A first step towards computing all hybridization networks for two rooted binary phylogenetic trees

Recently, considerable effort has been put into developing fast algorithms to reconstruct a rooted phylogenetic network that explains two rooted phylogenetic trees and has a minimum number of hybridization vertices. With the standard approach to tackle this problem being combinatorial, the reconstructed network is rarely unique. From a biological point of view, it is therefore of importance to not only compute one network, but all possible networks. In this paper, we make a first step towards approaching this goal by presenting the first algorithm---called allMAAFs---that calculates all maximum-acyclic-agreement forests for two rooted binary phylogenetic trees on the same set of taxa.Comment: 21 pages, 5 figure

OddzOn Products and Derivation of Invention: At Odds with the Purpose of Section 102(f) of the Patent Act of 1952?

Abstract Background Antimicrobial peptides are important components of the host defence with a broad range of functions including direct antimicrobial activity and modulation of inflammation. Lack of cathelin-related antimicrobial peptide (CRAMP) was associated with higher mortality and bacterial burden and impaired neutrophil granulocyte infiltration in a model of pneumococcal meningitis. The present study was designed to characterize the effects of CRAMP deficiency on glial response and phagocytosis after exposure to bacterial stimuli. Methods CRAMP-knock out and wildtype glial cells were exposed to bacterial supernatants from Streptococcus pneumoniae and Neisseria meningitides or the bacterial cell wall components lipopolysaccharide and peptidoglycan. Cell viability, expression of pro- and anti-inflammatory mediators and activation of signal transduction pathways, phagocytosis rate and glial cell phenotype were investigated by means of cell viability assays, immunohistochemistry, real-time RT-PCR and Western blot. Results CRAMP-deficiency was associated with stronger expression of pro-inflammatory and weakened expression of anti-inflammatory cytokines indicating a higher degree of glial cell activation even under resting-state conditions. Furthermore, increased translocation of nuclear factor ‘kappa-light-chain-enhancer’ of activated B-cells was observed and phagocytosis of S. pneumoniae was reduced in CRAMP-deficient microglia indicating impaired antimicrobial activity. Conclusions In conclusion, the present study detected severe alterations of the glial immune response due to lack of CRAMP. The results indicate the importance of CRAMP to maintain and regulate the delicate balance between beneficial and harmful immune response in the brain

Supersymmetric Inflation with the Ordinary Higgs?

We consider a model of D-term inflation in which the inflaton coincides with the standard Higgs doublet. Non-renormalizable terms are controlled by a discrete R-symmetry of the superpotential. We consider radiative corrections to the scalar potential and find that Higgs inflation in the slow-roll approximation is viable and consistent with CMB data, although with a rather large value of the non-renormalizable coupling involved.Comment: 7 pages, 1 figure, published version, comments and reference added, typos and factor of 2 corrected

A Statistical Equilibrium Model of Competitive Firms

We argue that the complex interactions of competitive heterogeneous firms lead to a statistical equilibrium distribution of firms? profit rates, which turns out to be an exponential power (or Subbotin) distribution. Moreover, we construct a diffusion process that has the Subbotin distribution as its stationary probability density, leading to a phenomenologically inspired interpretation of variations in the shape parameter of the statistical equilibrium distribution. Our main finding is that firms? idiosyncratic efforts and the tendency for competition to equalize profit rates are two sides of the same coin

A statistical equilibrium model of competitive firms

We find that the empirical density of firm profit rates, measured as returns on assets, is markedly non-Gaussian and reasonably well described by an exponential power (or Subbotin) distribution. We start from a statistical equilibrium model that leads to a stationary Subbotin density in the presence of complex interactions among competitive heterogeneous firms. To investigate the dynamics of firm profitability, we construct a diffusion process that has the Subbotin distribution as its stationary probability density. This leads to a phenomenologically inspired interpretation of variations in the shape parameter of the Subbotin distribution, which essentially measures the competitive pressure in and across industries. Our findings have profound implications both for the previous literature on the ‘persistence of profits’ as well as for understanding competition as a dynamic process. Our main formal finding is that firms' idiosyncratic efforts and the tendency for competition to equalize profit rates are two sides of the same coin, and that a ratio of these two effects ultimately determines the dispersion of the equilibrium distribution

Semileptonic Decays: an Update Down Under

Heavy-meson semileptonic decays calculations on the lattice are reviewed. The focus is upon obtaining reliable matrix elements. Errors that depend upon the lattice spacing, $a$, are an important source of systematic error. Full $O(a)$ improvement of matrix elements for arbitrary-mass four-component quarks is discussed. With improvement, bottom-quark matrix elements can be calculated directly using current lattices. Momentum dependent errors for $O(a)$-improved quarks and statistical noise limit momenta to around 1 GeV/c with current lattices. Hence, maximum recoil momenta can be reached for $D$ decays while only a fraction of the maximum recoil momentum can be reliably studied for the light-meson decay modes of the $B$. Differential decay rates and partial widths are phenomenologically important quantities in $B$ decays that can be reliably determined with present lattices.Comment: 14 pages, 9 postscript figures, requires espcrc2.st

Boltzmann brains and the scale-factor cutoff measure of the multiverse

To make predictions for an eternally inflating "multiverse", one must adopt a procedure for regulating its divergent spacetime volume. Recently, a new test of such spacetime measures has emerged: normal observers - who evolve in pocket universes cooling from hot big bang conditions - must not be vastly outnumbered by "Boltzmann brains" - freak observers that pop in and out of existence as a result of rare quantum fluctuations. If the Boltzmann brains prevail, then a randomly chosen observer would be overwhelmingly likely to be surrounded by an empty world, where all but vacuum energy has redshifted away, rather than the rich structure that we observe. Using the scale-factor cutoff measure, we calculate the ratio of Boltzmann brains to normal observers. We find the ratio to be finite, and give an expression for it in terms of Boltzmann brain nucleation rates and vacuum decay rates. We discuss the conditions that these rates must obey for the ratio to be acceptable, and we discuss estimates of the rates under a variety of assumptions.Comment: 32 pp, 2 figs. Modified to conform to the version accepted by Phys. Rev. D. The last paragraph of Sec. V-A, about Boltzmann brains in Minkowski space, has been significantly enlarged. Two sentences were added to the introduction concerning the classical approximation and the hope of finding a motivating principle for the measure. Several references were adde

Holographic Multiverse

We explore the idea that the dynamics of the inflationary multiverse is encoded in its future boundary, where it is described by a lower dimensional theory which is conformally invariant in the UV. We propose that a measure for the multiverse, which is needed in order to extract quantitative probabilistic predictions, can be derived in terms of the boundary theory by imposing a UV cutoff. In the inflationary bulk, this is closely related (though not identical) to the so-called scale factor cutoff measure.Comment: 23 pages, 4 figures. Replaced to match published versio

Running Inflation in the Standard Model

An interacting scalar field with largish coupling to curvature can support a distinctive inflationary universe scenario. Previously this has been discussed for the Standard Model Higgs field, treated classically or in a leading log approximation. Here we investigate the quantum theory using renormalization group methods. In this model the running of both the effective Planck mass and the couplings is important. The cosmological predictions are consistent with existing WMAP5 data, with 0.967 < n_s < 0.98 (for N_e = 60) and negligible gravity waves. We find a relationship between the spectral index and the Higgs mass that is sharply varying for m_h ~ 120-135 GeV (depending on the top mass); in the future, that relationship could be tested against data from PLANCK and LHC. We also comment briefly on how similar dynamics might arise in more general settings, and discuss our assumptions from the effective field theory point of view.Comment: 17 pages in Phys Lett B format, 5 figures; v3: updated to match published version, includes new Appendix B on EF