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

APOGEE DR14/DR15 Abundances in the Inner Milky Way

We present an overview of the distributions of 11 elemental abundances in the Milky Way's inner regions, as traced by APOGEE stars released as part of SDSS Data Release 14/15 (DR14/DR15), including O, Mg, Si, Ca, Cr, Mn, Co, Ni, Na, Al, and K. This sample spans ~4000 stars with R_GC<4 kpc, enabling the most comprehensive study to date of these abundances and their variations within the innermost few kiloparsecs of the Milky Way. We describe the observed abundance patterns ([X/Fe]-[Fe/H]), compare to previous literature results and to patterns in stars at the solar Galactic radius, and discuss possible trends with DR14/DR15 effective temperatures. We find that the position of the [Mg/Fe]-[Fe/H] "knee" is nearly constant with R_GC, indicating a well-mixed star-forming medium or high levels of radial migration in the early inner Galaxy. We quantify the linear correlation between pairs of elements in different subsamples of stars and find that these relationships vary; some abundance correlations are very similar between the alpha-rich and alpha-poor stars, but others differ significantly, suggesting variations in the metallicity dependencies of certain supernova yields. These empirical trends will form the basis for more detailed future explorations and for the refinement of model comparison metrics. That the inner Milky Way abundances appear dominated by a single chemical evolutionary track and that they extend to such high metallicities underscore the unique importance of this part of the Galaxy for constraining the ingredients of chemical evolution modeling and for improving our understanding of the evolution of the Galaxy as a whole.Comment: Submitted to AAS Journals; revised after referee repor

Target Selection for the SDSS-IV APOGEE-2 Survey

APOGEE-2 is a high-resolution, near-infrared spectroscopic survey observing roughly 300,000 stars across the entire sky. It is the successor to APOGEE and is part of the Sloan Digital Sky Survey IV (SDSS-IV). APOGEE-2 is expanding upon APOGEE's goals of addressing critical questions of stellar astrophysics, stellar populations, and Galactic chemodynamical evolution using (1) an enhanced set of target types and (2) a second spectrograph at Las Campanas Observatory in Chile. APOGEE-2 is targeting red giant branch (RGB) and red clump (RC) stars, RR Lyrae, low-mass dwarf stars, young stellar objects, and numerous other Milky Way and Local Group sources across the entire sky from both hemispheres. In this paper, we describe the APOGEE-2 observational design, target selection catalogs and algorithms, and the targeting-related documentation included in the SDSS data releases.Comment: 19 pages, 6 figures. Accepted to A

Calibrations of Atmospheric Parameters Obtained from the First Year of SDSS-III APOGEE Observations

The SDSS-III Apache Point Observatory Galactic Evolution Experiment (APOGEE) is a three year survey that is collecting 100,000 high-resolution spectra in the near-IR across multiple Galactic populations. To derive stellar parameters and chemical compositions from this massive data set, the APOGEE Stellar Parameters and Chemical Abundances Pipeline (ASPCAP) has been developed. Here, we describe empirical calibrations of stellar parameters presented in the first SDSS-III APOGEE data release (DR10). These calibrations were enabled by observations of 559 stars in 20 globular and open clusters. The cluster observations were supplemented by observations of stars in NASA's Kepler field that have well determined surface gravities from asteroseismic analysis. We discuss the accuracy and precision of the derived stellar parameters, considering especially effective temperature, surface gravity, and metallicity; we also briefly discuss the derived results for the abundances of the alpha-elements, carbon, and nitrogen. Overall, we find that ASPCAP achieves reasonably accurate results for temperature and metallicity, but suffers from systematic errors in surface gravity. We derive calibration relations that bring the raw ASPCAP results into better agreement with independently determined stellar parameters. The internal scatter of ASPCAP parameters within clusters suggests that, metallicities are measured with a precision better than 0.1 dex, effective temperatures better than 150 K, and surface gravities better than 0.2 dex. The understanding provided by the clusters and Kepler giants on the current accuracy and precision will be invaluable for future improvements of the pipeline.Comment: 40 pages, 15 figures, 4 tables, accepted to A

IN-SYNC. V. Stellar kinematics and dynamics in the Orion A Molecular Cloud

The kinematics and dynamics of young stellar populations enable us to test theories of star formation. With this aim, we continue our analysis of the SDSS-III/APOGEE IN-SYNC survey, a high resolution near infrared spectroscopic survey of young clusters. We focus on the Orion A star-forming region, for which IN-SYNC obtained spectra of $\sim2700$ stars. In Paper IV we used these data to study the young stellar population. Here we study the kinematic properties through radial velocities ($v_r$). The young stellar population remains kinematically associated with the molecular gas, following a $\sim10\:{\rm{km\:s}}^{-1}$ gradient along filament. However, near the center of the region, the $v_r$ distribution is slightly blueshifted and asymmetric; we suggest that this population, which is older, is slightly in foreground. We find evidence for kinematic subclustering, detecting statistically significant groupings of co-located stars with coherent motions. These are mostly in the lower-density regions of the cloud, while the ONC radial velocities are smoothly distributed, consistent with it being an older, more dynamically evolved cluster. The velocity dispersion $\sigma_v$ varies along the filament. The ONC appears virialized, or just slightly supervirial, consistent with an old dynamical age. Here there is also some evidence for on-going expansion, from a $v_r$--extinction correlation. In the southern filament, $\sigma_v$ is $\sim2$--$3$ times larger than virial in the L1641N region, where we infer a superposition along the line of sight of stellar sub-populations, detached from the gas. On the contrary, $\sigma_v$ decreases towards L1641S, where the population is again in agreement with a virial state.Comment: 14 pages, 13 figures, ApJ accepte

A Database and Evaluation for Classification of RNA Molecules Using Graph Methods

In this paper, we introduce a new graph dataset based on the representation of RNA. The RNA dataset includes 3178 RNA chains which are labelled in 8 classes according to their reported biological functions. The goal of this database is to provide a platform for investigating the classication of RNA using graph-based methods. The molecules are represented by graphs representing the sequence and base-pairs of the RNA, with a number of labelling schemes using base labels and local shape. We report the results of a number of state-of-the-art graph based methods on this dataset as a baseline comparison and investigate how these methods can be used to categorise RNA molecules on their type and functions. The methods applied are Weisfeiler Lehman and optimal assignment kernels, shortest paths kernel and the all paths and cycle methods. We also compare to the standard Needleman-Wunsch algorithm used in bioinformatics for DNA and RNA comparison, and demonstrate the superiority of graph kernels even on a string representation. The highest classication rate is obtained by the WL-OA algorithm using base labels and base-pair connections

Target Selection for the Apache Point Observatory Galactic Evolution Experiment (APOGEE)

The Apache Point Observatory Galactic Evolution Experiment (APOGEE) is a high-resolution infrared spectroscopic survey spanning all Galactic environments (i.e., bulge, disk, and halo), with the principal goal of constraining dynamical and chemical evolution models of the Milky Way. APOGEE takes advantage of the reduced effects of extinction at infrared wavelengths to observe the inner Galaxy and bulge at an unprecedented level of detail. The survey's broad spatial and wavelength coverage enables users of APOGEE data to address numerous Galactic structure and stellar populations issues. In this paper we describe the APOGEE targeting scheme and document its various target classes to provide the necessary background and reference information to analyze samples of APOGEE data with awareness of the imposed selection criteria and resulting sample properties. APOGEE's primary sample consists of ~100,000 red giant stars, selected to minimize observational biases in age and metallicity. We present the methodology and considerations that drive the selection of this sample and evaluate the accuracy, efficiency, and caveats of the selection and sampling algorithms. We also describe additional target classes that contribute to the APOGEE sample, including numerous ancillary science programs, and we outline the targeting data that will be included in the public data releases.Comment: Accepted to AJ. 31 pages, 11 figure