FLASH: ultra-fast protocol to identify RNA-protein interactions in cells

Determination of the in vivo binding sites of RNA-binding proteins (RBPs) is paramount to understanding their function and how they affect different aspects of gene regulation. With hundreds of RNA-binding proteins identified in human cells, a flexible, high-resolution, high-throughput, highly multiplexible and radioactivity-free method to determine their binding sites has not been described to date. Here we report FLASH (Fast Ligation of RNA after some sort of Affinity Purification for High-throughput Sequencing), which uses a special adapter design and an optimized protocol to determine protein-RNA interactions in living cells. The entire FLASH protocol, starting from cells on plates to a sequencing library, takes 1.5 days. We demonstrate the flexibility, speed and versatility of FLASH by using it to determine RNA targets of both tagged and endogenously expressed proteins under diverse conditions in vivo

Capacity Bounds and Concatenated Codes Over Segmented Deletion Channels

Cataloged from PDF version of article.We develop an information theoretic characterization and a practical coding approach for segmented deletion channels. Compared to channels with independent and identically distributed (i.i.d.) deletions, where each bit is independently deleted with an equal probability, the segmentation assumption imposes certain constraints, i.e., in a block of bits of a certain length, only a limited number of deletions are allowed to occur. This channel model has recently been proposed and motivated by the fact that for practical systems, when a deletion error occurs, it is more likely that the next one will not appear very soon. We first argue that such channels are information stable, hence their channel capacity exists. Then, we introduce several upper and lower bounds with two different methods in an attempt to understand the channel capacity behavior. The first scheme utilizes certain information provided to the transmitter and/or receiver while the second one explores the asymptotic behavior of the bounds when the average bit deletion rate is small. In the second part of the paper, we consider a practical channel coding approach over a segmented deletion channel. Specifically, we utilize outer LDPC codes concatenated with inner marker codes, and develop suitable channel detection algorithms for this scenario. Different maximum-a-posteriori (MAP) based channel synchronization algorithms operating at the bit and symbol levels are introduced, and specific LDPC code designs are explored. Simulation results clearly indicate the advantages of the proposed approach. In particular, for the entire range of deletion probabilities less than unity, our scheme offers a significantly larger transmission rate compared to the other existing solutions in the literature

The effect of sample properties on the electron velocity in quantum Hall bars

We report on our theoretical investigation of the effects of the confining potential profile and sample size on the electron velocity distribution in (narrow) quantum-Hall systems. The electrostatic properties of the electron system are obtained by the Thomas-Fermi-Poisson nonlinear screening theory. The electron velocity distribution as a function of the lateral coordinate is obtained from the slope of the screened potential at the Fermi level and within the incompressible strips (ISs). We compare our findings with the recent experiments.Comment: 8 pages, 6 figure

The dual parameterization of the proton generalized parton distribution functions H and E and description of the DVCS cross sections and asymmetries

We develop the minimal model of a new leading order parameterization of GPDs introduced by Shuvaev and Polyakov. The model for GPDs H and E is formulated in terms of the forward quark distributions, the Gegenbauer moments of the D-term and the forward limit of the GPD E. The model is designed primarely for small and medium-size values of x_B, x_B \leq 0.2. We examined two different models of the t-dependence of the GPDs: The factorized exponential model and the non-factorized Regge-motivated model. Using our model, we successfully described the DVCS cross section measured by H1 and ZEUS, the moments of the beam-spin A_{LU}^{\sin \phi}, beam-charge A_{C}^{\cos \phi} and transversely-polarized target A_{UT}^{\sin \phi \cos \phi} DVCS asymmetries measured by HERMES and A_{LU}^{\sin \phi} measured by CLAS. The data on A_{C}^{\cos \phi} prefers the Regge-motivated model of the t-dependence of the GPDs. The data on A_{UT}^{\sin \phi \cos \phi} indicates that the u and d quarks carry only a small fraction of the proton total angular momentum.Comment: 33 pages, 11 figure

Asymptotic directional structure of radiation for fields of algebraic type D

The directional behavior of dominant components of algebraically special spin-s fields near a spacelike, timelike or null conformal infinity is studied. By extending our previous general investigations we concentrate on fields which admit a pair of equivalent algebraically special null directions, such as the Petrov type D gravitational fields or algebraically general electromagnetic fields. We introduce and discuss a canonical choice of the reference tetrad near infinity in all possible situations, and we present the corresponding asymptotic directional structures using the most natural parametrizations.Comment: 20 pages, 6 figure

Polarization entangled photon-pair source based on quantum nonlinear photonics and interferometry

We present a versatile, high-brightness, guided-wave source of polarization entangled photons, emitted at a telecom wavelength. Photon-pairs are generated using an integrated type-0 nonlinear waveguide, and subsequently prepared in a polarization entangled state via a stabilized fiber interferometer. We show that the single photon emission wavelength can be tuned over more than 50 nm, whereas the single photon spectral bandwidth can be chosen at will over more than five orders of magnitude (from 25 MHz to 4 THz). Moreover, by performing entanglement analysis, we demonstrate a high degree of control of the quantum state via the violation of the Bell inequalities by more than 40 standard deviations. This makes this scheme suitable for a wide range of quantum optics experiments, ranging from fundamental research to quantum information applications. We report on details of the setup, as well as on the characterization of all included components, previously outlined in F. Kaiser et al. (2013 Laser Phys. Lett. 10, 045202).Comment: 16 pages, 7 figure

Nucleon Generalized Parton Distributions from Full Lattice QCD

We present a comprehensive study of the lowest moments of nucleon generalized parton distributions in N_f=2+1 lattice QCD using domain wall valence quarks and improved staggered sea quarks. Our investigation includes helicity dependent and independent generalized parton distributions for pion masses as low as 350 MeV and volumes as large as (3.5 fm)^3, for a lattice spacing of 0.124 fm. We use perturbative renormalization at one-loop level with an improvement based on the non-perturbative renormalization factor for the axial vector current, and only connected diagrams are included in the isosinglet channel.Comment: 40 pages, 49 figures; Revised chiral extrapolations in sections A-K, main conclusions unchange