IPD—the Immuno Polymorphism Database

The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors; IPD-MHC, a database of sequences of the Major Histocompatibility Complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. Those sections with similar data, such as IPD-KIR and IPD-MHC share the same database structure. The sharing of a common database structure makes it easier to implement common tools for data submission and retrieval. The data are currently available online from the website and ftp directory; files will also be made available in different formats to download from the website and ftp server. The data will also be included in SRS, BLAST and FASTA search engines at the European Bioinformatics Institute

Cool Companions to White Dwarfs from the 2MASS Second Incremental Data Release

We present near-infrared magnitudes for all white dwarfs (selected from the catalog of McCook & Sion) contained in the 2 Micron All Sky Survey Second Incremental Data Release(2MASS 2IDR). We show that the near-IR color-color diagram is an effective means of identifying candidate binary stars containing a WD and a low mass main sequence star. The loci of single WDs and WD + red dwarf binaries occupy distinct regions of the near-IR color-color diagram. We recovered all known unresolved WD + red dwarf binaries located in the 2IDR sky coverage, and also identified as many new candidate binaries (47 new candidates out of 95 total). Using observational near-IR data for WDs and M-L dwarfs, we have compared a sample of simulated WD + red dwarf binaries with our 2MASS data. The colors of the simulated binaries are dominated by the low mass companion through the late-M to early-L spectral types. As the spectral type of the companion becomes progressively later, however, the colors of unresolved binaries become progressively bluer. Binaries containing the lowest mass companions will be difficult to distinguish from single WDs solely on the basis of their near-IR colors.Comment: 18 pages, including 2 figures, accepted for publication in Ap

IPD-MHC 2.0:An improved inter-species database for the study of the major histocompatibility complex

The IPD-MHC Database project (http://www.ebi.ac.uk/ipd/mhc/) collects and expertly curates sequences of the major histocompatibility complex from non-human species and provides the infrastructure and tools to enable accurate analysis. Since the first release of the database in 2003, IPD-MHC has grown and currently hosts a number of specific sections, with more than 7000 alleles from 70 species, including non-human primates, canines, felines, equids, ovids, suids, bovins, salmonids and murids. These sequences are expertly curated and made publicly available through an open access website. The IPD-MHC Database is a key resource in its field, and this has led to an average of 1500 unique visitors and more than 5000 viewed pages per month. As the database has grown in size and complexity, it has created a number of challenges in maintaining and organizing information, particularly the need to standardize nomenclature and taxonomic classification, while incorporating new allele submissions. Here, we describe the latest database release, the IPD-MHC 2.0 and discuss planned developments. This release incorporates sequence updates and new tools that enhance database queries and improve the submission procedure by utilizing common tools that are able to handle the varied requirements of each MHC-group

First NuSTAR Limits on Quiet Sun Hard X-Ray Transient Events

We present the first results of a search for transient hard X-ray (HXR) emission in the quiet solar corona with the \textit{Nuclear Spectroscopic Telescope Array} (\textit{NuSTAR}) satellite. While \textit{NuSTAR} was designed as an astrophysics mission, it can observe the Sun above 2~keV with unprecedented sensitivity due to its pioneering use of focusing optics. \textit{NuSTAR} first observed quiet Sun regions on 2014 November 1, although out-of-view active regions contributed a notable amount of background in the form of single-bounce (unfocused) X-rays. We conducted a search for quiet Sun transient brightenings on time scales of 100 s and set upper limits on emission in two energy bands. We set 2.5--4~keV limits on brightenings with time scales of 100 s, expressed as the temperature T and emission measure EM of a thermal plasma. We also set 10--20~keV limits on brightenings with time scales of 30, 60, and 100 s, expressed as model-independent photon fluxes. The limits in both bands are well below previous HXR microflare detections, though not low enough to detect events of equivalent T and EM as quiet Sun brightenings seen in soft X-ray observations. We expect future observations during solar minimum to increase the \textit{NuSTAR} sensitivity by over two orders of magnitude due to higher instrument livetime and reduced solar background.Comment: 11 pages, 7 figures; accepted for publication in The Astrophysical Journa

The First Focused Hard X-ray Images of the Sun with NuSTAR

We present results from the the first campaign of dedicated solar observations undertaken by the \textit{Nuclear Spectroscopic Telescope ARray} ({\em NuSTAR}) hard X-ray telescope. Designed as an astrophysics mission, {\em NuSTAR} nonetheless has the capability of directly imaging the Sun at hard X-ray energies ($>$3~keV) with an increase in sensitivity of at least two magnitude compared to current non-focusing telescopes. In this paper we describe the scientific areas where \textit{NuSTAR} will make major improvements on existing solar measurements. We report on the techniques used to observe the Sun with \textit{NuSTAR}, their limitations and complications, and the procedures developed to optimize solar data quality derived from our experience with the initial solar observations. These first observations are briefly described, including the measurement of the Fe K-shell lines in a decaying X-class flare, hard X-ray emission from high in the solar corona, and full-disk hard X-ray images of the Sun.Comment: 11 pages, accepted to Ap

Permafrost Landscape History Shapes Fluvial Chemistry, Ecosystem Carbon Balance, and Potential Trajectories of Future Change

Intensifying permafrost thaw alters carbon cycling by mobilizing large amounts of terrestrial substrate into aquatic ecosystems. Yet, few studies have measured aquatic carbon fluxes and constrained drivers of ecosystem carbon balance across heterogeneous Arctic landscapes. Here, we characterized hydrochemical and landscape controls on fluvial carbon cycling, quantified fluvial carbon fluxes, and estimated fluvial contributions to ecosystem carbon balance across 33 watersheds in four ecoregions in the continuous permafrost zone of the western Canadian Arctic: unglaciated uplands, ice-rich moraine, and organic-rich lowlands and till plains. Major ions, stable isotopes, and carbon speciation and fluxes revealed patterns in carbon cycling across ecoregions defined by terrain relief and accumulation of organics. In previously unglaciated mountainous watersheds, bicarbonate dominated carbon export (70% of total) due to chemical weathering of bedrock. In lowland watersheds, where soil organic carbon stores were largest, lateral transport of dissolved organic carbon (50%) and efflux of biotic CO2 (25%) dominated. In watersheds affected by thaw-induced mass wasting, erosion of ice-rich tills enhanced chemical weathering and increased particulate carbon fluxes by two orders of magnitude. From an ecosystem carbon balance perspective, fluvial carbon export in watersheds not affected by thaw-induced wasting was, on average, equivalent to 6%–16% of estimated net ecosystem exchange (NEE). In watersheds affected by thaw-induced wasting, fluvial carbon export approached 60% of NEE. Because future intensification of thermokarst activity will amplify fluvial carbon export, determining the fate of carbon across diverse northern landscapes is a priority for constraining trajectories of permafrost region ecosystem carbon balance

Evidence of significant energy input in the late phase of a solar flare from NuSTAR x-ray observations

We present observations of the occulted active region AR 12222 during the third Nuclear Spectroscopic Telescope ARray (NuSTAR) solar campaign on 2014 December 11, with concurrent Solar Dynamics Observatory (SDO)/AIA and FOXSI-2 sounding rocket observations. The active region produced a medium-size solar flare 1 day before the observations, at ∼18 UT on 2014 December 10, with the post-flare loops still visible at the time of NuSTAR observations. The time evolution of the source emission in the SDO/AIA 335 Å channel reveals the characteristics of an extreme-ultraviolet late-phase event, caused by the continuous formation of new post-flare loops that arch higher and higher in the solar corona. The spectral fitting of NuSTAR observations yields an isothermal source, with temperature 3.8\ndash4.6 MK, emission measure (0.3\ndash1.8) × 10⁴⁶ cm‑3, and density estimated at (2.5\ndash6.0) × 10⁸ cm‑3. The observed AIA fluxes are consistent with the derived NuSTAR temperature range, favoring temperature values in the range of 4.0\ndash4.3 MK. By examining the post-flare loops\rsquo cooling times and energy content, we estimate that at least 12 sets of post-flare loops were formed and subsequently cooled between the onset of the flare and NuSTAR observations, with their total thermal energy content an order of magnitude larger than the energy content at flare peak time. This indicates that the standard approach of using only the flare peak time to derive the total thermal energy content of a flare can lead to a large underestimation of its value

The first X-ray imaging spectroscopy of quiescent solar active regions with NuSTAR

We present the first observations of quiescent active regions (ARs) using NuSTAR, a focusing hard X-ray telescope capable of studying faint solar emission from high temperature and non-thermal sources. We analyze the first directly imaged and spectrally resolved X-rays above 2~keV from non-flaring ARs, observed near the west limb on 2014 November 1. The NuSTAR X-ray images match bright features seen in extreme ultraviolet and soft X-rays. The NuSTAR imaging spectroscopy is consistent with isothermal emission of temperatures 3.1 − 4.4~MK and emission measures 1 – 8 × 10^(46)~cm^(−3). We do not observe emission above 5~MK but our short effective exposure times restrict the spectral dynamic range. With few counts above 6~keV, we can place constraints on the presence of an additional hotter component between 5 and 12~MK of ∼ 10^(46)cm^(−3) and ∼10^(43) cm^(−3), respectively, at least an order of magnitude stricter than previous limits. With longer duration observations and a weakening solar cycle (resulting in an increased livetime), future NuSTAR observations will have sensitivity to a wider range of temperatures as well as possible non-thermal emission