal definition on what constitutes a ‘dynamic’ method. Some of the methods are illustrated with real-life metabolomics examples

Titling community land to prevent deforestation: An evaluation of a best-case program in Morona-Santiago, Ecuador

Assigning land title to collective landholders is one of the primary policies land management agencies use to avoid deforestation worldwide. Such programs are designed to improve the ability of landholders to legally exclude competing users and thereby strengthen incentives to manage forests for long-term benefits. Despite the prevalence of this hypothesis, findings about the impacts of land titling programs on deforestation are mixed. Evidence is often unreliable because programs are targeted according to factors that independently influence the conversion of forests. We evaluate a donor-funded land titling and land management program for indigenous communities implemented in Morona-Santiago, Ecuador. This program offers a close to best case scenario for a land titling program to reduce deforestation because of colonization pressure, availability of payments when titled communities maintain forests, and limited opportunities for commercial agriculture. We match plots in program areas with similar plots outside program areas on covariates that influence the conversion of forests. Based on matched comparisons, we do not find evidence that land titling or community management plans reduced forest loss in the five years following legal recognition. The results call into question land titling as a direct deforestation strategy and suggests land titling is better viewed a precursor to other programs. (C) 2015 The Authors. Published by Elsevier Ltd

RANTES/CCL5 and risk for coronary events: Results from the MONICA/KORA Augsburg case-cohort, Athero-express and CARDIoGRAM studies

Background: The chemokine RANTES (regulated on activation, normal T-cell expressed and secreted)/CCL5 is involved in the pathogenesis of cardiovascular disease in mice, whereas less is known in humans. We hypothesised that its relevance for atherosclerosis should be reflected by associations between CCL5 gene variants, RANTES serum concentrations and protein levels in atherosclerotic plaques and risk for coronary events. Methods and Findings: We conducted a case-cohort study within the population-based MONICA/KORA Augsburg studies. Baseline RANTES serum levels were measured in 363 individuals with incident coronary events and 1,908 non-cases (mean follow-up: 10.2±

An international review of tobacco smoking in the medical profession: 1974–2004

Background\ud Tobacco smoking by physicians represents a contentious issue in public health, and regardless of what country it originates from, the need for accurate, historical data is paramount. As such, this article provides an international comparison of all modern literature describing the tobacco smoking habits of contemporary physicians.\ud \ud Methods\ud A keyword search of appropriate MeSH terms was initially undertaken to identify relevant material, after which the reference lists of manuscripts were also examined to locate further publications.\ud \ud Results\ud A total of 81 English-language studies published in the past 30 years met the inclusion criteria. Two distinct trends were evident. Firstly, most developed countries have shown a steady decline in physicians' smoking rates during recent years. On the other hand, physicians in some developed countries and newly-developing regions still appear to be smoking at high rates. The lowest smoking prevalence rates were consistently documented in the United States, Australia and the United Kingdom. Comparison with other health professionals suggests that fewer physicians smoke when compared to nurses, and sometimes less often than dentists.\ud \ud Conclusion\ud Overall, this review suggests that while physicians' smoking habits appear to vary from region to region, they are not uniformly low when viewed from an international perspective. It is important that smoking in the medical profession declines in future years, so that physicians can remain at the forefront of anti-smoking programs and lead the way as public health exemplars in the 21st century