Atomic and Molecular Data for Optical Stellar Spectroscopy

High-precision spectroscopy of large stellar samples plays a crucial role for several topical issues in astrophysics. Examples include studying the chemical structure and evolution of the Milky Way galaxy, tracing the origin of chemical elements, and characterizing planetary host stars. Data are accumulating from instruments that obtain high-quality spectra of stars in the ultraviolet, optical and infrared wavelength regions on a routine basis. These instruments are located at ground-based 2- to 10-m class telescopes around the world, in addition to the spectrographs with unique capabilities available at the Hubble Space Telescope. The interpretation of these spectra requires high-quality transition data for numerous species, in particular neutral and singly ionized atoms, and di- or triatomic molecules. We rely heavily on the continuous efforts of laboratory astrophysics groups that produce and improve the relevant experimental and theoretical atomic and molecular data. The compilation of the best available data is facilitated by databases and electronic infrastructures such as the NIST Atomic Spectra Database, the VALD database, or the Virtual Atomic and Molecular Data Centre (VAMDC). We illustrate the current status of atomic data for optical stellar spectra with the example of the Gaia-ESO Public Spectroscopic Survey. Data sources for 35 chemical elements were reviewed in an effort to construct a line list for a homogeneous abundance analysis of up to 100000 stars.Comment: Published 30 April 2015 in Physica Script

Promoter Variant of PIK3C3 Is Associated with Autoimmunity against Ro and Sm Epitopes in African-American Lupus Patients

The PIK3C3 locus was implicated in case-case genome-wide association study of systemic lupus erythematosus (SLE) which we had performed to detect genes associated with autoantibodies and serum interferon-alpha (IFN-α). Herein, we examine a PIK3C3 promoter variant (rs3813065/-442 C/T) in an independent multiancestral cohort of 478 SLE cases and 522 controls. rs3813065 C was strongly associated with the simultaneous presence of both anti-Ro and anti-Sm antibodies in African-American patients [OR = 2.24 (1.34–3.73), P = 2.0 × 10−3]. This autoantibody profile was associated with higher serum IFN-α (P = 7.6 × 10−6). In the HapMap Yoruba population, rs3813065 was associated with differential expression of ERAP2 (P = 2.0 × 10−5), which encodes an enzyme involved in MHC class I peptide processing. Thus, rs3813065 C is associated with a particular autoantibody profile and altered expression of an MHC peptide processing enzyme, suggesting that this variant modulates serologic autoimmunity in African-American SLE patients

Osteopontin Alleles Are Associated with Clinical Characteristics in Systemic Lupus Erythematosus

Variants of the osteopontin (OPN) gene have been associated with systemic lupus erythematosus (SLE) susceptibility and cytokine profiles in SLE patients. It is not known whether these alleles are associated with specific clinical phenotypes in SLE. We studied 252 well-characterized SLE patients from a multiethnic cohort, genotyping the rs11730582, rs28357094, rs6532040, and rs9138 SNPs in the OPN gene. Ancestry informative markers were used to control for genetic ancestry. The SLE-risk allele rs9138C in the 3′ UTR region was associated with photosensitivity in lupus patients across all ancestral backgrounds (meta-analysis OR = 3.2, 95% CI = 1.6–6.5, P = 1.0 × 10−3). Additionally, the promoter variant rs11730582C demonstrated suggestive evidence for association with two hematologic traits: thrombocytopenia (OR = 2.1, P = 0.023) and hemolytic anemia (OR = 2.6, P = 0.036). These clinical associations with SNPs in the promoter and 3′ UTR regions align with previously reported SLE-susceptibility SNPs in OPN and suggest potential roles for these variants in antibody-mediated cytopenias and skin inflammation in SLE

The Gaia-ESO Survey: Separating disk chemical substructures with cluster models

(Abridged) Recent spectroscopic surveys have begun to explore the Galactic disk system outside the solar neighborhood on the basis of large data samples. In this way, they provide valuable information for testing spatial and temporal variations of disk structure kinematics and chemical evolution. We used a Gaussian mixture model algorithm, as a rigurous mathematical approach, to separate in the [Mg/Fe] vs. [Fe/H] plane a clean disk star subsample from the Gaia-ESO survey internal data release 2. We find that the sample is separated into five groups associated with major Galactic components; the metal-rich end of the halo, the thick disk, and three subgroups for the thin disk sequence. This is confirmed with a sample of red clump stars from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) survey. The two metal-intermediate and metal-rich groups of the thin disk decomposition ([Fe/H]>-0.25 dex) highlight a change in the slope at solar metallicity. This holds true at different radial regions. The distribution of Galactocentric radial distances of the metal-poor part of the thin disk ([Fe/H]<-0.25 dex) is shifted to larger distances than those of the more metal-rich parts. Moreover, the metal-poor part of the thin disk presents indications of a scale height intermediate between those of the thick and the rest of the thin disk, and it displays higher azimuthal velocities than the latter. These stars might have formed and evolved in parallel and/or dissociated from the inside-out formation taking place in the internal thin disk. Their enhancement levels might be due to their origin from gas pre-enriched by outflows from the thick disk or the inner halo. The smooth trends of their properties (their spatial distribution with respect to the plane, in particular) with [Fe/H] and [Mg/Fe] suggested by the data indicates a quiet dynamical evolution, with no relevant merger events

The Gaia-ESO Survey: the chemical structure of the Galactic discs from the first internal data release

Most high-resolution spectroscopic studies of the Galactic discs were mostly confined to objects in the solar vicinity. Here we aim at enlarging the volume in which individual chemical abundances are used to characterise both discs, using the first internal data release of the Gaia-ESO survey. We derive and discuss the abundances of eight elements (Mg, Al, Si, Ca, Ti, Fe, Cr, Ni, and Y). The trends of these elemental abundances with iron are very similar to those in the solar neighbourhood. We find a natural division between alpha-rich and alpha-poor stars, best seen in the bimodality of the [Mg/M] distributions in bins of metallicity, which we attribute to thick- and thin-disc sequences, respectively. With the possible exception of Al, the observed dispersion around the trends is well described by the expected errors, leaving little room for astrophysical dispersion. Using previously derived distances from Recio-Blanco et al. (2014b), we further find that the thick-disc is more extended vertically and is more centrally concentrated towards the inner Galaxy than the thin-disc, which indicates a shorter scale-length. We derive the radial and vertical gradients in metallicity, iron, four alpha-element abundances, and Al for the two populations, taking into account the identified correlation between R_GC and |Z|. Radial metallicity gradient is found in the thin disc. The positive radial individual [alpha/M] gradients found are at variance from the gradients observed in the RAVE survey. The thin disc also hosts a negative vertical metallicity gradient, accompanied by positive individual [alpha/M] and [Al/M] gradients. The thick-disc, presents no radial metallicity gradient, a shallower vertical metallicity gradient than the thin-disc, an alpha-elements-to-iron radial gradient in the opposite sense than that of the thin disc, and positive vertical individual [alpha/M] and [Al/M] gradients.Comment: 24 pages, 10 figure

Trait-stratified genome-wide association study identifies novel and diverse genetic associations with serologic and cytokine phenotypes in systemic lupus erythematosus

INTRODUCTION: Systemic lupus erythematosus (SLE) is a highly heterogeneous disorder, characterized by differences in autoantibody profile, serum cytokines, and clinical manifestations. SLE-associated autoantibodies and high serum interferon alpha (IFN-α) are important heritable phenotypes in SLE which are correlated with each other, and play a role in disease pathogenesis. These two heritable risk factors are shared between ancestral backgrounds. The aim of the study was to detect genetic factors associated with autoantibody profiles and serum IFN-α in SLE. METHODS: We undertook a case-case genome-wide association study of SLE patients stratified by ancestry and extremes of phenotype in serology and serum IFN-α. Single nucleotide polymorphisms (SNPs) in seven loci were selected for follow-up in a large independent cohort of 538 SLE patients and 522 controls using a multi-step screening approach based on novel metrics and expert database review. The seven loci were: leucine-rich repeat containing 20 (LRRC20); protein phosphatase 1 H (PPM1H); lysophosphatidic acid receptor 1 (LPAR1); ankyrin repeat and sterile alpha motif domain 1A (ANKS1A); protein tyrosine phosphatase, receptor type M (PTPRM); ephrin A5 (EFNA5); and V-set and immunoglobulin domain containing 2 (VSIG2). RESULTS: SNPs in the LRRC20, PPM1H, LPAR1, ANKS1A, and VSIG2 loci each demonstrated strong association with a particular serologic profile (all odds ratios > 2.2 and P < 3.5 × 10(-4)). Each of these serologic profiles was associated with increased serum IFN-α. SNPs in both PTPRM and LRRC20 were associated with increased serum IFN-α independent of serologic profile (P = 2.2 × 10(-6 )and P = 2.6 × 10(-3 )respectively). None of the SNPs were strongly associated with SLE in case-control analysis, suggesting that the major impact of these variants will be upon subphenotypes in SLE. CONCLUSIONS: This study demonstrates the power of using serologic and cytokine subphenotypes to elucidate genetic factors involved in complex autoimmune disease. The distinct associations observed emphasize the heterogeneity of molecular pathogenesis in SLE, and the need for stratification by subphenotypes in genetic studies. We hypothesize that these genetic variants play a role in disease manifestations and severity in SLE

Beyond Gaia DR3: tracing the [{\alpha}/M]-[M/H] bimodality from the inner to the outer Milky Way disc with Gaia RVS and Convolutional Neural-Networks

Gaia DR3 has provided the community with about one million RVS spectra covering the CaII triplet region. In the next Gaia data releases, we anticipate the number of RVS spectra to successively increase from several 10 million spectra to eventually more than 200M spectra. Thus, stellar spectra are produced on an "industrial scale" with numbers well above those for current and anticipated ground based surveys. However, many of these spectra have low S/N (from 15 to 25 per pixel), such that they pose problems for classical spectral analysis pipelines and therefore alternative ways to tap into these large datasets need to be devised. We aim to leverage the versatility/capabilities of machine learning techniques for supercharged stellar parametrization, by combining Gaia RVS spectra with the full set of Gaia products and high-resolution, high-quality spectroscopic reference data sets. We develop a hybrid Convolutional Neural-Network (CNN) which combines the Gaia DR3 RVS spectra, photometry (G, Bp, Rp), parallaxes, and XP coefficients to derive atmospheric parameters (Teff, log(g), and overall [M/H]) and chemical abundances ([Fe/H] and [$\alpha$/M]). We trained the CNN with a high-quality training sample based on APOGEE DR17 labels. With this CNN, we derived homogeneous atmospheric parameters and abundances for 841300 stars, that remarkably compared to external data-sets. The CNN is robust against noise in the RVS data, and very precise labels are derived down to S/N=15. We managed to characterize the [$\alpha$/M]-[M/H] bimodality from the inner regions to the outer parts of the Milky Way, which has never been done using RVS spectra or similar datasets. This work is the first to combine machine-learning with such diverse datasets (spectroscopy, astrometry, and photometry), and paves the way for the large scale machine-learning analysis of Gaia-RVS spectra from future data releases.Comment: 24 pages, 24 figures, submitted to A&

The chemical composition of nearby young associations: s-process element abundances in AB Doradus, Carina-Near, and Ursa Major

Recently, several studies have shown that young, open clusters are characterised by a considerable over-abundance in their barium content. In particular, D'Orazi et al. (2009) reported that in some younger clusters [Ba/Fe] can reach values as high as ~0.6 dex. The work also identified the presence of an anti-correlation between [Ba/Fe] and cluster age. For clusters in the age range ~4.5 Gyr-500 Myr, this is best explained by assuming a higher contribution from low-mass asymptotic giant branch stars to the Galactic chemical enrichment. The purpose of this work is to investigate the ubiquity of the barium over-abundance in young stellar clusters. We analysed high-resolution spectroscopic data, focusing on the s-process elemental abundance for three nearby young associations, i.e. AB Doradus, Carina-Near, and Ursa Major. The clusters have been chosen such that their age spread would complement the D'Orazi et al. (2009) study. We find that while the s-process elements Y, Zr, La, and Ce exhibit solar ratios in all three associations, Ba is over-abundant by ~0.2 dex. Current theoretical models can not reproduce this abundance pattern, thus we investigate whether this unusually large Ba content might be related to chromospheric effects. Although no correlation between [Ba/Fe] and several activity indicators seems to be present, we conclude that different effects could be at work which may (directly or indirectly) be related to the presence of hot stellar chromospheres.Comment: Accepted for publication in MNRA

The Gaia-ESO Survey: {\alpha}-abundances of metal-poor stars

We performed a detailed study of the ratio of low-{\alpha} to high-{\alpha} stars in the Galactic halo as observed by the Gaia-ESO Survey. Using a sample of 381 metal-poor stars from the second internal data release, we found that the value of this ratio did not show evidence of systematic trends as a function of metallicity, surface gravity, Galactic latitude, Galactic longitude, height above the Galactic plane, and Galactocentric radius. We conclude that the {\alpha}-poor/{\alpha}-rich value of 0.28 $\pm$ 0.08 suggests that in the inner halo, the larger portion of stars were formed in a high star formation rate environment, and about 15% of the metal-poor stars originated from much lower star formation rate environments

The Gaia-ESO Survey: α-abundances of metal-poor stars

We performed a detailed study of the ratio of low-{\alpha} to high-{\alpha} stars in the Galactic halo as observed by the Gaia-ESO Survey. Using a sample of 381 metal-poor stars from the second internal data release, we found that the value of this ratio did not show evidence of systematic trends as a function of metallicity, surface gravity, Galactic latitude, Galactic longitude, height above the Galactic plane, and Galactocentric radius. We conclude that the {\alpha}-poor/{\alpha}-rich value of 0.28 $\pm$ 0.08 suggests that in the inner halo, the larger portion of stars were formed in a high star formation rate environment, and about 15% of the metal-poor stars originated from much lower star formation rate environments