Neighborhoods of trees in circular orderings

In phylogenetics, a common strategy used to construct an evolutionary tree for a set of species X is to search in the space of all such trees for one that optimizes some given score function (such as the minimum evolution, parsimony or likelihood score). As this can be computationally intensive, it was recently proposed to restrict such searches to the set of all those trees that are compatible with some circular ordering of the set X. To inform the design of efficient algorithms to perform such searches, it is therefore of interest to find bounds for the number of trees compatible with a fixed ordering in the neighborhood of a tree that is determined by certain tree operations commonly used to search for trees: the nearest neighbor interchange (nni), the subtree prune and regraft (spr) and the tree bisection and reconnection (tbr) operations. We show that the size of such a neighborhood of a binary tree associated with the nni operation is independent of the tree’s topology, but that this is not the case for the spr and tbr operations. We also give tight upper and lower bounds for the size of the neighborhood of a binary tree for the spr and tbr operations and characterize those trees for which these bounds are attained

Multiple recent horizontal transfers of the cox1 intron in Solanaceae and extended co-conversion of flanking exons

Background: The most frequent case of horizontal transfer in plants involves a group I intron in the mitochondrial gene cox1, which has been acquired via some 80 separate plant-to-plant transfer events among 833 diverse angiosperms examined. This homing intron encodes an endonuclease thought to promote the intron´s promiscuous behavior. A promising experimental approach to study endonuclease activity and intron transmission involves somatic cell hybridization, which in plants leads to mitochondrial fusion and genome recombination. However, the cox1 intron has not yet been found in the ideal group for plant somatic genetics - the Solanaceae. We therefore undertook an extensive survey of this family to find members with the intron and to learn more about the evolutionary history of this exceptionally mobile genetic element. Results: Although 409 of the 426 species of Solanaceae examined lack the cox1 intron, it is uniformly present in three phylogenetically disjunct clades. Despite strong overall incongruence of cox1 intron phylogeny with angiosperm phylogeny, two of these clades possess nearly identical intron sequences and are monophyletic in intron phylogeny. These two clades, and possibly the third also, contain a co-conversion tract (CCT) downstream of the intron that is extended relative to all previously recognized CCTs in angiosperm cox1. Re-examination of all published cox1 genes uncovered additional cases of extended co-conversion and identified a rare case of putative intron loss, accompanied by full retention of the CCT. Conclusions: We infer that the cox1 intron was separately and recently acquired by at least three different lineages of Solanaceae. The striking identity of the intron and CCT from two of these lineages suggests that one of these three intron captures may have occurred by a within-family transfer event. This is consistent with previous evidence that horizontal transfer in plants is biased towards phylogenetically local events. The discovery of extended co-conversion suggests that other cox1 conversions may be longer than realized but obscured by the exceptional conservation of plant mitochondrial sequences. Our findings provide further support for the rampant-transfer model of cox1 intron evolution and recommend the Solanaceae as a model system for the experimental analysis of cox1 intron transfer in plants.Fil: Sánchez Puerta, María Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaFil: Abbona, Cinthia Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaFil: Zhuo, Shi. Indiana University; Estados UnidosFil: Tepe, Eric J.. University of Cincinnati; Estados Unidos. University of Utah; Estados UnidosFil: Bohs, Lynn. University of Utah; Estados UnidosFil: Olmstead, Richard G.. University of Washington; Estados UnidosFil: Palmer, Jeffrey D.. Indiana University; Estados Unido

Ariel - Volume 8 Number 2

Executive Editor James W. Lockard , Jr. Issue Editor Doug Hiller Business Manager Neeraj K. Kanwal University News Richard J. Perry World News Doug Hiller Opinions Elizabeth A. McGuire Features Patrick P. Sokas Sports Desk Shahab S. Minassian Managing Editor Edward H. Jasper Managing Associate Brenda Peterson Photography Editor Robert D. Lehman, Jr. Graphics Christine M. Kuhnl

Orientational phase transitions in the hexagonal phase of a diblock copolymer melt under shear flow

We generalize the earlier theory by Fredrickson [J. Rheol. v.38, 1045 (1994)] to study the orientational behaviour of the hexagonal phase of diblock copolymer melt subjected to steady shear flow. We use symmetry arguments to show that the orientational ordering in the hexagonal phase is a much weaker effect than in the lamellae. We predict the parallel orientation to be stable at low and the perpendicular orientation at high shear rates. Our analysis reproduces the experimental results by Tepe et al. [Macromolecules v.28, 3008 (1995)] and explains the difficulties in experimental observation of the different orientations in the hexagonal phase.Comment: 21 pages, 6 eps figures, submitted to Physical Review

Determining neutrino oscillation parameters from atmospheric muon neutrino disappearance with three years of IceCube DeepCore data

We present a measurement of neutrino oscillations via atmospheric muon neutrino disappearance with three years of data of the completed IceCube neutrino detector. DeepCore, a region of denser instrumentation, enables the detection and reconstruction of atmospheric muon neutrinos between 10 GeV and 100 GeV, where a strong disappearance signal is expected. The detector volume surrounding DeepCore is used as a veto region to suppress the atmospheric muon background. Neutrino events are selected where the detected Cherenkov photons of the secondary particles minimally scatter, and the neutrino energy and arrival direction are reconstructed. Both variables are used to obtain the neutrino oscillation parameters from the data, with the best fit given by $\Delta m^2_{32}=2.72^{+0.19}_{-0.20}\times 10^{-3}\,\mathrm{eV}^2$ and $\sin^2\theta_{23} = 0.53^{+0.09}_{-0.12}$ (normal mass hierarchy assumed). The results are compatible and comparable in precision to those of dedicated oscillation experiments.Comment: 10 pages, 7 figure

Search for non-relativistic Magnetic Monopoles with IceCube

The IceCube Neutrino Observatory is a large Cherenkov detector instrumenting $1\,\mathrm{km}^3$ of Antarctic ice. The detector can be used to search for signatures of particle physics beyond the Standard Model. Here, we describe the search for non-relativistic, magnetic monopoles as remnants of the GUT (Grand Unified Theory) era shortly after the Big Bang. These monopoles may catalyze the decay of nucleons via the Rubakov-Callan effect with a cross section suggested to be in the range of $10^{-27}\,\mathrm{cm^2}$ to $10^{-21}\,\mathrm{cm^2}$. In IceCube, the Cherenkov light from nucleon decays along the monopole trajectory would produce a characteristic hit pattern. This paper presents the results of an analysis of first data taken from May 2011 until May 2012 with a dedicated slow-particle trigger for DeepCore, a subdetector of IceCube. A second analysis provides better sensitivity for the brightest non-relativistic monopoles using data taken from May 2009 until May 2010. In both analyses no monopole signal was observed. For catalysis cross sections of $10^{-22}\,(10^{-24})\,\mathrm{cm^2}$ the flux of non-relativistic GUT monopoles is constrained up to a level of $\Phi_{90} \le 10^{-18}\,(10^{-17})\,\mathrm{cm^{-2}s^{-1}sr^{-1}}$ at a 90% confidence level, which is three orders of magnitude below the Parker bound. The limits assume a dominant decay of the proton into a positron and a neutral pion. These results improve the current best experimental limits by one to two orders of magnitude, for a wide range of assumed speeds and catalysis cross sections.Comment: 20 pages, 20 figure

Searches for Extended and Point-like Neutrino Sources with Four Years of IceCube Data

We present results on searches for point-like sources of neutrinos using four years of IceCube data, including the first year of data from the completed 86-string detector. The total livetime of the combined dataset is 1,373 days. For an E$^{-2}$ spectrum the median sensitivity at 90\% C.L. is $\sim 10^{-12}$ TeV$^{-1}$cm$^{-2}$s$^{-1}$ for energies between 1 TeV$-$1 PeV in the northern sky and $\sim 10^{-11}$ TeV$^{-1}$cm$^{-2}$s$^{-1}$ for energies between 100 TeV $-$ 100 PeV in the southern sky. The sensitivity has improved from both the additional year of data and the introduction of improved reconstructions compared to previous publications. In addition, we present the first results from an all-sky search for extended sources of neutrinos. We update results of searches for neutrino emission from stacked catalogs of sources, and test five new catalogs; two of Galactic supernova remnants and three of active galactic nuclei. In all cases, the data are compatible with the background-only hypothesis, and upper limits on the flux of muon neutrinos are reported for the sources considered.Comment: 36 pages, 15 figures. Submitted to the Astrophysical Journa

Determining neutrino oscillation parameters from atmospheric muon neutrino disappearance with three years of IceCube DeepCore data

We present a measurement of neutrino oscillations via atmospheric muon neutrino disappearance with three years of data of the completed IceCube neutrino detector. DeepCore, a region of denser instrumentation, enables the detection and reconstruction of atmospheric muon neutrinos between 10 GeV and 100 GeV, where a strong disappearance signal is expected. The detector volume surrounding DeepCore is used as a veto region to suppress the atmospheric muon background. Neutrino events are selected where the detected Cherenkov photons of the secondary particles minimally scatter, and the neutrino energy and arrival direction are reconstructed. Both variables are used to obtain the neutrino oscillation parameters from the data, with the best fit given by $\Delta m^2_{32}=2.72^{+0.19}_{-0.20}\times 10^{-3}\,\mathrm{eV}^2$ and $\sin^2\theta_{23} = 0.53^{+0.09}_{-0.12}$ (normal mass hierarchy assumed). The results are compatible and comparable in precision to those of dedicated oscillation experiments.Comment: 10 pages, 7 figure

Calibration and Characterization of the IceCube Photomultiplier Tube

Over 5,000 PMTs are being deployed at the South Pole to compose the IceCube neutrino observatory. Many are placed deep in the ice to detect Cherenkov light emitted by the products of high-energy neutrino interactions, and others are frozen into tanks on the surface to detect particles from atmospheric cosmic ray showers. IceCube is using the 10-inch diameter R7081-02 made by Hamamatsu Photonics. This paper describes the laboratory characterization and calibration of these PMTs before deployment. PMTs were illuminated with pulses ranging from single photons to saturation level. Parameterizations are given for the single photoelectron charge spectrum and the saturation behavior. Time resolution, late pulses and afterpulses are characterized. Because the PMTs are relatively large, the cathode sensitivity uniformity was measured. The absolute photon detection efficiency was calibrated using Rayleigh-scattered photons from a nitrogen laser. Measured characteristics are discussed in the context of their relevance to IceCube event reconstruction and simulation efforts.Comment: 40 pages, 12 figure

Search for Prompt Neutrino Emission from Gamma-Ray Bursts with IceCube

We present constraints derived from a search of four years of IceCube data for a prompt neutrino flux from gamma-ray bursts (GRBs). A single low-significance neutrino, compatible with the atmospheric neutrino background, was found in coincidence with one of the 506 observed bursts. Although GRBs have been proposed as candidate sources for ultra-high energy cosmic rays, our limits on the neutrino flux disfavor much of the parameter space for the latest models. We also find that no more than $\sim1\%$ of the recently observed astrophysical neutrino flux consists of prompt emission from GRBs that are potentially observable by existing satellites.Comment: 15 pages, 3 figure