Hidden breakpoints in genome alignments

During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain and loss occurs in addition to other types of rearrangement, breakpoints of rearrangement can exist that are only detectable by comparison of three or more genomes. An arbitrarily large number of these "hidden" breakpoints can exist among genomes that exhibit no rearrangements in pairwise comparisons. We present an extension of the multichromosomal breakpoint median problem to genomes that have undergone gene gain and loss. We then demonstrate that the median distance among three genomes can be used to calculate a lower bound on the number of hidden breakpoints present. We provide an implementation of this calculation including the median distance, along with some practical improvements on the time complexity of the underlying algorithm. We apply our approach to measure the abundance of hidden breakpoints in simulated data sets under a wide range of evolutionary scenarios. We demonstrate that in simulations the hidden breakpoint counts depend strongly on relative rates of inversion and gene gain/loss. Finally we apply current multiple genome aligners to the simulated genomes, and show that all aligners introduce a high degree of error in hidden breakpoint counts, and that this error grows with evolutionary distance in the simulation. Our results suggest that hidden breakpoint error may be pervasive in genome alignments.Comment: 13 pages, 4 figure

The Fractionary Schr\"{o}dinger Equation, Green Functions and Ultradistributions

In this work, we generalize previous results about the Fractionary Schr\"{o}dinger Equation within the formalism of the theory of Tempered Ultradistributions. Several examples of the use of this theory are given. In particular we evaluate the Green's function for a free particle in the general case, for an arbitrary order of the derivative index.Comment: 32 pages. No figure

The Frequency Dependent Conductivity of Electron Glasses

Results of DC and frequency dependent conductivity in the quantum limit, i.e. hw > kT, for a broad range of dopant concentrations in nominally uncompensated, crystalline phosphorous doped silicon and amorphous niobium-silicon alloys are reported. These materials fall under the general category of disordered insulating systems, which are referred to as electron glasses. Using microwave resonant cavities and quasi-optical millimeter wave spectroscopy we are able to study the frequency dependent response on the insulating side of the metal-insulator transition. We identify a quantum critical regime, a Fermi glass regime and a Coulomb glass regime. Our phenomenological results lead to a phase diagram description, or taxonomy, of the electrodynamic response of electron glass systems

Desulfurization of Dibenzothiophene by Pseudomonas fluorescens (UCP 1514) Leading to the Production of Biphenyl

Dibenzothiophene (DBT) is a typical recalcitrant thiophenic sulfur component of fuels, and its desulphurization has been a model reaction in the treatment of these compounds. Based on this information, the potential of Pseudomonas fluorescens (UCP 1514) on the desulfurization of dibenzothiphene was studied, in order to use it for reducing the sulfur content of diesel oil in compliance with environmental regulations. The result of biodegradation by the bacteria was determined by undertaking high-performance liquid chromatography of the metabolites produced. These can also be identified by gas chromatography with a mass spectrometry detector, and doing so revealed a sulfur-free product, biphenyl, as the final product of the degradation process. The results showed a decrease of 73% in dibenzothiophene content, which means that P. fluorescens removes sulfur from dibenzothiophene with a good selectivity to form biphenyl. These promising results indicate that P. fluorescens has an interesting potential to degrade sulfur-containing compounds in diesel oil and thereby could help in removing sulfur content from diesel oil. The process of microbial desulfurization described herein can be used particularly after carrying out hydrodesulfurization. Consequently, the sulfur content could be reduced even further. Applying P. fluorescens UCP 1514 in dibenzothiophene could help to understand the nature of the biodegradation process and to achieve the regulatory standards for sulfur level in fossil fuels

High frequency oscillations during magnetar flares

The recent discovery of high frequency oscillations during giant flares from the Soft Gamma Repeaters SGR 1806-20 and SGR 1900+14 may be the first direct detection of vibrations in a neutron star crust. If this interpretation is correct it offers a novel means of testing the neutron star equation of state, crustal breaking strain, and magnetic field configuration. We review the observational data on the magnetar oscillations, including new timing analysis of the SGR 1806-20 giant flare using data from the Ramaty High Energy Solar Spectroscopic Imager (RHESSI) and the Rossi X-ray Timing Explorer (RXTE). We discuss the implications for the study of neutron star structure and crust thickness, and outline areas for future investigation.Comment: 5 pages, 1 figure, to appear in the proceedings of the conference "Isolated Neutron Stars: from the Interior to the Surface" (April 2006, London), eds. D. Page, R. Turolla, & S. Zane, Astrophysics & Space Science in pres

New strings for old Veneziano amplitudes II. Group-theoretic treatment

In this part of our four parts work (e.g see Part I, hep-th/0410242) we use the theory of polynomial invariants of finite pseudo-reflection groups in order to reconstruct both the Veneziano and Veneziano-like (tachyon-free) amplitudes and the generating function reproducing these amplitudes. We demonstrate that such generating function can be recovered with help of the finite dimensional exactly solvable N=2 supersymmetric quantum mechanical model known earlier from works by Witten, Stone and others. Using the Lefschetz isomorphisms theorem we replace traditional supersymmetric calculations by the group-theoretic thus solving the Veneziano model exactly using standard methods of representation theory. Mathematical correctness of our arguments relies on important theorems by Shepard and Todd, Serre and Solomon proven respectively in early fifties and sixties and documented in the monograph by Bourbaki. Based on these theorems we explain why the developed formalism leaves all known results of conformal field theories unchanged. We also explain why these theorems impose stringent requirements connecting analytical properties of scattering amplitudes with symmetries of space-time in which such amplitudes act.Comment: 57 pages J.Geom.Phys.(in press, available on line

Multimessenger astronomy with the Einstein Telescope

Gravitational waves (GWs) are expected to play a crucial role in the development of multimessenger astrophysics. The combination of GW observations with other astrophysical triggers, such as from gamma-ray and X-ray satellites, optical/radio telescopes, and neutrino detectors allows us to decipher science that would otherwise be inaccessible. In this paper, we provide a broad review from the multimessenger perspective of the science reach offered by the third generation interferometric GW detectors and by the Einstein Telescope (ET) in particular. We focus on cosmic transients, and base our estimates on the results obtained by ET's predecessors GEO, LIGO, and Virgo.Comment: 26 pages. 3 figures. Special issue of GRG on the Einstein Telescope. Minor corrections include

Quantifying stratospheric biases and identifying their potential sources in subseasonal forecast systems

The stratosphere can be a source of predictability for surface weather on timescales of several weeks to months. However, the potential predictive skill gained from stratospheric variability can be limited by biases in the representation of stratospheric processes and the coupling of the stratosphere with surface climate in forecast systems. This study provides a first systematic identification of model biases in the stratosphere across a wide range of subseasonal forecast systems. It is found that many of the forecast systems considered exhibit warm global-mean temperature biases from the lower to middle stratosphere, too strong/cold wintertime polar vortices, and too cold extratropical upper-troposphere/lowerstratosphere regions. Furthermore, tropical stratospheric anomalies associated with the Quasi-Biennial Oscillation tend to decay toward each system¿s climatology with lead time. In the Northern Hemisphere (NH), most systems do not capture the seasonal cycle of extreme-vortex-event probabilities, with an underestimation of sudden stratospheric warming events and an overestimation of strong vortex events in January. In the Southern Hemisphere (SH), springtime interannual variability in the polar vortex is generally underestimated, but the timing of the final breakdown of the polar vortex often happens too early in many of the prediction systems. These stratospheric biases tend to be considerably worse in systems with lower model lid heights. In both hemispheres, most systems with low-top atmospheric models also consistently underestimate the upward wave driving that affects the strength of the stratospheric polar vortex. We expect that the biases identified here will help guide model development for subseasonal-to-seasonal forecast systems and further our understanding of the role of the stratosphere in predictive skill in the troposphere.This work uses S2S Project data. S2S is a joint initiative of the World Weather Research Programme (WWRP) and the World Climate Research Programme (WCRP). This work was initiated by the Stratospheric Network for the Assessment of Predictability (SNAP), a joint activity of SPARC (WCRP) and the S2S Project (WWRP–WCRP). The work of Rachel W.-Y. Wu is funded through ETH grant ETH-05 19-1. Support from the Swiss National Science Foundation through projects PP00P2_170523 and PP00P2_198896 to Daniela I. V. Domeisen is gratefully acknowledged. Chaim I. Garfinkel and Chen Schwartz are supported by the ISF–NSFC joint research program (grant no. 3259/19). The work of Marisol Osman was supported by UBACyT20020170100428BA and PICT-2018-03046 projects. The work of Alvaro de la Cámara is funded by the Spanish Ministry of Science and Innovation through project PID2019-109107GB-I00. Blanca Ayarzagüena and Natalia Calvo acknowledge the support of the Spanish Ministry of Science and Innovation through the JeDiS (RTI2018-096402-B-I00) project. Froila M. Palmeiro and Javier García-Serrano have been partially supported by the Spanish ATLANTE project (PID2019-110234RB-C21) and Ramón y Cajal program (RYC-2016-21181), respectively. Neil P. Hindley and Corwin J. Wright are supported by UK Natural Environment Research Council (NERC), grant number NE/S00985X/1. Corwin J. Wright is also supported by a Royal Society University Research Fellowship UF160545. Seok-Woo Son and Hera Kim are supported by the Basic Science Research Program through the National Research Foundation of Korea (2017R1E1A1A01074889). This material is based upon work supported by the US Department of Energy, Office of Science, Office of Biological and Environmental Research (BER), Regional and Global Model Analysis (RGMA) component of the Earth and Environmental System Modeling program under award no. DE-SC0022070 and National Science Foundation (NSF) IA 1947282. This work was also supported by the National Center for Atmospheric Research (NCAR), which is a major facility sponsored by the NSF under cooperative agreement no. 1852977. Pu Lin is supported by award NA18OAR4320123 from the National Oceanic and Atmospheric Administration (NOAA), U.S. Department of Commerce. Zachary D. Lawrence was partially supported under NOAA award NA20NWS4680051; Zachary D. Lawrence and Judith Perlwitz also acknowledge support from US federally appropriated funds