18 research outputs found

    The Seventeenth Data Release of the Sloan Digital Sky Surveys: Complete Release of MaNGA, MaStar and APOGEE-2 Data

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    This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library (MaStar) accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) survey which publicly releases infra-red spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the sub-survey Time Domain Spectroscopic Survey (TDSS) data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey (SPIDERS) sub-survey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated Value Added Catalogs (VACs). This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper (MWM), Local Volume Mapper (LVM) and Black Hole Mapper (BHM) surveys

    SDSS-III: Massive Spectroscopic Surveys of the Distant Universe, the Milky Way Galaxy, and Extra-Solar Planetary Systems

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    Building on the legacy of the Sloan Digital Sky Survey (SDSS-I and II), SDSS-III is a program of four spectroscopic surveys on three scientific themes: dark energy and cosmological parameters, the history and structure of the Milky Way, and the population of giant planets around other stars. In keeping with SDSS tradition, SDSS-III will provide regular public releases of all its data, beginning with SDSS DR8 (which occurred in Jan 2011). This paper presents an overview of the four SDSS-III surveys. BOSS will measure redshifts of 1.5 million massive galaxies and Lya forest spectra of 150,000 quasars, using the BAO feature of large scale structure to obtain percent-level determinations of the distance scale and Hubble expansion rate at z<0.7 and at z~2.5. SEGUE-2, which is now completed, measured medium-resolution (R=1800) optical spectra of 118,000 stars in a variety of target categories, probing chemical evolution, stellar kinematics and substructure, and the mass profile of the dark matter halo from the solar neighborhood to distances of 100 kpc. APOGEE will obtain high-resolution (R~30,000), high signal-to-noise (S/N>100 per resolution element), H-band (1.51-1.70 micron) spectra of 10^5 evolved, late-type stars, measuring separate abundances for ~15 elements per star and creating the first high-precision spectroscopic survey of all Galactic stellar populations (bulge, bar, disks, halo) with a uniform set of stellar tracers and spectral diagnostics. MARVELS will monitor radial velocities of more than 8000 FGK stars with the sensitivity and cadence (10-40 m/s, ~24 visits per star) needed to detect giant planets with periods up to two years, providing an unprecedented data set for understanding the formation and dynamical evolution of giant planet systems. (Abridged)Comment: Revised to version published in The Astronomical Journa

    The 16th Data Release of the Sloan Digital Sky Surveys: First Release from the APOGEE-2 Southern Survey and Full Release of eBOSS Spectra

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    This paper documents the 16th data release (DR16) from the Sloan Digital Sky Surveys (SDSS), the fourth and penultimate from the fourth phase (SDSS-IV). This is the first release of data from the Southern Hemisphere survey of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2); new data from APOGEE-2 North are also included. DR16 is also notable as the final data release for the main cosmological program of the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), and all raw and reduced spectra from that project are released here. DR16 also includes all the data from the Time Domain Spectroscopic Survey and new data from the SPectroscopic IDentification of ERosita Survey programs, both of which were co-observed on eBOSS plates. DR16 has no new data from the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey (or the MaNGA Stellar Library "MaStar"). We also preview future SDSS-V operations (due to start in 2020), and summarize plans for the final SDSS-IV data release (DR17)

    The 16th Data Release of the Sloan Digital Sky Surveys : First Release from the APOGEE-2 Southern Survey and Full Release of eBOSS Spectra

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    This paper documents the 16th data release (DR16) from the Sloan Digital Sky Surveys (SDSS), the fourth and penultimate from the fourth phase (SDSS-IV). This is the first release of data from the Southern Hemisphere survey of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2); new data from APOGEE-2 North are also included. DR16 is also notable as the final data release for the main cosmological program of the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), and all raw and reduced spectra from that project are released here. DR16 also includes all the data from the Time Domain Spectroscopic Survey and new data from the SPectroscopic IDentification of ERosita Survey programs, both of which were co-observed on eBOSS plates. DR16 has no new data from the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey (or the MaNGA Stellar Library "MaStar"). We also preview future SDSS-V operations (due to start in 2020), and summarize plans for the final SDSS-IV data release (DR17).Peer reviewe

    Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study

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    Introduction: The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. Methods: In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ‚Č•18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. Findings: Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5¬∑0 months (IQR 4¬∑2‚Äď6¬∑3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p&lt;0¬∑0001) and independently associated with COVID-19 status (odds ratio [OR] 2¬∑9 [95% CI 1¬∑5‚Äď5¬∑8]; padjusted=0¬∑0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0¬∑0001; parenchymal abnormalities), brain abnormalities (p&lt;0¬∑0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0¬∑014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4‚Äď10]; mean age of 59¬∑8 years [SD 11¬∑7] with multiorgan abnormalities vs mean age of 52¬∑8 years [11¬∑9] without multiorgan abnormalities; p&lt;0¬∑0001), more likely to have three or more comorbidities (OR 2¬∑47 [1¬∑32‚Äď4¬∑82]; padjusted=0¬∑0059), and more likely to have a more severe acute infection (acute CRP &gt;5mg/L, OR 3¬∑55 [1¬∑23‚Äď11¬∑88]; padjusted=0¬∑025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. Interpretation: After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification

    Structure-Function Studies of Nitrate Reductase Enzymes

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    Nitrate reductase enzymes are a class of molybdenum-based enzymes that undergo a 2-electron redox reaction to reduce nitrate (NO3-) to nitrite (NO2-). This class of enzyme is very important in various geothermal cycles, the most prominent of which is the global nitrogen cycle. There are several types of nitrate reductase based on mechanism and overall structure from organisms such as eukaryotes to bacteria. The focus of this study is the periplasmic nitrate reductase from Campylobacter jejuni and the assimilatory nitrate reductase from Synechococcus elongatus. Both share identical primary coordination spheres at the catalytically essential molybdenum and are predicted to share an overall peptide fold motif. Importantly, for these enzymes, the primary coordination sphere and mechanism are open questions in the community and a focus of this work. Through a series of activity assays and analysis using electron paramagnetic resonance (EPR) spectroscopy, the kinetics, and reactivity of the nitrate reductases were probed in the hope of gaining a better understanding of what affects the reactivity of the Mo center, and what might potentially inhibit the enzyme\u27s activity. Kinetic activity assays using methyl viologen (MV) as an electron donator promoted the turnover of nitrate to nitrate, which allowed for the analysis of active enzymes to obtain the specific activity for both types of nitrate reductase. This assay proved that the synthesis methods of both enzymes were successful in producing active enzymes that could be used in further analysis, and also introduced the possibility that dithionite (DT) is not a good electron donator for these enzymes, but an inhibitor to turnover. Through EPR analysis of NapA, the mechanism behind the conversion of NO3- to NO2- was studied. WT CjNapA underwent turnover and the EPR was obtained before and after, which showed a 6-coordinate structure arising after turnover. This structure aligns with a ‚ÄúSulfur-shift reaction‚ÄĚ, that has been recently proposed in opposition to the previously stated ‚ÄúOxygen-atom reaction‚ÄĚ. This observation gives much more insight into not only the mechanism but also the binding pocket and potential reactivity of these types of enzymes. In addition to understanding the mechanism and reactivity of the enzymes, a new equation to help classify them was formed. This new ‚ÄúRhombicity‚ÄĚ equation was tested for a variety of different molybdenum enzymes, as well as for systems with different transition metals than Mo. This equation helps to classify and quantify the degree of separation of EPR spectra, which allows for better analysis of structure

    Detection and characterization of lung cancer using cell-free DNA fragmentomes

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    Non-invasive approaches for cell-free DNA (cfDNA) assessment provide an opportunity for cancer detection and intervention. Here, we use a machine learning model for detecting tumor-derived cfDNA through genome-wide analyses of cfDNA fragmentation in a prospective study of 365 individuals at risk for lung cancer. We validate the cancer detection model using an independent cohort of 385 non-cancer individuals and 46 lung cancer patients. Combining fragmentation features, clinical risk factors, and CEA levels, followed by CT imaging, detected 94% of patients with cancer across stages and subtypes, including 91% of stage I/II and 96% of stage III/IV, at 80% specificity. Genome-wide fragmentation profiles across ~13,000 ASCL1 transcription factor binding sites distinguished individuals with small cell lung cancer from those with non-small cell lung cancer with high accuracy (AUC‚ÄČ=‚ÄČ0.98). A higher fragmentation score represented an independent prognostic indicator of survival. This approach¬†provides a facile avenue¬†for non-invasive detection of lung cancer

    The Radial Velocity Experiment (RAVE):Second data release

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    We present the second data release of the Radial Velocity Experiment (RAVE), an ambitious spectroscopic survey to measure radial velocities (RVs) and stellar atmosphere parameters of up to one million stars using the 6dF multi-object spectrograph on the 1.2-m UK Schmidt Telescope of the Anglo-Australian Observatory (AAO). It is obtaining medium resolution spectra (median R=7,500) in the Ca-triplet region (8,410--8,795 \AA) for southern hemisphere stars in the magnitude range 9<I<12. Following the first data release (Steinmetz et al. 2006) the current release doubles the sample of published RVs, now containing 51,829 RVs for 49,327 individual stars observed on 141 nights between April 11 2003 and March 31 2005. Comparison with external data sets shows that the new data collected since April 3 2004 show a standard deviation of 1.3 km/s, about twice better than for the first data release. For the first time this data release contains values of stellar parameters from 22,407 spectra of 21,121 individual stars. They were derived by a penalized \chi^2 method using an extensive grid of synthetic spectra calculated from the latest version of Kurucz models. From comparison with external data sets, our conservative estimates of errors of the stellar parameters (for a spectrum with S/N=40) are 400 K in temperature, 0.5 dex in gravity, and 0.2 dex in metallicity. We note however that the internal errors estimated from repeat RAVE observations of 822 stars are at least a factor 2 smaller. We demonstrate that the results show no systematic offsets if compared to values derived from photometry or complementary spectroscopic analyses. The data release includes proper motion and photometric measurements. It can be accessed via the RAVE webpage: http://www.rave-survey.org and through CDS.
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