Combined burden and functional impact tests for cancer driver discovery using DriverPower

The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower's background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery

Chiral Symmetry and light resonances in hot and dense matter

We present a study of the $\pi\pi$ scattering amplitude in the $\sigma$ and $\rho$ channels at finite temperature and nuclear density within a chiral unitary framework. Meson resonances are dynamically generated in our approach, which allows us to analyze the behavior of their associated scattering poles when the system is driven towards chiral symmetry restoration. Medium effects are incorporated in three ways: (a) by thermal corrections of the unitarized scattering amplitudes, (b) by finite nuclear density effects associated to a renormalization of the pion decay constant, and complementarily (c) by extending our calculation of the scalar-isoscalar channel to account for finite nuclear density and temperature effects in a microscopic many-body implementation of pion dynamics. Our results are discussed in connection with several phenomenological aspects relevant for nuclear matter and Heavy-Ion Collision experiments, such as $\rho$ mass scaling vs broadening from dilepton spectra and chiral restoration signals in the $\sigma$ channel. We also elaborate on the molecular nature of $\pi\pi$ resonances.Comment: 14 pages, 14 figures. Contribution to Hard Probes 2008, Illa de A Toxa, Spain, June 8th-14th 200

Leading order determination of the gluon polarisation from DIS events with high-p_T hadron pairs

We present a determination of the gluon polarisation Delta g/g in the nucleon, based on the longitudinal double-spin asymmetry of DIS events with a pair of large transverse-momentum hadrons in the final state. The data were obtained by the COMPASS experiment at CERN using a 160 GeV/c polarised muon beam scattering off a polarised ^6LiD target. The gluon polarisation is evaluated by a Neural Network approach for three intervals of the gluon momentum fraction x_g covering the range 0.04 < x_g < 0.27. The values obtained at leading order in QCD do not show any significant dependence on x_g. Their average is Delta g/g = 0.125 +/- 0.060 (stat.) +/- 0.063 (syst.) at x_g=0.09 and a scale of mu^2 = 3 (GeV/c)^2.Comment: 13 pages, 6 figures and 3 table

Measurement of the Collins and Sivers asymmetries on transversely polarised protons

The Collins and Sivers asymmetries for charged hadrons produced in deeply inelastic scattering on transversely polarised protons have been extracted from the data collected in 2007 with the CERN SPS muon beam tuned at 160 GeV/c. At large values of the Bjorken x variable non-zero Collins asymmetries are observed both for positive and negative hadrons while the Sivers asymmetry for positive hadrons is slightly positive over almost all the measured x range. These results nicely support the present theoretical interpretation of these asymmetries, in terms of leading-twist quark distribution and fragmentation functions.Comment: 9 Pages, 5 figure

The Spin-dependent Structure Function of the Proton g_1^p and a Test of the Bjorken Sum Rule

The inclusive double-spin asymmetry, A_1^p, has been measured at COMPASS in deepinelastic polarised muon scattering off a large polarised NH3 target. The data, collected in the year 2007, cover the range Q2 > 1 (GeV/c)^2, 0.004 < x < 0.7 and improve the statistical precision of g_1^p(x) by a factor of two in the region x < 0.02. The new proton asymmetries are combined with those previously published for the deuteron to extract the non-singlet spin-dependent structure function g_1^NS(x,Q2). The isovector quark density, Delta_q_3(x,Q2), is evaluated from a NLO QCD fit of g_1^NS. The first moment of Delta_q3 is in good agreement with the value predicted by the Bjorken sum rule and corresponds to a ratio of the axial and vector coupling constants g_A/g_V = 1.28+-0.07(stat)+-0.10(syst).Comment: 12 pages, 5 figure

Quark helicity distributions from longitudinal spin asymmetries in muon-proton and muon-deuteron scattering

Double-spin asymmetries for production of charged pions and kaons in semi-inclusive deep-inelastic muon scattering have been measured by the COMPASS experiment at CERN. The data, obtained by scattering a 160 GeV muon beam off a longitudinally polarised NH_3 target, cover a range of the Bjorken variable x between 0.004 and 0.7. A leading order evaluation of the helicity distributions for the three lightest quarks and antiquark flavours derived from these asymmetries and from our previous deuteron data is presented. The resulting values of the sea quark distributions are small and do not show any sizable dependence on x in the range of the measurements. No significant difference is observed between the strange and antistrange helicity distributions, both compatible with zero. The integrated value of the flavour asymmetry of the helicity distribution of the light-quark sea, \Delta u-bar - \Delta d-bar, is found to be slightly positive, about 1.5 standard deviations away from zero.Comment: 13 pages, 5 figure

Azimuthal asymmetries of charged hadrons produced by high-energy muons scattered off longitudinally polarised deuterons

Azimuthal asymmetries in semi-inclusive production of positive (h^+) and negative hadrons (h^-) have been measured by scattering 160 GeV muons off longitudinally polarised deuterons at CERN. The asymmetries were decomposed in several terms according to their expected modulation in the azimuthal angle phi of the outgoing hadron. Each term receives contributions from one or several spin and transverse-momentum-dependent parton distribution and fragmentation functions. The amplitudes of all phi-modulation terms of the hadron asymmetries integrated over the kinematic variables are found to be consistent with zero within statistical errors, while the constant terms are nonzero and equal for h^+ and h^- within the statistical errors. The dependencies of the phi-modulated terms versus the Bjorken momentum fraction x, the hadron fractional momentum z, and the hadron transverse momentum p_h^T were studied. The x dependence of the constant terms for both positive and negative hadrons is in agreement with the longitudinal double-spin hadron asymmetries, measured in semi-inclusive deep-inelastic scattering. The x dependence of the sin phi-modulation term is less pronounced than that in the corresponding HERMES data. All other dependencies of the phi-modulation amplitudes are consistent with zero within the statistical errors.Comment: 12 pages, 11 Figures; revision 1 signs in Eq 5 corrected, polishe

Particle-yield modification in jet-like azimuthal di-hadron correlations in Pb-Pb collisions at sNN\sqrt{s_{\rm NN}} = 2.76 TeV

The yield of charged particles associated with high-$p_{\rm T}$ trigger particles ($8 < p_{\rm T} < 15$ GeV/$c$) is measured with the ALICE detector in Pb-Pb collisions at $\sqrt{s_{\rm NN}}$ = 2.76 TeV relative to proton-proton collisions at the same energy. The conditional per-trigger yields are extracted from the narrow jet-like correlation peaks in azimuthal di-hadron correlations. In the 5% most central collisions, we observe that the yield of associated charged particles with transverse momenta $p_{\rm T}> 3$ GeV/$c$ on the away-side drops to about 60% of that observed in pp collisions, while on the near-side a moderate enhancement of 20-30% is found.Comment: 15 pages, 2 captioned figures, 1 table, authors from page 10, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/350

Measurement of charm production at central rapidity in proton-proton collisions at s=2.76\sqrt{s} = 2.76 TeV

The $p_{\rm T}$-differential production cross sections of the prompt (B feed-down subtracted) charmed mesons D$^0$, D$^+$, and D$^{*+}$ in the rapidity range $|y|<0.5$, and for transverse momentum $1< p_{\rm T} <12$ GeV/$c$, were measured in proton-proton collisions at $\sqrt{s} = 2.76$ TeV with the ALICE detector at the Large Hadron Collider. The analysis exploited the hadronic decays D$^0 \rightarrow$K$\pi$, D$^+ \rightarrow$K$\pi\pi$, D$^{*+} \rightarrow$D$^0\pi$, and their charge conjugates, and was performed on a $L_{\rm int} = 1.1$ nb$^{-1}$ event sample collected in 2011 with a minimum-bias trigger. The total charm production cross section at $\sqrt{s} = 2.76$ TeV and at 7 TeV was evaluated by extrapolating to the full phase space the $p_{\rm T}$-differential production cross sections at $\sqrt{s} = 2.76$ TeV and our previous measurements at $\sqrt{s} = 7$ TeV. The results were compared to existing measurements and to perturbative-QCD calculations. The fraction of cdbar D mesons produced in a vector state was also determined.Comment: 20 pages, 5 captioned figures, 4 tables, authors from page 15, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/307