Novel Papillomaviruses in Free-Ranging Iberian Bats: No Virus-Host Co-evolution, No Strict Host Specificity, and Hints for Recombination

Papillomaviruses (PVs) are widespread pathogens. However, the extent of PV infections in bats remains largely unknown. This work represents the first comprehensive study of PVs in Iberian bats. We identified four novel PVs in the mucosa of free-ranging Eptesicus serotinus (EserPV1, EserPV2, and EserPV3) and Rhinolophus ferrumequinum (RferPV1) individuals and analyzed their phylogenetic relationships within the viral family. We further assessed their prevalence in different populations of E. serotinus and its close relative E. isabellinus. Although it is frequent to read that PVs co-evolve with their host, that PVs are highly species-specific, and that PVs do not usually recombine, our results suggest otherwise. First, strict virus-host co-evolution is rejected by the existence of five, distantly related bat PV lineages and by the lack of congruence between bats and bat PVs phylogenies. Second, the ability of EserPV2 and EserPV3 to infect two different bat species (E. serotinus and E. isabellinus) argues against strict host specificity. Finally, the description of a second noncoding region in the RferPV1 genome reinforces the view of an increased susceptibility to recombination in the E2-L2 genomic region. These findings prompt the question of whether the prevailing paradigms regarding PVs evolution should be reconsidered.

Measures of tuna abundance from purse-seine operations in the Eastern Pacific Ocean, adjusted for fleet-wide evolution of increased fishing power, 1960-1971

ENGLISH: The fishing power of the tuna purse-seine fleet of the eastern Pacific Ocean has increased since the early 1960's. Because the entire fleet seems to have adopted equipment and techniques to increase its efficiency in capturing tunas, traditional methods of adjusting catch rates to a reference vessel type of fixed efficiency to index tuna abundance from fishing success are inapplicable. Instead, a methodology for such adjustment based on a mathematical representation of purse seining activities is developed. Observed changes in efficiency in subprocesses of purse seining are then used to adjust catch rates when computing abundance histories for yellowfin and skipjack in large regions of the eastern Pacific Ocean. SPANISH: La eficacia de pesca de la flota de cerco atunera en el Océano Pacífico oriental ha aumentado desde el comienzo del decenio de 1960. Como toda la flota parece haber adoptado equipo y métodos para incrementar su eficaciaen capturar atunes, no se pueden aplicar los métodos tradicionales de ajustar los índices de captura a un tipo normalizado de barco (es decir de eficacia fija) para indicar la abundancia del atún según los resultados de pesca. En su lugar se ha desarrollado un método para realizar tal ajuste basado en una representación matemática de las actividades de las embarcaciones de cerco. Cuando se calcula la abundancia histórica del atún aleta amarilla y barrilete en grandes regiones del Océano Pacífico oriental, se usan entonces los cambios observados en la eficacia de los subprocesos cerqueros para ajustar los índices de captura. (PDF contains 120 pages.)

Atomistic Simulation On Size-Dependent Yield Strength And Defects Evolution Of Metal Nanowires

A simple derivation based on continuum mechanics is given, which shows the surface stress is critical for yield strength at ultra-small scales. Molecular dynamics (MD) simulations with modified embedded atom method (MEAM) are employed to investigate the mechanical behaviors of single-crystalline metal nanowires under tensile loading. The calculated yield strengths increasing with the decrease of the cross-sectional area of the nanowires are in accordance with the theoretical prediction. Reorientation induced by stacking faults is observed at the nanowire edge. In addition. the mechanism of yielding is discussed in details based on the snapshots of defects evolution. The nanowires in different crystallographic orientations behave differently in stretching deformation. This study on the plastic properties of metal nanowires will be helpful to further understanding of the mechanical properties of nanomaterials. (C) 2009 Elsevier B.V. All rights reserved.

Long-Term Evolution Of Delayed Ettringite And Gypsum In Portland Cement Mortars Under Sulfate Erosion

The magnitude evolution of ettringite and gypsum in hydrated Portland cement mortars due to sulfate attack was detected by X-ray powder diffraction. The influences of sulfate concentration and water-to-cement ratio on the evolution of ettringite and gypsum were investigated. Experimental results show that the magnitude of ettringite formation in sodium sulfate solution follows a three-stage process, namely, the 'penetration period', 'enhance period of strength', and 'macro-crack period'. The cracking of concrete materials is mainly attributed to the effect of ettringite. The gypsum formations occurred in two stages, the 'latent period' and the 'accelerated period'. The gypsum formation including ettringite formation was relative to the linear expansion of mortars to some extend. Both water-to-cement ratio and sulfate concentration play important roles in the evolution of ettringite and gypsum. (C) 2008 Elsevier Ltd. All rights reserved.

Generating artificial homologous proteins according to the representative family character in molecular mechanics properties - an attempt in validating an underlying rule of protein evolution

The molecular mechanics property is the foundation of many characters of proteins. Based on intramolecular hydrophobic force network, the representative family character underlying a protein’s mechanics property is described by a simple two-letter scheme. The tendency of a sequence to become a member of a protein family is scored according to this mathematical representation. Remote homologs of the WW-domain family could be easily designed using such a mechanistic signature of protein homology. Experimental validation showed that nearly all artificial homologs have the representative folding and bioactivity of their assigned family. Since the molecular mechanics property is the only consideration in this study, the results indicate its possible role in the generation of new members of a protein family during evolution.

Triangle Evolution-A Hybrid Heuristic for Global Optimization

Abstract This paper presents a hybrid heuristic{triangle evolution (TE) for global optimization. It is a real coded evolutionary algorithm. As in di®erential evolution (DE), TE targets each individual in current population and attempts to replace it by a new better individual. However, the way of generating new individuals is di®erent. TE generates new individuals in a Nelder- Mead way, while the simplices used in TE is 1 or 2 dimensional. The proposed algorithm is very easy to use and e±cient for global optimization problems with continuous variables. Moreover, it requires only one (explicit) control parameter. Numerical results show that the new algorithm is comparable with DE for low dimensional problems but it outperforms DE for high dimensional problems.

MODELING EVOLUTION OF INTERNAL WAVES IN SOUTH CHINA SEA

Internal waves are an important factor in the design of drill operations and production in deep water, because the waves have very large amplitude and may induce large horizontal velocity. How the internal waves occur and propagate over benthal terrain is of great concern for ocean engineers. In the present paper, we have formulated a mathematical model of internal wave propagation in a two-layer deep water, which involves the effects of friction, dissipation and shoaling, and is capable of manifesting the variation of the amplitude and the velocity pattern. After calibration by field data measured at the Continental Slope in the Northern South China Sea, we have applied the model to the South China Sea, investigating the westward propagation of internal waves from the Luzon Strait, where internal waves originate due to the interaction of benthal ridge and tides. We find that the internal wave induced velocity profile is obviously characterized by the opposite flow below and above the pycnocline, which results in a strong shear, threatening safety of ocean structures, such as mooring system of oil platform, risers, etc. When internal waves propagate westwards, the amplitude attenuates due to the effects of friction and dissipation. The preliminary results show that the amplitude is likely to become half of its initial value at Luzon Strait when the internal waves propagate about 400 kilometers westwards.

The stochastic exit problem for dynamical systems

The problem of "exit against a flow" for dynamical systems subject to small Gaussian white noise excitation is studied. Here the word "flow" refers to the behavior in phase space of the unperturbed system's state variables. "Exit against a flow" occurs if a perturbation causes the phase point to leave a phase space region within which it would normally be confined. In particular, there are two components of the problem of exit against a flow:

i) the mean exit time

ii) the phase-space distribution of exit locations.

When the noise perturbing the dynamical systems is small, the solution of each component of the problem of exit against a flow is, in general, the solution of a singularly perturbed, degenerate elliptic-parabolic boundary value problem.

Singular perturbation techniques are used to express the asymptotic solution in terms of an unknown parameter. The unknown parameter is determined using the solution of the adjoint boundary value problem.

The problem of exit against a flow for several dynamical systems of physical interest is considered, and the mean exit times and distributions of exit positions are calculated. The systems are then simulated numerically, using Monte Carlo techniques, in order to determine the validity of the asymptotic solutions.

I. Exact solution of some nonlinear evolution equations. II. The similarity solution for the Korteweg-De Vries equation and the related Painleve Transcendent

In Part I, a method for finding solutions of certain diffusive dispersive nonlinear evolution equations is introduced. The method consists of a straightforward iteration procedure, applied to the equation as it stands (in most cases), which can be carried out to all terms, followed by a summation of the resulting infinite series, sometimes directly and other times in terms of traces of inverses of operators in an appropriate space.

We first illustrate our method with Burgers' and Thomas' equations, and show how it quickly leads to the Cole-Hopft transformation, which is known to linearize these equations.

We also apply this method to the Korteweg and de Vries, nonlinear (cubic) Schrödinger, Sine-Gordon, modified KdV and Boussinesq equations. In all these cases the multisoliton solutions are easily obtained and new expressions for some of them follow. More generally we show that the Marcenko integral equations, together with the inverse problem that originates them, follow naturally from our expressions.

Only solutions that are small in some sense (i.e., they tend to zero as the independent variable goes to ∞) are covered by our methods. However, by the study of the effect of writing the initial iterate u_1 = u_(1)(x,t) as a sum u_1 = ^∼/u_1 + ^≈/u_1 when we know the solution which results if u_1 = ^∼/u_1, we are led to expressions that describe the interaction of two arbitrary solutions, only one of which is small. This should not be confused with Backlund transformations and is more in the direction of performing the inverse scattering over an arbitrary “base” solution. Thus we are able to write expressions for the interaction of a cnoidal wave with a multisoliton in the case of the KdV equation; these expressions are somewhat different from the ones obtained by Wahlquist (1976). Similarly, we find multi-dark-pulse solutions and solutions describing the interaction of envelope-solitons with a uniform wave train in the case of the Schrodinger equation.

Other equations tractable by our method are presented. These include the following equations: Self-induced transparency, reduced Maxwell-Bloch, and a two-dimensional nonlinear Schrodinger. Higher order and matrix-valued equations with nonscalar dispersion functions are also presented.

In Part II, the second Painleve transcendent is treated in conjunction with the similarity solutions of the Korteweg-de Vries equat ion and the modified Korteweg-de Vries equation.

Detailed properties of high redshift galaxies

Galaxies evolve throughout the history of the universe from the first star-forming sources, through gas-rich asymmetric structures with rapid star formation rates, to the massive symmetrical stellar systems observed at the present day. Determining the physical processes which drive galaxy formation and evolution is one of the most important questions in observational astrophysics. This thesis presents four projects aimed at improving our understanding of galaxy evolution from detailed measurements of star forming galaxies at high redshift.

We use resolved spectroscopy of gravitationally lensed z ≃ 2 - 3 star forming galaxies to measure their kinematic and star formation properties. The combination of lensing with adaptive optics yields physical resolution of ≃ 100 pc, sufficient to resolve giant Hii regions. We find that ~ 70 % of galaxies in our sample display ordered rotation with high local velocity dispersion indicating turbulent thick disks. The rotating galaxies are gravitationally unstable and are expected to fragment into giant clumps. The size and dynamical mass of giant Hii regions are in agreement with predictions for such clumps indicating that gravitational instability drives the rapid star formation. The remainder of our sample is comprised of ongoing major mergers. Merging galaxies display similar star formation rate, morphology, and local velocity dispersion as isolated sources, but their velocity fields are more chaotic with no coherent rotation.

We measure resolved metallicity in four lensed galaxies at z = 2.0 − 2.4 from optical emission line diagnostics. Three rotating galaxies display radial gradients with higher metallicity at smaller radii, while the fourth is undergoing a merger and has an inverted gradient with lower metallicity at the center. Strong gradients in the rotating galaxies indicate that they are growing inside-out with star formation fueled by accretion of metal-poor gas at large radii. By comparing measured gradients with an appropriate comparison sample at z = 0, we demonstrate that metallicity gradients in isolated galaxies must flatten at later times. The amount of size growth inferred by the gradients is in rough agreement with direct measurements of massive galaxies. We develop a chemical evolution model to interpret these data and conclude that metallicity gradients are established by a gradient in the outflow mass loading factor, combined with radial inflow of metal-enriched gas.

We present the first rest-frame optical spectroscopic survey of a large sample of low-luminosity galaxies at high redshift (L < L*, 1.5 < z < 3.5). This population dominates the star formation density of the universe at high redshifts, yet such galaxies are normally too faint to be studied spectroscopically. We take advantage of strong gravitational lensing magnification to compile observations for a sample of 29 galaxies using modest integration times with the Keck and Palomar telescopes. Balmer emission lines confirm that the sample has a median SFR ∼ 10 M_sun yr^−1 and extends to lower SFR than has been probed by other surveys at similar redshift. We derive the metallicity, dust extinction, SFR, ionization parameter, and dynamical mass from the spectroscopic data, providing the first accurate characterization of the star-forming environment in low-luminosity galaxies at high redshift. For the first time, we directly test the proposal that the relation between galaxy stellar mass, star formation rate, and gas phase metallicity does not evolve. We find lower gas phase metallicity in the high redshift galaxies than in local sources with equivalent stellar mass and star formation rate, arguing against a time-invariant relation. While our result is preliminary and may be biased by measurement errors, this represents an important first measurement that will be further constrained by ongoing analysis of the full data set and by future observations.

We present a study of composite rest-frame ultraviolet spectra of Lyman break galaxies at z = 4 and discuss implications for the distribution of neutral outflowing gas in the circumgalactic medium. In general we find similar spectroscopic trends to those found at z = 3 by earlier surveys. In particular, absorption lines which trace neutral gas are weaker in less evolved galaxies with lower stellar masses, smaller radii, lower luminosity, less dust, and stronger Lyα emission. Typical galaxies are thus expected to have stronger Lyα emission and weaker low-ionization absorption at earlier times, and we indeed find somewhat weaker low-ionization absorption at higher redshifts. In conjunction with earlier results, we argue that the reduced low-ionization absorption is likely caused by lower covering fraction and/or velocity range of outflowing neutral gas at earlier epochs. This result has important implications for the hypothesis that early galaxies were responsible for cosmic reionization. We additionally show that fine structure emission lines are sensitive to the spatial extent of neutral gas, and demonstrate that neutral gas is concentrated at smaller galactocentric radii in higher redshift galaxies.

The results of this thesis present a coherent picture of galaxy evolution at high redshifts 2 ≲ z ≲ 4. Roughly 1/3 of massive star forming galaxies at this period are undergoing major mergers, while the rest are growing inside-out with star formation occurring in gravitationally unstable thick disks. Star formation, stellar mass, and metallicity are limited by outflows which create a circumgalactic medium of metal-enriched material. We conclude by describing some remaining open questions and prospects for improving our understanding of galaxy evolution with future observations of gravitationally lensed galaxies.