omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data

CLIP-seq methods allow the generation of genome-wide maps of RNA binding protein - RNA interaction sites. However, due to differences between different CLIP-seq assays, existing computational approaches to analyze the data can only be applied to a subset of assays. Here, we present a probabilistic model called omniCLIP that can detect regulatory elements in RNAs from data of all CLIP-seq assays. omniCLIP jointly models data across replicates and can integrate background information. Therefore, omniCLIP greatly simplifies the data analysis, increases the reliability of results and paves the way for integrative studies based on data from different assays

A Nonrelativistic Chiral Soliton in One Dimension

I analyze the one-dimensional, cubic Schr\"odinger equation, with nonlinearity constructed from the current density, rather than, as is usual, from the charge density. A soliton solution is found, where the soliton moves only in one direction. Relation to higher-dimensional Chern--Simons theory is indicated. The theory is quantized and results for the two-body quantum problem agree at weak coupling with those coming from a semiclassical quantization of the soliton.Comment: 11 pages, Latex2

Precision Spectroscopy at Heavy Ion Ring Accelerator SIS300

Unique spectroscopic possibilities open up if a laser beam interacts with relativistic lithium-like ions stored in the heavy ion ring accelerator SIS300 at the future Facility for Antiproton and Ion Research FAIR in Darmstadt, Germany. At a relativistic factor gamma = 36 the 2P 1/2 level can be excited from the 2S 1/2 ground state for any element with frequency doubled dye-lasers in collinear geometry. Precise transition energy measurements can be performed if the fluorescence photons, boosted in forward direction into the X-ray region, are energetically analyzed with a single crystal monochromator. The hyperfine structure can be investigated at the 2P 1/2 - 2S 1/2 transition for all elements and at the 2P 3/2 - 2S 1/2 transition for elements with Z < 50. Isotope shifts and nuclear moments can be measured with unprecedented precision, in principle even for only a few stored radioactive species with known nuclear spin. A superior relative line width in the order of 5E-7 may be feasible after laser cooling, and even polarized external beams may be prepared by optical pumping

Complete NNLO QCD Analysis of B -> X_s l^+ l^- and Higher Order Electroweak Effects

We complete the next-to-next-to-leading order QCD calculation of the branching ratio for B -> X_s l^+ l^- including recent results for the three-loop anomalous dimension matrix and two-loop matrix elements. These new contributions modify the branching ratio in the low-q^2 region, BR_ll, by about +1% and -4%, respectively. We furthermore discuss the appropriate normalization of the electromagnetic coupling alpha and calculate the dominant higher order electroweak effects, showing that, due to accidental cancellations, they change BR_ll by only -1.5% if alpha(mu) is normalized at mu = O(m_b), while they shift it by about -8.5% if one uses a high scale normalization mu = O(M_W). The position of the zero of the forward-backward asymmetry, q_0^2, is changed by around +2%. After introducing a few additional improvements in order to reduce the theoretical error, we perform a comprehensive study of the uncertainty. We obtain BR_ll(1 GeV^2 <= q^2 <= 6 GeV^2) = (1.57 +- 0.16) x 10^-6 and q_0^2 = (3.76 +- 0.33) GeV^2 and note that the part of the uncertainty due to the b-quark mass can be easily reduced.Comment: 26 pages, 7 figures; v5: corrected normalisation in Eq. (5), numerical results unchange

Global identification of functional microRNA-mRNA interactions in Drosophila

MicroRNAs (miRNAs) are key mediators of post-transcriptional gene expression silencing. So far, no comprehensive experimental annotation of functional miRNA target sites exists in Drosophila. Here, we generated a transcriptome-wide in vivo map of miRNA-mRNA interactions in Drosophila melanogaster, making use of single nucleotide resolution in Argonaute1 (AGO1) crosslinking and immunoprecipitation (CLIP) data. Absolute quantification of cellular miRNA levels presents the miRNA pool in Drosophila cell lines to be more diverse than previously reported. Benchmarking two CLIP approaches, we identify a similar predictive potential to unambiguously assign thousands of miRNA-mRNA pairs from AGO1 interaction data at unprecedented depth, achieving higher signal-to-noise ratios than with computational methods alone. Quantitative RNA-seq and sub-codon resolution ribosomal footprinting data upon AGO1 depletion enabled the determination of miRNA-mediated effects on target expression and translation. We thus provide the first comprehensive resource of miRNA target sites and their quantitative functional impact in Drosophila

The non-linear Schr\"odinger equation and the conformal properties of non-relativistic space-time

The cubic non-linear Schr\"odinger equation where the coefficient of the nonlinear term is a function $F(t,x)$ only passes the Painlev\'e test of Weiss, Tabor, and Carnevale only for $F=(a+bt)^{-1}$, where $a$ and $b$ are constants. This is explained by transforming the time-dependent system into the constant-coefficient NLS by means of a time-dependent non-linear transformation, related to the conformal properties of non-relativistic space-time. A similar argument explains the integrability of the NLS in a uniform force field or in an oscillator background.Comment: Thoroughly revised version, in the light of new interest in non-relativistic conformal tranformation, with a new reference list. 8 pages, LaTex, no figures. To be published in Int. J. Theor. Phy