Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

P09-A130 Management of an eye bank with organ-cultured and hypothermic corneas: microbiology in endothelial grafts

Eye bank; Endothelial graftsBanco de ojos; Injertos endotelialesBanc d'ulls; Empelts endotelialsPurpose To analyse the microbiologic control results taken during the processing of hypothermic and cultured corneas for endothelial transplants comparing the two groups from January to September 2022. METHODS The microbiological controls of hypothermic corneas prepared for DSAEK or DMEK are: Transport Eusol control (pre-manipulation) and new Eusol control (post-manipulation). In cultured corneas the number of controls is increased to 4: first culture medium, evaluation culture medium, transport medium 24 hours post-evaluation and transport medium post-manipulation. RESULTS A total of 1438 corneas were processed for transplant during the 9 months studied (321 fresh corneas and 1113 cultured corneas). A total of 557 corneas were prepared for DSAEK or DMEK, from which 89 (15,98%) were hypothermic corneas and 468 (84.O2%) were cultured. From hypothermic corneas, 65 were cut for DSAEK and with 24 corneas, pre-stripping for DMEK was done. In the case of cultured corneas, 187 were cut for DSAEK and with 281 pre-stripping for DMEK was done. The number of corneas with positive results in the microbiological controls were 15 (16,85%) in the case of fresh corneas (in 7 corneas that were prepared for DSAEK and in 8 for DMEK) and 4 cases (0,85%) in cultured corneas (in 3 corneas for DSAEK and in 1 corneas for DMEK) resulting in a clear difference between both preservation methods. Bio-surveillance notifications notified during the studied period have been a total of 5, from which 2 were SAE in hypothermic corneas and other 2 were SAE and 1 SAR, in cultured corneas, all for endothelial transplantations. Conclusion The number of positive results for microorganisms was higher in the case of hypothermic corneas and the Bio-surveillance notifications were also a little bit higher in hypothermic corneas (2,25%) comparing to organ cultured corneas (0.64%). The management of an eye bank with both preservation systems is challenging with its advantages and disadvantages. The main disadvantage of hypothermic corneas is the risk of not detecting contaminations because the corneas are released without any definitive results but it is compensated by the fact that they allow us to respond to emergencies, tissue returns, apart from the economic aspect

Where Brain, Body and World Collide

The production cross section of electrons from semileptonic decays of beauty hadrons was measured at mid-rapidity (|y| < 0.8) in the transverse momentum range 1 < pt < 8 Gev/c with the ALICE experiment at the CERN LHC in pp collisions at a center of mass energy sqrt{s} = 7 TeV using an integrated luminosity of 2.2 nb^{-1}. Electrons from beauty hadron decays were selected based on the displacement of the decay vertex from the collision vertex. A perturbative QCD calculation agrees with the measurement within uncertainties. The data were extrapolated to the full phase space to determine the total cross section for the production of beauty quark-antiquark pairs

Particle production as a function of charged-particle flattenicity in pp collisions at s\sqrt{s} = 13 TeV

International audienceThis paper reports the first measurement of the transverse momentum ($p_{\mathrm{T}}$) spectra of primary charged pions, kaons, (anti)protons, and unidentified particles as a function of the charged-particle flattenicity in pp collisions at $\sqrt{s}=13$ TeV. Flattenicity is a novel event shape observable that is measured in the pseudorapidity intervals covered by the V0 detector, $2.8<\eta<5.1$ and $-3.7<\eta<-1.7$. According to QCD-inspired phenomenological models, it shows sensitivity to multiparton interactions and is less affected by biases towards larger $p_{\mathrm{T}}$ due to local multiplicity fluctuations in the V0 acceptance than multiplicity. The analysis is performed in minimum-bias (MB) as well as in high-multiplicity events up to $p_{\mathrm{T}}=20$ GeV/$c$. The event selection requires at least one charged particle produced in the pseudorapidity interval $|\eta|<1$. The measured $p_{\mathrm{T}}$ distributions, average $p_{\mathrm{T}}$, kaon-to-pion and proton-to-pion particle ratios, presented in this paper, are compared to model calculations using PYTHIA 8 based on color strings and EPOS LHC. The modification of the $p_{\mathrm{T}}$-spectral shapes in low-flattenicity events that have large event activity with respect to those measured in MB events develops a pronounced peak at intermediate $p_{\mathrm{T}}$ ($2<p_{\mathrm{T}}<8$ GeV/$c$), and approaches the vicinity of unity at higher $p_{\mathrm{T}}$. The results are qualitatively described by PYTHIA, and they show different behavior than those measured as a function of charged-particle multiplicity based on the V0M estimator

Exclusive four pion photoproduction in ultraperipheral Pb-Pb collisions at sNN=5.02\sqrt{s_{\rm NN}} = 5.02 TeV

International audienceThe intense photon fluxes from relativistic nuclei provide an opportunity to study photonuclear interactions in ultraperipheral collisions. The measurement of coherently photoproduced $\pi^+\pi^-\pi^+\pi^-$ final states in ultraperipheral Pb-Pb collisions at $\sqrt{s_{\mathrm{NN}}}=5.02$ TeV is presented for the first time. The cross section, d$\sigma$/d$y$, times the branching ratio ($\rho\rightarrow \pi^+ \pi^+ \pi^- \pi^-$) is found to be $47.8\pm2.3~\rm{(stat.)}\pm7.7~\rm{(syst.)}$ mb in the rapidity interval $|y| < 0.5$. The invariant mass distribution is not well described with a single Breit-Wigner resonance. The production of two interfering resonances, $\rho(1450)$ and $\rho(1700)$, provides a good description of the data. The values of the masses ($m$) and widths ($\Gamma$) of the resonances extracted from the fit are $m_{1}=1385\pm14~\rm{(stat.)}\pm3~\rm{(syst.)}$ MeV/$c^2$, $\Gamma_{1}=431\pm36~\rm{(stat.)}\pm82~\rm{(syst.)}$ MeV/$c^2$, $m_{2}=1663\pm13~\rm{(stat.)}\pm22~\rm{(syst.)}$ MeV/$c^2$ and $\Gamma_{2}=357 \pm31~\rm{(stat.)}\pm49~\rm{(syst.)}$ MeV/$c^2$, respectively. The measured cross sections times the branching ratios are compared to recent theoretical predictions

Measurement of Λ3H{}_{\Lambda}^{3}\mathrm{H} production in Pb-Pb collisions at sNN\sqrt{s_{\mathrm{NN}}} = 5.02 TeV

International audienceThe first measurement of $_{\Lambda}^{3}\mathrm{H}$ and $^3_ {\overline{\Lambda}}\overline{\mathrm{H}}$ differential production with respect to transverse momentum and centrality in Pb$-$Pb collisions at $\sqrt{s_{\mathrm{NN}}}=5.02$~TeV is presented. The $_{\Lambda}^{3}\mathrm{H}$ has been reconstructed via its two-charged-body decay channel, i.e., $_{\Lambda}^{3}\mathrm{H} \rightarrow {}^{3}\mathrm{He} + \pi^{-}$. A Blast-Wave model fit of the $p_{\rm T}$-differential spectra of all nuclear species measured by the ALICE collaboration suggests that the $_{\Lambda}^{3}\mathrm{H}$ kinetic freeze-out surface is consistent with that of other nuclei. The ratio between the integrated yields of $_{\Lambda}^{3}\mathrm{H}$ and $^3\mathrm{He}$ is compared to predictions from the statistical hadronisation model and the coalescence model, with the latter being favoured by the presented measurements

J/ψ\psi-hadron correlations at midrapidity in pp collisions at s\sqrt{s} = 13 TeV

International audienceWe report on the measurement of inclusive, non-prompt, and prompt J/$\psi$-hadron correlations by the ALICE Collaboration at the CERN Large Hadron Collider in pp collisions at a center-of-mass energy of 13 TeV. The correlations are studied at midrapidity ($|y| < 0.9$) in the transverse momentum ranges $p_{\rm T} < 40~\text{GeV}/c$ for the J/$\psi$ and $0.15 < p_{\rm T} < 10$ GeV/$c$ and $|\eta|<0.9$ for the associated hadrons. The measurement is based on minimum bias and high multiplicity data samples corresponding to integrated luminosities of $L_{\text{int}} = 34~\text{nb}^{-1}$ and $L_{\text{int}} = 6.9~\text{pb}^{-1}$, respectively. In addition, two more data samples are employed, requiring, on top of the minimum bias condition, a threshold on the tower energy of $E = 4$ and $9~\text{GeV}$ in the ALICE electromagnetic calorimeters, which correspond to integrated luminosities of $L_{\text{int}} = 0.9~\text{pb}^{-1}$ and $L_{\text{int}} = 8.4~\text{pb}^{-1}$, respectively. The results are presented as associated hadron yields per J/$\psi$ trigger as a function of the azimuthal angle difference between the associated hadrons and J/$\psi$ mesons. The integrated near-side and away-side correlated yields are also extracted as a function of the J/$\psi$ transverse momentum. The measurements are discussed in comparison to PYTHIA calculations

Charm fragmentation fractions and cc‾{\rm c\overline{c}} cross section in p−-Pb collisions at sNN=5.02\sqrt{s_{\rm NN}}=5.02 TeV

International audienceThe total charm-quark production cross section per unit of rapidity $\mathrm{d}\sigma({\rm c\overline{c}})/\mathrm{d}y$, and the fragmentation fractions of charm quarks to different charm-hadron species $f(\mathrm{c}\rightarrow {\rm h_{c}})$, are measured for the first time in p$-$Pb collisions at $\sqrt{s_\mathrm{NN}} = 5.02$ TeV at midrapidity ($-0.96<y<0.04$ in the centre-of-mass frame) using data collected by ALICE at the CERN LHC. The results are obtained based on all the available measurements of prompt production of ground-state charm-hadron species: $\mathrm{D}^{0}$, $\mathrm{D}^{+}$, $\mathrm{D}_\mathrm{s}^{+}$, and $\mathrm{J/\psi}$ mesons, and $\Lambda_\mathrm{c}^{+}$ and $\Xi_{\rm c}^{0}$ baryons. The resulting cross section is $\mathrm{d}\sigma({\rm c\overline{c}})/\mathrm{d}y =219.6 \pm 6.3\;(\mathrm{stat.}) {\;}_{-11.8}^{+10.5}\;(\mathrm{syst.}) {\;}_{-2.9}^{+7.6}\;(\mathrm{extr.})\pm 5.4\;(\mathrm{BR})\pm 4.6\;(\mathrm{lumi.}) \pm 19.5\;(\text{rapidity shape})+15.0\;(\Omega_{\rm c}^{0})$ mb, which is consistent with a binary scaling of pQCD calculations from pp collisions. The measured fragmentation fractions are compatible with those measured in pp collisions at $\sqrt{s} = 5.02$ and $13$ TeV, showing an increase in the relative production rates of charm baryons with respect to charm mesons in pp and p$-$Pb collisions compared with $\mathrm{e^{+}e^{-}}$ and $\mathrm{e^{-}p}$ collisions. The $p_\mathrm{T}$-integrated nuclear modification factor of charm quarks, $R_\mathrm{pPb}({\rm c\overline{c}})= 0.91 \pm 0.04\;{\rm (stat.)}{}^{+0.08}_{-0.09}\;{\rm (syst.)}{}^{+0.04}_{-0.03}\;{\rm (extr.)}{}\pm 0.03\;{\rm (lumi.)}$, is found to be consistent with unity and with theoretical predictions including nuclear modifications of the parton distribution functions