Novel Protein-Protein Interactions Inferred from Literature Context

We have developed a method that predicts Protein-Protein Interactions (PPIs) based on the similarity of the context in which proteins appear in literature. This method outperforms previously developed PPI prediction algorithms that rely on the conjunction of two protein names in MEDLINE abstracts. We show significant increases in coverage (76% versus 32%) and sensitivity (66% versus 41% at a specificity of 95%) for the prediction of PPIs currently archived in 6 PPI databases. A retrospective analysis shows that PPIs can efficiently be predicted before they enter PPI databases and before their interaction is explicitly described in the literature. The practical value of the method for discovery of novel PPIs is illustrated by the experimental confirmation of the inferred physical interaction between CAPN3 and PARVB, which was based on frequent co-occurrence of both proteins with concepts like Z-disc, dysferlin, and alpha-actinin. The relationships between proteins predicted by our method are broader than PPIs, and include proteins in the same complex or pathway. Dependent on the type of relationships deemed useful, the precision of our method can be as high as 90%. The full set of predicted interactions is available in a downloadable matrix and through the webtool Nermal, which lists the most likely interaction partners for a given protein. Our framework can be used for prioritizing potential interaction partners, hitherto undiscovered, for follow-up studies and to aid the generation of accurate protein interaction maps

2018 Research & Innovation Day Program

A one day showcase of applied research, social innovation, scholarship projects and activities.https://first.fanshawec.ca/cri_cripublications/1005/thumbnail.jp

phi-Meson production at forward rapidity in p-Pb collisions at root s(NN)=5.02 TeV and in pp collisions at root s=2.76 TeV

The first study of phi-meson production in p-Pb collisions at forward and backward rapidity, at a nucleonnucleon centre-of-mass energy root s(NN)= 5.02 TeV, has been performed with the ALICE apparatus at the LHC. The phi-mesons have been identified in the dimuon decay channel in the transverse momentum (p(T)) range 1 <p(T) <7GeV/c, both in the p-going (2.03 <y <3.53) and the Pb-going (-4.46 <y <-2.96) directions - where ystands for the rapidity in the nucleon-nucleon centre-of-mass - the integrated luminosity amounting to 5.01 +/- 0.19nb(-1) and 5.81 +/- 0.20nb(-1), respectively, for the two data samples. Differential cross sections as a function of transverse momentum and rapidity are presented. The forward-backward ratio for f-meson production is measured for 2.96Peer reviewe

Measurement of D-s(+) product ion and nuclear modification factor in Pb-Pb collisions at root S-NN=2.76 TeV

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Measurement of transverse energy at midrapidity in Pb-Pb collisions at root s(NN)=2.76 TeV

We report the transverse energy (ET) measured with ALICE at midrapidity in Pb-Pb collisions at root s(NN) = 2.76 TeV as a function of centrality. The transverse energy was measured using identified single-particle tracks. The measurement was cross checked using the electromagnetic calorimeters and the transverse momentum distributions of identified particles previously reported by ALICE. The results are compared to theoretical models as well as to results from other experiments. The mean ET per unit pseudorapidity (eta), , in 0%-5% central collisions is 1737 +/- 6(stat.) +/- 97(sys.) GeV. We find a similar centrality dependence of the shape of as a function of the number of participating nucleons to that seen at lower energies. The growth in at the LHC energies exceeds extrapolations of low-energy data. We observe a nearly linear scaling of with the number of quark participants. With the canonical assumption of a 1 fm/c formation time, we estimate that the energy density in 0%-5% central Pb-Pb collisions at root s(NN) = 2.76 TeV is 12.3 +/- 1.0 GeV/fm(3) and that the energy density at the most central 80 fm(2) of the collision is at least 21.5 +/- 1.7 GeV/fm(3). This is roughly 2.3 times that observed in 0%-5% central Au-Au collisions at root s(NN) = 200 GeV.Peer reviewe

D-meson production in p-Pb collisions at root S-NN=5.02 TeV and in pp collisions at root S=7 TeV

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Correlated Event-by-Event Fluctuations of Flow Harmonics in Pb-Pb Collisions at root S-NN=2.76 TeV

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J/Psi suppression at forward rapidity in Pb-Pb collisions at root s(NN)=5.02 TeV

The inclusive J/Psi production has been studied in Pb-Pb and pp collisions at the centre-of-mass energy per nucleon pair root sNN= 5.02TeV, using the ALICE detector at the CERN LHC. The J/Psi meson is reconstructed, in the centre-of-mass rapidity interval 2.5 <y <4and in the transverse- momentum range p(T)<12GeV/c, via its decay to a muon pair. In this Letter, we present results on the inclusive J/Psi cross section in pp collisions at root s= 5.02TeV and on the nuclear modification factor R-AA. The latter is presented as a function of the centrality of the collision and, for central collisions, as a function of the transverse momentum p(T) of the J/Psi. The measured R-AA values indicate a suppression of the J/Psi in nuclear collisions and are then compared to our previous results obtained in Pb-Pb collisions at root sNN= 2.76TeV. The ratio of the R-AA values at the two energies is also computed and compared to calculations of statistical and dynamical models. The numerical value of the ratio for central events (0-10% centrality) is 1.17 +/- 0.04( stat)+/- 0.20(syst). In central events, as a function of p(T), a slight increase of R-AA with collision energy is visible in the region 2 <p(T)<6GeV/c. Theoretical calculations qualitatively describe the measurements, within uncertainties. (C) 2017 The Author. Published by Elsevier B.V.Peer reviewe

Azimuthally Differential Pion Femtoscopy in Pb-Pb Collisions at root s(NN)=2.76 TeV

We present the first azimuthally differential measurements of the pion source size relative to the second harmonic event plane in Pb-Pb collisions at a center-of-mass energy per nucleon-nucleon pair of root(NN)-N-s = 2.76 TeV. The measurements have been performed in the centrality range 0%-50% and for pion pair transverse momenta 0.2 <k(T) <0.7 GeV/c. We find that the R-side and R-out radii, which characterize the pion source size in the directions perpendicular and parallel to the pion transverse momentum, oscillate out of phase, similar to what was observed at the Relativistic Heavy Ion Collider. The final-state source eccentricity, estimated via R-side oscillations, is found to be significantly smaller than the initial-state source eccentricity, but remains positive-indicating that even after a stronger expansion in the in-plane direction, the pion source at the freeze-out is still elongated in the out-of-plane direction. The 3 + 1D hydrodynamic calculations are in qualitative agreement with observed centrality and transverse momentum R-side oscillations, but systematically underestimate the oscillation magnitude.Peer reviewe