Measurement of the Oxidation State of Mitochondrial Cytochrome c from the Neocortex of the Mammalian Brain

Diffuse optical remission spectra from the mammalian neocortex at visible wavelengths contain spectral features originating from the mitochondria. A new algorithm is presented, based on analytically relating the first differential of the attenuation spectrum to the first differential of the chromophore spectra, that can separate and calculate the oxidation state of cytochrome c as well as the absolute concentration and saturation of hemoglobin. The algorithm is validated in phantoms and then tested on the neocortex of the rat during an anoxic challenge. Implementation of the algorithm will provide detailed information of mitochondrial oxygenation and mitochondrial function in physiological studies of the mammalian brain

The NStED Exoplanet Transit Survey Service

The NASA Star and Exoplanet Database (NStED) is a general purpose stellar archive with the aim of providing support for NASA's planet finding and characterization goals, stellar astrophysics, and the planning of NASA and other space missions. There are two principal components of NStED: a database of (currently) 140,000 nearby stars and exoplanet-hosting stars, and an archive dedicated to high-precision photometric surveys for transiting exoplanets. We present a summary of the latter component: the NStED Exoplanet Transit Survey Service (NStED-ETSS), along with its content, functionality, tools, and user interface. NStED-ETSS currently serves data from the TrES Survey of the Kepler Field as well as dedicated photometric surveys of four stellar clusters. NStED-ETSS aims to serve both the surveys and the broader astronomical community by archiving these data and making them available in a homogeneous format. Examples of usability of ETSS include investigation of any time-variable phenomena in data sets not studied by the original survey team, application of different techniques or algorithms for planet transit detections, combination of data from different surveys for given objects, statistical studies, etc. NStED-ETSS can be accessed at \tt{http://nsted.ipac.caltech.edu}Comment: To appear in the Proceedings of the 253rd IAU Symposium: "Transiting Planets", May 2008, Cambridge, MA. 4 pages, 2 figure

The NASA Exoplanet Archive: Data and Tools for Exoplanet Research

We describe the contents and functionality of the NASA Exoplanet Archive, a database and tool set funded by NASA to support astronomers in the exoplanet community. The current content of the database includes interactive tables containing properties of all published exoplanets, Kepler planet candidates, threshold-crossing events, data validation reports and target stellar parameters, light curves from the Kepler and CoRoT missions and from several ground-based surveys, and spectra and radial velocity measurements from the literature. Tools provided to work with these data include a transit ephemeris predictor, both for single planets and for observing locations, light curve viewing and normalization utilities, and a periodogram and phased light curve service. The archive can be accessed at http://exoplanetarchive.ipac.caltech.edu.Comment: Accepted for publication in the Publications of the Astronomical Society of the Pacific, 4 figure

The LAEX and NASA portals for CoRoT public data

* Aims. We describe here the main functionalities of the LAEX (Laboratorio de Astrofisica Estelar y Exoplanetas/Laboratory for Stellar Astrophysics and Exoplanets) and NASA portals for CoRoT Public Data. The CoRoT archive at LAEX was opened to the community in January 2009 and is managed in the framework of the Spanish Virtual Observatory. NStED (NASA Star and Exoplanet Database) serves as the CoRoT portal for the US astronomical community. NStED is a general purpose stellar and exoplanet archive with the aim of providing support for NASA planet finding and characterisation goals, and the planning and support of NASA and other space missions. CoRoT data at LAEX and NStED can be accessed at http://sdc.laeff.inta.es/corotfa/ and http://nsted.ipac.caltech.edu,respectively. * Methods. Based on considerable experience with astronomical archives, the aforementioned archives are designed with the aim of delivering science-quality data in a simple and efficient way. * Results. LAEX and NStED not only provide access to CoRoT Public Data but furthermore serve a variety of observed and calculated astrophysical data. In particular, NStED provides scientifically validated information on stellar and planetary data related to the search for and characterization of extrasolar planets, and LAEX makes any information from Virtual Observatory services available to the astronomical community.Comment: Accepted for publication in Astronomy & Astrophysic

The NASA Exoplanet Science Institute Archives: KOA and NStED

The NASA Exoplanet Science Institute (NExScI) maintains a series of archival services in support of NASA’s planet finding and characterization goals. Two of the larger archival services at NExScI are the Keck Observatory Archive (KOA) and the NASA Star and Exoplanet Database (NStED). KOA, a collaboration between the W. M. Keck Observatory and NExScI, serves raw data from the High Resolution Echelle Spectrograph (HIRES) and extracted spectral browse products. As of June 2009, KOA hosts over 28 million files (4.7 TB) from over 2,000 nights. In Spring 2010, it will begin to serve data from the Near-Infrared Echelle Spectrograph (NIRSPEC). NStED is a general purpose archive with the aim of providing support for NASA’s planet finding and characterization goals, and stellar astrophysics. There are two principal components of NStED: a database of (currently) all known exoplanets, and images; and an archive dedicated to high precision photometric surveys for transiting exoplanets. NStED is the US portal to the CNES mission CoRoT, the first space mission dedicated to the discovery and characterization of exoplanets. These archives share a common software and hardware architecture with the NASA/IPAC Infrared Science Archive (IRSA). The software architecture consists of standalone utilities that perform generic query and retrieval functions. They are called through program interfaces and plugged together to form applications through a simple executive library

The Keck Interferometer

The Keck Interferometer (KI) combined the two 10 m W. M. Keck Observatory telescopes on Mauna Kea, Hawaii, as a long-baseline near- and mid-infrared interferometer. Funded by NASA, it operated from 2001 until 2012. KI used adaptive optics on the two Keck telescopes to correct the individual wavefronts, as well as active fringe tracking in all modes for path-length control, including the implementation of cophasing to provide long coherent integration times. KI implemented high sensitivity fringe-visibility measurements at H (1.6 μm), K (2.2 μm), and L (3.8 μm) bands, and nulling measurements at N band (10 μm), which were used to address a broad range of science topics. Supporting these capabilities was an extensive interferometer infrastructure and unique instrumentation, including some additional functionality added as part of the NSF-funded ASTRA program. This paper provides an overview of the instrument architecture and some of the key design and implementation decisions, as well as a description of all of the key elements and their configuration at the end of the project. The objective is to provide a view of KI as an integrated system, and to provide adequate technical detail to assess the implementation. Included is a discussion of the operational aspects of the system, as well as of the achieved system performance. Finally, details on V^2 calibration in the presence of detector nonlinearities as applied in the data pipeline are provided

Detecting microsatellites within genomes: significant variation among algorithms

<p>Abstract</p> <p>Background</p> <p>Microsatellites are short, tandemly-repeated DNA sequences which are widely distributed among genomes. Their structure, role and evolution can be analyzed based on exhaustive extraction from sequenced genomes. Several dedicated algorithms have been developed for this purpose. Here, we compared the detection efficiency of five of them (TRF, Mreps, Sputnik, STAR, and RepeatMasker).</p> <p>Results</p> <p>Our analysis was first conducted on the human X chromosome, and microsatellite distributions were characterized by microsatellite number, length, and divergence from a pure motif. The algorithms work with user-defined parameters, and we demonstrate that the parameter values chosen can strongly influence microsatellite distributions. The five algorithms were then compared by fixing parameters settings, and the analysis was extended to three other genomes (<it>Saccharomyces cerevisiae</it>, <it>Neurospora crassa </it>and <it>Drosophila melanogaster</it>) spanning a wide range of size and structure. Significant differences for all characteristics of microsatellites were observed among algorithms, but not among genomes, for both perfect and imperfect microsatellites. Striking differences were detected for short microsatellites (below 20 bp), regardless of motif.</p> <p>Conclusion</p> <p>Since the algorithm used strongly influences empirical distributions, studies analyzing microsatellite evolution based on a comparison between empirical and theoretical size distributions should therefore be considered with caution. We also discuss why a typological definition of microsatellites limits our capacity to capture their genomic distributions.</p

Self-Phase-Referenced Spectro-Interferometry on the Keck Interferometer

As part of the astrometric and phase-referenced astronomy (ASTRA) project, three new science modes are being developed for the Keck Interferometer that extend the science capabilities of this instrument to include higher spectral resolution, fainter magnitudes, and astrometry. We report on the successful implementation of the first of these science modes, the self-phase-referencing mode, which provides a K-band (λ = 2.2 μm) spectral resolution of R ∼ 1000 on targets as faint as 7.8 mag with spatial resolution as fine as λ/B = 5 mas in the K band, with the 85 m interferometer baseline. This level of spectral resolution would not have been possible without a phase-referencing implementation extending the integration time limit imposed by atmospheric turbulence. For narrow spectral features, we demonstrate a precision of ± 0.01 on the differential V^2(λ), and ± 1.7 mrad on the differential phase Φ(λ), equivalent to a differential astrometry precision of ± 1.45 μas. This new Keck Interferometer instrument is typically used to study the geometry and location of narrow spectral features at high angular resolution, referenced to a continuum. By simultaneously providing spectral and spatial information, the geometry of velocity fields (e.g., rotating disks, inflows, outflows, etc.) larger than 150 km s^(-1) can also be explored