Planktonic foraminifera genomic variations reflect paleoceanographic changes in the Arctic: evidence from sedimentary ancient DNA

Deciphering the evolution of marine plankton is typically based on the study of microfossil groups. Cryptic speciation is common in these groups, and large intragenomic variations occur in ribosomal RNA genes of many morphospecies. In this study, we correlated the distribution of ribosomal amplicon sequence variants (ASVs) with paleoceanographic changes by analyzing the highthroughput sequence data assigned to Neogloboquadrina pachyderma in a 140,000-year-old sediment core from the Arctic Ocean. The sedimentary ancient DNA demonstrated the occurrence of various N. pachyderma ASVs whose occurrence and dominance varied through time. Most remarkable was the striking appearance of ASV18, which was nearly absent in older sediments but became dominant during the last glacial maximum and continues to persist today. Although the molecular ecology of planktonic foraminifera is still poorly known, the analysis of their intragenomic variations through time has the potential to provide new insight into the evolution of marine biodiversity and may lead to the development of new and important paleoceanographic proxies

Different distribution of CD4 and CD8 T cells in synovial membrane and peripheral blood of rheumatoid arthritis and osteoarthritis patients.

Rheumatoid arthritis (RA) and osteoarthritis (OA) are chronic diseases associated with morphological joint changes. Synovial membrane (SM) involvement was established for RA, but the data for OA are limited, because OA is usually regarded as noninflammatory disease. Changes in immune system in RA are not limited to joints, and the significant role of T cells of peripheral blood (PB) is not disputable. However, there is still an open debate about PB immunological profile in OA. Therefore, we decided to measure the distribution of CD4+ and CD8+ T cells, regarding CD28 expression, both in PB and SM of RA and OA patients, on the same day. Altogether, eleven RA patients, 11 OA patients and similar numbers of age-matched healthy controls were included into the study. Flow cytometry was used for T cells subpopulation distinguishing and quantification; monoclonal antibodies against CD3, CD4, CD8 and CD28 with different fluorochromes were used for stainings. The RA patients had significantly higher percentage of CD3+4+ cells in PB as compared to OA patients and relevant control group. Both within the CD4+ and CD8+ compartments, significantly lower percentages of cells bearing the CD28 marker were found in the PB of OA as compared to RA patients. The proportion of CD3+CD4+ cells in SM was dependent on age of OA patients, older OA patients had significantly higher value of their SM/blood ratio than RA patients. Older OA subjects were also characterized by higher values of the SM/blood ratio of both CD4+CD28+ and CD8+CD28+ subpopulations than RA or younger OA patients. In conclusion, in contrast to the traditional view of OA disease, our results give support to the hypothesis that OA may also (like RA) be a disease with a local immunological involvement

Impact of IL-28B polymorphisms on pegylated interferon plus ribavirin treatment response in children and adolescents infected with HCV genotypes 1 and 4

IL-28B polymorphisms are predictors of response to therapy in adults infected with hepatitis C. We do not know whether they are markers of response to therapy in children and adolescents. The aim of this study was to determine whether single-nucleotide polymorphisms (SNPs) in the IL-28B gene could influence the probability of response to therapy compared with other known baseline prognostic factors and correlate with clinical findings in pediatric patients infected with hepatitis C virus (HCV) genotypes 1 or 4. We determined three SNPs of IL-28B (rs12979860, rs12980275, and rs8099917) in 82 patients with chronic HCV infection treated with pegylated interferon alpha and ribavirin (peg-IFNα/RBV). Treatment response and clinical data were analyzed. Overall, sustained virological response (SVR) was achieved by 45 % of patients infected with difficult-to-treat HCV genotypes 1 and 4. Except for IL-28B polymorphisms, there was no association of SVR with any other clinical data. IL-28B rs12979860 CC [odds ratio (OR), 6.81; p = 0.001] and rs8099917 TT (OR, 3.14; p = 0.013) genotypes were associated with higher SVR rates. IL-28B rs12980275 was not significantly associated with SVR ( p = 0.058). Only the distribution between CC and CT-TT genotypes of rs12979860 significantly differentiated patients achieving early virological response (EVR) (OR, 10.0; p = 0.011). Children with the rs12979860 CC genotype had significantly higher baseline viral load compared with CT-TT patients ( p = 0.010). In children and adolescents chronically infected with HCV genotypes 1 and 4, IL-28B rs12979860 and rs8099917 polymorphisms were the only predictors of response to peg-IFN/RBV

HBV DNA suppression during entecavir treatment in previously treated children with chronic hepatitis B

The aim of this study was to assess HBV DNA suppression after 24 weeks of treatment with entecavir in previously treated children with CHB. Thirty children aged 5–17 years (25 males and 5 females) with CHB were treated with entecavir 0.5 or 1 mg daily. Twenty-two children were HBeAg-positive, eight were HBeAg-negative, and in eight HBV polymerase mutations were detected. After 24 weeks of treatment, mean and median HBV DNA levels and ALT activity were lower versus baseline, overall and in both subgroups. The overall median HBV DNA level decreased from 1.2 x 107 IU/mL to 3.3 x 102 IU/mL (p < 0.000004), in HBeAg-positive from 7.8x107 IU/mL to 6.3x103 IU/mL (p < 0.00004), and in HBeAg-negative from 2.5x104 IU/mL to 5.01x101 IU/mL (p < 0.03). The serum HBV DNA disappearance was observed in 7/8 (88%) HBeAg-negative and in 5/22 (23%) HBeAg-positive patients. The overall mean ALT activity decreased from 164+ 290 U/L to 34.1+ 18.9 U/L (p < 0.000007), in HBeAg-positive from 214+326 U/L to 38.59+19.2 U/L (p < 0.000074), and in HBeAg-negative from 27+14 U/L to 20+8 U/L (p < 0.03). Twenty-four weeks of treatment with entecavir results in suppression of HBV DNA in a substantial proportion of children previously treated ineffectively with CHB

Phase-space dependence of particle-ratio fluctuations in Pb+Pb collisions from 20A to 158A GeV beam energy

A novel approach, the identity method, was used for particle identification and the study of fluctuations of particle yield ratios in Pb+Pb collisions at the CERN Super Proton Synchrotron (SPS). This procedure allows to unfold the moments of the unknown multiplicity distributions of protons (p), kaons (K), pions ($\pi$) and electrons (e). Using these moments the excitation function of the fluctuation measure $\nu_{\text{\text{dyn}}}$[A,B] was measured, with A and B denoting different particle types. The obtained energy dependence of $\nu_{\text{dyn}}$ agrees with previously published NA49 results on the related measure $\sigma_{\text{dyn}}$. Moreover, $\nu_{\text{dyn}}$ was found to depend on the phase space coverage for [K,p] and [K,$\pi$] pairs. This feature most likely explains the reported differences between measurements of NA49 and those of STAR in central Au+Au collisions

Production of deuterium, tritium, and 3^3He in central Pb+Pb collisions at 20A, 30A, 40A, 80A, and 158A GeV at the CERN SPS

Production of $d$, $t$, and $^3$He nuclei in central Pb+Pb interactions was studied at five collision energies ($\sqrt{s_{NN}}=$ 6.3, 7.6, 8.8, 12.3, and 17.3 GeV) with the NA49 detector at the CERN SPS. Transverse momentum spectra, rapidity distributions, and particle ratios were measured. Yields are compared to predictions of statistical models. Phase-space distributions of light nuclei are discussed and compared to those of protons in the context of a coalescence approach. The coalescence parameters $B_2$ and $B_3$, as well as coalescence radii for $d$ and $^3$He were determined as a function of transverse mass at all energies.Comment: 22 pages, 29 figures, 8 tables, for submission to Phys. Rev.

Measurements of π±\pi^\pm, K±^\pm, p and pˉ\bar{\textrm{p}} spectra in proton-proton interactions at 20, 31, 40, 80 and 158 GeV/c with the NA61/SHINE spectrometer at the CERN SPS

Measurements of inclusive spectra and mean multiplicities of $\pi^\pm$, K$^\pm$, p and $\bar{\textrm{p}}$ produced in inelastic p+p interactions at incident projectile momenta of 20, 31, 40, 80 and 158 GeV/c ($\sqrt{s} =$ 6.3, 7.7, 8.8, 12.3 and 17.3 GeV, respectively) were performed at the CERN Super Proton Synchrotron using the large acceptance NA61/SHINE hadron spectrometer. Spectra are presented as function of rapidity and transverse momentum and are compared to predictions of current models. The measurements serve as the baseline in the NA61/SHINE study of the properties of the onset of deconfinement and search for the critical point of strongly interacting matter

Measurements of π±\pi^\pm, K±K^\pm, KS0K^0_S, Λ\Lambda and proton production in proton-carbon interactions at 31 GeV/cc with the NA61/SHINE spectrometer at the CERN SPS

Measurements of hadron production in p+C interactions at 31 GeV/c are performed using the NA61/ SHINE spectrometer at the CERN SPS. The analysis is based on the full set of data collected in 2009 using a graphite target with a thickness of 4% of a nuclear interaction length. Inelastic and production cross sections as well as spectra of $\pi^\pm$, $K^\pm$, p, $K^0_S$ and $\Lambda$ are measured with high precision. These measurements are essential for improved calculations of the initial neutrino fluxes in the T2K long-baseline neutrino oscillation experiment in Japan. A comparison of the NA61/SHINE measurements with predictions of several hadroproduction models is presented.Comment: v1 corresponds to the preprint CERN-PH-EP-2015-278; v2 matches the final published versio

Measurement of negatively charged pion spectra in inelastic p+p interactions at plabp_{lab} = 20, 31, 40, 80 and 158 GeV/c

We present experimental results on inclusive spectra and mean multiplicities of negatively charged pions produced in inelastic p+p interactions at incident projectile momenta of 20, 31, 40, 80 and 158 GeV/c ($\sqrt{s} =$ 6.3, 7.7, 8.8, 12.3 and 17.3 GeV, respectively). The measurements were performed using the large acceptance NA61/SHINE hadron spectrometer at the CERN Super Proton Synchrotron. Two-dimensional spectra are determined in terms of rapidity and transverse momentum. Their properties such as the width of rapidity distributions and the inverse slope parameter of transverse mass spectra are extracted and their collision energy dependences are presented. The results on inelastic p+p interactions are compared with the corresponding data on central Pb+Pb collisions measured by the NA49 experiment at the CERN SPS. The results presented in this paper are part of the NA61/SHINE ion program devoted to the study of the properties of the onset of deconfinement and search for the critical point of strongly interacting matter. They are required for interpretation of results on nucleus-nucleus and proton-nucleus collisions.Comment: Numerical results available at: https://edms.cern.ch/document/1314605 Updates in v3: Updated version, as accepted for publicatio

NA61/SHINE facility at the CERN SPS: beams and detector system

NA61/SHINE (SPS Heavy Ion and Neutrino Experiment) is a multi-purpose experimental facility to study hadron production in hadron-proton, hadron-nucleus and nucleus-nucleus collisions at the CERN Super Proton Synchrotron. It recorded the first physics data with hadron beams in 2009 and with ion beams (secondary 7Be beams) in 2011. NA61/SHINE has greatly profited from the long development of the CERN proton and ion sources and the accelerator chain as well as the H2 beamline of the CERN North Area. The latter has recently been modified to also serve as a fragment separator as needed to produce the Be beams for NA61/SHINE. Numerous components of the NA61/SHINE set-up were inherited from its predecessors, in particular, the last one, the NA49 experiment. Important new detectors and upgrades of the legacy equipment were introduced by the NA61/SHINE Collaboration. This paper describes the state of the NA61/SHINE facility - the beams and the detector system - before the CERN Long Shutdown I, which started in March 2013