| 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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| 11. |
- Lindström, Rakel, et al.
(författare)
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Li-intercalation behaviour of vanadium oxide thin film prepared by thermal oxidation of vanadium metal
- 2006
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Ingår i: Electrochimica Acta. - : Elsevier BV. - 0013-4686 .- 1873-3859. ; 51:23, s. 5001-5011
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Tidskriftsartikel (refereegranskat)abstract
- In order to produce thin films of crystalline V2O5, vanadium metal was thermally oxidised at 500 degrees C under oxygen pressures between 250 and 1000 mbar for 1-5 min. The oxide films were characterised by X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), X-ray diffraction (XRD) and Rutherford backscattering spectrometry (RBS). The lithium intercalation performance of the oxide films was investigated by cyclic voltammetry (CV), chronopotentiometry and electrochemical impedance spectroscopy (EIS). It was shown that the composition, the crystallinity and the related lithium intercalation properties of the thin oxide films were critically dependent on the oxidation conditions. The formation of crystalline V2O5 films was stimulated by higher oxygen pressure and longer oxidation time. Exposure for 5 min at 750 mbar 02 at 500 degrees C resulted in a surface oxide film composed of V2O5, and consisting of crystallites up to 200 nm in lateral size. The thickness of the layer was about 100 nm. This V2O5 oxide film was found to have good cycling performance in a potential window between 3.8 and 2.8 V, with a stable capacity of 117 +/- 10 mAh/g at an applied current density of 3.4 mu A/cm(2). The diffusion coefficients corresponding to the two plateaus at 3.4 and 3.2V were determined from the impedance measurements to (5.2 and 3.0) x 10(-13) cm(2) s(-1), respectively. Beneath the V2O5 layer, lower oxides (mainly VO2) were found close to the metal. At lower oxygen pressure and shorter exposure times, the oxide films were less crystalline and the amount of V4+ increased in the surface oxide film, as revealed by XPS. At intermediate oxygen pressures and exposure times a mixture of crystalline V2O5 and V6O13 was found in the oxide film.
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| 12. |
- Lindström, Rakel, et al.
(författare)
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Thin films of vanadium oxide grown on vanadium metal : oxidation conditions to produce V2O5 films for Li-intercalation applications and characterisation by XPS, AFM, RBS/NRA
- 2006
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Ingår i: Surface and Interface Analysis. - : Wiley. - 0142-2421 .- 1096-9918. ; 38:1, s. 6-18
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Tidskriftsartikel (refereegranskat)abstract
- Thin films of vanadium oxide were grown on vanadium metal surfaces W in air at ambient conditions, (ii) in 5 mm H2SO4 (aq), pH 3, (iii) by thermal oxidation at low oxygen pressure (10(-5) mbar) at temperatures between 350 and 550 degrees C and (iv) at near-atmospheric oxygen pressure (750 mbar) at 500 degrees C. The oxide films were investigated by atomic force microscopy (AIM), X-ray photoelectron spectroscopy (XPS), X-Ray diffraction (XRD) and Rutherford backscattering spectrometry (RBS) and nuclear reaction analysis (NRA). The lithium intercalation properties were studied by cyclic voltammetry (CV). The results show that the oxide films formed in air at room temperature (RT), in acidic aqueous solution, and at low oxygen pressure at elevated temperatures are composed Of V2O3. In air and in aqueous solution at RT, the oxide films are ultra-thin and hydroxylated. At 500 degrees C, nearly atmospheric oxygen pressure is required to form crystalline V2O5 films. The oxide films grown at pO(2) = 750 mbar for 5 min are about 260-nm thick, and consist of a 115-nm outer layer of crystalline V2O5. The inner oxide is mainly composed Of VO2. For all high temperature oxidations, the oxygen diffusion from the oxide film into the metal matrix was considerable. The oxygen saturation of the metal at 450 degrees C was found, by XPS, to be 27 at.% at the oxide/metal interface. The well-crystallized V2O5 film, formed by oxidation for 5 min at 500 degrees C and 750 mbar O-2, was shown to have good lithium intercalation properties and is a promising candidate as electrode material in lithium batteries.
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| 13. |
- Olsson, Mia, et al.
(författare)
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A Novel Unstable Duplication Upstream of HAS2 Predisposes to a Breed-Defining Skin Phenotype and a Periodic Fever Syndrome in Chinese Shar-Pei Dogs
- 2011
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Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 7:3, s. e1001332-
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Tidskriftsartikel (refereegranskat)abstract
- Hereditary periodic fever syndromes are characterized by recurrent episodes of fever and inflammation with no known pathogenic or autoimmune cause. In humans, several genes have been implicated in this group of diseases, but the majority of cases remain unexplained. A similar periodic fever syndrome is relatively frequent in the Chinese Shar-Pei breed of dogs. In the western world, Shar-Pei have been strongly selected for a distinctive thick and heavily folded skin. In this study, a mutation affecting both these traits was identified. Using genome-wide SNP analysis of Shar-Pei and other breeds, the strongest signal of a breed-specific selective sweep was located on chromosome 13. The same region also harbored the strongest genome-wide association (GWA) signal for susceptibility to the periodic fever syndrome (p(raw) = 2.3 x 10(-6), p(genome) = 0.01). Dense targeted resequencing revealed two partially overlapping duplications, 14.3 Kb and 16.1 Kb in size, unique to Shar-Pei and upstream of the Hyaluronic Acid Synthase 2 (HAS2) gene. HAS2 encodes the rate-limiting enzyme synthesizing hyaluronan (HA), a major component of the skin. HA is up-regulated and accumulates in the thickened skin of Shar-Pei. A high copy number of the 16.1 Kb duplication was associated with an increased expression of HAS2 as well as the periodic fever syndrome (p, < 0.0001). When fragmented, HA can act as a trigger of the innate immune system and stimulate sterile fever and inflammation. The strong selection for the skin phenotype therefore appears to enrich for a pleiotropic mutation predisposing these dogs to a periodic fever syndrome. The identification of HA as a major risk factor for this canine disease raises the potential of this glycosaminoglycan as a risk factor for human periodic fevers and as an important driver of chronic inflammation.
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| 14. |
- van Sebille, Erik, et al.
(författare)
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Lagrangian ocean analysis : Fundamentals and practices
- 2018
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Ingår i: Ocean Modelling. - : Elsevier BV. - 1463-5003 .- 1463-5011. ; 121, s. 49-75
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Forskningsöversikt (refereegranskat)abstract
- Lagrangian analysis is a powerful way to analyse the output of ocean circulation models and other ocean velocity data such as from altimetry. In the Lagrangian approach, large sets of virtual particles are integrated within the three-dimensional, time-evolving velocity fields. Over several decades, a variety of tools and methods for this purpose have emerged. Here, we review the state of the art in the field of Lagrangian analysis of ocean velocity data, starting from a fundamental kinematic framework and with a focus on large-scale open ocean applications. Beyond the use of explicit velocity fields, we consider the influence of unresolved physics and dynamics on particle trajectories. We comprehensively list and discuss the tools currently available for tracking virtual particles. We then showcase some of the innovative applications of trajectory data, and conclude with some open questions and an outlook. The overall goal of this review paper is to reconcile some of the different techniques and methods in Lagrangian ocean analysis, while recognising the rich diversity of codes that have and continue to emerge, and the challenges of the coming age of petascale computing.
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| 15. |
- Wang, Kai, et al.
(författare)
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Energy Levels, Lifetimes, and Transition Rates for P-like Ions from CrX to ZnXVI from Large-scale Relativistic Multiconfiguration Calculations
- 2018
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Ingår i: Astrophysical Journal Supplement Series. - : Bibliopolis, Edizioni di Filosofia e Scienze. - 0067-0049 .- 1538-4365. ; 235:2
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Tidskriftsartikel (refereegranskat)abstract
- The fully relativistic multiconfiguration Dirac-Hartree-Fock method is used to compute excitation energies and lifetimes for the 143 lowest states of the 3s(2)3p(3), 3s3p(4), 3s(2)3p(2)3d, 3s3p(3)3d, 3p(5), 3s(2)3p3d(2) configurations in P-like ions from Cr X to Zn XVI. Multipole (E1, M1, E2, M2) transition rates, line strengths, oscillator strengths, and branching fractions among these states are also given. Valence-valence and core-valence electron correlation effects are systematically accounted for using large basis function expansions. Computed excitation energies are compared with the NIST ASD and CHIANTI compiled values and previous calculations. The mean average absolute difference, removing obvious outliers, between computed and observed energies for the 41 lowest identified levels in Fe XII, is only 0.057%, implying that the computed energies are accurate enough to aid identification of new emission lines from the Sun and other astrophysical sources. The amount of energy and transition data of high accuracy are significantly increased for several P-like ions of astrophysics interest, where experimental data are still very scarce.
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| 16. |
- Wang, K., et al.
(författare)
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Large-scale Multiconfiguration Dirac-Hartree-Fock Calculations for Astrophysics : Cl-like Ions from Cr VIII to ZnXIV
- 2020
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Ingår i: Astrophysical Journal Supplement Series. - : Institute of Physics Publishing (IOPP). - 0067-0049 .- 1538-4365. ; 246:1
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Tidskriftsartikel (refereegranskat)abstract
- We use the multiconfiguration Dirac-Hartree-Fock (MCDHF) method combined with the relativistic configuration interaction approach (GRASP2K) to provide a consistent set of transition energies and radiative transition data for the lower n = 3 states in all Cl-like ions of astrophysical importance, from Cr VIII to Zn XIV. We also provide excitation energies calculated for Fe X using the many-body perturbation theory (MBPT, implemented within FAC). The comparison of the present MCDHF results with MBPT and with the available experimental energies indicates that the theoretical excitation energies are highly accurate, with uncertainties of only a few hundred cm(-1). Detailed comparisons for Fe X and Ni XII highlight discrepancies in the experimental energies found in the literature. Several new identifications are proposed.
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| 17. |
- Zhang, X. H., et al.
(författare)
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Benchmarking Multiconfiguration Dirac-Hartree-Fock Calculations for Astrophysics : Si-like Ions from Cr xi to Zn xvii
- 2021
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Ingår i: Astrophysical Journal Supplement Series. - : Institute of Physics Publishing (IOPP). - 0067-0049 .- 1538-4365. ; 257:2
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Tidskriftsartikel (refereegranskat)abstract
- The multiconfiguration Dirac-Hartree-Fock (MCDHF) and relativistic configuration interaction methods are used to provide excitation energies, lifetimes, and radiative transition data for the 604 (699, 702, 704, 704, 704, and 699) lowest levels of the 3s (2)3p (2), 3s3p (3), 3s (2)3p3d, 3p (4), 3s3p (2)3d, 3s (2)3d (2), 3p (3)3d, 3s3p3d (2), 3s3d (3), 3p3d (3), 3p (2)3d (2), 3s (2)3p4s, 3s (2)3p4p, 3s (2)3p4d, 3s (2)3p4f, 3s3p (2)4s, 3s3p (2)4p, 3s3p (2)4d, 3s3p (2)4f, 3s (2)3d4s, 3s (2)3d4p, 3p (3)4s, 3p (3)4p, 3s3p3d4s, 3s (2)3p5s, and 3s (2)3p5p configurations in Cr xi, (Mn xii, Fe xiii, Co xiv, Ni xv, Cu xvi, and Zn xvii). Previous line identifications of Fe xiii and Ni xv in the EUV and X-ray wavelength ranges are reviewed by comprehensively comparing the MCDHF theoretical results with available experimental data. Many recent identifications of Fe xiii and Ni xv lines are confirmed, and several new identifications for these two ions are proposed. A consistent atomic data set with spectroscopic accuracy is provided for the lowest hundreds of levels for Si-like ions of iron-group elements of astrophysical interest, for which experimental values are scarce. The uncertainty estimation method suggested by Kramida, applied to the comparison of the length and velocity line strength values, is used for ranking the transition data. The correlation of the latter with the gauge dependency patterns of the line strengths is investigated.
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