Development of 2MASS Catalog Server Kit

We develop a software kit called "2MASS Catalog Server Kit" to easily construct a high-performance database server for the 2MASS Point Source Catalog (includes 470,992,970 objects) and several all-sky catalogs. Users can perform fast radial search and rectangular search using provided stored functions in SQL similar to SDSS SkyServer. Our software kit utilizes open-source RDBMS, and therefore any astronomers and developers can install our kit on their personal computers for research, observation, etc. Out kit is tuned for optimal coordinate search performance. We implement an effective radial search using an orthogonal coordinate system, which does not need any techniques that depend on HTM or HEALpix. Applying the xyz coordinate system to the database index, we can easily implement a system of fast radial search for relatively small (less than several million rows) catalogs. To enable high-speed search of huge catalogs on RDBMS, we apply three additional techniques: table partitioning, composite expression index, and optimization in stored functions. As a result, we obtain satisfactory performance of radial search for the 2MASS catalog. Our system can also perform fast rectangular search. It is implemented using techniques similar to those applied for radial search. Our way of implementation enables a compact system and will give important hints for a low-cost development of other huge catalog databases.Comment: 2011 PASP accepte

The Montage Image Mosaic Service: Custom Image Mosaics On-Demand

The Montage software suite has proven extremely useful as a general engine for reprojecting, background matching, and mosaicking astronomical image data from a wide variety of sources. The processing algorithms support all common World Coordinate System (WCS) projections and have been shown to be both astrometrically accurate and flux conserving. The background ‘matching’ algorithm does not remove background flux but rather finds the best compromise background based on all the input and matches the individual images to that. The Infrared Science Archive (IRSA), part of the Infrared Processing and Analysis Center (IPAC) at Caltech, has now wrapped the Montage software as a CGI service and provided a compute and request management infrastructure capable of producing approximately 2 TBytes / day of image mosaic output (e.g. from 2MASS and SDSS data). Besides the basic Montage engine, this service makes use of a 16-node LINUX cluster (dual processor, dual core) and the ROME request management software developed by the National Virtual Observatory (NVO). ROME uses EJB/database technology to manage user requests, queue processing and load balance between users, and managing job monitoring and user notification. The Montage service will be extended to process userdefined data collections, including private data uploads

A Cross-Match of 2MASS and SDSS: Newly-Found L and T Dwarfs and an Estimate of the Space Densitfy of T Dwarfs

We report new L and T dwarfs found in a cross-match of the SDSS Data Release 1 and 2MASS. Our simultaneous search of the two databases effectively allows us to relax the criteria for object detection in either survey and to explore the combined databases to a greater completeness level. We find two new T dwarfs in addition to the 13 already known in the SDSS DR1 footprint. We also identify 22 new candidate and bona-fide L dwarfs, including a new young L2 dwarf and a peculiar L2 dwarf with unusually blue near-IR colors: potentially the result of mildly sub-solar metallicity. These discoveries underscore the utility of simultaneous database cross-correlation in searching for rare objects. Our cross-match completes the census of T dwarfs within the joint SDSS and 2MASS flux limits to the 97% level. Hence, we are able to accurately infer the space density of T dwarfs. We employ Monte Carlo tools to simulate the observed population of SDSS DR1 T dwarfs with 2MASS counterparts and find that the space density of T0-T8 dwarf systems is 0.0070 (-0.0030; +0.0032) per cubic parsec (95% confidence interval), i.e., about one per 140 cubic parsecs. Compared to predictions for the T dwarf space density that depend on various assumptions for the sub-stellar mass function, this result is most consistent with models that assume a flat sub-stellar mass function dN/dM ~ M^0. No >T8 dwarfs were discovered in the present cross-match, though less than one was expected in the limited area (2099 sq. degrees) of SDSS DR1.Comment: To appear in ApJ, Feb 10, 2008 issue. 37 pages, including 12 figures and 14 table

Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel

<b>BACKGROUND:</b> MicroRNAs (miRNAs) play key roles in regulating post-transcriptional gene expression and are essential for development in the free-living nematode Caenorhabditis elegans and in higher organisms. Whether microRNAs are involved in regulating developmental programs of parasitic nematodes is currently unknown. Here we describe the the miRNA repertoire of two important parasitic nematodes as an essential first step in addressing this question. <b>RESULTS:</b> The small RNAs from larval and adult stages of two parasitic species, Brugia pahangi and Haemonchus contortus, were identified using deep-sequencing and bioinformatic approaches. Comparative analysis to known miRNA sequences reveals that the majority of these miRNAs are novel. Some novel miRNAs are abundantly expressed and display developmental regulation, suggesting important functional roles. Despite the lack of conservation in the miRNA repertoire, genomic positioning of certain miRNAs within or close to specific coding genes is remarkably conserved across diverse species, indicating selection for these associations. Endogenous small-interfering RNAs and Piwi-interacting (pi)RNAs, which regulate gene and transposon expression, were also identified. piRNAs are expressed in adult stage H. contortus, supporting a conserved role in germline maintenance in some parasitic nematodes. <b>CONCLUSIONS:</b> This in-depth comparative analysis of nematode miRNAs reveals the high level of divergence across species and identifies novel sequences potentially involved in development. Expression of novel miRNAs may reflect adaptations to different environments and lifestyles. Our findings provide a detailed foundation for further study of the evolution and function of miRNAs within nematodes and for identifying potential targets for intervention

A Cost-Benefit Study of Doing Astrophysics On The Cloud: Production of Image Mosaics

Utility grids such as the Amazon EC2 and Amazon S3 clouds offer computational and storage resources that can be used on-demand for a fee by compute- and data-intensive applications. The cost of running an application on such a cloud depends on the compute, storage and communication resources it will provision and consume. Different execution plans of the same application may result in significantly different costs. We studied via simulation the cost performance trade-offs of different execution and resource provisioning plans by creating, under the Amazon cloud fee structure, mosaics with the Montage image mosaic engine, a widely used data- and compute-intensive application. Specifically, we studied the cost of building mosaics of 2MASS data that have sizes of 1, 2 and 4 square degrees, and a 2MASS all-sky mosaic. These are examples of mosaics commonly generated by astronomers. We also study these trade-offs in the context of the storage and communication fees of Amazon S3 when used for long-term application data archiving. Our results show that by provisioning the right amount of storage and compute resources cost can be significantly reduced with no significant impact on application performance

DNAPlotter: circular and linear interactive genome visualization

Summary: DNAPlotter is an interactive Java application for generating circular and linear representations of genomes. Making use of the Artemis libraries to provide a user-friendly method of loading in sequence files (EMBL, GenBank, GFF) as well as data from relational databases, it filters features of interest to display on separate user-definable tracks. It can be used to produce publication quality images for papers or web pages

HST Fine Guidance Sensor Astrometric Parallaxes for Three Dwarf Novae: SS Aurigae, SS Cygni, and U Geminorum

We report astrometric parallaxes for three well known dwarf novae obtained using the Fine Guidance Sensors on the Hubble Space Telescope. We found a parallax for SS Aurigae of Pi = 5.00 +/- 0.64 mas, for SS Cygni we found Pi = 6.02 +/- 0.46 mas, and for U Geminorum we obtained Pi = 10.37 +/- 0.50 mas. These represent the first true trigonometric parallaxes of any dwarf novae. We briefly compare these results with previous distance estimates. This program demonstrates that with a very modest amount of HST observing time, the Fine Guidance Sensors can deliver parallaxes of unrivaled precision.Comment: 15 pages, 2 Table

Parallax and Distance Estimates for Fourteen Cataclysmic Variable Stars

I used the 2.4 m Hiltner telescope at MDM Observatory in an attempt to measure trigonometric parallaxes for 14 cataclysmic variable stars. Techniques are described in detail. In the best cases the parallax uncertainties are below 1 mas, and significant parallaxes are found for most of the program stars. A Bayesian method which combines the parallaxes together with proper motions and absolute magnitude constraints is developed and used to derive distance estimates and confidence intervals. The most precise distance derived here is for WZ Sge, for which I find 43.3 (+1.6, -1.5) pc. Six Luyten Half-Second stars with previous precise parallax measurements were re-measured to test the techniques, and good agreement is found.Comment: 33 pages, 3 figures. Astronomical Journal, accepte

Single and Composite Hot Subdwarf Stars in the Light of 2MASS All-Sky Photometry

Utilizing the Two Micron All Sky Survey (2MASS) All-Sky Data Release Catalog, we have retrieved useful near-IR J, H, and Ks magnitudes for more than 800 hot subdwarfs (sdO and sdB stars) drawn from the "Catalogue of Spectroscopically Identified Hot Subdwarfs" (Kilkenny, Heber, & Drilling 1988, 1992). This sample size greatly exceeds previous studies of hot subdwarfs. We find that, of the hot subdwarfs in Kilkenny et al., ~40% in a magnitude limited sample have colors that are consistent with the presence of an unresolved late type (FGK) companion. Binary stars are over-represented in a magnitude limited sample. In an approximately volume limited sample the fraction of composite-color binaries is ~25%.Comment: 4 pages, 1 figure. To appear in "Extreme Horizontal Branch Stars and Related Objects", Astrophysics and Space Science, Kluwer Academic Publishers, proceedings of the meeting held in Keele, UK, June 16-20, 200