Folding and unfolding phylogenetic trees and networks

Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any phylogenetic network $N$ can be "unfolded" to obtain a MUL-tree $U(N)$ and, conversely, a MUL-tree $T$ can in certain circumstances be "folded" to obtain a phylogenetic network $F(T)$ that exhibits $T$. In this paper, we study properties of the operations $U$ and $F$ in more detail. In particular, we introduce the class of stable networks, phylogenetic networks $N$ for which $F(U(N))$ is isomorphic to $N$, characterise such networks, and show that they are related to the well-known class of tree-sibling networks.We also explore how the concept of displaying a tree in a network $N$ can be related to displaying the tree in the MUL-tree $U(N)$. To do this, we develop a phylogenetic analogue of graph fibrations. This allows us to view $U(N)$ as the analogue of the universal cover of a digraph, and to establish a close connection between displaying trees in $U(N)$ and reconcilingphylogenetic trees with networks

High-field Electron Spin Resonance of Cu_{1-x}Zn_{x}GeO_{3}

High-Field Electron Spin Resonance measurements were made on powder samples of Cu_{1-x}Zn_{x}GeO_{3} (x=0.00, 0.01, 0.02, 0.03 and 0.05) at different frequencies (95, 110, 190, 220, 330 and 440 GHz) at low temperatures. The spectra of the doped samples show resonances whose positions are dependent on Zn concentration, frequency and temperature. The analysis of intensity variation of these lines with temperature allows us to identify them as originating in transitions within states situated inside the Spin Peierls gap. A qualitative explanation of the details of the spectra is possible if we assume that these states in the gap are associated with "loose" spins created near the Zn impurities, as recently theoreticaly predicted. A new phenomenon of quenching of the ESR signal across the Dimerized to Incommensurate phase-boundary is observed.Comment: 4 pages, 5 ps figures in the text, submitted to Phys. Rev. Let

Stochastic processes, galactic star formation, and chemical evolution. Effects of accretion, stripping, and collisions in multiphase multi-zone models

This paper reports simulations allowing for stochastic accretion and mass loss within closed and open systems modeled using a previously developed multi-population, multi-zone (halo, thick disk, thin disk) treatment. The star formation rate is computed as a function of time directly from the model equations and all chemical evolution is followed without instantaneous recycling. Several types of simulations are presented here: (1) a closed system with bursty mass loss from the halo to the thick disk, and from the thick to the thin disk, in separate events to the thin disk; (2) open systems with random environmental (extragalactic) accretion, e.g. by infall of high velocity clouds directly to the thin disk; (3) schematic open system single and multiple collision events and intracluster stripping. For the open models, the mass of the Galaxy has been explicitly tracked with time. We present the evolution of the star formation rate, metallicity histories, and concentrate on the light elements. We find a wide range of possible outcomes, including an explanation for variations in the Galactic D/H ratio, and highlight the problems for uniquely reconstructing star forming histories from contemporary abundance measurements.Comment: 12 pages, 12 Postscript figures, uses A&A style macros. Accepted for publication by Astronomy & Astrophysic

A study of the deep structure of the energy landscape of glassy polystyrene: the exponential distribution of the energy-barriers revealed by high-field Electron Spin Resonance spectroscopy

The reorientation of one small paramagnetic molecule (spin probe) in glassy polystyrene (PS) is studied by high-field Electron Spin Resonance spectroscopy at two different Larmor frequencies (190 and 285 GHz). The exponential distribution of the energy-barriers for the rotational motion of the spin probe is unambigously evidenced at both 240K and 270K. The same shape for the distribution of the energy-barriers of PS was evidenced by the master curves provided by previous mechanical and light scattering studies. The breadth of the energy-barriers distribution of the spin probe is in the range of the estimates of the breadth of the PS energy-barriers distribution. The evidence that the deep structure of the energy landscape of PS exhibits the exponential shape of the energy-barriers distribution agrees with results from extreme-value statistics and the trap model by Bouchaud and coworkers.Comment: Final version in press as Letter to the Editor on J.Phys.:Condensed Matter. Changes in bol

Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets

Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set T of binary binets or trinets over a taxon set X, and constructing such a network whenever it exists. We show that this is NP-hard for trinets but polynomial-time solvable for binets. Moreover, we show that the problem is still polynomial-time solvable for inputs consisting of binets and trinets as long as the cycles in the trinets have size three. Finally, we present an O(3^{|X|} poly(|X|)) time algorithm for general sets of binets and trinets. The latter two algorithms generalise to instances containing level-1 networks with arbitrarily many leaves, and thus provide some of the first supernetwork algorithms for computing networks from a set of rooted 1 phylogenetic networks

A Novel Mutation in the Upstream Open Reading Frame of the CDKN1B Gene Causes a MEN4 Phenotype

PubMed ID: 23555276This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Measurement of the Branching Fraction of the Decay B+→π+π−ℓ+νℓ\boldsymbol{B^{+}\to\pi^{+}\pi^{-}\ell^{+}\nu_\ell} in Fully Reconstructed Events at Belle

We present an analysis of the exclusive $B^{+}\to\pi^{+}\pi^{-}\ell^{+}\nu_{\ell}$ decay, where $\ell$ represents an electron or a muon, with the assumption of charge-conjugation symmetry and lepton universality. The analysis uses the full $\Upsilon(4S)$ data sample collected by the Belle detector, corresponding to 711 fb$^{-1}$ of integrated luminosity. We select the events by fully reconstructing one $B$ meson in hadronic decay modes, subsequently determining the properties of the other $B$ meson. We extract the signal yields using a binned maximum-likelihood fit to the missing-mass squared distribution in bins of the invariant mass of the two pions or the momentum transfer squared. We measure a total branching fraction of ${{\cal B}(B^{+}\to \pi^{+}\pi^{-}\ell^{+}\nu_{\ell})= [22.7 ^{+1.9}_{-1.6} (\mathrm{stat}) \pm 3.5(\mathrm{syst}) ]\times 10^{-5}}$, where the uncertainties are statistical and systematic, respectively. This result is the first reported measurement of this decay.Comment: 23 pages, 19 figure

Hypoxia induces dilated cardiomyopathy in the chick embryo: mechanism, intervention, and long-term consequences

Background: Intrauterine growth restriction is associated with an increased future risk for developing cardiovascular diseases. Hypoxia in utero is a common clinical cause of fetal growth restriction. We have previously shown that chronic hypoxia alters cardiovascular development in chick embryos. The aim of this study was to further characterize cardiac disease in hypoxic chick embryos. Methods: Chick embryos were exposed to hypoxia and cardiac structure was examined by histological methods one day prior to hatching (E20) and at adulthood. Cardiac function was assessed in vivo by echocardiography and ex vivo by contractility measurements in isolated heart muscle bundles and isolated cardiomyocytes. Chick embryos were exposed to vascular endothelial growth factor (VEGF) and its scavenger soluble VEGF receptor-1 (sFlt-1) to investigate the potential role of this hypoxia-regulated cytokine. Principal Findings: Growth restricted hypoxic chick embryos showed cardiomyopathy as evidenced by left ventricular (LV) dilatation, reduced ventricular wall mass and increased apoptosis. Hypoxic hearts displayed pump dysfunction with decreased LV ejection fractions, accompanied by signs of diastolic dysfunction. Cardiomyopathy caused by hypoxia persisted into adulthood. Hypoxic embryonic hearts showed increases in VEGF expression. Systemic administration of rhVEGF165 to normoxic chick embryos resulted in LV dilatation and a dose-dependent loss of LV wall mass. Lowering VEGF levels in hypoxic embryonic chick hearts by systemic administration of sFlt-1 yielded an almost complete normalization of the phenotype. Conclusions/Significance: Our data show that hypoxia causes a decreased cardiac performance and cardiomyopathy in chick embryos, involving a significant VEGF-mediated component. This cardiomyopathy persists into adulthood

Observation of an alternative χc0(2P)\chi_{c0}(2P) candidate in e+e−→J/ψDDˉe^+ e^- \rightarrow J/\psi D \bar{D}

We perform a full amplitude analysis of the process $e^+ e^- \rightarrow J/\psi D \bar{D}$, where $D$ refers to either $D^0$ or $D^+$. A new charmoniumlike state $X^*(3860)$ that decays to $D \bar{D}$ is observed with a significance of $6.5\sigma$. Its mass is ($3862^{+26}_{-32}{}^{+40}_{-13}$) MeV/$c^2$ and width is ($201^{+154}_{-67}{}^{+88}_{-82}$) MeV. The $J^{PC}=0^{++}$ hypothesis is favored over the $2^{++}$ hypothesis at the level of $2.5\sigma$. The analysis is based on the 980 $\mathrm{fb}^{-1}$ data sample collected by the Belle detector at the asymmetric-energy $e^+ e^-$ collider KEKB.Comment: 17 pages, 11 figure