In-medium kaon and antikaon properties in the quark-meson coupling model

The properties of the kaon, $K$, and antikaon, \kbar, in nuclear medium are studied in the quark-meson coupling (QMC) model. Employing a constituent quark-antiquark (MIT bag model) picture, their excitation energies in a nuclear medium at zero momentum are calculated within mean field approximation. The scalar, and the vector mesons are assumed to couple directly to the nonstrange quarks and antiquarks in the $K$ and \kbar mesons. It is demonstrated that the $\rho$ meson induces different mean field potentials for each member of the isodoublets, $K$ and \kbar, when they are embedded in asymmetric nuclear matter. Furthermore, it is also shown that this $\rho$ meson potential is repulsive for the $K^-$ meson in matter with a neutron excess, and renders $K^-$ condensation less likely to occur.Comment: Latex, 11 pages, 4 Postscript figures, a few typos which can be important for an interpretation (but not reflected in the results) are corrected, as published in (E) Phys. Lett. B 436 (1998) 45

A Theory of Gamma-Ray Bursts

We present a specific scenario for the link between GRB and hypernovae, based on Blandford-Znajek extraction of black-hole spin energy. Such a mechanism requires a high angular momentum in the progenitor object. The observed association of gamma-ray bursts with type Ibc supernovae leads us to consider massive helium stars that form black holes at the end of their lives as progenitors. We combine the numerical work of MacFadyen & Woosley with analytic calculations, to show that about 1E53 erg each are available to drive the fast GRB ejecta and the supernova. The GRB ejecta are driven by the power output through the open field lines, whereas the supernova is powered by closed filed lines and jet shocks. We also present a much simplified approximate derivation of these energetics. Helium stars that leave massive black-hole remnants in special ways, namely via soft X-ray transients or very massive WNL stars. Since binaries naturally have high angular momentum, we propose a link between black-hole transients and gamma-ray bursts. Recent observations of one such transient, GRO J1655-40/Nova Scorpii 1994, explicitly support this connection: its high space velocity indicates that substantial mass was ejected in the formation of the black hole, and the overabundance of alpha-nuclei, especially sulphur, indicates that the explosion energy was extreme, as in SN 1998bw/GRB 980425. (abstract shortened)Comment: 32 pages, 8 figures, accepted for publication in New Astronom

Kaon mass in dense matter

The variation of kaon mass in dense, charge-neutral baryonic matter at beta-equilibrium has been investigated. The baryon interaction has been included by means of nonlinear Walecka model, with and without hyperons and the interaction of kaons with the baryons has been incorporated through the Nelson-Kaplan model. A self-consistant, one-loop level calculation has been carried out. We find that at the mean field level, the presence of the hyperons makes the density-dependence of the kaon mass softer. Thus, the kaon condensation threshold is pushed up in the baryon density. The loop diagrams tend to lower the kaon condensation point for lower values of $a_3 m_s$. We also find that the S-wave kaon-nucleon interaction plays the dominant role in determining the on-set of kaon condensation and the contribution of the P-wave interaction is insignificant.Comment: Four figures available on reques

A Novel Sequence-Based Antigenic Distance Measure for H1N1, with Application to Vaccine Effectiveness and the Selection of Vaccine Strains

H1N1 influenza causes substantial seasonal illness and was the subtype of the 2009 influenza pandemic. Precise measures of antigenic distance between the vaccine and circulating virus strains help researchers design influenza vaccines with high vaccine effectiveness. We here introduce a sequence-based method to predict vaccine effectiveness in humans. Historical epidemiological data show that this sequence-based method is as predictive of vaccine effectiveness as hemagglutination inhibition (HI) assay data from ferret animal model studies. Interestingly, the expected vaccine effectiveness is greater against H1N1 than H3N2, suggesting a stronger immune response against H1N1 than H3N2. The evolution rate of hemagglutinin in H1N1 is also shown to be greater than that in H3N2, presumably due to greater immune selection pressure.Comment: 26 pages, 7 figures, 2 tables, supplemen

Accurate exchange-correlation energies for the warm dense electron gas

Density matrix quantum Monte Carlo (DMQMC) is used to sample exact-on-average $N$-body density matrices for uniform electron gas systems of up to 10$^{124}$ matrix elements via a stochastic solution of the Bloch equation. The results of these calculations resolve a current debate over the accuracy of the data used to parametrize finite-temperature density functionals. Exchange-correlation energies calculated using the real-space restricted path-integral formalism and the $k$-space configuration path-integral formalism disagree by up to $\sim$$10$\% at certain reduced temperatures $T/T_F \le 0.5$ and densities $r_s \le 1$. Our calculations confirm the accuracy of the configuration path-integral Monte Carlo results available at high density and bridge the gap to lower densities, providing trustworthy data in the regime typical of planetary interiors and solids subject to laser irradiation. We demonstrate that DMQMC can calculate free energies directly and present exact free energies for $T/T_F \ge 1$ and $r_s \le 2$.Comment: Accepted version: added free energy data and restructured text. Now includes supplementary materia

A cancer cell-line titration series for evaluating somatic classification.

BackgroundAccurate detection of somatic single nucleotide variants and small insertions and deletions from DNA sequencing experiments of tumour-normal pairs is a challenging task. Tumour samples are often contaminated with normal cells confounding the available evidence for the somatic variants. Furthermore, tumours are heterogeneous so sub-clonal variants are observed at reduced allele frequencies. We present here a cell-line titration series dataset that can be used to evaluate somatic variant calling pipelines with the goal of reliably calling true somatic mutations at low allele frequencies.ResultsCell-line DNA was mixed with matched normal DNA at 8 different ratios to generate samples with known tumour cellularities, and exome sequenced on Illumina HiSeq to depths of >300×. The data was processed with several different variant calling pipelines and verification experiments were performed to assay >1500 somatic variant candidates using Ion Torrent PGM as an orthogonal technology. By examining the variants called at varying cellularities and depths of coverage, we show that the best performing pipelines are able to maintain a high level of precision at any cellularity. In addition, we estimate the number of true somatic variants undetected as cellularity and coverage decrease.ConclusionsOur cell-line titration series dataset, along with the associated verification results, was effective for this evaluation and will serve as a valuable dataset for future somatic calling algorithm development. The data is available for further analysis at the European Genome-phenome Archive under accession number EGAS00001001016. Data access requires registration through the International Cancer Genome Consortium's Data Access Compliance Office (ICGC DACO)