دورية أكاديمية
A New Standard DNA Damage (SDD) Data Format.
| العنوان: | A New Standard DNA Damage (SDD) Data Format. |
|---|---|
| المؤلفون: | Schuemann J; a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts., McNamara AL; a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts., Warmenhoven JW; b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom., Henthorn NT; b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom., Kirkby KJ; b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom., Merchant MJ; b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom., Ingram S; b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom., Paganetti H; a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts., Held KD; a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts., Ramos-Mendez J; c Department of Radiation Oncology, University of California San Francisco, San Francisco, California., Faddegon B; c Department of Radiation Oncology, University of California San Francisco, San Francisco, California., Perl J; d SLAC National Accelerator Laboratory, Menlo Park, California., Goodhead DT; e Medical Research Council, Harwell, United Kingdom., Plante I; f KBRwyle, Houston, Texas., Rabus H; g Physikalisch-Technische Bundesanstalt (PTB), Braunschweig, Germany.; h Task Group 6.2 'Computational Micro- and Nanodosimetry', European Radiation Dosimetry Group e.V., Neuherberg, Germany., Nettelbeck H; g Physikalisch-Technische Bundesanstalt (PTB), Braunschweig, Germany.; h Task Group 6.2 'Computational Micro- and Nanodosimetry', European Radiation Dosimetry Group e.V., Neuherberg, Germany., Friedland W; h Task Group 6.2 'Computational Micro- and Nanodosimetry', European Radiation Dosimetry Group e.V., Neuherberg, Germany.; i Institute of Radiation Protection, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany., Kundrát P; i Institute of Radiation Protection, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany., Ottolenghi A; j Physics Department, University of Pavia, Pavia, Italy., Baiocco G; h Task Group 6.2 'Computational Micro- and Nanodosimetry', European Radiation Dosimetry Group e.V., Neuherberg, Germany.; j Physics Department, University of Pavia, Pavia, Italy., Barbieri S; h Task Group 6.2 'Computational Micro- and Nanodosimetry', European Radiation Dosimetry Group e.V., Neuherberg, Germany.; j Physics Department, University of Pavia, Pavia, Italy., Dingfelder M; k Department of Physics, East Carolina University, Greenville, North Carolina., Incerti S; l CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France.; m University of Bordeaux, CENBG, UMR 5797, F-33170 Gradignan, France., Villagrasa C; h Task Group 6.2 'Computational Micro- and Nanodosimetry', European Radiation Dosimetry Group e.V., Neuherberg, Germany.; n Institut de Radioprotection et Sûreté Nucléaire, F-92262 Fontenay aux Roses Cedex, France., Bueno M; n Institut de Radioprotection et Sûreté Nucléaire, F-92262 Fontenay aux Roses Cedex, France., Bernal MA; o Applied Physics Department, Gleb Wataghin Institute of Physics, State University of Campinas, Campinas, SP, Brazil., Guatelli S; p Centre for Medical Radiation Physics, University of Wollongong, Wollongong, NSW, Australia., Sakata D; p Centre for Medical Radiation Physics, University of Wollongong, Wollongong, NSW, Australia., Brown JMC; q Department of Radiation Science and Technology, Delft University of Technology, Delft, The Netherlands., Francis Z; r Department of Physics, Faculty of Science, Saint Joseph University, Beirut, Lebanon., Kyriakou I; s Medical Physics Laboratory, University of Ioannina Medical School, Ioannina, Greece., Lampe N; l CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France., Ballarini F; j Physics Department, University of Pavia, Pavia, Italy.; t Italian National Institute of Nuclear Physics, Section of Pavia, I-27100 Pavia, Italy., Carante MP; j Physics Department, University of Pavia, Pavia, Italy.; t Italian National Institute of Nuclear Physics, Section of Pavia, I-27100 Pavia, Italy., Davídková M; u Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Řež, Czech Republic., Štěpán V; u Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Řež, Czech Republic., Jia X; v Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas., Cucinotta FA; w Health Physics and Diagnostic Sciences, University of Nevada Las Vegas, Las Vegas, Nevada., Schulte R; x Division of Biomedical Engineering Sciences, School of Medicine, Loma Linda University, Loma Linda, California., Stewart RD; y Department of Radiation Oncology, University of Washington, Seattle, Washington., Carlson DJ; z Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut., Galer S; aa Medical Radiation Science Group, National Physical Laboratory, Teddington, United Kingdom., Kuncic Z; bb School of Physics, University of Sydney, Sydney, NSW, Australia., Lacombe S; cc Institut des Sciences Moléculaires d'Orsay (UMR 8214) University Paris-Sud, CNRS, University Paris-Saclay, 91405 Orsay Cedex, France., Milligan J; dd Retired., Cho SH; ee Department of Radiation Physics and Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas., Sawakuchi G; ee Department of Radiation Physics and Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas., Inaniwa T; ff Department of Accelerator and Medical Physics, National Institute of Radiological Sciences, Chiba, Japan., Sato T; gg Japan Atomic Energy Agency, Nuclear Science and Engineering Center, Tokai 319-1196, Japan., Li W; i Institute of Radiation Protection, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.; hh Task Group 7.7 'Internal Micro- and Nanodosimetry', European Radiation Dosimetry Group e.V., Neuherberg, Germany., Solov'yov AV; ii MBN Research Center, 60438 Frankfurt am Main, Germany., Surdutovich E; jj Department of Physics, Oakland University, Rochester, Michigan., Durante M; kk GSI Helmholtzzentrum für Schwerionenforschung, Biophysics Department, Darmstadt, Germany., Prise KM; ll Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, United Kingdom., McMahon SJ; ll Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, United Kingdom. |
| المصدر: | Radiation research [Radiat Res] 2019 Jan; Vol. 191 (1), pp. 76-92. Date of Electronic Publication: 2018 Nov 08. |
| نوع المنشور: | Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: Radiation Research Society Country of Publication: United States NLM ID: 0401245 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1938-5404 (Electronic) Linking ISSN: 00337587 NLM ISO Abbreviation: Radiat Res Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: Bozeman, MT : Radiation Research Society Original Publication: Charlottesville, VA : Kluge Carden Jennnings Pub. Co. |
| مواضيع طبية MeSH: | DNA Damage*, Computer Simulation ; DNA Repair ; Linear Energy Transfer ; Models, Theoretical ; Monte Carlo Method |
| مستخلص: | Our understanding of radiation-induced cellular damage has greatly improved over the past few decades. Despite this progress, there are still many obstacles to fully understand how radiation interacts with biologically relevant cellular components, such as DNA, to cause observable end points such as cell killing. Damage in DNA is identified as a major route of cell killing. One hurdle when modeling biological effects is the difficulty in directly comparing results generated by members of different research groups. Multiple Monte Carlo codes have been developed to simulate damage induction at the DNA scale, while at the same time various groups have developed models that describe DNA repair processes with varying levels of detail. These repair models are intrinsically linked to the damage model employed in their development, making it difficult to disentangle systematic effects in either part of the modeling chain. These modeling chains typically consist of track-structure Monte Carlo simulations of the physical interactions creating direct damages to DNA, followed by simulations of the production and initial reactions of chemical species causing so-called "indirect" damages. After the induction of DNA damage, DNA repair models combine the simulated damage patterns with biological models to determine the biological consequences of the damage. To date, the effect of the environment, such as molecular oxygen (normoxic vs. hypoxic), has been poorly considered. We propose a new standard DNA damage (SDD) data format to unify the interface between the simulation of damage induction in DNA and the biological modeling of DNA repair processes, and introduce the effect of the environment (molecular oxygen or other compounds) as a flexible parameter. Such a standard greatly facilitates inter-model comparisons, providing an ideal environment to tease out model assumptions and identify persistent, underlying mechanisms. Through inter-model comparisons, this unified standard has the potential to greatly advance our understanding of the underlying mechanisms of radiation-induced DNA damage and the resulting observable biological effects when radiation parameters and/or environmental conditions change. |
| References: | Phys Med Biol. 2000 Nov;45(11):3319-30. (PMID: 11098906) Radiat Res. 2001 May;155(5):703-15. (PMID: 11302768) Adv Space Res. 1989;9(10):15-20. (PMID: 11537287) Radiat Res. 2001 Nov;156(5 Pt 2):577-83. (PMID: 11604075) Radiat Res. 2004 Apr;161(4):451-7. (PMID: 15038766) Radiat Environ Biophys. 2004 May;43(1):23-33. (PMID: 15042380) Phys Med Biol. 2004 Jul 7;49(13):2811-25. (PMID: 15285249) Radiat Res. 2005 Aug;164(2):180-93. (PMID: 16038589) Radiat Res. 2005 Aug;164(2):194-201. (PMID: 16038590) Phys Med Biol. 2006 Apr 7;51(7):1693-706. (PMID: 16552098) Int J Radiat Biol. 1991 Mar;59(3):625-42. (PMID: 1672353) Int J Radiat Biol. 2007 Jan;83(1):27-39. (PMID: 17357437) Nucleic Acids Res. 2007;35(17):5755-62. (PMID: 17717001) Biochem Biophys Res Commun. 2008 May 9;369(3):982-8. (PMID: 18054777) Radiat Res. 2008 Apr;169(4):447-59. (PMID: 18363426) Int J Radiat Oncol Biol Phys. 2008 Jul 1;71(3):866-72. (PMID: 18430521) Int J Radiat Biol. 2008 Nov;84(11):916-29. (PMID: 19016140) Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Jan;79(1 Pt 1):011909. (PMID: 19257071) Radiat Environ Biophys. 2010 Nov;49(4):693-703. (PMID: 20574841) Med Phys. 2010 Sep;37(9):4692-708. (PMID: 20964188) Phys Med Biol. 2010 Nov 21;55(22):6721-37. (PMID: 21030747) Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Nov;82(5 Pt 1):051915. (PMID: 21230508) Mutat Res. 2011 Jun 3;711(1-2):28-40. (PMID: 21281649) J Theor Biol. 2011 Aug 21;283(1):122-35. (PMID: 21635903) Radiat Res. 2011 Nov;176(5):587-602. (PMID: 21823972) Int J Radiat Biol. 2012 Jan;88(1-2):87-97. (PMID: 22081899) Int J Radiat Oncol Biol Phys. 2012 May 1;83(1):442-50. (PMID: 22099045) Int J Radiat Oncol Biol Phys. 2012 Sep 1;84(1):250-6. (PMID: 22285663) Acta Oncol. 2013 Apr;52(3):580-8. (PMID: 22909391) J Comput Chem. 2012 Nov 15;33(30):2412-39. (PMID: 22965786) Radiat Res. 2013 May;179(5):540-8. (PMID: 23560631) Radiat Res. 2013 May;179(5):530-9. (PMID: 23560635) Radiat Res. 2013 Jul;180(1):100-9. (PMID: 23682596) Radiat Res. 2013 Nov;180(5):524-38. (PMID: 24138482) PLoS One. 2014 Feb 10;9(2):e85816. (PMID: 24520318) Sci Transl Med. 2014 Jul 16;6(245):245ra93. (PMID: 25031268) Int J Radiat Biol. 1989 Apr;55(4):513-29. (PMID: 2564863) Int J Radiat Biol. 1989 Jul;56(1):1-19. (PMID: 2569005) Phys Med Biol. 2015 Apr 21;60(8):3271-86. (PMID: 25826534) Radiat Prot Dosimetry. 2015 Sep;166(1-4):19-23. (PMID: 25870431) Radiat Prot Dosimetry. 2015 Sep;166(1-4):66-70. (PMID: 25877535) Radiat Prot Dosimetry. 2015 Sep;166(1-4):75-9. (PMID: 25877543) PLoS One. 2015 Jun 11;10(6):e0129416. (PMID: 26067661) Cancer Radiother. 2015 Oct;19(6-7):526-31. (PMID: 26277238) Phys Med Biol. 2015 Nov 7;60(21):8249-74. (PMID: 26449929) Phys Med Biol. 2015 Nov 7;60(21):8399-416. (PMID: 26459756) Int J Radiat Oncol Biol Phys. 2015 Nov 1;93(3):557-68. (PMID: 26460998) Phys Med Biol. 2015 Nov 7;60(21):8583-99. (PMID: 26501434) Phys Med. 2015 Dec;31(8):861-874. (PMID: 26653251) Sci Rep. 2016 Jun 14;6:27654. (PMID: 27297618) Phys Med Biol. 1989 Jun;34(6):691-705. (PMID: 2740437) Sci Rep. 2016 Sep 14;6:33290. (PMID: 27624453) Rep Prog Phys. 2016 Nov;79(11):116601. (PMID: 27652826) Sci Rep. 2016 Sep 22;6:34033. (PMID: 27654349) Phys Med. 2016 Oct;32(10):1187-1200. (PMID: 27659007) Phys Med. 2017 Jan;33:207-215. (PMID: 28017738) Sci Rep. 2017 Mar 27;7:45161. (PMID: 28345622) Nanoscale. 2017 May 11;9(18):5843-5853. (PMID: 28429022) Radiat Res. 2017 Sep;188(3):355-368. (PMID: 28650774) Radiat Res. 2017 Dec;188(6):690-703. (PMID: 28792846) DNA Repair (Amst). 2017 Oct;58:38-46. (PMID: 28863396) Sci Rep. 2017 Sep 7;7(1):10790. (PMID: 28883414) Sci Rep. 2017 Sep 20;7(1):11923. (PMID: 28931851) Phys Med Biol. 2017 Nov 21;62(24):9260-9281. (PMID: 29053105) Phys Med. 2017 Nov;43:120-126. (PMID: 29195554) Phys Med. 2018 Apr;48:146-155. (PMID: 29371062) Sci Rep. 2018 Feb 8;8(1):2654. (PMID: 29422642) Phys Med Biol. 2018 Mar 26;63(7):075007. (PMID: 29508768) Radiat Res. 2018 Jun;189(6):597-604. (PMID: 29624483) Phys Med. 2018 Apr;48:135-145. (PMID: 29628360) Phys Med Biol. 2018 May 17;63(10):105014. (PMID: 29697057) Int J Radiat Biol Relat Stud Phys Chem Med. 1987 Apr;51(4):573-89. (PMID: 3034813) Int J Radiat Biol Relat Stud Phys Chem Med. 1988 Mar;53(3):353-65. (PMID: 3257951) Radiat Environ Biophys. 1980 Feb;17(2):95-113. (PMID: 6768098) Phys Med Biol. 1983 May;28(5):485-92. (PMID: 6867109) Radiat Res. 1994 Dec;140(3):366-74. (PMID: 7972689) Int J Radiat Biol. 1997 May;71(5):467-83. (PMID: 9191891) Radiat Res. 1998 Aug;150(2):170-82. (PMID: 9692362) |
| معلومات مُعتمدة: | R01 CA187003 United States CA NCI NIH HHS; U19 CA021239 United States CA NCI NIH HHS |
| تواريخ الأحداث: | Date Created: 20181109 Date Completed: 20190405 Latest Revision: 20201211 |
| رمز التحديث: | 20221213 |
| مُعرف محوري في PubMed: | PMC6407706 |
| DOI: | 10.1667/RR15209.1 |
| PMID: | 30407901 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 1938-5404 |
|---|---|
| DOI: | 10.1667/RR15209.1 |