miRDB: An online database for prediction of functional microRNA targets

MicroRNAs (miRNAs) are small noncoding RNAs that act as master regulators in many biological processes. miRNAs function mainly by downregulating the expression of their gene targets. Thus, accurate prediction of miRNA targets is critical for characterization of miRNA functions. To this end, we have developed an online database, miRDB, for miRNA target prediction and functional annotations. Recently, we have performed major updates for miRDB. Specifically, by employing an improved algorithm for miRNA target prediction, we now present updated transcriptome-wide target prediction data in miRDB, including 3.5 million predicted targets regulated by 7000 miRNAs in five species. Further, we have implemented the new prediction algorithm into a web server, allowing custom target prediction with user-provided sequences. Another new database feature is the prediction of cell-specific miRNA targets. miRDB now hosts the expression profiles of over 1000 cell lines and presents target prediction data that are tailored for specific cell models. At last, a new web query interface has been added to miRDB for prediction of miRNA functions by integrative analysis of target prediction and Gene Ontology data. All data in miRDB are freely accessible at http://mirdb.org

Cross-Entropy of Uncertain Variables

In order to deal with the divergence of uncertain variables from a prior one, this paper is devoted to introduce the concept of cross-entropy for uncertain variables and study the minimum cross-entropy principle

Whose input counts and which paradigm prevails?: a content analysis of mass-mediated debate on U.S.-China relations in 1990\u27s and a policy critique on republican virtue of the policy tradeoff

This dissertation examines the public opinion-public policy nexus with regard to the making of U.S.-China policy during the Clinton administration (1992-2000). The researcher investigates how the mass media discourse on U.S.-China relations relates to the policy tradeoff between economic interdependence and confrontation on human rights. Particularly, the quantitative study of the media discourse is placed within a Communitarian perspective to determine: (1) whether the policy tradeoff can claim to have the support of public opinion; (2) whether the media discourse originated from the active civic participation; and (3) how the policy tradeoff broke its promise. As a result, the researcher concludes that the eclipse of co-operative inquiry of the U.S. public, the ascendancy of issue management of special stakeholders, and the entanglement between newsmaking and policy-making may have jeopardized the republican virtue of U.S. diplomacy. First, the researcher contextualizes U.S.-China relations and relates it to the dynamics of U.S. foreign policy choices among four national interests: power, prosperity, principle, and peace. Then, the researcher sets the Communitarian theory of the press as a normative theory of media democracy and incorporates other positive theories of political communication to make sense of the dilemma of the current media democracy. Following that, a content analysis of the New York Times and Cable News Network examined: (1) who said what; (2) which perspective prevails; (3) the correlation between newsmaking and policy-making; and (4) the congruence/dissension between policy beltway and other social groups. The finding suggests a significant correlation between/among the policy proposal, the author of that proposal, and the issue/frame espoused; on the other hand, the conspicuous differences among policy-makers, ordinary citizens (issue public), and professional communicators in regard to the policy trade-off indicates a low public accountability of the policy tradeoff. To explain the discrepancy, the investigator examined corporate America\u27s issue management of U.S.-China trade and put the policy tradeoff into the perspective of capitalistic globalization theory. Finally, the lack of republican virtue is explained as a result of corporate-driven diplomacy and the media discourse short of civic participation. Henceforward, a Communitarian press becomes recommendable for the rejuvenation of media democracy

Stellar loci I. Metallicity dependence and intrinsic widths

Stellar loci are widely used for selection of interesting outliers, reddening determinations, and calibrations. However, hitherto the dependence of stellar loci on metallicity has not been fully explored and their intrinsic widths are unclear. In this paper, by combining the spectroscopic and re-calibrated imaging data of the SDSS Stripe 82, we have built a large, clean sample of dwarf stars with accurate colors and well determined metallicities to investigate the metallicity dependence and intrinsic widths of the SDSS stellar loci. Typically, one dex decrease in metallicity causes 0.20 and 0.02 mag decrease in colors u-g and g-r, and 0.02 and 0.02 mag increase in colors r-i and i-z, respectively. The variations are larger for metal-rich stars than for metal-poor ones, and for F/G/K stars than for A/M ones. Using the sample, we have performed two dimensional polynomial fitting to the u-g, g-r, r-i, and i-z colors as a function of color g-i and metallicity [Fe/H]. The residuals, at the level of 0.029, 0.008, 0.008 and 0.011 mag for the u-g, g-r, r-i, and i-z colors, respectively can be fully accounted for by the photometric errors and metallicity uncertainties, suggesting that the intrinsic widths of the loci are at maximum a few mmag. The residual distributions are asymmetric, revealing that a significant fraction of stars are binaries. In a companion paper, we will present an unbiased estimate of the binary fraction for field stars. Other potential applications of the metallicity dependent stellar loci are briefly discussed.Comment: 6 pages, 4 figures, 1 table, ApJ in pres