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

Data_Sheet_1_Associations of central obesity and habitual food consumption with saliva microbiota and its enzymatic profiles – a pilot study in Finnish children.DOCX

BackgroundVariation in diversity and composition of saliva microbiota has been linked to weight status, but findings have been inconsistent. Focusing on clinically relevant conditions such as central obesity and using advanced sequencing techniques might fill in the gaps of knowledge.AimsWe investigated saliva microbiota with shallow metagenome sequencing in children with (n = 14) and without (n = 36) central obesity. Additionally, we examined the role of habitual food consumption on microbial enzymatic repertoire.MethodsData comprised 50 children (50% male) with a mean age of 14.2 (SD 0.3) years, selected from the Finnish Health in Teens (Fin-HIT) cohort. Dietary scores for consumption frequency of sweet treats (STI), dairy products (DCI) and plants (PCI) were derived based on a self-administered food frequency questionnaire. Central obesity was defined based on waist–height ratio using the cut-off 0.5. Saliva samples were subjected to whole-metagenome shotgun sequencing, and taxonomic and functional profiling was achieved with METAnnotatorX2 bioinformatics platform.ResultsGroups had an average 20 (95% CI 14–27) cm difference in waist circumference. We identified the lack of Pseudomonas guguagenesis and Prevotella scopos, oulorum and oris as putative biomarkers associated with central obesity and observed a total of 16 enzymatic reactions differing between the groups. DCI was associated with the highest number of enzyme profiles (122), followed by STI (60) and DCI (25) (Pearson correlation p ConclusionClinically relevant differences in central obesity were only modestly reflected in the composition of saliva microbiota. Habitual consumption of sweet treats was a strong determinant of enzymatic reactions of saliva microbiota in children with and without central obesity. The clinical relevance of these findings warrants further studies.</p

Table_1_Associations of central obesity and habitual food consumption with saliva microbiota and its enzymatic profiles – a pilot study in Finnish children.XLSX

BackgroundVariation in diversity and composition of saliva microbiota has been linked to weight status, but findings have been inconsistent. Focusing on clinically relevant conditions such as central obesity and using advanced sequencing techniques might fill in the gaps of knowledge.AimsWe investigated saliva microbiota with shallow metagenome sequencing in children with (n = 14) and without (n = 36) central obesity. Additionally, we examined the role of habitual food consumption on microbial enzymatic repertoire.MethodsData comprised 50 children (50% male) with a mean age of 14.2 (SD 0.3) years, selected from the Finnish Health in Teens (Fin-HIT) cohort. Dietary scores for consumption frequency of sweet treats (STI), dairy products (DCI) and plants (PCI) were derived based on a self-administered food frequency questionnaire. Central obesity was defined based on waist–height ratio using the cut-off 0.5. Saliva samples were subjected to whole-metagenome shotgun sequencing, and taxonomic and functional profiling was achieved with METAnnotatorX2 bioinformatics platform.ResultsGroups had an average 20 (95% CI 14–27) cm difference in waist circumference. We identified the lack of Pseudomonas guguagenesis and Prevotella scopos, oulorum and oris as putative biomarkers associated with central obesity and observed a total of 16 enzymatic reactions differing between the groups. DCI was associated with the highest number of enzyme profiles (122), followed by STI (60) and DCI (25) (Pearson correlation p ConclusionClinically relevant differences in central obesity were only modestly reflected in the composition of saliva microbiota. Habitual consumption of sweet treats was a strong determinant of enzymatic reactions of saliva microbiota in children with and without central obesity. The clinical relevance of these findings warrants further studies.</p

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

<i>Lactococcus garvieae</i>: Where Is It From? A First Approach to Explore the Evolutionary History of This Emerging Pathogen

<div><p>The population structure and diversity of <i>Lactococcus garvieae</i>, an emerging pathogen of increasing clinical significance, was determined at both gene and genome level. Selected lactococcal isolates of various origins were analyzed by a multi locus sequence typing (MLST). This gene-based analysis was compared to genomic characteristics, estimated through the complete genome sequences available in database. The MLST identified two branches containing the majority of the strains and two branches bearing one strain each. One strain was particularly differentiated from the other <i>L. garvieae</i> strains, showing a significant genetic distance. The genomic characteristics, correlated to the MLST-based phylogeny, indicated that this “separated strain” appeared first and could be considered the evolutionary intermediate between <i>Lactococcus lactis</i> and <i>L. garvieae</i> main clusters. A preliminary genome analysis of <i>L. garvieae</i> indicated a pan-genome constituted of about 4100 genes, which included 1341 core genes and 2760 genes belonging to the dispensable genome. A total of 1491 Clusters of Orthologous Genes (COGs) were found to be specific to the 11 <i>L. garvieae</i> genomes, with the genome of the “separated strain” showing the highest presence of unique genes.</p></div

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

Major rule consensus tree based on Clonal Frame analysis of concatenated sequences of all loci, for the total population.

<p>The X-axis represents the estimated time to the most recent common ancestor of <i>L. garvieae</i>. Open and closed squares correspond to subgroups S_B and S_A, respectively.</p

Polymorphism observed in seven housekeeping genes in <i>L. garvieae.</i>

<p>Conc: concatenated sequences of seven loci.</p><p>S_A = Subgroup A, S_B = Subgroup B.</p><p>^a Statistical significance: Not significant, p>0.10.</p><p>^b Statistical significance: Not significant, 0.10</p><p>^c linkage disequilibrium detected.</p><p>/: not determined.</p><p>π = defined as the average number of nucleotide differences per site for a group of DNA sequences sampled.</p><p>π _{MAX<b> = </b>}maximal nucleotide diversity, defined as the number of nucleotide differences per site between the two most divergent sequences within the population.</p

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