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  • Open Access English
    Authors: 
    Shah, A. M.; Morrill, C.; Gille, E. P.; Gross, W. S.; Anderson, D. M.; Bauer, B. A.; Buckner, R.; Hartman, M.;
    Publisher: Hindawi Publishing Corporation

    This synthesis of thirty-six sites (sixty cores with over 27 000 measurements) located around the world facilitates scientific research on the climate of the last 21 000 years ago obtained from oxygen isotope ( or delta-O-18) measurements. Oxygen isotopes in speleothem calcite record the influence of ambient temperature and the isotopic composition of the source water, the latter providing evidence of hydrologic variability and change. Compared to paleoclimate proxies from sedimentary archives, the age uncertainty is unusually small, around +/−100 years for the last 21 000-year interval. Using data contributed to the World Data Center (WDC) for Paleoclimatology, we have created consistently formatted data files for individual sites as well as composite dataset of annual to millennial resolution. These individual files also contain the chronology information about the sites. The data are useful in understanding hydrologic variability at local and regional scales, such as the Asian summer monsoon and the Intertropical Convergence Zone (as discussed in the underlying source publications), and should also be useful in understanding large-scale aspects of hydrologic change since the Last Glacial Maximum (LGM).

  • Open Access English
    Authors: 
    Ling, Maurice H. T.; Rabara, Roel C.; Tripathi, Prateek; Rushton, Paul J.; Ge, Xijin;
    Publisher: Hindawi Publishing Corporation
    Project: NIH | Large-scale expression an... (1R01GM083226-01A1)

    Microarrays are a large-scale expression profiling method which has been used to study the transcriptome of plants under various environmental conditions. However, manual inspection of microarray data is difficult at the genome level because of the large number of genes (normally at least 30 000) and the many different processes that occur within any given plant. MapMan software, which was initially developed to visualize microarray data for Arabidopsis, has been adapted to other plant species by mapping other species onto MapMan ontology. This paper provides a detailed procedure and the relevant computing codes to generate a MapMan ontology mapping file for tobacco (Nicotiana tabacum L.) using potato and Arabidopsis as intermediates. The mapping file can be used directly with our custom-made NimbleGen oligoarray, which contains gene sequences from both the tobacco gene space sequence and the tobacco gene index 4 (NTGI4) collection of ESTs. The generated dataset will be informative for scientists working on tobacco as their model plant by providing a MapMan ontology mapping file to tobacco, homology between tobacco coding sequences and that of potato and Arabidopsis, as well as adapting our procedure and codes for other plant species where the complete genome is not yet available.

  • Open Access English
    Authors: 
    Cannon, Ethalinda K. S.; Cannon, Steven B.;
    Publisher: Hindawi Publishing Corporation
    Project: NSF | Sequencing the Gene Space... (0321460)

    CViT (chromosome visualization tool) is a Perl utility for quickly generating images of features on a whole genome at once. It reads GFF3-formated data representing chromosomes (linkage groups or pseudomolecules) and sets of features on those chromosomes. It can display features on any chromosomal unit system, including genetic (centimorgan), cytological (centiMcClintock), and DNA unit (base-pair) coordinates. CViT has been used to track sequencing progress (status of genome sequencing, location and number of gaps), to visualize BLAST hits on a whole genome view, to associate maps with one another, to locate regions of repeat densities to display syntenic regions, and to visualize centromeres and knobs on chromosomes.

  • Open Access English
    Authors: 
    Seman, Ali; Abu Bakar, Zainab; Isa, Mohamed Nizam;
    Publisher: Hindawi Publishing Corporation

    The Y-chromosome short tandem repeat (Y-STR) data are mainly collected for a performance benchmarking result in clustering methods. There are six Y-STR dataset items, divided into two categories: Y-STR surname and Y-haplogroup data presented here. The Y-STR data are categorical, unique, and different from the other categorical data. They are composed of a lot of similar and almost similar objects. This characteristic of the Y-STR data has caused certain problems of the existing clustering algorithms in clustering them.

  • Open Access English
    Authors: 
    Hu, Zhiqiu; Xu, Shizhong;
    Publisher: Hindawi Publishing Corporation
    Project: NSF | Optimal Utilization of Ge... (0345205)

    Statistical analysis system (SAS) is the most comprehensive statistical analysis software package in the world. It offers data analysis for almost all experiments under various statistical models. Each analysis is performed using a particular subroutine, called a procedure (PROC). For example, PROC ANOVA performs analysis of variances. PROC QTL is a user-defined SAS procedure for mapping quantitative trait loci (QTL). It allows users to perform QTL mapping for continuous and discrete traits within the SAS platform. Users of PROC QTL are able to take advantage of all existing features offered by the general SAS software, for example, data management and graphical treatment. The current version of PROC QTL can perform QTL mapping for all line crossing experiments using maximum likelihood (ML), least square (LS), iteratively reweighted least square (IRLS), Fisher scoring (FISHER), Bayesian (BAYES), and empirical Bayes (EBAYES) methods.

  • Open Access English
    Authors: 
    Roopnarine, Peter D.; Hertog, Rachel;
    Publisher: Hindawi Publishing Corporation

    Food webs represent one of the most complex aspects of community biotic interactions. Complex food webs are represented as networks of interspecific interactions, where nodes represent species or groups of species, and links are predator-prey interactions. This paper presents reconstructions of coral reef food webs in three Greater Antillean regions of the Caribbean: the Cayman Islands, Cuba, and Jamaica. Though not taxonomically comprehensive, each food web nevertheless comprises producers and consumers, single-celled and multicellular organisms, and species foraging on reefs and adjacent seagrass beds. Species are grouped into trophic guilds if their prey and predator links are indistinguishable. The data list guilds, taxonomic composition, prey guilds/species, and predators. Primary producer and invertebrate richness are regionally uniform, but vertebrate richness varies on the basis of more detailed occurrence data. Each region comprises 169 primary producers, 513 protistan and invertebrate consumer species, and 159, 178, and 170 vertebrate species in the Cayman Islands, Cuba, and Jamaica, respectively. Caribbean coral reefs are among the world's most endangered by anthropogenic activities. The datasets presented here will facilitate comparisons of historical and regional variation, the assessment of impacts of species loss and invasion, and the application of food webs to ecosystem analyses.

  • Open Access English
    Authors: 
    Seigel, Gail M.; Salvi, Richard J.;
    Publisher: Hindawi Publishing Corporation
    Project: NIH | Diversity Supplement Magn... (3U54CA143876-05S1), NIH | ACQUIRED HEARING LOSS (3P01DC003600-04S1), NIH | Tumor initiating cells in... (1R21CA127061-01A1)

    The R28 rat retinal progenitor cell line was developed from postnatal day six rat retina immortalized with the 12S E1A gene of adenovirus. R28 cells have been distributed to over 100 laboratories worldwide, with over 60 publications on topics that include in vitro toxicology, cellular physiology, gene expression analysis, and experimental transplantation. In this paper, we present a microarray dataset of R28 cells that describes the presence or absence of 8799 genes and ESTs that may be relevant to current and future studies of R28 retinal precursor cells.

  • Open Access English
    Authors: 
    Namusoke, Fatuma; Rasti, Niloofar; Kironde, Fred; Wahlgren, Mats; Mirembe, Florence;
    Publisher: SAGE-Hindawi Access to Research
  • Open Access English
    Authors: 
    Chan, P. K.; Zhao, X.-P.; Heidinger, A. K.;
    Publisher: Hindawi Publishing Corporation

    Aerosol optical thickness (AOT) was retrieved using the Advanced Very High Resolution Radiometer (AVHRR) PATMOS-x Level-2b gridded radiances and the two-channel algorithm of the National Climatic Data Center (NCDC). The primary retrieval product is AOT at 0.63 μm channel. AOT is also retrieved at 0.83 μm or 1.61 μm channel for consistent check. The retrieval was made during day time, under clear sky and snow-free conditions, and over the global oceans. The spatial resolution is 0.1×0.1 degree grid and the temporal resolution is both daily and monthly. The resultant AVHRR AOT climate data record (CDR) spans from August 1981 to December 2009 and provides the longest aerosol CDR currently available from operational satellites. This dataset is useful in studying aerosol climate forcing, monitoring long-term aerosol trends, and evaluating global air pollution and aerosol transport models over the global ocean.

  • Open Access English
    Authors: 
    Ballas, Samir K.; Kesen, Muge R.; Goldberg, Morton F.; Lutty, Gerard A.; Dampier, Carlton; Osunkwo, Ifeyinwa; Wang, Winfred C.; Hoppe, Carolyn; Hagar, Ward; Darbari, Deepika S.; +1 more
    Publisher: Hindawi Publishing Corporation
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