Effects of initial-state dynamics on collective flow within a coupled transport and viscous hydrodynamic approach

We evaluate the effects of preequilibrium dynamics on observables in ultrarelativistic heavy-ion collisions. We simulate the initial nonequilibrium phase within A MultiPhase Transport (AMPT) model, while the subsequent near-equilibrium evolution is modeled using (2+1)-dimensional relativistic viscous hydrodynamics. We match the two stages of evolution carefully by calculating the full energy-momentum tensor from AMPT and using it as input for the hydrodynamic evolution. We find that when the preequilibrium evolution is taken into account, final-state observables are insensitive to the switching time from AMPT to hydrodynamics. Unlike some earlier treatments of preequilibrium dynamics, we do not find the initial shear viscous tensor to be large. With a shear viscosity to entropy density ratio of $0.12$, our model describes quantitatively a large set of experimental data on Pb+Pb collisions at the Large Hadron Collider(LHC) over a wide range of centrality: differential anisotropic flow $v_n(p_T) ~(n=2-6)$, event-plane correlations, correlation between $v_2$ and $v_3$, and cumulant ratio $v_2\{4\}/v_2\{2\}$.Comment: 10 pages, v2: minor revisio

Cattle manure and the spread of bovine tuberculosis

Department of Agriculture, Food and the MarineTeagascDeposited by bulk impor

Additional file 3: Figure S2. of Ancient bacteria of the Ötzi’s microbiome: a genomic tale from the Copper Age

Cytosine to thymine substitution frequency at the 5′ end of the sequenced reads. The plot displays the cytosine deamination pattern of the Clostridium sp. CADE, C. algidicarnis CALG, C. perfringens CPER, P. fluorescens PFLU, and P. veronii PVER selected reads from the Ötzi’s metagenomic samples. The y axis reports the C to T substitution frequency, while the x axis indicates the distance from the 5′ end of the sequence reads

Additional file 7: Figure S6. of Ancient bacteria of the Ötzi’s microbiome: a genomic tale from the Copper Age

Comparative genomic analysis of Clostridium sp. CADE, C. algidicarnis CALG, and C. perfringens CPER with other fully sequenced strains. Panel a displays the circular genome atlas of Clostridium sp. CADE (red circle) with mapped orthologues (defined as reciprocal best BLASTp hits with more than 50% identity over at least 50% of both protein lengths) in public available Clostridium sp. Ade.TY genome (orange circle). Internal circles illustrate GC% deviation and GC skew (G − C/G + C). Panel b and c shows the same circular genome atlas of C. algidicarnis CALG and C. perfringens CPER, respectively

Additional file 2: Figure S1. of Ancient bacteria of the Ötzi’s microbiome: a genomic tale from the Copper Age

Bacterial abundance in Ötzi’s gut. Panel a displays a bar plot with the abundance of the major species identified in the Tyrolean Iceman gut using MEGAN5 software. The x axis represents the identified bacterial species, while the y axis represents the number of reads. Each color reflects a specific sample, i.e., B0625 (lower part of the large intestine), C1824 and C1825 (upper part of the large intestine), and B0621 (small intestine). Panel b visually displays the observed abundance of the identified species

Additional file 1: of Ancient bacteria of the Ötzi’s microbiome: a genomic tale from the Copper Age

Tables S1, S2, S3, S4, and S5

Occurrence of CRISPR-Cas systems in bifidobacteria.

<p>Occurrence of CRISPR-Cas systems in bifidobacteria.</p

CRISPR repeat-spacer array size distribution.

<p>The graph shows the variability in size of the repeat-spacer arrays using number of spacers in each array, from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133661#pone.0133661.t001" target="_blank">Table 1</a>. The error bars show the range of the locus size.</p

Clustering of Cas1 into distinct phylogenetic groups.

<p>Cas1 protein sequences were aligned using the MUSCLE algorithm and used to generate a UPMGA tree to show the divergence of different CRISPR-Cas systems. The system type and sub-type is noted on the right. The (*) indicates <i>B</i>. <i>moukalabense</i> which contained an “Undetermined” CRISPR-Cas system.</p

CRISPR-Cas locus architecture.

<p>One representative for each unique CRISPR subtypes represents the locus architecture of <i>cas</i> genes, CRISPR repeats, spacers and other system-specific components (e.g. tracrRNA). The signature gene for each subtype is colored in red (<i>cas3</i> or <i>cas9</i> for Type I and II, respectively). The universal <i>cas1</i> and <i>cas2</i> genes are colored in blue. Accessory genes are grey. The tracrRNA for Type II systems is shown in yellow. The direction of the arrows indicates directionality of the coding sequences. The repeat-spacer array only shows the CRISPR repeats (black rectangles). Each operon is shown at a scale of 11,000 base pairs. Long repeat-spacer arrays were shortened for simplicity indicated by a double line break. Numbers under the arrays indicate the first and last spacer location, showing the size of the array.</p