The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis.

Ribosome profiling is a technique that permits genome-wide, quantitative analysis of translation and has found broad application in recent years. Here we describe a modified profiling protocol and software package designed to benefit more broadly the translation community in terms of simplicity and utility. The protocol, applicable to diverse organisms, including organelles, is based largely on previously published profiling methodologies, but uses duplex-specific nuclease (DSN) as a convenient, species-independent way to reduce rRNA contamination. We show that DSN-based depletion compares favorably with other commonly used rRNA depletion strategies and introduces little bias. The profiling protocol typically produces high levels of triplet periodicity, facilitating the detection of coding sequences, including upstream, downstream, and overlapping open reading frames (ORFs) and an alternative ribosome conformation evident during termination of protein synthesis. In addition, we provide a software package that presents a set of methods for parsing ribosomal profiling data from multiple samples, aligning reads to coding sequences, inferring alternative ORFs, and plotting average and transcript-specific aspects of the data. Methods are also provided for extracting the data in a form suitable for differential analysis of translation and translational efficiency.This work was supported by an EMBL long-term postdoctoral fellowship to B.Y.C., Sir Henry Wellcome Fellowships to B.Y.C. and N.I., a Wellcome Trust PhD scholarship to J.D.J., a Wellcome Trust Fellowship to A.E.F. (088789), and UK Biotechnology and Biological Sciences Research Council grants to I.B. (BB/L000334/ 1) and A.E.F. (BB/J007072/1). Work in the Baulcombe laboratory is supported by The Gatsby Charitable Foundation and the European Research Council Advanced Investigator grant TRIBE. D.C.B. is the Royal Society Edward Penley Abraham Research Professor. We wish to thank Professor Stuart G. Siddell, University of Bristol, for providing the murine 17 clone 1 cellsThis is the final version of the article. It was first available from Cold Springs Harbor Press via http://dx.doi.org/10.1261/rna.052548.11

Elastic electron deuteron scattering with consistent meson exchange and relativistic contributions of leading order

The influence of relativistic contributions to elastic electron deuteron scattering is studied systematically at low and intermediate momentum transfers ($Q^2\leq 30$ fm$^{-2}$). In a $(p/M)$-expansion, all leading order relativistic $\pi$-exchange contributions consistent with the Bonn OBEPQ models are included. In addition, static heavy meson exchange currents including boost terms and lowest order $\rho\pi\gamma$-currents are considered. Sizeable effects from the various relativistic two-body contributions, mainly from $\pi$-exchange, have been found in form factors, structure functions and the tensor polarization $T_{20}$. Furthermore, static properties, viz. magnetic dipole and charge quadrupole moments and the mean square charge radius are evaluated.Comment: 15 pages Latex including 5 figures, final version accepted for publication in Phys.Rev.C Details of changes: (i) The notation of the curves in Figs. 1 and 2 have been clarified with respect to left and right panels. (ii) In Figs. 3 and 4 an experimental point for T_20 has been added and a corresponding reference [48] (iii) At the end of the text we have added a paragraph concerning the quality of the Bonn OBEPQ potential

Centrality Dependence of Charged Particle Multiplicity in Au-Au Collisions at sqrt(s_NN)=130 GeV

We present results for the charged-particle multiplicity distribution at mid-rapidity in Au - Au collisions at sqrt(s_NN)=130 GeV measured with the PHENIX detector at RHIC. For the 5% most central collisions we find $dN_{ch}/d\eta_{|\eta=0} = 622 \pm 1 (stat) \pm 41 (syst)$. The results, analyzed as a function of centrality, show a steady rise of the particle density per participating nucleon with centrality.Comment: 307 authors, 43 institutions, 6 pages, 4 figures, 1 table Minor changes to figure labels and text to meet PRL requirements. One author added: M. Hibino of Waseda Universit

Near-Infrared Properties of Metal-poor Globular Clusters in the Galactic Bulge Direction

Aims. J, H, and K' images obtained from the near-infrared imager CFHTIR on the Canada-France-Hawaii Telescope are used to derive the morphological parameters of the red giant branch (RGB) in the near-infrared color-magnitude diagrams for 12 metal-poor globular clusters in the Galactic bulge direction. Using the compiled data set of the RGB parameters for the observed 12 clusters, in addition to the previously studied 5 clusters, we discuss the properties of the RGB morphology for the clusters and compare them with the calibration relations for the metal-rich bulge clusters and the metal-poor halo clusters. Methods. The photometric RGB shape indices such as colors at fixed magnitudes of MK = MH = (-5.5, -5, -4, and -3), magnitudes at fixed colors of (J - K)o = (J - H)o = 0.7, and the RGB slope are measured from the fiducial normal points defined in the near- infrared color-magnitude diagrams for each cluster. The magnitudes of RGB bump and tip are also estimated from the differential and cumulative luminosity functions of the selected RGB stars. The derived RGB parameters have been used to examine the overall behaviors of the RGB morphology as a function of cluster metallicity. Results. The correlations between the near-infrared photometric RGB shape indices and the cluster metallicity for the programme clusters compare favorably with the previous observational calibration relations for metal-rich clusters in the Galactic bulge and the metal-poor halo clusters. The observed near-infrared magnitudes of the RGB bump and tip for the investigated clusters are also in accordance with the previous calibration relations for the Galactic bulge clusters.Comment: 12 pages, 9 figures, accepted for publication in Astronomy & Astrophysic

Clustering in Highest Energy Cosmic Rays: Physics or Statistics?

Directional clustering can be expected in cosmic ray observations due to purely statistical fluctuations for sources distributed randomly in the sky. We develop an analytic approach to estimate the probability of random cluster configurations, and use these results to study the strong potential of the HiRes, Auger, Telescope Array and EUSO/OWL/AirWatch facilities for deciding whether any observed clustering is most likely due to non-random sources.Comment: 19 pages, LaTeX, 3 figure

Vibrational Spectra of a Mechanosensitive Channel

We report the simulated vibrational spectra of a mechanosensitive membrane channel in different gating states. Our results show that while linear absorption is insensitive to structural differences, linear dichroism and sum-frequency generation spectroscopies are sensitive to the orientation of the transmembrane helices, which is changing during the opening process. Linear dichroism cannot distinguish an intermediate structure from the closed structure, but sum-frequency generation can. In addition, we find that two-dimensional infrared spectroscopy can be used to distinguish all three investigated gating states of the mechanosensitive membrane channel.

Burkhardt-Cottingham sum rule and forward spin polarizabilities in Heavy Baryon Chiral Perturbation Theory

We study spin-dependent sum rules for forward virtual Compton scattering(VVCS) off the nucleon in heavy baryon chiral perturbation theory at order $O(p^4)$. We show how these sum rules can be evaluated from low energy expansions (in the virtual photon energy) of the forward VVCS amplitudes. We study in particular the Burkhardt -Cottingham sum rule in HBChPT and higher terms in the low energy expansion, which can be related to the generalized forward spin polarizabilities of the nucleon. The dependence of these observables on the photon virtuality $Q^2$ can be accessed, at small and intermediate $Q^2$ values, from existing and forthcoming data at Jefferson Lab.Comment: 16 pages,4 fig

Inclusive charged hadron elliptic flow in Au + Au collisions at sNN\sqrt{s_{NN}} = 7.7 - 39 GeV

A systematic study is presented for centrality, transverse momentum ($p_T$) and pseudorapidity ($\eta$) dependence of the inclusive charged hadron elliptic flow ($v_2$) at midrapidity($|\eta| < 1.0$) in Au+Au collisions at $\sqrt{s_{NN}}$ = 7.7, 11.5, 19.6, 27 and 39 GeV. The results obtained with different methods, including correlations with the event plane reconstructed in a region separated by a large pseudorapidity gap and 4-particle cumulants ($v_2{4}$), are presented in order to investigate non-flow correlations and $v_2$ fluctuations. We observe that the difference between $v_2{2}$ and $v_2{4}$ is smaller at the lower collision energies. Values of $v_2$, scaled by the initial coordinate space eccentricity, $v_{2}/\varepsilon$, as a function of $p_T$ are larger in more central collisions, suggesting stronger collective flow develops in more central collisions, similar to the results at higher collision energies. These results are compared to measurements at higher energies at the Relativistic Heavy Ion Collider ($\sqrt{s_{NN}}$ = 62.4 and 200 GeV) and at the Large Hadron Collider (Pb + Pb collisions at $\sqrt{s_{NN}}$ = 2.76 TeV). The $v_2(p_T)$ values for fixed $p_T$ rise with increasing collision energy within the $p_T$ range studied ($< 2 {\rm GeV}/c$). A comparison to viscous hydrodynamic simulations is made to potentially help understand the energy dependence of $v_{2}(p_{T})$. We also compare the $v_2$ results to UrQMD and AMPT transport model calculations, and physics implications on the dominance of partonic versus hadronic phases in the system created at Beam Energy Scan (BES) energies are discussed.Comment: 20 pages, 12 figures. Version accepted by PR

Centrality categorization for R_{p(d)+A} in high-energy collisions

High-energy proton- and deuteron-nucleus collisions provide an excellent tool for studying a wide array of physics effects, including modifications of parton distribution functions in nuclei, gluon saturation, and color neutralization and hadronization in a nuclear environment, among others. All of these effects are expected to have a significant dependence on the size of the nuclear target and the impact parameter of the collision, also known as the collision centrality. In this article, we detail a method for determining centrality classes in p(d)+A collisions via cuts on the multiplicity at backward rapidity (i.e., the nucleus-going direction) and for determining systematic uncertainties in this procedure. For d+Au collisions at sqrt(s_NN) = 200 GeV we find that the connection to geometry is confirmed by measuring the fraction of events in which a neutron from the deuteron does not interact with the nucleus. As an application, we consider the nuclear modification factors R_{p(d)+A}, for which there is a potential bias in the measured centrality dependent yields due to auto-correlations between the process of interest and the backward rapidity multiplicity. We determine the bias correction factor within this framework. This method is further tested using the HIJING Monte Carlo generator. We find that for d+Au collisions at sqrt(s_NN)=200 GeV, these bias corrections are small and vary by less than 5% (10%) up to p_T = 10 (20) GeV. In contrast, for p+Pb collisions at sqrt(s_NN) = 5.02 TeV we find these bias factors are an order of magnitude larger and strongly p_T dependent, likely due to the larger effect of multi-parton interactions.Comment: 375 authors, 18 pages, 16 figures, 4 tables. Submitted to Phys. Rev. C. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Upsilon (1S+2S+3S) production in d+Au and p+p collisions at sqrt(s_NN)=200 GeV and cold-nuclear matter effects

The three Upsilon states, Upsilon(1S+2S+3S), are measured in d+Au and p+p collisions at sqrt(s_NN)=200 GeV and rapidities 1.2<|y|<2.2 by the PHENIX experiment at the Relativistic Heavy-Ion Collider. Cross sections for the inclusive Upsilon(1S+2S+3S) production are obtained. The inclusive yields per binary collision for d+Au collisions relative to those in p+p collisions (R_dAu) are found to be 0.62 +/- 0.26 (stat) +/- 0.13 (syst) in the gold-going direction and 0.91 +/- 0.33 (stat) +/- 0.16 (syst) in the deuteron-going direction. The measured results are compared to a nuclear-shadowing model, EPS09 [JHEP 04, 065 (2009)], combined with a final-state breakup cross section, sigma_br, and compared to lower energy p+A results. We also compare the results to the PHENIX J/psi results [Phys. Rev. Lett. 107, 142301 (2011)]. The rapidity dependence of the observed Upsilon suppression is consistent with lower energy p+A measurements.Comment: 495 authors, 11 pages, 9 figures, 5 tables. Submitted to Phys. Rev. C. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm