| 1. |
- Dubernet, M. L., et al.
(författare)
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The virtual atomic and molecular data centre (VAMDC) consortium
- 2016
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Ingår i: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 49:7
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Tidskriftsartikel (refereegranskat)abstract
- The Virtual Atomic and Molecular Data Centre (VAMDC) Consortium is a worldwide consortium which federates atomic and molecular databases through an e-science infrastructure and an organisation to support this activity. About 90% of the inter-connected databases handle data that are used for the interpretation of astronomical spectra and for modelling in many fields of astrophysics. Recently the VAMDC Consortium has connected databases from the radiation damage and the plasma communities, as well as promoting the publication of data from Indian institutes. This paper describes how the VAMDC Consortium is organised for the optimal distribution of atomic and molecular data for scientific research. It is noted that the VAMDC Consortium strongly advocates that authors of research papers using data cite the original experimental and theoretical papers as well as the relevant databases.
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| 2. |
- Barnes, DR, et al.
(författare)
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Breast and Prostate Cancer Risks for Male BRCA1 and BRCA2 Pathogenic Variant Carriers Using Polygenic Risk Scores
- 2022
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 1460-2105 .- 0027-8874. ; 114:1, s. 109-122
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundRecent population-based female breast cancer and prostate cancer polygenic risk scores (PRS) have been developed. We assessed the associations of these PRS with breast and prostate cancer risks for male BRCA1 and BRCA2 pathogenic variant carriers.Methods483 BRCA1 and 1318 BRCA2 European ancestry male carriers were available from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). A 147-single nucleotide polymorphism (SNP) prostate cancer PRS (PRSPC) and a 313-SNP breast cancer PRS were evaluated. There were 3 versions of the breast cancer PRS, optimized to predict overall (PRSBC), estrogen receptor (ER)–negative (PRSER-), or ER-positive (PRSER+) breast cancer risk.ResultsPRSER+ yielded the strongest association with breast cancer risk. The odds ratios (ORs) per PRSER+ standard deviation estimates were 1.40 (95% confidence interval [CI] =1.07 to 1.83) for BRCA1 and 1.33 (95% CI = 1.16 to 1.52) for BRCA2 carriers. PRSPC was associated with prostate cancer risk for BRCA1 (OR = 1.73, 95% CI = 1.28 to 2.33) and BRCA2 (OR = 1.60, 95% CI = 1.34 to 1.91) carriers. The estimated breast cancer odds ratios were larger after adjusting for female relative breast cancer family history. By age 85 years, for BRCA2 carriers, the breast cancer risk varied from 7.7% to 18.4% and prostate cancer risk from 34.1% to 87.6% between the 5th and 95th percentiles of the PRS distributions.ConclusionsPopulation-based prostate and female breast cancer PRS are associated with a wide range of absolute breast and prostate cancer risks for male BRCA1 and BRCA2 carriers. These findings warrant further investigation aimed at providing personalized cancer risks for male carriers and informing clinical management.
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| 3. |
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| 4. |
- Porth, Oliver, et al.
(författare)
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The Event Horizon General Relativistic Magnetohydrodynamic Code Comparison Project
- 2019
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Ingår i: Astrophysical Journal, Supplement Series. - : American Astronomical Society. - 1538-4365 .- 0067-0049. ; 243:2
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Tidskriftsartikel (refereegranskat)abstract
- Recent developments in compact object astrophysics, especially the discovery of merging neutron stars by LIGO, the imaging of the black hole in M87 by the Event Horizon Telescope, and high- precision astrometry of the Galactic Center at close to the event horizon scale by the GRAVITY experiment motivate the development of numerical source models that solve the equations of general relativistic magnetohydrodynamics (GRMHD). Here we compare GRMHD solutions for the evolution of a magnetized accretion flow where turbulence is promoted by the magnetorotational instability from a set of nine GRMHD codes: Athena++, BHAC, Cosmos++, ECHO, H-AMR, iharm3D, HARM-Noble, IllinoisGRMHD, and KORAL. Agreement among the codes improves as resolution increases, as measured by a consistently applied, specially developed set of code performance metrics. We conclude that the community of GRMHD codes is mature, capable, and consistent on these test problems.
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| 5. |
- Del Dotto, V., et al.
(författare)
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SSBP1 mutations cause mtDNA depletion underlying a complex optic atrophy disorder
- 2020
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Ingår i: Journal of Clinical Investigation. - : American Society for Clinical Investigation. - 0021-9738 .- 1558-8238. ; 130:1, s. 108-125
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Tidskriftsartikel (refereegranskat)abstract
- Inherited optic neuropathies include complex phenotypes, mostly driven by mitochondrial dysfunction. We report an optic atrophy spectrum disorder, including retinal macular dystrophy and kidney insufficiency leading to transplantation, associated with mitochondrial DNA (mtDNA) depletion without accumulation of multiple deletions. By whole-exome sequencing, we identified mutations affecting the mitochondrial single-strand binding protein (SSBP1) in 4 families with dominant and 1 with recessive inheritance. We show that SSBP1 mutations in patient-derived fibroblasts variably affect the amount of SSBP1 protein and alter multimer formation, but not the binding to ssDNA. SSBP1 mutations impaired mtDNA, nucleoids, and 7S-DNA amounts as well as mtDNA replication, affecting replisome machinery. The variable mtDNA depletion in cells was reflected in severity of mitochondrial dysfunction, including respiratory efficiency, OXPHOS subunits, and complex amount and assembly. mtDNA depletion and cytochrome c oxidase-negative cells were found ex vivo in biopsies of affected tissues, such as kidney and skeletal muscle. Reduced efficiency of mtDNA replication was also reproduced in vitro, confirming the pathogenic mechanism. Furthermore, ssbp1 suppression in zebrafish induced signs of nephropathy and reduced optic nerve size, the latter phenotype complemented by WT mRNA but not by SSBP1 mutant transcripts. This previously unrecognized disease of mtDNA maintenance implicates SSBP1 mutations as a cause of human pathology.
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| 6. |
- Li, J. Q., et al.
(författare)
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Large-scale Multiconfiguration Dirac-Hartree-Fock Calculations for Astrophysics : C-like Ions from O iii to Mg vii
- 2022
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Ingår i: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 260:2, s. 1-23
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Tidskriftsartikel (refereegranskat)abstract
- Large-scale multiconfiguration Dirac-Hartree-Fock calculations are provided for the n <= 5 states in C-like ions from O iii to Mg vii. Electron correlation effects are accounted for by using large configuration state function expansions, built from sets of orbitals with principal quantum numbers n <= 10. An accurate and complete data set of excitation energies, wavelengths, radiative transition parameters, and lifetimes is offered for the 156 (196, 215, 272, 318) lowest states of the 2s (2)2p (2), 2s2p (3), 2p (4), 2s (2)2p3s, 2s (2)2p3p, 2s (2)2p3d, 2s2p (2)3s, 2s2p (2)3p, 2s2p (2)3d, 2p (3)3s, 2p (3)3p, 2p (3)3d, 2s (2)2p4s, 2s (2)2p4p, 2s (2)2p4d, 2s (2)2p4f, 2s2p (2)4s, 2s2p (2)4p, 2s2p (2)4d, 2s2p (2)4f, 2s (2)2p5s, 2s (2)2p5p, 2s (2)2p5d, 2s (2)2p5f, and 2s (2)2p5g configurations in O iii (F iv, Ne v, Na vi, Mg vii). By comparing available experimental wavelengths with the MCDHF results, the previous line identifications for the n = 5, 4, 3 -> n = 2 transitions of Na vi in the X-ray and EUV wavelength range are revised. For several previous identifications discrepancies are found, and tentative new (or revised) identifications are proposed. A consistent atomic data set including both energy and transition data with spectroscopic accuracy is provided for the lowest hundreds of states for C-like ions from O iii to Mg vii.
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| 7. |
- Song, C.X., et al.
(författare)
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Large-scale multiconfiguration Dirac-Hartree-Fock calculations for astrophysics : n=4 levels in P-like ions from Mn XIto Ni XIV
- 2020
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Ingår i: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 247:70, s. 1-11
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Tidskriftsartikel (refereegranskat)abstract
- Using the multiconfiguration Dirac–Hartree–Fock and the relativistic configuration interaction methods, a consistent set of transition energies and radiative transition data for the lowest 546 (623, 701, and 745) states of the , , , , , , , , , , , , , , , and configurations in Mn xi (Fe xii, Co xiii, and Ni xiv) is provided. The comparison between calculated excitation energies for the n = 4 states and available experimental values for Fe xii indicate that the calculations are highly accurate, with uncertainties of only a few hundred cm−1. Lines from these states are prominent in the soft X-rays. With the present calculations, several recent new identifications are confirmed. Other identifications involving levels in Fe xii that were found to be questionable are discussed and a few new assignments are recommended. As some n = 4 states of the other ions also show large discrepancies between experimental and calculated energies, we reassess their identification. The present study provides highly accurate atomic data for the n = 4 states of P-like ions of astrophysical interest, for which experimental data are scarce.
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| 8. |
- Wang, K., et al.
(författare)
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Benchmarking Atomic Data from Large-scale Multiconfiguration Dirac Hartree Fock Calculations for Astrophysics : S-like Ions from Cr IX to Cu XIV
- 2018
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Ingår i: Astrophysical Journal Supplement Series. - : Bibliopolis, Edizioni di Filosofia e Scienze. - 0067-0049 .- 1538-4365. ; 239:2
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Tidskriftsartikel (refereegranskat)abstract
- We present a consistent set of calculated energies and El, Ml, E2, M2 radiative transition data for the main n = 3 levels from the 3s(2)3p(4), 3p(6), 3s3p(4)3d, 3s(2)3p(2)3d(2), 3s3p(5), 3s(2)3p(3)3d, and 3s3p(3)3d(2) configurations for S-like ions from Cr TX to Cu XIV. The fully relativistic multiconfiguration Dirac Hartree Fock method implemented in the GRASP2K code is used to perform the present calculations. The excitation energies of the lowest 47 levels from the 3s(2)3p(4), 3s3p(5), and 3s(2)3p3 3d configurations, producing the strongest lines, are found to be in good agreement, reaching spectroscopic accuracy, with the latest experimental values for Fe XI evaluated by Del Zanna. Our energies can reliably be used to identify in astrophysical and laboratory spectra the 3s(2)3p(3) 3d levels in other S-like ions, which are mostly unknown. On the contrary, significant discrepancies with the 3s3p(4)3d levels were found, emphasizing the need for more detailed experimental studies. A few new tentative identifications are suggested. The benchmarks we present indicate that our consistent set of radiative data is accurate and can be used for spectral line modeling.
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| 9. |
- Albert, Damien, et al.
(författare)
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A Decade with VAMDC : Results and Ambitions
- 2020
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Ingår i: Atoms. - : MDPI. - 2218-2004. ; 8:4
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents an overview of the current status of the Virtual Atomic and Molecular Data Centre (VAMDC) e-infrastructure, including the current status of the VAMDC-connected (or to be connected) databases, updates on the latest technological development within the infrastructure and a presentation of some application tools that make use of the VAMDC e-infrastructure. We analyse the past 10 years of VAMDC development and operation, and assess their impact both on the field of atomic and molecular (A&M) physics itself and on heterogeneous data management in international cooperation. The highly sophisticated VAMDC infrastructure and the related databases developed over this long term make them a perfect resource of sustainable data for future applications in many fields of research. However, we also discuss the current limitations that prevent VAMDC from becoming the main publishing platform and the main source of A&M data for user communities, and present possible solutions under investigation by the consortium. Several user application examples are presented, illustrating the benefits of VAMDC in current research applications, which often need the A&M data from more than one database. Finally, we present our vision for the future of VAMDC.
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| 10. |
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