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  • American Institute of Physics (AIP)  (1)
  • Oxford University Press  (1)
  • 2015-2019  (2)
  • 1920-1924
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  • 1
    Publication Date: 2015-12-18
    Description: : Chemical mapping experiments allow for nucleotide resolution assessment of RNA structure. We demonstrate that different strategies of integrating probing data with thermodynamics-based RNA secondary structure prediction algorithms can be implemented by means of soft constraints. This amounts to incorporating suitable pseudo-energies into the standard energy model for RNA secondary structures. As a showcase application for this new feature of the ViennaRNA Package we compare three distinct, previously published strategies to utilize SHAPE reactivities for structure prediction. The new tool is benchmarked on a set of RNAs with known reference structure. Availability and implementation : The capability for SHAPE directed RNA folding is part of the upcoming release of the ViennaRNA Package 2.2, for which a preliminary release is already freely available at http://www.tbi.univie.ac.at/RNA . Contact : michael.wolfinger@univie.ac.at Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 2
    Publication Date: 2015-01-17
    Description: Due to the present shortage of 3 He and the associated tremendous increase of its price, the supply of large neutron detection systems with 3 He becomes unaffordable. Alternative neutron detection concepts, therefore, have been invented based on solid 10 B converters. These concepts require development in thin film deposition technique regarding high adhesion, thickness uniformity and chemical purity of the converter coating on large area substrates. We report on the sputter deposition of highly uniform large-area 10 B 4 C coatings of up to 2  μ m thickness with a thickness deviation below 4% using the Helmholtz-Zentrum Geesthacht large area sputtering system. The 10 B 4 C coatings are x-ray amorphous and highly adhesive to the substrate. Material analysis by means of X-ray-Photoelectron Spectroscopy, Secondary-Ion-Mass-Spectrometry, and Rutherford-Back-Scattering (RBS) revealed low impurities concentration in the coatings. The isotope composition determined by Secondary-Ion-Mass-Spectrometry, RBS, and inelastic nuclear reaction analysis of the converter coatings evidences almost identical 10 B isotope contents in the sputter target and in the deposited coating. Neutron conversion and detection test measurements with variable irradiation geometry of the converter coating demonstrate an average relative quantum efficiency ranging from 65% to 90% for cold neutrons as compared to a black 3 He-monitor. Thus, these converter coatings contribute to the development of 3 He-free prototype detectors based on neutron grazing incidence. Transferring the developed coating process to an industrial scale sputtering system can make alternative 3 He-free converter elements available for large area neutron detection systems.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
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