Why old duplicated genes are not thrown away in (paleo)polyploids? Example from the petC gene in Brassica napus

Duplication of genes at different time period, through recurrent and frequent polyploidization events, have played a major role in plant evolution, adaptation and diversification. Interestingly, some of the ancestral duplicated genes (referred as paleologs), have been maintained for millions of years, and there is still a poor knowledge of the reasons of their retention, especially when testing the phenotypic effect of individual copies by using functional genetic approaches. To fill this gap, we performed functional genetic (CRISPR-Cas9), physiological, transcriptomic and evolutionary studies to finely investigate this open question, taking the example of the petC gene (involved in cytochrome b6/f and thus impacting photosynthesis) that is present in four paleologous copies in the oilseed crop Brassica napus. RNA-Seq and selective pressure analyses suggested that all paleologous copies conserved the same function and that they were all highly transcribed. Thereafter, the Knock Out (K.O.) of one, several or all petC copies highlighted that all paleologous copies have to be K.O. to suppress the gene function. In addition, we could determine that phenotypic effects in single and double mutants could only be deciphered in high light conditions. Interestingly, we did not detect any significant differences between single mutants K.O. for either the A03 or A09 copy (despite being differentially transcribed), or even between mutants for a single or two petC copies. Altogether, this work revealed that petC paleologs have retained their ancestral function and that the retention of these copies is explained by their compensatory role, especially in optimal environmental conditions.

Phase stabilization and optical response in the ultraviolet range, due to terbium concentration in hafnium oxide nanoparticles

This work reports the influence of terbium trivalent ions on growing kinetics and the phase in hafnium oxide nanoparticles, as well as response to radiation in the range from 256 to 286. The nanoparticles were obtained by the hydrothermal route maintaining the temperature constant and varying the reaction time and the terbium concentration. The results show a gradual change in the phase with the concentration of terbium trivalent ions, going from the monoclinic phase, present at low concentrations, to the tetragonal phase, which appears from dopant concentrations greater than 5% at., increasing in amount with concentration of dopant. These phases appear as two perfectly defined morphologies. Furthermore, there is a significant change in radiative lifetimes when the tetragonal phase appears.

Evaluation of genome and base editing tools in maize protoplasts

INTRODUCTION

Despite its rapid worldwide adoption as an efficient mutagenesis tool, plant genome editing remains a labor-intensive process requiring often several months of in vitro culture to obtain mutant plantlets. To avoid a waste in time and money and to test, in only a few days, the efficiency of molecular constructs or novel Cas9 variants (clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9) prior to stable transformation, rapid analysis tools are helpful.

METHODS

To this end, a streamlined maize protoplast system for transient expression of CRISPR/Cas9 tools coupled to NGS (next generation sequencing) analysis and a novel bioinformatics pipeline was established.

RESULTS AND DISCUSSION

Mutation types found with high frequency in maize leaf protoplasts had a trend to be the ones observed after stable transformation of immature maize embryos. The protoplast system also allowed to conclude that modifications of the sgRNA (single guide RNA) scaffold leave little room for improvement, that relaxed PAM (protospacer adjacent motif) sites increase the choice of target sites for genome editing, albeit with decreased frequency, and that efficient base editing in maize could be achieved for certain but not all target sites. Phenotypic analysis of base edited mutant maize plants demonstrated that the introduction of a stop codon but not the mutation of a serine predicted to be phosphorylated in the bHLH (basic helix loop helix) transcription factor ZmICEa (INDUCER OF CBF EXPRESSIONa) caused abnormal stomata, pale leaves and eventual plant death two months after sowing.

D-Meson Azimuthal Anisotropy in Midcentral Pb-Pb Collisions at sqrt[s]_{NN}=5.02 TeV

The azimuthal anisotropy coefficient v_{2} of prompt D^{0}, D^{+}, D^{*+}, and D_{s}^{+} mesons was measured in midcentral (30%-50% centrality class) Pb-Pb collisions at a center-of-mass energy per nucleon pair sqrt[s_{NN}]=5.02  TeV, with the ALICE detector at the LHC. The D mesons were reconstructed via their hadronic decays at midrapidity, |y|<0.8, in the transverse momentum interval 1<p_{T}<24  GeV/c. The measured D-meson v_{2} has similar values as that of charged pions. The D_{s}^{+} v_{2}, measured for the first time, is found to be compatible with that of nonstrange D mesons. The measurements are compared with theoretical calculations of charm-quark transport in a hydrodynamically expanding medium and have the potential to constrain medium parameters.

J/ψ Elliptic Flow in Pb-Pb Collisions at sqrt[s_{NN}]=5.02 TeV

We report a precise measurement of the J/ψ elliptic flow in Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV with the ALICE detector at the LHC. The J/ψ mesons are reconstructed at midrapidity (|y|<0.9) in the dielectron decay channel and at forward rapidity (2.5<y<4.0) in the dimuon channel, both down to zero transverse momentum. At forward rapidity, the elliptic flow v_{2} of the J/ψ is studied as a function of the transverse momentum and centrality. A positive v_{2} is observed in the transverse momentum range 2<p_{T}<8  GeV/c in the three centrality classes studied and confirms with higher statistics our earlier results at sqrt[s_{NN}]=2.76  TeV in semicentral collisions. At midrapidity, the J/ψ  v_{2} is investigated as a function of the transverse momentum in semicentral collisions and found to be in agreement with the measurements at forward rapidity. These results are compared to transport model calculations. The comparison supports the idea that at low p_{T} the elliptic flow of the J/ψ originates from the thermalization of charm quarks in the deconfined medium but suggests that additional mechanisms might be missing in the models.

Anomalous Evolution of the Near-Side Jet Peak Shape in Pb-Pb Collisions at sqrt[s_{NN}]=2.76 TeV

The measurement of two-particle angular correlations is a powerful tool to study jet quenching in a p_{T} region inaccessible by direct jet identification. In these measurements pseudorapidity (Δη) and azimuthal (Δφ) differences are used to extract the shape of the near-side peak formed by particles associated with a higher p_{T} trigger particle (1<p_{T,trig}<8  GeV/c). A combined fit of the near-side peak and long-range correlations is applied to the data allowing the extraction of the centrality evolution of the peak shape in Pb-Pb collisions at sqrt[s_{NN}]=2.76  TeV. A significant broadening of the peak in the Δη direction at low p_{T} is found from peripheral to central collisions, which vanishes above 4  GeV/c, while in the Δφ direction the peak is almost independent of centrality. For the 10% most central collisions and 1<p_{T,assoc}<2  GeV/c, 1<p_{T,trig}<3  GeV/c a novel feature is observed: a depletion develops around the center of the peak. The results are compared to pp collisions at the same center of mass energy and ampt model simulations. The comparison to the investigated models suggests that the broadening and the development of the depletion is connected to the strength of radial and longitudinal flow.

Energy dependence of forward-rapidity [Formula: see text] and [Formula: see text] production in pp collisions at the LHC

We present results on transverse momentum ([Formula: see text]) and rapidity ([Formula: see text]) differential production cross sections, mean transverse momentum and mean transverse momentum square of inclusive [Formula: see text] and [Formula: see text] at forward rapidity ([Formula: see text]) as well as [Formula: see text]-to-[Formula: see text] cross section ratios. These quantities are measured in pp collisions at center of mass energies [Formula: see text] and 13 TeV with the ALICE detector. Both charmonium states are reconstructed in the dimuon decay channel, using the muon spectrometer. A comprehensive comparison to inclusive charmonium cross sections measured at [Formula: see text], 7 and 8 TeV is performed. A comparison to non-relativistic quantum chromodynamics and fixed-order next-to-leading logarithm calculations, which describe prompt and non-prompt charmonium production respectively, is also presented. A good description of the data is obtained over the full [Formula: see text] range, provided that both contributions are summed. In particular, it is found that for [Formula: see text] GeV/c the non-prompt contribution reaches up to 50% of the total charmonium yield.

Production of Σ(1385)± and Ξ(1530)0 in p-Pb collisions at sNN=5.02 TeV

The transverse momentum distributions of the strange and double-strange hyperon resonances (Σ ( 1385 ) ± , Ξ ( 1530 ) 0 ) produced in p-Pb collisions at s NN = 5.02 TeV were measured in the rapidity range - 0.5 < y CMS < 0 for event classes corresponding to different charged-particle multiplicity densities, ⟨ dN ch /dη lab ⟩ . The mean transverse momentum values are presented as a function of ⟨ dN ch /dη lab ⟩ , as well as a function of the particle masses and compared with previous results on hyperon production. The integrated yield ratios of excited to ground-state hyperons are constant as a function of ⟨ dN ch /dη lab ⟩ . The equivalent ratios to pions exhibit an increase with ⟨ dN ch /dη lab ⟩ , depending on their strangeness content.

Production of [Formula: see text] and [Formula: see text] mesons up to high transverse momentum in pp collisions at 2.76 TeV

The invariant differential cross sections for inclusive [Formula: see text] and [Formula: see text] mesons at midrapidity were measured in pp collisions at [Formula: see text] TeV for transverse momenta [Formula: see text] GeV/c and [Formula: see text] GeV/c, respectively, using the ALICE detector. This large range in [Formula: see text] was achieved by combining various analysis techniques and different triggers involving the electromagnetic calorimeter (EMCal). In particular, a new single-cluster, shower-shape based method was developed for the identification of high-[Formula: see text] neutral pions, which exploits that the showers originating from their decay photons overlap in the EMCal. Above 4 GeV/[Formula: see text], the measured cross sections are found to exhibit a similar power-law behavior with an exponent of about 6.3. Next-to-leading-order perturbative QCD calculations differ from the measured cross sections by about 30% for the [Formula: see text], and between 30-50% for the [Formula: see text] meson, while generator-level simulations with PYTHIA 8.2 describe the data to better than 10-30%, except at [Formula: see text] GeV/[Formula: see text]. The new data can therefore be used to further improve the theoretical description of [Formula: see text] and [Formula: see text] meson production.

Flow Dominance and Factorization of Transverse Momentum Correlations in Pb-Pb Collisions at the LHC

We present the first measurement of the two-particle transverse momentum differential correlation function, P_{2}≡⟨Δp_{T}Δp_{T}⟩/⟨p_{T}⟩^{2}, in Pb-Pb collisions at sqrt[s_{NN}]=2.76  TeV. Results for P_{2} are reported as a function of the relative pseudorapidity (Δη) and azimuthal angle (Δφ) between two particles for different collision centralities. The Δϕ dependence is found to be largely independent of Δη for |Δη|≥0.9. In the 5% most central Pb-Pb collisions, the two-particle transverse momentum correlation function exhibits a clear double-hump structure around Δφ=π (i.e., on the away side), which is not observed in number correlations in the same centrality range, and thus provides an indication of the dominance of triangular flow in this collision centrality. Fourier decompositions of P_{2}, studied as a function of the collision centrality, show that correlations at |Δη|≥0.9 can be well reproduced by a flow ansatz based on the notion that measured transverse momentum correlations are strictly determined by the collective motion of the system.

Measurement of azimuthal correlations of D mesons with charged particles in pp collisions at [Formula: see text] TeV and p-Pb collisions at [Formula: see text] TeV

The azimuthal correlations of D mesons with charged particles were measured with the ALICE apparatus in pp collisions at [Formula: see text] and p-Pb collisions at [Formula: see text] at the Large Hadron Collider. [Formula: see text], [Formula: see text], and [Formula: see text] mesons and their charge conjugates with transverse momentum [Formula: see text] and rapidity in the nucleon-nucleon centre-of-mass system [Formula: see text] (pp collisions) and [Formula: see text] (p-Pb collisions) were correlated to charged particles with [Formula: see text]. The yield of charged particles in the correlation peak induced by the jet containing the D meson and the peak width are compatible within uncertainties in the two collision systems. The data are described within uncertainties by Monte-Carlo simulations based on PYTHIA, POWHEG, and EPOS 3 event generators.

Correlated Event-by-Event Fluctuations of Flow Harmonics in Pb-Pb Collisions at sqrt[s_{NN}]=2.76 TeV

We report the measurements of correlations between event-by-event fluctuations of amplitudes of anisotropic flow harmonics in nucleus-nucleus collisions, obtained for the first time using a new analysis method based on multiparticle cumulants in mixed harmonics. This novel method is robust against systematic biases originating from nonflow effects and by construction any dependence on symmetry planes is eliminated. We demonstrate that correlations of flow harmonics exhibit a better sensitivity to medium properties than the individual flow harmonics. The new measurements are performed in Pb-Pb collisions at the center-of-mass energy per nucleon pair of sqrt[s_{NN}]=2.76  TeV by the ALICE experiment at the Large Hadron Collider. The centrality dependence of correlation between event-by-event fluctuations of the elliptic v_{2} and quadrangular v_{4} flow harmonics, as well as of anticorrelation between v_{2} and triangular v_{3} flow harmonics are presented. The results cover two different regimes of the initial state configurations: geometry dominated (in midcentral collisions) and fluctuation dominated (in the most central collisions). Comparisons are made to predictions from Monte Carlo Glauber, viscous hydrodynamics, ampt, and hijing models. Together with the existing measurements of the individual flow harmonics the presented results provide further constraints on the initial conditions and the transport properties of the system produced in heavy-ion collisions.

Centrality Dependence of the Charged-Particle Multiplicity Density at Midrapidity in Pb-Pb Collisions at sqrt[s_{NN}]=5.02 TeV

The pseudorapidity density of charged particles, dN_{ch}/dη, at midrapidity in Pb-Pb collisions has been measured at a center-of-mass energy per nucleon pair of sqrt[s_{NN}]=5.02  TeV. For the 5% most central collisions, we measure a value of 1943±54. The rise in dN_{ch}/dη as a function of sqrt[s_{NN}] is steeper than that observed in proton-proton collisions and follows the trend established by measurements at lower energy. The increase of dN_{ch}/dη as a function of the average number of participant nucleons, ⟨N_{part}⟩, calculated in a Glauber model, is compared with the previous measurement at sqrt[s_{NN}]=2.76  TeV. A constant factor of about 1.2 describes the increase in dN_{ch}/dη from sqrt[s_{NN}]=2.76 to 5.02 TeV for all centrality classes, within the measured range of 0%-80% centrality. The results are also compared to models based on different mechanisms for particle production in nuclear collisions.

Measurement of an Excess in the Yield of J/ψ at Very Low p_{T} in Pb-Pb Collisions at sqrt[s]_{NN}=2.76 TeV

We report on the first measurement of an excess in the yield of J/ψ at very low transverse momentum (p_{T}<0.3  GeV/c) in peripheral hadronic Pb-Pb collisions at sqrt[s_{NN}]=2.76  TeV, performed by ALICE at the CERN LHC. Remarkably, the measured nuclear modification factor of J/ψ in the rapidity range 2.5<y<4 reaches about 7 (2) in the p_{T} range 0-0.3  GeV/c in the 70%-90% (50%-70%) centrality class. The J/ψ production cross section associated with the observed excess is obtained under the hypothesis that coherent photoproduction of J/ψ is the underlying physics mechanism. If confirmed, the observation of J/ψ coherent photoproduction in Pb-Pb collisions at impact parameters smaller than twice the nuclear radius opens new theoretical and experimental challenges and opportunities. In particular, coherent photoproduction accompanying hadronic collisions may provide insight into the dynamics of photoproduction and nuclear reactions, as well as become a novel probe of the quark-gluon plasma.

Centrality dependence of charged jet production in p-Pb collisions at [Formula: see text] = 5.02 TeV

Measurements of charged jet production as a function of centrality are presented for  p-Pb  collisions recorded at [Formula: see text] TeV with the ALICE detector. Centrality classes are determined via the energy deposit in neutron calorimeters at zero degree, close to the beam direction, to minimise dynamical biases of the selection. The corresponding number of participants or binary nucleon-nucleon collisions is determined based on the particle production in the Pb-going rapidity region. Jets have been reconstructed in the central rapidity region from charged particles with the anti-[Formula: see text] algorithm for resolution parameters [Formula: see text] and [Formula: see text] in the transverse momentum range 20 to 120 GeV/c. The reconstructed jet momentum and yields have been corrected for detector effects and underlying-event background. In the five centrality bins considered, the charged jet production in  p-Pb   collisions is consistent with the production expected from binary scaling from pp collisions. The ratio of jet yields reconstructed with the two different resolution parameters is also independent of the centrality selection, demonstrating the absence of major modifications of the radial jet structure in the reported centrality classes.

Production of K[Formula: see text](892)[Formula: see text] and [Formula: see text](1020) in p-Pb collisions at [Formula: see text] = 5.02 TeV

The production of K[Formula: see text](892)[Formula: see text] and [Formula: see text](1020) mesons has been measured in p-Pb collisions at [Formula: see text][Formula: see text] 5.02 TeV. K[Formula: see text] and [Formula: see text] are reconstructed via their decay into charged hadrons with the ALICE detector in the rapidity range [Formula: see text]. The transverse momentum spectra, measured as a function of the multiplicity, have a p[Formula: see text] range from 0 to 15 GeV/c for K[Formula: see text] and from 0.3 to 21 GeV/c for [Formula: see text]. Integrated yields, mean transverse momenta and particle ratios are reported and compared with results in pp collisions at [Formula: see text][Formula: see text] 7 TeV and Pb-Pb collisions at [Formula: see text][Formula: see text] 2.76 TeV. In Pb-Pb and p-Pb collisions, K[Formula: see text] and [Formula: see text] probe the hadronic phase of the system and contribute to the study of particle formation mechanisms by comparison with other identified hadrons. For this purpose, the mean transverse momenta and the differential proton-to-[Formula: see text] ratio are discussed as a function of the multiplicity of the event. The short-lived K[Formula: see text] is measured to investigate re-scattering effects, believed to be related to the size of the system and to the lifetime of the hadronic phase.

Inclusive quarkonium production at forward rapidity in pp collisions at [Formula: see text]TeV

We report on the inclusive production cross sections of [Formula: see text], [Formula: see text], [Formula: see text](1S), [Formula: see text](2S) and [Formula: see text](3S), measured at forward rapidity with the ALICE detector in [Formula: see text] collisions at a center-of-mass energy [Formula: see text] TeV. The analysis is based on data collected at the LHC and corresponds to an integrated luminosity of 1.23 pb[Formula: see text]. Quarkonia are reconstructed in the dimuon-decay channel. The differential production cross sections are measured as a function of the transverse momentum [Formula: see text] and rapidity y, over the [Formula: see text] ranges [Formula: see text] GeV/c for [Formula: see text], [Formula: see text] GeV/c for all other resonances, and for [Formula: see text]. The cross sections, integrated over [Formula: see text] and y, and assuming unpolarized quarkonia, are [Formula: see text] [Formula: see text]b, [Formula: see text] [Formula: see text]b, [Formula: see text] nb, [Formula: see text] nb and [Formula: see text] nb, where the first uncertainty is statistical and the second one is systematic. These values agree, within at most [Formula: see text], with measurements performed by the LHCb collaboration in the same rapidity range.

Anisotropic Flow of Charged Particles in Pb-Pb Collisions at √[s{NN}]=5.02 TeV

We report the first results of elliptic (v_{2}), triangular (v_{3}), and quadrangular (v_{4}) flow of charged particles in Pb-Pb collisions at a center-of-mass energy per nucleon pair of sqrt[s_{NN}]=5.02  TeV with the ALICE detector at the CERN Large Hadron Collider. The measurements are performed in the central pseudorapidity region |η|<0.8 and for the transverse momentum range 0.2<p_{T}<5  GeV/c. The anisotropic flow is measured using two-particle correlations with a pseudorapidity gap greater than one unit and with the multiparticle cumulant method. Compared to results from Pb-Pb collisions at sqrt[s_{NN}]=2.76  TeV, the anisotropic flow coefficients v_{2}, v_{3}, and v_{4} are found to increase by (3.0±0.6)%, (4.3±1.4)%, and (10.2±3.8)%, respectively, in the centrality range 0%-50%. This increase can be attributed mostly to an increase of the average transverse momentum between the two energies. The measurements are found to be compatible with hydrodynamic model calculations. This comparison provides a unique opportunity to test the validity of the hydrodynamic picture and the power to further discriminate between various possibilities for the temperature dependence of shear viscosity to entropy density ratio of the produced matter in heavy-ion collisions at the highest energies.

Multiplicity and transverse momentum evolution of charge-dependent correlations in pp, p-Pb, and Pb-Pb collisions at the LHC

We report on two-particle charge-dependent correlations in pp, p-Pb, and Pb-Pb collisions as a function of the pseudorapidity and azimuthal angle difference, [Formula: see text] and [Formula: see text] respectively. These correlations are studied using the balance function that probes the charge creation time and the development of collectivity in the produced system. The dependence of the balance function on the event multiplicity as well as on the trigger and associated particle transverse momentum ([Formula: see text]) in pp, p-Pb, and Pb-Pb collisions at [Formula: see text] 7, 5.02, and 2.76 TeV, respectively, are presented. In the low transverse momentum region, for [Formula: see text] GeV/c, the balance function becomes narrower in both [Formula: see text] and [Formula: see text] directions in all three systems for events with higher multiplicity. The experimental findings favor models that either incorporate some collective behavior (e.g. AMPT) or different mechanisms that lead to effects that resemble collective behavior (e.g. PYTHIA8 with color reconnection). For higher values of transverse momenta the balance function becomes even narrower but exhibits no multiplicity dependence, indicating that the observed narrowing with increasing multiplicity at low [Formula: see text] is a feature of bulk particle production.

Measurement of pion, kaon and proton production in proton-proton collisions at [Formula: see text] TeV

The measurement of primary [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] production at mid-rapidity ([Formula: see text] 0.5) in proton-proton collisions at [Formula: see text][Formula: see text] 7 TeV performed with a large ion collider experiment at the large hadron collider (LHC) is reported. Particle identification is performed using the specific ionisation energy-loss and time-of-flight information, the ring-imaging Cherenkov technique and the kink-topology identification of weak decays of charged kaons. Transverse momentum spectra are measured from 0.1 up to 3 GeV/[Formula: see text] for pions, from 0.2 up to 6 GeV/[Formula: see text] for kaons and from 0.3 up to 6 GeV/[Formula: see text] for protons. The measured spectra and particle ratios are compared with quantum chromodynamics-inspired models, tuned to reproduce also the earlier measurements performed at the LHC. Furthermore, the integrated particle yields and ratios as well as the average transverse momenta are compared with results at lower collision energies.

Molecular evolution and transcriptional regulation of the oilseed rape proline dehydrogenase genes suggest distinct roles of proline catabolism during development

Six BnaProDH1 and two BnaProDH2 genes were identified in Brassica napus genome. The BnaProDH1 genes are mainly expressed in pollen and roots' organs while BnaProDH2 gene expression is associated with leaf vascular tissues at senescence. Proline dehydrogenase (ProDH) catalyzes the first step in the catabolism of proline. The ProDH gene family in oilseed rape (Brassica napus) was characterized and compared to other Brassicaceae ProDH sequences to establish the phylogenetic relationships between genes. Six BnaProDH1 genes and two BnaProDH2 genes were identified in the B. napus genome. Expression of the three paralogous pairs of BnaProDH1 genes and the two homoeologous BnaProDH2 genes was measured by real-time quantitative RT-PCR in plants at vegetative and reproductive stages. The BnaProDH2 genes are specifically expressed in vasculature in an age-dependent manner, while BnaProDH1 genes are strongly expressed in pollen grains and roots. Compared to the abundant expression of BnaProDH1, the overall expression of BnaProDH2 is low except in roots and senescent leaves. The BnaProDH1 paralogs showed different levels of expression with BnaA&C.ProDH1.a the most strongly expressed and BnaA&C.ProDH1.c the least. The promoters of two BnaProDH1 and two BnaProDH2 genes were fused with uidA reporter gene (GUS) to characterize organ and tissue expression profiles in transformed B. napus plants. The transformants with promoters from different genes showed contrasting patterns of GUS activity, which corresponded to the spatial expression of their respective transcripts. ProDHs probably have non-redundant functions in different organs and at different phenological stages. In terms of molecular evolution, all BnaProDH sequences appear to have undergone strong purifying selection and some copies are becoming subfunctionalized. This detailed description of oilseed rape ProDH genes provides new elements to investigate the function of proline metabolism in plant development.

Production of [Formula: see text] and [Formula: see text] in proton-proton collisions at [Formula: see text] 7 TeV

The production of the strange and double-strange baryon resonances ([Formula: see text], [Formula: see text]) has been measured at mid-rapidity ([Formula: see text][Formula: see text]) in proton-proton collisions at [Formula: see text] [Formula: see text] 7 TeV with the ALICE detector at the LHC. Transverse momentum spectra for inelastic collisions are compared to QCD-inspired models, which in general underpredict the data. A search for the [Formula: see text] pentaquark, decaying in the [Formula: see text] channel, has been carried out but no evidence is seen.

Use of simulations to enhance knowledge integration and livestock producers’ adaptation to variability in the climate in northern Uruguay

Basaltic soils have an extremely reduced capacity to accumulate water in Uruguay where they occupy 3.5 m ha (25% of the area of Uruguay) and are mainly exploited by extensive cattle production systems. Drought can have a negative effect on forage growth and cattle production and can have a devastating impact on the economy of livestock producers, and damage the entire beef-supply chain. To improve the livestock producers ability to adapt to climate variability, the past effects of droughts were modelled to understand the dynamics of droughts at the level of the production unit through the development of an interactive agent-based simulation model. The simulator was constructed in four steps by simulating: (i) forage growth using a logistic growth equation calibrated with data originated from the Moderate resolution imaging spectroradiometer (MODIS) satellite, (ii) the life cycle of livestock, (iii) the interaction between forage and livestock, and (iv) different strategies of management. Outputs of simulations were explored in five workshops with 82 livestock farmers and development actors. In these workshops, both biophysical models and those related to farm management were recognised as valid, and the typologies used were identified as realistic. Through the workshops and discussions about the models, the producers’ understanding of droughts was investigated. It was found that two types of information were important in encouraging better adaptation: (i) information that allowed a better understanding of the complex system and (ii) information that supported action. The workshops were found to valuable in generating a motivation to analyse and discuss climate variability.

Exclusive J/ψ photoproduction off protons in ultraperipheral p-Pb collisions at √(s(NN))=5.02 TeV

We present the first measurement at the LHC of exclusive J/ψ photoproduction off protons, in ultraperipheral proton-lead collisions at sqrt[s_{NN}]=5.02  TeV. Events are selected with a dimuon pair produced either in the rapidity interval, in the laboratory frame, 2.5<y<4 (p-Pb) or -3.6<y<-2.6 (Pb-p), and no other particles observed in the ALICE acceptance. The measured cross sections σ(γ+p→J/ψ+p) are 33.2±2.2(stat)±3.2(syst)±0.7(theor)  nb in p-Pb and 284±36(stat)_{-32}^{+27}(syst)±26(theor)  nb in Pb-p collisions. We measure this process up to about 700 GeV in the γp center of mass, which is a factor of two larger than the highest energy studied at HERA. The data are consistent with a power law dependence of the J/ψ photoproduction cross section in γp energies from about 20 to 700 GeV, or equivalently, from Bjorken x scaling variable between ∼2×10^{-2} and ∼2×10^{-5}, thus indicating no significant change in the gluon density behavior of the proton between HERA and LHC energies.

Measurement of prompt D-meson production in p-Pb collisions at √(s(NN))=5.02 TeV

The p_{T}-differential production cross sections of the prompt charmed mesons D^{0}, D^{+}, D^{*+}, and D_{s}^{+} and their charge conjugate in the rapidity interval -0.96<y_{cms}<0.04 were measured in p-Pb collisions at a center-of-mass energy sqrt[s_{NN}]=5.02  TeV with the ALICE detector at the LHC. The nuclear modification factor R_{pPb}, quantifying the D-meson yield in p-Pb collisions relative to the yield in pp collisions scaled by the number of binary nucleon-nucleon collisions, is compatible within the 15%-20% uncertainties with unity in the transverse momentum interval 1<p_{T}<24  GeV/c. No significant difference among the R_{pPb} of the four D-meson species is observed. The results are described within uncertainties by theoretical calculations that include initial-state effects. The measurement adds experimental evidence that the modification of the momentum spectrum of D mesons observed in Pb-Pb collisions with respect to pp collisions is due to strong final-state effects induced by hot partonic matter.

Measurement of quarkonium production at forward rapidity in [Formula: see text] collisions at [Formula: see text]TeV

The inclusive production cross sections at forward rapidity of [Formula: see text], [Formula: see text], [Formula: see text](1S) and [Formula: see text](2S) are measured in [Formula: see text] collisions at [Formula: see text] with the ALICE detector at the LHC. The analysis is based on a data sample corresponding to an integrated luminosity of 1.35 pb[Formula: see text]. Quarkonia are reconstructed in the dimuon-decay channel and the signal yields are evaluated by fitting the [Formula: see text] invariant mass distributions. The differential production cross sections are measured as a function of the transverse momentum [Formula: see text] and rapidity [Formula: see text], over the ranges [Formula: see text] GeV/c for [Formula: see text], [Formula: see text] GeV/c for all other resonances and for [Formula: see text]. The measured cross sections integrated over [Formula: see text] and [Formula: see text], and assuming unpolarized quarkonia, are: [Formula: see text] [Formula: see text]b, [Formula: see text] [Formula: see text]b, [Formula: see text] nb and [Formula: see text] nb, where the first uncertainty is statistical and the second one is systematic. The results are compared to measurements performed by other LHC experiments and to theoretical models.

Energy dependence of the transverse momentum distributions of charged particles in pp collisions measured by ALICE

Differential cross sections of charged particles in inelastic pp collisions as a function of p_T have been measured at [Formula: see text] at the LHC. The p_T spectra are compared to NLO-pQCD calculations. Though the differential cross section for an individual [Formula: see text] cannot be described by NLO-pQCD, the relative increase of cross section with [Formula: see text] is in agreement with NLO-pQCD. Based on these measurements and observations, procedures are discussed to construct pp reference spectra at [Formula: see text] up to p_T=50 GeV/c as required for the calculation of the nuclear modification factor in nucleus-nucleus and proton-nucleus collisions.

Directed flow of charged particles at midrapidity relative to the spectator plane in Pb-Pb collisions at √(s(NN))=2.76 TeV

The directed flow of charged particles at midrapidity is measured in Pb-Pb collisions at √(s(NN))=2.76 TeV relative to the collision symmetry plane defined by the spectator nucleons. A negative slope of the rapidity-odd directed flow component with approximately 3 times smaller magnitude than found at the highest RHIC energy is observed. This suggests a smaller longitudinal tilt of the initial system and disfavors the strong fireball rotation predicted for the LHC energies. The rapidity-even directed flow component is measured for the first time with spectators and found to be independent of pseudorapidity with a sign change at transverse momenta p(T) between 1.2 and 1.7  GeV/c. Combined with the observation of a vanishing rapidity-even p(T) shift along the spectator deflection this is strong evidence for dipolelike initial density fluctuations in the overlap zone of the nuclei. Similar trends in the rapidity-even directed flow and the estimate from two-particle correlations at midrapidity, which is larger by about a factor of 40, indicate a weak correlation between fluctuating participant and spectator symmetry planes. These observations open new possibilities for investigation of the initial conditions in heavy-ion collisions with spectator nucleons.

K(S)0 and Λ production in Pb-Pb collisions at √(s(NN))=2.76 TeV

The ALICE measurement of K(S)(0) and Λ production at midrapidity in Pb-Pb collisions at √(s(NN))=2.76 TeV is presented. The transverse momentum (p(T)) spectra are shown for several collision centrality intervals and in the p(T) range from 0.4 GeV/c (0.6 GeV/c for Λ) to 12 GeV/c. The p(T) dependence of the Λ/K(S)(0) ratios exhibits maxima in the vicinity of 3 GeV/c, and the positions of the maxima shift towards higher p(T) with increasing collision centrality. The magnitude of these maxima increases by almost a factor of three between most peripheral and most central Pb-Pb collisions. This baryon excess at intermediate p(T) is not observed in pp interactions at √s=0.9 TeV and at √s=7 TeV. Qualitatively, the baryon enhancement in heavy-ion collisions is expected from radial flow. However, the measured p(T) spectra above 2 GeV/c progressively decouple from hydrodynamical-model calculations. For higher values of p(T), models that incorporate the influence of the medium on the fragmentation and hadronization processes describe qualitatively the p(T) dependence of the Λ/K(S)(0) ratio.

Charmonium and e+e- pair photoproduction at mid-rapidity in ultra-peripheral Pb-Pb collisions at [Formula: see text]

The ALICE Collaboration at the LHC has measured the J/ψ and ψ' photoproduction at mid-rapidity in ultra-peripheral Pb-Pb collisions at [Formula: see text]. The charmonium is identified via its leptonic decay for events where the hadronic activity is required to be minimal. The analysis is based on an event sample corresponding to an integrated luminosity of about 23 μb-1. The cross section for coherent and incoherent J/ψ production in the rapidity interval -0.9 Collapse

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J/ψ elliptic flow in Pb-Pb collisions at √(s(NN))=2.76 TeV

We report on the first measurement of inclusive J/ψ elliptic flow v2 in heavy-ion collisions at the LHC. The measurement is performed with the ALICE detector in Pb-Pb collisions at √(s(NN))=2.76 TeV in the rapidity range 2.5<y<4.0. The dependence of the J/ψ v2 on the collision centrality and on the J/ψ transverse momentum is studied in the range 0≤p(T)<10 GeV/c. For semicentral Pb-Pb collisions at √(s(NN))=2.76 TeV, an indication of nonzero v2 is observed with a largest measured value of v2=0.116±0.046(stat)±0.029(syst) for J/ψ in the transverse momentum range 2≤p(T)<4 GeV/c. The elliptic flow measurement complements the previously reported ALICE results on the inclusive J/ψ nuclear modification factor and favors the scenario of a significant fraction of J/ψ production from charm quarks in a deconfined partonic phase.

D meson elliptic flow in noncentral Pb-Pb collisions at sqrt[sNN]=2.76 Tev

Azimuthally anisotropic distributions of D0, D+, and D*+ mesons were studied in the central rapidity region (|y|<0.8) in Pb-Pb collisions at a center-of-mass energy sqrt[sNN]=2.76  TeV per nucleon-nucleon collision, with the ALICE detector at the LHC. The second Fourier coefficient v2 (commonly denoted elliptic flow) was measured in the centrality class 30%-50% as a function of the D meson transverse momentum pT, in the range 2-16  GeV/c. The measured v2 of D mesons is comparable in magnitude to that of light-flavor hadrons. It is positive in the range 2<pT<6  GeV/c with 5.7σ significance, based on the combination of statistical and systematic uncertainties.

Measurement of inelastic, single- and double-diffraction cross sections in proton-proton collisions at the LHC with ALICE

Measurements of cross sections of inelastic and diffractive processes in proton-proton collisions at LHC energies were carried out with the ALICE detector. The fractions of diffractive processes in inelastic collisions were determined from a study of gaps in charged particle pseudorapidity distributions: for single diffraction (diffractive mass MX <200 GeV/c2) [Formula: see text], and [Formula: see text], respectively at centre-of-mass energies [Formula: see text]; for double diffraction (for a pseudorapidity gap Δη>3) σDD/σINEL=0.11±0.03,0.12±0.05, and [Formula: see text], respectively at [Formula: see text]. To measure the inelastic cross section, beam properties were determined with van der Meer scans, and, using a simulation of diffraction adjusted to data, the following values were obtained: [Formula: see text] mb at [Formula: see text] and [Formula: see text] at [Formula: see text]. The single- and double-diffractive cross sections were calculated combining relative rates of diffraction with inelastic cross sections. The results are compared to previous measurements at proton-antiproton and proton-proton colliders at lower energies, to measurements by other experiments at the LHC, and to theoretical models.

Wuschel overexpression promotes somatic embryogenesis and induces organogenesis in cotton (Gossypium hirsutum L.) tissues cultured in vitro

This work shows that overexpression of the WUS gene from Arabidopsis enhanced the expression of embryogenic competence and triggered organogenesis from some cells of the regenerated embryo-like structures. Agrobacterium-mediated genetic transformation of cotton was described in the late 1980s, but is still time consuming and largely genotype dependant due to poor regeneration. To help solve this bottleneck, we over-expressed the WUSCHEL (WUS) gene, a homeobox transcription factor cloned in Arabidopsis thaliana, known to stimulate organogenesis and/or somatic embryogenesis in Arabidopsis tissues cultured in vitro. The AtWUS gene alone, and AtWUS gene fused to the GFP marker were compared to the GFP gene alone and to an empty construct used as a control. Somatic embryogenesis was improved in WUS expressed calli, as the percentage of explants giving rise to embryogenic tissues was significantly higher (×3) when WUS gene was over-expressed than in the control. An interesting result was that WUS embryogenic lines evolved in green embryo-like structures giving rise to ectopic organogenesis never observed in any of our previous transformation experiments. Using our standard in vitro culture protocol, the overexpression of AtWUS in tissues of a recalcitrant variety did not result in the production of regenerated plants. This achievement will still require the optimization of other non-genetic factors, such as the balance of exogenous phytohormones. However, our results suggest that targeted expression of the WUS gene is a promising strategy to improve gene transfer in recalcitrant cotton cultivars.

Net-charge fluctuations in Pb-Pb collisions at sqrt[sNN]=2.76 TeV

We report the first measurement of the net-charge fluctuations in Pb-Pb collisions at sqrt[sNN]=2.76  TeV, measured with the ALICE detector at the CERN Large Hadron Collider. The dynamical fluctuations per unit entropy are observed to decrease when going from peripheral to central collisions. An additional reduction in the amount of fluctuations is seen in comparison to the results from lower energies. We examine the dependence of fluctuations on the pseudorapidity interval, which may account for the dilution of fluctuations during the evolution of the system. We find that the fluctuations at the LHC are smaller compared to the measurements at the BNL Relativistic Heavy Ion Collider, and as such, closer to what has been theoretically predicted for the formation of a quark-gluon plasma.

Transverse momentum distribution and nuclear modification factor of charged particles in p+Pb collisions at sqrt[s(NN)] = 5.02 TeV

The transverse momentum (p(T)) distribution of primary charged particles is measured in minimum bias (non-single-diffractive) p+Pb collisions at sqrt[s(NN)]=5.02 TeV with the ALICE detector at the LHC. The p(T) spectra measured near central rapidity in the range 0.5<p(T) <20 GeV/c exhibit a weak pseudorapidity dependence. The nuclear modification factor R(pPb) is consistent with unity for p(T) above 2 GeV/c. This measurement indicates that the strong suppression of hadron production at high p(T) observed in Pb+Pb collisions at the LHC is not due to an initial-state effect. The measurement is compared to theoretical calculations.

Pseudorapidity density of charged particles in p+Pb collisions at √(s(NN))=5.02 TeV

The charged-particle pseudorapidity density measured over four units of pseudorapidity in nonsingle-diffractive p+Pb collisions at a center-of-mass energy per nucleon pair √(s(NN))=5.02 TeV is presented. The average value at midrapidity is measured to be 16.81±0.71 (syst), which corresponds to 2.14±0.17 (syst) per participating nucleon, calculated with the Glauber model. This is 16% lower than in nonsingle-diffractive pp collisions interpolated to the same collision energy and 84% higher than in d+Au collisions at s√(s(NN))=0.2 TeV. The measured pseudorapidity density in p+Pb collisions is compared to model predictions and provides new constraints on the description of particle production in high-energy nuclear collisions.

Charge separation relative to the reaction plane in Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV

Measurements of charge-dependent azimuthal correlations with the ALICE detector at the LHC are reported for Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV. Two- and three-particle charge-dependent azimuthal correlations in the pseudorapidity range |η| < 0.8 are presented as a function of the collision centrality, particle separation in pseudorapidity, and transverse momentum. A clear signal compatible with a charge-dependent separation relative to the reaction plane is observed, which shows little or no collision energy dependence when compared to measurements at RHIC energies. This provides a new insight for understanding the nature of the charge-dependent azimuthal correlations observed at RHIC and LHC energies.

Pion, kaon, and proton production in central Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV

In this Letter we report the first results on π(±), K(±), p, and p production at midrapidity (|y|<0.5) in central Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV, measured by the ALICE experiment at the LHC. The p(T) distributions and yields are compared to previous results at sqrt[s(NN)] = 200 GeV and expectations from hydrodynamic and thermal models. The spectral shapes indicate a strong increase of the radial flow velocity with sqrt[s(NN)], which in hydrodynamic models is expected as a consequence of the increasing particle density. While the K/π ratio is in line with predictions from the thermal model, the p/π ratio is found to be lower by a factor of about 1.5. This deviation from thermal model expectations is still to be understood.

Measurement of the cross section for electromagnetic dissociation with neutron emission in Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV

The first measurement of neutron emission in electromagnetic dissociation of ^{208}Pb nuclei at the LHC is presented. The measurement is performed using the neutron zero degree calorimeters of the ALICE experiment, which detect neutral particles close to beam rapidity. The measured cross sections of single and mutual electromagnetic dissociation of Pb nuclei at sqrt[s(NN)]=2.76 TeV with neutron emission are σ(singleEMD)=187.4 ± 0.2(stat)(-11.2)(+13.2) (syst) b and σ(mutualEMD) = 5.7 ± 0.1(stat) ± 0.4(syst) b, respectively. The experimental results are compared to the predictions from a relativistic electromagnetic dissociation model.

Production of muons from heavy flavor decays at forward rapidity in pp and Pb-Pb collisions at sqrt[s(NN)]=2.76 TeV

The ALICE Collaboration has measured the inclusive production of muons from heavy-flavor decays at forward rapidity, 2.5<y<4, in pp and Pb-Pb collisions at sqrt[s(NN)]=2.76  TeV. The p(t)-differential inclusive cross section of muons from heavy-flavor decays in pp collisions is compared to perturbative QCD calculations. The nuclear modification factor is studied as a function of p(t) and collision centrality. A weak suppression is measured in peripheral collisions. In the most central collisions, a suppression of a factor of about 3-4 is observed in 6<p(t)<10  GeV/c. The suppression shows no significant p(t) dependence.

J/ψ suppression at forward rapidity in Pb-Pb collisions at √s(NN) = 2.76 TeV

The ALICE experiment has measured the inclusive J/ψ production in Pb-Pb collisions at √s(NN) = 2.76 TeV down to zero transverse momentum in the rapidity range 2.5 < y < 4. A suppression of the inclusive J/ψ yield in Pb-Pb is observed with respect to the one measured in pp collisions scaled by the number of binary nucleon-nucleon collisions. The nuclear modification factor, integrated over the 0%-80% most central collisions, is 0.545 ± 0.032(stat) ± 0.083(syst) and does not exhibit a significant dependence on the collision centrality. These features appear significantly different from measurements at lower collision energies. Models including J/ψ production from charm quarks in a deconfined partonic phase can describe our data.

Particle-yield modification in jetlike azimuthal dihadron correlations in Pb-Pb collisions at √s(NN)=2.76 TeV

The yield of charged particles associated with high-p(t) trigger particles (8<p(t)<15 GeV/c) is measured with the ALICE detector in Pb-Pb collisions at √s(NN)=2.76 TeV relative to proton-proton collisions at the same energy. The conditional per-trigger yields are extracted from the narrow jetlike correlation peaks in azimuthal dihadron correlations. In the 5% most central collisions, we observe that the yield of associated charged particles with transverse momenta p(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.