A Study of the Near-Ultraviolet Spectrum of Vega

UV, optical, and near-IR spectra of Vega have been combined to test our understanding of stellar atmospheric opacities, and to examine the possibility of constraining chemical abundances from low-resolution UV fluxes. We have carried out a detailed analysis assuming Local Thermodynamic Equilibrium (LTE) to identify the most important contributors to the UV continuous opacity: H, H$^{-}$, C I, and Si II. Our analysis also assumes that Vega is spherically symmetric and its atmosphere is well described with the plane parallel approximation. Comparing observations and computed fluxes we have been able to discriminate between two different flux scales that have been proposed, the IUE-INES and the HST scales, favoring the latter. The effective temperature and angular diameter derived from the analysis of observed optical and near-UV spectra are in very good agreement with previous determinations based on different techniques. The silicon abundance is poorly constrained by the UV observations of the continuum and strong lines, but the situation is more favorable for carbon and the abundances inferred from the UV continuum and optical absorption lines are in good agreement. Some spectral intervals in the UV spectrum of Vega that the calculations do not reproduce well are likely affected by deviations from LTE, but we conclude that our understanding of UV atmospheric opacities is fairly complete for early A-type stars.Comment: 13 pages, 9 figures, to be published in Ap

Chemical Abundances in Field Red Giants from High-Resolution H-Band Spectra using the APOGEE Spectral Linelist

High-resolution H-band spectra of five bright field K, M, and MS giants, obtained from the archives of the Kitt Peak National Observatory (KPNO) Fourier Transform Spectrometer (FTS), are analyzed to determine chemical abundances of 16 elements. The abundances were derived via spectrum synthesis using the detailed linelist prepared for the SDSS III Apache Point Galactic Evolution Experiment (APOGEE), which is a high-resolution near-infrared spectroscopic survey to derive detailed chemical abundance distributions and precise radial velocities for 100,000 red giants sampling all Galactic stellar populations. Measured chemical abundances include the cosmochemically important isotopes 12C, 13C, 14N, and 16O, along with Mg, Al, Si, K, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, and Cu. A comparison of the abundances derived here with published values for these stars reveals consistent results to ~0.1 dex. The APOGEE spectral region and linelist is, thus, well-suited for probing both Galactic chemical evolution, as well as internal nucleosynthesis and mixing in populations of red giants using high-resolution spectroscopy.Comment: Accepted for publication in The Astrophysical Journal. 42 pages, 12 figure

Spectroscopic Observations of Convective Patterns in the Atmospheres of Metal-Poor Stars

Convective line asymmetries in the optical spectrum of two metal-poor stars, Gmb1830 and HD140283, are compared to those observed for solar metallicity stars. The line bisectors of the most metal-poor star, the subgiant HD140283, show a significantly larger velocity span that the expectations for a solar-metallicity star of the same spectral type and luminosity class. The enhanced line asymmetries are interpreted as the signature of the lower metal content, and therefore opacity, in the convective photospheric patterns. These findings point out the importance of three-dimensional convective velocity fields in the interpretation of the observed line asymmetries in metal-poor stars, and in particular, urge for caution when deriving isotopic ratios from observed line shapes and shifts using one-dimensional model atmospheres. The mean line bisector of the photospheric atomic lines is compared with those measured for the strong Mg I b1 and b2 features. The upper part of the bisectors are similar, and assuming they overlap, the bottom end of the stronger lines, which are formed higher in the atmosphere, goes much further to the red. This is in agreement with the expected decreasing of the convective blue-shifts in upper atmospheric layers, and compatible with the high velocity redshifts observed in the chromosphere, transition region, and corona of late-type stars.Comment: 27 pages, LaTeX; 10 Figures (14 PostScript files); to be published in The Astrophysical Journa

Validation of a DNA methylation microarray for 285,000 CpG sites in the mouse genome

Mouse has been extensively used as a model organism in many studies to characterize biological pathways and drug effects and to mimic human diseases. Similar DNA sequences between both species facilitate these types of experiments. However, much less is known about the mouse epigenome, particularly for DNA methylation. Progress in delivering mouse DNA methylomes has been slow due to the currently available time-consuming and expensive methodologies. Following the great acceptance of the human DNA methylation microarrays, we have herein validated a newly developed DNA methylation microarray (Infinium Mouse Methylation BeadChip) that interrogates 280,754 unique CpG sites within the mouse genome. The CpGs included in the platform cover CpG Islands, shores, shelves and open sea sequences, and loci surrounding transcription start sites and gene bodies. From a functional standpoint, mouse ENCODE representative DNase hypersensitivity sites (rDHSs) and candidate cis-Regulatory Elements (cCREs) are also included. Herein, we show that the profiled mouse DNA methylation microarray provides reliable values among technical replicates; matched results from fresh frozen versus formalin-fixed samples; detects hemimethylated X-chromosome and imprinted CpG sites; and is able to determine CpG methylation changes in mouse cell lines treated with a DNA demethylating agent or upon genetic disruption of a DNA methyltransferase. Most important, using unsupervised hierarchical clustering and t-SNE approaches, the platform is able to classify all types of normal mouse tissues and organs. These data underscore the great features of the assessed microarray to obtain comprehensive DNA methylation profiles of the mouse genome.We thank the CERCA Programme/Generalitat de Catalunya for institutional support. This work was supported by the Health Department PERIS-project no. SLT/002/16/00374 and AGAUR-project no. 2017SGR1080 of the Catalan Government (Generalitat de Catalunya); Ministerio de Ciencia e Innovación (MCI), Agencia Estatal de Investigación (AEI), and European Regional Development Fund (ERDF) project no. RTI2018-094049-B-I00 and PID2020-117284RB-I00; the Cellex Foundation; Marie Sklodowska-Curie Fellowship no. 895979 from the European Commission (BNV); and ‘la Caixa’ Banking Foundation (LCF/PR/GN18/51140001).Peer ReviewedPostprint (published version

the SDSS-III APOGEE Spectral Line List for H-Band Spectroscopy

We present the H-band spectral line lists adopted by the Apache Point Observatory Galactic Evolution Experiment (APOGEE). The APOGEE line lists comprise astrophysical, theoretical, and laboratory sources from the literature, as well as newly evaluated astrophysical oscillator strengths and damping parameters. We discuss the construction of the APOGEE line list, which is one of the critical inputs for the APOGEE Stellar Parameters and Chemical Abundances Pipeline, and present three different versions that have been used at various stages of the project. The methodology for the newly calculated astrophysical line lists is reviewed. The largest of these three line lists contains 134,457 molecular and atomic transitions. In addition to the format adopted to store the data, the line lists are available in MOOG, Synspec, and Turbospectrum formats. The limitations of the line lists along with guidance for its use on different spectral types are discussed. We also present a list of H-band spectral features that are either poorly represented or completely missing in our line list. This list is based on the average of a large number of spectral fit residuals for APOGEE observations spanning a wide range of stellar parameters.Alfred P. Sloan FoundationNational Science FoundationU.S. Department of Energy Office of ScienceJanos Bolyai Research Scholarship of the Hungarian Academy of SciencesSpanish Ministry of Economy and Competitiveness AYA-2011-27754, AYA-2014-58082-PRSF 14-50-00043McDonald Observator

Culture expansion of CAR T cells results in aberrant DNA methylation that is associated with adverse clinical outcome

Chimeric antigen receptor (CAR) T cells provide new perspectives for treatment of hematological malignancies. Manufacturing of these cellular products includes culture expansion procedures, which may affect cellular integrity and therapeutic outcome. In this study, we investigated culture-associated epigenetic changes in CAR T cells and found continuous gain of DNAm, particularly within genes that are relevant for T cell function. Hypermethylation in many genes, such as TCF7, RUNX1, and TOX, was reflected by transcriptional downregulation. 332 CG dinucleotides (CpGs) showed an almost linear gain in methylation with cell culture time, albeit neighboring CpGs were not coherently regulated on the same DNA strands. An epigenetic signature based on 14 of these culture-associated CpGs predicted cell culture time across various culture conditions. Notably, even in CAR T cell products of similar culture time higher DNAm levels at these CpGs were associated with significantly reduced long-term survival post transfusion. Our data demonstrate that cell culture expansion of CAR T cells evokes DNA hypermethylation at specific sites in the genome and the signature may also reflect loss of potential in CAR T cell products. Hence, reduced cultivation periods are beneficial to avoid dysfunctional methylation programs that seem to be associated with worse therapeutic outcome.This research was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation − 363055819/GRK2415; WA1706/11–1; WA 1706/12–2 within CRU344/417911533; WA1706/14–1; and SFB 1506/1); and the ForTra gGmbH für Forschungstransfer der Else Kröner-Fresenius-Stiftung. Furthermore, we thank CERCA Programme / Generalitat de Catalunya for institutional support. The research leading to these results has received funding from MCIN/AEI/10.13039/501100011033 and European Commission “Next GenerationEU”/PRTR (PDC2022–133476-I00); Ministry of Research and Universities of the Catalan Government (2021 PROD 00020); and the Cellex Foundation.Peer ReviewedPostprint (published version

Chemical abundance gradients from open clusters in the Milky Way disk: results from the APOGEE survey

Metallicity gradients provide strong constraints for understanding the chemical evolution of the Galaxy. We report on radial abundance gradients of Fe, Ni, Ca, Si, and Mg obtained from a sample of 304 red-giant members of 29 disk open clusters, mostly concentrated at galactocentric distances between ~8 - 15 kpc, but including two open clusters in the outer disk. The observations are from the APOGEE survey. The chemical abundances were derived automatically by the ASPCAP pipeline and these are part of the SDSS III Data Release 12. The gradients, obtained from least squares fits to the data, are relatively flat, with slopes ranging from -0.026 to -0.033 dex/kpc for the alpha-elements [O/H], [Ca/H], [Si/H] and [Mg/H] and -0.035 dex/kpc and -0.040 dex/kpc for [Fe/H] and [Ni/H], respectively. Our results are not at odds with the possibility that metallicity ([Fe/H]) gradients are steeper in the inner disk (R_GC ~7 - 12 kpc) and flatter towards the outer disk. The open cluster sample studied spans a significant range in age. When breaking the sample into age bins, there is some indication that the younger open cluster population in our sample (log age < 8.7) has a flatter metallicity gradient when compared with the gradients obtained from older open clusters.Comment: 4 pages, 3 figures, To appear in Astronomische Nachrichten, special issue "Reconstruction the Milky Way's History: Spectroscopic surveys, Asteroseismology and Chemo-dynamical models", Guest Editors C. Chiappini, J. Montalb\'an, and M. Steffen, AN 2016 (in press)

BACCHUS Analysis of Weak Lines in APOGEE Spectra (BAWLAS)

Elements with weak and blended spectral features in stellar spectra are challenging to measure and require specialized analysis methods to precisely measure their chemical abundances. In this work, we have created a catalog of approximately 120,000 giants with high signal-to-noise APOGEE DR17 spectra, for which we explore weak and blended species to measure Na, P, S, V, Cu, Ce, and Nd abundances and $^{12}$C/$^{13}$C isotopic ratios. We employ an updated version of the BACCHUS (Brussels Automatic Code for Characterizing High accUracy Spectra) code to derive these abundances using the stellar parameters measured by APOGEE's DR17 ASPCAP pipeline, quality flagging to identify suspect spectral lines, and a prescription for upper limits. Combined these allow us to provide our BACCHUS Analysis of Weak Lines in APOGEE Spectra (BAWLAS) catalog of precise chemical abundances for these weak and blended species that agrees well with literature and improves upon APOGEE abundances for these elements, some of which are unable to be measured with APOGEE's current, grid-based approach without computationally expensive expansions. This new catalog can be used alongside APOGEE and provide measurements for many scientific applications ranging from nuclear physics to Galactic chemical evolution and Milky Way population studies. To illustrate this we show some examples of uses for this catalog, such as, showing that we observe stars with enhanced s-process abundances or that we can use the our $^{12}$C/$^{13}$C ratios to explore extra mixing along the red giant branch.Comment: 49 Pages, 30 figures, 7 Tables. Accepted for publishing in The Astrophysical Journal Supplement Series. The BAWLAS chemical abundance catalog to be made publicly available as an SDSS DR17 value-added catalog: https://www.sdss.org/dr17/data_access/value-added-catalogs

A Consistency Test of Spectroscopic Gravities for Late-Type Stars

Chemical analyses of late-type stars are usually carried out following the classical recipe: LTE line formation and homogeneous, plane-parallel, flux-constant, and LTE model atmospheres. We review different results in the literature that have suggested significant inconsistencies in the spectroscopic analyses, pointing out the difficulties in deriving independent estimates of the stellar fundamental parameters and hence,detecting systematic errors. The trigonometric parallaxes measured by the HIPPARCOS mission provide accurate appraisals of the stellar surface gravity for nearby stars, which are used here to check the gravities obtained from the photospheric iron ionization balance. We find an approximate agreement for stars in the metallicity range -1 <= [Fe/H] <= 0, but the comparison shows that the differences between the spectroscopic and trigonometric gravities decrease towards lower metallicities for more metal-deficient dwarfs (-2.5 <= [Fe/H] <= -1.0), which casts a shadow upon the abundance analyses for extreme metal-poor stars that make use of the ionization equilibrium to constrain the gravity. The comparison with the strong-line gravities derived by Edvardsson (1988) and Fuhrmann (1998a) confirms that this method provides systematically larger gravities than the ionization balance. The strong-line gravities get closer to the physical ones for the stars analyzed by Fuhrmann, but they are even further away than the iron ionization gravities for the stars of lower gravities in Edvardsson's sample. The confrontation of the deviations of the iron ionization gravities in metal-poor stars reported here with departures from the excitation balance found in the literature, show that they are likely to be induced by the same physical mechanism(s).Comment: AAS LaTeX v4.0, 35 pages, 10 PostScript files; to appear in The Astrophysical Journa

Non-LTE Model Atmospheres for Late-Type Stars II. Restricted NLTE Calculations for a Solar-Like Atmosphere

We test our knowledge of the atomic opacity in the solar UV spectrum. Using the atomic data compiled in Paper I from modern, publicly available, databases, we perform calculations that are confronted with space-based observations of the Sun. At wavelengths longer than about 260 nm, LTE modeling can reproduce quite closely the observed fluxes; uncertainties in the atomic line data account fully for the differences between calculated and observed fluxes. At shorter wavelengths, departures from LTE appear to be important, as our LTE and restricted NLTE calculations differ. Analysis of visible-near infrared Na I and O I lines, two species that produce a negligible absorption in the UV, shows that observed departures from LTE for theses species can be reproduced very accurately with restricted (fixed atmospheric structure) NLTE calculations.Comment: 13 pages, 11 figures, to appear in Ap