Bringing PLOS Genetics Editors to Preprint Servers

What's the first thing you do after making a cool new discovery? If you're like us, you run up and down the hallway, propelled by excitement, eager to show your latest result to your colleagues. But the hallway is a pretty limited audience, so we soon turn to publishing our work in a peer-reviewed journal to show it to the whole world (assuming it is an open-access journal). That's when the fun of discovery can come to a screeching halt and turn into dreary hours of formatting and online form submission only to wait weeks, if not months, for your manuscript to wend its way through the peer-review system. Preprint servers (PPS) can short-circuit those cheerless steps, at least for a time, and allow the fruits of your labor to be seen immediately by all who are interested. In addition to increasing the visibility of authors' work, PPS provide opportunities for journals to identify manuscripts that are good fit for their audience. In that vein, PLOS Genetics is pleased to announce a new initiative to use PPS for identifying and soliciting manuscripts, as part of PLOS' overall mission to improve the efficiency and accessibility of science communication (and, of course, to make the process less cheerless for authors). As part of that effort, we now have a dedicated team of editors who will focus on identifying manuscripts on PPS that are potentially suitable for publication in PLOS Genetics

Properties of branes in curved spacetimes

A generic property of curved manifolds is the existence of focal points. We show that branes located at focal points of the geometry satisfy special properties. Examples of backgrounds to which our discussion applies are AdS_m x S^n and plane wave backgrounds. As an example, we show that a pair of AdS_2 branes located at the north and south pole of the S^5 in AdS_5 x S^5 are half supersymmetric and that they are dual to a two-monopole solution of N=4 SU(N) SYM theory. Our second example involves spacelike branes in the (Lorentzian) plane wave. We develop a modified lightcone gauge for the open string channel, analyze in detail the cylinder diagram and establish open-closed duality. When the branes are located at focal points of the geometry the amplitude acquires most of the characteristics of flat space amplitudes. In the open string channel the special properties are due to stringy modes that become massless.Comment: 41 pages; v2:typos corrected, ref adde

Loop Groups, Kaluza-Klein Reduction and M-Theory

We show that the data of a principal G-bundle over a principal circle bundle is equivalent to that of a \hat{LG} = U(1) |x LG bundle over the base of the circle bundle. We apply this to the Kaluza-Klein reduction of M-theory to IIA and show that certain generalized characteristic classes of the loop group bundle encode the Bianchi identities of the antisymmetric tensor fields of IIA supergravity. We further show that the low dimensional characteristic classes of the central extension of the loop group encode the Bianchi identities of massive IIA, thereby adding support to the conjectures of hep-th/0203218.Comment: 26 pages, LaTeX, utarticle.cls, v2:clarifications and refs adde

Aspects of U-duality in BLG models with Lorentzian metric 3-algebras

In our previous paper, it was shown that BLG model based on a Lorentzian metric 3-algebra gives Dp-brane action whose worldvolume is compactified on torus T^d (d=p-2). Here the 3-algebra was a generalized one with d+1 pairs of Lorentzian metric generators and expressed in terms of a loop algebra with central extensions. In this paper, we derive the precise relation between the coupling constant of the super Yang-Mills, the moduli of T^d and some R-R flux with VEV's of ghost fields associated with Lorentzian metric generators. In particular, for d=1, we derive the Yang-Mills action with theta term and show that SL(2,Z) Montonen-Olive duality is realized as the rotation of two VEV's. Furthermore, some moduli parameters such as NS-NS 2-form flux are identified as the deformation parameters of the 3-algebras. By combining them, we recover most of the moduli parameters which are required by U-duality symmetry.Comment: 27 pages, v2: minor correction

EGIA–evolutionary optimisation of gene regulatory networks, an integrative approach

Quantitative modelling of gene regulatory networks (GRNs) is still limited by data issues such as noise and the restricted length of available time series, creating an under-determination problem. However, large amounts of other types of biological data and knowledge are available, such as knockout experiments, annotations and so on, and it has been postulated that integration of these can improve model quality. However, integration has not been fully explored, to date. Here, we present a novel integrative framework for different types of data that aims to enhance model inference. This is based on evolutionary computation and uses different types of knowledge to introduce a novel customised initialisation and mutation operator and complex evaluation criteria, used to distinguish between candidate models. Specifically, the algorithm uses information from (i) knockout experiments, (ii) annotations of transcription factors, (iii) binding site motifs (expressed as position weight matrices) and (iv) DNA sequence of gene promoters, to drive the algorithm towards more plausible network structures. Further, the evaluation basis is also extended to include structure information included in these additional data. This framework is applied to both synthetic and real gene expression data. Models obtained by data integration display both quantitative and qualitative improvement

A Measurement of Time-Averaged Aerosol Optical Depth using Air-Showers Observed in Stereo by HiRes

Air fluorescence measurements of cosmic ray energy must be corrected for attenuation of the atmosphere. In this paper we show that the air-showers themselves can yield a measurement of the aerosol attenuation in terms of optical depth, time-averaged over extended periods. Although the technique lacks statistical power to make the critical hourly measurements that only specialized active instruments can achieve, we note the technique does not depend on absolute calibration of the detector hardware, and requires no additional equipment beyond the fluorescence detectors that observe the air showers. This paper describes the technique, and presents results based on analysis of 1258 air-showers observed in stereo by the High Resolution Fly's Eye over a four year span.Comment: 7 pages, 3 figures, accepted for publication by Astroparticle Physics Journa

Flux Backgrounds in 2D String Theory

We study RR flux backgrounds in two dimensional type 0 string theories. In particular, we study the relation between the 0A matrix model and the extremal black hole in two dimensions. Using T-duality we find a dual flux background in type 0B theory and propose its matrix model description. When the Fermi level is set to zero this system remains weakly coupled and exhibits a larger symmetry related to the structure of flux vacua. Finally, we construct a two dimensional type IIB background as an orbifold of the 0B background.Comment: Harvmac, 40 pages, 6 figs, minor changes, references adde

Search for Global Dipole Enhancements in the HiRes-I Monocular Data above 10^{18.5} eV

Several proposed source models for Ultra-High Energy Cosmic Rays (UHECRs) consist of dipole distributions oriented towards major astrophysical landmarks such as the galactic center, M87, or Centaurus A. We use a comparison between real data and simulated data to show that the HiRes-I monocular data for energies above 10^{18.5} eV is, in fact, consistent with an isotropic source model. We then explore methods to quantify our sensitivity to dipole source models oriented towards the Galactic Center, M87, and Centaurus A.Comment: 17 pages, 31 figure

Observation of the Ankle and Evidence for a High-Energy Break in the Cosmic Ray Spectrum

We have measured the cosmic ray spectrum at energies above $10^{17}$ eV using the two air fluorescence detectors of the High Resolution Fly's Eye experiment operating in monocular mode. We describe the detector, PMT and atmospheric calibrations, and the analysis techniques for the two detectors. We fit the spectrum to models describing galactic and extragalactic sources. Our measured spectrum gives an observation of a feature known as the ``ankle'' near $3\times 10^{18}$ eV, and strong evidence for a suppression near $6\times 10^{19}$ eV.Comment: 14 pages, 9 figures. To appear in Physics Letters B. Accepted versio