Electroweak baryogenesis

Electroweak baryogenesis (EWBG) remains a theoretically attractive and experimentally testable scenario for explaining the cosmic baryon asymmetry. We review recent progress in computations of the baryon asymmetry within this framework and discuss their phenomenological consequences. We pay particular attention to methods for analyzing the electroweak phase transition and calculating CP-violating asymmetries, the development of Standard Model extensions that may provide the necessary ingredients for EWBG, and searches for corresponding signatures at the high energy, intensity, and cosmological frontiers.Comment: 42 pages, 13 figures, invited review for the New Journal of Physics focus issue on 'Origin of Matter

Moisture transport by Atlantic tropical cyclones onto the North American continent

Tropical Cyclones (TCs) are an important source of freshwater for the North American continent. Many studies have tried to estimate this contribution by identifying TC-induced precipitation events, but few have explicitly diagnosed the moisture fluxes across continental boundaries. We design a set of attribution schemes to isolate the column-integrated moisture fluxes that are directly associated with TCs and to quantify the flux onto the North American Continent due to TCs. Averaged over the 2004–2012 hurricane seasons and integrated over the western, southern and eastern coasts of North America, the seven schemes attribute 7 to 18 % (mean 14 %) of total net onshore flux to Atlantic TCs. A reduced contribution of 10 % (range 9 to 11 %) was found for the 1980–2003 period, though only two schemes could be applied to this earlier period. Over the whole 1980–2012 period, a further 8 % (range 6 to 9 % from two schemes) was attributed to East Pacific TCs, resulting in a total TC contribution of 19 % (range 17 to 22 %) to the ocean-to-land moisture transport onto the North American continent between May and November. Analysis of the attribution uncertainties suggests that incorporating details of individual TC size and shape adds limited value to a fixed radius approach and TC positional errors in the ERA-Interim reanalysis do not affect the results significantly, but biases in peak wind speeds and TC sizes may lead to underestimates of moisture transport. The interannual variability does not appear to be strongly related to the El Nino-Southern Oscillation phenomenon

Warped Radion Inflation

We show that the radion in a warped geometry bounded by two branes can have a potential suitable for inflation. Our construction is based upon a solution known in string theory as the linear dilaton, in which the back-reaction from a bulk scalar \Phi is exactly accounted for. The radion, stabilized by \Phi, is much heavier than the TeV scale and its couplings to the standard model are much more suppressed than in the usual Randall-Sundrum solution. We present a new formalism for obtaining approximate time-dependent solutions, based on perturbing the exact solution to the coupled Einstein and scalar field equations in the bulk. It allows the radion potential to be computed directly in terms of the brane potentials for \Phi. We show that simple exponential potentials on the branes can lead to a 4D radion potential with a flattened hilltop form, yielding inflation with a spectral index of typically n_s=0.96 and no higher than 0.99. With more complicated brane potentials, the descent from the hilltop can be a linear potential, giving a tensor-to-scalar ratio as large as r=0.07 with n_s=0.974. The couplings of the radion to the standard model particles are dictated by general covariance, so the details of reheating are explicitly calculable, leading to a reheat temperature of at least 10^7 GeV. The quantum corrections to the inflaton potential from its couplings to matter are also calculable and are shown to be small, so that the prediction for the shape of the potential is under theoretical control, even with superPlanckian field excursions.Comment: 32 pages, 15 figure

High throughput mutagenesis for identification of residues regulating human prostacyclin (hIP) receptor

The human prostacyclin receptor (hIP receptor) is a seven-transmembrane G protein-coupled receptor (GPCR) that plays a critical role in vascular smooth muscle relaxation and platelet aggregation. hIP receptor dysfunction has been implicated in numerous cardiovascular abnormalities, including myocardial infarction, hypertension, thrombosis and atherosclerosis. Genomic sequencing has discovered several genetic variations in the PTGIR gene coding for hIP receptor, however, its structure-function relationship has not been sufficiently explored. Here we set out to investigate the applicability of high throughput random mutagenesis to study the structure-function relationship of hIP receptor. While chemical mutagenesis was not suitable to generate a mutagenesis library with sufficient coverage, our data demonstrate error-prone PCR (epPCR) mediated mutagenesis as a valuable method for the unbiased screening of residues regulating hIP receptor function and expression. Here we describe the generation and functional characterization of an epPCR derived mutagenesis library compromising >4000 mutants of the hIP receptor. We introduce next generation sequencing as a useful tool to validate the quality of mutagenesis libraries by providing information about the coverage, mutation rate and mutational bias. We identified 18 mutants of the hIP receptor that were expressed at the cell surface, but demonstrated impaired receptor function. A total of 38 non-synonymous mutations were identified within the coding region of the hIP receptor, mapping to 36 distinct residues, including several mutations previously reported to affect the signaling of the hIP receptor. Thus, our data demonstrates epPCR mediated random mutagenesis as a valuable and practical method to study the structurefunction relationship of GPCRs. © 2014 Bill et al

Genoviz Software Development Kit: Java tool kit for building genomics visualization applications

<p>Abstract</p> <p>Background</p> <p>Visualization software can expose previously undiscovered patterns in genomic data and advance biological science.</p> <p>Results</p> <p>The Genoviz Software Development Kit (SDK) is an open source, Java-based framework designed for rapid assembly of visualization software applications for genomics. The Genoviz SDK framework provides a mechanism for incorporating adaptive, dynamic zooming into applications, a desirable feature of genome viewers. Visualization capabilities of the Genoviz SDK include automated layout of features along genetic or genomic axes; support for user interactions with graphical elements (Glyphs) in a map; a variety of Glyph sub-classes that promote experimentation with new ways of representing data in graphical formats; and support for adaptive, semantic zooming, whereby objects change their appearance depending on zoom level and zooming rate adapts to the current scale. Freely available demonstration and production quality applications, including the Integrated Genome Browser, illustrate Genoviz SDK capabilities.</p> <p>Conclusion</p> <p>Separation between graphics components and genomic data models makes it easy for developers to add visualization capability to pre-existing applications or build new applications using third-party data models. Source code, documentation, sample applications, and tutorials are available at <url>http://genoviz.sourceforge.net/</url>.</p

Dichromatic dark matter

Both the robust INTEGRAL 511 keV gamma-ray line and the recent tentative hint of the 135 GeV gamma-ray line from Fermi-LAT have similar signal morphologies, and may be produced from the same dark matter annihilation. Motivated by this observation, we construct a dark matter model to explain both signals and to accommodate the two required annihilation cross sections that are different by more than six orders of magnitude. In our model, to generate the low-energy positrons for INTEGRAL, dark matter particles annihilate into a complex scalar that couples to photon via a charge-radius operator. The complex scalar contains an excited state decaying into the ground state plus an off-shell photon to generate a pair of positron and electron. Two charged particles with non-degenerate masses are necessary for generating this charge-radius operator. One charged particle is predicted to be long-lived and have a mass around 3.8 TeV to explain the dark matter thermal relic abundance from its late decay. The other charged particle is predicted to have a mass below 1 TeV given the ratio of the two signal cross sections. The 14 TeV LHC will concretely test the main parameter space of this lighter charged particle.University of Wisconsin--Madison (Start-up funds)SLAC National Accelerator Laboratory (US DOE contract DE-AC02-76SF00515)Aspen Center for Physics (NSF Grant No. 1066293)United States. National Aeronautics and Space Administration (Einstein Postdoctoral Fellowship grant number PF2-130102)Smithsonian Astrophysical Observatory (Chandra X-ray Center, NASA under contract NAS8-03060

An X-ray Pulsar with a Superstrong Magnetic Field in the Soft Gamma-Ray Repeater SGR1806-20

Soft gamma-ray repeaters (SGRs) emit multiple, brief (approximately O.1 s) intense outbursts of low-energy gamma-rays. They are extremely rare; three are known in our galaxy and one in the Large Magellanic Cloud. Two SGRs are associated with young supernova remnants (SNRs), and therefore most probably with neutron stars, but it remains a puzzle why SGRs are so different from 'normal' radio pulsars. Here we report the discovery of pulsations in the persistent X-ray flux of SGR1806-20, with a period of 7.47 s and a spindown rate of 2.6 x 10(exp -3) s/yr. We argue that the spindown is due to magnetic dipole emission and find that the pulsar age and (dipolar) magnetic field strength are approximately 1500 years and 8 x 10(exp 14) gauss, respectively. Our observations demonstrate the existence of 'magnetars', neutron stars with magnetic fields about 100 times stronger than those of radio pulsars, and support earlier suggestions that SGR bursts are caused by neutron-star 'crust-quakes' produced by magnetic stresses. The 'magnetar' birth rate is about one per millenium, a substantial fraction of that of radio pulsars. Thus our results may explain why some SNRs have no radio pulsars

f(R) theories

Over the past decade, f(R) theories have been extensively studied as one of the simplest modifications to General Relativity. In this article we review various applications of f(R) theories to cosmology and gravity - such as inflation, dark energy, local gravity constraints, cosmological perturbations, and spherically symmetric solutions in weak and strong gravitational backgrounds. We present a number of ways to distinguish those theories from General Relativity observationally and experimentally. We also discuss the extension to other modified gravity theories such as Brans-Dicke theory and Gauss-Bonnet gravity, and address models that can satisfy both cosmological and local gravity constraints.Comment: 156 pages, 14 figures, Invited review article in Living Reviews in Relativity, Published version, Comments are welcom

Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

One of the central issues in evolutionary developmental biology is how we can formulate the relationships between evolutionary and developmental processes. Two major models have been proposed: the 'funnel-like' model, in which the earliest embryo shows the most conserved morphological pattern, followed by diversifying later stages, and the 'hourglass' model, in which constraints are imposed to conserve organogenesis stages, which is called the phylotypic period. Here we perform a quantitative comparative transcriptome analysis of several model vertebrate embryos and show that the pharyngula stage is most conserved, whereas earlier and later stages are rather divergent. These results allow us to predict approximate developmental timetables between different species, and indicate that pharyngula embryos have the most conserved gene expression profiles, which may be the source of the basic body plan of vertebrates

A biologically inspired network design model

A network design problem is to select a subset of links in a transport network that satisfy passengers or cargo transportation demands while minimizing the overall costs of the transportation. We propose a mathematical model of the foraging behaviour of slime mould P. polycephalum to solve the network design problem and construct optimal transport networks. In our algorithm, a traffic flow between any two cities is estimated using a gravity model. The flow is imitated by the model of the slime mould. The algorithm model converges to a steady state, which represents a solution of the problem. We validate our approach on examples of major transport networks in Mexico and China. By comparing networks developed in our approach with the man-made highways, networks developed by the slime mould, and a cellular automata model inspired by slime mould, we demonstrate the flexibility and efficiency of our approach