Protist predation can favour cooperation within bacterial species

Here, we studied how protist predation affects cooperation in the opportunistic pathogen bacterium Pseudomonas aeruginosa, which uses quorum sensing (QS) cell-to-cell signalling to regulate the production of public goods. By competing wild-type bacteria with QS mutants (cheats), we show that a functioning QS system confers an elevated resistance to predation. Surprisingly, cheats were unable to exploit this resistance in the presence of cooperators, which suggests that resistance does not appear to result from activation of QS-regulated public goods. Instead, elevated resistance of wild-type bacteria was related to the ability to form more predation-resistant biofilms. This could be explained by the expression of QS-regulated resistance traits in densely populated biofilms and floating cell aggregations, or alternatively, by a pleiotropic cost of cheating where less resistant cheats are selectively removed from biofilms. These results show that trophic interactions among species can maintain cooperation within species, and have further implications for P. aeruginosa virulence in environmental reservoirs by potentially enriching the cooperative and highly infective strains with functional QS system

Topo-Geometric Filtration Scheme for Geometric Active Contours and Level Sets: Application to Cerebrovascular Segmentation

One of the main problems of the existing methods for the segmentation of cerebral vasculature is the appearance in the segmentation result of wrong topological artefacts such as the kissing vessels. In this paper, a new approach for the detection and correction of such errors is presented. The proposed technique combines robust topological information given by Persistent Homology with complementary geometrical information of the vascular tree. The method was evaluated on 20 images depicting cerebral arteries. Detection and correction success rates were 81.80% and 68.77%, respectively

Relativistic hydrodynamics for heavy-ion collisions

Relativistic hydrodynamics is essential to our current understanding of nucleus-nucleus collisions at ultrarelativistic energies (current experiments at the Relativistic Heavy Ion Collider, forthcoming experiments at the CERN Large Hadron Collider). This is an introduction to relativistic hydrodynamics for graduate students. It includes a detailed derivation of the equations, and a description of the hydrodynamical evolution of a heavy-ion collisions. Some knowledge of thermodynamics and special relativity is assumed.Comment: Lectures given at the Advanced School on Quark-Gluon Plasma, Indian Institute of Technology, Bombay, 3-13 July, 200

Mapping the phase diagram of strongly interacting matter

We employ a conformal mapping to explore the thermodynamics of strongly interacting matter at finite values of the baryon chemical potential $\mu$. This method allows us to identify the singularity corresponding to the critical point of a second-order phase transition at finite $\mu$, given information only at $\mu=0$. The scheme is potentially useful for computing thermodynamic properties of strongly interacting hot and dense matter in lattice gauge theory. The technique is illustrated by an application to a chiral effective model.Comment: 5 pages, 3 figures; published versio

Bulk viscosity in superfluid neutron star cores. I. Direct Urca processes in npe\mu matter

The bulk viscosity of the neutron star matter due to the direct Urca processes involving nucleons, electrons and muons is studied taking into account possible superfluidity of nucleons in the neutron star cores. The cases of singlet-state pairing or triplet-state pairing (without and with nodes of the superfluid gap at the Fermi surface) of nucleons are considered. It is shown that the superfluidity may strongly reduce the bulk viscosity. The practical expressions for the superfluid reduction factors are obtained. For illustration, the bulk viscosity is calculated for two models of dense matter composed of neutrons, protons,electrons and muons. The presence of muons affects the bulk viscosity due to the direct Urca reactions involving electrons and produces additional comparable contribution due to the direct Urca reactions involving muons. The results can be useful for studying damping of vibrations of neutron stars with superfluid cores.Comment: 14 pages, 7 figures, latex, uses aa.cls, to be published in Astronomy and Astrophysic

The effects of antibiotic combination treatments on Pseudomonas aeruginosa tolerance evolution and coexistence with Stenotrophomonas maltophilia

Pseudomonas aeruginosa bacterium is a common pathogen of Cystic Fibrosis (CF) patients due to its ability to evolve resistance to antibiotics during treatments. While P. aeruginosa resistance evolution is well characterised in monocultures, it is less well understood in polymicrobial CF infections. Here, we investigated how exposure to ciprofloxacin, colistin, or tobramycin antibiotics, administered at sub-MIC doses alone and in combination, shaped the tolerance evolution of P. aeruginosa (PAO1 lab and clinical CF LESB58 strains) in the absence and presence of a commonly co-occurring species, Stenotrophomonas maltophilia. Increases in antibiotic tolerances were primarily driven by the presence of that antibiotic in the treatment. We observed a reciprocal cross-tolerance between ciprofloxacin and tobramycin, and when combined these antibiotics selected increased MICs for all antibiotics. Though the presence of S. maltophilia did not affect the tolerance or the MIC evolution, it drove P. aeruginosa into extinction more frequently in the presence of tobramycin due to its relatively greater innate tobramycin tolerance. In contrast, P. aeruginosa dominated and drove S. maltophilia extinct in most other treatments. Together, our findings suggest that besides driving high-level antibiotic tolerance evolution, sub-MIC antibiotic exposure can alter competitive bacterial interactions, leading to target pathogen extinctions in multi-species communities.Funding provided by: University of YorkCrossref Funder Registry ID: http://dx.doi.org/10.13039/100009001Award Number:See Methods in paper for collection. MIC values (MIC data.csv) derived from visual inspection of antibiotic growth measurements plotted as a growth curve. Optical density data has been blank-corrected, and in the case of the antibiotic growth measurements (Antibiotic growth data.csv) averaged over ≤3 technical replicates

Extraction of Airways with Probabilistic State-space Models and Bayesian Smoothing

Segmenting tree structures is common in several image processing applications. In medical image analysis, reliable segmentations of airways, vessels, neurons and other tree structures can enable important clinical applications. We present a framework for tracking tree structures comprising of elongated branches using probabilistic state-space models and Bayesian smoothing. Unlike most existing methods that proceed with sequential tracking of branches, we present an exploratory method, that is less sensitive to local anomalies in the data due to acquisition noise and/or interfering structures. The evolution of individual branches is modelled using a process model and the observed data is incorporated into the update step of the Bayesian smoother using a measurement model that is based on a multi-scale blob detector. Bayesian smoothing is performed using the RTS (Rauch-Tung-Striebel) smoother, which provides Gaussian density estimates of branch states at each tracking step. We select likely branch seed points automatically based on the response of the blob detection and track from all such seed points using the RTS smoother. We use covariance of the marginal posterior density estimated for each branch to discriminate false positive and true positive branches. The method is evaluated on 3D chest CT scans to track airways. We show that the presented method results in additional branches compared to a baseline method based on region growing on probability images.Comment: 10 pages. Pre-print of the paper accepted at Workshop on Graphs in Biomedical Image Analysis. MICCAI 2017. Quebec Cit

Non-equilibrium beta processes in superfluid neutron star cores

The influence of nucleons superfluidity on the beta relaxation time of degenerate neutron star cores, composed of neutrons, protons and electrons, is investigated. We numerically calculate the implied reduction factors for both direct and modified Urca reactions, with isotropic pairing of protons or anisotropic pairing of neutrons. We find that due to the non-zero value of the temperature and/or to the vanishing of anisotropic gaps in some directions of the phase-space, superfluidity does not always completely inhibit beta relaxation, allowing for some reactions if the superfluid gap amplitude is not too large in respect to both the typical thermal energy and the chemical potential mismatch. We even observe that if the ratio between the critical temperature and the actual temperature is very small, a suprathermal regime is reached for which superfluidity is almost irrelevant. On the contrary, if the gap is large enough, the composition of the nuclear matter can stay frozen for very long durations, unless the departure from beta equilibrium is at least as important as the gap amplitude. These results are crucial for precise estimation of the superfluidity effect on the cooling/slowing-down of pulsars and we provide online subroutines to be implemented in codes for simulating such evolutions.Comment: 11 pages, 6 Figs., published, minor changes, subroutines can be found on line at http://luth2.obspm.fr/~etu/villain/Micro/Resolution.htm

Net-proton probability distribution in heavy ion collisions

We compute net-proton probability distributions in heavy ion collisions within the hadron resonance gas model. The model results are compared with data taken by the STAR Collaboration in Au-Au collisions at sqrt(s_{NN})= 200 GeV for different centralities. We show that in peripheral Au-Au collisions the measured distributions, and the resulting first four moments of net-proton fluctuations, are consistent with results obtained from the hadron resonance gas model. However, data taken in central Au-Au collisions differ from the predictions of the model. The observed deviations can not be attributed to uncertainties in model parameters. We discuss possible interpretations of the observed deviations.Comment: 4 pages, 2 figure