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  • Oxford University Press  (218)
  • Wiley-Blackwell  (92)
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  • 1
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    Novel bioinformatics quality control metric for next-generation sequencing experiments in the clinical context (2019)
    Oxford University Press
    Details
    Publication Date: 2019-09-12
    Description: As the use of next-generation sequencing (NGS) for the Mendelian diseases diagnosis is expanding, the performance of this method has to be improved in order to achieve higher quality. Typically, performance measures are considered to be designed in the context of each application and, therefore, account for a spectrum of clinically relevant variants. We present EphaGen, a new computational methodology for bioinformatics quality control (QC). Given a single NGS dataset in BAM format and a pre-compiled VCF-file of targeted clinically relevant variants it associates this dataset with a single arbiter parameter. Intrinsically, EphaGen estimates the probability to miss any variant from the defined spectrum within a particular NGS dataset. Such performance measure virtually resembles the diagnostic sensitivity of given NGS dataset. Here we present case studies of the use of EphaGen in context of BRCA1/2 and CFTR sequencing in a series of 14 runs across 43 blood samples and 504 publically available NGS datasets. EphaGen is superior to conventional bioinformatics metrics such as coverage depth and coverage uniformity. We recommend using this software as a QC step in NGS studies in the clinical context. Availability: https://github.com/m4merg/EphaGen or https://hub.docker.com/r/m4merg/ephagen.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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    PAPER CURRENT
  • 2
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    The Palaeocene ‘‘top chron C27n’’ transient greenhouse episode: evidence from marine pelagic Atlantic and peri-Tethyan sections (2012)
    Wiley-Blackwell
    Details
    Publication Date: 2022-05-24
    Description: The early Cenozoic, which is punctuated by several negative carbon isotope excursions (CIEs), was a time of climatic and oceanographic transition from ’Greenhouse’ to ’Icehouse’ conditions. The occurrence of a 0.5& CIE starting at the top of Chron C27n (TC27N) is reconfirmed with stable isotope data from Zumaia (Spain) and Bjala (Bulgaria) localities. Spectral analysis on respective carbonate ⁄magnetic susceptibility proxy records substantiates the orbital cyclostratigraphy allowing correlation to a high-resolution benthic foraminifera isotope record from ODP Pacific Site 1209, that indicates a coeval 2 C transient warming. The hyperthermal event lasts 200 ka, contrasting with other short-lived events from the Eocene, and displays a relatively rapid onset and a longer tailing back to pre-event values similar to the Palaeocene–Eocene Thermal Maximum (PETM), though lower in amplitude. That a causal trigger for the TC27N event may be the onset of volcanism in the North Atlantic Igneous Province (NAIP) can be inferred from a 200-m-thick lava pile erupted during C27n ⁄ C26r polarity transition in the E Greenland margin.
    Description: Published
    Description: 477-486
    Description: 2.2. Laboratorio di paleomagnetismo
    Description: JCR Journal
    Description: reserved
    Keywords: hyperthermal ; isotope excursion ; TC27N event ; Zumaia ; 03. Hydrosphere::03.01. General::03.01.06. Paleoceanography and paleoclimatology ; 04. Solid Earth::04.04. Geology::04.04.08. Sediments: dating, processes, transport ; 04. Solid Earth::04.04. Geology::04.04.10. Stratigraphy
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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    PAPER (OA)
  • 3
    Electronic Resource
    Electronic Resource
    Mass spectrometric study of vaporization processes and thermodynamic properties in the GeO2·P2O5 system (1990)
    New York, NY : Wiley-Blackwell
    Rapid Communications in Mass Spectrometry 4 (1990), S. 510-512 
    Details
    ISSN: 0951-4198
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Physics
    Notes: The Knudsen effusion mass spectrometric method was used to study the vaporization processes and thermodynamic properties of the GeO2·P2O5 system at 1423 K. GeO, PO2, P4O10, GePO3 and O2 molecules were identified in the gas phase above the GeO2·P2O5 system. A correlation was shown between the phase diagram and the thermodynamic properties attained in the GeO2·P2O5 system.
    Additional Material: 2 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/rcm.1290041208
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  • 4
    Electronic Resource
    Electronic Resource
    High temperature mass spectrometric study of the B2O3—Al2O3 system at 1248-1850 K (1995)
    New York, NY : Wiley-Blackwell
    Rapid Communications in Mass Spectrometry 9 (1995), S. 1244-1251 
    Details
    ISSN: 0951-4198
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Physics
    Notes: The high-temperature mass spectrometric Knudsen effusion method has been used to study the vaporization processes and thermodynamic properties of the B2O3—Al2O3 system in the temperature range 1248-1850 K. Data on the B2O3 partial vapour pressures and the B2O3 activities in the system under consideration were obtained. The enthalpies of formation of Al4B2O9 and Al18B4O33 have been evaluated from the values of the enthalpies of B2O3 sublimation from boron oxide and from these compounds. Comparison is made between the available phase diagram of the B2O3—Al2O3 system and the results obtained in the present study, using the complete isothermal vaporization method.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/rcm.1290091306
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  • 5
    Electronic Resource
    Electronic Resource
    Electronic structure, insulator-metal transition and superconductivity in κ-ET2X salts (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Advanced Materials for Optics and Electronics 8 (1998), S. 53-60 
    Details
    ISSN: 1057-9257
    Keywords: organic conductors ; electron correlations ; dielectric-metal transition ; superconductivity ; Fermi surface ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
    Notes: The electronic structure and superconductivity of layered organic materials based on the bis(ethylenedithio)tetrathiafulvalene molecule (BEDT-TTF, hereafter ET) with essential intra-ET correlations of electrons are analysed. Taking into account the Fermi surface topology, the superconducting electronic density of states (DOS) is calculated for a realistic model of κ-ET2X salts. A d-symmetry of the superconducting order parameter is obtained and a relation is found between its nodes on the Fermi surface and the superconducting phase characteristics. The results are in agreement with the measured non-activated temperature dependences of the superconducting specific heat and NMR relaxation rate of central 13C atoms in ET. © 1998 John Wiley & Sons, Ltd.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Mass spectrometric study of laser-induced pyrolytic decomposition of TMA (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Advanced Materials for Optics and Electronics 1 (1992), S. 287-292 
    Details
    ISSN: 1057-9257
    Keywords: LCVD ; TMA ; Pyrolysis ; Copper bromide vapour laser ; Mass spectrometry ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
    Notes: The composition of the gaseous phase during pyrolytic laser-induced chemical vapour deposition (LCVD) of aluminium from trimethylaluminium (TMA) was determined. The analysis was carried out in situ by means of a quadrupole mass spectrometer (QMS) in a closed reaction cell. The decomposition of the aluminium alkyl was induced by a copper bromide vapour laser on the surface of (111) silicon monocrystalline wafer at 0.22 GW m-2 average power density, 120 μm s-1 scanning speed and 100 Pa (1 mbar) partial pressure of TMA. The detected gaseous products of the pyrolysis of TMA were ethane, ethylene, methane and hydrogen. The presence of ethane and ethylene was probably due to the unconventional way of decomposition caused by pulsed laser irradiation. The mass peak dynamics of the created pyrolytic products at m/e = 28, 16 and 2 indicated significant production of ethane + ethylene, methane and hydrogen in the ratio 1:5:1.75.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/amo.860010605
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  • 7
    Electronic Resource
    Electronic Resource
    Synthesis of a copolymer of tetrafluoroethylene and 1-fluorosulfonyl-difluoroacetylfluoride (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Applied Polymer Science 42 (1991), S. 2761-2766 
    Details
    ISSN: 0021-8995
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Tetrafluoroethylene (TFE) was copolymerized with 1-fluorosulfonyl-difluoroacetylfluoride (FSDFAF) in both the bulk and solution by using a free radical initiator at temperature 50°C. The presence of sulfonyl fluoride (—SO2F) functional groups in the copolymers was proved by infrared (IR) spectroscopy. The copolymers were subjected to alkaline hydrolysis followed by an acid treatment and the —SO2F groups content was found not to exceed 0.40-0.50 meq/g with polymer yield ranging between 1 and 36%. Copolymerization in solution of 1,1,2-trichloro-1,2,2-trifluoroethane (Freon 113) under TFE pressure about 1.0 MPa and TFE/FSDFAF mole ratio 1.5-2.0 was proposed for further investigations. A random distribution of single FSDFAF units along the polymeric chain consisting mainly of TFE fragments was considered to exist. The copolymers had melting temperatures within 10-15°C lower than polytetrafluoroethylene and their thermal stability was 360-380°C.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/app.1991.070421014
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  • 8
    Electronic Resource
    Electronic Resource
    Study on the synthesis of perfluorovinyl-sulfonic functional monomer and its copolymerization with tetrafluoroethylene (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Applied Polymer Science 47 (1993), S. 735-741 
    Details
    ISSN: 0021-8995
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Tetrafiuoroethylene (TFE) and hexafluoropropylene (HFP) were subjected to reactions with freshly distilled sulfur trioxide to obtain 1-fluorosulfonyldifluoro-acetylfluoride (FSDFAF, yield 65-70%) and pentafluoro-2-propenylfluorosulfate (PPFS, yield up to 50%). A subsequent reaction of FSDFAF with PPFS under anhydrous conditions led to a preparation of 2-(1-pentafluoro-2-propenyloxy)tetrafluoroethanesulfonyl fluoride (PPOTESF, yield 40-41%) whose structure was proved by both infrared (IR) spectroscopy and nuclear magnetic resonance (19F NMR). TFE was copolymerized with PPOTESF in bulk by using a free radical initiator of the hydrocarbon type at a temperature of 50°C. Various TFE/PPOTESF mole ratios were employed and the presence of sulfonyl fluoride (—SO2F) functional groups in the copolymers was proven by IR spectroscopy. The copolymers were subjected to alkaline hydrolysis and the —SO2F content was found not to exceed 0.70-0.80 mEq/g with polymer yields in the range of 11-31%. The reactivity ratios r1 and r2 related to TFE and PPOTESF, respectively, were determined by using the Fineman-Ross method. A random distribution of PPOTESF units along the polymeric chain, consisting mainly of TFE fragments, was found to exist. The copolymers had melting temperatures 40-45°C lower than polytetrafluoroethylene and were thermally stable to 305-315°C. © 1993 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/app.1993.070470417
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  • 9
    Electronic Resource
    Electronic Resource
    Polymer-supported molybdenum and vanadium catalysts for epoxidation of alkenes by alkyl hydroperoxides (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Applied Polymer Science 42 (1991), S. 807-812 
    Details
    ISSN: 0021-8995
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Polymer-supported molybdenum and vanadium catalysts were synthesized using gel-type crosslinked copolymers with microheterogeneous structure. The supports were composed of inert ethylene-propylene rubber and crosslinked high molecular weight poly(ethylene oxide) matrices and polymeric ligands grafted or forming interpenetrating networks: poly(acrylic acid), poly(methacrylic acid), poly(4-vinylpyridine), and polyvinyl alcohol. Catalytic activity and selectivity of some of these complexes were tested in epoxidation of styrene by ethylbenzene hydroperoxide. Molybdenyl cations are strongly coordinated with pyridine-containing copolymers giving catalysts of high activity and selectivity. They provide conversion and selectivity above 70%. Because of the microheterogeneous mosaic-like structure of the supports, better accessibility of the active sites is achieved.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/app.1991.070420325
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  • 10
    Electronic Resource
    Electronic Resource
    Dispersion coalescence: Kinetic stability of creamed dispersions (1993)
    Hoboken, NJ : Wiley-Blackwell
    AIChE Journal 39 (1993), S. 322-334 
    Details
    ISSN: 0001-1541
    Keywords: Chemistry ; Chemical Engineering
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A Model is developed to predict the coalescence behavior in liquid-liquid dispersions. Coalescence times are based on the lifetimes of the single films that are formed between adjoining drops in a creamed or sedimented dispersion. The model is developed for smaller drop sized dispersions (〈100 μm) in which the drops are not substantially deformed due to gravitational forces. The model predicts that coalescence occurs between the emulsion drops without the gross separation of the dispersed phase (that is, the dispersion does not separate into distinct oil and water phases). As a result of interdrop coalescence, the mean drop size of the dispersed phase increases along with an increase in the polydispersity of the drop size. The model's predictions are used to develop a quantitative relationship between the lifetime of the single film and the rate of increase of the mean drop size of the dispersion. The model also accounts for the effect on dispersion stability via the models of single film drainage in the presence of surfactant.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/aic.690390212
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