Sequence analysis and distribution of an IS3-like insertion element isolated from Salmonella enteritidis

The nucleotide sequence of a 3 kb region immediately upstream of the sef operon operon of Salmonella enteritidis was determined. A 1230 base pair insertion sequence which shared sequence identity (> 75%) with members of the IS3 family was revealed. This element, designated IS1230, had almost identical (90% identity) terminal inverted repeats to Escherichia coli IS3 but unlike other IS3-like sequences lacked the two characteristic open reading frames which encode the putative transposase. S. enteritidis possessed only one copy of this insertion sequence although Southern hybridisation analysis of restriction digests of genomic DNA revealed another fragment located in a region different from the sef operon which hybridised weakly which suggested the presence of an IS1230 homologue. The distribution of IS1230 and IS1230-like elements was shown to be widespread amongst salmonellas and the patterns of restriction fragments which hybridised differed significantly between Salmonella serotypes and it is suggested that IS1230 has potential for development as a differential diagnostic tool.

Oxygen isotope ratios in the shell of Mytilus edulis: archives of glacier meltwater in Greenland?

Melting of the Greenland Ice Sheet (GrIS) is accelerating and will contribute significantly to global sea level rise during the 21st century. Instrumental data on GrIS melting only cover the last few decades, and proxy data extending our knowledge into the past are vital for validating models predicting the influence of ongoing climate change. We investigated a potential meltwater proxy in Godthåbsfjord (West Greenland), where glacier meltwater causes seasonal excursions with lower oxygen isotope water (δ18Ow) values and salinity. The blue mussel (Mytilus edulis) potentially records these variations, because it precipitates its shell calcite in oxygen isotopic equilibrium with ambient seawater. As M. edulis shells are known to occur in raised shorelines and archaeological shell middens from previous Holocene warm periods, this species may be ideal in reconstructing past meltwater dynamics. We investigate its potential as a palaeo-meltwater proxy. First, we confirmed that M. edulis shell calcite oxygen isotope (δ18Oc) values are in equilibrium with ambient water and generally reflect meltwater conditions. Subsequently we investigated if this species recorded the full range of δ18Ow values occurring during the years 2007 to 2010. Results show that δ18Ow values were not recorded at very low salinities (< ~ 19), because the mussels appear to cease growing. This implies that Mytilus edulis δ18Oc values are suitable in reconstructing past meltwater amounts in most cases, but care has to be taken that shells are collected not too close to a glacier, but rather in the mid-region or mouth of the fjord. The focus of future research will expand on the geographical and temporal range of the shell measurements by sampling mussels in other fjords in Greenland along a south–north gradient, and by sampling shells from raised shorelines and archaeological shell middens from prehistoric settlements in Greenland.

Co3(SO4)3(OH)2[enH2]: a newS= 3/2 Kagome-type layered sulfate with a unique connectivity

The Kagome lattice, comprising a two-dimensional array of corner-sharing equilateral triangles, is central to the exploration of magnetic frustration. In such a lattice, antiferromagnetic coupling between ions in triangular plaquettes prevents all of the exchange interactions being simultaneously satisfied and a variety of novel magnetic ground states may result at low temperature. Experimental realization of a Kagome lattice remains difficult. The jarosite family of materials of nominal composition AM3(SO4)2(OH)6 (A = monovalent cation; M= Fe3+, Cr3+), offers perhaps one of the most promising manifestations of the phenomenon of magnetic frustration in two dimensions. The magnetic properties of jarosites are however extremely sensitive to the degree of coverage of magnetic sites. Consequently, there is considerable interest in the use of soft chemical techniques for the design and synthesis of novel materials in which to explore the effects of spin, degree of site coverage and connectivity on magnetic frustration.

First order k-th moment finite element analysis of nonlinear operator equations with stochastic data

We develop and analyze a class of efficient Galerkin approximation methods for uncertainty quantification of nonlinear operator equations. The algorithms are based on sparse Galerkin discretizations of tensorized linearizations at nominal parameters. Specifically, we consider abstract, nonlinear, parametric operator equations J(\alpha ,u)=0 for random input \alpha (\omega ) with almost sure realizations in a neighborhood of a nominal input parameter \alpha _0. Under some structural assumptions on the parameter dependence, we prove existence and uniqueness of a random solution, u(\omega ) = S(\alpha (\omega )). We derive a multilinear, tensorized operator equation for the deterministic computation of k-th order statistical moments of the random solution's fluctuations u(\omega ) - S(\alpha _0). We introduce and analyse sparse tensor Galerkin discretization schemes for the efficient, deterministic computation of the k-th statistical moment equation. We prove a shift theorem for the k-point correlation equation in anisotropic smoothness scales and deduce that sparse tensor Galerkin discretizations of this equation converge in accuracy vs. complexity which equals, up to logarithmic terms, that of the Galerkin discretization of a single instance of the mean field problem. We illustrate the abstract theory for nonstationary diffusion problems in random domains.

A high frequency $hp$ boundary element method for scattering by convex polygons

In this paper we propose and analyze a hybrid $hp$ boundary element method for the solution of problems of high frequency acoustic scattering by sound-soft convex polygons, in which the approximation space is enriched with oscillatory basis functions which efficiently capture the high frequency asymptotics of the solution. We demonstrate, both theoretically and via numerical examples, exponential convergence with respect to the order of the polynomials, moreover providing rigorous error estimates for our approximations to the solution and to the far field pattern, in which the dependence on the frequency of all constants is explicit. Importantly, these estimates prove that, to achieve any desired accuracy in the computation of these quantities, it is sufficient to increase the number of degrees of freedom in proportion to the logarithm of the frequency as the frequency increases, in contrast to the at least linear growth required by conventional methods.

Gradient recovery in adaptive finite-element methods for parabolic problems

We derive energy-norm a posteriori error bounds, using gradient recovery (ZZ) estimators to control the spatial error, for fully discrete schemes for the linear heat equation. This appears to be the �rst completely rigorous derivation of ZZ estimators for fully discrete schemes for evolution problems, without any restrictive assumption on the timestep size. An essential tool for the analysis is the elliptic reconstruction technique.Our theoretical results are backed with extensive numerical experimentation aimed at (a) testing the practical sharpness and asymptotic behaviour of the error estimator against the error, and (b) deriving an adaptive method based on our estimators. An extra novelty provided is an implementation of a coarsening error "preindicator", with a complete implementation guide in ALBERTA in the appendix.

A finite element method for nonlinear elliptic problems

We present a Galerkin method with piecewise polynomial continuous elements for fully nonlinear elliptic equations. A key tool is the discretization proposed in Lakkis and Pryer, 2011, allowing us to work directly on the strong form of a linear PDE. An added benefit to making use of this discretization method is that a recovered (finite element) Hessian is a byproduct of the solution process. We build on the linear method and ultimately construct two different methodologies for the solution of second order fully nonlinear PDEs. Benchmark numerical results illustrate the convergence properties of the scheme for some test problems as well as the Monge–Amp`ere equation and the Pucci equation.

A finite element method for second order nonvariational elliptic problems

We propose a numerical method to approximate the solution of second order elliptic problems in nonvariational form. The method is of Galerkin type using conforming finite elements and applied directly to the nonvariational (nondivergence) form of a second order linear elliptic problem. The key tools are an appropriate concept of “finite element Hessian” and a Schur complement approach to solving the resulting linear algebra problem. The method is illustrated with computational experiments on three linear and one quasi-linear PDE, all in nonvariational form.

Arrays of chiral nanotubes and a layered coordination polymer containing gallium-sulfide supertetrahedral clusters

We report here a unique chiral hybrid gallium sulfide, [NC2H8]2[Ga10S16(N2C12H12)(NC2H7)2] 1, consisting of helical chains of organically-functionalised supertetrahedral clusters which form quadruple-stranded helical nanotubes of ca. 3 nm diameter. This material therefore consists of discrete metal-organic nanotubes which, to the best of our knowledge, are extremely rare. Whilst solvothermal reactions involving 1,2-di(4-pyridyl)ethylene (DPE) resulted in the formation of such single-walled chiral nanotubes, the use of longer 4,4’-trimethylenedipyridine (TMP) ligands resulted in the synthesis of a two-dimensional hybrid gallium sulfide, [C5H6N]3[Ga10S16(OH)(N2C13H14)] 2 in which, for the first time, inorganic and organic linkages between supertetrahedral clusters coexist.

A finite element-spherical harmonics model for radiative transfer in inhomogeneous clouds. Part II. some applications

EVENT has been used to examine the effects of 3D cloud structure, distribution, and inhomogeneity on the scattering of visible solar radiation and the resulting 3D radiation field. Large eddy simulation and aircraft measurements are used to create realistic cloud fields which are continuous or broken with smooth or uneven tops. The values, patterns and variance in the resulting downwelling and upwelling radiation from incident visible solar radiation at different angles are then examined and compared to measurements. The results from EVENT confirm that 3D cloud structure is important in determining the visible radiation field, and that these results are strongly influenced by the solar zenith angle. The results match those from other models using visible solar radiation, and are supported by aircraft measurements of visible radiation, providing confidence in the new model.