Transcriptional regulatory elements (TREs), including enhancers and promoters, determine the transcription levels of associated genes. We have recently shown that global run-on and sequencing (GRO-seq) with enrichment for 5'-capped RNAs reveals active TREs with high accuracy. Here, we demonstrate that active TREs can be identified by applying sensitive machine-learning methods to standard GRO-seq data. This approach allows TREs to be assayed together with gene expression levels and other transcriptional features in a single experiment. Our prediction method, called discriminative Regulatory Element detection from GRO-seq (dREG), summarizes GRO-seq read counts at multiple scales and uses support vector regression to identify active TREs. The predicted TREs are more strongly enriched for several marks of transcriptional activation, including eQTL, GWAS-associated SNPs, H3K27ac, and transcription factor binding than those identified by alternative functional assays. Using dREG, we survey TREs in eight human cell types and provide new insights into global patterns of TRE function.

We investigate a model of the interacting holographic dark energy with cold dark matter (CDM). If the holographic energy density decays into CDM, we find two types of the effective equation of state. In this case we have to use the effective equations of state ($\omega^{\rm eff}_{\rm \Lambda}$) instead of the equation of state ($\omega_{\rm \Lambda})$. For a fixed ratio of two energy densities, their effective equations of state are given by the same negative constant. Actually, the cosmic anti-friction arisen from the vacuum decay process may induce the acceleration with $\omega^{\rm eff}_{\rm \Lambda}<-1/3$. For a variable ratio, their effective equations of state are slightly different, but they approach the same negative constant in the far future. Consequently, we show that such an interacting holographic energy model cannot accommodate a transition from the dark energy with $\omega^{\rm eff}_{\rm \Lambda}\ge-1$ to the phantom regime with $\omega^{\rm eff}_{\rm \Lambda}<-1$.Comment: 11 pages, 2 eps figures, final version to appear in PL

We investigate the agegraphic dark energy models which were recently proposed to explain the dark energy-dominated universe. For this purpose, we calculate their equation of states and squared speeds of sound. We find that the squared speed for agegraphic dark energy is always negative. This means that the perfect fluid for agegraphic dark energy is classically unstable. Furthermore, it is shown that the new agegraphic dark energy model could describe the matter (radiation)-dominated universe in the far past only when the parameter $n$ is chosen to be $n>n_c$, where the critical values are determined to be $n_c=2.6878(2.5137752)$ numerically. It seems that the new agegraphic dark energy model is no better than the holographic dark energy model for the description of the dark energy-dominated universe, even though it resolves the causality problem.Comment: 15 pages 4 figure

No abstract

No abstract

Contents (11 pages and 7 tables)Table S1. GC/MS peak areas of evolved compounds of reaction region during thermal and catalytic pyrolysis of cellulose.

No abstract

No abstract