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Bernd Weisshaar - One of the best experts on this subject based on the ideXlab platform.

  • A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock 'Börner' (Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping.
    Frontiers in Plant Science, 2020
    Co-Authors: Daniela Holtgräwe, Thomas Rosleff Soerensen, Ludger Hausmann, Boas Pucker, Prisca Viehöver, Reinhard Töpfer, Bernd Weisshaar
    Abstract:

    Grapevine breeding has become highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Vitis vinifera. In modern breeding programs, therefore, genetic Marker technologies and genomic data are used to develop new cultivars with defined and stacked resistance loci. Potential sources of resistance are wild species of American or Asian origin. The interspecific hybrid of Vitis riparia Gm 183 x Vitis cinerea Arnold, available as the rootstock cultivar 'Borner,' carries several relevant resistance loci. We applied next-generation sequencing to enable the reliable identification of simple sequence repeats (SSR), and we also generated a draft genome sequence assembly of 'Borner' to access genome-wide sequence variations in a comprehensive and highly reliable way. These data were used to cover the 'Borner' genome with genetic Marker Positions. A subset of these Marker Positions was used for targeted mapping of the P. viticola resistance locus, Rpv14, to validate the Marker Position list. Based on the reference genome sequence PN40024, the Position of this resistance locus can be narrowed down to less than 0.5 Mbp on chromosome 5.

  • A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock 'Börner' (Vitis riparia x Vitis cinerea) and its Exploitation for Marker Development and Targeted Mapping
    2019
    Co-Authors: Daniela Holtgräwe, Thomas Rosleff Soerensen, Ludger Hausmann, Boas Pucker, Prisca Viehöver, Reinhard Töpfer, Bernd Weisshaar
    Abstract:

    Grapevine breeding becomes highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Vitis vinifera. Therefore, in modern breeding programs genetic Marker technologies and genomic data are used to develop new cultivars with defined and stacked resistance loci. Potential sources of resistance are wild species of American or Asian origin. The interspecific hybrid of Vitis riparia Gm 183 x V. cinerea Arnold, available as the rootstock cultivar 9Borner9, carries several relevant resistance loci. We applied next generation sequencing to enable the reliable identification of simple sequence repeats (SSR) and also generated a draft genome sequence assembly of 9Borner9 to access genome wide sequence variations in a comprehensive and highly reliable way. These data were used to cover the 9Borner9 genome with genetic Marker Positions. A subset of these Marker Positions was used for targeted mapping of the P. viticola resistance locus, Rpv14, to validate the Marker Position list. Based on the reference genome sequence PN40024, the Position of this resistance locus can be narrowed down to less than 0.5 Mbp on chromosome 5.

K Ocran - One of the best experts on this subject based on the ideXlab platform.

  • image guided respiratory gated hypofractionated stereotactic body radiation therapy h sbrt for liver and lung tumors initial experience
    Acta Oncologica, 2006
    Co-Authors: Reinhard Wurm, Stephan Erbel, L Schlenger, Dirk Scheffler, D Agaoglu, Reinhard Schild, B Gebauer, P Rogalla, M Plotkin, K Ocran
    Abstract:

    To evaluate our initial experience with image guided respiratory gated H-SBRT for liver and lung tumors. The system combines a stereoscopic x-ray imaging system (ExacTrac® X-Ray 6D) with a dedicated conformal stereotactic radiosurgery and radiotherapy linear accelerator (Novalis) and ExacTrac® Adaptive Gating for dynamic adaptive treatment. Moving targets are located and tracked by x-ray imaging of implanted fiducial Markers defined in the treatment planning computed tomography (CT). The Marker Position is compared with the Position in verification stereoscopic x-ray images, using fully automated Marker detection software. The required shift for a correct, gated set-up is calculated and automatically applied. We present our acceptance testing and initial experience in patients with liver and lung tumors. For treatment planning CT and Fluorodeoxyglucose-Positron Emission Tomography (FDG-PET) as well as magnetic resonance imaging (MRI) taken at free breathing and expiration breath hold with internal and ext...

Weisshaar Bernd - One of the best experts on this subject based on the ideXlab platform.

  • A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock ‘Börner’ (Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping
    'Frontiers Media SA', 2020
    Co-Authors: Holtgräwe Daniela, Rosleff Soerensen Thomas, Hausmann Ludger, Pucker Boas, Viehöver Prisca, Töpfer Reinhard, Weisshaar Bernd
    Abstract:

    Holtgräwe D, Rosleff Soerensen T, Hausmann L, et al. A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock ‘Börner’ (Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping. Frontiers in Plant Science. 2020;11: 156.Grapevine breeding has become highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Vitis vinifera. In modern breeding programs, therefore, genetic Marker technologies and genomic data are used to develop new cultivars with defined and stacked resistance loci. Potential sources of resistance are wild species of American or Asian origin. The interspecific hybrid of Vitis riparia Gm 183 x Vitis cinerea Arnold, available as the rootstock cultivar ‘Börner,’ carries several relevant resistance loci. We applied next-generation sequencing to enable the reliable identification of simple sequence repeats (SSR), and we also generated a draft genome sequence assembly of ‘Börner’ to access genome-wide sequence variations in a comprehensive and highly reliable way. These data were used to cover the ‘Börner’ genome with genetic Marker Positions. A subset of these Marker Positions was used for targeted mapping of the P. viticola resistance locus, Rpv14, to validate the Marker Position list. Based on the reference genome sequence PN40024, the Position of this resistance locus can be narrowed down to less than 0.5 Mbp on chromosome 5

Daniela Holtgräwe - One of the best experts on this subject based on the ideXlab platform.

  • A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock 'Börner' (Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping.
    Frontiers in Plant Science, 2020
    Co-Authors: Daniela Holtgräwe, Thomas Rosleff Soerensen, Ludger Hausmann, Boas Pucker, Prisca Viehöver, Reinhard Töpfer, Bernd Weisshaar
    Abstract:

    Grapevine breeding has become highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Vitis vinifera. In modern breeding programs, therefore, genetic Marker technologies and genomic data are used to develop new cultivars with defined and stacked resistance loci. Potential sources of resistance are wild species of American or Asian origin. The interspecific hybrid of Vitis riparia Gm 183 x Vitis cinerea Arnold, available as the rootstock cultivar 'Borner,' carries several relevant resistance loci. We applied next-generation sequencing to enable the reliable identification of simple sequence repeats (SSR), and we also generated a draft genome sequence assembly of 'Borner' to access genome-wide sequence variations in a comprehensive and highly reliable way. These data were used to cover the 'Borner' genome with genetic Marker Positions. A subset of these Marker Positions was used for targeted mapping of the P. viticola resistance locus, Rpv14, to validate the Marker Position list. Based on the reference genome sequence PN40024, the Position of this resistance locus can be narrowed down to less than 0.5 Mbp on chromosome 5.

  • A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock 'Börner' (Vitis riparia x Vitis cinerea) and its Exploitation for Marker Development and Targeted Mapping
    2019
    Co-Authors: Daniela Holtgräwe, Thomas Rosleff Soerensen, Ludger Hausmann, Boas Pucker, Prisca Viehöver, Reinhard Töpfer, Bernd Weisshaar
    Abstract:

    Grapevine breeding becomes highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Vitis vinifera. Therefore, in modern breeding programs genetic Marker technologies and genomic data are used to develop new cultivars with defined and stacked resistance loci. Potential sources of resistance are wild species of American or Asian origin. The interspecific hybrid of Vitis riparia Gm 183 x V. cinerea Arnold, available as the rootstock cultivar 9Borner9, carries several relevant resistance loci. We applied next generation sequencing to enable the reliable identification of simple sequence repeats (SSR) and also generated a draft genome sequence assembly of 9Borner9 to access genome wide sequence variations in a comprehensive and highly reliable way. These data were used to cover the 9Borner9 genome with genetic Marker Positions. A subset of these Marker Positions was used for targeted mapping of the P. viticola resistance locus, Rpv14, to validate the Marker Position list. Based on the reference genome sequence PN40024, the Position of this resistance locus can be narrowed down to less than 0.5 Mbp on chromosome 5.

Ross Berbeco - One of the best experts on this subject based on the ideXlab platform.

  • automatic Marker detection and 3d Position reconstruction using cine epid images for sbrt verification
    Medical Physics, 2009
    Co-Authors: Sangjune Park, Dan Ionascu, Fred Hacker, Harvey J. Mamon, Ross Berbeco
    Abstract:

    In previous studies, an electronic portal imaging device(EPID) in cine mode was used for validating respiratory gating and stereotactic body radiation therapy(SBRT) by tracking implanted fiducials. The manual Marker tracking methods that were used were time and labor intensive, limiting the utility of the validation. The authors have developed an automatic algorithm to quickly and accurately extract the Markers in EPIDimages and reconstruct their 3D Positions. Studies have been performed with gold fiducials placed in solid water and dynamic thorax phantoms. In addition, the authors have examined the cases of five patients being treated under an SBRT protocol for hepatic metastases. For each case, a sequence of images was created by collecting the exit radiation using the EPID. The Markers were detected and recognized using an image processing algorithm based on the Laplacian of Gaussian function. To reduce false Marker detection, a Marker registration technique was applied using image intensity as well as the geometric spatial transformations between the reference Marker Positions produced from the projection of 3D CTimages and the estimated Marker Positions. An average Marker Position in 3D was reconstructed by backprojecting, towards the source, the Position of each Marker on the 2D image plane. From the static phantom study, spatial accuracies of 1 mm were achieved in both 2D and 3D Marker locations. From the dynamic phantom study, using only the Laplacian of the Gaussian algorithm, the Marker detection success rate was 88.8%. However, adding a Marker registration technique which utilizes prior CT information, the detection success rate was increased to 100%. From the SBRT patient study, intrafractional tumor motion (3.1–11.3 mm) in the SI direction was measured using the 2D images. The interfractional patient setup errors (0.1–12.7 mm) in the SI, AP, and LR directions were obtained from the average Marker locations reconstructed in 3D and compared to the reference planning CTimage. The authors have developed an automatic algorithm to extract Marker locations from MV images and have evaluated its performance. The measured intrafractional tumor motion and the interfractional daily patient setup error can be used for off-line retrospective verification of SBRT.

  • SU-DD-A3-06: Fully Automated Internal Marker Tracking Algorithm for Cine EPID Images
    Medical Physics, 2009
    Co-Authors: So Yeon Park, Dan Ionascu, Fred Hacker, Harvey J. Mamon, Ross Berbeco
    Abstract:

    Introduction: An electronic portal imaging device(EPID) in cine mode can be used for validating respiratory gating and stereotactic body radiation therapy(SBRT) by tracking implanted fiducials. Manual tracking methods are time and labor intensive, limiting the utility of the validation. We have developed a fully automated algorithm to quickly and accurately extract the Markers in EPIDimages and reconstruct their 3D Positions. Materials and Methods: The Markers were detected and recognized using an image processing algorithm based on the Laplacian of Gaussian (LoG) filter. To reduce false Marker detection, a Marker registration technique was applied using image intensity as well as the geometric spatial transformations between the reference Marker Positions produced from the projection of 3D CTimages and the estimated Marker Positions. An average Marker Position in 3D was reconstructed by backprojecting, towards the source, the Position of each Marker on the 2D image.Results: From phantom studies, spatial accuracies of