REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments

RNA editing is a relevant epitranscriptome phenomenon able to increase the transcriptome and proteome diversity of eukaryotic organisms. ADAR mediated RNA editing is widespread in humans in which millions of A-to-I changes modify thousands of primary transcripts. RNA editing has pivotal roles in the regulation of gene expression or modulation of the innate immune response or functioning of several neurotransmitter receptors. Massive transcriptome sequencing has fostered the research in this field. Nonetheless, different aspects of the RNA editing biology are still unknown and need to be elucidated. To support the study of A-to-I RNA editing we have updated our REDIportal catalogue raising its content to about 16 millions of events detected in 9642 human RNAseq samples from the GTEx project by using a dedicated pipeline based on the HPC version of the REDItools software. REDIportal now allows searches at sample level, provides overviews of RNA editing profiles per each RNAseq experiment, implements a Gene View module to look at individual events in their genic context and hosts the CLAIRE database. Starting from this novel version, REDIportal will start collecting non-human RNA editing changes for comparative genomics investigations. The database is freely available at http://srv00.recas.ba.infn.it/atlas/index.html

INDIGO-DataCloud: A data and computing platform to facilitate seamless access to e-infrastructures

This paper describes the achievements of the H2020 project INDIGO-DataCloud. The project has provided e-infrastructures with tools, applications and cloud framework enhancements to manage the demanding requirements of scientific communities, either locally or through enhanced interfaces. The middleware developed allows to federate hybrid resources, to easily write, port and run scientific applications to the cloud. In particular, we have extended existing PaaS (Platform as a Service) solutions, allowing public and private e-infrastructures, including those provided by EGI, EUDAT, and Helix Nebula, to integrate their existing services and make them available through AAI services compliant with GEANT interfederation policies, thus guaranteeing transparency and trust in the provisioning of such services. Our middleware facilitates the execution of applications using containers on Cloud and Grid based infrastructures, as well as on HPC clusters. Our developments are freely downloadable as open source components, and are already being integrated into many scientific applications

Azimuthal anisotropy of charged jet production in root s(NN)=2.76 TeV Pb-Pb collisions

We present measurements of the azimuthal dependence of charged jet production in central and semi-central root s(NN) = 2.76 TeV Pb-Pb collisions with respect to the second harmonic event plane, quantified as nu(ch)(2) (jet). Jet finding is performed employing the anti-k(T) algorithm with a resolution parameter R = 0.2 using charged tracks from the ALICE tracking system. The contribution of the azimuthal anisotropy of the underlying event is taken into account event-by-event. The remaining (statistical) region-to-region fluctuations are removed on an ensemble basis by unfolding the jet spectra for different event plane orientations independently. Significant non-zero nu(ch)(2) (jet) is observed in semi-central collisions (30-50% centrality) for 20 <p(T)(ch) (jet) <90 GeV/c. The azimuthal dependence of the charged jet production is similar to the dependence observed for jets comprising both charged and neutral fragments, and compatible with measurements of the nu(2) of single charged particles at high p(T). Good agreement between the data and predictions from JEWEL, an event generator simulating parton shower evolution in the presence of a dense QCD medium, is found in semi-central collisions. (C) 2015 CERN for the benefit of the ALICE Collaboration. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).Peer reviewe

Forward-central two-particle correlations in p-Pb collisions at root s(NN)=5.02 TeV

Two-particle angular correlations between trigger particles in the forward pseudorapidity range (2.5 2GeV/c. (C) 2015 CERN for the benefit of the ALICE Collaboration. Published by Elsevier B. V.Peer reviewe

Event-shape engineering for inclusive spectra and elliptic flow in Pb-Pb collisions at root(NN)-N-S=2.76 TeV

Peer reviewe

Pseudorapidity and transverse-momentum distributions of charged particles in proton-proton collisions at root s=13 TeV

The pseudorapidity (eta) and transverse-momentum (p(T)) distributions of charged particles produced in proton-proton collisions are measured at the centre-of-mass energy root s = 13 TeV. The pseudorapidity distribution in vertical bar eta vertical bar <1.8 is reported for inelastic events and for events with at least one charged particle in vertical bar eta vertical bar <1. The pseudorapidity density of charged particles produced in the pseudorapidity region vertical bar eta vertical bar <0.5 is 5.31 +/- 0.18 and 6.46 +/- 0.19 for the two event classes, respectively. The transverse-momentum distribution of charged particles is measured in the range 0.15 <p(T) <20 GeV/c and vertical bar eta vertical bar <0.8 for events with at least one charged particle in vertical bar eta vertical bar <1. The evolution of the transverse momentum spectra of charged particles is also investigated as a function of event multiplicity. The results are compared with calculations from PYTHIA and EPOS Monte Carlo generators. (C) 2015 CERN for the benefit of the ALICE Collaboration. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).Peer reviewe

Elliptic flow of muons from heavy-flavour hadron decays at forward rapidity in Pb-Pb collisions at root s(NN)=2.76TeV

The elliptic flow, v(2), of muons from heavy-flavour hadron decays at forward rapidity (2.5 <y <4) is measured in Pb-Pb collisions at root s(NN)= 2.76TeVwith the ALICE detector at the LHC. The scalar product, two- and four-particle Q cumulants and Lee-Yang zeros methods are used. The dependence of the v(2) of muons from heavy-flavour hadron decays on the collision centrality, in the range 0-40%, and on transverse momentum, p(T), is studied in the interval 3 <p(T)<10 GeV/c. A positive v(2) is observed with the scalar product and two-particle Q cumulants in semi-central collisions (10-20% and 20-40% centrality classes) for the p(T) interval from 3 to about 5GeV/c with a significance larger than 3 sigma, based on the combination of statistical and systematic uncertainties. The v(2) magnitude tends to decrease towards more central collisions and with increasing pT. It becomes compatible with zero in the interval 6 <p(T)<10 GeV/c. The results are compared to models describing the interaction of heavy quarks and open heavy-flavour hadrons with the high-density medium formed in high-energy heavy-ion collisions. (C) 2015 CERN for the benefit of the ALICE Collaboration. Published by Elsevier B.V.Peer reviewe

Centrality evolution of the charged-particle pseudorapidity density over a broad pseudorapidity range in Pb-Pb collisions at root s(NN)=2.76TeV

Peer reviewe

Identified charged hadron production in Pb-Pb collisions with event shape engineering

The Event Shape Engineering technique allows the selection of different event shapes for a definite centrality and colliding system. The event selection is based on the azimuthal distribution of produced particles, using the so-called flow vector. For such shape selected events, the elliptic flow coefficient (v(2)) is significantly different with respect to the unbiased events. Moreover, recent Monte-Carlo studies show a strong correlation between the (final state) event shape selection and the (initial state) eccentricity of the collision. This opens the opportunity to characterize events according to the initial geometry. An approach to select the eccentricity of the event with the Event Shape Engineering is presented. Then the effect of this selection on identified particle spectra, mean transverse momentum and v(2) of charged particles in heavy-ion collisions at $\sqrt{s_{NN}}$ = 2.76 TeV center-of-mass energy is discussed

Study of the effect of the initial geometry on elliptic flow and charged hadron production in Pb-Pb collisions with ALICE

The aim of the ALICE experiment (A Large Ion Collider Experiment) at the LHC is the study of the nuclear matter under conditions of extreme energy density and temperature. Under these conditions the formation of a deconfined phase called Quark Gluon Plasma (QGP) is predicted by lattice QCD. In this phase, quarks and gluons are no longer confined to individual nucleons. A transition from the QGP state into a hadronic state should have occurred during the early stages of Universe, due to its expansion and to the consequent decrease of the temperature. Collisions of heavy nucleons at relativistic energy create in the laboratory the conditions for the hot and dense environment required for the phase transition. The ALICE experiment is dedicated to the study of the deconfined state of strongly interacting matter. Heavy-ions are extended object and the system created in central nucleus- nucleus collisions is different from the one created in peripheral collisions. In par- ticular, for non-central collisions, in the plane perpendicular to the beam direction, the geometrical overlap region is highly anisotropic. This initial spatial asymmetry is converted via interactions into an anisotropy in the momentum space. Measure- ments of this modulation, known as anisotropic transverse flow, provide insight into the collective evolution and the early stages of a relativistic heavy-ion collision. The QGP exhibits strong collectivity, behaving as a nearly perfect liquid as observed at RHIC. The collective properties of the system can be stud- ied through the transverse momentum (pT ) distributions and the measurement of the anisotropy of the particle distributions. The pT distributions allow to extract information about the collective transverse expansion (radial flow) and the tem- perature at the moment when the hadrons decouple from the system. On the other hand the magnitude of the anisotropic flow can be characterized by the coefficients in the Fourier expansion of the azimuthal distribution of particles. The dominant coefficient for non central collision is the second harmonic, v2, which is called elliptic flow. It has been observed and extensively studied in nuclear collisions from sub-relativistic energies on up to RHIC and LHC energies. For the collisions of two smooth spheres, one would expect all odd harmonics to vanish due to symmetry reasons. However, due to event-by-event fluctuations in the positions of the participating nucleons inside the nuclei, the shape of the initial energy density of the heavy-ion collision is, in general, not symmetric with respect to the reaction plane, defined by the beam direction and the impact parameter. This gives rise to non-zero odd harmonic coefficients. In recent years the understanding of the initial geometry fluctuations and their role in the formation of final state anisotropic flow has significantly improved. Con- trolling the initial conditions in heavy-ion collisions would provide the possibility of detailed studies of the properties of the high density hot QCD matter. The Event Shape Engineering (ESE) technique allows the selection of different event shapes for a definite centrality and colliding system. The event selection is based on the azimuthal distribution of produced particles, using the so-called flow vector. Recent Monte-Carlo studies show a strong correlation between the (final state) event shape selection and the (initial state) eccentricity of the collision. This opens many new possibilities to study the properties of the system created in high energy nucleus-nucleus collisions, allowing to characterize events according to the initial geometry. In particular the event shape selection allows investigating the non trivial cor- relation between elliptic and radial flow. In this thesis we present a measurement of the pT distributions of primary particles in strongly or weakly anisotropic envi- ronments, at fixed impact parameter. In the first chapter a brief introduction to the physics of the QGP is given, focusing on the global characteristics of heavy ion collisions and the time evolution of the created system. A brief overview of the most recent results at RHIC and LHC experiments is also presented. In the second chapter we present a basic introduction to hydrodynamic models, which provide the theoretical framework, for the understanding the connection be- tween initial condition dynamic and the hydrodynamic response of the system cre- ated in nucleus-nucleus collisions. Furthermore, recent measurements of a large set of flow observables associated with event-shape fluctuations and collective expan- sion in heavy ion collisions are discussed. The experimental results are presented and compared to theoretical calculations. New types of fluctuation measurements, that can further improve our understanding of the event-shape fluctuations and collective expansion dynamics, are discussed. The third chapter is devoted to the description of the ALICE experiment. After a general overview of the apparatus, the the ALICE particle identification capabilities are described. In chapter 5 an approach to select the eccentricity of the event with the Event Shape Engineering is presented. The effect of this selection on the elliptic flow coefficient and identified particle spectra in Pb–Pb collisions at \sqrt{s_{NN}} = 2.76 TeV center-of-mass energy are discussed in chapter 6 and 7, respectively. The final results on the elliptic flow and the pT distributions of charged hadrons in event shape selected events are discussed in chapter 8