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  • 1
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    Imaging zero-offset 3-D P-cable data with CRS method (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Standard seismic acquisition and processing require appropriate source–receiver offsets. P-cable technology represents the opposite, namely, very short source–receiver offsets at the price of increased spatial and lateral resolution with a high-frequency source. To use this advantage, a processing flow excluding offset information is required. This aim can be achieved with a processing tuned to diffractions because point diffractions scatter the same information in the offset and midpoint direction. Usually, diffractions are small amplitude events and a careful diffraction separation is required as a first step. We suggest the strategy to use a multiparameter stacking operator, for example, common-reflection surface, and stack along the midpoint direction. The obtained kinematic wave-front attributes are used to calculate time-migration velocities. A diffractivity map serves as a filter to refine the velocities. This strategy is applied to a 3-D P-cable data set to obtain a time-migrated image.〈/span〉
    Print ISSN: 2051-1965
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 2
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    Glycoproteomic characterization of recombinant mouse {alpha}-dystroglycan (2012)
    Oxford University Press
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    Publication Date: 2012-04-05
    Description: α-Dystroglycan (DG) is a key component of the dystrophin–glycoprotein complex. Aberrant glycosylation of the protein has been linked to various forms of congenital muscular dystrophy. Unusually α-DG has previously been demonstrated to be modified with both O - N -acetylgalactosamine and O -mannose initiated glycans. In the present study, Fc-tagged recombinant mouse α-DG was expressed and purified from human embryonic kidney 293T cells. α-DG glycopeptides were characterized by glycoproteomic strategies using both nano-liquid chromatography matrix-assisted laser desorption ionization and electrospray tandem mass spectrometry. A total of 14 different peptide sequences and 38 glycopeptides were identified which displayed heterogeneous O-glycosylation. These data provide new insights into the complex domain-specific O-glycosylation of α-DG.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 3
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    On the approximation order of triangular Shepard interpolation (2016)
    Oxford University Press
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    Publication Date: 2016-01-26
    Description: Shepard's method is a well-known technique for interpolating large sets of scattered data. The classical Shepard operator reconstructs an unknown function as a normalized blend of the function values at the scattered points, using the inverse distances to the scattered points as weight functions. Based on the general idea of defining interpolants by convex combinations, Little suggested extending the bivariate Shepard operator in two ways. On the one hand, he considers a triangulation of the scattered points and substitutes function values with linear polynomials which locally interpolate the given data at the vertices of each triangle. On the other hand, he modifies the classical point-based weight functions and defines instead a normalized blend of the locally interpolating polynomials with triangle-based weight functions which depend on the product of inverse distances to the three vertices of the corresponding triangle. The resulting triangular Shepard operator interpolates all data required for its definition and reproduces polynomials up to degree $1$ , whereas the classical Shepard operator reproduces only constants. In this paper, we show that this interpolation operator consequentially has quadratic approximation order, which is confirmed by our numerical results.
    Print ISSN: 0272-4979
    Electronic ISSN: 1464-3642
    Topics: Mathematics
    Published by Oxford University Press
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  • 4
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    Cdx2 homeoprotein inhibits non-homologous end joining in colon cancer but not in leukemia cells (2012)
    Oxford University Press
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    Publication Date: 2012-04-24
    Description: Cdx2, a gene of the paraHox cluster, encodes a homeodomain transcription factor that plays numerous roles in embryonic development and in homeostasis of the adult intestine. Whereas Cdx2 exerts a tumor suppressor function in the gut, its abnormal ectopic expression in acute leukemia is associated to a pro-oncogenic function. To try to understand this duality, we have hypothesized that Cdx2 may interact with different protein partners in the two tissues and set up experiments to identify them by tandem affinity purification. We show here that Cdx2 interacts with the Ku heterodimer specifically in intestinal cells, but not in leukemia cells, via its homeodomain. Ku proteins do not affect Cdx2 transcriptional activity. However, Cdx2 inhibits in vivo and in vitro the DNA repair activity mediated by Ku proteins in intestinal cells. Whereas Cdx2 does not affect the recruitment of Ku proteins and DNA-PKcs into the DNA repair complex, it inhibits DNA-PKcs activity. Thus, we report here a new function of Cdx2, acting as an inhibitor of the DNA repair machinery, that may contribute to its tumor suppressor function specifically in the gut.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Letter to the Glycoforum Transforming Glycoscience: An Australian Perspective (2013)
    Oxford University Press
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    Publication Date: 2013-12-07
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 6
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    Common-reflection-surface-based workflow for diffraction imaging (2011)
    Society of Exploration Geophysicists (SEG)
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    Publication Date: 2011-09-01
    Description: Imaging of diffractions is a challenge in seismic processing. Standard seismic processing is tuned to enhance reflections. Separation of diffracted from reflected events is frequently used to achieve an optimized image of diffractions. We present a method to effectively separate and image diffracted events in the time domain. The method is based on the common-reflection-surface-based diffraction stacking and the application of a diffraction-filter. The diffraction-filter uses kinematic wavefield attributes determined by the common-reflection-surface approach. After the separation of seismic events, poststack time-migration velocity analysis is applied to obtain migration velocities. The velocity analysis uses a semblance based method of diffraction traveltimes. The procedure is incorporated into the conventional common-reflection-surface workflow. We apply the procedure to 2D synthetic data. The application of the method to simple and complex synthetic data shows promising results.
    Print ISSN: 0016-8033
    Electronic ISSN: 1942-2156
    Topics: Geosciences , Physics
    Published by Society of Exploration Geophysicists (SEG)
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  • 7
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    Prestack time migration by common-migrated-reflector-element stacking (2012)
    Society of Exploration Geophysicists (SEG)
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    Publication Date: 2012-05-01
    Description: Time migration is an attractive tool to produce a subsurface image because it is faster and less sensitive to velocities errors than depth migration. However, a highly focused time image is only achievable with well-determined time-migration velocities. Therefore, a refinement of the initial time-migration velocities often is required. We introduced a new technique for prestack time migration, based on the common-migrated-reflector-element stack of common scatterpoint gathers, including an automatic update of time-migration velocities. The common scatterpoint gathers are generated using a new formulation of the double-square-root equation that is parametrized with the common-offset apex time. The common-migrated-reflector-element stack is a multiparameter stacking technique based on the Taylor expansion of traveltimes of time-migrated reflections in the paraxial vicinity of the image ray. Our 2D synthetic and field data examples demonstrated that the proposed method provides updated time-migration velocities that are more robust and have higher resolution compared with the initial time-migration velocities. The prestack time migration method also showed a clear improvement of the focusing of reflections for such geologic features as faults and salt structures.
    Print ISSN: 0016-8033
    Electronic ISSN: 1942-2156
    Topics: Geosciences , Physics
    Published by Society of Exploration Geophysicists (SEG)
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  • 8
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    MIRAGE: The minimum information required for a glycomics experiment (2014)
    Oxford University Press
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    Publication Date: 2014-04-05
    Description: The MIRAGE (minimum information required for a glycomics experiment) initiative was founded in Seattle, WA, in November 2011 in order to develop guidelines for reporting the qualitative and quantitative results obtained by diverse types of glycomics analyses, including the conditions and techniques that were applied to prepare the glycans for analysis and generate the primary data along with the tools and parameters that were used to process and annotate this data. These guidelines must address a broad range of issues, as glycomics data are inherently complex and are generated using diverse methods, including mass spectrometry (MS), chromatography, glycan array-binding assays, nuclear magnetic resonance (NMR) and other rapidly developing technologies. The acceptance of these guidelines by scientists conducting research on biological systems in which glycans have a significant role will facilitate the evaluation and reproduction of glycomics experiments and data that is reported in scientific journals and uploaded to glycomics databases. As a first step, MIRAGE guidelines for glycan analysis by MS have been recently published (Kolarich D, Rapp E, Struwe WB, Haslam SM, Zaia J., et al. 2013. The minimum information required for a glycomics experiment (MIRAGE) project – Improving the standards for reporting mass spectrometry-based glycoanalytic data. Mol. Cell Proteomics. 12:991–995), allowing them to be implemented and evaluated in the context of real-world glycobiology research. In this paper, we set out the historical context, organization structure and overarching objectives of the MIRAGE initiative.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 9
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    Using seismic diffractions for assessment of tectonic overprint and fault interpretation (2018)
    Society of Exploration Geophysicists (SEG)
    Details
    Publication Date: 2018
    Description: 〈span〉〈div〉ABSTRACT〈/div〉Assessment of the area of interest on tectonic overprint is a key aspect during various geoscientific exploration endeavors. Conventionally, 3D reflection imaging is used because it provides the highest resolution of the subsurface image. Tectonic features, e.g., faults or fractures, are imaged indirectly by means of discontinuities of the specular reflections. Specular reflections, however, are only a part of the backscattering wavefield. Geologic heterogeneities in the subsurface can act as scattering points or scattering edges, which both evoke diffracted waves. Thus, diffracted waves are a direct seismic response from subsurface heterogeneities, which have a size comparable with the prevailing wavelength or a curvature growing locally to infinity. We investigate a dedicated processing of diffracted waves, which allows direct imaging of such heterogeneities. The method is based on separation of reflections from diffractions with subsequent diffraction focusing. We apply a combination of frequency-wavenumber filtering and an adaptive-subtraction engine to isolate diffractions. Once the reflections are removed from a data set, diffracted waves are focused into their apexes yielding an image of scatter points, which can be interpreted as an indicator for the extent of the degree of inhomogeneities or can be used to map structural elements or fracture density. We use a modified coherence analysis as a focusing tool. Diffractions from the scattering points have a different phase response than diffractions from the edges. These differences can be distinguished and further guide the geologic interpretation.〈/span〉
    Print ISSN: 0016-8033
    Electronic ISSN: 1942-2156
    Topics: Geosciences , Physics
    Published by Society of Exploration Geophysicists (SEG)
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  • 10
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    The minimum information required for a glycomics experiment (MIRAGE) project: sample preparation guidelines for reliable reporting of glycomics datasets (2016)
    Oxford University Press
    Details
    Publication Date: 2016-10-08
    Description: The minimum information required for a glycomics experiment (MIRAGE) project was established in 2011 to provide guidelines to aid in data reporting from all types of experiments in glycomics research including mass spectrometry (MS), liquid chromatography, glycan arrays, data handling and sample preparation. MIRAGE is a concerted effort of the wider glycomics community that considers the adaptation of reporting guidelines as an important step towards critical evaluation and dissemination of datasets as well as broadening of experimental techniques worldwide. The MIRAGE Commission published reporting guidelines for MS data and here we outline guidelines for sample preparation. The sample preparation guidelines include all aspects of sample generation, purification and modification from biological and/or synthetic carbohydrate material. The application of MIRAGE sample preparation guidelines will lead to improved recording of experimental protocols and reporting of understandable and reproducible glycomics datasets.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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