PubServer: literature searches by homology.

PubServer, available at http://pubserver.burnham.org/, is a tool to automatically collect, filter and analyze publications associated with groups of homologous proteins. Protein entries in databases such as Entrez Protein database at NCBI contain information about publications associated with a given protein. The scope of these publications varies a lot: they include studies focused on biochemical functions of individual proteins, but also reports from genome sequencing projects that introduce tens of thousands of proteins. Collecting and analyzing publications related to sets of homologous proteins help in functional annotation of novel protein families and in improving annotations of well-studied protein families or individual genes. However, performing such collection and analysis manually is a tedious and time-consuming process. PubServer automatically collects identifiers of homologous proteins using PSI-Blast, retrieves literature references from corresponding database entries and filters out publications unlikely to contain useful information about individual proteins. It also prepares simple vocabulary statistics from titles, abstracts and MeSH terms to identify the most frequently occurring keywords, which may help to quickly identify common themes in these publications. The filtering criteria applied to collected publications are user-adjustable. The results of the server are presented as an interactive page that allows re-filtering and different presentations of the output

PubServer: literature searches by homology.

PubServer, available at http://pubserver.burnham.org/, is a tool to automatically collect, filter and analyze publications associated with groups of homologous proteins. Protein entries in databases such as Entrez Protein database at NCBI contain information about publications associated with a given protein. The scope of these publications varies a lot: they include studies focused on biochemical functions of individual proteins, but also reports from genome sequencing projects that introduce tens of thousands of proteins. Collecting and analyzing publications related to sets of homologous proteins help in functional annotation of novel protein families and in improving annotations of well-studied protein families or individual genes. However, performing such collection and analysis manually is a tedious and time-consuming process. PubServer automatically collects identifiers of homologous proteins using PSI-Blast, retrieves literature references from corresponding database entries and filters out publications unlikely to contain useful information about individual proteins. It also prepares simple vocabulary statistics from titles, abstracts and MeSH terms to identify the most frequently occurring keywords, which may help to quickly identify common themes in these publications. The filtering criteria applied to collected publications are user-adjustable. The results of the server are presented as an interactive page that allows re-filtering and different presentations of the output

Multiplicity dependence of light (anti-)nuclei production in p–Pb collisions at sNN=5.02 TeV

The measurement of the deuteron and anti-deuteron production in the rapidity range −1 < y < 0 as a function of transverse momentum and event multiplicity in p–Pb collisions at √sNN = 5.02 TeV is presented. (Anti-)deuterons are identified via their specific energy loss dE/dx and via their time-of- flight. Their production in p–Pb collisions is compared to pp and Pb–Pb collisions and is discussed within the context of thermal and coalescence models. The ratio of integrated yields of deuterons to protons (d/p) shows a significant increase as a function of the charged-particle multiplicity of the event starting from values similar to those observed in pp collisions at low multiplicities and approaching those observed in Pb–Pb collisions at high multiplicities. The mean transverse particle momenta are extracted from the deuteron spectra and the values are similar to those obtained for p and particles. Thus, deuteron spectra do not follow mass ordering. This behaviour is in contrast to the trend observed for non-composite particles in p–Pb collisions. In addition, the production of the rare 3He and 3He nuclei has been studied. The spectrum corresponding to all non-single diffractive p-Pb collisions is obtained in the rapidity window −1 < y < 0 and the pT-integrated yield dN/dy is extracted. It is found that the yields of protons, deuterons, and 3He, normalised by the spin degeneracy factor, follow an exponential decrease with mass number

Measurement of the Cross Sections of Ξc0\Xi^0_{c} and Ξc+\Xi^+_{c} Baryons and of the Branching-Fraction Ratio BR(Ξc0→Ξ−e+νe\Xi^0_{c} \rightarrow \Xi^-{e}^+\nu_{ e})/BR(Ξc0→Ξ−π+\Xi^0_{c} \rightarrow \Xi^-\pi^+) in pp collisions at 13 TeV

The $p_T$-differential cross sections of prompt charm-strange baryons Ξ$_c^0$ and Ξ$_c^+$ were measured at midrapidity (|y|<0.5) in proton-proton (pp) collisions at a center-of-mass energy $\sqrt{s}$ = 13 TeV with the ALICE detector at the LHC. The Ξ$_c^0$ baryon was reconstructed via both the semileptonic decay (Ξ$^-$e$^+$ν$_e$) and the hadronic decay (Ξ$^-$π$^+$) channels. The Ξ$_c^+$ baryon was reconstructed via the hadronic decay (Ξ$^-$π$^+$π$^+$) channel. The branching-fraction ratio BR(Ξ$_c^0$→Ξ$^-$e$^+$ν$_e$)/BR(Ξ$_c^0$→Ξ$^-$π$^+$) = 1.38±0.14(stat)±0.22(syst) was measured with a total uncertainty reduced by a factor of about 3 with respect to the current world average reported by the Particle Data Group. The transverse momentum ($p_T$) dependence of the Ξ$_c^0-$ and Ξ$_c^+$-baryon production relative to the D$^0$ meson and to the Σ$_c^{0,+,++}$- and Λ$_c^+$-baryon production are reported. The baryon-to-meson ratio increases toward low $p_T$ up to a value of approximately 0.3. The measurements are compared with various models that take different hadronization mechanisms into consideration. The results provide stringent constraints to these theoretical calculations and additional evidence that different processes are involved in charm hadronization in electron-positron (e$^+$e$^-$) and hadronic collisions

Measurements of the groomed and ungroomed jet angularities in pp collisions at s \sqrt{s} = 5.02 TeV

International audienceThe jet angularities are a class of jet substructure observables which characterize the angular and momentum distribution of particles within jets. These observables are sensitive to momentum scales ranging from perturbative hard scatterings to nonperturbative fragmentation into final-state hadrons. We report measurements of several groomed and ungroomed jet angularities in pp collisions at $\sqrt{s}$ = 5.02 TeV with the ALICE detector. Jets are reconstructed using charged particle tracks at midrapidity (|η| < 0.9). The anti-k$_{T}$ algorithm is used with jet resolution parameters R = 0.2 and R = 0.4 for several transverse momentum {p}_{\mathrm{T}}^{\mathrm{ch}} ^{jet} intervals in the 20–100 GeV/c range. Using the jet grooming algorithm Soft Drop, the sensitivity to softer, wide-angle processes, as well as the underlying event, can be reduced in a way which is well-controlled in theoretical calculations. We report the ungroomed jet angularities, λ$_{α}$, and groomed jet angularities, λ$_{α,g}$, to investigate the interplay between perturbative and nonperturbative effects at low jet momenta. Various angular exponent parameters α = 1, 1.5, 2, and 3 are used to systematically vary the sensitivity of the observable to collinear and soft radiation. Results are compared to analytical predictions at next-to-leading-logarithmic accuracy, which provide a generally good description of the data in the perturbative regime but exhibit discrepancies in the nonperturbative regime. Moreover, these measurements serve as a baseline for future ones in heavy-ion collisions by providing new insight into the interplay between perturbative and nonperturbative effects in the angular and momentum substructure of jets. They supply crucial guidance on the selection of jet resolution parameter, jet transverse momentum, and angular scaling variable for jet quenching studies.[graphic not available: see fulltext

Measurement of K∗^{*}(892)±^{\mathrm{\pm}} production in inelastic pp collisions at the LHC

International audienceThe first results on K⁎(892)± resonance production in inelastic pp collisions at LHC energies of s=5.02, 8, and 13 TeV are presented. The K⁎(892)± has been reconstructed via its hadronic decay channel K⁎(892)→±KS0+π± with the ALICE detector. Measurements of transverse momentum distributions, pT-integrated yields, and mean transverse momenta for charged K⁎(892) are found to be consistent with previous ALICE measurements for neutral K⁎(892) within uncertainties. For pT&gt;1 GeV/c the K⁎(892)± transverse momentum spectra become harder with increasing centre-of-mass energy from 5.02 to 13 TeV, similar to what previously observed for charged kaons and pions. For pT&lt;1 GeV/c the K⁎(892)± yield does not evolve significantly and the abundance of K⁎(892)± relative to K is rather independent of the collision energy. The transverse momentum spectra, measured for K⁎(892)± at midrapidity in the interval 0 &lt;pT&lt;15 GeV/c, are not well described by predictions of different versions of PYTHIA 6, PYTHIA 8 and EPOS-LHC event generators. These generators reproduce the measured pT-integrated K⁎±/K ratios and describe well the momentum dependence for pT&lt;2 GeV/c

Hypertriton production in p–Pb collisions at √sNN = 5.02 TeV

The study of nuclei and antinuclei production has proven to be a powerful tool to investigate the formation mechanism of loosely bound states in high-energy hadronic collisions. The first measurement of the production of 3ΛH in p-Pb collisions at sNN−−−√ = 5.02 TeV is presented in this Letter. Its production yield measured in the rapidity interval −1<y<0 for the 40% highest multiplicity p-Pb collisions is dN/dy=[6.3±1.8(stat.)±1.2(syst.)]×10−7. The measurement is compared with the expectations of statistical hadronisation and coalescence models, which describe the nucleosynthesis in hadronic collisions. These two models predict very different yields of the hypertriton in charged particle multiplicity environments relevant to small collision systems such as p-Pb and therefore the measurement of dN/dy is crucial to distinguish between them. The precision of this measurement leads to the exclusion with a significance larger than 6.9σ of some configurations of the statistical hadronization model, thus constraining the theory behind the production of loosely bound states at hadron colliders

Production of K∗(892)0^{*}(892)^{0} and ϕ(1020)\phi(1020) in pp and Pb-Pb collisions at sNN=5.02\sqrt{s_{\rm NN}} = 5.02 TeV

The production of K$^{*}(892)^{0}$ and $\phi(1020)$ mesons in proton-proton (pp) and lead-lead (Pb-Pb) collisions at $\sqrt{s_\mathrm{NN}} = 5.02$ TeV has been measured using the ALICE detector at the Large Hadron Collider (LHC). The transverse momentum ($p_{\mathrm{T}}$) distributions of K$^{*}(892)^{0}$ and $\phi(1020)$ mesons have been measured at midrapidity $(|y| 8$ GeV$/c$, the $R_{\rm AA}$ values of K$^{*}(892)^{0}$ and $\phi(1020)$ are below unity and observed to be similar to those of pions, kaons, and (anti)protons. The $R_{\rm AA}$ values at high $p_{\mathrm T}$ for K$^{*}(892)^{0}$ and $\phi(1020)$ mesons are in agreement within uncertainties for $\sqrt{s_\mathrm{NN}} = 5.02$ and 2.76 TeV

Charm-quark fragmentation fractions and production cross section at midrapidity in pp collisions at the LHC

International audienceRecent pT-integrated cross-section measurements of the ground-state charm mesons and baryons, D0, D+, Ds+, Λc+, and Ξc0, are used to evaluate the charm fragmentation fractions and production cross section per unit of rapidity at midrapidity (|y|&lt;0.5), in pp collisions at s=5.02  TeV at the LHC. The latter is dσcc¯/dy||y|&lt;0.5=1165±44(stat)-101+134(syst)  μb. These measurements were obtained for the first time in hadronic collisions at the LHC, including the charm baryon states, recently measured by ALICE at midrapidity. The charm fragmentation fractions differ significantly from the values measured in e+e- and ep collisions, providing evidence of the dependence of the parton-to-hadron fragmentation fractions on the collision system, indicating that the assumption of their universality is not supported by the measured cross sections. An increase of a factor of about 3.3 for the fragmentation fraction for the Λc+ with a significance of 5σ between the values obtained in pp collisions and those obtained in e+e- (ep) collisions is reported. The fragmentation fraction for the Ξc0 was obtained for the first time in any collision system. The measured fragmentation fractions were used to update the cc¯ cross sections per unit of rapidity at |y|&lt;0.5 at s=2.76 and 7 TeV, which are about 40% higher than the previously published results. The data were compared with perturbative-QCD calculations and lie at the upper edge of the theoretical bands