Spatially explicit structural equation modeling

Structural equation modeling (SEM) is a powerful statistical approach for the testing of networks of direct and indirect theoretical causal relationships in complex data sets with intercorrelated dependent and independent variables. SEM is commonly applied in ecology, but the spatial information commonly found in ecological data remains difficult to model in a SEM framework. Here we propose a simple method for spatially explicit SEM (SE-SEM) based on the analysis of variance/covariance matrices calculated across a range of lag distances. This method provides readily interpretable plots of the change in path coefficients across scale and can be implemented using any standard SEM software package. We demonstrate the application of this method using three studies examining the relationships between environmental factors, plant community structure, nitrogen fixation, and plant competition. By design, these data sets had a spatial component, but were previously analyzed using standard SEM models. Using these data sets, we demonstrate the application of SE-SEM to regularly spaced, irregularly spaced, and ad hoc spatial sampling designs and discuss the increased inferential capability of this approach compared with standard SEM. We provide an R package, sesem, to easily implement spatial structural equation modeling.

Secondary structure element alignment kernel method for prediction of protein structural classes

In this paper, we aim at predicting protein structural classes for low-homology data sets based on predicted secondary structures. We propose a new and simple kernel method, named as SSEAKSVM, to predict protein structural classes. The secondary structures of all protein sequences are obtained by using the tool PSIPRED and then a linear kernel on the basis of secondary structure element alignment scores is constructed for training a support vector machine classifier without parameter adjusting. Our method SSEAKSVM was evaluated on two low-homology datasets 25PDB and 1189 with sequence homology being 25% and 40%, respectively. The jackknife test is used to test and compare our method with other existing methods. The overall accuracies on these two data sets are 86.3% and 84.5%, respectively, which are higher than those obtained by other existing methods. Especially, our method achieves higher accuracies (88.1% and 88.5%) for differentiating the α + β class and the α/β class compared to other methods. This suggests that our method is valuable to predict protein structural classes particularly for low-homology protein sequences. The source code of the method in this paper can be downloaded at http://math.xtu.edu.cn/myphp/math/research/source/SSEAK_source_code.rar.

Evolution of a ~2.7 Ga large igneous province: A volcanological, geochemical and geochronological study of the Agnew Greenstone Belt, and new regional correlations for the Kalgoorlie Terrane (Yilgarn Craton, Western Australia)

The thick package of ~2.7 Ga mafic and ultramafic lavas and intrusions preserved among the Neoarchean of the Kalgoorlie Terrene in Western Australia provides valuable insight into geological processes controlling the most prodigious episode of growth and preservation of juvenile continental crust in Earth’s history. Limited exposure of these rocks results in uncertainty about their age, physical and chemical characteristics, and stratigraphic relationships. This in turn prevents confident correlation of regional occurrences of mafic and ultramafic successions (both intrusive and extrusive) and hinders the interpretation of tectonic setting and magmatic evolution. A recent stratigraphic drilling program of the Neoarchean stratigraphy of the Agnew Greenstone Belt in Western Australia has provided continuous exposures through a c. 7 km thick sequence of mafic and ultramafic units. In this study, we present a volcanological, lithogeochemical and chronological study of the Agnew Greenstone Belt, and provide the first pre-2690 Ma regional correlation across the Kalgoorlie Terrane. The Agnew Greenstone Belt records ~30 m.y. of episodic ultramafic-mafic magmatism that includes two cycles, each defined by a komatiite that is overlain by units that become more evolved and contaminated with time. The sequence is divided into nine conformable packages, each consisting of stacked subaqueous lava flows and comagmatic intrusions, as well as two sills without associated extrusions. Lavas, with the exception of intercalations between two units, form a layer-cake stratigraphy and were likely erupted from a system of fissures tapping the same magma source. The komatiites are not contaminated by continental crust ([La/Sm]PM ~0.7) and are of the Al-undepleted Munro-type. Crustal contamination is evident in many units (Songvang Basalt, Never Can Tell Basalt, Redeemer Basalt, and Turrett Dolerite), as judged by [La/Sm]>1, negative Nb and Ti anomalies, and geochemical mixing trends towards felsic contaminants. Crystal fractionation was also significant, with early olivine and chromite (Mg#>65) followed by plagioclase and clinopyroxene removal (Mg<65), and in the most evolved case, titanomagnetite accumulation. Three new TIMS dates on granophyric zones of mafic sills and one ICP-MS date from an interflow felsic tuff are presented and used for regional stratigraphic correlation. Cycle I magmatism began at ~2720 Ma and ended ~2705 Ma, whereas cycle II began ~2705 Ma and ended at 2690.7±1.2 Ma. Regional correlations indicate the western Kalgoorlie Terrane consists of a remarkably similar stratigraphy that can be recognised at Agnew, Ora Banda and Coolgardie, whereas the eastern part of the terrane (e.g., Kambalda Domain) does not include cycle I, but correlates well with cycle II. This research supports an autochthonous model of greenstone formation, in which one large igneous province, represented by two complete cycles, is constructed on sialic crust. New stratigraphic correlations for the Kalgoorlie Terrane indicate that many units can be traced over distances >100 km, which has implications for exploration targeting for stratigraphically hosted ultramafic Ni and VMS deposits.

Evolution of multivariant microstructures with anisotropic misfit: A phase field study

We study, in two dimensions, the effect of misfit anisotropy on microstructural evolution during precipitation of an ordered beta phase from a disordered alpha matrix; these phases have, respectively, 2- and 6-fold rotation symmetries. Thus, precipitation produces three orientational variants of beta phase particles, and they have an anisotropic (and crystallographically equivalent) misfit strain with the matrix. The anisotropy in misfit is characterized using a parameter t = epsilon(yy)/epsilon(xx), where epsilon(xx) and epsilon(yy) are the principal components of the misfit strain tensor. Our phase field, simulations show that the morphology of beta phase particles is significantly influenced by 1, the level of misfit anisotropy. Particles are circular in systems with dilatational misfit (t = 1), elongated along the direction of lower principal misfit when 0 < t < 1 and elongated along the invariant direction when - 1 <= t <= 0. In the special case of a pure shear misfit strain (t = - 1), the microstructure exhibits star, wedge and checkerboard patterns; these microstructural features are in agreement with those in Ti-Al-Nb alloys.

Nonlinear Enzyme Kinetics Can Lead to High Metabolic Flux Control Coefficients: Implications for the Evolution of Dominance

In a classic study, Kacser & Burns (1981, Genetics 97, 639-666) demonstrated that given certain plausible assumptions, the flux in a metabolic pathway was more or less indifferent to the activity of any of the enzymes in the pathway taken singly. It was inferred from this that the observed dominance of most wild-type alleles with respect to loss-of-function mutations did not require an adaptive, meaning selectionist, explanation. Cornish-Bowden (1987, J. theor. Biol. 125, 333-338) showed that the Kacser-Burns inference was not valid when substrate concentrations were large relative to the relevant Michaelis constants. We find that in a randomly constructed functional pathway, even when substrate levels are small, one can expect high values of control coefficients for metabolic flux in the presence of significant nonlinearities as exemplified by enzymes with Hill coefficients ranging from two to six, or by the existence of oscillatory loops. Under these conditions the flux can be quite sensitive to changes in enzyme activity as might be caused by inactivating one of the two alleles in a diploid. Therefore, the phenomenon of dominance cannot be a trivial ''default'' consequence of physiology but must be intimately linked to the manner in which metabolic networks have been moulded by natural selection.

Structural and lithium ion transport studies in sol-gel-prepared lithium silicophosphate glasses

Lithium silicophosphate glasses have been prepared by a sol-gel route over a wide range of compositions. Their structural and electrical properties have been investigated. Infrared spectroscopic studies show the presence of hydroxyl groups attached to Si and P. MAS NMR investigations provide evidence for the presence of different phosphatic units in the structure. The variations of de conductivities at 423 K and activation energies have been studied as a function of composition, and both exhibit an increasing trend with the ratio of nonbridging oxygen to bridging oxygen in the structure. Ac conductivity behavior shows that the power law exponent, s, is temperature dependent and exhibits a minimum. Relaxation behavior has been examined in detail using an electrical modulus formalism, and modulus data were fitted to Kohlraush-William-Watts stretched exponential function. A structural model has been proposed and the unusual properties exhibited by this unique system of glasses have been rationalized using this model. Ion transport in these glasses appears to be confined to unidimensional conduits defined by modified phosphate chains and interspersed with unmodified silica units.

Structural correlations in GexSe1-x glasses - a neutron diffraction study

Neutron diffraction measurement is carried out on GexSe1-x glasses, where 0.1 less than or equal to x less than or equal to 0.4, in a Q interval of 0.55-13.8 Angstrom(-1). The first sharp diffraction peak (FSDP) in the structure factor, S(Q), shows a systematic increase in the intensity and shifts to a lower Q with increasing Ge concentration. The coherence length of FSDP increases with x and becomes maximum for 0.33 less than or equal to x less than or equal to 0.4. The Monte-Carlo method, due to Soper, is used to generate S(Q) and also the pair correlation function, g(r). The generated S(Q) is in agreement with the experimental data for all x. Analysis of the first four peaks in the total correlation function, T(r), shows that the short range order in GeSe2 glass is due to Ge(Se-1/2)(4) tetrahedra, in agreement with earlier reports. Se-rich glasses contain Se-chains which are cross-linked with Ge(Se-1/2)(4) tetrahedra. Ge-2(Se-1/2)(6) molecular units are the basic structural units in Ge-rich, x = 0.4, glass. For x = 0.2, 0.33 and 0.4 there is evidence for some of the tetrahedra being in an edge-shared configuration. The number of edge-shared tetrahedra in these glasses increase with increasing Ge content.

Finite volume evolution Galerkin method for hyperbolic conservation laws with spatially varying flux functions

We present a generalization of the finite volume evolution Galerkin scheme [M. Lukacova-Medvid'ova,J. Saibertov'a, G. Warnecke, Finite volume evolution Galerkin methods for nonlinear hyperbolic systems, J. Comp. Phys. (2002) 183 533-562; M. Luacova-Medvid'ova, K.W. Morton, G. Warnecke, Finite volume evolution Galerkin (FVEG) methods for hyperbolic problems, SIAM J. Sci. Comput. (2004) 26 1-30] for hyperbolic systems with spatially varying flux functions. Our goal is to develop a genuinely multi-dimensional numerical scheme for wave propagation problems in a heterogeneous media. We illustrate our methodology for acoustic waves in a heterogeneous medium but the results can be generalized to more complex systems. The finite volume evolution Galerkin (FVEG) method is a predictor-corrector method combining the finite volume corrector step with the evolutionary predictor step. In order to evolve fluxes along the cell interfaces we use multi-dimensional approximate evolution operator. The latter is constructed using the theory of bicharacteristics under the assumption of spatially dependent wave speeds. To approximate heterogeneous medium a staggered grid approach is used. Several numerical experiments for wave propagation with continuous as well as discontinuous wave speeds confirm the robustness and reliability of the new FVEG scheme.

Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families

Background: Disulphide bridges are well known to play key roles in stability, folding and functions of proteins. Introduction or deletion of disulphides by site-directed mutagenesis have produced varying effects on stability and folding depending upon the protein and location of disulphide in the 3-D structure. Given the lack of complete understanding it is worthwhile to learn from an analysis of extent of conservation of disulphides in homologous proteins. We have also addressed the question of what structural interactions replaces a disulphide in a homologue in another homologue. Results: Using a dataset involving 34,752 pairwise comparisons of homologous protein domains corresponding to 300 protein domain families of known 3-D structures, we provide a comprehensive analysis of extent of conservation of disulphide bridges and their structural features. We report that only 54% of all the disulphide bonds compared between the homologous pairs are conserved, even if, a small fraction of the non-conserved disulphides do include cytoplasmic proteins. Also, only about one fourth of the distinct disulphides are conserved in all the members in protein families. We note that while conservation of disulphide is common in many families, disulphide bond mutations are quite prevalent. Interestingly, we note that there is no clear relationship between sequence identity between two homologous proteins and disulphide bond conservation. Our analysis on structural features at the sites where cysteines forming disulphide in one homologue are replaced by non-Cys residues show that the elimination of a disulphide in a homologue need not always result in stabilizing interactions between equivalent residues. Conclusion: We observe that in the homologous proteins, disulphide bonds are conserved only to a modest extent. Very interestingly, we note that extent of conservation of disulphide in homologous proteins is unrelated to the overall sequence identity between homologues. The non-conserved disulphides are often associated with variable structural features that were recruited to be associated with differentiation or specialisation of protein function.

Synthesis, reactivity and structural characterisation of bicyclic tetraphosphapentazanes

The diphenoxy bicyclic tetraphosphapentazane derivatives (EtN)(5)P-4(OPh)(2) 2 and its monoxide (EtN)(5)P-4(O)(OPh)(2) 3 have been prepared. Both 2 and 3 exist as a mixture of two isomers. One isomer of (EtN)(5)P-4(O)(OPh)(2) 3a has been isolated and its reaction with tetrachloro-1,2-benzoquinone yielded (EtN)(5)P-4(O)(OPh)(2)(O2C6Cl4) 5 in which the junction phosphorus atom becomes five-co-ordinated. Treatment of 2 or 3a with [Mo(CO)(4)(nbd)] (nbd = norbornadiene, bicyclo[2.2.1]hepta-2,5-diene), on the other hand, yielded the chelate complex [Mo(CO)(4){(EtN)(5)P-4(O)(n)(OPh)(2)}] (n = 0 or 1; 6 or 7) in which the peripheral phosphorus atoms are bonded to the metal. The structures of 3a and 5-7 have been confirmed by single-crystal X-ray diffraction studies. The two P3N3 rings in 3a and 5 adopt twist/twist and irregular/twist conformations respectively; the phenoxy substituents occupy the 'pseudo axial' positions. However, an ideal chair conformation is observed for the P3N3 rings in 6 and 7 with the phenoxy substituents taking up the 'pseudo equatorial' positions. The NMR spectroscopic data for the compounds are discussed.

Unoccupied electronic states in NiS2-xSex across the metal-insulator transition

We investigate the evolution of the electronic structure across the insulator-metal transition in NiS2-xSex with changing composition, but in the absence of any structural or magnetic changes. A comparison of the inverse photoemission spectra with band-structure calculations establishes the importance of correlation effects in these systems. Systematic changes in the spectral distribution establish the persistence of the upper Hubbard band well into the metallic regime, with the insulator-to-metal transition being driven by a transfer of spectral weight from the Hubbard band to states close to the Fermi energy.

Micropillar compression studies on a bulk metallic glass in different structural states

Uniaxial compression experiments on 0.3, 1 and 3 mu m diameter micropillars of a Zr-based bulk metallic glass in as-cast, shot-peened and structurally relaxed conditions were conducted. Shear band formation and stable propagation is observed to be the plastic deformation mode in all cases, with no detectable difference in yield strength according to either size or condition. The limitations of uniaxial compression tests in assessing the influence of various material conditions on plasticity, when it is inhomogeneous in nature, are illustrated.

Thermal evolution of the submonolayer near-surface alloy of ZnPd on Pd (111)

We have performed a high-resolution synchrotron radiation photoelectron spectroscopy study of the initial growth stages of the ZnPd near-surface alloy on Pd(111), complemented by scanning tunnelling microscopy data. We show that the chemical environment for surfaces containing less than half of one monolayer of Zn is chemically distinct from subsequent layers. Surfaces where the deposition is performed at room temperature contain ZnPd islands surrounded by a substrate with dilute Zn substitutions. Annealing these surfaces drives the Zn towards the substrate top-layer, and favours the completion of the first 1 : 1 monolayer before the onset of growth in the next layer.

Boundary element analysis of reinforced concrete structural elements

A simple and practical technique for the discrete representation of reinforcement in two-dimensional boundary element analysis of reinforced concrete structural elements is presented. The bond developed over the surface of contact between the reinforcing steel and concrete is represented using fictitious one-dimensional spring elements. Potentials of the model developed are demonstrated using a number of numerical examples. The results are seen to be in good agreement with the results obtained using standard finite element software.

Structural characteristics of a giant tropical liana and its mode of canopy spread in an alien environment

To circumvent the practical difficulties in research on tropical rainforest lianas in their natural habitat due to prevailing weather conditions, dense camouflaging vegetation and problems in transporting equipment for experimental investigations, Entada pursaetha DC (syn. Entada scandens Benth., Leguminosae) was grown inside a research campus in a dry subtropical environment. A solitary genet has attained a gigantic size in 17 years, infesting crowns of semi-evergreen trees growing in an area roughly equivalent to 1.6 ha. It has used aerially formed, cable-like stolons for navigating and spreading its canopy across tree gaps. Some of its parts which had remained unseen in its natural habitat due to dense vegetation are described. The attained size of this liana in a climatically different environment raises the question as to why it is restricted to evergreen rainforests. Some research problems for which this liana will be useful are pointed out.