Almost all human genes resulted from ancient duplication

Results of protein sequence comparison at open criterion show a very large number of relationships that have, up to now, gone unreported. The relationships suggest many ancient events of gene duplication. It is well known that gene duplication has been a major process in the evolution of genomes. A collection of human genes that have known functions have been examined for a history of gene duplications detected by means of amino acid sequence similarity by using BLASTp with an expectation of two or less (open criterion). Because the collection of genes in build 35 includes sets of transcript variants, all genes of known function were collected, and only the longest transcription variant was included, yielding a 13,298-member library called KGMV (for known genes maximum variant). When all lengths of matches are accepted, >97% of human genes show significant matches to each other. Many form matches with a large number of other different proteins, showing that most genes are made up from parts of many others as a result of ancient events of duplication. To support the use of the open criterion, all of the members of the KGMV library were twice replaced with random protein sequences of the same length and average composition, and all were compared with each other with BLASTp at expectation two or less. The set of matches averaged 0.35% of that observed for the KGMV set of proteins

County-Specific Net Migration by Five-Year Age Groups, Hispanic Origin, Race and Sex 2000-2010

This report documents the methodology used to prepare county-level, net migration estimates by five-year age cohorts and sex, and by race and Hispanic origin, for the intercensal period from 2000 to 2010. The estimates were prepared using a vital statistics version of the forward cohort residual method (Siegel and Hamilton 1952) following the techniques used to prepare the 1990 to 2000 net migration estimates (Voss, McNiven, Johnson, Hammer, and Fuguitt 2004) as described in detail below. These numbers (and the net migration rates derivable from them) extend the set of decennial estimates of net migration that have been produced following each decennial census beginning with 1960 (net migration for the 1950s: Bowles and Tarver, 1965; 1960s: Bowles, Beale and Lee, 1975; 1970s: White, Mueser and Tierney, 1987; 1980s: Fuguitt, Beale, and Voss 2010; and 1990s: Voss, McNiven, Hammer, Johnson and Fuguitt, 2004)

Comparisons between Nimbus 6 satellite and rawinsonde soundings for several geographical areas

Good agreement between satellite and weighted (linearly interpolated) rawinsonde temperature and temperature derived parameters was found in most instances with the poorest agreement either near the tropopause region or near the ground. However, satellite moisture data are highly questionable. The smallest discrepancy between satellite and weighted mean rawinsonde temperature and parameters derived from temperature was found over water and the largest discrepancy was found over mountains. Cumulative frequency distributions show that discrepancies between satellite and rawinsonde data can be represented by a normal distribution except for dew point temperature

Advanced biofuel technologies : status and barriers

Large-scale production of crop based (first generation) biofuels may not be feasible without adversely affecting global food supply or encroaching on other important land uses. Because alternatives to liquid fossil fuels are important to develop in order to address greenhouse gas mitigation and other energy policy objectives, the potential for increased use of advanced (non-crop, second generation) biofuel production technologies has significant policy relevance. This study reviews the current status ofseveral advanced biofuel technologies. Technically, it would be possible to produce a large portion of transportation fuels using advanced biofuel technologies, specifically those that can be grown using a small portion of the world's land area (for example, microalgae), or those grown on arable lands without affecting food supply (for example, agricultural residues). However, serious technical barriers limit the near-term commercial application of advanced biofuels technologies. Key technical barriers include low conversion efficiency from biomass to fuel, limits on supply of key enzymes used in conversion, large energy requirements for operation, and dependence in many cases on commercially unproven technology. Despite a large future potential, large-scale expansion of advanced biofuels technologies is unlikely unless and until further research and development lead to lowering these barriers.Energy Production and Transportation,Climate Change Mitigation and Green House Gases,Renewable Energy,Crops&Crop Management Systems,Sanitation and Sewerage

Average-Atom Model for X-ray Scattering from Warm Dense Matter

A scheme for analyzing Thomson scattering of x-rays by warm dense matter, based on the average-atom model, is developed. Emphasis is given to x-ray scattering by bound electrons. Contributions to the scattered x-ray spectrum from elastic scattering by electrons moving with the ions and from inelastic scattering by free and bound electrons are evaluated using parameters (chemical potential, average ionic charge, free electron density, bound and continuum wave functions, and occupation numbers) taken from the average-atom model. The resulting scheme provides a relatively simple diagnostic for use in connection with x-ray scattering measurements. Applications are given to dense hydrogen, beryllium, aluminum, titanium, and tin plasmas. At high momentum transfer, contributions from inelastic scattering by bound electrons are dominant features of the scattered x-ray spectrum for aluminum, titanium, and tin.Comment: 22 pages, 10 figures Presentation at Workshop IV: Computational Challenges in Warm Dense Matter at IPAM (UCLA) May 21 - 25, 201

Using the X-FEL to understand X-ray Thomson scattering for partially ionized plasmas

For the last decade numerous researchers have been trying to develop experimental techniques to use X-ray Thomson scattering as a method to measure the temperature, electron density, and ionization state of high energy density plasmas such as those used in inertial confinement fusion. With the advent of the X-ray free electron laser (X-FEL) at the SLAC Linac Coherent Light Source (LCLS) we now have such a source available in the keV regime. One challenge with X-ray Thomson scattering experiments is understanding how to model the scattering for partially ionized plasmas. Most Thomson scattering codes used to model experimental data greatly simplify or neglect the contributions of the bound electrons to the scattered intensity. In this work we take the existing models of Thomson scattering that include elastic ion-ion scattering and the electron-electron plasmon scattering and add the contribution of the bound electrons in the partially ionized plasmas. Except for hydrogen plasmas almost every plasma that is studied today has bound electrons and it is important to understand their contribution to the Thomson scattering, especially as new X-ray sources such as the X-FEL will allow us to study much higher Z plasmas. Currently most experiments have looked at hydrogen or beryllium. We will first look at the bound electron contributions to beryllium by analysing existing experimental data. We then consider several higher Z materials such as Cr and predict the existence of additional peaks in the scattering spectrum that requires new computational tools to understand. For a Sn plasma we show that the bound contributions changes the shape of the scattered spectrum in a way that would change the plasma temperature and density inferred by the experiment.Comment: 13th International Conference on X-ray Lasers Paris, France June 10, 2012 through June 15, 201

Haar expectations of ratios of random characteristic polynomials

We compute Haar ensemble averages of ratios of random characteristic polynomials for the classical Lie groups K = O(N), SO(N), and USp(N). To that end, we start from the Clifford-Weyl algebera in its canonical realization on the complex of holomorphic differential forms for a C-vector space V. From it we construct the Fock representation of an orthosymplectic Lie superalgebra osp associated to V. Particular attention is paid to defining Howe's oscillator semigroup and the representation that partially exponentiates the Lie algebra representation of sp in osp. In the process, by pushing the semigroup representation to its boundary and arguing by continuity, we provide a construction of the Shale-Weil-Segal representation of the metaplectic group. To deal with a product of n ratios of characteristic polynomials, we let V = C^n \otimes C^N where C^N is equipped with its standard K-representation, and focus on the subspace of K-equivariant forms. By Howe duality, this is a highest-weight irreducible representation of the centralizer g of Lie(K) in osp. We identify the K-Haar expectation of n ratios with the character of this g-representation, which we show to be uniquely determined by analyticity, Weyl group invariance, certain weight constraints and a system of differential equations coming from the Laplace-Casimir invariants of g. We find an explicit solution to the problem posed by all these conditions. In this way we prove that the said Haar expectations are expressed by a Weyl-type character formula for all integers N \ge 1. This completes earlier work by Conrey, Farmer, and Zirnbauer for the case of U(N).Comment: LaTeX, 70 pages, Complex Analysis and its Synergies (2016) 2: