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Heat stress transcription factors (HSFs) regulate transcriptional response to a large number of environmental influences, such as temperature fluctuations and chemical compound applications. Plant HSFs represent a large and diverse gene family. The HSF members vary substantially both in gene expression patterns and molecular functions. HEATSTER is a web resource for mining, annotating, and analyzing members of the different classes of HSFs in plants. A web-interface allows the identification and class assignment of HSFs, intuitive searches in the database and visualization of conserved motifs, and domains to classify novel HSFs.
Adjuvanted influenza vaccines constitute a key element towards inducing neutralizing antibody responses in populations with reduced responsiveness, such as infants and elderly subjects, as well as in devising antigen-sparing strategies. In particular, squalene-containing adjuvants have been observed to induce enhanced antibody responses, as well as having an influence on cross-reactive immunity. To explore the effects of adjuvanted vaccine formulations on antibody response and their relation to protein-specific immunity, we propose different mathematical models of antibody production dynamics in response to influenza vaccination. Data from ferrets immunized with commercial H1N1pdm09 vaccine antigen alone or formulated with different adjuvants was instrumental to adjust model parameters. While the affinity maturation process complexity is abridged, the proposed model is able to recapitulate the essential features of the observed dynamics. Our numerical results suggest that there exists a qualitative shift in protein-specific antibody response, with enhanced production of antibodies targeting the NA protein in adjuvanted versus non-adjuvanted formulations, in conjunction with a protein-independent boost that is over one order of magnitude larger for squalene-containing adjuvants. Furthermore, simulations predict that vaccines formulated with squalene-containing adjuvants are able to induce sustained antibody titers in a robust way, with little impact of the time interval between immunizations.
An overt pro-inflammatory immune response is a key factor contributing to lethal pneumococcal infection in an influenza pre-infected host and represents a potential target for therapeutic intervention. However, there is a paucity of knowledge about the level of contribution of individual cytokines. Based on the predictions of our previous mathematical modeling approach, the potential benefit of IFN-γ- and/or IL-6-specific antibody-mediated cytokine neutralization was explored in C57BL/6 mice infected with the influenza A/PR/8/34 strain, which were subsequently infected with the Streptococcus pneumoniae strain TIGR4 on day 7 post influenza. While single IL-6 neutralization had no effect on respiratory bacterial clearance, single IFN-γ neutralization enhanced local bacterial clearance in the lungs. Concomitant neutralization of IFN-γ and IL-6 significantly reduced the degree of pneumonia as well as bacteremia compared to the control group, indicating a positive effect for the host during secondary bacterial infection. The results of our model-driven experimental study reveal that the predicted therapeutic value of IFN-γ and IL-6 neutralization in secondary pneumococcal infection following influenza infection is tightly dependent on the experimental protocol while at the same time paving the way toward the development of effective immune therapies.
Multi-view microscopy techniques are used to increase the resolution along the optical axis for 3D imaging. Without this, the resolution is insufficient to resolve subcellular events. In addition, parts of the images of opaque specimens are often highly degraded or masked. Both problems motivate scientists to record the same specimen from multiple directions. The images, then have to be digitally fused into a single high-quality image. Selective-plane illumination microscopy has proven to be a powerful imaging technique due to its unsurpassed acquisition speed and gentle optical sectioning. However, even in the case of multi view imaging techniques that illuminate and image the sample from multiple directions, light scattering inside tissues often severely impairs image contrast.
Here we show that for c-elegans embryos multi view registration can be achieved based on segmented nuclei. However, segmentation of nuclei in high density distribution like c-elegans embryo is challenging. We propose a method which uses 3D Mexican hat filter for preprocessing and 3D Gaussian curvature for the post-processing step to separate nuclei. We used this method successfully on 3 data sets of c-elegans embryos in 3 different views. The result of segmentation outperforms previous methods. Moreover, we provide a simple GUI for manual correction and adjusting the parameters for different data.
We then proposed a method that combines point and voxel registration for an accurate multi view reg- istration of c-elegans embryo, which does not need any special experimental preparation. We demonstrate the performance of our approach on data acquired from fixed embryos of c-elegans worms. This multi step approach is successfully evaluated by comparison to different methods and also by using synthetic data. The proposed method could overcome the typically low resolution along the optical axis and enable stitching to- gether the different parts of the embryo available through the different views. A tool for running the code and analyzing the results is developed.
We calculate ratios of higher-order susceptibilities quantifying fluctuations in the number of net-protons and in the net-electric charge using the Hadron Resonance Gas (HRG) model. We take into account the effect of resonance decays, the kinematic acceptance cuts in rapidity, pseudo-rapidity and transverse momentum used in the experimental analysis, as well as a randomization of the isospin of nucleons in the hadronic phase. By comparing these results to the latest experimental data from the STAR Collaboration, we determine the freeze-out conditions from net-electric charge and net-proton distributions and discuss their consistency.
Following a brief review of current efforts to identify the neuronal correlates of conscious processing (NCCP) an attempt is made to bridge the gap between the material neuronal processes and the immaterial dimensions of subjective experience. It is argued that this "hard problem" of consciousness research cannot be solved by only considering the neuronal underpinnings of cognition. The proposal is that the hard problem can be treated within a naturalistic framework if one considers not only the biological but also the socio-cultural dimensions of evolution. The argument is based on the following premises: perceptions are the result of a constructivist process that depends on priors. This applies both for perceptions of the outer world and the perception of oneself. Social interactions between agents endowed with the cognitive abilities of humans generated immaterial realities, addressed as social or cultural realities. This novel class of realities assumed the role of priors for the perception of oneself and the embedding world. A natural consequence of these extended perceptions is a dualist classification of observables into material and immaterial phenomena nurturing the concept of ontological substance dualism. It is argued that perceptions shaped by socio-cultural priors lead to the construction of a self-model that has both a material and an immaterial dimension. As priors are implicit and not amenable to conscious recollection the perceived immaterial dimension is experienced as veridical and not derivable from material processes—which is the hallmark of the hard problem. These considerations let the hard problem appear as the result of cognitive constructs that are amenable to naturalistic explanations in an evolutionary framework.
PURPOSE: The purpose of this work is to analyze whether the Monte Carlo codes penh, fluka, and geant4/topas are suitable to calculate absorbed doses and fQ/fQ0 ratios in therapeutic high-energy photon and proton beams.
METHODS: We used penh, fluka, geant4/topas, and egsnrc to calculate the absorbed dose to water in a reference water cavity and the absorbed dose to air in two air cavities representative of a plane-parallel and a cylindrical ionization chamber in a 1.25 MeV photon beam and a 150 MeV proton beam - egsnrc was only used for the photon beam calculations. The physics and transport settings in each code were adjusted to simulate the particle transport as detailed as reasonably possible. From these absorbed doses, fQ0 factors, fQ factors, and fQ/fQ0 ratios (which are the basis of Monte Carlo calculated beam quality correction factors kQ,Q0 ) were calculated and compared between the codes. Additionally, we calculated the spectra of primary particles and secondary electrons in the reference water cavity, as well as the integrated depth-dose curve of 150 MeV protons in water.
RESULTS: The absorbed doses agreed within 1.4% or better between the individual codes for both the photon and proton simulations. The fQ0 and fQ factors agreed within 0.5% or better for the individual codes for both beam qualities. The resulting fQ/fQ0 ratios for 150 MeV protons agreed within 0.7% or better. For the 1.25 MeV photon beam, the spectra of photons and secondary electrons agreed almost perfectly. For the 150 MeV proton simulation, we observed differences in the spectra of secondary protons whereas the spectra of primary protons and low-energy delta electrons also agreed almost perfectly. The first 2 mm of the entrance channel of the 150 MeV proton Bragg curve agreed almost perfectly while for greater depths, the differences in the integrated dose were up to 1.5%.
CONCLUSION: penh, fluka, and geant4/topas are capable of calculating beam quality correction factors in proton beams. The differences in the fQ0 and fQ factors between the codes are 0.5% at maximum. The differences in the fQ/fQ0 ratios are 0.7% at maximum.
The differences between contemporary Monte Carlo generators of high energy hadronic interactions are discussed and their impact on the interpretation of experimental data on ultra-high energy cosmic rays (UHECRs) is studied. Key directions for further model improvements are outlined. The prospect for a coherent interpretation of the data in terms of the UHECR composition is investigated.
We present a model for the autonomous and simultaneous learning of active binocular and motion vision. The model is based on the Active Efficient Coding (AEC) framework, a recent generalization of classic efficient coding theories to active perception. The model learns how to efficiently encode the incoming visual signals generated by an object moving in 3-D through sparse coding. Simultaneously, it learns how to produce eye movements that further improve the efficiency of the sensory coding. This learning is driven by an intrinsic motivation to maximize the system's coding efficiency. We test our approach on the humanoid robot iCub using simulations. The model demonstrates self-calibration of accurate object fixation and tracking of moving objects. Our results show that the model keeps improving until it hits physical constraints such as camera or motor resolution, or limits on its internal coding capacity. Furthermore, we show that the emerging sensory tuning properties are in line with results on disparity, motion, and motion-in-depth tuning in the visual cortex of mammals. The model suggests that vergence and tracking eye movements can be viewed as fundamentally having the same objective of maximizing the coding efficiency of the visual system and that they can be learned and calibrated jointly through AEC.
A hypothesis regarding the development of imitation learning is presented that is rooted in intrinsic motivations. It is derived from a recently proposed form of intrinsically motivated learning (IML) for efficient coding in active perception, wherein an agent learns to perform actions with its sense organs to facilitate efficient encoding of the sensory data. To this end, actions of the sense organs that improve the encoding of the sensory data trigger an internally generated reinforcement signal. Here it is argued that the same IML mechanism might also support the development of imitation when general actions beyond those of the sense organs are considered: The learner first observes a tutor performing a behavior and learns a model of the the behavior's sensory consequences. The learner then acts itself and receives an internally generated reinforcement signal reflecting how well the sensory consequences of its own behavior are encoded by the sensory model. Actions that are more similar to those of the tutor will lead to sensory signals that are easier to encode and produce a higher reinforcement signal. Through this, the learner's behavior is progressively tuned to make the sensory consequences of its actions match the learned sensory model. I discuss this mechanism in the context of human language acquisition and bird song learning where similar ideas have been proposed. The suggested mechanism also offers an account for the development of mirror neurons and makes a number of predictions. Overall, it establishes a connection between principles of efficient coding, intrinsic motivations and imitation.
Steep rise of parton densities in the limit of small parton momentum fraction x poses a challenge for describing the observed energy-dependence of the total and inelastic proton-proton cross sections σtot/inelpp : considering a realistic parton spatial distribution, one obtains a too-strong increase of σtot/inelpp in the limit of very high energies. We discuss various mechanisms which allow one to tame such a rise, paying special attention to the role of parton-parton correlations. In addition, we investigate a potential impact on model predictions for σtotpp, related to dynamical higher twist corrections to parton-production process.
The capability of directing gaze to relevant parts in the environment is crucial for our survival. Computational models have proposed quantitative accounts of human gaze selection in a range of visual search tasks. Initially, models suggested that gaze is directed to the locations in a visual scene at which some criterion such as the probability of target location, the reduction of uncertainty or the maximization of reward appear to be maximal. But subsequent studies established, that in some tasks humans instead direct their gaze to locations, such that after the single next look the criterion is expected to become maximal. However, in tasks going beyond a single action, the entire action sequence may determine future rewards thereby necessitating planning beyond a single next gaze shift. While previous empirical studies have suggested that human gaze sequences are planned, quantitative evidence for whether the human visual system is capable of finding optimal eye movement sequences according to probabilistic planning is missing. Here we employ a series of computational models to investigate whether humans are capable of looking ahead more than the next single eye movement. We found clear evidence that subjects’ behavior was better explained by the model of a planning observer compared to a myopic, greedy observer, which selects only a single saccade at a time. In particular, the location of our subjects’ first fixation differed depending on the stimulus and the time available for the search, which was well predicted quantitatively by a probabilistic planning model. Overall, our results are the first evidence that the human visual system’s gaze selection agrees with optimal planning under uncertainty.
Spatial neuronal synchronization and the waveform of oscillations : implications for EEG and MEG
(2019)
Neuronal oscillations are ubiquitous in the human brain and are implicated in virtually all brain functions. Although they can be described by a prominent peak in the power spectrum, their waveform is not necessarily sinusoidal and shows rather complex morphology. Both frequency and temporal descriptions of such non-sinusoidal neuronal oscillations can be utilized. However, in non-invasive EEG/MEG recordings the waveform of oscillations often takes a sinusoidal shape which in turn leads to a rather oversimplified view on oscillatory processes. In this study, we show in simulations how spatial synchronization can mask non-sinusoidal features of the underlying rhythmic neuronal processes. Consequently, the degree of non-sinusoidality can serve as a measure of spatial synchronization. To confirm this empirically, we show that a mixture of EEG components is indeed associated with more sinusoidal oscillations compared to the waveform of oscillations in each constituent component. Using simulations, we also show that the spatial mixing of the non-sinusoidal neuronal signals strongly affects the amplitude ratio of the spectral harmonics constituting the waveform. Finally, our simulations show how spatial mixing can affect the strength and even the direction of the amplitude coupling between constituent neuronal harmonics at different frequencies. Validating these simulations, we also demonstrate these effects in real EEG recordings. Our findings have far reaching implications for the neurophysiological interpretation of spectral profiles, cross-frequency interactions, as well as for the unequivocal determination of oscillatory phase.
We consider a simple model of modified gravity interacting with a single scalar field ϕ with weakly coupled exponential potential within the framework of non-Riemannian spacetime volume-form formalism. The specific form of the action is fixed by the requirement of invariance under global Weyl-scale symmetry. Upon passing to the physical Einstein frame we show how the non-Riemannian volume elements create a second canonical scalar field u and dynamically generate a non-trivial two-scalar-field potential Ueff(u,ϕ) with two remarkable features: (i) it possesses a large flat region for large u describing a slow-roll inflation; (ii) it has a stable low-lying minimum w.r.t. (u,ϕ) representing the dark energy density in the “late universe”. We study the corresponding two-field slow-roll inflation and show that the pertinent slow-roll inflationary curve ϕ = ϕ(u) in the two-field space (u,ϕ) has a very small curvature, i.e., ϕ changes very little during the inflationary evolution of u on the flat region of Ueff(u,ϕ). Explicit expressions are found for the slow-roll parameters which differ from those in the single-field inflationary counterpart. Numerical solutions for the scalar spectral index and the tensor-to-scalar ratio are derived agreeing with the observational data.
We present a study of the elliptic flow and RAA of D and D¯ mesons in Au+Au collisions at FAIR energies. We propagate the charm quarks and the D mesons following a previously applied Langevin dynamics. The evolution of the background medium is modeled in two different ways: (I) we use the UrQMD hydrodynamics + Boltzmann transport hybrid approach including a phase transition to QGP and (II) with the coarse-graining approach employing also an equation of state with QGP. The latter approach has previously been used to describe di-lepton data at various energies very successfully. This comparison allows us to explore the effects of partial thermalization and viscous effects on the charm propagation. We explore the centrality dependencies of the collisions, the variation of the decoupling temperature and various hadronization parameters. We find that the initial partonic phase is responsible for the creation of most of the D/D¯ mesons elliptic flow and that the subsequent hadronic interactions seem to play only a minor role. This indicates that D/D¯ mesons elliptic flow is a smoking gun for a partonic phase at FAIR energies. However, the results suggest that the magnitude and the details of the elliptic flow strongly depend on the dynamics of the medium and on the hadronization procedure, which is related to the medium properties as well. Therefore, even at FAIR energies the charm quark might constitute a very useful tool to probe the quark–gluon plasma and investigate its physics.
The coordinate and momentum space configurations of the net baryon number in heavy ion collisions that undergo spinodal decomposition, due to a first-order phase transition, are investigated using state-of-the-art machine-learning methods. Coordinate space clumping, which appears in the spinodal decomposition, leaves strong characteristic imprints on the spatial net density distribution in nearly every event which can be detected by modern machine learning techniques. On the other hand, the corresponding features in the momentum distributions cannot clearly be detected, by the same machine learning methods, in individual events. Only a small subset of events can be systematically differ- entiated if only the momentum space information is available. This is due to the strong similarity of the two event classes, with and without spinodal decomposition. In such sce- narios, conventional event-averaged observables like the baryon number cumulants signal a spinodal non-equilibrium phase transition. Indeed the third-order cumulant, the skewness, does exhibit a peak at the beam energy (Elab = 3–4 A GeV), where the transient hot and dense system created in the heavy ion collision reaches the first-order phase transition.
The effect of a non-zero strangeness chemical potential on the strong interaction phase diagram has been studied within the framework of the SU(3) quark-hadron chiral parity-doublet model. Both, the nuclear liquid-gas and the chiral/deconfinement phase transitions are modified. The first-order line in the chiral phase transition is observed to vanish completely, with the entire phase boundary becoming a crossover. These changes in the nature of the phase transitions are expected to modify various susceptibilities, the effects of which might be detectable in particle-number distributions resulting from moderate-temperature and high-density heavy-ion collision experiments.
Classical Hodgkin lymphoma (cHL) is one of the most common malignant lymphomas in Western Europe. The nodular sclerosing subtype of cHL (NS cHL) is characterized by a proliferation of fibroblasts in the tumor microenvironment, leading to fibrotic bands surrounding the lymphoma infiltrate. Several studies have described a crosstalk between the tumour cells of cHL, the Hodgkin- and Reed-Sternberg (HRS) cells, and cancer-associated fibroblasts. However, to date a deep molecular characterization of these fibroblasts is lacking. Thus, the aim of the present study is a comprehensive characterization of these fibroblasts. Gene expression profiling and methylation profiles of fibroblasts isolated from primary lymph node suspensions revealed persistent differences between fibroblasts obtained from NS cHL and lymphadenitis. NS cHL derived fibroblasts exhibit a myofibroblastic phenotype characterized by myocardin (MYOCD) expression. Moreover, TIMP3, an inhibitor of matrix metalloproteinases, was strongly upregulated in NS cHL fibroblasts, likely contributing to the accumulation of collagen in sclerotic bands of NS cHL. As previously shown for other types of cancer-associated fibroblasts, treatment by luteolin could reverse this fibroblast phenotype and decrease TIMP3 secretion. NS cHL fibroblasts showed enhanced proliferation when they were exposed to soluble factors released from HRS cells. For HRS cells, soluble factors from fibroblasts were not sufficient to protect them from Brentuximab-Vedotin induced cell death. However, HRS cells adherent to fibroblasts were protected from Brentuximab-Vedotin induced injury. In summary, we confirm the importance of fibroblasts for HRS cell survival and identify TIMP3 which probably contributes as a major factor to the typical fibrosis observed in NS cHL.
Anaplastic large cell lymphoma (ALCL) and classical Hodgkin lymphoma (cHL) are lymphomas that contain CD30-expressing tumor cells and have numerous pathological similarities. Whereas ALCL is usually diagnosed at an advanced stage, cHL more frequently presents with localized disease. The aim of the present study was to elucidate the mechanisms underlying the different clinical presentation of ALCL and cHL. Chemokine and chemokine receptor expression were similar in primary ALCL and cHL cases apart from the known overexpression of the chemokines CCL17 and CCL22 in the Hodgkin and Reed-Sternberg (HRS) cells of cHL. Consistent with the overexpression of these chemokines, primary cHL cases encountered a significantly denser T cell microenvironment than ALCL. Additionally to differences in the interaction with their microenvironment, cHL cell lines presented a lower and less efficient intrinsic cell motility than ALCL cell lines, as assessed by time-lapse microscopy in a collagen gel and transwell migration assays. We thus propose that the combination of impaired basal cell motility and differences in the interaction with the microenvironment hamper the dissemination of HRS cells in cHL when compared with the tumor cells of ALCL.
Use-dependent long-term changes of neuronal response properties must be gated to prevent irrelevant activity from inducing inappropriate modifications. Here we test the hypothesis that local network dynamics contribute to such gating. As synaptic modifications depend on temporal contiguity between presynaptic and postsynaptic activity, we examined the effect of synchronized gamma (ɣ) oscillations on stimulation-dependent modifications of orientation selectivity in adult cat visual cortex. Changes of orientation maps were induced by pairing visual stimulation with electrical activation of the mesencephalic reticular formation. Changes in orientation selectivity were assessed with optical recording of intrinsic signals and multiunit recordings. When conditioning stimuli were associated with strong ɣ-oscillations, orientation domains matching the orientation of the conditioning grating stimulus became more responsive and expanded, because neurons with preferences differing by less than 30° from the orientation of the conditioning grating shifted their orientation preference toward the conditioned orientation. When conditioning stimuli induced no or only weak ɣ-oscillations, responsiveness of neurons driven by the conditioning stimulus decreased. These differential effects depended on the power of oscillations in the low ɣ-band (20 Hz to 48 Hz) and not on differences in discharge rate of cortical neurons, because there was no correlation between the discharge rates during conditioning and the occurrence of changes in orientation preference. Thus, occurrence and polarity of use-dependent long-term changes of cortical response properties appear to depend on the occurrence of ɣ-oscillations during induction and hence on the degree of temporal coherence of the change-inducing network activity.
Measurements of the π±, K±, and proton double differential yields emitted from the surface of the 90-cm-long carbon target (T2K replica) were performed for the incoming 31 GeV/c protons with the NA61/SHINE spectrometer at the CERN SPS using data collected during 2010 run. The double differential π± yields were measured with increased precision compared to the previously published NA61/SHINE results, while the K± and proton yields were obtained for the first time. A strategy for dealing with the dependence of the results on the incoming proton beam profile is proposed. The purpose of these measurements is to reduce significantly the (anti)neutrino flux uncertainty in the T2K long-baseline neutrino experiment by constraining the production of (anti)neutrino ancestors coming from the T2K target.
Bardeen black hole chemistry
(2019)
In the present paper we try to connect the Bardeen black hole with the concept of the recently proposed black hole chemistry. We study thermodynamic properties of the regular black hole with an anti-deSitter background. The negative cosmological constant Λ plays the role of the positive thermodynamic pressure of the system. After studying the thermodynamic variables, we derive the corresponding equation of state and we show that a neutral Bardeen-anti-deSitter black hole has similar phenomenology to the chemical Van der Waals fluid. This is equivalent to saying that the system exhibits criticality and a first order small/large black hole phase transition reminiscent of the liquid/gas coexistence.
The properties of open strange meson K1± in nuclear matter are estimated in the QCD sum rule approach. We obtain a relation between the in-medium mass and width of K1− (K1+) in nuclear matter, and show that the upper limit of the mass shift is as large as −249 (−35) MeV. The spectral modification of the K1 meson is possible to be probed by using kaon beams at J-PARC. Such measurement together with that of K⁎ will shed light on how chiral symmetry is partially restored in nuclear matter.
We study the production of entropy in the context of a nonequilibrium chiral phase transition. The dynamical symmetry breaking is modeled by a Langevin equation for the order parameter coupled to the Bjorken dynamics of a quark plasma. We investigate the impact of dissipation and noise on the entropy and explore the possibility of reheating for crossover and first-order phase transitions, depending on the expansion rate of the fluid. The relative increase in is estimated to range from 10% for a crossover to 100% for a first-order phase transition at low beam energies, which could be detected in the pion-to-proton ratio as a function of beam energy.
We present a study of the inclusive charged-particle transverse momentum (pT) spectra as a function of charged-particle multiplicity density at mid-pseudorapidity, dNch/dη, in pp collisions at s√=5.02 and 13 TeV covering the kinematic range |η|<0.8 and 0.15<pT<20 GeV/c. The results are presented for events with at least one charged particle in |η|<1 (INEL>0). The pT spectra are reported for two multiplicity estimators covering different pseudorapidity regions. The pT spectra normalized to that for INEL>0 show little energy dependence. Moreover, the high-pT yields of charged particles increase faster than the charged-particle multiplicity density. The average pT as a function of multiplicity and transverse spherocity is reported for pp collisions at s√=13 TeV. For low- (high-) spherocity events, corresponding to jet-like (isotropic) events, the average pT is higher (smaller) than that measured in INEL>0 pp collisions. Within uncertainties, the functional form of ⟨pT⟩(Nch) is not affected by the spherocity selection. While EPOS LHC gives a good description of many features of data, PYTHIA overestimates the average pT in jet-like events.
Measurement of the production of charm jets tagged with D0 mesons in pp collisions at √s = 7 TeV
(2019)
The production of charm jets in proton-proton collisions at a center-of-mass energy of s√=7 TeV was measured with the ALICE detector at the CERN Large Hadron Collider. The measurement is based on a data sample corresponding to a total integrated luminosity of 6.23 nb−1, collected using a minimum-bias trigger. Charm jets are identified by the presence of a D0 meson among their constituents. The D0 mesons are reconstructed from their hadronic decay D0 →K−π+. The D0-meson tagged jets are reconstructed using tracks of charged particles (track-based jets) with the anti-kT algorithm in the jet transverse momentum range 5<pchT,jet< 30 GeV/c and pseudorapidity |ηjet| < 0.5. The fraction of charged jets containing a D0-meson increases with pchT,jet from 0.042 ± 0.004 (stat) ± 0.006 (syst) to 0.080 ± 0.009 (stat) ± 0.008 (syst). The distribution of D0-meson tagged jets as a function of the jet momentum fraction carried by the D0 meson in the direction of the jet axis (zch∥) is reported for two ranges of jet transverse momenta, 5<pchT,jet< 15 GeV/c and 15<pchT,jet< 30 GeV/c in the intervals 0.2<zch∥∥<1.0 and 0.4<zch∥∥<1.0, respectively. The data are compared with results from Monte Carlo event generators (PYTHIA 6, PYTHIA 8 and Herwig 7) and with a Next-to-Leading-Order perturbative Quantum Chromodynamics calculation, obtained with the POWHEG method and interfaced with PYTHIA 6 for the generation of the parton shower, fragmentation, hadronisation and underlying event.
Charged-particle pseudorapidity density at mid-rapidity in p-Pb collisions at √sNN = 8.16 TeV
(2019)
The pseudorapidity density of charged particles, dNch/dη, in p–Pb collisions has been measured at a centre-of-mass energy per nucleon–nucleon pair of sNN−−−√ = 8.16 TeV at mid-pseudorapidity for non-single-diffractive events. The results cover 3.6 units of pseudorapidity, |η|<1.8. The dNch/dη value is 19.1±0.7 at |η|<0.5. This quantity divided by ⟨Npart⟩ / 2 is 4.73±0.20, where ⟨Npart⟩is the average number of participating nucleons, is 9.5% higher than the corresponding value for p–Pb collisions at sNN−−−√ = 5.02 TeV. Measurements are compared with models based on different mechanisms for particle production. All models agree within uncertainties with data in the Pb-going side, while HIJING overestimates, showing a symmetric behaviour, and EPOS underestimates the p-going side of the dNch/dη distribution. Saturation-based models reproduce the distributions well for η>−1.3. The dNch/dη is also measured for different centrality estimators, based both on the charged-particle multiplicity and on the energy deposited in the Zero-Degree Calorimeters. A study of the implications of the large multiplicity fluctuations due to the small number of participants for systems like p–Pb in the centrality calculation for multiplicity-based estimators is discussed, demonstrating the advantages of determining the centrality with energy deposited near beam rapidity.
Measurement of the inclusive isolated photon production cross section in pp collisions at √s = 7 TeV
(2019)
The production cross section of inclusive isolated photons has been measured by the ALICE experiment at the CERN LHC in pp collisions at a centre-of-momentum energy of s√= 7 TeV. The measurement is performed with the electromagnetic calorimeter EMCal and the central tracking detectors, covering a range of |η|<0.27 in pseudorapidity and a transverse momentum range of 10<pγT<60 GeV/c. The result extends the pT coverage of previously published results of the ATLAS and CMS experiments at the same collision energy to smaller pT. The measurement is compared to next-to-leading order perturbative QCD calculations and to the results from the ATLAS and CMS experiments. All measurements and theory predictions are in agreement with each other.
Measurement of ϒ(1S) elliptic flow at forward rapidity in Pb-Pb collisions at √sNN = 5.02 TeV
(2019)
The first measurement of the ϒ(1S) elliptic flow coefficient (v2) is performed at forward rapidity (2.5 < y < 4) in Pb–Pb collisions at √sNN = 5.02 TeV with the ALICE detector at the LHC. The results are obtained with the scalar product method and are reported as a function of transverse momentum (pT) up to 15 GeV/c in the 5%–60% centrality interval. The measured Υ(1S)v2 is consistent with 0 and with the small positive values predicted by transport models within uncertainties. The v2 coefficient in 2 < pT < 15 GeV/c is lower than that of inclusive J/ψ mesons in the same pT interval by 2.6 standard deviations. These results, combined with earlier suppression measurements, are in agreement with a scenario in which the Υ(1S) production in Pb–Pb collisions at LHC energies is dominated by dissociation limited to the early stage of the collision, whereas in the J/ψ case there is substantial experimental evidence of an additional regeneration component.
The production yield of prompt D mesons and their elliptic flow coefficient v2 were measured with the Event-Shape Engineering (ESE) technique applied to mid-central (10–30% and 30–50% centrality classes) Pb-Pb collisions at the centre-of-mass energy per nucleon pair sNN−−−√=5.02 TeV, with the ALICE detector at the LHC. The ESE technique allows the classification of events, belonging to the same centrality, according to the azimuthal anisotropy of soft particle production in the collision. The reported measurements give the opportunity to investigate the dynamics of charm quarks in the Quark-Gluon Plasma and provide information on their participation in the collective expansion of the medium. D mesons were reconstructed via their hadronic decays at mid-rapidity, |η| < 0.8, in the transverse momentum interval 1 < pT < 24 GeV/c. The v2 coefficient is found to be sensitive to the event-shape selection confirming a correlation between the D-meson azimuthal anisotropy and the collective expansion of the bulk matter, while the per-event D-meson yields do not show any significant modification within the current uncertainties.
The ALICE Collaboration has measured the energy dependence of exclusive photoproduction of J/ψ vector mesons off proton targets in ultra–peripheral p–Pb collisions at a centre-of-mass energy per nucleon pair sNN−−−√=5.02 TeV. The e+e− and μ+μ− decay channels are used to measure the cross section as a function of the rapidity of the J/ψ in the range −2.5<y<2.7, corresponding to an energy in the γp centre-of-mass in the interval 40<Wγp<550 GeV. The measurements, which are consistent with a power law dependence of the exclusive J/ψ photoproduction cross section, are compared to previous results from HERA and the LHC and to several theoretical models. They are found to be compatible with previous measurements.
The measurements of the production of prompt D0, D+, D∗+, and D+s mesons in proton–proton (pp) collisions at s√=5.02 TeV with the ALICE detector at the Large Hadron Collider (LHC) are reported. D mesons were reconstructed at mid-rapidity (|y|<0.5) via their hadronic decay channels D0→K−π+, D+→K−π+π+, D∗+→D0π+→K−π+π+, D+s→ϕπ+→K+K−π+, and their charge conjugates. The production cross sections were measured in the transverse momentum interval 0<pT<36 GeV/c for D0, 1<pT<36 GeV/c for D+ and D∗+, and in 2<pT<24 GeV/c for D+s mesons. Thanks to the higher integrated luminosity, an analysis in finer pT bins with respect to the previous measurements at s√=7 TeV was performed, allowing for a more detailed description of the cross-section pT shape. The measured pT-differential production cross sections are compared to the results at s√=7 TeV and to four different perturbative QCD calculations. Its rapidity dependence is also tested combining the ALICE and LHCb measurements in pp collisions at s√=5.02 TeV. This measurement will allow for a more accurate determination of the nuclear modification factor in p–Pb and Pb–Pb collisions performed at the same nucleon–nucleon centre-of-mass energy.
Two-particle correlations in high-energy collision experiments enable the extraction of particle source radii by using the Bose-Einstein enhancement of pion production at low relative momentum q ∝ 1/R. It was previously observed that in pp collisions at s√ = 7TeV the average pair transverse momentum kT range of such analyses is limited due to large background correlations which were attributed to mini-jet phenomena. To investigate this further, an event-shape dependent analysis of Bose-Einstein correlations for pion pairs is performed in this work. By categorizing the events by their transverse sphericity ST into spherical (ST > 0:7) and jet-like (ST < 0:3) events a method was developed that allows for the determination of source radii for much larger values of kT for the first time. Spherical events demonstrate little or no background correlations while jet-like events are dominated by them. This observation agrees with the hypothesis of a mini-jet origin of the non-femtoscopic background correlations and gives new insight into the physics interpretation of the kT dependence of the radii. The emission source size in spherical events shows a substantially diminished kT dependence, while jet-like events show indications of a negative trend with respect to kT in the highest multiplicity events. Regarding the emission source shape, the correlation functions for both event sphericity classes show good agreement with an exponential shape, rather than a Gaussian one.
The transverse structure of jets was studied via jet fragmentation transverse momentum (jT) distributions, obtained using two-particle correlations in proton-proton and proton-lead collisions, measured with the ALICE experiment at the LHC. The highest transverse momentum particle in each event is used as the trigger particle and the region 3 < pTt < 15GeV/c is explored in this study. The measured distributions show a clear narrow Gaussian component and a wide non-Gaussian one. Based on Pythia simulations, the narrow component can be related to non-perturbative hadronization and the wide component to quantum chromodynamical splitting. The width of the narrow component shows a weak dependence on the transverse momentum of the trigger particle, in agreement with the expectation of universality of the hadronization process. On the other hand, the width of the wide component shows a rising trend suggesting increased branching for higher transverse momentum. The results obtained in pp collisions at s√=7 TeV and in p–Pb collisions at sNN−−−√=5.02 TeV are compatible within uncertainties and hence no significant cold nuclear matter effects are observed. The results are compared to previous measurements from CCOR and PHENIX as well as to PYTHIA 8 and Herwig 7 simulations.
The second (v2) and third (v3) flow harmonic coefficients of J/ψ mesons are measured at forward rapidity (2.5 < y < 4.0) in Pb-Pb collisions at sNN−−−√=5.02 TeV with the ALICE detector at the LHC. Results are obtained with the scalar product method and reported as a function of transverse momentum, pT, for various collision centralities. A positive value of J/ψ v3 is observed with 3.7σ significance. The measurements, compared to those of prompt D0 mesons and charged particles at mid-rapidity, indicate an ordering with vn(J/ψ) < vn(D0) < vn(h±) (n = 2, 3) at low and intermediate pT up to 6 GeV/c and a convergence with v2(J/ψ) ≈ v2(D0) ≈ v2(h±) at high pT above 6–8 GeV/c. In semi-central collisions (5–40% and 10–50% centrality intervals) at intermediate pT between 2 and 6 GeV/c, the ratio v3/v2 of J/ψ mesons is found to be significantly lower (4.6σ) with respect to that of charged particles. In addition, the comparison to the prompt D0-meson ratio in the same pT interval suggests an ordering similar to that of the v2 and v3 coefficients. The J/ψ v2 coefficient is further studied using the Event Shape Engineering technique. The obtained results are found to be compatible with the expected variations of the eccentricity of the initial-state geometry.
Gravitational waves, electromagnetic radiation, and the emission of high energy particles probe the phase structure of the equation of state of dense matter produced at the crossroad of the closely related relativistic collisions of heavy ions and of binary neutron stars mergers. 3 + 1 dimensional special- and general relativistic hydrodynamic simulation studies reveal a unique window of opportunity to observe phase transitions in compressed baryon matter by laboratory based experiments and by astrophysical multimessenger observations. The astrophysical consequences of a hadron-quark phase transition in the interior of a compact star will be focused within this article. Especially with a future detection of the post-merger gravitational wave emission emanated from a binary neutron star merger event, it would be possible to explore the phase structure of quantum chromodynamics. The astrophysical observables of a hadron-quark phase transition in a single compact star system and binary hybrid star merger scenario will be summarized within this article. The FAIR facility at GSI Helmholtzzentrum allows one to study the universe in the laboratory, and several astrophysical signatures of the quark-gluon plasma have been found in relativistic collisions of heavy ions and will be explored in future experiments.
In this work, we discuss the dense matter equation of state (EOS) for the extreme range of conditions encountered in neutron stars and their mergers. The calculation of the properties of such an EOS involves modeling different degrees of freedom (such as nuclei, nucleons, hyperons, and quarks), taking into account different symmetries, and including finite density and temperature effects in a thermodynamically consistent manner. We begin by addressing subnuclear matter consisting of nucleons and a small admixture of light nuclei in the context of the excluded volume approach. We then turn our attention to supranuclear homogeneous matter as described by the Chiral Mean Field (CMF) formalism. Finally, we present results from realistic neutron-star-merger simulations performed using the CMF model that predict signatures for deconfinement to quark matter in gravitational wave signals.
Inclusive J/ψ production is studied in minimum-bias proton-proton collisions at a centre-of-mass energy of s√ = 5.02 TeV by ALICE at the CERN LHC. The measurement is performed at mid-rapidity (|y| < 0.9) in the dielectron decay channel down to zero transverse momentum pT, using a data sample corresponding to an integrated luminosity of Lint = 19.4 ± 0.4 nb−1. The measured pT-integrated inclusive J/ψ production cross sec- tion is dσ/dy = 5.64 ± 0.22(stat.) ± 0.33(syst.) ± 0.12(lumi.) μb. The pT-differential cross section d2σ/dpTdy is measured in the pT range 0–10 GeV/c and compared with state-of- the-art QCD calculations. The J/ψ 〈pT〉 and ⟨p2T⟩ are extracted and compared with results obtained at other collision energies.
Charged-particle spectra at midrapidity are measured in Pb–Pb collisions at the centre-of-mass energy per nucleon–nucleon pair √sNN = 5.02 TeV and presented in centrality classes ranging from most central (0–5%) to most peripheral (95–100%) collisions. Possible medium effects are quantified using the nuclear modification factor (RAA) by comparing the measured spectra with those from proton–proton collisions, scaled by the number of independent nucleon–nucleon collisions obtained from a Glauber model. At large transverse momenta (8 < pT < 20 GeV/c), the average RAA is found to increase from about 0.15 in 0–5% central to a maximum value of about 0.8 in 75–85% peripheral collisions, beyond which it falls off strongly to below 0.2 for the most peripheral collisions. Furthermore, RAA initially exhibits a positive slope as a function of pT in the 8–20 GeV/c interval, while for collisions beyond the 80% class the slope is negative. To reduce uncertainties related to event selection and normalization, we also provide the ratio of RAA in adjacent centrality intervals. Our results in peripheral collisions are consistent with a PYTHIA-based model without nuclear modification, demonstrating that biases caused by the event selection and collision geometry can lead to the apparent suppression in peripheral collisions. This explains the unintuitive observation that RAA is below unity in peripheral Pb–Pb, but equal to unity in minimum-bias p–Pb collisions despite similar charged-particle multiplicities.
The measurement of the production of prompt D0, D+, D*+, and D+S mesons in proton–lead (p–Pb) collisions at the centre-of-mass energy per nucleon pair of sNN−−−√ = 5.02 TeV, with an integrated luminosity of 292 ± 11 μb−1, are reported. Differential production cross sections are measured at mid-rapidity (−0.96 < ycms< 0.04) as a function of transverse momentum (pT) in the intervals 0 < pT< 36 GeV/c for D0, 1 < pT< 36 GeV/c for D+ and D*+, and 2 < pT< 24 GeV/c for D+ mesons. For each species, the nuclear modification factor RpPb is calculated as a function of pT using a proton-proton (pp) ref- erence measured at the same collision energy. The results are compatible with unity in the whole pT range. The average of the non-strange D mesons RpPb is compared with theoretical model predictions that include initial-state effects and parton transport model predictions. The pT dependence of the D0, D+, and D*+ nuclear modification factors is also reported in the interval 1 < pT< 36 GeV/c as a function of the collision centrality, and the central-to-peripheral ratios are computed from the D-meson yields measured in different centrality classes. The results are further compared with charged-particle measurements and a similar trend is observed in all the centrality classes. The ratios of the pT-differential cross sections of D0, D+, D*+, and D+S mesons are also reported. The D+S and D+ yields are compared as a function of the charged-particle multiplicity for several pT intervals. No modification in the relative abundances of the four species is observed with respect to pp collisions within the statistical and systematic uncertainties.
First results on K/π, p/π and K/p fluctuations are obtained with the ALICE detector at the CERN LHC as a function of centrality in Pb--Pb collisions at sNN−−−√=2.76 TeV. The observable νdyn, which is defined in terms of the moments of particle multiplicity distributions, is used to quantify the magnitude of dynamical fluctuations of relative particle yields and also provides insight into the correlation between particle pairs. This study is based on a novel experimental technique, called the Identity Method, which allows one to measure the moments of multiplicity distributions in case of incomplete particle identification. The results for p/π show a change of sign in νdyn from positive to negative towards more peripheral collisions. For central collisions, the results follow the smooth trend of the data at lower energies and νdyn exhibits a change in sign for p/π and K/p.
Feathers are arranged in a precise pattern in avian skin. They first arise during development in a row along the dorsal midline, with rows of new feather buds added sequentially in a spreading wave. We show that the patterning of feathers relies on coupled fibroblast growth factor (FGF) and bone morphogenetic protein (BMP) signalling together with mesenchymal cell movement, acting in a coordinated reaction-diffusion-taxis system. This periodic patterning system is partly mechanochemical, with mechanical-chemical integration occurring through a positive feedback loop centred on FGF20, which induces cell aggregation, mechanically compressing the epidermis to rapidly intensify FGF20 expression. The travelling wave of feather formation is imposed by expanding expression of Ectodysplasin A (EDA), which initiates the expression of FGF20. The EDA wave spreads across a mesenchymal cell density gradient, triggering pattern formation by lowering the threshold of mesenchymal cells required to begin to form a feather bud. These waves, and the precise arrangement of feather primordia, are lost in the flightless emu and ostrich, though via different developmental routes. The ostrich retains the tract arrangement characteristic of birds in general but lays down feather primordia without a wave, akin to the process of hair follicle formation in mammalian embryos. The embryonic emu skin lacks sufficient cells to enact feather formation, causing failure of tract formation, and instead the entire skin gains feather primordia through a later process. This work shows that a reaction-diffusion-taxis system, integrated with mechanical processes, generates the feather array. In flighted birds, the key role of the EDA/Ectodysplasin A receptor (EDAR) pathway in vertebrate skin patterning has been recast to activate this process in a quasi-1-dimensional manner, imposing highly ordered pattern formation.
Production cross sections of muons from semi-leptonic decays of charm and beauty hadrons were measured at forward rapidity (2.5 < y < 4) in proton-proton (pp) collisions at a centre-of-mass energy s√ = 5.02 TeV with the ALICE detector at the CERN LHC. The results were obtained in an extended transverse momentum interval, 2 < pT< 20 GeV/c, and with an improved precision compared to previous measurements performed in the same rapidity interval at centre-of-mass energies s√ = 2.76 and 7 TeV. The pT- and y-differential production cross sections as well as the pT-differential production cross section ratios between different centre-of-mass energies and different rapidity intervals are described, within experimental and theoretical uncertainties, by predictions based on perturbative QCD.
Measurements of anisotropic flow coefficients with two- and multi-particle cumulants for inclusive charged particles in Pb-Pb collisions at sNN−−−√=5.02 and 2.76 TeV are reported in the pseudorapidity range |η|<0.8 and transverse momentum 0.2<pT<50 GeV/c. The full data sample collected by the ALICE detector in 2015 (2010), corresponding to an integrated luminosity of 12.7 (2.0) μb−1 in the centrality range 0-80%, is analysed. Flow coefficients up to the sixth flow harmonic (v6) are reported and a detailed comparison among results at the two energies is carried out. The pT dependence of anisotropic flow coefficients and its evolution with respect to centrality and harmonic number n are investigated. An approximate power-law scaling of the form vn(pT)∼pn/3T is observed for all flow harmonics at low pT (0.2<pT<3 GeV/c). At the same time, the ratios vn/vn/mm are observed to be essentially independent of pT for most centralities up to about pT=10 GeV/c. Analysing the differences among higher-order cumulants of elliptic flow (v2), which have different sensitivities to flow fluctuations, a measurement of the standardised skewness of the event-by-event v2 distribution P(v2) is reported and constraints on its higher moments are provided. The Elliptic Power distribution is used to parametrise P(v2), extracting its parameters from fits to cumulants. The measurements are compared to different model predictions in order to discriminate among initial-state models and to constrain the temperature dependence of the shear viscosity to entropy-density ratio.
Scattering studies with low-energy kaon-proton femtoscopy in
proton–proton collisions at the LHC
(2019)
The study of the strength and behaviour of the antikaon-nucleon (K¯¯¯¯N) interaction constitutes one of the key focuses of the strangeness sector in low-energy Quantum Chromodynamics (QCD). In this letter a unique high-precision measurement of the strong interaction between kaons and protons, close and above the kinematic threshold, is presented. The femtoscopic measurements of the correlation function at low pair-frame relative momentum of (K+ p ⊕ K− p¯¯¯) and (K− p ⊕ K+ p¯¯¯) pairs measured in pp collisions at s√ = 5, 7 and 13 TeV are reported. A structure observed around a relative momentum of 58 MeV/c in the measured correlation function of (K− p ⊕ K+ p¯¯¯) constitutes the first experimental evidence for the opening of the (K¯¯¯¯0n⊕K0n¯¯¯) isospin breaking channel due to the mass difference between charged and neutral kaons. The measured correlation functions have been compared to several models. The high-precision data at low relative momenta presented in this work prove femtoscopy to be a powerful complementary tool to scattering experiments and provide new constraints above the K¯¯¯¯N threshold for low-energy QCD chiral models.
The elliptic (v2), triangular (v3), and quadrangular (v4) flow coefficients of π±, K±, p+p¯¯¯, Λ+Λ¯¯¯¯, K0S, and the ϕ-meson are measured in Pb-Pb collisions at sNN−−−√=5.02 TeV. Results obtained with the scalar product method are reported for the rapidity range |y|< 0.5 as a function of transverse momentum, pT, at different collision centrality intervals between 0-70%, including ultra-central (0-1%) collisions for π±, K±, and p+p¯¯¯. For pT<3 GeV/c, the flow coefficients exhibit a particle mass dependence. At intermediate transverse momenta (3<pT<~8-10 GeV/c), particles show an approximate grouping according to their type (i.e., mesons and baryons). The ϕ-meson v2, which tests both particle mass dependence and type scaling, follows p+p¯¯¯ v2 at low pT and π± v2 at intermediate pT. The evolution of the shape of vn(pT) as a function of centrality and harmonic number n is studied for the various particle species. Flow coefficients of π±, K±, and p+p¯¯¯ for pT<3 GeV/c are compared to iEBE-VISHNU and MUSIC hydrodynamical calculations coupled to a hadronic cascade model (UrQMD). The iEBE-VISHNU calculations describe the results fairly well for pT<2.5 GeV/c, while MUSIC calculations reproduce the measurements for pT<1 GeV/c. A comparison to vn coefficients measured in Pb-Pb collisions at sNN−−−√ = 2.76 TeV is also provided.
ϕ meson measurements provide insight into strangeness production, which is one of the key observables for the hot medium formed in high-energy heavy-ion collisions. ALICE measured ϕ production through its decay in muon pairs in Pb-Pb collisions at sNN−−−√ = 2.76 TeV in the intermediate transverse momentum range 2<pT<5 GeV/c and in the rapidity interval 2.5<y<4. The ϕ yield was measured as a function of the transverse momentum and collision centrality. The nuclear modification factor was obtained as a function of the average number of participating nucleons. Results were compared with the ones obtained via the kaon decay channel in the same pT range at midrapidity. The values of the nuclear modification factor in the two rapidity regions are in agreement within uncertainties.
Measurement of the inclusive J/ψ polarization at forward rapidity in pp collisions at √s = 8 TeV
(2019)
We report on the measurement of the inclusive J/ψ polarization parameters in pp collisions at a center of mass energy s√=8 TeV with the ALICE detector at the LHC. The analysis is based on a data sample corresponding to an integrated luminosity of 1.23 pb−1. J/ψ resonances are reconstructed in their di-muon decay channel in the rapidity interval 2.5<y<4.0 and over the transverse-momentum interval 2<pT<15 GeV/c. The three polarization parameters (λθ, λφ, λθφ) are measured as a function of pT both in the helicity and Collins-Soper reference frames. The measured J/ψ polarization parameters are found to be compatible with zero within uncertainties, contrary to expectations from all available predictions. The results are compared with the measurement in pp collisions at s√=7 TeV.
The production of the Λ(1520) baryonic resonance has been measured at midrapidity in inelastic pp collisions at s√ = 7 TeV and in p-Pb collisions at sNN−−−√ = 5.02 TeV for non-single diffractive events and in multiplicity classes. The resonance is reconstructed through its hadronic decay channel Λ(1520) → pK− and the charge conjugate with the ALICE detector. The integrated yields and mean transverse momenta are calculated from the measured transverse momentum distributions in pp and p-Pb collisions. The mean transverse momenta follow mass ordering as previously observed for other hyperons in the same collision systems. A Blast-Wave function constrained by other light hadrons (π, K, K0S, p, Λ) describes the shape of the Λ(1520) transverse momentum distribution up to 3.5 GeV/c in p-Pb collisions. In the framework of this model, this observation suggests that the Λ(1520) resonance participates in the same collective radial flow as other light hadrons. The ratio of the yield of Λ(1520) to the yield of the ground state particle Λ remains constant as a function of charged-particle multiplicity, suggesting that there is no net effect of the hadronic phase in p-Pb collisions on the Λ(1520) yield.