1,042 research outputs found

    TomograPy: A Fast, Instrument-Independent, Solar Tomography Software

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    Solar tomography has progressed rapidly in recent years thanks to the development of robust algorithms and the availability of more powerful computers. It can today provide crucial insights in solving issues related to the line-of-sight integration present in the data of solar imagers and coronagraphs. However, there remain challenges such as the increase of the available volume of data, the handling of the temporal evolution of the observed structures, and the heterogeneity of the data in multi-spacecraft studies. We present a generic software package that can perform fast tomographic inversions that scales linearly with the number of measurements, linearly with the length of the reconstruction cube (and not the number of voxels) and linearly with the number of cores and can use data from different sources and with a variety of physical models: TomograPy (http://nbarbey.github.com/TomograPy/), an open-source software freely available on the Python Package Index. For performance, TomograPy uses a parallelized-projection algorithm. It relies on the World Coordinate System standard to manage various data sources. A variety of inversion algorithms are provided to perform the tomographic-map estimation. A test suite is provided along with the code to ensure software quality. Since it makes use of the Siddon algorithm it is restricted to rectangular parallelepiped voxels but the spherical geometry of the corona can be handled through proper use of priors. We describe the main features of the code and show three practical examples of multi-spacecraft tomographic inversions using STEREO/EUVI and STEREO/COR1 data. Static and smoothly varying temporal evolution models are presented.Comment: 21 pages, 6 figures, 5 table

    Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses

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    Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three computationally inexpensive simulation methods-normal mode analysis using the elastic network model, rigidity analysis using the pebble game algorithm, and geometric simulation of protein motion-to explore conformational change along normal mode eigenvectors. Using a combination of ELNEMO and FIRST/FRODA software, large-amplitude motions in proteins with hundreds or thousands of residues can be rapidly explored within minutes using desktop computing resources. We apply the method to a representative set of six proteins covering a range of sizes and structural characteristics and show that the method identifies specific types of motion in each case and determines their amplitude limits.Comment: 34 pages, 22 Figures, Phys. Biol. 9 (2012

    Forecasting snowmelt flooding over Britain using the Grid-to-Grid model: a review and assessment of methods

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    In many regions of high annual snowfall, snowmelt modelling can prove to be a vital component of operational flood forecasting and warning systems. Although Britain as a whole does not experience prolonged periods of lying snow, with the exception of the Scottish Highlands, the inclusion of snowmelt modelling can still have a significant impact on the skill of flood forecasts. Countrywide operational flood forecasts over Britain are produced using the national Grid-to-Grid (G2G) distributed hydrological model. For Scotland, snowmelt is included in these forecasts through a G2G snow hydrology module involving temperature-based snowfall/rainfall partitioning and functions for temperature-excess snowmelt, snowpack storage and drainage. Over England and Wales, the contribution of snowmelt is included by pre-processing the precipitation prior to input into G2G. This removes snowfall diagnosed from weather model outputs and adds snowmelt from an energy budget land surface scheme to form an effective liquid water gridded input to G2G. To review the operational options for including snowmelt modelling in G2G over Britain, a project was commissioned by the Environment Agency through the Flood Forecasting Centre (FFC) for England and Wales and in partnership with the Scottish Environment Protection Agency (SEPA) and Natural Resources Wales (NRW). Results obtained from this snowmelt review project will be reported on here. The operational methods used by the FFC and SEPA are compared on past snowmelt floods, alongside new alternative methods of treating snowmelt. Both case study and longer-term analyses are considered, covering periods selected from the winters 2009-2010, 2012-2013, 2013-2014 and 2014-2015. Over Scotland, both of the snowmelt methods used operationally by FFC and SEPA provided a clear improvement to the river flow simulations. Over England and Wales, fewer and less significant snowfall events occurred, leading to less distinction in the results between the methods. It is noted that, for all methods considered,large uncertainties remain in flood forecasts influenced by snowmelt. Understanding and quantifying these uncertainties should lead to more informed flood forecasts and associated guidance information

    The position of graptolites within Lower Palaeozoic planktic ecosystems.

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    An integrated approach has been used to assess the palaeoecology of graptolites both as a discrete group and also as a part of the biota present within Ordovician and Silurian planktic realms. Study of the functional morphology of graptolites and comparisons with recent ecological analogues demonstrates that graptolites most probably filled a variety of niches as primary consumers, with modes of life related to the colony morphotype. Graptolite coloniality was extremely ordered, lacking any close morphological analogues in Recent faunas. To obtain maximum functional efficiency, graptolites would have needed varying degrees of coordinated automobility. A change in lifestyle related to ontogenetic changes was prevalent within many graptolite groups. Differing lifestyle was reflected by differing reproductive strategies, with synrhabdosomes most likely being a method for rapid asexual reproduction. Direct evidence in the form of graptolithophage 'coprolitic' bodies, as well as indirect evidence in the form of probable defensive adaptations, indicate that graptolites comprised a food item for a variety of predators. Graptolites were also hosts to a variety of parasitic organisms and provided an important nutrient source for scavenging organisms

    Prevention of childhood poisoning in the home: overview of systematic reviews and a systematic review of primary studies

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    Unintentional poisoning is a significant child public health problem. This systematic overview of reviews, supplemented with a systematic review of recently published primary studies synthesizes evidence on non-legislative interventions to reduce childhood poisonings in the home with particular reference to interventions that could be implemented by Children's Centres in England or community health or social care services in other high income countries. Thirteen systematic reviews, two meta-analyses and 47 primary studies were identified. The interventions most commonly comprised education, provision of cupboard/drawer locks, and poison control centre (PCC) number stickers. Meta-analyses and primary studies provided evidence that interventions improved poison prevention practices. Twenty eight per cent of studies reporting safe medicine storage (OR from meta-analysis 1.57, 95% CI 1.22–2.02), 23% reporting safe storage of other products (OR from meta-analysis 1.63, 95% CI 1.22–2.17) and 46% reporting availability of PCC numbers (OR from meta-analysis 3.67, 95% CI 1.84–7.33) demonstrated significant effects favouring the intervention group. There was a lack of evidence that interventions reduced poisoning rates. Parents should be provided with poison prevention education, cupboard/drawer locks and emergency contact numbers to use in the event of a poisoning. Further research is required to determine whether improving poison prevention practices reduces poisoning rates

    Volumetric texture description and discriminant feature selection for MRI

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    This paper considers the problem of classification of Magnetic Resonance Images using 2D and 3D texture measures. Joint statistics such as co-occurrence matrices are common for analysing texture in 2D since they are simple and effective to implement. However, the computational complexity can be prohibitive especially in 3D. In this work, we develop a texture classification strategy by a sub-band filtering technique that can be extended to 3D. We further propose a feature selection technique based on the Bhattacharyya distance measure that reduces the number of features required for the classification by selecting a set of discriminant features conditioned on a set training texture samples. We describe and illustrate the methodology by quantitatively analysing a series of images: 2D synthetic phantom, 2D natural textures, and MRI of human knees

    Thermodynamic properties of excess-oxygen-doped La2CuO4.11 near a simultaneous transition to superconductivity and long-range magnetic order

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    We have measured the specific heat and magnetization {\it versus} temperature in a single crystal sample of superconducting La2_{2}CuO4.11_{4.11} and in a sample of the same material after removing the excess oxygen, in magnetic fields up to 15 T. Using the deoxygenated sample to subtract the phonon contribution, we find a broad peak in the specific heat, centered at 50 K. This excess specific heat is attributed to fluctuations of the Cu spins possibly enhanced by an interplay with the charge degrees of freedom, and appears to be independent of magnetic field, up to 15 T. Near the superconducting transition TcT_{c}(HH=0)= 43 K, we find a sharp feature that is strongly suppressed when the magnetic field is applied parallel to the crystallographic c-axis. A model for 3D vortex fluctuations is used to scale magnetization measured at several magnetic fields. When the magnetic field is applied perpendicular to the c-axis, the only observed effect is a slight shift in the superconducting transition temperature.Comment: 8 pages, 8 figure

    STAT3 differential scanning fluorimetry and differential scanning light scattering assays: Addressing a missing link in the characterization of STAT3 inhibitor interactions

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    STAT3 protein is an established target for the development of new cancer therapeutic agents. Despite lacking a traditional binding site for small molecule inhibitors, many STAT3 inhibitors have been identified and explored for their anti-cancer activity. Because STAT3 signaling is mediated by protein-protein interactions, indirect methods are often employed to determine if proposed STAT3 inhibitors bind to STAT3 protein. While established STAT3 inhibition assays (such as the fluorescence polarization assay, electrophoretic mobility shift assay and ELISAs) have been used to identify novel inhibitors of STAT3 signaling, methods that directly assess STAT3 protein-inhibitor interactions could facilitate the development of novel inhibitors. In this context, we herein report new STAT3 binding assays based on differential scanning fluorimetry (DSF) and differential scanning light scattering (DSLS) to characterize interactions between STAT3 protein and inhibitors. Several peptide and small molecule STAT3 inhibitors have been evaluated, and new insight into how these compounds may interact with STAT3 is provided
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