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We present a dataset of free-viewing eye-movement recordings that contains more than 2.7 million fixation locations from 949 observers on more than 1000 images from different categories. This dataset aggregates and harmonizes data from 23 different studies conducted at the Institute of Cognitive Science at Osnabrück University and the University Medical Center in Hamburg-Eppendorf. Trained personnel recorded all studies under standard conditions with homogeneous equipment and parameter settings. All studies allowed for free eye-movements, and differed in the age range of participants (~7–80 years), stimulus sizes, stimulus modifications (phase scrambled, spatial filtering, mirrored), and stimuli categories (natural and urban scenes, web sites, fractal, pink-noise, and ambiguous artistic figures). The size and variability of viewing behavior within this dataset presents a strong opportunity for evaluating and comparing computational models of overt attention, and furthermore, for thoroughly quantifying strategies of viewing behavior. This also makes the dataset a good starting point for investigating whether viewing strategies change in patient groups.
The ability to learn sequential behaviors is a fundamental property of our brains. Yet a long stream of studies including recent experiments investigating motor sequence learning in adult human subjects have produced a number of puzzling and seemingly contradictory results. In particular, when subjects have to learn multiple action sequences, learning is sometimes impaired by proactive and retroactive interference effects. In other situations, however, learning is accelerated as reflected in facilitation and transfer effects. At present it is unclear what the underlying neural mechanism are that give rise to these diverse findings. Here we show that a recently developed recurrent neural network model readily reproduces this diverse set of findings. The self-organizing recurrent neural network (SORN) model is a network of recurrently connected threshold units that combines a simplified form of spike-timing dependent plasticity (STDP) with homeostatic plasticity mechanisms ensuring network stability, namely intrinsic plasticity (IP) and synaptic normalization (SN). When trained on sequence learning tasks modeled after recent experiments we find that it reproduces the full range of interference, facilitation, and transfer effects. We show how these effects are rooted in the network’s changing internal representation of the different sequences across learning and how they depend on an interaction of training schedule and task similarity. Furthermore, since learning in the model is based on fundamental neuronal plasticity mechanisms, the model reveals how these plasticity mechanisms are ultimately responsible for the network’s sequence learning abilities. In particular, we find that all three plasticity mechanisms are essential for the network to learn effective internal models of the different training sequences. This ability to form effective internal models is also the basis for the observed interference and facilitation effects. This suggests that STDP, IP, and SN may be the driving forces behind our ability to learn complex action sequences.
Dendrites form predominantly binary trees that are exquisitely embedded in the networks of the brain. While neuronal computation is known to depend on the morphology of dendrites, their underlying topological blueprint remains unknown. Here, we used a centripetal branch ordering scheme originally developed to describe river networks—the Horton-Strahler order (SO)–to examine hierarchical relationships of branching statistics in reconstructed and model dendritic trees. We report on a number of universal topological relationships with SO that are true for all binary trees and distinguish those from SO-sorted metric measures that appear to be cell type-specific. The latter are therefore potential new candidates for categorising dendritic tree structures. Interestingly, we find a faithful correlation of branch diameters with centripetal branch orders, indicating a possible functional importance of SO for dendritic morphology and growth. Also, simulated local voltage responses to synaptic inputs are strongly correlated with SO. In summary, our study identifies important SO-dependent measures in dendritic morphology that are relevant for neural function while at the same time it describes other relationships that are universal for all dendrites.
Working memory and conscious perception are thought to share similar brain mechanisms, yet recent reports of non-conscious working memory challenge this view. Combining visual masking with magnetoencephalography, we investigate the reality of non-conscious working memory and dissect its neural mechanisms. In a spatial delayed-response task, participants reported the location of a subjectively unseen target above chance-level after several seconds. Conscious perception and conscious working memory were characterized by similar signatures: a sustained desynchronization in the alpha/beta band over frontal cortex, and a decodable representation of target location in posterior sensors. During non-conscious working memory, such activity vanished. Our findings contradict models that identify working memory with sustained neural firing, but are compatible with recent proposals of ‘activity-silent’ working memory. We present a theoretical framework and simulations showing how slowly decaying synaptic changes allow cell assemblies to go dormant during the delay, yet be retrieved above chance-level after several seconds.
Motivated by a recent finding of an exact solution of the relativistic Boltzmann equation in a Friedmann–Robertson–Walker spacetime, we implement this metric into the newly developed transport approach Simulating Many Accelerated Strongly-interacting Hadrons (SMASH). We study the numerical solution of the transport equation and compare it to this exact solution for massless particles. We also compare a different initial condition, for which the transport equation can be independently solved numerically. Very nice agreement is observed in both cases. Having passed these checks for the SMASH code, we study a gas of massive particles within the same spacetime, where the particle decoupling is forced by the Hubble expansion. In this simple scenario we present an analysis of the freeze-out times, as function of the masses and cross sections of the particles. The results might be of interest for their potential application to relativistic heavy-ion collisions, for the characterization of the freeze-out process in terms of hadron properties.
I summarize recent developments in the hard-thermal-loop approach to QCD. I first discuss a finite-temperature and -density calculation of QCD thermodynamics at NNLO from the hard-thermal-loop perturbation theory. I then discuss a generalization of the hard-thermal-loop framework to the magnetic scale g2T, from which a novel non-Abelian massless mode is uncovered.
The detailed biophysical mechanisms through which transcranial magnetic stimulation (TMS) activates cortical circuits are still not fully understood. Here we present a multi-scale computational model to describe and explain the activation of different pyramidal cell types in motor cortex due to TMS. Our model determines precise electric fields based on an individual head model derived from magnetic resonance imaging and calculates how these electric fields activate morphologically detailed models of different neuron types. We predict neural activation patterns for different coil orientations consistent with experimental findings. Beyond this, our model allows us to calculate activation thresholds for individual neurons and precise initiation sites of individual action potentials on the neurons’ complex morphologies. Specifically, our model predicts that cortical layer 3 pyramidal neurons are generally easier to stimulate than layer 5 pyramidal neurons, thereby explaining the lower stimulation thresholds observed for I-waves compared to D-waves. It also shows differences in the regions of activated cortical layer 5 and layer 3 pyramidal cells depending on coil orientation. Finally, it predicts that under standard stimulation conditions, action potentials are mostly generated at the axon initial segment of cortical pyramidal cells, with a much less important activation site being the part of a layer 5 pyramidal cell axon where it crosses the boundary between grey matter and white matter. In conclusion, our computational model offers a detailed account of the mechanisms through which TMS activates different cortical pyramidal cell types, paving the way for more targeted application of TMS based on individual brain morphology in clinical and basic research settings.
The detailed biophysical mechanisms through which transcranial magnetic stimulation (TMS) activates cortical circuits are still not fully understood. Here we present a multi-scale computational model to describe and explain the activation of different pyramidal cell types in motor cortex due to TMS. Our model determines precise electric fields based on an individual head model derived from magnetic resonance imaging and calculates how these electric fields activate morphologically detailed models of different neuron types. We predict neural activation patterns for different coil orientations consistent with experimental findings. Beyond this, our model allows us to calculate activation thresholds for individual neurons and precise initiation sites of individual action potentials on the neurons’ complex morphologies. Specifically, our model predicts that cortical layer 3 pyramidal neurons are generally easier to stimulate than layer 5 pyramidal neurons, thereby explaining the lower stimulation thresholds observed for I-waves compared to D-waves. It also shows differences in the regions of activated cortical layer 5 and layer 3 pyramidal cells depending on coil orientation. Finally, it predicts that under standard stimulation conditions, action potentials are mostly generated at the axon initial segment of cortical pyramidal cells, with a much less important activation site being the part of a layer 5 pyramidal cell axon where it crosses the boundary between grey matter and white matter. In conclusion, our computational model offers a detailed account of the mechanisms through which TMS activates different cortical pyramidal cell types, paving the way for more targeted application of TMS based on individual brain morphology in clinical and basic research settings.
We investigate the effect of large magnetic fields on the (2 + 1)-dimensional reduced-magnetohydrodynamical expansion of hot and dense nuclear matter produced in √sNN = 200 GeV Au+Au collisions. For the sake of simplicity,we consider the casewhere themagnetic field points in the direction perpendicular to the reaction plane. We also consider this field to be external, with energy density parametrized as a two-dimensional Gaussian. The width of the Gaussian along the directions orthogonal to the beam axis varies with the centrality of the collision. The dependence of the magnetic field on proper time (τ ) for the case of zero electrical conductivity of the QGP is parametrized following Deng et al. [Phys. Rev. C 85, 044907 (2012)], and for finite electrical conductivity following Tuchin [Phys. Rev. C 88, 024911 (2013)].We solve the equations of motion of ideal hydrodynamics for such an external magnetic field. For collisions with nonzero impact parameter we observe considerable changes in the evolution of the momentum eccentricities of the fireball when comparing the case when the magnetic field decays in a conducting QGP medium and when no magnetic field is present. The elliptic-flow coefficient v2 of π− is shown to increase in the presence of an external magnetic field and the increment in v2 is found to depend on the evolution and the initial magnitude of the magnetic field.
Neurogenesis of hippocampal granule cells (GCs) persists throughout mammalian life and is important for learning and memory. How newborn GCs differentiate and mature into an existing circuit during this time period is not yet fully understood. We established a method to visualize postnatally generated GCs in organotypic entorhino-hippocampal slice cultures (OTCs) using retroviral (RV) GFP-labeling and performed time-lapse imaging to study their morphological development in vitro. Using anterograde tracing we could, furthermore, demonstrate that the postnatally generated GCs in OTCs, similar to adult born GCs, grow into an existing entorhino-dentate circuitry. RV-labeled GCs were identified and individual cells were followed for up to four weeks post injection. Postnatally born GCs exhibited highly dynamic structural changes, including dendritic growth spurts but also retraction of dendrites and phases of dendritic stabilization. In contrast, older, presumably prenatally born GCs labeled with an adeno-associated virus (AAV), were far less dynamic. We propose that the high degree of structural flexibility seen in our preparations is necessary for the integration of newborn granule cells into an already existing neuronal circuit of the dentate gyrus in which they have to compete for entorhinal input with cells generated and integrated earlier.
We present the black hole accretion code (BHAC), a new multidimensional general-relativistic magnetohydrodynamics module for the MPI-AMRVAC framework. BHAC has been designed to solve the equations of ideal general-relativistic magnetohydrodynamics in arbitrary spacetimes and exploits adaptive mesh refinement techniques with an efficient block-based approach. Several spacetimes have already been implemented and tested. We demonstrate the validity of BHAC by means of various one-, two-, and three-dimensional test problems, as well as through a close comparison with the HARM3D code in the case of a torus accreting onto a black hole. The convergence of a turbulent accretion scenario is investigated with several diagnostics and we find accretion rates and horizon-penetrating fluxes to be convergent to within a few percent when the problem is run in three dimensions. Our analysis also involves the study of the corresponding thermal synchrotron emission, which is performed by means of a new general-relativistic radiative transfer code, BHOSS. The resulting synthetic intensity maps of accretion onto black holes are found to be convergent with increasing resolution and are anticipated to play a crucial role in the interpretation of horizon-scale images resulting from upcoming radio observations of the source at the Galactic Center.
The global energy system is undergoing a major transition, and in energy planning and decision-making across governments, industry and academia, models play a crucial role. Because of their policy relevance and contested nature, the transparency and open availability of energy models and data are of particular importance. Here we provide a practical how-to guide based on the collective experience of members of the Open Energy Modelling Initiative (Openmod). We discuss key steps to consider when opening code and data, including determining intellectual property ownership, choosing a licence and appropriate modelling languages, distributing code and data, and providing support and building communities. After illustrating these decisions with examples and lessons learned from the community, we conclude that even though individual researchers' choices are important, institutional changes are still also necessary for more openness and transparency in energy research.
The goal of heavy ion reactions at low beam energies is to explore the QCD phase diagram at high net baryon chemical potential. To relate experimental observations with a first order phase transition or a critical endpoint, dynamical approaches for the theoretical description have to be developed. In this summary of the corresponding plenary talk, the status of the dynamical modeling including the most recent advances is presented. The remaining challenges are highlighted and promising experimental measurements are pointed out.
Criticality meets learning : criticality signatures in a self-organizing recurrent neural network
(2017)
Many experiments have suggested that the brain operates close to a critical state, based on signatures of criticality such as power-law distributed neuronal avalanches. In neural network models, criticality is a dynamical state that maximizes information processing capacities, e.g. sensitivity to input, dynamical range and storage capacity, which makes it a favorable candidate state for brain function. Although models that self-organize towards a critical state have been proposed, the relation between criticality signatures and learning is still unclear. Here, we investigate signatures of criticality in a self-organizing recurrent neural network (SORN). Investigating criticality in the SORN is of particular interest because it has not been developed to show criticality. Instead, the SORN has been shown to exhibit spatio-temporal pattern learning through a combination of neural plasticity mechanisms and it reproduces a number of biological findings on neural variability and the statistics and fluctuations of synaptic efficacies. We show that, after a transient, the SORN spontaneously self-organizes into a dynamical state that shows criticality signatures comparable to those found in experiments. The plasticity mechanisms are necessary to attain that dynamical state, but not to maintain it. Furthermore, onset of external input transiently changes the slope of the avalanche distributions – matching recent experimental findings. Interestingly, the membrane noise level necessary for the occurrence of the criticality signatures reduces the model’s performance in simple learning tasks. Overall, our work shows that the biologically inspired plasticity and homeostasis mechanisms responsible for the SORN’s spatio-temporal learning abilities can give rise to criticality signatures in its activity when driven by random input, but these break down under the structured input of short repeating sequences.
The Karl Schwarzschild Meeting 2017 (KSM2017) has been the third instalment of the conference dedicated to the great Frankfurter scientist, who derived the first black hole solution of Einstein's equations about 100 years ago.
The event has been a 5 day meeting in the field of black holes, AdS/CFT correspondence and gravitational physics. Like the two previous instalments, the conference continued to attract a stellar ensemble of participants from the world's most renowned institutions. The core of the meeting has been a series of invited talks from eminent experts (keynote speakers) as well as the presence of plenary research talks by students and junior speakers.
List of Conference photo and poster, Sponsors and funding acknowledgments, Committees and List of participants are available in this PDF.
Ebola virus (EBOV) infection causes a high death toll, killing a high proportion of EBOV-infected patients within 7 days. Comprehensive data on EBOV infection are fragmented, hampering efforts in developing therapeutics and vaccines against EBOV. Under this circumstance, mathematical models become valuable resources to explore potential controlling strategies. In this paper, we employed experimental data of EBOV-infected nonhuman primates (NHPs) to construct a mathematical framework for determining windows of opportunity for treatment and vaccination. Considering a prophylactic vaccine based on recombinant vesicular stomatitis virus expressing the EBOV glycoprotein (rVSV-EBOV), vaccination could be protective if a subject is vaccinated during a period from one week to four months before infection. For the case of a therapeutic vaccine based on monoclonal antibodies (mAbs), a single dose might resolve the invasive EBOV replication even if it was administrated as late as four days after infection. Our mathematical models can be used as building blocks for evaluating therapeutic and vaccine modalities as well as for evaluating public health intervention strategies in outbreaks. Future laborator experiments will help to validate and refine the estimates of the windows of opportunity proposed here.
We study the effect of the chiral symmetry restoration (CSR) on heavy-ion collisions observables in the energy range sNN=3–20GeV within the Parton-Hadron-String Dynamics (PHSD) transport approach. The PHSD includes the deconfinement phase transition as well as essential aspects of CSR in the dense and hot hadronic medium, which are incorporated in the Schwinger mechanism for particle production. Our systematic studies show that chiral symmetry restoration plays a crucial role in the description of heavy-ion collisions at sNN=3–20GeV, realizing an increase of the hadronic particle production in the strangeness sector with respect to the non-strange one. Our results provide a microscopic explanation for the horn structure in the excitation function of the K+/π+ ratio: the CSR in the hadronic phase produces the steep increase of this particle ratio up to sNN≈7GeV, while the drop at higher energies is associated to the appearance of a deconfined partonic medium. Furthermore, the appearance/disappearance of the horn structure is investigated as a function of the system size. We additionally present an analysis of strangeness production in the (T,μB)-plane (as extracted from the PHSD for central Au+Au collisions) and discuss the perspectives to identify a possible critical point in the phase diagram.
In this work, largely based on [J. L. Albacete, A. Soto-Ontoso, Hot spots and the hollowness of proton-proton interactions at high energies, arXiv:1605.09176; J. L. Albacete, H. Petersen, A. Soto-Ontoso, Correlated wounded hot spots in proton-proton interactions, arXiv:1612.06274], we present a novel initial state geometry for proton-proton interactions. We rely on gluonic hot spots as effective degrees of freedom whose transverse positions inside the proton are correlated. We explore the impact of these non-trivial spatial correlations on the eccentricity and triangularity of the system following a Monte Carlo Glauber approach.
We compute the fermion spin distribution in the vortical fluid created in off-central high energy heavy-ion collisions. We employ the event-by-event (3+1)D viscous hydrodynamic model. The spin polarization density is proportional to the local fluid vorticity in quantum kinetic theory. As a result of strong collectivity, the spatial distribution of the local vorticity on the freeze-out hyper-surface strongly correlates to the rapidity and azimuthal angle distribution of fermion spins. We investigate the sensitivity of the local polarization to the initial fluid velocity in the hydrodynamic model and compute the global polarization of Λ hyperons by the AMPT model. The energy dependence of the global polarization agrees with the STAR data.
Distillation of scalar exchange by coherent hypernucleus production in antiproton–nucleus collisions
(2017)
The total and angular differential cross sections of the coherent process p¯ + A Z → A (Z − 1) + ¯ are evaluated at the beam momenta 1.5 ÷ 20 GeV/c within the meson exchange model with bound proton and -hyperon wave functions. It is shown that the shape of the beam momentum dependence of the hypernucleus production cross sections with various discrete states is strongly sensitive to the presence of the scalar κ-meson exchange in the p p¯ → ¯ amplitude. This can be used as a clean test of the exchange by scalar π K correlation in coherent p A¯ reactions.
Transcranial electrical stimulation has widespread clinical and research applications, yet its effect on ongoing neural activity in humans is not well established. Previous reports argue that transcranial alternating current stimulation (tACS) can entrain and enhance neural rhythms related to memory, but the evidence from non-invasive recordings has remained inconclusive. Here, we measure endogenous spindle and theta activity intracranially in humans during low-frequency tACS and find no stable entrainment of spindle power during non-REM sleep, nor of theta power during resting wakefulness. As positive controls, we find robust entrainment of spindle activity to endogenous slow-wave activity in 66% of electrodes as well as entrainment to rhythmic noise-burst acoustic stimulation in 14% of electrodes. We conclude that low-frequency tACS at common stimulation intensities neither acutely modulates spindle activity during sleep nor theta activity during waking rest, likely because of the attenuated electrical fields reaching the cortical surface.
Overrepresentation of bidirectional connections in local cortical networks has been repeatedly reported and is a focus of the ongoing discussion of nonrandom connectivity. Here we show in a brief mathematical analysis that in a network in which connection probabilities are symmetric in pairs, Pij = Pji, the occurrences of bidirectional connections and nonrandom structures are inherently linked; an overabundance of reciprocally connected pairs emerges necessarily when some pairs of neurons are more likely to be connected than others. Our numerical results imply that such overrepresentation can also be sustained when connection probabilities are only approximately symmetric.
Current theories of schizophrenia (ScZ) posit that the symptoms and cognitive dysfunctions arise from a dysconnection syndrome. However, studies that have examined this hypothesis with physiological data at realistic time scales are so far scarce. The current study employed a state-of-the-art approach using Magnetoencephalography (MEG) to test alterations in large-scale phase synchronization in a sample of n = 16 chronic ScZ patients, 10 males and n = 19 healthy participants, 10 males, during a perceptual closure task. We identified large-scale networks from source reconstructed MEG data using data-driven analyses of neuronal synchronization. Oscillation amplitudes and interareal phase-synchronization in the 3–120 Hz frequency range were estimated for 400 cortical parcels and correlated with clinical symptoms and neuropsychological scores. ScZ patients were characterized by a reduction in γ-band (30–120 Hz) oscillation amplitudes that was accompanied by a pronounced deficit in large-scale synchronization at γ-band frequencies. Synchronization was reduced within visual regions as well as between visual and frontal cortex and the reduction of synchronization correlated with elevated clinical disorganization. Accordingly, these data highlight that ScZ is associated with a profound disruption of transient synchronization, providing critical support for the notion that core aspect of the pathophysiology arises from an impairment in coordination of distributed neural activity.
We present entropy-limited hydrodynamics (ELH): a new approach for the computation of numerical fluxes arising in the discretization of hyperbolic equations in conservation form. ELH is based on the hybridisation of an unfiltered high-order scheme with the first-order Lax-Friedrichs method. The activation of the low-order part of the scheme is driven by a measure of the locally generated entropy inspired by the artificial-viscosity method proposed by Guermond et al. (J. Comput. Phys. 230(11):4248-4267, 2011, doi:10.1016/j.jcp.2010.11.043). Here, we present ELH in the context of high-order finite-differencing methods and of the equations of general-relativistic hydrodynamics. We study the performance of ELH in a series of classical astrophysical tests in general relativity involving isolated, rotating and nonrotating neutron stars, and including a case of gravitational collapse to black hole. We present a detailed comparison of ELH with the fifth-order monotonicity preserving method MP5 (Suresh and Huynh in J. Comput. Phys. 136(1):83-99, 1997, doi:10.1006/jcph.1997.5745), one of the most common high-order schemes currently employed in numerical-relativity simulations. We find that ELH achieves comparable and, in many of the cases studied here, better accuracy than more traditional methods at a fraction of the computational cost (up to ∼50% speedup). Given its accuracy and its simplicity of implementation, ELH is a promising framework for the development of new special- and general-relativistic hydrodynamics codes well adapted for massively parallel supercomputers.
A key hallmark of visual perceptual awareness is robustness to instabilities arising from unnoticeable eye and eyelid movements. In previous human intracranial (iEEG) work (Golan et al., 2016) we found that excitatory broadband high-frequency activity transients, driven by eye blinks, are suppressed in higher-level but not early visual cortex. Here, we utilized the broad anatomical coverage of iEEG recordings in 12 eye-tracked neurosurgical patients to test whether a similar stabilizing mechanism operates following small saccades. We compared saccades (1.3°−3.7°) initiated during inspection of large individual visual objects with similarly-sized external stimulus displacements. Early visual cortex sites responded with positive transients to both conditions. In contrast, in both dorsal and ventral higher-level sites the response to saccades (but not to external displacements) was suppressed. These findings indicate that early visual cortex is highly unstable compared to higher-level visual regions which apparently constitute the main target of stabilizing extra-retinal oculomotor influences.
Two theories address the origin of repeating patterns, such as hair follicles, limb digits, and intestinal villi, during development. The Turing reaction–diffusion system posits that interacting diffusible signals produced by static cells first define a prepattern that then induces cell rearrangements to produce an anatomical structure. The second theory, that of mesenchymal self-organisation, proposes that mobile cells can form periodic patterns of cell aggregates directly, without reference to any prepattern. Early hair follicle development is characterised by the rapid appearance of periodic arrangements of altered gene expression in the epidermis and prominent clustering of the adjacent dermal mesenchymal cells. We assess the contributions and interplay between reaction–diffusion and mesenchymal self-organisation processes in hair follicle patterning, identifying a network of fibroblast growth factor (FGF), wingless-related integration site (WNT), and bone morphogenetic protein (BMP) signalling interactions capable of spontaneously producing a periodic pattern. Using time-lapse imaging, we find that mesenchymal cell condensation at hair follicles is locally directed by an epidermal prepattern. However, imposing this prepattern’s condition of high FGF and low BMP activity across the entire skin reveals a latent dermal capacity to undergo spatially patterned self-organisation in the absence of epithelial direction. This mesenchymal self-organisation relies on restricted transforming growth factor (TGF) β signalling, which serves to drive chemotactic mesenchymal patterning when reaction–diffusion patterning is suppressed, but, in normal conditions, facilitates cell movement to locally prepatterned sources of FGF. This work illustrates a hierarchy of periodic patterning modes operating in organogenesis.
Unparticle Casimir effect
(2017)
In this paper we present the un-Casimir effect, namely the study of the Casimir energy in the presence of an unparticle component in addition to the electromagnetic field contribution. The distinctive feature of the un-Casimir effect is a fractalization of metallic plates. This result emerges through a new dependence of the Casimir energy on the plate separation that scales with a continuous power controlled by the unparticle dimension. As long as the perfect conductor approximation is valid, we find bounds on the unparticle scale that are independent of the effective coupling constant between the scale invariant sector and ordinary matter. We find regions of the parameter space such that for plate distances around 5 μm and larger the un-Casimir bound wins over the other bounds.
As the density of matter increases, atomic nuclei disintegrate into nucleons and, eventually, the nucleons themselves disintegrate into quarks. The phase transitions (PT's) between these phases can vary from steep first order to smooth crossovers, depending on certain conditions. First-order PT's with more than one globally conserved charge, so-called non-congruent PT's, have characteristic differences compared to congruent PT's. In this conference proceeding we discuss the non-congruence of the quark deconfinement PT at high densities and/or temperatures relevant for heavy-ion collisions, neutron stars, proto-neutron stars, supernova explosions, and compact-star mergers.
When binary systems of neutron stars merge, a very small fraction of their rest mass is ejected, either dynamically or secularly. This material is neutron-rich and its nucleosynthesis provides the astrophysical site for the production of heavy elements in the Universe, together with a kilonova signal confirming neutron-star mergers as the origin of short gamma-ray bursts. We perform full general-relativistic simulations of binary neutron-star mergers employing three different nuclear-physics equations of state (EOSs), considering both equal- and unequal-mass configurations, and adopting a leakage scheme to account for neutrino radiative losses. Using a combination of techniques, we carry out an extensive and systematic study of the hydrodynamical, thermodynamical, and geometrical properties of the matter ejected dynamically, employing the WinNet nuclear-reaction network to recover the relative abundances of heavy elements produced by each configurations. Among the results obtained, three are particularly important. First, we find that, within the sample considered here, both the properties of the dynamical ejecta and the nucleosynthesis yields are robust against variations of the EOS and masses. Second, using a conservative but robust criterion for unbound matter, we find that the amount of ejected mass is ≲10−3 M⊙, hence at least one order of magnitude smaller than what normally assumed in modelling kilonova signals. Finally, using a simplified and gray-opacity model we assess the observability of the infrared kilonova emission finding, that for all binaries the luminosity peaks around ∼1=2 day in the H-band, reaching a maximum magnitude of −13, and decreasing rapidly after one day.
Compartmental models are the theoretical tool of choice for understanding single neuron computations. However, many models are incomplete, built ad hoc and require tuning for each novel condition rendering them of limited usability. Here, we present T2N, a powerful interface to control NEURON with Matlab and TREES toolbox, which supports generating models stable over a broad range of reconstructed and synthetic morphologies. We illustrate this for a novel, highly detailed active model of dentate granule cells (GCs) replicating a wide palette of experiments from various labs. By implementing known differences in ion channel composition and morphology, our model reproduces data from mouse or rat, mature or adult-born GCs as well as pharmacological interventions and epileptic conditions. This work sets a new benchmark for detailed compartmental modeling. T2N is suitable for creating robust models useful for large-scale networks that could lead to novel predictions. We discuss possible T2N application in degeneracy studies.
BACKGROUND: The analysis of microarray time series promises a deeper insight into the dynamics of the cellular response following stimulation. A common observation in this type of data is that some genes respond with quick, transient dynamics, while other genes change their expression slowly over time. The existing methods for detecting significant expression dynamics often fail when the expression dynamics show a large heterogeneity. Moreover, these methods often cannot cope with irregular and sparse measurements.
RESULTS: The method proposed here is specifically designed for the analysis of perturbation responses. It combines different scores to capture fast and transient dynamics as well as slow expression changes, and performs well in the presence of low replicate numbers and irregular sampling times. The results are given in the form of tables including links to figures showing the expression dynamics of the respective transcript. These allow to quickly recognise the relevance of detection, to identify possible false positives and to discriminate early and late changes in gene expression. An extension of the method allows the analysis of the expression dynamics of functional groups of genes, providing a quick overview of the cellular response. The performance of this package was tested on microarray data derived from lung cancer cells stimulated with epidermal growth factor (EGF).
CONCLUSION: Here we describe a new, efficient method for the analysis of sparse and heterogeneous time course data with high detection sensitivity and transparency. It is implemented as R package TTCA (transcript time course analysis) and can be installed from the Comprehensive R Archive Network, CRAN. The source code is provided with the Additional file 1.
We present measurements of ρ0, ω and K∗0 spectra in π−+ C production interactions at 158 GeV / c and ρ0 spectra at 350 GeV / c using the NA61/SHINE spectrometer at the CERN SPS. Spectra are presented as a function of the Feynman’s variable xF in the range 0<xF<1 and 0<xF<0.5 for 158 and 350 GeV / c respectively. Furthermore, we show comparisons with previous measurements and predictions of several hadronic interaction models. These measurements are essential for a better understanding of hadronic shower development and for improving the modeling of cosmic ray air showers.
The transverse momentum distributions of the strange and double-strange hyperon resonances (Σ(1385)±, Ξ(1530)0) produced in p–Pb collisions at sNN−−−√=5.02 TeV were measured in the rapidity range −0.5<yCMS<0 for event classes corresponding to different charged-particle multiplicity densities, ⟨dNch/dηlab⟩. The mean transverse momentum values are presented as a function of ⟨dNch/dηlab⟩, 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 ⟨dNch/dηlab⟩. The equivalent ratios to pions exhibit an increase with ⟨dNch/dηlab⟩, depending on their strangeness content.
The transverse momentum distributions of the strange and double-strange hyperon resonances (Σ(1385)±,Ξ(1530)0) produced in p–Pb collisions at √sNN = 5.02 TeV were measured in the rapidity range −0.5<yCMS<0 for event classes corresponding to different charged-particle multiplicity densities, ⟨dNch/dηlab⟩. The mean transverse momentum values are presented as a function of ⟨dNch/dηlab⟩, 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 ⟨dNch/dηlab⟩. The equivalent ratios to pions exhibit an increase with ⟨dNch/dηlab⟩, depending on their strangeness content.
The first study of ϕ-meson production in p–Pb collisions at forward and backward rapidity, at a nucleon–nucleon centre-of-mass energy √sNN=5.02 TeV, has been performed with the ALICE apparatus at the LHC. The ϕ-mesons have been identified in the dimuon decay channel in the transverse momentum (pT) range 1<pT<7 GeV/c, both in the p-going (2.03<y<3.53) and the Pb-going (−4.46<y<−2.96) directions — where y stands for the rapidity in the nucleon–nucleon centre-of-mass — the integrated luminosity amounting to 5.01±0.19 nb−1 and 5.81±0.20 nb−1, respectively, for the two data samples. Differential cross sections as a function of transverse momentum and rapidity are presented. The forward–backward ratio for ϕ-meson production is measured for 2.96<|y|<3.53, resulting in a ratio ∼0.5 with no significant pT dependence within the uncertainties. The pT dependence of the ϕ nuclear modification factor RpPb exhibits an enhancement up to a factor 1.6 at pT=3–4 GeV/c in the Pb-going direction. The pT dependence of the ϕ-meson cross section in pp collisions at √s=2.76 TeV, which is used to determine a reference for the p–Pb results, is also presented here for 1<pT<5 GeV/c and 2.5<y<4, for a 78±3 nb−1 integrated luminosity sample.
A detailed study of pseudorapidity densities and multiplicity distributions of primary charged particles produced in proton-proton collisions, at s√= 0.9, 2.36, 2.76, 7 and 8 TeV, in the pseudorapidity range |η|<2, was carried out using the ALICE detector. Measurements were obtained for three event classes: inelastic, non-single diffractive and events with at least one charged particle in the pseudorapidity interval |η|<1. The use of an improved track-counting algorithm combined with ALICE's measurements of diffractive processes allows a higher precision compared to our previous publications. A KNO scaling study was performed in the pseudorapidity intervals |η|< 0.5, 1.0 and 1.5. The data are compared to other experimental results and to models as implemented in Monte Carlo event generators PHOJET and recent tunes of PYTHIA6, PYTHIA8 and EPOS.
The azimuthal correlations of D mesons with charged particles were measured with the ALICE apparatus in pp collisions at s√=7 TeV and p–Pb collisions at sNN−−−√=5.02 TeV at the Large Hadron Collider. D0, D+, and D∗+ mesons and their charge conjugates with transverse momentum 3<pT<16 GeV/c and rapidity in the nucleon-nucleon centre-of-mass system |ycms|<0.5 (pp collisions) and −0.96<ycms<0.04 (p–Pb collisions) were correlated to charged particles with pT>0.3 GeV/c. 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.
At sufficiently high temperature and energy density, nuclear matter undergoes a transition to a phase in which quarks and gluons are not confined: the quark–gluon plasma (QGP)1. Such an exotic state of strongly interacting quantum chromodynamics matter is produced in the laboratory in heavy nuclei high-energy collisions, where an enhanced production of strange hadrons is observed2,3,4,5,6. Strangeness enhancement, originally proposed as a signature of QGP formation in nuclear collisions7, is more pronounced for multi-strange baryons. Several effects typical of heavy-ion phenomenology have been observed in high-multiplicity proton–proton (pp) collisions8,9, but the enhanced production of multi-strange particles has not been reported so far. Here we present the first observation of strangeness enhancement in high-multiplicity proton–proton collisions. We find that the integrated yields of strange and multi-strange particles, relative to pions, increases significantly with the event charged-particle multiplicity. The measurements are in remarkable agreement with the p–Pb collision results10,11, indicating that the phenomenon is related to the final system created in the collision. In high-multiplicity events strangeness production reaches values similar to those observed in Pb–Pb collisions, where a QGP is formed.
The production of beauty hadrons was measured via semi-leptonic decays at mid-rapidity with the ALICE detector at the LHC in the transverse momentum interval 1<p T < 8 GeV/c in minimum-bias p-Pb collisions at sNN−−−√=5.02 TeV and in 1.3 < p T < 8 GeV/c in the 20% most central Pb-Pb collisions at sNN−−−√=2.76 TeV. The pp reference spectra at sNN−−−√=5.02 TeV and s√=2.76 TeV, needed for the calculation of the nuclear modification factors R pPb and R PbPb, were obtained by a pQCD-driven scaling of the cross section of electrons from beauty-hadron decays measured at s√=7 TeV. In the p T interval 3 < p T < 8 GeV/c, a suppression of the yield of electrons from beauty-hadron decays is observed in Pb-Pb compared to pp collisions. Towards lower p T, the R PbPb values increase with large systematic uncertainties. The R pPb is consistent with unity within systematic uncertainties and is well described by theoretical calculations that include cold nuclear matter effects in p-Pb collisions. The measured R pPb and these calculations indicate that cold nuclear matter effects are small at high transverse momentum also in Pb-Pb collisions. Therefore, the observed reduction of R PbPb below unity at high p T may be ascribed to an effect of the hot and dense medium formed in Pb-Pb collisions.
The inclusive J/ψ production has been studied in Pb–Pb and pp collisions at the centre-of-mass energy per nucleon pair √sNN=5.02 TeV, using the ALICE detector at the CERN LHC. The J/ψ meson is reconstructed, in the centre-of-mass rapidity interval 2.5<y<4 and in the transverse-momentum range pT<12 GeV/c, via its decay to a muon pair. In this Letter, we present results on the inclusive J/ψ cross section in pp collisions at √s=5.02 TeV and on the nuclear modification factor RAA. The latter is presented as a function of the centrality of the collision and, for central collisions, as a function of the transverse momentum pT of the J/ψ. The measured RAA values indicate a suppression of the J/ψ in nuclear collisions and are then compared to our previous results obtained in Pb–Pb collisions at √sNN=2.76 TeV. The ratio of the RAA values at the two energies is also computed and compared to calculations of statistical and dynamical models. The numerical value of the ratio for central events (0–10% centrality) is 1.17±0.04(stat)±0.20(syst). In central events, as a function of pT, a slight increase of RAA with collision energy is visible in the region 2<pT<6 GeV/c. Theoretical calculations qualitatively describe the measurements, within uncertainties.
Two-particle angular correlations were measured in pp collisions at s√=7 TeV for pions, kaons, protons, and lambdas, for all particle/anti-particle combinations in the pair. Data for mesons exhibit an expected peak dominated by effects associated with mini-jets and are well reproduced by general purpose Monte Carlo generators. However, for baryon–baryon and anti-baryon–anti-baryon pairs, where both particles have the same baryon number, a near-side anti-correlation structure is observed instead of a peak. This effect is interpreted in the context of baryon production mechanisms in the fragmentation process. It currently presents a challenge to Monte Carlo models and its origin remains an open question.
Particle identification is an important feature of the ALICE detector at the LHC. In particular, for particle identification via the time-of-flight technique, the precise determination of the event collision time represents an important ingredient of the quality of the measurement. In this paper, the different methods used for such a measurement in ALICE by means of the T0 and the TOF detectors are reviewed. Efficiencies, resolution and the improvement of the particle identification separation power of the methods used are presented for the different LHC colliding systems (pp , p-Pb and Pb-Pb) during the first period of data taking of LHC (Run 1).
The measurement of two-particle angular correlations is a powerful tool to study jet quenching in a pT 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 to a higher pT trigger particle (1<pT,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 sNN−−−√ = 2.76 TeV. A significant broadening of the peak in the Δη direction at low pT 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<pT,assoc< 2 GeV/c, 1<pT,trig< 3 GeV/c a novel feature is observed: a depletion develops around the centre of the peak. The results are compared to pp collisions at the same centre of mass energy and to 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.
In two-particle angular correlation measurements, jets give rise to a near-side peak, formed by particles associated to a higher pT trigger particle. Measurements of these correlations as a function of pseudorapidity (Δη) and azimuthal (Δφ) differences are used to extract the centrality and pT dependence of the shape of the near-side peak in the pT range 1<pT< 8 GeV/c in Pb-Pb and pp collisions at sNN−−−√ = 2.76 TeV. A combined fit of the near-side peak and long-range correlations is applied to the data and the peak shape is quantified by the variance of the distributions. While the width of the peak in the Δφ direction is almost independent of centrality, a significant broadening in the Δη direction is found from peripheral to central collisions. This feature is prominent for the low pT region and vanishes above 4 GeV/c. The widths measured in peripheral collisions are equal to those in pp in the Δφ direction and above 3 GeV/c in the Δη direction. Furthermore, for the 10\% most central collisions and 1<pT,assoc< 2 GeV/c, 1<pT,trig< 3 GeV/c a departure from a Gaussian shape is found: a depletion develops around the centre of the peak. The results are compared to AMPT model simulations as well as other theoretical calculations indicating that the broadening and the development of the depletion is connected to the strength of radial and longitudinal flow.
The W and Z boson production was measured via the muonic decay channel in proton-lead collisions at sNN−−−√=5.02 TeV at the Large Hadron Collider with the ALICE detector. The measurement covers backward (−4.46<ycms<−2.96) and forward (2.03<ycms<3.53) rapidity regions, corresponding to Pb-going and p-going directions, respectively. The Z-boson production cross section, with dimuon invariant mass of 60<mμμ<120 GeV/c2 and muon transverse momentum (pμT) larger than 20 GeV/c, is measured. The production cross section and charge asymmetry of muons from W-boson decays with pμT>10 GeV/c are determined. The results are compared to theoretical calculations both with and without including the nuclear modification of the parton distribution functions. The W-boson production is also studied as a function of the collision centrality: the cross section of muons from W-boson decays is found to scale with the average number of binary nucleon-nucleon collisions within uncertainties.
The production cross sections of the prompt charmed mesons D0, D+, D∗+ and D+s were measured at mid-rapidity in proton-proton collisions at a centre-of-mass energy s√=7 TeV with the ALICE detector at the Large Hadron Collider (LHC). D mesons were reconstructed from their decays D0→K−π+, D+→K−π+π+, D∗+→D0π+, D+s→ϕπ+→K−K+π+, and their charge conjugates. With respect to previous measurements in the same rapidity region, the coverage in transverse momentum (pT) is extended and the uncertainties are reduced by a factor of about two. The accuracy on the estimated total cc¯¯ production cross section is likewise improved. The measured pT-differential cross sections are compared with the results of three perturbative QCD calculations.
The production of muons from heavy-flavour hadron decays in p–Pb collisions at t √sNN=5.02 TeV was studied for 2<pT<16 GeV/c with the ALICE detector at the CERN LHC. The measurement was performed at forward (p-going direction) and backward (Pb-going direction) rapidity, in the ranges of rapidity in the centre-of-mass system (cms) 2.03<ycms<3.53 and −4.46<ycms<−2.96, respectively. The production cross sections and nuclear modification factors are presented as a function of transverse momentum (pT). At forward rapidity, the nuclear modification factor is compatible with unity while at backward rapidity, in the interval 2.5<pT<3.5 GeV/c, it is above unity by more than 2σ. The ratio of the forward-to-backward production cross sections is also measured in the overlapping interval 2.96<|ycms|<3.53 and is smaller than unity by 3.7σ in 2.5<pT<3.5 GeV/c. The data are described by model calculations including cold nuclear matter effects.
The invariant differential cross sections for inclusive π0 and η mesons at midrapidity were measured in pp collisions at s√=2.76 TeV for transverse momenta 0.4<pT<40 GeV/c and 0.6<pT<20 GeV/c, respectively, using the ALICE detector. This large range in pT 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-pT neutral pions, which exploits that the showers originating from their decay photons overlap in the EMCal. Above 4 GeV/c, 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 π0, and between 30–50% for the η meson, while generator-level simulations with PYTHIA 8.2 describe the data to better than 10–30%, except at pT<1 GeV/c. The new data can therefore be used to further improve the theoretical description of π0 and η meson production.