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Sample records for complex kohn variational

  1. Improvements to the "STANDARD" Complex Kohn Variational Method: Towards the Development of AN "R-MATRIX Theory Without a BOX"

    NASA Astrophysics Data System (ADS)

    Rescigno, T. N.; McCurdy, C. W.

    The complex Kohn variational method is among the most successful ab initio techniques currently being used to study electron-molecule collisions. We review the essential features of the standard method and then discuss a few recent developments that allow us to relax some of the simplifying approximations that have been used in the past and reduce the size of the expansion basis sets needed for convergence. We also discuss an extension that allows one to evaluate scattering amplitudes as a continuous function of energy, much like R-matrix theory, but without the R-matrix "box".

  2. Complex Kohn calculations on an overset grid

    NASA Astrophysics Data System (ADS)

    Greenman, Loren; Lucchese, Robert; McCurdy, C. William

    2016-05-01

    An implentation of the overset grid method for complex Kohn scattering calculations is presented, along with static exchange calculations of electron-molecule scattering for small molecules including methane. The overset grid method uses multiple numerical grids, for instance Finite Element Method - Discrete Variable Representation (FEM-DVR) grids, expanded radially around multiple centers (corresponding to the individual atoms in each molecule as well as the center-of-mass of the molecule). The use of this flexible grid allows the complex angular dependence of the wavefunctions near the atomic centers to be well-described, but also allows scattering wavefunctions that oscillate rapidly at large distances to be accurately represented. Additionally, due to the use of multiple grids (and also grid shells), the method is easily parallelizable. The method has been implemented in ePolyscat, a multipurpose suite of programs for general molecular scattering calculations. It is interfaced with a number of quantum chemistry programs (including MolPro, Gaussian, GAMESS, and Columbus), from which it can read molecular orbitals and wavefunctions obtained using standard computational chemistry methods. The preliminary static exchange calculations serve as a test of the applicability.

  3. Generalization of the variational principle and the Hohenberg and Kohn theorems for excited states of Fermion systems

    NASA Astrophysics Data System (ADS)

    Gonis, A.

    2017-01-01

    Through the entanglement of a collection of K non-interacting replicas of a system of N interacting Fermions, and making use of the properties of reduced density matrices the variational principle and the theorems of Hohenberg and Kohn are generalized to excited states. The generalization of the variational principle makes use of the natural orbitals of an N-particle density matrix describing the state of lowest energy of the entangled state. The extension of the theorems of Hohenberg and Kohn is based on the ground-state formulation of density functional theory but with a new interpretation of the concept of a ground state: It is the state of lowest energy of a system of KN Fermions that is described in terms of the excited states of the N-particle interacting system. This straightforward implementation of the line of reasoning of ground-state density functional theory to a new domain leads to a unique and logically valid extension of the theory to excited states that allows the systematic treatment of all states in the spectrum of the Hamiltonian of an interacting system.

  4. Complex Correlation Kohn-T Method of Calculating Total and Elastic Cross Sections. Part 1; Electron-Hydrogen Elastic Scattering

    NASA Technical Reports Server (NTRS)

    Bhatia, A. K.; Temkin, A.; Fisher, Richard R. (Technical Monitor)

    2001-01-01

    We report on the first part of a study of electron-hydrogen scattering, using a method which allows for the ab initio calculation of total and elastic cross sections at higher energies. In its general form the method uses complex 'radial' correlation functions, in a (Kohn) T-matrix formalism. The titled method, abbreviated Complex Correlation Kohn T (CCKT) method, is reviewed, in the context of electron-hydrogen scattering, including the derivation of the equation for the (complex) scattering function, and the extraction of the scattering information from the latter. The calculation reported here is restricted to S-waves in the elastic region, where the correlation functions can be taken, without loss of generality, to be real. Phase shifts are calculated using Hylleraas-type correlation functions with up to 95 terms. Results are rigorous lower bounds; they are in general agreement with those of Schwartz, but they are more accurate and outside his error bounds at a couple of energies,

  5. The calculation of the contributions to low energy e+H2 scattering from sigma u+ and Pion u symmetries using the Kohn variational method

    NASA Technical Reports Server (NTRS)

    Armour, E. A. G.; Baker, D. J.; Plummer, M.

    1990-01-01

    Above incident energies of about 2 eV, the contribution to the total cross section in positron+H2 scattering from the sigma g+ symmetry is insufficient to account for the experimental value. Calculations carried out of the lowest partial waves of sigma u+ symmetry and Pion u symmetry using the Kohn variational method are described. The contributions to the total cross section from the two equivalent partial waves of Pion u symmetry significantly reduce the discrepancy with experiment up to incident energies of 4 to 5 eV. Comparisons are made with recent R-matrix calculations performed by Danby and Tennyson.

  6. Competition: Was Kohn Right?

    ERIC Educational Resources Information Center

    Shields, David Light; Bredemeier, Brenda Light

    2010-01-01

    Alfie Kohn made the case for competition being destructive to education. The truth may be that there are two separate ways to contest: true competition, which is a healthy desire to excel, and decompetition, which is the unhealthy desire merely to beat the opponent. Decompetition leads to the ills that Kohn enumerated. Educators should teach their…

  7. A ground-state-directed optimization scheme for the Kohn-Sham energy.

    PubMed

    Høst, Stinne; Jansík, Branislav; Olsen, Jeppe; Jørgensen, Poul; Reine, Simen; Helgaker, Trygve

    2008-09-21

    Kohn-Sham density-functional calculations are used in many branches of science to obtain information about the electronic structure of molecular systems and materials. Unfortunately, the traditional method for optimizing the Kohn-Sham energy suffers from fundamental problems that may lead to divergence or, even worse, convergence to an energy saddle point rather than to the ground-state minimum--in particular, for the larger and more complicated electronic systems that are often studied by Kohn-Sham theory nowadays. We here present a novel method for Kohn-Sham energy minimization that does not suffer from the flaws of the conventional approach, combining reliability and efficiency with linear complexity. In particular, the proposed method converges by design to a minimum, avoiding the sometimes spurious solutions of the traditional method and bypassing the need to examine the structure of the provided solution.

  8. Kohn singularity and Kohn anomaly in conventional superconductors--role of pairing mechanism.

    PubMed

    Chaudhury, Ranjan; Das, Mukunda P

    2013-03-27

    We present a theoretical analysis of the Kohn singularity and Kohn anomaly in the superconducting phase of a three-dimensional metallic system. We show that a phonon mechanism-based Cooper pairing in a Fermi liquid metal can lead to these phenomena quite naturally. The results are discussed against the background of some recent experimental findings.

  9. Tucker-tensor algorithm for large-scale Kohn-Sham density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Motamarri, Phani; Gavini, Vikram; Blesgen, Thomas

    2016-03-01

    In this work, we propose a systematic way of computing a low-rank globally adapted localized Tucker-tensor basis for solving the Kohn-Sham density functional theory (DFT) problem. In every iteration of the self-consistent field procedure of the Kohn-Sham DFT problem, we construct an additive separable approximation of the Kohn-Sham Hamiltonian. The Tucker-tensor basis is chosen such as to span the tensor product of the one-dimensional eigenspaces corresponding to each of the spatially separable Hamiltonians, and the localized Tucker-tensor basis is constructed from localized representations of these one-dimensional eigenspaces. This Tucker-tensor basis forms a complete basis, and is naturally adapted to the Kohn-Sham Hamiltonian. Further, the locality of this basis in real-space allows us to exploit reduced-order scaling algorithms for the solution of the discrete Kohn-Sham eigenvalue problem. In particular, we use Chebyshev filtering to compute the eigenspace of the Kohn-Sham Hamiltonian, and evaluate nonorthogonal localized wave functions spanning the Chebyshev filtered space, all represented in the Tucker-tensor basis. We thereby compute the electron-density and other quantities of interest, using a Fermi-operator expansion of the Hamiltonian projected onto the subspace spanned by the nonorthogonal localized wave functions. Numerical results on benchmark examples involving pseudopotential calculations suggest an exponential convergence of the ground-state energy with the Tucker rank. Interestingly, the rank of the Tucker-tensor basis required to obtain chemical accuracy is found to be only weakly dependent on the system size, which results in close to linear-scaling complexity for Kohn-Sham DFT calculations for both insulating and metallic systems. A comparative study has revealed significant computational efficiencies afforded by the proposed Tucker-tensor approach in comparison to a plane-wave basis.

  10. Crystallization of macromolecular complexes:. stoichiometric variation screening

    NASA Astrophysics Data System (ADS)

    Stura, Enrico A.; Graille, Marc; Taussig, Michael J.; Sutton, Brian; Gore, Michael G.; Silverman, Gregg J.; Charbonnier, Jean-Baptiste

    2001-11-01

    Theoretically a crystal may contain both complexed and uncomplexed molecules simultaneously in the same lattice. Since we seldom screen for such possibilities, such occurrences are only rarely reported. Here we propose that stoichiometry should be one of the parameters to be screened in the crystallization of macromolecular complexes. By allowing for non-biologically significant stoichiometries, we may increase the chances of crystallizing a macromolecular complex and of selecting arrangements which crystallize better or yield more ordered crystals. Although biological forces tend to be stronger than lattice-building interactions, in the crystal the latter will dominate numerically. By allowing for a varied stoichiometry we permit a wider selection of lattice-building contacts and increase the probability of crystallization. From these theoretical considerations we have developed methodology compatible with classical solubility screening and other well-established crystallization principles. We discuss this technique, stoichiometric variation screening (SVS), as part of a multicomponent system for the enhancement of crystallization of macromolecular complexes. We present this technique as an extension of reverse screening and illustrate the complementarity in the methodology. We present two examples of the use of SVS: the complexes between an immunoglobulin Fab fragment and two bacterial proteins, namely the D domain of protein A from Staphylococcus aureus (SpA) and a single domain of protein L from Peptostreptococcus magnus (PpL). In the first example there are 3 Fab molecules and only 2 SpA D domains (domD) (2 complexed and 1 unliganded Fab), in the second 2 Fabs and only 1 PpL domain (1 complexed and 1 unliganded Fab). SVS has the added and unique advantage that in the same crystal we have information on both the unliganded and complexed states under precisely identical conditions: one structure, two answers. Together with a combinatorial method for complex

  11. Kohn anomaly in phonon driven superconductors

    NASA Astrophysics Data System (ADS)

    Das, M. P.; Chaudhury, R.

    2014-08-01

    Anomalies often occur in the physical world. Sometimes quite unexpectedly anomalies may give rise to new insight to an unrecognized phenomenon. In this paper we shall discuss about Kohn anomaly in a conventional phonon-driven superconductor by using a microscopic approach. Recently Aynajian et al.'s experiment showed a striking feature; the energy of phonon at a particular wave-vector is almost exactly equal to twice the energy of the superconducting gap. Although the phonon mechanism of superconductivity is well known for many conventional superconductors, as has been noted by Scalapino, the new experimental results reveal a genuine puzzle. In our recent work we have presented a detailed theoretical analysis with the help of microscopic calculations to unravel this mystery. We probe this aspect of phonon behaviour from the properties of electronic polarizability function in the superconducting phase of a Fermi liquid metal, leading to the appearance of a Kohn singularity. We show the crossover to the standard Kohn anomaly of the normal phase for temperatures above the transition temperature. Our analysis provides a nearly complete explanation of this new experimentally discovered phenomenon. This report is a shorter version of our recent work in JPCM.

  12. On the Kohn-Luttinger conundrum

    SciTech Connect

    Hirata, So; He Xiao

    2013-05-28

    Kohn and Luttinger [Phys. Rev. 118, 41 (1960)] showed that the conventional finite-temperature extension of the second-order many-body perturbation theory had the incorrect zero-temperature limit in metals and, on this basis, argued that the theory was incorrect. We show that this inconsistency arises from the noninclusion of the temperature effect in the energies of the zeroth-order eigenstates of the perturbation theory, which causes not only the Kohn-Luttinger conundrum but also another inconsistency with the zero-temperature many-body perturbation theory, namely, the different rates of divergence of the correlation energy in a homogeneous electron gas (HEG). We propose a renormalized many-body perturbation theory derivable from the finite-temperature extension of the normal-ordered second quantization applied to the denominators of the energy expression, which involves the energies of the zeroth-order states, as well as to the numerators. The renormalized theory is shown to have the correct zero-temperature limit and the same rate of divergence in a HEG as the zero-temperature counterpart, and is, therefore, the correct finite-temperature many-body perturbation theory.

  13. Lie Conformal Algebra Cohomology and the Variational Complex

    NASA Astrophysics Data System (ADS)

    de Sole, Alberto; Kac, Victor G.

    2009-12-01

    We find an interpretation of the complex of variational calculus in terms of the Lie conformal algebra cohomology theory. This leads to a better understanding of both theories. In particular, we give an explicit construction of the Lie conformal algebra cohomology complex, and endow it with a structure of a {mathfrak{g}}-complex. On the other hand, we give an explicit construction of the complex of variational calculus in terms of skew-symmetric poly-differential operators.

  14. Time-dependent Kohn-Sham approach to quantum electrodynamics

    SciTech Connect

    Ruggenthaler, M.; Mackenroth, F.; Bauer, D.

    2011-10-15

    We prove a generalization of the van Leeuwen theorem toward quantum electrodynamics, providing the formal foundations of a time-dependent Kohn-Sham construction for coupled quantized matter and electromagnetic fields. We circumvent the symmetry-causality problems associated with the action-functional approach to Kohn-Sham systems. We show that the effective external four-potential and four-current of the Kohn-Sham system are uniquely defined and that the effective four-current takes a very simple form. Further we rederive the Runge-Gross theorem for quantum electrodynamics.

  15. Hohenberg-Kohn theorems in electrostatic and uniform magnetostatic fields

    SciTech Connect

    Pan, Xiao-Yin; Sahni, Viraht

    2015-11-07

    The Hohenberg-Kohn (HK) theorems of bijectivity between the external scalar potential and the gauge invariant nondegenerate ground state density, and the consequent Euler variational principle for the density, are proved for arbitrary electrostatic field and the constraint of fixed electron number. The HK theorems are generalized for spinless electrons to the added presence of an external uniform magnetostatic field by introducing the new constraint of fixed canonical orbital angular momentum. Thereby, a bijective relationship between the external scalar and vector potentials, and the gauge invariant nondegenerate ground state density and physical current density, is proved. A corresponding Euler variational principle in terms of these densities is also developed. These theorems are further generalized to electrons with spin by imposing the added constraint of fixed canonical orbital and spin angular momenta. The proofs differ from the original HK proof and explicitly account for the many-to-one relationship between the potentials and the nondegenerate ground state wave function. A Percus-Levy-Lieb constrained-search proof expanding the domain of validity to N-representable functions, and to degenerate states, again for fixed electron number and angular momentum, is also provided.

  16. Terrace width variations in complex lunar craters

    NASA Technical Reports Server (NTRS)

    Pearce, Steven J.; Melosh, H. J.

    1986-01-01

    The widths of terrace structures in complex craters on the moon are compared to existing theoretical models of their origin. Terrace widths in an individual crater increase monotonically outward toward the crater rim. Similarly, the width W of the terraces lying closest to the rim of a crater of diameter D increases monotonically, obeying a least-squares power-law relation WS (km) = 0.09D exp 0.87 km). A simple model of slumping that ignores inertial forces and assumes a constant bedrock yield strength is in good agreement with the observations.

  17. Explaining additional genetic variation in complex traits

    PubMed Central

    Robinson, Matthew R.; Wray, Naomi R.; Visscher, Peter M.

    2015-01-01

    Genome-wide association studies (GWAS) have provided valuable insights into the genetic basis of complex traits, discovering >6000 variants associated with >500 quantitative traits and common complex diseases in humans. The associations identified so far represent only a fraction of those which influence phenotype, as there are likely to be very many variants across the entire frequency spectrum, each of which influences multiple traits, with only a small average contribution to the phenotypic variance. This presents a considerable challenge to further dissection of the remaining unexplained genetic variance within populations, which limits our ability to predict disease risk, identify new drug targets, improve and maintain food sources, and understand natural diversity. This challenge will be met within the current framework through larger sample size, better phenotyping including recording of non-genetic risk factors, focused study designs, and an integration of multiple sources of phenotypic and genetic information. The current evidence supports the application of quantitative genetic approaches, and we argue that one should retain simpler theories until simplicity can be traded for greater explanatory power. PMID:24629526

  18. The role of variation, error, and complexity in manufacturing defects

    SciTech Connect

    Hinckley, C.M.; Barkan, P.

    1994-03-01

    Variation in component properties and dimensions is a widely recognized factor in product defects which can be quantified and controlled by Statistical Process Control methodologies. Our studies have shown, however, that traditional statistical methods are ineffective in characterizing and controlling defects caused by error. The distinction between error and variation becomes increasingly important as the target defect rates approach extremely low values. Motorola data substantiates our thesis that defect rates in the range of several parts per million can only be achieved when traditional methods for controlling variation are combined with methods that specifically focus on eliminating defects due to error. Complexity in the product design, manufacturing processes, or assembly increases the likelihood of defects due to both variation and error. Thus complexity is also a root cause of defects. Until now, the absence of a sound correlation between defects and complexity has obscured the importance of this relationship. We have shown that assembly complexity can be quantified using Design for Assembly (DFA) analysis. High levels of correlation have been found between our complexity measures and defect data covering tens of millions of assembly operations in two widely different industries. The availability of an easily determined measure of complexity, combined with these correlations, permits rapid estimation of the relative defect rates for alternate design concepts. This should prove to be a powerful tool since it can guide design improvement at an early stage when concepts are most readily modified.

  19. Natural Allelic Variations in Highly Polyploidy Saccharum Complex

    PubMed Central

    Song, Jian; Yang, Xiping; Resende, Marcio F. R.; Neves, Leandro G.; Todd, James; Zhang, Jisen; Comstock, Jack C.; Wang, Jianping

    2016-01-01

    Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWA-mem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes. PMID:27375658

  20. Natural Allelic Variations in Highly Polyploidy Saccharum Complex.

    PubMed

    Song, Jian; Yang, Xiping; Resende, Marcio F R; Neves, Leandro G; Todd, James; Zhang, Jisen; Comstock, Jack C; Wang, Jianping

    2016-01-01

    Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWA-mem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.

  1. Adaptive Finite Element Method for Solving the Exact Kohn-Sham Equation of Density Functional Theory

    SciTech Connect

    Bylaska, Eric J.; Holst, Michael; Weare, John H.

    2009-04-14

    Results of the application of an adaptive finite element (FE) based solution using the FETK library of M. Holst to Density Functional Theory (DFT) approximation to the electronic structure of atoms and molecules are reported. The severe problem associated with the rapid variation of the electronic wave functions in the near singular regions of the atomic centers is treated by implementing completely unstructured simplex meshes that resolve these features around atomic nuclei. This concentrates the computational work in the regions in which the shortest length scales are necessary and provides for low resolution in regions for which there is no electron density. The accuracy of the solutions significantly improved when adaptive mesh refinement was applied, and it was found that the essential difficulties of the Kohn-Sham eigenvalues equation were the result of the singular behavior of the atomic potentials. Even though the matrix representations of the discrete Hamiltonian operator in the adaptive finite element basis are always sparse with a linear complexity in the number of discretization points, the overall memory and computational requirements for the solver implemented were found to be quite high. The number of mesh vertices per atom as a function of the atomic number Z and the required accuracy e (in atomic units) was esitmated to be v (e;Z) = 122:37 * Z2:2346 /1:1173 , and the number of floating point operations per minimization step for a system of NA atoms was found to be 0(N3A*v(e,Z0) (e.g. Z=26, e=0.0015 au, and NA=100, the memory requirement and computational cost would be ~0.2 terabytes and ~25 petaflops). It was found that the high cost of the method could be reduced somewhat by using a geometric based refinement strategy to fix the error near the singularities.

  2. Must Kohn-Sham oscillator strengths be accurate at threshold?

    SciTech Connect

    Yang Zenghui; Burke, Kieron; Faassen, Meta van

    2009-09-21

    The exact ground-state Kohn-Sham (KS) potential for the helium atom is known from accurate wave function calculations of the ground-state density. The threshold for photoabsorption from this potential matches the physical system exactly. By carefully studying its absorption spectrum, we show the answer to the title question is no. To address this problem in detail, we generate a highly accurate simple fit of a two-electron spectrum near the threshold, and apply the method to both the experimental spectrum and that of the exact ground-state Kohn-Sham potential.

  3. Natural allelic variations in highly polyploidy Saccharum complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sugarcane (Saccharum spp.) as important sugar and biofuel crop are highly polypoid with complex genomes. A large amount of natural phenotypic variation exists in sugarcane germplasm. Understanding its allelic variance has been challenging but is a critical foundation for discovery of the genomic seq...

  4. Calculus structure on the Lie conformal algebra complex and the variational complex

    SciTech Connect

    De Sole, Alberto; Hekmati, Pedram; Kac, Victor G.

    2011-05-15

    We construct a calculus structure on the Lie conformal algebra cochain complex. By restricting to degree one chains, we recover the structure of a g-complex introduced in [A. De Sole and V. G. Kac, Commun. Math. Phys. 292, 667 (2009)]. A special case of this construction is the variational calculus, for which we provide explicit formulas.

  5. Complex variational mode decomposition for signal processing applications

    NASA Astrophysics Data System (ADS)

    Wang, Yanxue; Liu, Fuyun; Jiang, Zhansi; He, Shuilong; Mo, Qiuyun

    2017-03-01

    Complex-valued signals occur in many areas of science and engineering and are thus of fundamental interest. The complex variational mode decomposition (CVMD) is proposed as a natural and a generic extension of the original VMD algorithm for the analysis of complex-valued data in this work. Moreover, the equivalent filter bank structure of the CVMD in the presence of white noise, and the effects of initialization of center frequency on the filter bank property are both investigated via numerical experiments. Benefiting from the advantages of CVMD algorithm, its bi-directional Hilbert time-frequency spectrum is developed as well, in which the positive and negative frequency components are formulated on the positive and negative frequency planes separately. Several applications in the real-world complex-valued signals support the analysis.

  6. Extended variational theory of complex rays in heterogeneous Helmholtz problem

    NASA Astrophysics Data System (ADS)

    Li, Hao; Ladeveze, Pierre; Riou, Hervé

    2017-02-01

    In the past years, a numerical technique method called Variational Theory of Complex Rays (VTCR) has been developed for vibration problems in medium frequency. It is a Trefftz Discontinuous Galerkin method which uses plane wave functions as shape functions. However this method is only well developed in homogeneous case. In this paper, VTCR is extended to the heterogeneous Helmholtz problem by creating a new base of shape functions. Numerical examples give a scope of the performances of such an extension of VTCR.

  7. Major histocompatibility complex variation in the endangered Przewalski's horse.

    PubMed Central

    Hedrick, P W; Parker, K M; Miller, E L; Miller, P S

    1999-01-01

    The major histocompatibility complex (MHC) is a fundamental part of the vertebrate immune system, and the high variability in many MHC genes is thought to play an essential role in recognition of parasites. The Przewalski's horse is extinct in the wild and all the living individuals descend from 13 founders, most of whom were captured around the turn of the century. One of the primary genetic concerns in endangered species is whether they have ample adaptive variation to respond to novel selective factors. In examining 14 Przewalski's horses that are broadly representative of the living animals, we found six different class II DRB major histocompatibility sequences. The sequences showed extensive nonsynonymous variation, concentrated in the putative antigen-binding sites, and little synonymous variation. Individuals had from two to four sequences as determined by single-stranded conformation polymorphism (SSCP) analysis. On the basis of the SSCP data, phylogenetic analysis of the nucleotide sequences, and segregation in a family group, we conclude that four of these sequences are from one gene (although one sequence codes for a nonfunctional allele because it contains a stop codon) and two other sequences are from another gene. The position of the stop codon is at the same amino-acid position as in a closely related sequence from the domestic horse. Because other organisms have extensive variation at homologous loci, the Przewalski's horse may have quite low variation in this important adaptive region. PMID:10430594

  8. A complex Noether approach for variational partial differential equations

    NASA Astrophysics Data System (ADS)

    Naz, R.; Mahomed, F. M.

    2015-10-01

    Scalar complex partial differential equations which admit variational formulations are studied. Such a complex partial differential equation, via a complex dependent variable, splits into a system of two real partial differential equations. The decomposition of the Lagrangian of the complex partial differential equation in the real domain is shown to yield two real Lagrangians for the split system. The complex Maxwellian distribution, transonic gas flow, Maxwellian tails, dissipative wave and Klein-Gordon equations are considered. The Noether symmetries and gauge terms of the split system that correspond to both the Lagrangians are constructed by the Noether approach. In the case of coupled split systems, the same Noether symmetries are obtained. The Noether symmetries for the uncoupled split systems are different. The conserved vectors of the split system which correspond to both the Lagrangians are compared to the split conserved vectors of the complex partial differential equation for the examples. The split conserved vectors of the complex partial differential equation are the same as the conserved vectors of the split system of real partial differential equations in the case of coupled systems. Moreover a Noether-like theorem for the split system is proved which provides the Noether-like conserved quantities of the split system from knowledge of the Noether-like operators. An interesting result on the split characteristics and the conservation laws is shown as well. The Noether symmetries and gauge terms of the Lagrangian of the split system with the split Noether-like operators and gauge terms of the Lagrangian of the given complex partial differential equation are compared. Folklore suggests that the split Noether-like operators of a Lagrangian of a complex Euler-Lagrange partial differential equation are symmetries of the Lagrangian of the split system of real partial differential equations. This is not the case. They are proved to be the same if the

  9. Korringa-Kohn-Rostoker electronic structure method for space-filling cell potentials

    SciTech Connect

    Gonis, A.; Butler, W.H.; Zhang, X.-G.

    1991-12-31

    The multiple scattering theory (MST) method of Korringa, and of Kohn and Rostoker for determining the electronic structure of solids, originally developed in connection with potentials bounded by non-overlapping spheres (muffin-tin (MT) potentials), is generalized to the case of space-filling potential cells of arbitrary shape through the use of a variational formalism. This generalized version of MST retains the separability of structure and potential characteristic of the application of MST to MT potentials. However, in contrast to the MT case, different forms of MST exhibit different convergence rates for the energy and the wave function. Numerical results are presented which illustrate the differing convergence rates of the variational and nonvariational forms of MST for space-filling potentials.

  10. Exact Kohn-Sham potential of strongly correlated finite systems

    SciTech Connect

    Helbig, N.; Rubio, A.

    2009-12-14

    The dissociation of molecules, even the most simple hydrogen molecule, cannot be described accurately within density functional theory because none of the currently available functionals accounts for strong on-site correlation. This problem led to a discussion of properties that the local Kohn-Sham potential has to satisfy in order to correctly describe strongly correlated systems. We derive an analytic expression for the nontrivial form of the Kohn-Sham potential in between the two fragments for the dissociation of a single bond. We show that the numerical calculations for a one-dimensional two-electron model system indeed approach and reach this limit. It is shown that the functional form of the potential is universal, i.e., independent of the details of the two fragments.

  11. Calculus structure on the Lie conformal algebra complex and the variational complex

    NASA Astrophysics Data System (ADS)

    De Sole, Alberto; Hekmati, Pedram; Kac, Victor G.

    2011-05-01

    We construct a calculus structure on the Lie conformal algebra cochain complex. By restricting to degree one chains, we recover the structure of a {mathfrak g}-complex introduced in [A. De Sole and V. G. Kac, Commun. Math. Phys. 292, 667 (2009), 10.1007/s00220-009-0886-1]. A special case of this construction is the variational calculus, for which we provide explicit formulas.

  12. On the Kohn-Sham density response in a localized basis set

    NASA Astrophysics Data System (ADS)

    Foerster, Dietrich; Koval, Peter

    2009-07-01

    We construct the Kohn-Sham density response function χ0 in a previously described basis of the space of orbital products. The calculational complexity of our construction is O(N2Nω) for a molecule of N atoms and in a spectroscopic window of Nω frequency points. As a first application, we use χ0 to calculate the molecular spectra from the Petersilka-Gossmann-Gross equation. With χ0 as input, we obtain the correct spectra with an extra computational effort that grows also as O(N2Nω) and, therefore, less steeply in N than the O(N3) complexity of solving Casida's equations. Our construction should be useful for the study of excitons in molecular physics and in related areas where χ0 is a crucial ingredient.

  13. Schizophrenia risk from complex variation of complement component 4

    PubMed Central

    Sekar, Aswin; Bialas, Allison R.; de Rivera, Heather; Davis, Avery; Hammond, Timothy R.; Kamitaki, Nolan; Tooley, Katherine; Presumey, Jessy; Baum, Matthew; Van Doren, Vanessa; Genovese, Giulio; Rose, Samuel A.; Handsaker, Robert E.; Daly, Mark J.; Carroll, Michael C.; Stevens, Beth; McCarroll, Steven A.

    2016-01-01

    Schizophrenia is a heritable brain illness with unknown pathogenic mechanisms. Schizophrenia’s strongest genetic association at a population level involves variation in the Major Histocompatibility Complex (MHC) locus, but the genes and molecular mechanisms accounting for this have been challenging to recognize. We show here that schizophrenia’s association with the MHC locus arises in substantial part from many structurally diverse alleles of the complement component 4 (C4) genes. We found that these alleles promoted widely varying levels of C4A and C4B expression and associated with schizophrenia in proportion to their tendency to promote greater expression of C4A in the brain. Human C4 protein localized at neuronal synapses, dendrites, axons, and cell bodies. In mice, C4 mediated synapse elimination during postnatal development. These results implicate excessive complement activity in the development of schizophrenia and may help explain the reduced numbers of synapses in the brains of individuals affected with schizophrenia. PMID:26814963

  14. Schizophrenia risk from complex variation of complement component 4.

    PubMed

    Sekar, Aswin; Bialas, Allison R; de Rivera, Heather; Davis, Avery; Hammond, Timothy R; Kamitaki, Nolan; Tooley, Katherine; Presumey, Jessy; Baum, Matthew; Van Doren, Vanessa; Genovese, Giulio; Rose, Samuel A; Handsaker, Robert E; Daly, Mark J; Carroll, Michael C; Stevens, Beth; McCarroll, Steven A

    2016-02-11

    Schizophrenia is a heritable brain illness with unknown pathogenic mechanisms. Schizophrenia's strongest genetic association at a population level involves variation in the major histocompatibility complex (MHC) locus, but the genes and molecular mechanisms accounting for this have been challenging to identify. Here we show that this association arises in part from many structurally diverse alleles of the complement component 4 (C4) genes. We found that these alleles generated widely varying levels of C4A and C4B expression in the brain, with each common C4 allele associating with schizophrenia in proportion to its tendency to generate greater expression of C4A. Human C4 protein localized to neuronal synapses, dendrites, axons, and cell bodies. In mice, C4 mediated synapse elimination during postnatal development. These results implicate excessive complement activity in the development of schizophrenia and may help explain the reduced numbers of synapses in the brains of individuals with schizophrenia.

  15. Human copy number variation and complex genetic disease.

    PubMed

    Girirajan, Santhosh; Campbell, Catarina D; Eichler, Evan E

    2011-01-01

    Copy number variants (CNVs) play an important role in human disease and population diversity. Advancements in technology have allowed for the analysis of CNVs in thousands of individuals with disease in addition to thousands of controls. These studies have identified rare CNVs associated with neuropsychiatric diseases such as autism, schizophrenia, and intellectual disability. In addition, copy number polymorphisms (CNPs) are present at higher frequencies in the population, show high diversity in copy number, sequence, and structure, and have been associated with multiple phenotypes, primarily related to immune or environmental response. However, the landscape of copy number variation still remains largely unexplored, especially for smaller CNVs and those embedded within complex regions of the human genome. An integrated approach including characterization of single nucleotide variants and CNVs in a large number of individuals with disease and normal genomes holds the promise of thoroughly elucidating the genetic basis of human disease and diversity.

  16. Climatic variation and the distribution of an amphibian polyploid complex

    USGS Publications Warehouse

    Otto, C.R.V.; Snodgrass, J.W.; Forester, D.C.; Mitchell, J.C.; Miller, R.W.

    2007-01-01

    1. The establishment of polyploid populations involves the persistence and growth of the polyploid in the presence of the progenitor species. Although there have been a number of animal polyploid species documented, relatively few inquiries have been made into the large-scale mechanisms of polyploid establishment in animal groups. Herein we investigate the influence of regional climatic conditions on the distributional patterns of a diploid-tetraploid species pair of gray treefrogs, Hyla chrysoscelis and H. versicolor (Anura: Hylidae) in the mid-Atlantic region of eastern North America. 2. Calling surveys at breeding sites were used to document the distribution of each species. Twelve climatic models and one elevation model were generated to predict climatic and elevation values for gray treefrog breeding sites. A canonical analysis of discriminants was used to describe relationships between climatic variables, elevation and the distribution of H. chrysoscelis and H. versicolor. 3. There was a strong correlation between several climatic variables, elevation and the distribution of the gray treefrog complex. Specifically, the tetraploid species almost exclusively occupied areas of higher elevation, where climatic conditions were relatively severe (colder, drier, greater annual variation). In contrast, the diploid species was restricted to lower elevations, where climatic conditions were warmer, wetter and exhibited less annual variation. 4. Clusters of syntopic sites were associated with areas of high variation in annual temperature and precipitation during the breeding season. 5. Our data suggest that large-scale climatic conditions have played a role in the establishment of the polyploid H. versicolor in at least some portions of its range. The occurrence of the polyploid and absence of the progenitor in colder, drier and more varied environments suggests the polyploid may posses a tolerance of severe environmental conditions that is not possessed by the diploid

  17. Major histocompatibility complex variation in the Arabian oryx.

    PubMed

    Hedrick, P W; Parker, K M; Gutiérrez-Espeleta, G A; Rattink, A; Lievers, K

    2000-12-01

    In the 1960s, the Arabian oryx was one of the most endangered species in the world, extinct in the wild and surviving in only a few captive herds. The present day population of over 2000 descends from a small number of founders and may have restricted genetic variation for important adaptive genes. We have examined the amount of genetic variation for a class II gene in the major histocompatibility complex thought to be the most important genetic basis for pathogen resistance in vertebrates. We found three very divergent alleles, which on average, differed by 24 nucleotides and 15 amino acids in the 236-bp fragment we examined. Using single-strand conformation polymorphism, we found that in a sample of 57 animals, the alleles were in Hardy-Weinberg proportions, although one allele was found only in four heterozygous individuals. The average heterozygosity for the 22 amino acid positions involved in antigen binding was 0.165, three times as high as that for the 56 amino acids not involved with antigen binding. Because the three alleles have such divergent sequences, it is likely that they may recognize peptides from quite different pathogens. As a result, maintenance of these variants should be considered as a goal in the captive breeding program of the Arabian oryx.

  18. Element orbitals for Kohn-Sham density functional theory

    SciTech Connect

    Lin, Lin; Ying, Lexing

    2012-05-08

    We present a method to discretize the Kohn-Sham Hamiltonian matrix in the pseudopotential framework by a small set of basis functions automatically contracted from a uniform basis set such as planewaves. Each basis function is localized around an element, which is a small part of the global domain containing multiple atoms. We demonstrate that the resulting basis set achieves meV accuracy for 3D densely packed systems with a small number of basis functions per atom. The procedure is applicable to insulating and metallic systems.

  19. Asymptotic form of the Kohn-Sham correlation potential

    SciTech Connect

    Joubert, D. P.

    2007-07-15

    The density-functional correlation potential of a finite system is shown to asymptotically approach a nonzero constant along a nodal surface of the energetically highest occupied orbital and zero everywhere else. This nonuniform asymptotic form of the correlation potential exactly cancels the nonuniform asymptotic behavior of the exact exchange potential discussed by Della Sala and Goerling [Phys. Rev. Lett. 89, 33003 (2002)]. The sum of the exchange and correlation potentials therefore asymptotically tends to -1/r everywhere, consistent with the asymptotic form of the Kohn-Sham potential as analyzed by Almbladh and von Barth [Phys. Rev. B 31, 3231 (1985)].

  20. Structural genomic variation in childhood epilepsies with complex phenotypes

    PubMed Central

    Helbig, Ingo; Swinkels, Marielle E M; Aten, Emmelien; Caliebe, Almuth; van 't Slot, Ruben; Boor, Rainer; von Spiczak, Sarah; Muhle, Hiltrud; Jähn, Johanna A; van Binsbergen, Ellen; van Nieuwenhuizen, Onno; Jansen, Floor E; Braun, Kees P J; de Haan, Gerrit-Jan; Tommerup, Niels; Stephani, Ulrich; Hjalgrim, Helle; Poot, Martin; Lindhout, Dick; Brilstra, Eva H; Møller, Rikke S; Koeleman, Bobby PC

    2014-01-01

    A genetic contribution to a broad range of epilepsies has been postulated, and particularly copy number variations (CNVs) have emerged as significant genetic risk factors. However, the role of CNVs in patients with epilepsies with complex phenotypes is not known. Therefore, we investigated the role of CNVs in patients with unclassified epilepsies and complex phenotypes. A total of 222 patients from three European countries, including patients with structural lesions on magnetic resonance imaging (MRI), dysmorphic features, and multiple congenital anomalies, were clinically evaluated and screened for CNVs. MRI findings including acquired or developmental lesions and patient characteristics were subdivided and analyzed in subgroups. MRI data were available for 88.3% of patients, of whom 41.6% had abnormal MRI findings. Eighty-eight rare CNVs were discovered in 71 out of 222 patients (31.9%). Segregation of all identified variants could be assessed in 42 patients, 11 of which were de novo. The frequency of all structural variants and de novo variants was not statistically different between patients with or without MRI abnormalities or MRI subcategories. Patients with dysmorphic features were more likely to carry a rare CNV. Genome-wide screening methods for rare CNVs may provide clues for the genetic etiology in patients with a broader range of epilepsies than previously anticipated, including in patients with various brain anomalies detectable by MRI. Performing genome-wide screens for rare CNVs can be a valuable contribution to the routine diagnostic workup in patients with a broad range of childhood epilepsies. PMID:24281369

  1. Chirality-Induced Dynamic Kohn Anomalies in Graphene

    NASA Astrophysics Data System (ADS)

    Tse, Wang-Kong; Hu, Ben Yu-Kuang; Das Sarma, S.

    2008-08-01

    We develop a theory for the renormalization of the phonon energy dispersion in graphene due to the combined effects of both Coulomb and electron-phonon (e-ph) interactions. We obtain the renormalized phonon energy spectrum by an exact analytic derivation of the phonon self-energy, finding three distinct Kohn anomalies (KAs) at the phonon wave vector q=ω/v, 2kF±ω/v for LO phonons and one at q=ω/v for TO phonons. The presence of these new KAs in graphene, in contrast to the usual KA q=2kF in ordinary metals, originates from the dynamical screening of e-ph interaction (with a concomitant breakdown of the Born-Oppenheimer approximation) and the peculiar chirality of the graphene e-ph coupling.

  2. Luminescence modulations of rhenium tricarbonyl complexes induced by structural variations.

    PubMed

    Bertrand, Hélène C; Clède, Sylvain; Guillot, Régis; Lambert, François; Policar, Clotilde

    2014-06-16

    Octahedral d(6) low-spin Re(I) tricarbonyl complexes are of considerable interest as noninvasive imaging probes and have been deeply studied owing to their biological stability, low toxicity, large Stokes shifts, and long luminescence lifetimes. We reported recently the bimodal IR and luminescence imaging of a Re(I) tricarbonyl complex with a Pyta ligand (4-(2-pyridyl)-1,2,3-triazole) in cells and labeled such metal-carbonyl complexes SCoMPIs for single-core multimodal probes for imaging. Re(I) tricarbonyl complexes have unique photophysical properties allowing for their unequivocal detection in cells but also present some weaknesses such as a very low luminescence quantum yield in aqueous medium. Further optimizations would thus be desirable. We therefore developed new Re(I) tricarbonyl complexes prepared from different ancillary ligands. Complexes with benzothiadiazole-triazole ligands show interesting luminescent quantum yields in acetonitrile and may constitute valuable luminescent metal complexes in organic media. A series of complexes with bidentate 1-(2-quinolinyl)-1,2,3-triazole (Taquin) and 1-(2-pyridyl)-1,2,3-triazole (Tapy) ligands bearing various 4-substituted alkyl side chains has been designed and synthesized with efficient procedures. Their photophysical properties have been characterized in acetonitrile and in a H2O/DMSO (98/2) mixture and compared with those of the parent Quinta- and Pyta-based complexes. Tapy complexes bearing long alkyl chains show impressive enhancement of their luminescent properties relative to the parent Pyta complex. Theoretical calculations have been performed to further characterize this new class of rhenium tricarbonyl complexes. Preliminary cellular imaging studies in MDA-MB231 breast cancer cells reveal a strong increase in the luminescence signal in cells incubated with the Tapy complex substituted with a C12 alkyl chain. This study points out the interesting potential of the Tapy ligand in coordination chemistry

  3. Perspective: Kohn-Sham density functional theory descending a staircase

    NASA Astrophysics Data System (ADS)

    Yu, Haoyu S.; Li, Shaohong L.; Truhlar, Donald G.

    2016-10-01

    This article presents a perspective on Kohn-Sham density functional theory (KS-DFT) for electronic structure calculations in chemical physics. This theory is in widespread use for applications to both molecules and solids. We pay special attention to several aspects where there are both concerns and progress toward solutions. These include: 1. The treatment of open-shell and inherently multiconfigurational systems (the latter are often called multireference systems and are variously classified as having strong correlation, near-degeneracy correlation, or high static correlation; KS-DFT must treat these systems with broken-symmetry determinants). 2. The treatment of noncovalent interactions. 3. The choice between developing new functionals by parametrization, by theoretical constraints, or by a combination. 4. The ingredients of the exchange-correlation functionals used by KS-DFT, including spin densities, the magnitudes of their gradients, spin-specific kinetic energy densities, nonlocal exchange (Hartree-Fock exchange), nonlocal correlation, and subshell-dependent corrections (DFT+U). 5. The quest for a universal functional, where we summarize some of the success of the latest Minnesota functionals, namely MN15-L and MN15, which were obtained by optimization against diverse databases. 6. Time-dependent density functional theory, which is an extension of DFT to treat time-dependent problems and excited states. The review is a snapshot of a rapidly moving field, and—like Marcel Duchamp—we hope to convey progress in a stimulating way.

  4. Perspective: Kohn-Sham density functional theory descending a staircase.

    PubMed

    Yu, Haoyu S; Li, Shaohong L; Truhlar, Donald G

    2016-10-07

    This article presents a perspective on Kohn-Sham density functional theory (KS-DFT) for electronic structure calculations in chemical physics. This theory is in widespread use for applications to both molecules and solids. We pay special attention to several aspects where there are both concerns and progress toward solutions. These include: 1. The treatment of open-shell and inherently multiconfigurational systems (the latter are often called multireference systems and are variously classified as having strong correlation, near-degeneracy correlation, or high static correlation; KS-DFT must treat these systems with broken-symmetry determinants). 2. The treatment of noncovalent interactions. 3. The choice between developing new functionals by parametrization, by theoretical constraints, or by a combination. 4. The ingredients of the exchange-correlation functionals used by KS-DFT, including spin densities, the magnitudes of their gradients, spin-specific kinetic energy densities, nonlocal exchange (Hartree-Fock exchange), nonlocal correlation, and subshell-dependent corrections (DFT+U). 5. The quest for a universal functional, where we summarize some of the success of the latest Minnesota functionals, namely MN15-L and MN15, which were obtained by optimization against diverse databases. 6. Time-dependent density functional theory, which is an extension of DFT to treat time-dependent problems and excited states. The review is a snapshot of a rapidly moving field, and-like Marcel Duchamp-we hope to convey progress in a stimulating way.

  5. Complex Variation in Measures of General Intelligence and Cognitive Change

    PubMed Central

    Rowe, Suzanne J.; Rowlatt, Amy; Davies, Gail; Harris, Sarah E.; Porteous, David J.; Liewald, David C.; McNeill, Geraldine; Starr, John M.

    2013-01-01

    Combining information from multiple SNPs may capture a greater amount of genetic variation than from the sum of individual SNP effects and help identifying missing heritability. Regions may capture variation from multiple common variants of small effect, multiple rare variants or a combination of both. We describe regional heritability mapping of human cognition. Measures of crystallised (gc) and fluid intelligence (gf) in late adulthood (64–79 years) were available for 1806 individuals genotyped for 549,692 autosomal single nucleotide polymorphisms (SNPs). The same individuals were tested at age 11, enabling us the rare opportunity to measure cognitive change across most of their lifespan. 547,750 SNPs ranked by position are divided into 10, 908 overlapping regions of 101 SNPs to estimate the genetic variance each region explains, an approach that resembles classical linkage methods. We also estimate the genetic variation explained by individual autosomes and by SNPs within genes. Empirical significance thresholds are estimated separately for each trait from whole genome scans of 500 permutated data sets. The 5% significance threshold for the likelihood ratio test of a single region ranged from 17–17.5 for the three traits. This is the equivalent to nominal significance under the expectation of a chi-squared distribution (between 1df and 0) of P<1.44×10−5. These thresholds indicate that the distribution of the likelihood ratio test from this type of variance component analysis should be estimated empirically. Furthermore, we show that estimates of variation explained by these regions can be grossly overestimated. After applying permutation thresholds, a region for gf on chromosome 5 spanning the PRRC1 gene is significant at a genome-wide 10% empirical threshold. Analysis of gene methylation on the temporal cortex provides support for the association of PRRC1 and fluid intelligence (P = 0.004), and provides a prime candidate gene for high throughput

  6. Evaluating Long-Term Complex Professional Development: Using a Variation of the Cohort Control Design

    ERIC Educational Resources Information Center

    Sample Mcmeeking, Laura B.; Cobb, R. Brian; Basile, Carole

    2010-01-01

    This paper introduces a variation on the post-test only cohort control design and addresses questions concerning both the methodological credibility and the practical utility of employing this design variation in evaluations of large-scale complex professional development programmes in mathematics education. The original design and design…

  7. Calculation of the defect kinetic energy in Kohn-Sham theory by means of local-scaling transformations

    NASA Astrophysics Data System (ADS)

    Ludeña, Eduardo V.; López-Boada, Roberto; Maldonado, Jorge; Koga, Toshikatsu; Kryachko, Eugene S.

    1993-09-01

    The kinetic-energy difference ΔT=T-Ts[ρ0] is calculated for the helium isoelectronic series and for the beryllium atom. Ts[ρ0] is in this case the kinetic energy corresponding to a noninteracting N-particle system which, however, has the same density ρ0 as the exact interacting system. These densities ρ0 were assumed in the present case to be well represented by those coming from the optimal Hylleraas-type expansions for the He isoelectronic series and by the Bunge-Esquivel 650-term configuration-interaction wave function for Be. The calculations are carried out by means of a constrained variational method based on local-scaling transformations. The connection between this approach and the one based on the Kohn-Sham equations is discussed.

  8. Immunological consequences of strain variation within the Mycobacterium tuberculosis complex

    PubMed Central

    Tientcheu, Leopold D.; Ndengane, Mthawelenga; Andoseh, Genevieve; Kampmann, Beate; Wilkinson, Robert J

    2017-01-01

    In 2015, there were an estimated 10.4 million new cases of tuberculosis (TB) globally, making it one of the leading causes of death due to an infectious disease. TB is caused by members of the Mycobacterium tuberculosis complex (MTBC), with human disease resulting from infection by M. tuberculosis sensu stricto and M. africanum. Recent progress in genotyping techniques, in particular the increasing availability of whole genome sequence data, has revealed previously under appreciated levels of genetic diversity within the MTBC. Several studies have shown that this genetic diversity may translate into differences in TB transmission, clinical manifestations of disease, and host immune responses. This suggests the existence of MTBC genotype‐dependent host–pathogen interactions which may influence the outcome of infection and progression of disease. In this review, we highlight the studies demonstrating differences in innate and adaptive immunological outcomes consequent on MTBC genetic diversity, and discuss how these differences in immune response might influence the development of TB vaccines, diagnostics and new therapies. PMID:28150302

  9. Kohn-Sham potential for a strongly correlated finite system with fractional occupancy

    NASA Astrophysics Data System (ADS)

    Benítez, A.; Proetto, C. R.

    2016-11-01

    Using a simplified one-dimensional model of a diatomic molecule, the associated interacting density and corresponding Kohn-Sham (KS) potential have been obtained analytically for all fractional molecule occupancies N between 0 and 2. For the homonuclear case, and in the dissociation limit, the exact Kohn-Sham potential builds a barrier at the midpoint between the two atoms, whose strength increases linearly with N , with 1 Kohn-Sham potential with regards to the strength of the electron-electron repulsion is clearly displayed by our model; without this property both the unusual barrier and the plateau features will be absent.

  10. Adaptive solver of a Kohn-Sham equation for an atom

    NASA Astrophysics Data System (ADS)

    Romanowski, Zbigniew

    2009-06-01

    An adaptive numerical algorithm solving a Kohn-Sham equation for an atom confined in a spherical cavity is presented. The Kohn-Sham equation is solved by the high order finite element method with Lobatto polynomials as the basis set. Based on this method the adaptive algorithm is proposed, which leads to a simple and efficient algorithm. The details of the adaptive algorithm are discussed. Numerical results for N, Al, Ga and In atoms are provided. Using this procedure very high accuracy was obtained with a very small number of mesh nodes.

  11. On the Nature of Syntactic Variation: Evidence from Complex Predicates and Complex Word-Formation.

    ERIC Educational Resources Information Center

    Snyder, William

    2001-01-01

    Provides evidence from child language acquisition and comparative syntax for existence of a syntactic parameter in the classical sense of Chomsky (1981), with simultaneous effects on syntactic argument structure. Implications are that syntax is subject to points of substantive parametric variation as envisioned in Chomsky, and the time course of…

  12. A new view of transcriptome complexity and regulation through the lens of local splicing variations

    PubMed Central

    Vaquero-Garcia, Jorge; Barrera, Alejandro; Gazzara, Matthew R; González-Vallinas, Juan; Lahens, Nicholas F; Hogenesch, John B; Lynch, Kristen W; Barash, Yoseph

    2016-01-01

    Alternative splicing (AS) can critically affect gene function and disease, yet mapping splicing variations remains a challenge. Here, we propose a new approach to define and quantify mRNA splicing in units of local splicing variations (LSVs). LSVs capture previously defined types of alternative splicing as well as more complex transcript variations. Building the first genome wide map of LSVs from twelve mouse tissues, we find complex LSVs constitute over 30% of tissue dependent transcript variations and affect specific protein families. We show the prevalence of complex LSVs is conserved in humans and identify hundreds of LSVs that are specific to brain subregions or altered in Alzheimer's patients. Amongst those are novel isoforms in the Camk2 family and a novel poison exon in Ptbp1, a key splice factor in neurogenesis. We anticipate the approach presented here will advance the ability to relate tissue-specific splice variation to genetic variation, phenotype, and disease. DOI: http://dx.doi.org/10.7554/eLife.11752.001 PMID:26829591

  13. Microsatellite and major histocompatibility complex variation in an endangered rattlesnake, the Eastern Massasauga (Sistrurus catenatus).

    PubMed

    Jaeger, Collin P; Duvall, Melvin R; Swanson, Bradley J; Phillips, Christopher A; Dreslik, Michael J; Baker, Sarah J; King, Richard B

    2016-06-01

    Genetic diversity is fundamental to maintaining the long-term viability of populations, yet reduced genetic variation is often associated with small, isolated populations. To examine the relationship between demography and genetic variation, variation at hypervariable loci (e.g., microsatellite DNA loci) is often measured. However, these loci are selectively neutral (or near neutral) and may not accurately reflect genomewide variation. Variation at functional trait loci, such as the major histocompatibility complex (MHC), can provide a better assessment of adaptive genetic variation in fragmented populations. We compared patterns of microsatellite and MHC variation across three Eastern Massasauga (Sistrurus catenatus) populations representing a gradient of demographic histories to assess the relative roles of natural selection and genetic drift. Using 454 deep amplicon sequencing, we identified 24 putatively functional MHC IIB exon 2 alleles belonging to a minimum of six loci. Analysis of synonymous and nonsynonymous substitution rates provided evidence of historical positive selection at the nucleotide level, and Tajima's D provided support for balancing selection in each population. As predicted, estimates of microsatellite allelic richness, observed, heterozygosity, and expected heterozygosity varied among populations in a pattern qualitatively consistent with demographic history and abundance. While MHC allelic richness at the population and individual levels revealed similar trends, MHC nucleotide diversity was unexpectedly high in the smallest population. Overall, these results suggest that genetic variation in the Eastern Massasauga populations in Illinois has been shaped by multiple evolutionary mechanisms. Thus, conservation efforts should consider both neutral and functional genetic variation when managing captive and wild Eastern Massasauga populations.

  14. The variation game: Cracking complex genetic disorders with NGS and omics data.

    PubMed

    Cui, Hongzhu; Dhroso, Andi; Johnson, Nathan; Korkin, Dmitry

    2015-06-01

    Tremendous advances in Next Generation Sequencing (NGS) and high-throughput omics methods have brought us one step closer towards mechanistic understanding of the complex disease at the molecular level. In this review, we discuss four basic regulatory mechanisms implicated in complex genetic diseases, such as cancer, neurological disorders, heart disease, diabetes, and many others. The mechanisms, including genetic variations, copy-number variations, posttranscriptional variations, and epigenetic variations, can be detected using a variety of NGS methods. We propose that malfunctions detected in these mechanisms are not necessarily independent, since these malfunctions are often found associated with the same disease and targeting the same gene, group of genes, or functional pathway. As an example, we discuss possible rewiring effects of the cancer-associated genetic, structural, and posttranscriptional variations on the protein-protein interaction (PPI) network centered around P53 protein. The review highlights multi-layered complexity of common genetic disorders and suggests that integration of NGS and omics data is a critical step in developing new computational methods capable of deciphering this complexity.

  15. Minisatellite and microsatellite length variation at a complex bovine VNTR locus.

    PubMed

    Nave, A; Kashi, Y; Soller, M

    1997-02-01

    Length variation at the BTGL1 variable number of tandem repeat (VNTR) locus, which includes both minisatellite and microsatellite motifs, was examined in a wide sample of cattle. A total of 22 alleles were uncovered. The distribution of allele size variation implicated mechanisms involving both minisatellite and microsatellite sequences. This was confirmed by direct sequences of two alleles. Differences between the two alleles involved repeat number variation of microsatellite motifs and a complex event involving the minisatellite motif, but point mutations were not observed.

  16. Is the Kohn-Sham Oscillator Strength Exact at the Ionization Threshold?

    NASA Astrophysics Data System (ADS)

    Yang, Zenghui; van Faassen, Meta; Burke, Kieron

    2009-03-01

    It is well-established that the highest occupied orbital of the exact Kohn-Sham potential of any system is at -I, where I is the ionization energy. Therefore, in optical response, the non-interacting Kohn-Sham electrons in the ground-state potential have a first ionization threshold that exactly matches that of the real system[1]. We show that corresponding the Kohn-Sham oscillator strength is not exact at the first ionization threshold by explicit demonstration for the helium atom. We use a simple fit of the entire photoabsorption spectrum of both the Kohn-Sham potential for helium and that of real helium. We use oscillator strength sum rules[2] to determine the fit parameters, so this fit should be generally useful. [1] M. A. L. Marques, C. A. Ullrich, F. Nogueira, et al. Time-Dependent Density Functional Theory. Springer-Verlag, Berlin, 2006 [2] U. Fano and J. W. Cooper. Rev. Mod. Phys., 40(3), 441-507, 1968

  17. Why Students Lose When "Tougher Standards" Win: A Conversation with Alfie Kohn.

    ERIC Educational Resources Information Center

    O'Neil, John; Tell, Carol

    1999-01-01

    Kohn believes the "tougher standards" movement is incompatible with personalized learning, excellence, and marginalized kids' interests. Horizontal standards that shift how teaching and learning happen in classrooms are terrific, but vertical standards using traditional pedagogy are macho and mindless. Kids need freedom to design their…

  18. "Fighting the Toxic Status Quo": Alfie Kohn on Standardized Tests and Teacher Education.

    ERIC Educational Resources Information Center

    Appleman, Deborah; Thompson, Micheal J.

    2002-01-01

    Considers how many teacher educators feel caught between the need to comply with state and federal laws governing the approval of their teacher education programs and the desire to resist what many feel to be another example of "testing gone wild." Presents a conversation with Alfie Kohn on high stakes tests for teachers and for students. (SG)

  19. Paradoxical Pathways: An Ethnographic Extension of Kohn's Findings on Class and Childrearing

    ERIC Educational Resources Information Center

    Weininger, Elliot B.; Lareau, Annette

    2009-01-01

    Stratification is a central issue in family research, yet relatively few studies highlight its impact on family processes. Drawing on in-depth interviews (N = 137) and observational data (N = 12), we extend Melvin Kohn's research on childrearing values by examining how parental commitments to self-direction and conformity are enacted in daily…

  20. Morphological variation in the horse: defining complex traits of body size and shape.

    PubMed

    Brooks, S A; Makvandi-Nejad, S; Chu, E; Allen, J J; Streeter, C; Gu, E; McCleery, B; Murphy, B A; Bellone, R; Sutter, N B

    2010-12-01

    Horses, like many domesticated species, have been selected for broad variation in skeletal size. This variation is not only an interesting model of rapid evolutionary change during domestication, but is also directly applicable to the horse industry. Breeders select for complex traits like body size and skeletal conformation to improve marketability, function, soundness and performance in the show ring. Using a well-defined set of 35 measurements, we have identified and quantified skeletal variation in the horse species. We collected measurements from 1215 horses representing 65 breeds of diverse conformation such as the American Miniature, Shetland Pony, Arabian Horse, Thoroughbred, Shire and Clydesdale. Principal components analysis has identified two key dimensions of skeletal variation in the horse. Principal component 1 is positively correlated with every measurement and quantifies overall body size. Principal component 2 captures a pattern of bone widths vs. lengths and thus quantifies variation in overall bone thickness. By defining these complex skeletal traits, we have created a framework for whole genome association studies to identify quantitative trait loci that contribute to this variation.

  1. Genetic Variation of Major Histocompatibility Complex and Microsatellite Loci: A Comparison in Bighorn Sheep

    PubMed Central

    Boyce, W. M.; Hedrick, P. W.; Muggli-Cockett, N. E.; Kalinowski, S.; Penedo, MCT.; Ramey-II, R. R.

    1997-01-01

    Examining and comparing genetic variation for major histocompatibility complex (MHC) and microsatellite (MS) loci in the same individuals provides an opportunity to understand the forces influencing genetic variation. We examined five MHC and three MS loci in 235 bighorn sheep (Ovis canadensis) from 14 populations and found that both types of loci were highly variable and were in Hardy-Weinberg proportions. Mean F(ST) values for both markers were very similar and MHC and MS genetic variability was predominantly distributed within rather than among populations. However, analyses of genetic distances and tree topologies revealed different spatial patterns of variation for the two types of loci. Collectively, these results indicated that neutral forces substantially influenced MS and MHC variation, and they provided limited evidence for selection acting on the MHC. PMID:9071595

  2. Genetic variation of major histocompatibility complex and microsatellite loci: a comparison in bighorn sheep.

    PubMed

    Boyce, W M; Hedrick, P W; Muggli-Cockett, N E; Kalinowski, S; Penedo, M C; Ramey, R R

    1997-02-01

    Examining and comparing genetic variation for major histocompatibility complex (MHC) and micro-satellite (MS) loci in the same individuals provides an opportunity to understand the forces influencing genetic variation. We examined five MHC and three MS loci in 235 bighorn sheep (Ovis canadensis) from 14 populations and found that both types of loci were highly variable and were in Hardy-Weinberg proportions. Mean FST values for both markers were very similar and MHC and MS genetic variability was predominantly distributed within rather than among populations. However, analyses of genetic distances and tree topologies revealed different spatial patterns of variation for the two types of loci. Collectively, these results indicated that neutral forces substantially influenced MS and MHC variation, and they provided limited evidence for selection acting on the MHC.

  3. Cytogeography and genome size variation in the Claytonia perfoliata (Portulacaceae) polyploid complex

    PubMed Central

    McIntyre, Patrick J.

    2012-01-01

    Background and Aims Genome duplication is a central process in plant evolution and contributes to patterns of variation in genome size within and among lineages. Studies that combine cytogeography with genome size measurements contribute to our basic knowledge of cytotype distributions and their associations with variation in genome size. Methods Ploidy and genome size were assessed with direct chromosome counts and flow cytometry for 78 populations within the Claytonia perfoliata complex, comprised of three diploid taxa with numerous polyploids that range to the decaploid level. The relationship between genome size and temperature and precipitation was investigated within and across cytotypes to test for associations between environmental factors and nuclear DNA content. Key Results A euploid series (n = 6) of diploids to octoploids was documented through chromosome counts, and decaploids were suggested by flow cytometry. Increased variation in genome size among populations was found at higher ploidy levels, potentially associated with differential contributions of diploid parental genomes, variation in rates of genomic loss or gain, or undetected hybridization. Several accessions were detected with atypical genome sizes, including a diploid population of C. parviflora ssp. grandiflora with an 18 % smaller genome than typical, and hexaploids of C. perfoliata and C. parviflora with genomes 30 % larger than typical. There was a slight but significant association of larger genome sizes with colder winter temperature across the C. perfoliata complex as a whole, and a strong association between lower winter temperatures and large genome size for tetraploid C. parviflora. Conclusions The C. perfoliata complex is characterized by polyploids ranging from tetraploid to decaploid, with large magnitude variation in genome size at higher ploidy levels, associated in part with environmental variation in temperature. PMID:22962302

  4. Complex potential surface for the {sup 2}B{sub 1} metastable state of the water anion

    SciTech Connect

    Haxton, Daniel J.; Zhang, Zhiyong; McCurdy, C. William; Rescigno, Thomas N.

    2004-04-23

    The potential energy surface corresponding the complex resonance energy of the 2B1 Feshbach resonance state of the water anion is constructed in its full dimensionality. Complex Kohn variational scattering calculations are used to compute the resonance width, while large-scale Configuration Interaction calculations are used to compute the resonance energy. Near the equilibrium geometry, an accompanying ground state potential surface is constructed from Configuration Interaction calculations that treat correlation at a level similar to that used in the calculations on the anion.

  5. SANS with contrast variation study of the bacteriorhodopsin-octyl glucoside complex

    NASA Astrophysics Data System (ADS)

    Mo, Yiming; Heller, William T.

    2010-11-01

    Membrane proteins (MPs), which play vital roles in trans-membrane trafficking and signalling between cells and their external environment, comprise a major fraction of the expressed proteomes of many organisms. MP production for biophysical characterization requires detergents for extracting MPs from their native membrane and to solubilize the MP in solution for purification and study. In a proper detergent solution, the detergent-associated MPs retain their native fold and oligomerization state, key requirements for biophysical characterization and crystallization. SANS with contrast variation was performed to characterize BR in complex with OG to better understand the MP-detergent complex. Contrast variation makes it possible to not only probe the conformation of the entire structure but also investigate the conformation of the polypeptide chain within the BR-OG complex. The BR-OG SANS contrast variation series is not consistent with a compact structure, such as a trimeric BR complex surrounded by a belt of detergent. The data strongly suggest that the protein is partially unfolded through its association with the detergent micelles.

  6. SANS with Contrast Variation Study of the Bacteriorhodopsin-octyl Glucoside Complex

    SciTech Connect

    Heller, William T; Mo, Yiming

    2010-01-01

    Membrane proteins (MPs), which play vital roles in trans-membrane trafficking and signaling between cells and their external environment, comprise a major fraction of the expressed proteomes of many organisms. MP production for biophysical characterization requires detergents for extracting MPs from their native membrane and to solubilize the MP in solution for purification and study. In a proper detergent solution, the detergent-associated MPs retain their native fold and oligomerization state, key requirements for biophysical characterization and crystallization. SANS with contrast variation was performed to characterize BR in complex with OG to better understand the MP-detergent complex. Contrast variation makes it possible to not only probe the conformation of the entire structure but also investigate the conformation of the polypeptide chain within the BR-OG complex. The BR-OG SANS contrast variation series is not consistent with a compact structure, such as a trimeric BR complex surrounded by a belt of detergent. The data strongly suggest that the protein is partially unfolded through its association with the detergent micelles.

  7. Few-body collective excitations beyond Kohn's theorem in quantum Hall systems

    NASA Astrophysics Data System (ADS)

    Wooten, R. E.; Yan, B.; Greene, Chris H.

    2017-01-01

    A relative coordinate breathing mode in the quantum Hall system is predicted to exist with different behavior under either Coulomb or dipole-dipole interactions. While Kohn's theorem [W. Kohn, Phys. Rev. 123, 1242 (1961), 10.1103/PhysRev.123.1242] predicts that any relative coordinate interaction will fail to alter the center-of-mass energy spectrum, it can affect excitations in the relative coordinates. One such collective excitation, which we call the hyperradial breathing mode, emerges naturally from a few-body, hyperspherical representation of the problem and depends on the interparticle interactions, the ground state wave function, and the number of particles participating in the excitation. Possible observations of this excitation will be discussed in the context of both conventional quantum Hall experiments and cold, rotating atomic simulations.

  8. Ab-initio study of the Kohn anomalies in strained graphene

    NASA Astrophysics Data System (ADS)

    Cifuentes-Quintal, M. E.; de Coss, R.; de La Peña-Seaman, O.; Heid, R.; Bohnen, K.-P.

    2011-03-01

    Recent experimental studies have show that the electronic and vibrational properties of graphene can be modulated by means of strain. However, there are not studies on strain effects on the Kohn anomalies, which is a principal key to understand the electron phonon coupling in graphene. In this work we have studied the phonon band structure of graphene under biaxial and uniaxial strain using the mixed basis pseudopotential method, within the framework of the density functional perturbation theory. For tensile/compressive biaxial strain, we found an increasing/decreasing behavior on the slop of the phonon frequencies close to Kohn anomalies. Under uniaxial strain, the two highest optical branches show a discontinuity in the frequency derivative at gamma point, instead of only one branch like in the biaxial and unstrained case. The present results suggest that the electron-phonon coupling in graphene can be modulated via strain. This research was supported by Conacyt-Mexico under Grant No. 83604.

  9. A phenomenographic study of the ability to address complex socio-technical systems via variation theory

    NASA Astrophysics Data System (ADS)

    Mendoza Garcia, John A.

    Sometimes engineers fail when addressing the inherent complexity of socio-technical systems because they lack the ability to address the complexity of socio-technical systems. Teaching undergraduate engineering students how to address complex socio-technical systems, has been an educational endeavor at different levels ranging from kindergarten to post-graduate education. The literature presents different pedagogical strategies and content to reach this goal. However, there are no existing empirically-based assessments guided by a learning theory. This may be because at the same time explanations of how the skill is developed are scarce. My study bridges this gap, and I propose a developmental path for the ability to address the complex socio-technical systems via Variation Theory, and according to the conceptual framework provided by Variation Theory, my research question was "What are the various ways in which engineers address complex socio-technical systems?" I chose the research approach of phenomenography to answer my research question. I also chose to use a blended approach, Marton's approach for finding the dimensions of variation, and the developmental approach (Australian) for finding a hierarchical relationship between the dimensions. Accordingly, I recruited 25 participants with different levels of experience with addressing complex socio-technical systems and asked them all to address the same two tasks: A design of a system for a county, and a case study in a manufacturing firm. My outcome space is a nona-dimensional (nine) developmental path for the ability to address the complexity in socio-technical systems, and I propose 9 different ways of experiencing the complexity of a socio-technical system. The findings of this study suggest that the critical aspects that are needed to address the complexity of socio-technical systems are: being aware of the use of models, the ecosystem around, start recognizing different boundaries, being aware of time as a

  10. Variation.

    ERIC Educational Resources Information Center

    Hamilton City Board of Education (Ontario).

    Suggestions for studying the topic of variation of individuals and objects (balls) to help develop elementary school students' measurement, comparison, classification, evaluation, and data collection and recording skills are made. General suggestions of variables that can be investigated are made for the study of human variation. Twelve specific…

  11. Variation in complex semiochemical signals arising from insects and host plants.

    PubMed

    Aukema, Brian H; Powell, Jaimie S; Clayton, Murray K; Raffa, Kenneth F

    2010-06-01

    Chemical communication by many insect species involves complex signals of both insect and plant origin. Much attention has been focused on the behavioral activities of these components but less on their sources of variation, despite implications for evolutionary theory and pest management. We studied variation in chemical signaling at host, tree-within-host, and beetle-on-tree scales using tunneling male pine engravers [Ips pini (Say)] on jack, Pinus banksiana Lamb, red, P. resinosa Aiton, and white, P. strobus L. pines. Pine engravers are distributed transcontinentally, and stereoisomeric ratios of their principal pheromone component ipsdienol varies regionally. Linear mixed-effects models were used to examine variation in monoterpene and pheromone volatile profiles, determined by gas chromatography. Phloem from white pine had the greatest concentration of monoterpenes, although insects tunneling in white pine produced the smallest ratios of monoterpenes to pheromones (1:2) in their volatile plumes relative to jack and red pine (1:1). Beetle-to-beetle variation in plume composition was approximately 2-9 times greater than the inter-tree variation within a tree species. The stereoisomeric ratio of ipsdienol was highly consistent within the pheromone component of the plume. The little variation present existed almost entirely at the level of the insects. Within the pheromone component of the plume in a given host species, there was up to 13 times more beetle-to-beetle than tree-to-tree variation. This magnitude was almost double the magnitudes of the ratios among components within the entire plumes. Implications to the behavioral ecology of bark beetle communication, such as potential strategies of cheating and predator avoidance, are discussed.

  12. Syntactic Complexity, Lexical Variation and Accuracy as a Function of Task Complexity and Proficiency Level in L2 Writing and Speaking

    ERIC Educational Resources Information Center

    Kuiken, Folkert; Vedder, Ineke

    2012-01-01

    The research project reported in this chapter consists of three studies in which syntactic complexity, lexical variation and fluency appear as dependent variables. The independent variables are task complexity and proficiency level, as the three studies investigate the effect of task complexity on the written and oral performance of L2 learners of…

  13. A spectral scheme for Kohn-Sham density functional theory of clusters

    NASA Astrophysics Data System (ADS)

    Banerjee, Amartya S.; Elliott, Ryan S.; James, Richard D.

    2015-04-01

    Starting from the observation that one of the most successful methods for solving the Kohn-Sham equations for periodic systems - the plane-wave method - is a spectral method based on eigenfunction expansion, we formulate a spectral method designed towards solving the Kohn-Sham equations for clusters. This allows for efficient calculation of the electronic structure of clusters (and molecules) with high accuracy and systematic convergence properties without the need for any artificial periodicity. The basis functions in this method form a complete orthonormal set and are expressible in terms of spherical harmonics and spherical Bessel functions. Computation of the occupied eigenstates of the discretized Kohn-Sham Hamiltonian is carried out using a combination of preconditioned block eigensolvers and Chebyshev polynomial filter accelerated subspace iterations. Several algorithmic and computational aspects of the method, including computation of the electrostatics terms and parallelization are discussed. We have implemented these methods and algorithms into an efficient and reliable package called ClusterES (Cluster Electronic Structure). A variety of benchmark calculations employing local and non-local pseudopotentials are carried out using our package and the results are compared to the literature. Convergence properties of the basis set are discussed through numerical examples. Computations involving large systems that contain thousands of electrons are demonstrated to highlight the efficacy of our methodology. The use of our method to study clusters with arbitrary point group symmetries is briefly discussed.

  14. Kohn-Luttinger superconductivity in monolayer and bilayer semimetals with the Dirac spectrum

    SciTech Connect

    Kagan, M. Yu.; Mitskan, V. A.; Korovushkin, M. M.

    2014-12-15

    The effect of Coulomb interaction in an ensemble of Dirac fermions on the formation of superconducting pairing in monolayer and bilayer doped graphene is studied using the Kohn-Luttinger mechanism disregarding the Van der Waals potential of the substrate and impurities. The electronic structure of graphene is described using the Shubin-Vonsovsky model taking into account the intratomic, interatomic, and interlayer (in the case of bilayer graphene) Coulomb interactions between electrons. The Cooper instability is determined by solving the Bethe-Saltpeter integral equation. The renormalized scattering amplitude is obtained with allowance for the Kohn-Luttinger polarization contributions up to the second order of perturbation theory in the Coulomb interaction. It plays the role of effective interaction in the Bethe-Salpeter integral equation. It is shown that the allowance for the Kohn-Luttinger renormalizations as well as intersite Coulomb interaction noticeably affects the competition between the superconducting phases with the f-wave and d + id-wave symmetries of the order parameter. It is demonstrated that the superconducting transition temperature for an idealized graphene bilayer with significant interlayer Coulomb interaction between electrons is noticeably higher than in the monolayer case.

  15. ACKS2: Atom-condensed Kohn-Sham DFT approximated to second order

    NASA Astrophysics Data System (ADS)

    Verstraelen, T.; Ayers, P. W.; Van Speybroeck, V.; Waroquier, M.

    2013-02-01

    A new polarizable force field (PFF), namely atom-condensed Kohn-Sham density functional theory approximated to second order (ACKS2), is proposed for the efficient computation of atomic charges and linear response properties of extended molecular systems. It is derived from Kohn-Sham density functional theory (KS-DFT), making use of two novel ingredients in the context of PFFs: (i) constrained atomic populations and (ii) the Legendre transform of the Kohn-Sham kinetic energy. ACKS2 is essentially an extension of the Electronegativity Equalization Method (EEM) [W. J. Mortier, S. K. Ghosh, and S. Shankar, J. Am. Chem. Soc. 108, 4315 (1986)], 10.1021/ja00275a013 in which two major EEM shortcomings are fixed: ACKS2 predicts a linear size-dependence of the dipole polarizability in the macroscopic limit and correctly describes the charge distribution when a molecule dissociates. All ACKS2 parameters are defined as atoms-in-molecules expectation values. The implementation of ACKS2 is very similar to that of EEM, with only a small increase in computational cost.

  16. Excitation Energies from Real-Time Propagation of the Four-Component Dirac-Kohn-Sham Equation.

    PubMed

    Repisky, Michal; Konecny, Lukas; Kadek, Marius; Komorovsky, Stanislav; Malkin, Olga L; Malkin, Vladimir G; Ruud, Kenneth

    2015-03-10

    We report the first implementation of real-time time-dependent density functional theory (RT-TDDFT) at the relativistic four-component level of theory. In contrast to the perturbative linear-response TDDFT approach (LR-TDDFT), the RT-TDDFT approach performs an explicit time propagation of the Dirac-Kohn-Sham density matrix, offering the possibility to simulate molecular spectroscopies involving strong electromagnetic fields while, at the same time, treating relativistic scalar and spin-orbit corrections variationally. The implementation is based on the matrix representation of the Dirac-Coulomb Hamiltonian in the basis of restricted kinetically balanced Gaussian-type functions, exploiting the noncollinear Kramers unrestricted formalism implemented in the program ReSpect. We also present an analytic form for the delta-type impulse commonly used in RT-TDDFT calculations, as well as a dipole-weighted transition matrix analysis, facilitating the interpretation of spectral transitions in terms of ground-state molecular orbitals. The possibilities offered by the methodology are illustrated by investigating vertical excitation energies and oscillator strengths for ground-state to excited-state transitions in the Group 12 atoms and in heavy-element hydrides. The accuracy of the method is assessed by comparing the excitation energies obtained with earlier relativistic linear response TDDFT results and available experimental data.

  17. DNA variation of the mammalian major histocompatibility complex reflects genomic diversity and population history.

    PubMed Central

    Yuhki, N; O'Brien, S J

    1990-01-01

    The major histocompatibility complex (MHC) is a multigene complex of tightly linked homologous genes that encode cell surface antigens that play a key role in immune regulation and response to foreign antigens. In most species, MHC gene products display extreme antigenic polymorphism, and their variability has been interpreted to reflect an adaptive strategy for accommodating rapidly evolving infectious agents that periodically afflict natural populations. Determination of the extent of MHC variation has been limited to populations in which skin grafting is feasible or for which serological reagents have been developed. We present here a quantitative analysis of restriction fragment length polymorphism of MHC class I genes in several mammalian species (cats, rodents, humans) known to have very different levels of genetic diversity based on functional MHC assays and on allozyme surveys. When homologous class I probes were employed, a notable concordance was observed between the extent of MHC restriction fragment variation and functional MHC variation detected by skin grafts or genome-wide diversity estimated by allozyme screens. These results confirm the genetically depauperate character of the African cheetah, Acinonyx jubatus, and the Asiatic lion, Panthera leo persica; further, they support the use of class I MHC molecular reagents in estimating the extent and character of genetic diversity in natural populations. Images PMID:1967831

  18. DNA variation of the mammalian major histocompatibility complex reflects genomic diversity and population history.

    PubMed

    Yuhki, N; O'Brien, S J

    1990-01-01

    The major histocompatibility complex (MHC) is a multigene complex of tightly linked homologous genes that encode cell surface antigens that play a key role in immune regulation and response to foreign antigens. In most species, MHC gene products display extreme antigenic polymorphism, and their variability has been interpreted to reflect an adaptive strategy for accommodating rapidly evolving infectious agents that periodically afflict natural populations. Determination of the extent of MHC variation has been limited to populations in which skin grafting is feasible or for which serological reagents have been developed. We present here a quantitative analysis of restriction fragment length polymorphism of MHC class I genes in several mammalian species (cats, rodents, humans) known to have very different levels of genetic diversity based on functional MHC assays and on allozyme surveys. When homologous class I probes were employed, a notable concordance was observed between the extent of MHC restriction fragment variation and functional MHC variation detected by skin grafts or genome-wide diversity estimated by allozyme screens. These results confirm the genetically depauperate character of the African cheetah, Acinonyx jubatus, and the Asiatic lion, Panthera leo persica; further, they support the use of class I MHC molecular reagents in estimating the extent and character of genetic diversity in natural populations.

  19. Major histocompatibility complex variation in the endangered crested ibis Nipponia nippon and implications for reintroduction.

    PubMed

    Zhang, Bei; Fang, Sheng-Guo; Xi, Yong-Mei

    2006-04-01

    The major histocompatibility complex (MHC), with its extraordinary levels of genetic variation, is thought to be an essential aspect of the ability of an organism to recognize different parasites and pathogens. It has also been proposed to regulate reproductive processes in many aspects. Here we examine the genetic variation of the second exon of the MHC class II B genes of the crested ibis, an endangered species known to descend from just two breeding pairs rediscovered in 1981. Only five alleles are identified by single-strand conformation polymorphism (SSCP) analysis of 36 samples taken from both wild and captive populations, and a comparatively low level of divergence between MHC alleles is observed. We suggest that representative sampling of individuals with most of the different MHC allele genotypes to constitute a founder population, together with the monitoring of the pathogen status of candidate sites before release, is of great importance for raising the success rate of reintroduction for the crested ibis.

  20. Genetic Variation in Human Vitamin C Transporter Genes in Common Complex Diseases123

    PubMed Central

    Shaghaghi, Mandana Amir; Kloss, Olena

    2016-01-01

    Adequate plasma, cellular, and tissue vitamin C concentrations are required for maintaining optimal health through suppression of oxidative stress and optimizing functions of certain enzymes that require vitamin C as a cofactor. Polymorphisms in the vitamin C transporter genes, compromising genes encoding sodium-dependent ascorbate transport proteins, and also genes encoding facilitative transporters of dehydroascorbic acid, are associated with plasma and tissue cellular ascorbate status and hence cellular redox balance. This review summarizes our current knowledge of the links between variations in vitamin C transporter genes and common chronic diseases. We conclude that emerging genetic knowledge has a good likelihood of defining future personalized dietary recommendations and interventions; however, further validations through biological studies as well as controlled dietary trials are required to identify predictive and actionable genetic biomarkers. We further advocate the need to consider genetic variation of vitamin C transporters in future clinical and epidemiologic studies on common complex diseases. PMID:26980812

  1. Major histocompatibility complex (MHC) variation in the endangered Mexican wolf and related canids.

    PubMed

    Hedrick, P W; Lee, R N; Parker, K M

    2000-12-01

    We have examined in Mexican wolves and related canids the amount of genetic variation for a class II gene in the major histocompatibility complex (MHC), thought to be part of the most important genetic basis for pathogen resistance in vertebrates. In Mexican wolves, descended from only seven founders over three lineages, there were five different alleles. These were in three phylogenetic groups, only one of which was shared between lineages. Using single stand conformation polymorphism (SSCP), we found that in samples of animals from the two polymorphic lineages, the observed heterozygosity was 0.74 and the genotypes were not different statistically from Hardy-Weinberg proportions. The Ghost Ranch lineage of Mexican wolves was monomorphic for the locus, consistent with the lower level of variation found previously for microsatellite loci and predicted from pedigree analysis. Samples of grey wolves, red wolves, and coyotes had 16 additional alleles. One Mexican wolf allele was also found in grey wolves and another allele was shared between grey and red wolves. Most of the nucleotide variation resulted in amino acid variation and there were five different amino acids found at two different positions. Only two of the 21 variable amino acid positions had solely synonymous nucleotide variation. The average heterozygosity for eight individual amino acid positions in the Mexican wolves was greater than 0.4. The estimated rate of nonsynonymous substitution was 2.5 times higher than that for synonymous substitution for the putative antigen binding site positions, indicative of positive selection acting on these positions. Examination of the known dog sequences for this locus showed that one of the Mexican wolf alleles was found in dogs and that the allele found in both grey and red wolves is also found in dogs.

  2. Variation in complex olfactory stimuli and its influence on odour recognition.

    PubMed Central

    Wrigh, Geraldine A.; Smith, Brian H.

    2004-01-01

    Natural olfactory stimuli are often complex and highly variable. The olfactory systems of animals are likely to have evolved to use specific features of olfactory stimuli for identification and discrimination. Here, we train honeybees to learn chemically defined odorant mixtures that systematically vary from trial to trial and then examine how they generalize to each odorant present in the mixture. An odorant that was present at a constant concentration in a mixture becomes more representative of the mixture than other variable odorants. We also show that both variation and intensity of a complex olfactory stimulus affect the rate of generalization by honeybees to subsequent olfactory stimuli. These results have implications for the way that all animals perceive and attend to features of olfactory stimuli. PMID:15058390

  3. Human radiation studies: Remembering the early years: Oral history of radiologist Henry I. Kohn, M.D., Ph.D., conducted September 13, 1994

    SciTech Connect

    1995-06-01

    This report is a transcript of an interview of Dr. Henry I. Kohn by representatives of the US DOE Office of Human Radiation Experiments. Dr. Kohn was selected for this interview because of the positions he held at Oak Ridge National Laboratory, University of California at San Francisco, and Harvard Medical School. Dr. Kohn discussed his remembrances of his experiences in blood chemistry of animals and patients exposed to radiation, and his remembrances of several radiobiologists.

  4. Variational regularization of complex deautoconvolution and phase retrieval in ultrashort laser pulse characterization

    NASA Astrophysics Data System (ADS)

    Anzengruber, Stephan W.; Bürger, Steven; Hofmann, Bernd; Steinmeyer, Günter

    2016-03-01

    The SD-SPIDER method for the characterization of ultrashort laser pulses requires the solution of a nonlinear integral equation of autoconvolution type with a device-based kernel function. Taking into account the analytical background of a variational regularization approach for solving the corresponding ill-posed operator equation formulated in complex-valued L2-spaces over finite real intervals, we suggest and evaluate numerical procedures using NURBS and the TIGRA method for calculating the regularized solutions in a stable manner. In this context, besides the complex deautoconvolution problem with noisy but full data, a phase retrieval problem is introduced which adapts to the experimental state of the art in laser optics. For the treatment of this problem facet, which is formulated as a tensor product operator equation, we derive the well-posedness of variational regularization methods. Case studies with synthetic and real optical data show the capability of the implemented approach as well as its limitations due to measurement deficits.

  5. Model Organisms Retain an “Ecological Memory” of Complex Ecologically Relevant Environmental Variation

    PubMed Central

    Beer, Karlyn D.; Wurtmann, Elisabeth J.; Pinel, Nicolás

    2014-01-01

    Although tractable model organisms are essential to characterize the molecular mechanisms of evolution and adaptation, the ecological relevance of their behavior is not always clear because certain traits are easily lost during long-term laboratory culturing. Here, we demonstrate that despite their long tenure in the laboratory, model organisms retain “ecological memory” of complex environmental changes. We have discovered that Halobacterium salinarum NRC-1, a halophilic archaeon that dominates microbial communities in a dynamically changing hypersaline environment, simultaneously optimizes fitness to total salinity, NaCl concentration, and the [K]/[Mg] ratio. Despite being maintained under controlled conditions over the last 50 years, peaks in the three-dimensional fitness landscape occur in salinity and ionic compositions that are not replicated in laboratory culturing but are routinely observed in the natural hypersaline environment of this organism. Intriguingly, adaptation to variations in ion composition was associated with differential regulation of anaerobic metabolism genes, suggesting an intertwined relationship between responses to oxygen and salinity. Our results suggest that the ecological memory of complex environmental variations is imprinted in the networks for coordinating multiple cellular processes. These coordination networks are also essential for dealing with changes in other physicochemically linked factors present during routine laboratory culturing and, hence, retained in model organisms. PMID:24413600

  6. Higher-order adaptive finite-element methods for Kohn-Sham density functional theory

    NASA Astrophysics Data System (ADS)

    Motamarri, P.; Nowak, M. R.; Leiter, K.; Knap, J.; Gavini, V.

    2013-11-01

    We present an efficient computational approach to perform real-space electronic structure calculations using an adaptive higher-order finite-element discretization of Kohn-Sham density-functional theory (DFT). To this end, we develop an a priori mesh-adaption technique to construct a close to optimal finite-element discretization of the problem. We further propose an efficient solution strategy for solving the discrete eigenvalue problem by using spectral finite-elements in conjunction with Gauss-Lobatto quadrature, and a Chebyshev acceleration technique for computing the occupied eigenspace. The proposed approach has been observed to provide a staggering 100-200-fold computational advantage over the solution of a generalized eigenvalue problem. Using the proposed solution procedure, we investigate the computational efficiency afforded by higher-order finite-element discretizations of the Kohn-Sham DFT problem. Our studies suggest that staggering computational savings-of the order of 1000-fold-relative to linear finite-elements can be realized, for both all-electron and local pseudopotential calculations, by using higher-order finite-element discretizations. On all the benchmark systems studied, we observe diminishing returns in computational savings beyond the sixth-order for accuracies commensurate with chemical accuracy, suggesting that the hexic spectral-element may be an optimal choice for the finite-element discretization of the Kohn-Sham DFT problem. A comparative study of the computational efficiency of the proposed higher-order finite-element discretizations suggests that the performance of finite-element basis is competing with the plane-wave discretization for non-periodic local pseudopotential calculations, and compares to the Gaussian basis for all-electron calculations to within an order of magnitude. Further, we demonstrate the capability of the proposed approach to compute the electronic structure of a metallic system containing 1688 atoms using

  7. Learned vocal variation is associated with abrupt cryptic genetic change in a parrot species complex.

    PubMed

    Ribot, Raoul F H; Buchanan, Katherine L; Endler, John A; Joseph, Leo; Bennett, Andrew T D; Berg, Mathew L

    2012-01-01

    Contact zones between subspecies or closely related species offer valuable insights into speciation processes. A typical feature of such zones is the presence of clinal variation in multiple traits. The nature of these traits and the concordance among clines are expected to influence whether and how quickly speciation will proceed. Learned signals, such as vocalizations in species having vocal learning (e.g. humans, many birds, bats and cetaceans), can exhibit rapid change and may accelerate reproductive isolation between populations. Therefore, particularly strong concordance among clines in learned signals and population genetic structure may be expected, even among continuous populations in the early stages of speciation. However, empirical evidence for this pattern is often limited because differences in vocalisations between populations are driven by habitat differences or have evolved in allopatry. We tested for this pattern in a unique system where we may be able to separate effects of habitat and evolutionary history. We studied geographic variation in the vocalizations of the crimson rosella (Platycercus elegans) parrot species complex. Parrots are well known for their life-long vocal learning and cognitive abilities. We analysed contact calls across a ca 1300 km transect encompassing populations that differed in neutral genetic markers and plumage colour. We found steep clinal changes in two acoustic variables (fundamental frequency and peak frequency position). The positions of the two clines in vocal traits were concordant with a steep cline in microsatellite-based genetic variation, but were discordant with the steep clines in mtDNA, plumage and habitat. Our study provides new evidence that vocal variation, in a species with vocal learning, can coincide with areas of restricted gene flow across geographically continuous populations. Our results suggest that traits that evolve culturally can be strongly associated with reduced gene flow between

  8. Complex patterns of cis-regulatory polymorphisms in ebony underlie standing pigmentation variation in Drosophila melanogaster.

    PubMed

    Miyagi, Ryutaro; Akiyama, Noriyoshi; Osada, Naoki; Takahashi, Aya

    2015-12-01

    Pigmentation traits in adult Drosophila melanogaster were used in this study to investigate how phenotypic variations in continuous ecological traits can be maintained in a natural population. First, pigmentation variation in the adult female was measured at seven different body positions in 20 strains from the Drosophila melanogaster Genetic Reference Panel (DGRP) originating from a natural population in North Carolina. Next, to assess the contributions of cis-regulatory polymorphisms of the genes involved in the melanin biosynthesis pathway, allele-specific expression levels of four genes were quantified by amplicon sequencing using a 454 GS Junior. Among those genes, ebony was significantly associated with pigmentation intensity of the thoracic segment. Detailed sequence analysis of the gene regulatory regions of this gene indicated that many different functional cis-regulatory alleles are segregating in the population and that variations outside the core enhancer element could potentially play important roles in the regulation of gene expression. In addition, a slight enrichment of distantly associated SNP pairs was observed in the ~10 kb cis-regulatory region of ebony, which suggested the presence of interacting elements scattered across the region. In contrast, sequence analysis in the core cis-regulatory region of tan indicated that SNPs within the region are significantly associated with allele-specific expression level of this gene. Collectively, the data suggest that the underlying genetic differences in the cis-regulatory regions that control intraspecific pigmentation variation can be more complex than those of interspecific pigmentation trait differences, where causal genetic changes are typically confined to modular enhancer elements.

  9. Existence of minimizers for Kohn-Sham within the local spin density approximation

    NASA Astrophysics Data System (ADS)

    Gontier, David

    2015-01-01

    The purpose of this article is to extend the work by Anantharaman and Cancès (2009 Ann. Inst. Henri Poincaré (C) 26 2425-55) and prove the existence of minimizers for the spin-polarized Kohn-Sham model in the presence of a magnetic field within the local spin density approximation. We show that for any magnetic field that vanishes at infinity, the existence of minimizers is ensured for neutral or positively charged systems. The proof relies on classical concentration-compactness techniques.

  10. Dynamical Correction to Linear Kohn-Sham Conductances from Static Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Kurth, S.; Stefanucci, G.

    2013-07-01

    For molecules weakly coupled to leads the exact linear Kohn-Sham (KS) conductance can be orders of magnitude larger than the true linear conductance due to the lack of dynamical exchange-correlation (xc) corrections. In this work we show how to incorporate dynamical effects in KS transport calculations. The only quantity needed is the static xc potential in the molecular junction. Our scheme provides a comprehensive description of Coulomb blockade without breaking the spin symmetry. This is explicitly demonstrated in single-wall nanotubes where the corrected conductance is in good agreement with experimental data whereas the KS conductance fails dramatically.

  11. Numerical Methods for a Kohn-Sham Density Functional Model Based on Optimal Transport.

    PubMed

    Chen, Huajie; Friesecke, Gero; Mendl, Christian B

    2014-10-14

    In this paper, we study numerical discretizations to solve density functional models in the "strictly correlated electrons" (SCE) framework. Unlike previous studies, our work is not restricted to radially symmetric densities. In the SCE framework, the exchange-correlation functional encodes the effects of the strong correlation regime by minimizing the pairwise Coulomb repulsion, resulting in an optimal transport problem. We give a mathematical derivation of the self-consistent Kohn-Sham-SCE equations, construct an efficient numerical discretization for this type of problem for N = 2 electrons, and apply it to the H2 molecule in its dissociating limit.

  12. Genetic specificity of a plant–insect food web: Implications for linking genetic variation to network complexity

    PubMed Central

    Barbour, Matthew A.; Fortuna, Miguel A.; Bascompte, Jordi; Nicholson, Joshua R.; Julkunen-Tiitto, Riitta; Jules, Erik S.; Crutsinger, Gregory M.

    2016-01-01

    Theory predicts that intraspecific genetic variation can increase the complexity of an ecological network. To date, however, we are lacking empirical knowledge of the extent to which genetic variation determines the assembly of ecological networks, as well as how the gain or loss of genetic variation will affect network structure. To address this knowledge gap, we used a common garden experiment to quantify the extent to which heritable trait variation in a host plant determines the assembly of its associated insect food web (network of trophic interactions). We then used a resampling procedure to simulate the additive effects of genetic variation on overall food-web complexity. We found that trait variation among host-plant genotypes was associated with resistance to insect herbivores, which indirectly affected interactions between herbivores and their insect parasitoids. Direct and indirect genetic effects resulted in distinct compositions of trophic interactions associated with each host-plant genotype. Moreover, our simulations suggest that food-web complexity would increase by 20% over the range of genetic variation in the experimental population of host plants. Taken together, our results indicate that intraspecific genetic variation can play a key role in structuring ecological networks, which may in turn affect network persistence. PMID:26858398

  13. Canine parvovirus enteritis, canine distemper, and major histocompatibility complex genetic variation in Mexican wolves.

    PubMed

    Hedrick, Philip W; Lee, Rhonda N; Buchanan, Colleen

    2003-10-01

    The endangered Mexican wolf (Canis lupus baileyi) was recently reintroduced into Arizona and New Mexico (USA). In 1999 and 2000, pups from three litters that were part of the reintroduction program died of either canine parvovirus or canine distemper. Overall, half (seven of 14) of the pups died of either canine parvovirus or canine distemper. The parents and their litters were analyzed for variation at the class II major histocompatibility complex (MHC) gene DRB1. Similar MHC genes are related to disease resistance in other species. All six of the surviving pups genotyped for the MHC gene were heterozygous while five of the pups that died were heterozygous and one was homozygous. Resistance to pathogens is an important aspect of the management and long-term survival of endangered taxa, such as the Mexican wolf.

  14. The Nature of Genetic Variation for Complex Traits Revealed by GWAS and Regional Heritability Mapping Analyses

    PubMed Central

    Caballero, Armando; Tenesa, Albert; Keightley, Peter D.

    2015-01-01

    We use computer simulations to investigate the amount of genetic variation for complex traits that can be revealed by single-SNP genome-wide association studies (GWAS) or regional heritability mapping (RHM) analyses based on full genome sequence data or SNP chips. We model a large population subject to mutation, recombination, selection, and drift, assuming a pleiotropic model of mutations sampled from a bivariate distribution of effects of mutations on a quantitative trait and fitness. The pleiotropic model investigated, in contrast to previous models, implies that common mutations of large effect are responsible for most of the genetic variation for quantitative traits, except when the trait is fitness itself. We show that GWAS applied to the full sequence increases the number of QTL detected by as much as 50% compared to the number found with SNP chips but only modestly increases the amount of additive genetic variance explained. Even with full sequence data, the total amount of additive variance explained is generally below 50%. Using RHM on the full sequence data, a slightly larger number of QTL are detected than by GWAS if the same probability threshold is assumed, but these QTL explain a slightly smaller amount of genetic variance. Our results also suggest that most of the missing heritability is due to the inability to detect variants of moderate effect (∼0.03–0.3 phenotypic SDs) segregating at substantial frequencies. Very rare variants, which are more difficult to detect by GWAS, are expected to contribute little genetic variation, so their eventual detection is less relevant for resolving the missing heritability problem. PMID:26482794

  15. Major histocompatibility complex class II genetic variation in forest musk deer (Moschus berezovskii) in China.

    PubMed

    Yao, Gang; Zhu, Ying; Wan, Qiu-Hong; Fang, Sheng-Guo

    2015-10-01

    The major histocompatibility complex (MHC) plays an important role in the immune system of vertebrates. We used the second exon of four MHC class II genes (DRA, DQA1, DQA2 and DRB3) to assess the overall MHC variation in forest musk deer (Moschus berezovskii). We also compared the MHC variation in captive and wild populations. We observed 22 alleles at four loci (four at DRA, four at DQA1, four at DQA2 and 10 at DRB3), 15 of which were newly identified alleles. Results suggest that forest musk deer maintain relatively high MHC variation, which may result from balancing selection. Moreover, considerable diversity was observed at the DRA locus. We found a high frequency of Mobe-DRA*02, Mobe-DQA1*01 and Mobe-DQA2*05 alleles, which may be important for pathogen resistance. A Ewens-Watterson test showed that the DRB3 locus in the wild population had experienced recent balancing selection. We detected a small divergence at the DRA locus, suggesting the effect of weak positive selection on the DRA gene. Alternatively, this locus may be young and not yet adapted a wide spectrum of alleles for pathogen resistance. The significant heterozygosity deficit observed at the DQA1 and DRB3 loci in the captive population and at all four loci in the wild population may be the result of a population bottleneck. Additionally, MHC genetic diversity was higher in the wild population than in the captive, suggesting that the wild population may have the ability to respond to a wider range of pathogens.

  16. Efficient iterative method for solving the Dirac-Kohn-Sham density functional theory

    SciTech Connect

    Lin, Lin; Shao, Sihong; E, Weinan

    2012-11-06

    We present for the first time an efficient iterative method to directly solve the four-component Dirac-Kohn-Sham (DKS) density functional theory. Due to the existence of the negative energy continuum in the DKS operator, the existing iterative techniques for solving the Kohn-Sham systems cannot be efficiently applied to solve the DKS systems. The key component of our method is a novel filtering step (F) which acts as a preconditioner in the framework of the locally optimal block preconditioned conjugate gradient (LOBPCG) method. The resulting method, dubbed the LOBPCG-F method, is able to compute the desired eigenvalues and eigenvectors in the positive energy band without computing any state in the negative energy band. The LOBPCG-F method introduces mild extra cost compared to the standard LOBPCG method and can be easily implemented. We demonstrate our method in the pseudopotential framework with a planewave basis set which naturally satisfies the kinetic balance prescription. Numerical results for Pt$_{2}$, Au$_{2}$, TlF, and Bi$_{2}$Se$_{3}$ indicate that the LOBPCG-F method is a robust and efficient method for investigating the relativistic effect in systems containing heavy elements.

  17. Generalization of the Kohn-Sham system that can represent arbitrary one-electron density matrices

    NASA Astrophysics Data System (ADS)

    van Dam, Hubertus J. J.

    2016-05-01

    Density functional theory is currently the most widely applied method in electronic structure theory. The Kohn-Sham method, based on a fictitious system of noninteracting particles, is the workhorse of the theory. The particular form of the Kohn-Sham wave function admits only idempotent one-electron density matrices whereas wave functions of correlated electrons in post-Hartree-Fock methods invariably have fractional occupation numbers. Here we show that by generalizing the orbital concept and introducing a suitable dot product as well as a probability density, a noninteracting system can be chosen that can represent the one-electron density matrix of any system, even one with fractional occupation numbers. This fictitious system ensures that the exact electron density is accessible within density functional theory. It can also serve as the basis for reduced density matrix functional theory. Moreover, to aid the analysis of the results the orbitals may be assigned energies from a mean-field Hamiltonian. This produces energy levels that are akin to Hartree-Fock orbital energies such that conventional analyses based on Koopmans' theorem are available. Finally, this system is convenient in formalisms that depend on creation and annihilation operators as they are trivially applied to single-determinant wave functions.

  18. Generalization of the Kohn-Sham system that can represent arbitrary one-electron density matrices

    SciTech Connect

    Hubertus J. J. van Dam

    2016-04-27

    Density functional theory is currently the most widely applied method in electronic structure theory. The Kohn-Sham method, based on a fictitious system of noninteracting particles, is the workhorse of the theory. The particular form of the Kohn-Sham wave function admits only idempotent one-electron density matrices whereas wave functions of correlated electrons in post-Hartree-Fock methods invariably have fractional occupation numbers. Here we show that by generalizing the orbital concept and introducing a suitable dot product as well as a probability density, a noninteracting system can be chosen that can represent the one-electron density matrix of any system, even one with fractional occupation numbers. This fictitious system ensures that the exact electron density is accessible within density functional theory. It can also serve as the basis for reduced density matrix functional theory. Moreover, to aid the analysis of the results the orbitals may be assigned energies from a mean-field Hamiltonian. This produces energy levels that are akin to Hartree-Fock orbital energies such that conventional analyses based on Koopmans' theorem are available. Lastly, this system is convenient in formalisms that depend on creation and annihilation operators as they are trivially applied to single-determinant wave functions.

  19. Generalization of the Kohn-Sham system that can represent arbitrary one-electron density matrices

    DOE PAGES

    Hubertus J. J. van Dam

    2016-04-27

    Density functional theory is currently the most widely applied method in electronic structure theory. The Kohn-Sham method, based on a fictitious system of noninteracting particles, is the workhorse of the theory. The particular form of the Kohn-Sham wave function admits only idempotent one-electron density matrices whereas wave functions of correlated electrons in post-Hartree-Fock methods invariably have fractional occupation numbers. Here we show that by generalizing the orbital concept and introducing a suitable dot product as well as a probability density, a noninteracting system can be chosen that can represent the one-electron density matrix of any system, even one with fractionalmore » occupation numbers. This fictitious system ensures that the exact electron density is accessible within density functional theory. It can also serve as the basis for reduced density matrix functional theory. Moreover, to aid the analysis of the results the orbitals may be assigned energies from a mean-field Hamiltonian. This produces energy levels that are akin to Hartree-Fock orbital energies such that conventional analyses based on Koopmans' theorem are available. Lastly, this system is convenient in formalisms that depend on creation and annihilation operators as they are trivially applied to single-determinant wave functions.« less

  20. Peroxidase complex with concomitant anodal and cathodal variation in red-fruited tomato species.

    PubMed

    Rick, C M; Fobes, J F

    1976-03-01

    Four groups of bands (a-d) are controlled by 19 alleles of the Peroxidase-4 (Prx-4) complex in the red-fruited tomato species, Lycopersicon esculentum and L. pimpinellifolium. Heterozygotes can be detected by virtue of codominance in all combinations except a few in which bands of single groups are absent ("semi-null" alleles). No recombinations were detected in 7419 F(2) segregants of 53 different combinations of alleles. A maximum fiducial limit (P = 0.01) of 0.08% crossing-over between any Prx-4 band groups is estimated. Variation of the anodal b bands is absolutely associated with that of the cathodal d band in respect to presence versus absence and direction of migration. In respect to the origin of these variants, the probability of 18 instances of simultaneous mutation of genes at two loci, always in such complete agreement, is so remote that no more than one locus could conceivably govern b and d. The disposition of a is not similarly associated with that of the other bands, while that of the faint-staining c could not always be reliably resolved. The negation of all save extremely low recombination rates and the observed concomitant variation of b and d strongly support the concept of single locus control of all Prx-4 banding, this hypothesis being espoused until rejection should be required be required by future research. Models of single locus control of several isozymes are discussed.

  1. Diploptene δ13C values from contemporary thermokarst lake sediments show complex spatial variation

    NASA Astrophysics Data System (ADS)

    Davies, Kimberley L.; Pancost, Richard D.; Edwards, Mary E.; Anthony, Katey M. Walter; Langdon, Peter G.; Chaves Torres, Lidia

    2016-05-01

    Cryospheric changes in northern high latitudes are linked to significant greenhouse gas flux to the atmosphere, for example, methane that originates from organic matter decomposition in thermokarst lakes. The set of pathways that link methane production in sediments, via oxidation in the lake system, to the flux of residual methane to the atmosphere is complex and exhibits temporal and spatial variation. The isotopic signal of bacterial biomarkers (hopanoids, e.g. diploptene) in sediments has been used to identify contemporary ocean-floor methane seeps and, in the geological record, periods of enhanced methane production (e.g. the PETM). The biomarker approach could potentially be used to assess temporal changes in lake emissions through the Holocene via the sedimentary biomarker record. However, there are no data on the consistency of the signal of isotopic depletion in relation to source or on the amount of noise (unexplained variation) in biomarker values from modern lake sediments. We assessed methane oxidation as represented by the isotopic signal of biomarkers from methane oxidising bacteria (MOB) in multiple surface sediment samples in three distinct areas known to emit varying levels of methane in two shallow Alaskan thermokarst lakes. Diploptene was present and had δ13C values lower than -38 ‰ in all sediments analysed, suggesting methane oxidation was widespread. However, there was considerable variation in δ13C values within each area. The most 13C-depleted diploptene was found in an area of high methane ebullition in Ace Lake (diploptene δ13C values between -68.2 and -50.1 ‰). In contrast, significantly higher diploptene δ13C values (between -42.9 and -38.8 ‰) were found in an area of methane ebullition in Smith Lake. δ13C values of diploptene between -56.8 and -46.9 ‰ were found in the centre of Smith Lake, where ebullition rates are low but diffusive methane efflux occurs. The small-scale heterogeneity of the samples may reflect patchy

  2. O the Topological Complexity of the Cost Function in Variational Data Assimilation

    NASA Astrophysics Data System (ADS)

    Li, Yong

    We investigate here the causes and implications of topological complexity in the cost function in the context of the variational data assimilation. This complexity, which can take many forms from multiple minima to very flat regions with almost no curvature, causes severe problems for minimization algorithms and can lead to a retrieved state that is strongly related to the initial guess, i.e., non-uniqueness. To determine the origin of multiple minima, we first utilize guess, simple dynamical systems: the chaotic logistic equation, Duffing's equation, and Burgers equation. We demonstrate that multiple minima are associated with nonlinear dynamics, and that the length of the assimilation window and data availability also exert a strong influence over the topology of the cost function. This finding is validated for the somewhat more complicated resonant Rossby wave model. Having established the principal causes of topological complexity in the cost function, we extend our work to the convective regime by performing retrievals using simulated data from a 3-D Boussinesq model and its adjoint. We find that the complexity of the cost function is not as serious a problem as shown in the simple nonlinear systems. Only in an extreme case, where the first guess is chosen to differ substantially from the true solution, does the retrieved state depart from the control, and even then it does so only superficially. This result could be due to the high dimensionality (i.e., greater degrees of freedom) of the Boussinesq flow. By including a penalty term, consisting of second-order temporal derivatives of the model state variables, the cost function is regularized and an improved retrieval is obtained. Such a penalty term can also improve the conditioning of the Hessian and thus the efficiency of the minimization process. The role of diffusion in data retrieval is also examined, and a linear analysis based on the one-dimensional diffusion equation shows that the retrieved initial

  3. Construction of integrable model Kohn-Sham potentials by analysis of the structure of functional derivatives

    SciTech Connect

    Gaiduk, Alex P.; Staroverov, Viktor N.

    2011-01-15

    A directly approximated exchange-correlation potential should, by construction, be a functional derivative of some density functional in order to avoid unphysical results. Using generalized gradient approximations (GGAs) as an example, we show that functional derivatives of explicit density functionals have a very rigid inner structure, the knowledge of which allows one to build the entire functional derivative from a small part. Based on this analysis, we develop a method for direct construction of integrable Kohn-Sham potentials. As an illustration, we transform the model potential of van Leeuwen and Baerends (which is not a functional derivative) into a semilocal exchange potential that has a parent GGA, yields accurate energies, and is free from the artifacts inherent in existing semilocal potential approximations.

  4. Configuration interaction with Kohn Sham orbitals and their relation to excited electronic states

    NASA Astrophysics Data System (ADS)

    Bouř, Petr

    2001-09-01

    Kohn-Sham (KS) orbitals in CH 2, formaldehyde and acetone molecules were used as reference states for configuration interaction (CI) instead of the usual Hartree-Fock (HF) orbitals. A little difference in overall accuracy of electronic excitation energies was found between these schemes. However, analysis of the wave functions indicated that Slater determinant with the KS orbitals is more suitable for construction of the electronic states. Typically, the main expansion coefficients for the CI/KS procedure were closer to unity than those for HF. The difference was most pronounced for the lowest-energy transitions, while the two methods provided more comparable results for the higher-energy states. Similar behaviour of singlet and triplet states was observed. The results justify the common practice of using the KS determinant as a wave function, for example in sum-over-states theories.

  5. Effects of edge magnetism on the Kohn anomalies of zigzag graphene nanoribbons.

    PubMed

    Culchac, F J; Capaz, Rodrigo B

    2016-02-12

    The effects of edge magnetism on the Kohn anomaly (KA) of the G-band phonons of zigzag graphene nanoribbons (ZGNRs) are studied using a combination of the tight-binding and mean-field Hubbard models. We show that the opening of an energy gap, induced by magnetic ordering, significantly changes the KA effects, particularly for narrow ribbons in which the gap is larger than the phonon energy. Therefore, the G-band phonon frequency and lifetime are altered for a magnetically-ordered edge state with respect to an unpolarized edge state. The effects of temperature, ZGNR width, doping and transverse electric fields are systematically investigated. We propose using this effect to probe the magnetic order of edge states in graphene nanoribbons using Raman spectroscopy.

  6. Major-histocompatibility-complex variation in two species of cichlid fishes from Lake Malawi.

    PubMed

    Ono, H; O'hUigin, C; Tichy, H; Klein, J

    1993-09-01

    Lake Malawi in eastern Africa harbors > 500 endemic species of cichlid fishes, all of which are believed to have emerged from a single founding population in the past 2 Myr. Molecular characterization of differences among the species could provide important information about the nature of speciation in the period of adaptive radiation. Because of the close relationship, however, molecular variation among the species has been difficult to ascertain. In this communication, we provide evidence for extensive differences, in major-histocompatibility-complex (Mhc) class II genes, between two related species, Pseudotropheus zebra and Melanochromis auratus. We used specific primers to amplify and sequence intron 1 and exon 2 of the class II genes from 18 individuals. Although we found 20 different sequences among the 42 that we produced, there was not a single sequence shared by the two species. Thus the study suggests that different cichlid species of Lake Malawi have different profiles of class II alleles, presumably because the polymorphism present in the ancestral founding population segregated differentially into the various species. These results make Mhc genes an important tool for elucidating speciation.

  7. Variations in plasma motilin, somatostatin, and pancreatic polypeptide concentrations and the interdigestive myoelectric complex in dog.

    PubMed

    Poitras, P; Lemoyne, M; Tasse, D; Trudel, L; Yamada, T; Taylor, I L

    1985-12-01

    We have looked at the plasma concentrations of motilin, pancreatic polypeptide (PP), and somatostatin (STS) during the various phases of the interdigestive motor complex (IDMC) in dogs. As expected, motilin cyclical increase was always associated with the phase III of the IDMC. Statistical analysis of PP variations revealed a significant rise 10 min before duodenal phase III; however, in individual animals, this relationship was inconsistent. Although a dose-related increase in PP blood levels was induced by administration of synthetic canine motilin (0-200 ng kg-1 iv), fasting plasma levels of PP were not correlated with the concentrations of circulating endogenous motilin. After truncal vagotomy, while motilin release and the intestinal motility pattern remained unaltered, the phase III associated cyclical increases of PP disappeared. Infusion of physiological amounts of PP (1 microgram kg-1 h-1 for 3 h) mimicking the postprandial release failed to reproduce a fed pattern type of intestinal motility and of motilin secretion. No statistical correlation could be established between STS plasma levels and the motor activity of the intestine. STS plasma levels were not correlated with circulating concentrations of motilin and the exogenous administration of physiological doses of synthetic canine motilin failed to modify STS plasma levels. Morphine (200 micrograms kg-1 iv) stimulated only the release of motilin. These data suggest that the role played by circulating concentrations of PP and STS in the control of the IDMC in dog is at most minimal.

  8. The Microgeographical Patterns of Morphological and Molecular Variation of a Mixed Ploidy Population in the Species Complex Actinidia chinensis

    PubMed Central

    Liu, Yifei; Li, Dawei; Yan, Ling; Huang, Hongwen

    2015-01-01

    Polyploidy and hybridization are thought to have significant impacts on both the evolution and diversification of the genus Actinidia, but the structure and patterns of morphology and molecular diversity relating to ploidy variation of wild Actinidia plants remain much less understood. Here, we examine the distribution of morphological variation and ploidy levels along geographic and environmental variables of a large mixed-ploidy population of the A. chinensis species complex. We then characterize the extent of both genetic and epigenetic diversity and differentiation exhibited between individuals of different ploidy levels. Our results showed that while there are three ploidy levels in this population, hexaploids were constituted the majority (70.3%). Individuals with different ploidy levels were microgeographically structured in relation to elevation and extent of niche disturbance. The morphological characters examined revealed clear difference between diploids and hexaploids, however tetraploids exhibited intermediate forms. Both genetic and epigenetic diversity were high but the differentiation among cytotypes was weak, suggesting extensive gene flow and/or shared ancestral variation occurred in this population even across ploidy levels. Epigenetic variation was clearly correlated with changes in altitudes, a trend of continuous genetic variation and gradual increase of epigenomic heterogeneities of individuals was also observed. Our results show that complex interactions between the locally microgeographical environment, ploidy and gene flow impact A. chinensis genetic and epigenetic variation. We posit that an increase in ploidy does not broaden the species habitat range, but rather permits A. chinensis adaptation to specific niches. PMID:25658107

  9. Capturing variations in inundation with satellite remote sensing in a morphologically complex, large lake

    NASA Astrophysics Data System (ADS)

    Wu, Guiping; Liu, Yuanbo

    2015-04-01

    Poyang Lake is the largest freshwater lake in China, with high morphological complexity from south to north. In recent years, the lake has experienced expansion and shrinkage processes over both short- and long-term scales, resulting in significant hydrological, ecological and economic problems. Exactly how and how rapidly the processes of spatial change have occurred in the lake during the expansion and shrinkage periods is unknown. Such knowledge is of great importance for policymakers as it may help with flood/drought prevention, land use planning and lake ecological conservation. In this study, we investigated the spatial-temporal distribution and changing processes of inundation in Poyang Lake based on Moderate Resolution Imaging Spectroradiometer (MODIS) Level-1B data from 2000 to 2011. A defined water variation rate (WVR) and inundation frequency (IF) indicator revealed the water surface submersion and exposure processes of lake expansion and shrinkage in different zones which were divided according to the lake's hydrological and topographic features. Regional differences and significant seasonality variability were found in the annual and monthly mean IF. The monthly mean IF increased slowly from north to south during January-August but decreased quickly from south to north during September-December. During the lake expansion period, the lake-type water body zone (Zone II) had the fastest expansion rate, with a mean monthly WVR value of 34.47% in February-March, and was followed by the channel-type water body zone (Zone I) in March-May (22.47%). However, during the lake shrinkage period, rapid shrinkage first appeared around the alluvial delta zones in August-October. The sequence of lake surface shrinkage from August to December is exactly opposite to that of lake expansion from February to July. These complex inundation characteristics and changing process were driven by the high temporal variability of the river flows, the morphological diversity of the

  10. Latitudinal Variation of a Defensive Symbiosis in the Bugula neritina (Bryozoa) Sibling Species Complex

    PubMed Central

    Linneman, Jonathan; Paulus, Darcy; Lim-Fong, Grace; Lopanik, Nicole B.

    2014-01-01

    Mutualistic relationships are beneficial for both partners and are often studied within a single environment. However, when the range of the partners is large, geographical differences in selective pressure may shift the relationship outcome from positive to negative. The marine bryozoan Bugula neritina is a colonial invertebrate common in temperate waters worldwide. It is the source of bioactive polyketide metabolites, the bryostatins. Evidence suggests that an uncultured vertically transmitted symbiont, “Candidatus Endobugula sertula”, hosted by B. neritina produces the bryostatins, which protect the vulnerable larvae from predation. Studies of B. neritina along the North American Atlantic coast revealed a complex of two morphologically similar sibling species separated by an apparent biogeographic barrier: the Type S sibling species was found below Cape Hatteras, North Carolina, while Type N was found above. Interestingly, the Type N colonies lack “Ca. Endobugula sertula” and, subsequently, defensive bryostatins; their documented northern distribution was consistent with traditional biogeographical paradigms of latitudinal variation in predation pressure. Upon further sampling of B. neritina populations, we found that both host types occur in wider distribution, with Type N colonies living south of Cape Hatteras, and Type S to the north. Distribution of the symbiont, however, was not restricted to Type S hosts. Genetic and microscopic evidence demonstrates the presence of the symbiont in some Type N colonies, and larvae from these colonies are endowed with defensive bryostatins and contain “Ca. Endobugula sertula”. Molecular analysis of the symbiont from Type N colonies suggests an evolutionarily recent acquisition, which is remarkable for a symbiont thought to be transmitted only vertically. Furthermore, most Type S colonies found at higher latitudes lack the symbiont, suggesting that this host-symbiont relationship is more flexible than previously

  11. Molecular variation in the Paragonimus heterotremus complex in Thailand and Myanmar.

    PubMed

    Sanpool, Oranuch; Intapan, Pewpan M; Thanchomnang, Tongjit; Janwan, Penchom; Nawa, Yukifumi; Blair, David; Maleewong, Wanchai

    2013-12-01

    Paragonimiasis is an important food-borne parasitic zoonosis caused by infection with lung flukes of the genus Paragonimus. Of the 7 members of the genus known in Thailand until recently, only P. heterotremus has been confirmed as causing human disease. An 8th species, P. pseudoheterotremus, has recently been proposed from Thailand, and has been found in humans. Molecular data place this species as a sister species to P. heterotremus, and it is likely that P. pseudoheterotremus is not specifically distinct from P. heterotremus. In this study, we collected metacercariae of both nominal species (identification based on metacercarial morphology) from freshwater crabs from Phetchabun Province in northern Thailand, Saraburi Province in central Thailand, and Surat Thani Province in southern Thailand. In addition, we purchased freshwater crabs imported from Myanmar at Myawaddy Province, western Thailand, close to the Myanmar-Thailand border. The DNAs extracted from excysted metacercariae were PCR-amplified and sequenced for ITS2 and cox1 genes. The ITS2 sequences were nearly identical among all samples (99-100%). Phylogenies inferred from all available partial cox1 sequences contained several clusters. Sequences from Indian P. heterotremus formed a sister group to sequences from P. pseudoheterotremus-type metacercariae. Sequences of P. heterotremus from Thailand, Vietnam, and China formed a separate distinct clade. One metacercaria from Phitsanulok Province was distinct from all others. There is clearly considerable genetic variation in the P. heterotremus complex in Thailand and the form referred to as P. pseudoheterotremus is widely distributed in Thailand and the Thai-Myanmar border region.

  12. Latitudinal variation of a defensive symbiosis in the Bugula neritina (Bryozoa) sibling species complex.

    PubMed

    Linneman, Jonathan; Paulus, Darcy; Lim-Fong, Grace; Lopanik, Nicole B

    2014-01-01

    Mutualistic relationships are beneficial for both partners and are often studied within a single environment. However, when the range of the partners is large, geographical differences in selective pressure may shift the relationship outcome from positive to negative. The marine bryozoan Bugula neritina is a colonial invertebrate common in temperate waters worldwide. It is the source of bioactive polyketide metabolites, the bryostatins. Evidence suggests that an uncultured vertically transmitted symbiont, "Candidatus Endobugula sertula", hosted by B. neritina produces the bryostatins, which protect the vulnerable larvae from predation. Studies of B. neritina along the North American Atlantic coast revealed a complex of two morphologically similar sibling species separated by an apparent biogeographic barrier: the Type S sibling species was found below Cape Hatteras, North Carolina, while Type N was found above. Interestingly, the Type N colonies lack "Ca. Endobugula sertula" and, subsequently, defensive bryostatins; their documented northern distribution was consistent with traditional biogeographical paradigms of latitudinal variation in predation pressure. Upon further sampling of B. neritina populations, we found that both host types occur in wider distribution, with Type N colonies living south of Cape Hatteras, and Type S to the north. Distribution of the symbiont, however, was not restricted to Type S hosts. Genetic and microscopic evidence demonstrates the presence of the symbiont in some Type N colonies, and larvae from these colonies are endowed with defensive bryostatins and contain "Ca. Endobugula sertula". Molecular analysis of the symbiont from Type N colonies suggests an evolutionarily recent acquisition, which is remarkable for a symbiont thought to be transmitted only vertically. Furthermore, most Type S colonies found at higher latitudes lack the symbiont, suggesting that this host-symbiont relationship is more flexible than previously thought. Our

  13. Introgression from domestic goat generated variation at the major histocompatibility complex of Alpine ibex.

    PubMed

    Grossen, Christine; Keller, Lukas; Biebach, Iris; Croll, Daniel

    2014-06-01

    The major histocompatibility complex (MHC) is a crucial component of the vertebrate immune system and shows extremely high levels of genetic polymorphism. The extraordinary genetic variation is thought to be ancient polymorphisms maintained by balancing selection. However, introgression from related species was recently proposed as an additional mechanism. Here we provide evidence for introgression at the MHC in Alpine ibex (Capra ibex ibex). At a usually very polymorphic MHC exon involved in pathogen recognition (DRB exon 2), Alpine ibex carried only two alleles. We found that one of these DRB alleles is identical to a DRB allele of domestic goats (Capra aegagrus hircus). We sequenced 2489 bp of the coding and non-coding regions of the DRB gene and found that Alpine ibex homozygous for the goat-type DRB exon 2 allele showed nearly identical sequences (99.8%) to a breed of domestic goats. Using Sanger and RAD sequencing, microsatellite and SNP chip data, we show that the chromosomal region containing the goat-type DRB allele has a signature of recent introgression in Alpine ibex. A region of approximately 750 kb including the DRB locus showed high rates of heterozygosity in individuals carrying one copy of the goat-type DRB allele. These individuals shared SNP alleles both with domestic goats and other Alpine ibex. In a survey of four Alpine ibex populations, we found that the region surrounding the DRB allele shows strong linkage disequilibria, strong sequence clustering and low diversity among haplotypes carrying the goat-type allele. Introgression at the MHC is likely adaptive and introgression critically increased MHC DRB diversity in the genetically impoverished Alpine ibex. Our finding contradicts the long-standing view that genetic variability at the MHC is solely a consequence of ancient trans-species polymorphism. Introgression is likely an underappreciated source of genetic diversity at the MHC and other loci under balancing selection.

  14. Vesicularity variation to pyroclasts from silicic eruptions at Laguna del Maule volcanic complex, Chile

    NASA Astrophysics Data System (ADS)

    Wright, H. M. N.; Fierstein, J.; Amigo, A.; Miranda, J.

    2014-12-01

    Crystal-poor rhyodacitic to rhyolitic volcanic eruptions at Laguna del Maule volcanic complex, Chile have produced an astonishing range of textural variation to pyroclasts. Here, we focus on eruptive deposits from two Quaternary eruptions from vents on the northwestern side of the Laguna del Maule basin: the rhyolite of Loma de Los Espejos and the rhyodacite of Laguna Sin Puerto. Clasts in the pyroclastic fall and pyroclastic flow deposits from the rhyolite of Loma de Los Espejos range from dense, non-vesicular (obsidian) to highly vesicular, frothy (coarsely vesicular reticulite); where vesicularity varies from <1% to >90%. Bulk compositions range from 75.6-76.7 wt.% SiO2. The highest vesicularity clasts are found in early fall deposits and widely dispersed pyroclastic flow deposits; the frothy carapace to lava flows is similarly highly vesicular. Pyroclastic deposits also contain tube pumice, and macroscopically folded, finely vesicular, breadcrusted, and heterogeneously vesiculated textures. We speculate that preservation of the highest vesicularities requires relatively low decompression rates or open system degassing such that relaxation times were sufficient to allow extensive vesiculation. Such an inference is in apparent contradiction to documentation of Plinian dispersal to the eruption. Clasts in the pyroclastic fall deposit of the rhyodacite (68-72 wt.% SiO2) of Laguna Sin Puerto are finely vesicular, with vesicularity modes at ~50% and ~68% corresponding to gray and white pumice colors, respectively. Some clasts are banded in color (and vesicularity). All clasts were fragmented into highly angular particles, with subplanar to slightly concave exterior surfaces (average Wadell Roundness of clast margins between 0.32 and 0.39), indicating brittle fragmentation. In contrast to Loma de Los Espejos, high bubble number densities to Laguna Sin Puerto rhyodacite imply high decompression rates.

  15. Major histocompatibility complex variation in red wolves: evidence for common ancestry with coyotes and balancing selection.

    PubMed

    Hedrick, P W; Lee, R N; Garrigan, D

    2002-10-01

    We examined variation at a class II major histocompatibility complex (MHC) gene (DRB1) in the captive red wolf population and samples of coyotes from Texas and North Carolina. We found 4 alleles in the 48 red wolves, 8 alleles in the 10 coyotes from Texas and 15 alleles in the 29 coyotes from North Carolina. Two of the four alleles found in red wolves, Caru-2 and Caru-4, were found in both the Texas and North Carolina coyote samples. Allele Caru-1, previously found in gray wolves, was also found in the North Carolina sample. The most frequent red wolf allele, Caru-3, was not found in any of the coyote samples. However, an allele found in both the Texas and North Carolina coyote samples is only one nucleotide (one amino acid) different from this red wolf allele. Overall, it appears from examination of this MHC gene that red wolves are more closely related to coyotes than to gray wolves. There were a number of different types of evidence supporting the action of balancing selection in red wolves. Namely, there was: (i) an excess of heterozygotes compared with expectations; (ii) a higher rate of nonsynonymous than synonymous substitution for the functionally important antigen-binding site positions; (iii) an eight times higher average heterozygosity of individual amino acids at the positions identified as part of the antigen-binding site than those not associated with it; (iv) the amino acid divergence of four red wolf alleles was greater than that expected from a simulation of genetic drift; and (v) the distribution of alleles, and the distributions of amino acids at many positions were more even than expected from neutrality. Examination of the level and pattern of linkage disequilibria between pairs of sites suggest that the heterozygosity, substitution and frequencies at individual amino acids are not highly dependent upon each other.

  16. Visual Complexity in Orthographic Learning: Modeling Learning across Writing System Variations

    ERIC Educational Resources Information Center

    Chang, Li-Yun; Plaut, David C.; Perfetti, Charles A.

    2016-01-01

    The visual complexity of orthographies varies across writing systems. Prior research has shown that complexity strongly influences the initial stage of reading development: the perceptual learning of grapheme forms. This study presents a computational simulation that examines the degree to which visual complexity leads to grapheme learning…

  17. Orbital-free extension to Kohn-Sham density functional theory equation of state calculations: Application to silicon dioxide

    DOE PAGES

    Sjostrom, Travis; Crockett, Scott

    2015-09-02

    The liquid regime equation of state of silicon dioxide SiO2 is calculated via quantum molecular dynamics in the density range of 5 to 15 g/cc and with temperatures from 0.5 to 100 eV, including the α-quartz and stishovite phase Hugoniot curves. Below 8 eV calculations are based on Kohn-Sham density functional theory (DFT), and above 8 eV a new orbital-free DFT formulation, presented here, based on matching Kohn-Sham DFT calculations is employed. Recent experimental shock data are found to be in very good agreement with the current results. Finally both experimental and simulation data are used in constructing a newmore » liquid regime equation of state table for SiO2.« less

  18. Orbital-free extension to Kohn-Sham density functional theory equation of state calculations: Application to silicon dioxide

    SciTech Connect

    Sjostrom, Travis; Crockett, Scott

    2015-09-02

    The liquid regime equation of state of silicon dioxide SiO2 is calculated via quantum molecular dynamics in the density range of 5 to 15 g/cc and with temperatures from 0.5 to 100 eV, including the α-quartz and stishovite phase Hugoniot curves. Below 8 eV calculations are based on Kohn-Sham density functional theory (DFT), and above 8 eV a new orbital-free DFT formulation, presented here, based on matching Kohn-Sham DFT calculations is employed. Recent experimental shock data are found to be in very good agreement with the current results. Finally both experimental and simulation data are used in constructing a new liquid regime equation of state table for SiO2.

  19. Orbital-free extension to Kohn-Sham density functional theory equation of state calculations: Application to silicon dioxide

    NASA Astrophysics Data System (ADS)

    Sjostrom, Travis; Crockett, Scott

    2015-09-01

    The liquid regime equation of state of silicon dioxide SiO2 is calculated via quantum molecular dynamics in the density range of 5 -15 g/cm 3 and with temperatures from 0.5 to 100 eV, including the α -quartz and stishovite phase Hugoniot curves. Below 8 eV calculations are based on Kohn-Sham density functional theory (DFT), and above 8 eV a new orbital-free DFT formulation, presented here, based on matching Kohn-Sham DFT calculations is employed. Recent experimental shock data are found to be in very good agreement with the current results. Finally both experimental and simulation data are used in constructing a new liquid regime equation of state table for SiO2.

  20. The filial piety complex: variations on the Oedipus theme in Chinese literature and culture.

    PubMed

    Gu, Ming Dong

    2006-01-01

    The Oedipus complex is central to Western tradition, but not to Chinese culture. Occurrence of oedipal themes in Chinese literature is almost negligible. This phenomenon seems to support a contra-Freud claim: that a theory of European origin, the Oedipus complex, is not universal to human experience in non-Western cultures. However, this article suggests that powerful moral repression may cause the Oedipus complex to undergo structural transformations in some cultures. Through studying a sample of Chinese literary and film representations, the author argues that the Oedipus complex in Chinese culture has been transformed into a filial piety complex. Some conceptual issues are considered from a cross-cultural perspective.

  1. [Nictemeral variation of physical and chemical variables in the Paticos wetland, Ayapel swamp complex, Colombia].

    PubMed

    Montoya M, Yimmy; Aguirre R, Néstor

    2009-09-01

    The nictemeral variation of abiotic factors in a key factor for tropical organisms. We evaluated some climatic, physical and chemical variables during four surveys of the hydrologic cycle in the Paticos wetland (8 degrees 21'08.2" N, 75 degrees 08'45.7" W). Of climatic variables, pluviosity presented the highest variation (C.V. = 1 022%) followed by air temperature (C.V. = 19.7%). There was a high relation in the coefficients of variation for these variables (84:1). This relation may be associated with altitude. Throughout the day-night cycle, most variables presented significant differences; except for pluviosity, air and water temperature (because of their high variability). Variables most related with nictemeral variation were pluviosity, wind speed and direction, air temperature and dissolved oxygen.

  2. Physical Meaning of Virtual Kohn-Sham Orbitals and Orbital Energies: An Ideal Basis for the Description of Molecular Excitations.

    PubMed

    van Meer, R; Gritsenko, O V; Baerends, E J

    2014-10-14

    In recent years, several benchmark studies on the performance of large sets of functionals in time-dependent density functional theory (TDDFT) calculations of excitation energies have been performed. The tested functionals do not approximate exact Kohn-Sham orbitals and orbital energies closely. We highlight the advantages of (close to) exact Kohn-Sham orbitals and orbital energies for a simple description, very often as just a single orbital-to-orbital transition, of molecular excitations. Benchmark calculations are performed for the statistical average of orbital potentials (SAOP) functional for the potential [J. Chem. Phys. 2000, 112, 1344; 2001, 114, 652], which approximates the true Kohn-Sham potential much better than LDA, GGA, mGGA, and hybrid potentials do. An accurate Kohn-Sham potential does not only perform satisfactorily for calculated vertical excitation energies of both valence and Rydberg transitions but also exhibits appealing properties of the KS orbitals including occupied orbital energies close to ionization energies, virtual-occupied orbital energy gaps very close to excitation energies, realistic shapes of virtual orbitals, leading to straightforward interpretation of most excitations as single orbital transitions. We stress that such advantages are completely lost in time-dependent Hartree-Fock and partly in hybrid approaches. Many excitations and excitation energies calculated with local density, generalized gradient, and hybrid functionals are spurious. There is, with an accurate KS, or even the LDA or GGA potentials, nothing problematic about the "band gap" in molecules: the HOMO-LUMO gap is close to the first excitation energy (the optical gap).

  3. Restricted open-shell Kohn-Sham theory for π-π* transitions. I. Polyenes, cyanines, and protonated imines

    NASA Astrophysics Data System (ADS)

    Grimm, Stephan; Nonnenberg, Christel; Frank, Irmgard

    2003-12-01

    We present a self-consistent field algorithm for the restricted open-shell Kohn-Sham method which can be used to calculate excited states that have the same spatial symmetry as the corresponding ground states. The method is applied to π-π* transitions in polyenes, cyanines, and protonated imines. Excitation energies obtained with gradient corrected functionals are found to be significantly redshifted; the shift is constant within a homologous series. Planar excited state geometries have been optimized for all systems.

  4. Spectrum-splitting approach for Fermi-operator expansion in all-electron Kohn-Sham DFT calculations

    NASA Astrophysics Data System (ADS)

    Motamarri, Phani; Gavini, Vikram; Bhattacharya, Kaushik; Ortiz, Michael

    2017-01-01

    We present a spectrum-splitting approach to conduct all-electron Kohn-Sham density functional theory (DFT) calculations by employing Fermi-operator expansion of the Kohn-Sham Hamiltonian. The proposed approach splits the subspace containing the occupied eigenspace into a core subspace, spanned by the core eigenfunctions, and its complement, the valence subspace, and thereby enables an efficient computation of the Fermi-operator expansion by reducing the expansion to the valence-subspace projected Kohn-Sham Hamiltonian. The key ideas used in our approach are as follows: (i) employ Chebyshev filtering to compute a subspace containing the occupied states followed by a localization procedure to generate nonorthogonal localized functions spanning the Chebyshev-filtered subspace; (ii) compute the Kohn-Sham Hamiltonian projected onto the valence subspace; (iii) employ Fermi-operator expansion in terms of the valence-subspace projected Hamiltonian to compute the density matrix, electron density, and band energy. We demonstrate the accuracy and performance of the method on benchmark materials systems involving silicon nanoclusters up to 1330 electrons, a single gold atom, and a six-atom gold nanocluster. The benchmark studies on silicon nanoclusters revealed a staggering fivefold reduction in the Fermi-operator expansion polynomial degree by using the spectrum-splitting approach for accuracies in the ground-state energies of ˜10-4Ha/atom with respect to reference calculations. Further, numerical investigations on gold suggest that spectrum splitting is indispensable to achieve meaningful accuracies, while employing Fermi-operator expansion.

  5. Advances in biotechnology and linking outputs to variation in complex traits: Plant and Animal Genome meeting January 2012.

    PubMed

    Appels, R; Barrero, R; Bellgard, M

    2012-03-01

    The Plant and Animal Genome (PAG, held annually) meeting in January 2012 provided insights into the advances in plant, animal, and microbe genome studies particularly as they impact on our understanding of complex biological systems. The diverse areas of biology covered included the advances in technologies, variation in complex traits, genome change in evolution, and targeting phenotypic changes, across the broad spectrum of life forms. This overview aims to summarize the major advances in research areas presented in the plenary lectures and does not attempt to summarize the diverse research activities covered throughout the PAG in workshops, posters, presentations, and displays by suppliers of cutting-edge technologies.

  6. Full Parallel Implementation of an All-Electron Four-Component Dirac-Kohn-Sham Program.

    PubMed

    Rampino, Sergio; Belpassi, Leonardo; Tarantelli, Francesco; Storchi, Loriano

    2014-09-09

    A full distributed-memory implementation of the Dirac-Kohn-Sham (DKS) module of the program BERTHA (Belpassi et al., Phys. Chem. Chem. Phys. 2011, 13, 12368-12394) is presented, where the self-consistent field (SCF) procedure is replicated on all the parallel processes, each process working on subsets of the global matrices. The key feature of the implementation is an efficient procedure for switching between two matrix distribution schemes, one (integral-driven) optimal for the parallel computation of the matrix elements and another (block-cyclic) optimal for the parallel linear algebra operations. This approach, making both CPU-time and memory scalable with the number of processors used, virtually overcomes at once both time and memory barriers associated with DKS calculations. Performance, portability, and numerical stability of the code are illustrated on the basis of test calculations on three gold clusters of increasing size, an organometallic compound, and a perovskite model. The calculations are performed on a Beowulf and a BlueGene/Q system.

  7. All-electron Kohn-Sham density functional theory on hierarchic finite element spaces

    NASA Astrophysics Data System (ADS)

    Schauer, Volker; Linder, Christian

    2013-10-01

    In this work, a real space formulation of the Kohn-Sham equations is developed, making use of the hierarchy of finite element spaces from different polynomial order. The focus is laid on all-electron calculations, having the highest requirement onto the basis set, which must be able to represent the orthogonal eigenfunctions as well as the electrostatic potential. A careful numerical analysis is performed, which points out the numerical intricacies originating from the singularity of the nuclei and the necessity for approximations in the numerical setting, with the ambition to enable solutions within a predefined accuracy. In this context the influence of counter-charges in the Poisson equation, the requirement of a finite domain size, numerical quadratures and the mesh refinement are examined as well as the representation of the electrostatic potential in a high order finite element space. The performance and accuracy of the method is demonstrated in computations on noble gases. In addition the finite element basis proves its flexibility in the calculation of the bond-length as well as the dipole moment of the carbon monoxide molecule.

  8. Orbitals from local RDMFT: Are they Kohn-Sham or natural orbitals?

    SciTech Connect

    Theophilou, Iris; Helbig, Nicole; Lathiotakis, Nektarios N.; Gidopoulos, Nikitas I.; Rubio, Angel

    2015-08-07

    Recently, an approximate theoretical framework was introduced, called local reduced density matrix functional theory (local-RDMFT), where functionals of the one-body reduced density matrix (1-RDM) are minimized under the additional condition that the optimal orbitals satisfy a single electron Schrödinger equation with a local potential. In the present work, we focus on the character of these optimal orbitals. In particular, we compare orbitals obtained by local-RDMFT with those obtained with the full minimization (without the extra condition) by contrasting them against the exact NOs and orbitals from a density functional calculation using the local density approximation (LDA). We find that the orbitals from local-RMDFT are very close to LDA orbitals, contrary to those of the full minimization that resemble the exact NOs. Since local RDMFT preserves the good quality of the description of strong static correlation, this finding opens the way to a mixed density/density matrix scheme, where Kohn-Sham orbitals obtain fractional occupations from a minimization of the occupation numbers using 1-RDM functionals. This will allow for a description of strong correlation at a cost only minimally higher than a density functional calculation.

  9. Optimized unrestricted Kohn-Sham potentials from ab initio spin densities

    NASA Astrophysics Data System (ADS)

    Boguslawski, Katharina; Jacob, Christoph R.; Reiher, Markus

    2013-01-01

    The reconstruction of the exchange-correlation potential from accurate ab initio electron densities can provide insights into the limitations of the currently available approximate functionals and provide guidance for devising improved approximations for density-functional theory (DFT). For open-shell systems, the spin density is introduced as an additional fundamental variable in spin-DFT. Here, we consider the reconstruction of the corresponding unrestricted Kohn-Sham (KS) potentials from accurate ab initio spin densities. In particular, we investigate whether it is possible to reconstruct the spin exchange-correlation potential, which determines the spin density in unrestricted KS-DFT, despite the numerical difficulties inherent to the optimization of potentials with finite orbital basis sets. We find that the recently developed scheme for unambiguously singling out an optimal optimized potential [Ch. R. Jacob, J. Chem. Phys. 135, 244102 (2011), 10.1063/1.3670414] can provide such spin potentials accurately. This is demonstrated for two test cases, the lithium atom and the dioxygen molecule, and target (spin) densities from full configuration interaction and complete active space self-consistent field calculations, respectively.

  10. Kohn-Sham density functional theory prediction of fracture in silicon carbide under mixed mode loading

    NASA Astrophysics Data System (ADS)

    Leung, K. W. K.; Pan, Z. L.; Warner, D. H.

    2016-03-01

    The utility of silicon carbide (SiC) for high temperature structural application has been limited by its brittleness. To improve its ductility, it is paramount to develop a sound understanding of the mechanisms controlling crack propagation. In this manuscript, we present direct ab initio predictions of fracture in SiC under pure mode I and mixed mode loading, utilizing a Kohn-Sham Density Functional Theory (KSDFT) framework. Our results show that in both loading cases, cleavage occurs at a stress intensity factor (SIF) only slightly higher than the Griffith toughness, focusing on a (1 1 1) [1 \\bar{1} 0] crack in the 3C-SiC crystal structure. This lattice trapping effect is shown to decrease with mode mixity, due to the formation of a temporary surface bond that forms during decohesion under shear. Comparing the critical mode I SIF to the value obtained in experiments suggests that some plasticity may occur near a crack tip in SiC even at low temperatures. Ultimately, these findings provide a solid foundation upon which to study the influence of impurities on brittleness, and upon which to develop empirical potentials capable of realistically simulating fracture in SiC.

  11. Development of the cyclic cluster model formalism for Kohn-Sham auxiliary density functional theory methods.

    PubMed

    Janetzko, Florian; Köster, Andreas M; Salahub, Dennis R

    2008-01-14

    The development of the cyclic cluster model (CCM) formalism for Kohn-Sham auxiliary density functional theory (KS-ADFT) methods is presented. The CCM is a direct space approach for the calculation of perfect and defective systems under periodic boundary conditions. Translational symmetry is introduced in the CCM by integral weighting. A consistent weighting scheme for all two-center and three-center interactions appearing in the KS-ADFT method is presented. For the first time, an approach for the numerical integration of the exchange-correlation potential within the cyclic cluster formalism is derived. The presented KS-ADFT CCM implementation was applied to covalent periodic systems. The results of cyclic and molecular cluster model (MCM) calculations for trans-polyacetylene, graphene, and diamond are discussed as examples for systems periodic in one, two, and three dimensions, respectively. All structures were optimized. It is shown that the CCM results represent the results of MCM calculations in the limit of infinite molecular clusters. By analyzing the electronic structure, we demonstrate that the symmetry of the corresponding periodic systems is retained in CCM calculations. The obtained geometric and electronic structures are compared with available data from the literature.

  12. Variation of entropic elasticity of DNA-Psoralen complex under UV light

    NASA Astrophysics Data System (ADS)

    Rocha, M. S.; Mesquita, O. N.

    2005-08-01

    We measure the entropic elasticity of a single λ-DNA molecule and of a single DNA-Psoralen complex by doing stretching experiments with an optical tweezers. Psoralen is a photosensitive drug used in the treatment of many skin diseases, by impeding DNA replication. Psolaren intercalates the DNA and can form crosslinks with pyrimidine basis in opposite strands of DNA, when illuminated with UVA light. As crosslinks form the persistence length of the complex increases, indicating an increase in rigidity of the complex. We study the kinetics of DNA-Psoralen crosslink formation via changes in entropic elasticity of the complex.

  13. A global conformance quality model. A new strategic tool for minimizing defects caused by variation, error, and complexity

    SciTech Connect

    Hinckley, C. Martin

    1994-01-01

    The performance of Japanese products in the marketplace points to the dominant role of quality in product competition. Our focus is motivated by the tremendous pressure to improve conformance quality by reducing defects to previously unimaginable limits in the range of 1 to 10 parts per million. Toward this end, we have developed a new model of conformance quality that addresses each of the three principle defect sources: (1) Variation, (2) Human Error, and (3) Complexity. Although the role of variation in conformance quality is well documented, errors occur so infrequently that their significance is not well known. We have shown that statistical methods are not useful in characterizing and controlling errors, the most common source of defects. Excessive complexity is also a root source of defects, since it increases errors and variation defects. A missing link in the defining a global model has been the lack of a sound correlation between complexity and defects. We have used Design for Assembly (DFA) methods to quantify assembly complexity and have shown that assembly times can be described in terms of the Pareto distribution in a clear exception to the Central Limit Theorem. Within individual companies we have found defects to be highly correlated with DFA measures of complexity in broad studies covering tens of millions of assembly operations. Applying the global concepts, we predicted that Motorola`s Six Sigma method would only reduce defects by roughly a factor of two rather than orders of magnitude, a prediction confirmed by Motorola`s data. We have also shown that the potential defects rates of product concepts can be compared in the earliest stages of development. The global Conformance Quality Model has demonstrated that the best strategy for improvement depends upon the quality control strengths and weaknesses.

  14. Evaluation of the diurnal variation of near-surface temperature and winds from WRF numerical simulations over complex terrain

    NASA Astrophysics Data System (ADS)

    Zhang, H.; Pace, C.; Pu, Z.

    2011-12-01

    Near-surface atmospheric conditions, especially the temperature and winds, are characterized by their diurnal variations. Accurate representation and forecast of the diurnal variations are the essential components of numerical modeling and weather prediction. However, it is commonly challenging to accurately simulate and predict diurnal variations of near-surface atmospheric conditions over complex terrain, especially over the mountainous areas. In this study we evaluate the diurnal variation of near-surface temperature and winds from the numerical simulations generated by mesoscale community Weather Research and Forecasting (WRF) model. The model simulated surface temperature at 2-meter height and winds at 10-meter height are compared with these observations from surface mesonet observations in several different weather scenarios (winter inversion, cold front and low-level jet etc.) over the Inter-mountain West of US. Preliminary results show large discrepancies between model generated diurnal variations and observations in some cases. The mechanism and causes of these differences are further investigated. Implications of these results for model improvement and data assimilation are also discussed.

  15. A density matrix-based quasienergy formulation of the Kohn-Sham density functional response theory using perturbation- and time-dependent basis sets.

    PubMed

    Thorvaldsen, Andreas J; Ruud, Kenneth; Kristensen, Kasper; Jørgensen, Poul; Coriani, Sonia

    2008-12-07

    A general method is presented for the calculation of molecular properties to arbitrary order at the Kohn-Sham density functional level of theory. The quasienergy and Lagrangian formalisms are combined to derive response functions and their residues by straightforward differentiation of the quasienergy derivative Lagrangian using the elements of the density matrix in the atomic orbital representation as variational parameters. Response functions and response equations are expressed in the atomic orbital basis, allowing recent advances in the field of linear-scaling methodology to be used. Time-dependent and static perturbations are treated on an equal footing, and atomic basis sets that depend on the applied frequency-dependent perturbations may be used, e.g., frequency-dependent London atomic orbitals. The 2n+1 rule may be applied if computationally favorable, but alternative formulations using higher-order perturbed density matrices are also derived. These may be advantageous in order to minimize the number of response equations that needs to be solved, for instance, when one of the perturbations has many components, as is the case for the first-order geometrical derivative of the hyperpolarizability.

  16. A density matrix-based quasienergy formulation of the Kohn-Sham density functional response theory using perturbation- and time-dependent basis sets

    NASA Astrophysics Data System (ADS)

    Thorvaldsen, Andreas J.; Ruud, Kenneth; Kristensen, Kasper; Jørgensen, Poul; Coriani, Sonia

    2008-12-01

    A general method is presented for the calculation of molecular properties to arbitrary order at the Kohn-Sham density functional level of theory. The quasienergy and Lagrangian formalisms are combined to derive response functions and their residues by straightforward differentiation of the quasienergy derivative Lagrangian using the elements of the density matrix in the atomic orbital representation as variational parameters. Response functions and response equations are expressed in the atomic orbital basis, allowing recent advances in the field of linear-scaling methodology to be used. Time-dependent and static perturbations are treated on an equal footing, and atomic basis sets that depend on the applied frequency-dependent perturbations may be used, e.g., frequency-dependent London atomic orbitals. The 2n+1 rule may be applied if computationally favorable, but alternative formulations using higher-order perturbed density matrices are also derived. These may be advantageous in order to minimize the number of response equations that needs to be solved, for instance, when one of the perturbations has many components, as is the case for the first-order geometrical derivative of the hyperpolarizability.

  17. Deformation characteristics and associated clay-mineral variation in 2-3 km buried Hota accretionary complex, central Japan

    NASA Astrophysics Data System (ADS)

    Yamamoto, Y.; Kameda, J.; Yamaguchi, H.

    2009-12-01

    Although deformation and physical/chemical properties variation in aseismic-seismic transition zone were essential to examine critical changes in environmental parameters that result in earthquake, they are poorly understood because the appropriate samples buried 2-4 km have not been collected yet (scientific drilling has never reached there and most of ancient examples experienced the deeper burial depth and suffered thermal and physical overprinting). The lower to middle Miocene Hota accretionary complex is a unique example of on land accretionary complex, representing deformation and its physical/chemical properties of sediments just prior to entering the seismogenic realm. The maximum paleotemperature was estimated approximately 55-70°C (based on vitrinite reflectance) indicative of a maximum burial depth about 2-3 km assuming a paleo-geothermal gradient as 25-35°C/km. Accretionary complex in this temperature/depth range corresponds with an intermediate range between the core samples collected from the modern accretionary prism (e.g. Nankai, Barbados, and so on) and rocks in the ancient accretionary complexes on land. This presentation will treat the detailed structural and chemical analyses of the Hota accretionary complex to construct deformation properties of décollement zone and accretionary complex in its 2-3 km depth range and to discuss the interrelation between the early diagenesis (hydrocarbon/cations generation and sediment dewatering, etc.) and transition of the deformation properties. The deformation in this accretionary complex is characterized by two deformation styles: one is a few centimeter-scale phacoidal deformation representing clay minerals preferred orientation in the outer rim, whereas random fabric in the core, quite similar texture to the rocks in the present-Nankai décollement. The other is S-C style deformation (similar deformation to the mélanges in ancient accretionary complex on land) exhibiting block-in-matrix texture and

  18. Characterization of Native Protein Complexes and Protein Isoform Variation Using Size-fractionation-based Quantitative Proteomics*

    PubMed Central

    Kirkwood, Kathryn J.; Ahmad, Yasmeen; Larance, Mark; Lamond, Angus I.

    2013-01-01

    Proteins form a diverse array of complexes that mediate cellular function and regulation. A largely unexplored feature of such protein complexes is the selective participation of specific protein isoforms and/or post-translationally modified forms. In this study, we combined native size-exclusion chromatography (SEC) with high-throughput proteomic analysis to characterize soluble protein complexes isolated from human osteosarcoma (U2OS) cells. Using this approach, we have identified over 71,500 peptides and 1,600 phosphosites, corresponding to over 8,000 proteins, distributed across 40 SEC fractions. This represents >50% of the predicted U2OS cell proteome, identified with a mean peptide sequence coverage of 27% per protein. Three biological replicates were performed, allowing statistical evaluation of the data and demonstrating a high degree of reproducibility in the SEC fractionation procedure. Specific proteins were detected interacting with multiple independent complexes, as typified by the separation of distinct complexes for the MRFAP1-MORF4L1-MRGBP interaction network. The data also revealed protein isoforms and post-translational modifications that selectively associated with distinct subsets of protein complexes. Surprisingly, there was clear enrichment for specific Gene Ontology terms associated with differential size classes of protein complexes. This study demonstrates that combined SEC/MS analysis can be used for the system-wide annotation of protein complexes and to predict potential isoform-specific interactions. All of these SEC data on the native separation of protein complexes have been integrated within the Encyclopedia of Proteome Dynamics, an online, multidimensional data-sharing resource available to the community. PMID:24043423

  19. A Longitudinal Study of Complexity, Accuracy and Fluency Variation in Second Language Development

    ERIC Educational Resources Information Center

    Ferraris, Stefania

    2012-01-01

    This chapter presents the results of a study on interlanguage variation. The production of four L2 learners of Italian, tested four times at yearly intervals while engaged in four oral tasks, is compared to that of two native speakers, and analysed with quantitative CAF measures. Thus, time, task type, nativeness, as well as group vs. individual…

  20. Genetic variation in isolates of the Fusarium incarnatum-equiseti species complex recovered from cereals

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Fusarium incarnatum-equiseti species complex (FIESC) includes mycotoxigenic species associated with several diseases of cereals and other crops. These species are considered moderately aggressive and are reported to produce multiple mycotoxins, including beauvericin, zearalenone, equisetin, fusa...

  1. Rate-dependent variation in the duration of the QRS complex with left anterior fascicular block.

    PubMed

    Mirvis, D M; Bandura, J P; Brody, D A

    1977-10-01

    The case of a 67-year-old man with combined ischemic and valvular heart disease is presented. Electrocardiographic abnormalities included left anterior fascicular block with a variable duration of the QRS complex. The width of the QRS complex was dependent on the length of the cycle, being broader with short than with long preceding R-R intervals. This is interpreted as a tachycardia-dependent focal block coexisting with a fixed delay in fascicular conduction.

  2. Landscape complexity and soil moisture variation in south Georgia, USA, for remote sensing applications

    USGS Publications Warehouse

    Giraldo, M.A.; Bosch, D.; Madden, M.; Usery, L.; Kvien, Craig

    2008-01-01

    This research addressed the temporal and spatial variation of soil moisture (SM) in a heterogeneous landscape. The research objective was to investigate soil moisture variation in eight homogeneous 30 by 30 m plots, similar to the pixel size of a Landsat Thematic Mapper (TM) or Enhanced Thematic Mapper plus (ETM+) image. The plots were adjacent to eight stations of an in situ soil moisture network operated by the United States Department of Agriculture-Agriculture Research Service USDA-ARS in Tifton, GA. We also studied five adjacent agricultural fields to examine the effect of different landuses/land covers (LULC) (grass, orchard, peanuts, cotton and bare soil) on the temporal and spatial variation of soil moisture. Soil moisture field data were collected on eight occasions throughout 2005 and January 2006 to establish comparisons within and among eight homogeneous plots. Consistently throughout time, analysis of variance (ANOVA) showed high variation in the soil moisture behavior among the plots and high homogeneity in the soil moisture behavior within them. A precipitation analysis for the eight sampling dates throughout the year 2005 showed similar rainfall conditions for the eight study plots. Therefore, soil moisture variation among locations was explained by in situ local conditions. Temporal stability geostatistical analysis showed that soil moisture has high temporal stability within the small plots and that a single point reading can be used to monitor soil moisture status for the plot within a maximum 3% volume/volume (v/v) soil moisture variation. Similarly, t-statistic analysis showed that soil moisture status in the upper soil layer changes within 24 h. We found statistical differences in the soil moisture between the different LULC in the agricultural fields as well as statistical differences between these fields and the adjacent 30 by 30 m plots. From this analysis, it was demonstrated that spatial proximity is not enough to produce similar soil

  3. Landscape complexity and soil moisture variation in south Georgia, USA, for remote sensing applications

    NASA Astrophysics Data System (ADS)

    Giraldo, Mario A.; Bosch, David; Madden, Marguerite; Usery, Lynn; Kvien, Craig

    2008-08-01

    SummaryThis research addressed the temporal and spatial variation of soil moisture (SM) in a heterogeneous landscape. The research objective was to investigate soil moisture variation in eight homogeneous 30 by 30 m plots, similar to the pixel size of a Landsat Thematic Mapper (TM) or Enhanced Thematic Mapper plus (ETM+) image. The plots were adjacent to eight stations of an in situ soil moisture network operated by the United States Department of Agriculture-Agriculture Research Service USDA-ARS in Tifton, GA. We also studied five adjacent agricultural fields to examine the effect of different landuses/land covers (LULC) (grass, orchard, peanuts, cotton and bare soil) on the temporal and spatial variation of soil moisture. Soil moisture field data were collected on eight occasions throughout 2005 and January 2006 to establish comparisons within and among eight homogeneous plots. Consistently throughout time, analysis of variance (ANOVA) showed high variation in the soil moisture behavior among the plots and high homogeneity in the soil moisture behavior within them. A precipitation analysis for the eight sampling dates throughout the year 2005 showed similar rainfall conditions for the eight study plots. Therefore, soil moisture variation among locations was explained by in situ local conditions. Temporal stability geostatistical analysis showed that soil moisture has high temporal stability within the small plots and that a single point reading can be used to monitor soil moisture status for the plot within a maximum 3% volume/volume (v/v) soil moisture variation. Similarly, t-statistic analysis showed that soil moisture status in the upper soil layer changes within 24 h. We found statistical differences in the soil moisture between the different LULC in the agricultural fields as well as statistical differences between these fields and the adjacent 30 by 30 m plots. From this analysis, it was demonstrated that spatial proximity is not enough to produce similar

  4. Correlating genetic variation in carbon isotopic composition with complex climatic gradients.

    PubMed Central

    Comstock, J P; Ehleringer, J R

    1992-01-01

    Genetic variation in both carbon isotope discrimination and the proportions of leaf and photosynthetic twig tissues were observed in ecotypes of Hymenoclea salsola T.G., a common shrub in the deserts of the western United States, when grown under common garden conditions. These variations were correlated with climatic conditions in the habitats of origin through a model that described the leaf-to-air water vapor gradients experienced by plants during the growing season. Both carbon isotope discrimination and the proportion of leaves in the canopy were lower in plants derived from habitats with higher leaf-to-air vapor gradients, despite the fact that some of these sites received relatively high amounts of annual precipitation. These patterns were consistent with the notion that plants are able to maintain substantial control of water-use efficiency over large environmental gradients of temperature and moisture availability. PMID:1502194

  5. Exact exchange potential evaluated from occupied Kohn-Sham and Hartree-Fock solutions

    SciTech Connect

    Cinal, M.; Holas, A.

    2011-06-15

    The reported algorithm determines the exact exchange potential v{sub x} in an iterative way using energy shifts (ESs) and orbital shifts (OSs) obtained with finite-difference formulas from the solutions (occupied orbitals and their energies) of the Hartree-Fock-like equation and the Kohn-Sham-like equation, the former used for the initial approximation to v{sub x} and the latter for increments of ES and OS due to subsequent changes of v{sub x}. Thus, the need for solution of the differential equations for OSs, used by Kuemmel and Perdew [Phys. Rev. Lett. 90, 043004 (2003)], is bypassed. The iterated exchange potential, expressed in terms of ESs and OSs, is improved by modifying ESs at odd iteration steps and OSs at even steps. The modification formulas are related to the optimized-effective-potential equation (satisfied at convergence) written as the condition of vanishing density shift (DS). They are obtained, respectively, by enforcing its satisfaction through corrections to approximate OSs and by determining the optimal ESs that minimize the DS norm. The proposed method, successfully tested for several closed-(sub)shell atoms, from Be to Kr, within the density functional theory exchange-only approximation, proves highly efficient. The calculations using the pseudospectral method for representing orbitals give iterative sequences of approximate exchange potentials (starting with the Krieger-Li-Iafrate approximation) that rapidly approach the exact v{sub x} so that, for Ne, Ar, and Zn, the corresponding DS norm becomes less than 10{sup -6} after 13, 13, and 9 iteration steps for a given electron density. In self-consistent density calculations, orbital energies of 10{sup -4} hartree accuracy are obtained for these atoms after, respectively, 9, 12, and 12 density iteration steps, each involving just two steps of v{sub x} iteration, while the accuracy limit of 10{sup -6} to 10{sup -7} hartree is reached after 20 density iterations.

  6. Differential Regulation of Cryptic Genetic Variation Shapes the Genetic Interactome Underlying Complex Traits

    PubMed Central

    Yadav, Anupama; Dhole, Kaustubh

    2016-01-01

    Cryptic genetic variation (CGV) refers to genetic variants whose effects are buffered in most conditions but manifest phenotypically upon specific genetic and environmental perturbations. Despite having a central role in adaptation, contribution of CGV to regulation of quantitative traits is unclear. Instead, a relatively simplistic architecture of additive genetic loci is known to regulate phenotypic variation in most traits. In this paper, we investigate the regulation of CGV and its implication on the genetic architecture of quantitative traits at a genome-wide level. We use a previously published dataset of biparental recombinant population of Saccharomyces cerevisiae phenotyped in 34 diverse environments to perform single locus, two-locus, and covariance mapping. We identify loci that have independent additive effects as well as those which regulate the phenotypic manifestation of other genetic variants (variance QTL). We find that whereas additive genetic variance is predominant, a higher order genetic interaction network regulates variation in certain environments. Despite containing pleiotropic loci, with effects across environments, these genetic networks are highly environment specific. CGV is buffered under most allelic combinations of these networks and perturbed only in rare combinations resulting in high phenotypic variance. The presence of such environment specific genetic networks is the underlying cause of abundant gene–environment interactions. We demonstrate that overlaying identified molecular networks on such genetic networks can identify potential candidate genes and underlying mechanisms regulating phenotypic variation. Such an integrated approach applied to human disease datasets has the potential to improve the ability to predict disease predisposition and identify specific therapeutic targets. PMID:28172852

  7. Extensive recombination rate variation in the house mouse species complex inferred from genetic linkage maps.

    PubMed

    Dumont, Beth L; White, Michael A; Steffy, Brian; Wiltshire, Tim; Payseur, Bret A

    2011-01-01

    The rate of recombination is a key genomic parameter that displays considerable variation among taxa. Species comparisons have demonstrated that the rate of evolution in recombination rate is strongly dependent on the physical scale of measurement. Individual recombination hotspots are poorly conserved among closely related taxa, whereas genomic-scale recombination rate variation bears a strong signature of phylogenetic history. In contrast, the mode and tempo of evolution in recombination rates measured on intermediate physical scales is poorly understood. Here, we conduct a detailed statistical comparison between two whole-genome F₂ genetic linkage maps constructed from experimental intercrosses between closely related house mouse subspecies (Mus musculus). Our two maps profile a common wild-derived inbred strain of M. m. domesticus crossed to distinct wild-derived inbred strains representative of two other house mouse subspecies, M. m. castaneus and M. m. musculus. We identify numerous orthologous genomic regions with significant map length differences between these two crosses. Because the genomes of these recently diverged house mice are highly collinear, observed differences in map length (centimorgans) are suggestive of variation in broadscale recombination rate (centimorgans per megabase) within M. musculus. Collectively, these divergent intervals span 19% of the house mouse genome, disproportionately aggregating on the X chromosome. In addition, we uncover strong statistical evidence for a large effect, sex-linked, site-specific modifier of recombination rate segregating within M. musculus. Our findings reveal considerable variation in the megabase-scale recombination landscape among recently diverged taxa and underscore the continued importance of genetic linkage maps in the post-genome era.

  8. Read clouds uncover variation in complex regions of the human genome.

    PubMed

    Bishara, Alex; Liu, Yuling; Weng, Ziming; Kashef-Haghighi, Dorna; Newburger, Daniel E; West, Robert; Sidow, Arend; Batzoglou, Serafim

    2015-10-01

    Although an increasing amount of human genetic variation is being identified and recorded, determining variants within repeated sequences of the human genome remains a challenge. Most population and genome-wide association studies have therefore been unable to consider variation in these regions. Core to the problem is the lack of a sequencing technology that produces reads with sufficient length and accuracy to enable unique mapping. Here, we present a novel methodology of using read clouds, obtained by accurate short-read sequencing of DNA derived from long fragment libraries, to confidently align short reads within repeat regions and enable accurate variant discovery. Our novel algorithm, Random Field Aligner (RFA), captures the relationships among the short reads governed by the long read process via a Markov Random Field. We utilized a modified version of the Illumina TruSeq synthetic long-read protocol, which yielded shallow-sequenced read clouds. We test RFA through extensive simulations and apply it to discover variants on the NA12878 human sample, for which shallow TruSeq read cloud sequencing data are available, and on an invasive breast carcinoma genome that we sequenced using the same method. We demonstrate that RFA facilitates accurate recovery of variation in 155 Mb of the human genome, including 94% of 67 Mb of segmental duplication sequence and 96% of 11 Mb of transcribed sequence, that are currently hidden from short-read technologies.

  9. Toward Failure Modeling In Complex Dynamic Systems: Impact of Design and Manufacturing Variations

    NASA Technical Reports Server (NTRS)

    Tumer, Irem Y.; McAdams, Daniel A.; Clancy, Daniel (Technical Monitor)

    2001-01-01

    When designing vehicle vibration monitoring systems for aerospace devices, it is common to use well-established models of vibration features to determine whether failures or defects exist. Most of the algorithms used for failure detection rely on these models to detect significant changes during a flight environment. In actual practice, however, most vehicle vibration monitoring systems are corrupted by high rates of false alarms and missed detections. Research conducted at the NASA Ames Research Center has determined that a major reason for the high rates of false alarms and missed detections is the numerous sources of statistical variations that are not taken into account in the. modeling assumptions. In this paper, we address one such source of variations, namely, those caused during the design and manufacturing of rotating machinery components that make up aerospace systems. We present a novel way of modeling the vibration response by including design variations via probabilistic methods. The results demonstrate initial feasibility of the method, showing great promise in developing a general methodology for designing more accurate aerospace vehicle vibration monitoring systems.

  10. Sources of variation in the mutagenic potency of complex chemical mixtures based on the salmonella/microsome assay

    SciTech Connect

    Krewski, D.; Leroux, B.G.; Creason, J.; Claxton, L.

    1992-01-01

    Twenty laboratories worldwide participated in a collaborative trial sponsored by the International Program on Chemical Safety on the mutagenicity of complex mixtures as expressed in the Salmonella/microsome assay. The U.S. National Institute of Standards and Technology provided homogeneous reference samples of urban air and diesel particles and a coal tar solution to each participating laboratory, along with samples of benzo(a)pyrene and 1-nitropyrene which served as positive controls. Mutagenic potency was characterized by the slope of the initial linear component of the dose response curve. Analysis of variance revealed significant interlaboratory variation in mutagenic potency, which accounted for 57-96% of the total variance on a logarithmic scale, depending on the sample, strain and activation conditions. No significant differences were noted in the average potency reported for air and diesel particles between laboratories using soxhlet extracts and those using sonication, although there was larger interlaboratory variation for the soxhlet method.

  11. Finding the molecular basis of complex genetic variation in humans and mice

    PubMed Central

    Mott, Richard

    2006-01-01

    I survey the state of the art in complex trait analysis, including the use of new experimental and computational technologies and resources becoming available, and the challenges facing us. I also discuss how the prospects of rodent model systems compare with association mapping in humans. PMID:16524828

  12. Intragenomic rDNA ITS2 Variation in the Neotropical Anopheles (Nyssorhynchus) albitarsis Complex (Diptera: Culicidae)

    DTIC Science & Technology

    2006-12-07

    However, in Allopb,/er, there are examples of rONA intragenomic variation (\\X’ilkerson et al. 2004; Fairley et al. 2005), but its prevalence and...Anopheles species (Onyabe and Conn 1999; Wilkerson et al. 2004; Fairley et aI. 200S) and in other mos- quitoes in subfamily Culicinae (Black et a!. 1989...DNA 1TS2 sequences. J :-.led Entomo!’ 33:109-116. Dover GA. 1982. Molecular dri"e: a cnhesive mode of species evolution. Nature. 299:111-117. Fairley

  13. Direct calculation of the reactive transition matrix by L-squared quantum mechanical variational methods with complex boundary conditions

    NASA Technical Reports Server (NTRS)

    Sun, Yan; Yu, Chin-Hui; Kouri, Donald J.; Schwenke, David W.; Halvick, Philippe

    1989-01-01

    A new formalism of the generalized Newton variational principle for the calculation of quantum mechanical state-to-state reaction probabilities is presented. The reformulation involves solving directly for the transition matrix rather than the reactance mtrix so that calculations may be carried out for individual columns of the transition matrix without obtaining solutions for all possible initial channels. The convergence of calculations with real and complex boundary conditions are compared for H + H2 - H2 + H, O + H2 - OH + H, and O + HD - OH + D and OD + H.

  14. Chemical data and variation diagrams of igneous rocks from the Timber Mountain-Oasis Valley Caldera Complex, southern Nevada

    USGS Publications Warehouse

    Quinlivan, W.D.; Byers, F.M.

    1977-01-01

    Silica variation diagrams presented here are based on 162 chemical analyses of tuffs, lavas, and intrusives, representative of volcanic centers of the Timber Mountain-Oasis Valley caldera complex and cogenetic rocks of the Silent Canyon ca1dera. Most of the volcanic units sampled are shown on the U.S. Geological Survey geologic map of the Timber Mountain caldera area (I-891) and are described in U.S. Geological Survey Professional Paper 919. Early effusives of the complex, although slightly altered, are probably chemically, and petrographically, more like the calc-alkalic Fraction Tuff (Miocene) of the northern Nellis Air Force Base Bombing and Gunnery Range to the north, whereas effusives of later Miocene age, such as the Paintbrush and Timber Mountain Tuffs, are alkali-calcic.

  15. The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.

    PubMed

    Astle, William J; Elding, Heather; Jiang, Tao; Allen, Dave; Ruklisa, Dace; Mann, Alice L; Mead, Daniel; Bouman, Heleen; Riveros-Mckay, Fernando; Kostadima, Myrto A; Lambourne, John J; Sivapalaratnam, Suthesh; Downes, Kate; Kundu, Kousik; Bomba, Lorenzo; Berentsen, Kim; Bradley, John R; Daugherty, Louise C; Delaneau, Olivier; Freson, Kathleen; Garner, Stephen F; Grassi, Luigi; Guerrero, Jose; Haimel, Matthias; Janssen-Megens, Eva M; Kaan, Anita; Kamat, Mihir; Kim, Bowon; Mandoli, Amit; Marchini, Jonathan; Martens, Joost H A; Meacham, Stuart; Megy, Karyn; O'Connell, Jared; Petersen, Romina; Sharifi, Nilofar; Sheard, Simon M; Staley, James R; Tuna, Salih; van der Ent, Martijn; Walter, Klaudia; Wang, Shuang-Yin; Wheeler, Eleanor; Wilder, Steven P; Iotchkova, Valentina; Moore, Carmel; Sambrook, Jennifer; Stunnenberg, Hendrik G; Di Angelantonio, Emanuele; Kaptoge, Stephen; Kuijpers, Taco W; Carrillo-de-Santa-Pau, Enrique; Juan, David; Rico, Daniel; Valencia, Alfonso; Chen, Lu; Ge, Bing; Vasquez, Louella; Kwan, Tony; Garrido-Martín, Diego; Watt, Stephen; Yang, Ying; Guigo, Roderic; Beck, Stephan; Paul, Dirk S; Pastinen, Tomi; Bujold, David; Bourque, Guillaume; Frontini, Mattia; Danesh, John; Roberts, David J; Ouwehand, Willem H; Butterworth, Adam S; Soranzo, Nicole

    2016-11-17

    Many common variants have been associated with hematological traits, but identification of causal genes and pathways has proven challenging. We performed a genome-wide association analysis in the UK Biobank and INTERVAL studies, testing 29.5 million genetic variants for association with 36 red cell, white cell, and platelet properties in 173,480 European-ancestry participants. This effort yielded hundreds of low frequency (<5%) and rare (<1%) variants with a strong impact on blood cell phenotypes. Our data highlight general properties of the allelic architecture of complex traits, including the proportion of the heritable component of each blood trait explained by the polygenic signal across different genome regulatory domains. Finally, through Mendelian randomization, we provide evidence of shared genetic pathways linking blood cell indices with complex pathologies, including autoimmune diseases, schizophrenia, and coronary heart disease and evidence suggesting previously reported population associations between blood cell indices and cardiovascular disease may be non-causal.

  16. Alkali Metal Variation and Twisting of the FeNNFe Core in Bridging Diiron Dinitrogen Complexes.

    PubMed

    McWilliams, Sean F; Rodgers, Kenton R; Lukat-Rodgers, Gudrun; Mercado, Brandon Q; Grubel, Katarzyna; Holland, Patrick L

    2016-03-21

    Alkali metal cations can interact with Fe-N2 complexes, potentially enhancing back-bonding or influencing the geometry of the iron atom. These influences are relevant to large-scale N2 reduction by iron, such as in the FeMoco of nitrogenase and the alkali-promoted Haber-Bosch process. However, to our knowledge there have been no systematic studies of a large range of alkali metals regarding their influence on transition metal-dinitrogen complexes. In this work, we varied the alkali metal in [alkali cation]2[LFeNNFeL] complexes (L = bulky β-diketiminate ligand) through the size range from Na(+) to K(+), Rb(+), and Cs(+). The FeNNFe cores have similar Fe-N and N-N distances and N-N stretching frequencies despite the drastic change in alkali metal cation size. The two diketiminates twist relative to one another, with larger dihedral angles accommodating the larger cations. In order to explain why the twisting has so little influence on the core, we performed density functional theory calculations on a simplified LFeNNFeL model, which show that the two metals surprisingly do not compete for back-bonding to the same π* orbital of N2, even when the ligand planes are parallel. This diiron system can tolerate distortion of the ligand planes through compensating orbital energy changes, and thus, a range of ligand orientations can give very similar energies.

  17. Variation in the biomolecular interactions of nickel(II) hydrazone complexes upon tuning the hydrazide fragment.

    PubMed

    Krishnamoorthy, Paramasivam; Sathyadevi, Palanisamy; Butorac, Rachel R; Cowley, Alan H; Bhuvanesh, Nattamai S P; Dharmaraj, Nallasamy

    2012-06-14

    Three new bivalent nickel hydrazone complexes have been synthesised from the reactions of [NiCl(2)(PPh(3))(2)] with H(2)L {L = dianion of the hydrazones derived from the condensation of o-hydroxynaphthaldehyde with furoic acid hydrazide (H(2)L(1)) (1)/thiophene-2-acid hydrazide (H(2)L(2)) (2)/isonicotinic acid hydrazide (H(2)L(3)) (3)} and formulated as [Ni(L(1))(PPh(3))] (4), [Ni(L(2))(PPh(3))] (5) and [Ni(L(3))(PPh(3))] (6). Structural characterization of these compounds 4-6 were accomplished by using various physico-chemical techniques. Single crystal X-ray diffraction data of complexes 4 and 5 proved their distorted square planar geometry. In order to ascertain the potential of the above synthesised compounds towards biomolecular interactions, additional experiments involving interaction with calf thymus DNA (CT DNA) and bovine serum albumin (BSA) were carried out. All the ligands and corresponding nickel(ii) chelates have been screened for their scavenging effect towards O(2)(-), OH and NO radicals. The efficiency of complexes 4-6 to arrest the growth of HeLa, HepG-2 and A431 tumour cell lines has been studied along with the cell viability test against the non-cancerous NIH 3T3 cells under in vitro conditions.

  18. Alkali Metal Variation and Twisting of the FeNNFe Core in Bridging Diiron Dinitrogen Complexes

    PubMed Central

    2016-01-01

    Alkali metal cations can interact with Fe–N2 complexes, potentially enhancing back-bonding or influencing the geometry of the iron atom. These influences are relevant to large-scale N2 reduction by iron, such as in the FeMoco of nitrogenase and the alkali-promoted Haber–Bosch process. However, to our knowledge there have been no systematic studies of a large range of alkali metals regarding their influence on transition metal–dinitrogen complexes. In this work, we varied the alkali metal in [alkali cation]2[LFeNNFeL] complexes (L = bulky β-diketiminate ligand) through the size range from Na+ to K+, Rb+, and Cs+. The FeNNFe cores have similar Fe–N and N–N distances and N–N stretching frequencies despite the drastic change in alkali metal cation size. The two diketiminates twist relative to one another, with larger dihedral angles accommodating the larger cations. In order to explain why the twisting has so little influence on the core, we performed density functional theory calculations on a simplified LFeNNFeL model, which show that the two metals surprisingly do not compete for back-bonding to the same π* orbital of N2, even when the ligand planes are parallel. This diiron system can tolerate distortion of the ligand planes through compensating orbital energy changes, and thus, a range of ligand orientations can give very similar energies. PMID:26925968

  19. Gold–superheavy-element interaction in diatomics and cluster adducts: A combined four-component Dirac-Kohn-Sham/charge-displacement study

    SciTech Connect

    Rampino, Sergio Belpassi, Leonardo

    2015-07-14

    The chemistry of superheavy elements (Z ≥ 104) is actively investigated in atom-at-a-time experiments of volatility through adsorption on gold surfaces. In this context, common guidelines for interpretation based on group trends in the periodic table should be used cautiously, because relativistic effects play a central role and may cause predictions to fall short. In this paper, we present an all-electron four-component Dirac-Kohn-Sham comparative study of the interaction of gold with Cn (Z = 112), Fl (Z = 114), and Uuo (Z = 118) versus their lighter homologues of the 6th period, Hg, Pb, and Rn plus the noble gas Xe. Calculations were carried out for Au–E (E = Hg, Cn, Pb, Fl, Xe, Rn, Uuo), Au{sub 7}– and Au{sub 20}–E (E = Hg, Cn, Pb, Fl, Rn) complexes, where Au{sub 7} (planar) and Au{sub 20} (pyramidal) are experimentally determined clusters having structures of increasing complexity. Results are analysed both in terms of the energetics of the complexes and of the electron charge rearrangement accompanying their formation. In line with the available experimental data, Cn and more markedly Fl are found to be less reactive than their lighter homologues. On the contrary, Uuo is found to be more reactive than Rn and Xe. Cn forms the weakest bond with the gold atom, compared to Fl and Uuo. The reactivity of Fl decreases with increasing gold-fragment size more rapidly than that of Cn and, as a consequence, the order of the reactivity of these two elements is inverted upon reaching the Au{sub 20}-cluster adduct. Density difference maps between adducts and fragments reveal similarities in the behaviour of Cn and Xe, and in that of Uuo and the more reactive species Hg and Pb. These findings are given a quantitative ground via charge-displacement analysis.

  20. Gold-superheavy-element interaction in diatomics and cluster adducts: A combined four-component Dirac-Kohn-Sham/charge-displacement study.

    PubMed

    Rampino, Sergio; Storchi, Loriano; Belpassi, Leonardo

    2015-07-14

    The chemistry of superheavy elements (Z ≥ 104) is actively investigated in atom-at-a-time experiments of volatility through adsorption on gold surfaces. In this context, common guidelines for interpretation based on group trends in the periodic table should be used cautiously, because relativistic effects play a central role and may cause predictions to fall short. In this paper, we present an all-electron four-component Dirac-Kohn-Sham comparative study of the interaction of gold with Cn (Z = 112), Fl (Z = 114), and Uuo (Z = 118) versus their lighter homologues of the 6th period, Hg, Pb, and Rn plus the noble gas Xe. Calculations were carried out for Au-E (E = Hg, Cn, Pb, Fl, Xe, Rn, Uuo), Au7- and Au20-E (E = Hg, Cn, Pb, Fl, Rn) complexes, where Au7 (planar) and Au20 (pyramidal) are experimentally determined clusters having structures of increasing complexity. Results are analysed both in terms of the energetics of the complexes and of the electron charge rearrangement accompanying their formation. In line with the available experimental data, Cn and more markedly Fl are found to be less reactive than their lighter homologues. On the contrary, Uuo is found to be more reactive than Rn and Xe. Cn forms the weakest bond with the gold atom, compared to Fl and Uuo. The reactivity of Fl decreases with increasing gold-fragment size more rapidly than that of Cn and, as a consequence, the order of the reactivity of these two elements is inverted upon reaching the Au20-cluster adduct. Density difference maps between adducts and fragments reveal similarities in the behaviour of Cn and Xe, and in that of Uuo and the more reactive species Hg and Pb. These findings are given a quantitative ground via charge-displacement analysis.

  1. Gold-superheavy-element interaction in diatomics and cluster adducts: A combined four-component Dirac-Kohn-Sham/charge-displacement study

    NASA Astrophysics Data System (ADS)

    Rampino, Sergio; Storchi, Loriano; Belpassi, Leonardo

    2015-07-01

    The chemistry of superheavy elements (Z ≥ 104) is actively investigated in atom-at-a-time experiments of volatility through adsorption on gold surfaces. In this context, common guidelines for interpretation based on group trends in the periodic table should be used cautiously, because relativistic effects play a central role and may cause predictions to fall short. In this paper, we present an all-electron four-component Dirac-Kohn-Sham comparative study of the interaction of gold with Cn (Z = 112), Fl (Z = 114), and Uuo (Z = 118) versus their lighter homologues of the 6th period, Hg, Pb, and Rn plus the noble gas Xe. Calculations were carried out for Au-E (E = Hg, Cn, Pb, Fl, Xe, Rn, Uuo), Au7- and Au20-E (E = Hg, Cn, Pb, Fl, Rn) complexes, where Au7 (planar) and Au20 (pyramidal) are experimentally determined clusters having structures of increasing complexity. Results are analysed both in terms of the energetics of the complexes and of the electron charge rearrangement accompanying their formation. In line with the available experimental data, Cn and more markedly Fl are found to be less reactive than their lighter homologues. On the contrary, Uuo is found to be more reactive than Rn and Xe. Cn forms the weakest bond with the gold atom, compared to Fl and Uuo. The reactivity of Fl decreases with increasing gold-fragment size more rapidly than that of Cn and, as a consequence, the order of the reactivity of these two elements is inverted upon reaching the Au20-cluster adduct. Density difference maps between adducts and fragments reveal similarities in the behaviour of Cn and Xe, and in that of Uuo and the more reactive species Hg and Pb. These findings are given a quantitative ground via charge-displacement analysis.

  2. On horizontal Hardy, Rellich, Caffarelli-Kohn-Nirenberg and p-sub-Laplacian inequalities on stratified groups

    NASA Astrophysics Data System (ADS)

    Ruzhansky, Michael; Suragan, Durvudkhan

    2017-02-01

    In this paper, we present a version of horizontal weighted Hardy-Rellich type and Caffarelli-Kohn-Nirenberg type inequalities on stratified groups and study some of their consequences. Our results reflect on many results previously known in special cases. Moreover, a new simple proof of the Badiale-Tarantello conjecture [2] on the best constant of a Hardy type inequality is provided. We also show a family of Poincaré inequalities as well as inequalities involving the weighted and unweighted p-sub-Laplacians.

  3. Computationally simple, analytic, closed form solution of the Coulomb self-interaction problem in Kohn Sham density functional theory

    SciTech Connect

    Gonis, Antonios; Daene, Markus W; Nicholson, Don M; Stocks, George Malcolm

    2012-01-01

    We have developed and tested in terms of atomic calculations an exact, analytic and computationally simple procedure for determining the functional derivative of the exchange energy with respect to the density in the implementation of the Kohn Sham formulation of density functional theory (KS-DFT), providing an analytic, closed-form solution of the self-interaction problem in KS-DFT. We demonstrate the efficacy of our method through ground-state calculations of the exchange potential and energy for atomic He and Be atoms, and comparisons with experiment and the results obtained within the optimized effective potential (OEP) method.

  4. Local variation and parallel evolution: morphological and genetic diversity across a species complex of neotropical crater lake cichlid fishes

    PubMed Central

    Elmer, Kathryn R.; Kusche, Henrik; Lehtonen, Topi K.; Meyer, Axel

    2010-01-01

    The polychromatic and trophically polymorphic Midas cichlid fish species complex (Amphilophus cf. citrinellus) is an excellent model system for studying the mechanisms of speciation and patterns of phenotypic diversification in allopatry and in sympatry. Here, we first review research to date on the species complex and the geological history of its habitat. We analyse body shape variation from all currently described species in the complex, sampled from six crater lakes (maximally 1.2–23.9 kyr old) and both great lakes in Nicaragua. We find that Midas cichlid populations in each lake have their own characteristic body shape. In lakes with multiple sympatric species of Midas cichlid, each species has a distinct body shape. Across the species complex, most body shape change relates to body depth, head, snout and mouth shape and caudal peduncle length. There is independent parallel evolution of an elongate limnetic species in at least two crater lakes. Mitochondrial genetic diversity is higher in crater lakes with multiple species. Midas cichlid species richness increases with the size and age of the crater lakes, though no such relationship exists for the other syntopic fishes. We suggest that crater lake Midas cichlids follow the predicted pattern of an adaptive radiation, with early divergence of each crater lake colonization, followed by intralacustrine diversification and speciation by ecological adaptation and sexual selection. PMID:20439280

  5. A comprehensive custom panel design for routine hereditary cancer testing: preserving control, improving diagnostics and revealing a complex variation landscape.

    PubMed

    Castellanos, Elisabeth; Gel, Bernat; Rosas, Inma; Tornero, Eva; Santín, Sheila; Pluvinet, Raquel; Velasco, Juan; Sumoy, Lauro; Del Valle, Jesús; Perucho, Manuel; Blanco, Ignacio; Navarro, Matilde; Brunet, Joan; Pineda, Marta; Feliubadaló, Lidia; Capellá, Gabi; Lázaro, Conxi; Serra, Eduard

    2017-01-04

    We wanted to implement an NGS strategy to globally analyze hereditary cancer with diagnostic quality while retaining the same degree of understanding and control we had in pre-NGS strategies. To do this, we developed the I2HCP panel, a custom bait library covering 122 hereditary cancer genes. We improved bait design, tested different NGS platforms and created a clinically driven custom data analysis pipeline. The I2HCP panel was developed using a training set of hereditary colorectal cancer, hereditary breast and ovarian cancer and neurofibromatosis patients and reached an accuracy, analytical sensitivity and specificity greater than 99%, which was maintained in a validation set. I2HCP changed our diagnostic approach, involving clinicians and a genetic diagnostics team from panel design to reporting. The new strategy improved diagnostic sensitivity, solved uncertain clinical diagnoses and identified mutations in new genes. We assessed the genetic variation in the complete set of hereditary cancer genes, revealing a complex variation landscape that coexists with the disease-causing mutation. We developed, validated and implemented a custom NGS-based strategy for hereditary cancer diagnostics that improved our previous workflows. Additionally, the existence of a rich genetic variation in hereditary cancer genes favors the use of this panel to investigate their role in cancer risk.

  6. A comprehensive custom panel design for routine hereditary cancer testing: preserving control, improving diagnostics and revealing a complex variation landscape

    PubMed Central

    Castellanos, Elisabeth; Gel, Bernat; Rosas, Inma; Tornero, Eva; Santín, Sheila; Pluvinet, Raquel; Velasco, Juan; Sumoy, Lauro; del Valle, Jesús; Perucho, Manuel; Blanco, Ignacio; Navarro, Matilde; Brunet, Joan; Pineda, Marta; Feliubadaló, Lidia; Capellá, Gabi; Lázaro, Conxi; Serra, Eduard

    2017-01-01

    We wanted to implement an NGS strategy to globally analyze hereditary cancer with diagnostic quality while retaining the same degree of understanding and control we had in pre-NGS strategies. To do this, we developed the I2HCP panel, a custom bait library covering 122 hereditary cancer genes. We improved bait design, tested different NGS platforms and created a clinically driven custom data analysis pipeline. The I2HCP panel was developed using a training set of hereditary colorectal cancer, hereditary breast and ovarian cancer and neurofibromatosis patients and reached an accuracy, analytical sensitivity and specificity greater than 99%, which was maintained in a validation set. I2HCP changed our diagnostic approach, involving clinicians and a genetic diagnostics team from panel design to reporting. The new strategy improved diagnostic sensitivity, solved uncertain clinical diagnoses and identified mutations in new genes. We assessed the genetic variation in the complete set of hereditary cancer genes, revealing a complex variation landscape that coexists with the disease-causing mutation. We developed, validated and implemented a custom NGS-based strategy for hereditary cancer diagnostics that improved our previous workflows. Additionally, the existence of a rich genetic variation in hereditary cancer genes favors the use of this panel to investigate their role in cancer risk. PMID:28051113

  7. Major QTLs for critical photoperiod and vernalization underlie extensive variation in flowering in the Mimulus guttatus species complex.

    PubMed

    Friedman, Jannice; Willis, John H

    2013-07-01

    Species with extensive ranges experience highly variable environments with respect to temperature, light and soil moisture. Synchronizing the transition from vegetative to floral growth is important to employ favorable conditions for reproduction. Optimal timing of this transition might be different for semelparous annual plants and iteroparous perennial plants. We studied variation in the critical photoperiod necessary for floral induction and the requirement for a period of cold-chilling (vernalization) in 46 populations of annuals and perennials in the Mimulus guttatus species complex. We then examined critical photoperiod and vernalization QTLs in growth chambers using F(2) progeny from annual and perennial parents that differed in their requirements for flowering. We identify extensive variation in critical photoperiod, with most annual populations requiring substantially shorter day lengths to initiate flowering than perennial populations. We discover a novel type of vernalization requirement in perennial populations that is contingent on plants experiencing short days first. QTL analyses identify two large-effect QTLs which influence critical photoperiod. In two separate vernalization experiments we discover each set of crosses contain different large-effect QTLs for vernalization. Mimulus guttatus harbors extensive variation in critical photoperiod and vernalization that may be a consequence of local adaptation.

  8. Variational approach to studying solitary waves in the nonlinear Schrödinger equation with complex potentials.

    PubMed

    Mertens, Franz G; Cooper, Fred; Arévalo, Edward; Khare, Avinash; Saxena, Avadh; Bishop, A R

    2016-09-01

    We discuss the behavior of solitary wave solutions of the nonlinear Schrödinger equation (NLSE) as they interact with complex potentials, using a four-parameter variational approximation based on a dissipation functional formulation of the dynamics. We concentrate on spatially periodic potentials with the periods of the real and imaginary part being either the same or different. Our results for the time evolution of the collective coordinates of our variational ansatz are in good agreement with direct numerical simulation of the NLSE. We compare our method with a collective coordinate approach of Kominis and give examples where the two methods give qualitatively different answers. In our variational approach, we are able to give analytic results for the small oscillation frequency of the solitary wave oscillating parameters which agree with the numerical solution of the collective coordinate equations. We also verify that instabilities set in when the slope dp(t)/dv(t) becomes negative when plotted parametrically as a function of time, where p(t) is the momentum of the solitary wave and v(t) the velocity.

  9. Complex Copy Number Variation of AMY1 does not Associate with Obesity in two East Asian Cohorts.

    PubMed

    Yong, Rita Y Y; Mustaffa, Su'Aidah B; Wasan, Pavandip S; Sheng, Liang; Marshall, Christian R; Scherer, Stephen W; Teo, Yik-Ying; Yap, Eric P H

    2016-07-01

    The human amylase gene locus at chromosome 1p21.1 is structurally complex. This region contains two pancreatic amylase genes, AMY2B, AMY2A, and a salivary gene AMY1. The AMY1 gene harbors extensive copy number variation (CNV), and recent studies have implicated this variation in adaptation to starch-rich diets and in association to obesity for European and Asian populations. In this study, we showed that by combining quantitative PCR and digital PCR, coupled with careful experimental design and calibration, we can improve the resolution of genotyping CNV with high copy numbers (CNs). In two East Asian populations of Chinese and Malay ethnicity studied, we observed a unique non-normal distribution of AMY1 diploid CN genotypes with even:odd CNs ratio of 4.5 (3.3-4.7), and an association between the common AMY2A CN = 2 genotype and odd CNs of AMY1, that could be explained by the underlying haplotypic structure. In two further case-control cohorts (n = 932 and 145, for Chinese and Malays, respectively), we did not observe the previously reported association between AMY1 and obesity or body mass index. Improved methods for accurately genotyping multiallelic CNV loci and understanding the haplotype complexity at the AMY1 locus are necessary for population genetics and association studies.

  10. Delocalization error and "functional tuning" in Kohn-Sham calculations of molecular properties.

    PubMed

    Autschbach, Jochen; Srebro, Monika

    2014-08-19

    Kohn-Sham theory (KST) is the "workhorse" of numerical quantum chemistry. This is particularly true for first-principles calculations of ground- and excited-state properties for larger systems, including electronic spectra, electronic dynamic and static linear and higher order response properties (including nonlinear optical (NLO) properties), conformational or dynamic averaging of spectra and response properties, or properties that are affected by the coupling of electron and nuclear motion. This Account explores the sometimes dramatic impact of the delocalization error (DE) and possible benefits from the use of long-range corrections (LC) and "tuning" of functionals in KST calculations of molecular ground-state and response properties. Tuning refers to a nonempirical molecule-specific determination of adjustable parameters in functionals to satisfy known exact conditions, for instance, that the energy of the highest occupied molecular orbital (HOMO) should be equal to the negative vertical ionization potential (IP) or that the energy as a function of fractional electron numbers should afford straight-line segments. The presentation is given from the viewpoint of a chemist interested in computations of a variety of molecular optical and spectroscopic properties and of a theoretician developing methods for computing such properties with KST. In recent years, the use of LC functionals, functional tuning, and quantifying the DE explicitly have provided valuable insight regarding the performance of KST for molecular properties. We discuss a number of different molecular properties, with examples from recent studies from our laboratory and related literature. The selected properties probe different aspects of molecular electronic structure. Electric field gradients and hyperfine coupling constants can be exquisitely sensitive to the DE because it affects the ground-state electron density and spin density distributions. For π-conjugated molecules, it is shown how the

  11. Transcontinental latitudinal variation in song performance and complexity in house wrens (Troglodytes aedon)

    PubMed Central

    Kaluthota, Chinthaka; Brinkman, Benjamin E.; dos Santos, Ednei B.; Rendall, Drew

    2016-01-01

    There is growing interest in latitudinal effects on animal behaviour and life history. One recent focus is on birdsong, which is hypothesized to be more elaborated or complex in the north temperate zone compared with the tropics. Current evidence is mixed and based on cross-species comparisons, or single species with restricted distributions. We circumvent these limitations using a transcontinental sample of 358 songs from house wrens (Troglodytes aedon) at 281 locations spanning more than 100° of latitude (52° N–55° S) across the Americas. We found a significant latitudinal gradient in several basic elements of song performance and complexity between north temperate and tropical populations. Furthermore, we document convergence in song patterns between populations at higher latitudes in the Northern and Southern Hemispheres. Effects were strongest for the number of elements in a song, and the rate of element production, both increasing towards the poles, with similar but weaker effects for other song dimensions (e.g. number of unique elements, trills and trill rate). We consider possible causes related to variable habitats and morphology, concluding that the shorter breeding seasons at higher latitudes in both hemispheres may favour greater song elaboration to mediate territory competition and mate choice. PMID:26865297

  12. Major histocompatibility complex variation in insular populations of the Egyptian vulture: inferences about the roles of genetic drift and selection.

    PubMed

    Agudo, Rosa; Alcaide, Miguel; Rico, Ciro; Lemus, Jesus A; Blanco, Guillermo; Hiraldo, Fernando; Donázar, Jose A

    2011-06-01

    Insular populations have attracted the attention of evolutionary biologists because of their morphological and ecological peculiarities with respect to their mainland counterparts. Founder effects and genetic drift are known to distribute neutral genetic variability in these demes. However, elucidating whether these evolutionary forces have also shaped adaptive variation is crucial to evaluate the real impact of reduced genetic variation in small populations. Genes of the major histocompatibility complex (MHC) are classical examples of evolutionarily relevant loci because of their well-known role in pathogen confrontation and clearance. In this study, we aim to disentangle the partial roles of genetic drift and natural selection in the spatial distribution of MHC variation in insular populations. To this end, we integrate the study of neutral (22 microsatellites and one mtDNA locus) and MHC class II variation in one mainland (Iberia) and two insular populations (Fuerteventura and Menorca) of the endangered Egyptian vulture (Neophron percnopterus). Overall, the distribution of the frequencies of individual MHC alleles (n=17 alleles from two class II B loci) does not significantly depart from neutral expectations, which indicates a prominent role for genetic drift over selection. However, our results point towards an interesting co-evolution of gene duplicates that maintains different pairs of divergent alleles in strong linkage disequilibrium on islands. We hypothesize that the co-evolution of genes may counteract the loss of genetic diversity in insular demes, maximize antigen recognition capabilities when gene diversity is reduced, and promote the co-segregation of the most efficient allele combinations to cope with local pathogen communities.

  13. Variation in canopy duration in the perennial biofuel crop Miscanthus reveals complex associations with yield.

    PubMed

    Robson, Paul R H; Farrar, Kerrie; Gay, Alan P; Jensen, Elaine F; Clifton-Brown, John C; Donnison, Iain S

    2013-05-01

    Energy crops can provide a sustainable source of power and fuels, and mitigate the negative effects of CO2 emissions associated with fossil fuel use. Miscanthus is a perennial C4 energy crop capable of producing large biomass yields whilst requiring low levels of input. Miscanthus is largely unimproved and therefore there could be significant opportunities to increase yield. Further increases in yield will improve the economics, energy balance, and carbon mitigation of the crop, as well as reducing land-take. One strategy to increase yield in Miscanthus is to maximize the light captured through an extension of canopy duration. In this study, canopy duration was compared among a diverse collection of 244 Miscanthus genotypes. Canopy duration was determined by calculating the number of days between canopy establishment and senescence. Yield was positively correlated with canopy duration. Earlier establishment and later senescence were also both separately correlated with higher yield. However, although genotypes with short canopy durations were low yielding, not all genotypes with long canopy durations were high yielding. Differences of yield between genotypes with long canopy durations were associated with variation in stem and leaf traits. Different methodologies to assess canopy duration traits were investigated, including visual assessment, image analysis, light interception, and different trait thresholds. The highest correlation coefficients were associated with later assessments of traits and the use of quantum sensors for canopy establishment. A model for trait optimization to enable yield improvement in Miscanthus and other bioenergy crops is discussed.

  14. Influence of complex childhood diseases on variation in growth and skeletal development.

    PubMed

    Zemel, Babette S

    2017-03-01

    The study of human growth and skeletal development by human biologists is framed by the larger theoretical concerns regarding the underpinnings of population variation and human evolution. This unique perspective is directly relevant to the assessment of child health and well-being at the individual and group level, as well as the construction of growth charts. Environmental, behavioral (nutrition and physical activity), and disease-related factors can prevent attainment of full genetic potential for growth. Undernutrition is most often the cause of growth faltering and poor skeletal development. Disease related factors, such as malabsorption, inflammation, and immobility also have profound effects. These effects will be illustrated with examples from diseases such as cystic fibrosis, inflammatory bowel disease, and Down syndrome. The need for separate growth charts for children with genetic disorders is often controversial because of potential medical and/or nutritional complications associated with some disorders. Children with Alagille syndrome and Down syndrome will be used to illustrate the advantages and limitations of syndrome-specific charts. This overview of health and disease effects on growth and skeletal development provides insights into the plasticity of human growth and its sensitivity to overall health and well-being.

  15. Variation in number of hits for complex searches in Google Scholar

    PubMed Central

    Bramer, Wichor Matthijs

    2016-01-01

    Objective Google Scholar is often used to search for medical literature. Numbers of results reported by Google Scholar outperform the numbers reported by traditional databases. How reliable are these numbers? Why are often not all available 1,000 references shown? Methods For several complex search strategies used in systematic review projects, the number of citations and the total number of versions were calculated. Several search strategies were followed over a two-year period, registering fluctuations in reported search results. Results Changes in numbers of reported search results varied enormously between search strategies and dates. Theories for calculations of the reported and shown number of hits were not proved. Conclusions The number of hits reported in Google Scholar is an unreliable measure. Therefore, its repeatability is problematic, at least when equal results are needed. PMID:27076802

  16. A comparative overview of the sperm centriolar complex in mammals and birds: Variations on a theme.

    PubMed

    Soley, John T

    2016-06-01

    This paper presents an overview of the structure, function and anomalies of the sperm centriolar complex (CC) on a comparative basis between mammals and birds. The information is based on selected references from the literature supplemented by original observations on spermiogenesis and sperm structure in disparate mammalian (cheetah and cane rat) and avian (ostrich, rhea and emu) species. Whereas the basic structure of the CC (a diplosome surrounded by pericentriolar material) is similar in Aves and Mammalia, certain differences are apparent. Centriole reduction does not generally occur in birds, but when present as in oscines, involves the loss of the proximal centriole. In ratites, the distal centriole forms the core of the entire midpiece and incorporates the outer dense fibres in addition to initiating axoneme formation. The elements of the connecting piece are not segmented in birds and less complex in basic design than in mammals. The functions of the various components of the CC appear to be similar in birds and mammals. Despite obvious differences in sperm head shape, the centrosomal anomalies afflicting both vertebrate groups demonstrate structural uniformity across species and display a similar range of defects. Most abnormalities result from defective migration and alignment of the CC relative to the nucleus. The most severe manifestation is that of acephalic sperm, while angled tail attachment, abaxial and multiflagellate sperm reflect additional defective forms. The stump-tail defect is not observed in birds. A comparison of defective sperm formation and centrosomal dysfunction at the molecular level is currently difficult owing to the paucity of relevant information on avian sperm.

  17. Complex offspring size effects: variations across life stages and between species

    PubMed Central

    Sun, Zhao; Hamel, Jean-François; Parrish, Christopher C; Mercier, Annie

    2015-01-01

    Classical optimality models of offspring size and number assume a monotonically increasing relationship between offspring size and performance. In aquatic organisms with complex life cycles, the size–performance function is particularly hard to grasp because measures of performance are varied and their relationships with size may not be consistent throughout early ontogeny. Here, we examine size effects in premetamorphic (larval) and postmetamorphic (juvenile) stages of brooding marine animals and show that they vary contextually in strength and direction during ontogeny and among species. Larger offspring of the sea anemone Urticina felina generally outperformed small siblings at the larval stage (i.e., greater settlement and survival rates under suboptimal conditions). However, results differed when analyses were conducted at the intrabrood versus across-brood levels, suggesting that the relationship between larval size and performance is mediated by parentage. At the juvenile stage (15 months), small offspring were less susceptible than large ones to predation by subadult nudibranchs and both sizes performed similarly when facing adult nudibranchs. In a sympatric species with a different life history (Aulactinia stella), all juveniles suffered similar predation rates by subadult nudibranchs, but smaller juveniles performed better (lower mortalities) when facing adult nudibranchs. Size differences in premetamorphic performance of U. felina were linked to total lipid contents of larvae, whereas size-specific predation of juvenile stages followed the general predictions of the optimal foraging strategy. These findings emphasize the challenge in gathering empirical support for a positive monotonic size–performance function in taxa that exhibit complex life cycles, which are dominant in the sea. PMID:25798228

  18. A Survey of Genetic Variation and Genome Evolution within the Invasive Fallopia Complex

    PubMed Central

    Bzdega, Katarzyna; Janiak, Agnieszka; Książczyk, Tomasz; Lewandowska, Agata; Gancarek, Małgorzata; Sliwinska, Elwira; Tokarska-Guzik, Barbara

    2016-01-01

    The knotweed taxa Fallopia japonica, F. sachalinensis and their interspecific hybrid F. × bohemica are some of the most aggressive invaders in Europe and North America and they are serious threats to native biodiversity. At the same time, they constitute a unique model system for the creation of hybrids and studies of the initiation of evolutionary processes. In the presented study, we focused on (i) examining genetic diversity in selected populations of three Fallopia taxa in the invaded (Poland) and native ranges (Japan), (ii) establishing genome size and ploidy levels and (iii) identifying ribosomal DNA (rDNA)-bearing chromosomes in all of the taxa from the invaded range. We found that the genetic diversity within particular taxa was generally low regardless of their geographical origin. A higher level of clonality was observed for the Polish populations compared to the Japanese populations. Our study suggests that the co-occurrence of F. sachalinensis together with the other two taxa in the same stand may be the source of the higher genetic variation within the F. × bohemica hybrid. Some shift towards the contribution of F. japonica alleles was also observed for selected F. × bohemica individuals, which indicates the possibility of producing more advanced generations of F. × bohemica hybrids. All of the F. sachalinensis individuals were hexaploid (2n = 6x = 66; 2C = 6.01 pg), while those of F. japonica were mostly octoploid (2n = 8x = 88; 2C = 8.87 pg) and all of the F. × bohemica plants except one were hexaploid (2n = 6x = 66; 2C = 6.46 pg). Within the chromosome complement of F. japonica, F. sachalinensis and F. × bohemica, the physical mapping of the rDNA loci provided markers for 16, 13 and 10 chromosomes, respectively. In F. × bohemica, a loss of some of rDNA loci was observed, which indicates the occurrence of genome changes in the hybrid. PMID:27575805

  19. Kohn-Sham approach to quantum electrodynamical density-functional theory: Exact time-dependent effective potentials in real space.

    PubMed

    Flick, Johannes; Ruggenthaler, Michael; Appel, Heiko; Rubio, Angel

    2015-12-15

    The density-functional approach to quantum electrodynamics extends traditional density-functional theory and opens the possibility to describe electron-photon interactions in terms of effective Kohn-Sham potentials. In this work, we numerically construct the exact electron-photon Kohn-Sham potentials for a prototype system that consists of a trapped electron coupled to a quantized electromagnetic mode in an optical high-Q cavity. Although the effective current that acts on the photons is known explicitly, the exact effective potential that describes the forces exerted by the photons on the electrons is obtained from a fixed-point inversion scheme. This procedure allows us to uncover important beyond-mean-field features of the effective potential that mark the breakdown of classical light-matter interactions. We observe peak and step structures in the effective potentials, which can be attributed solely to the quantum nature of light; i.e., they are real-space signatures of the photons. Our findings show how the ubiquitous dipole interaction with a classical electromagnetic field has to be modified in real space to take the quantum nature of the electromagnetic field fully into account.

  20. The Kohn-Luttinger mechanism and phase diagram of the superconducting state in the Shubin-Vonsovsky model

    SciTech Connect

    Kagan, M. Yu.; Val'kov, V. V.; Mitskan, V. A.; Korovuskin, M. M.

    2013-10-15

    Using the Shubin-Vonsovsky model in the weak-coupling regime W > U > V (W is the bandwidth, U is the Hubbard onsite repulsion, and V is the Coulomb interaction at neighboring sites) based on the Kohn-Luttinger mechanism, we determined the regions of the existence of the superconducting phases with the d{sub xy}, p, s, and d{sub x{sup 2}-y{sup 2}} symmetry types of the order parameter. It is shown that the effective interaction in the Cooper channel considerably depends not only on single-site but also on intersite Coulomb correlations. This is demonstrated by the example of the qualitative change and complication of the phase diagram of the superconducting state. The superconducting (SC) phase induction mechanism is determined taking into account polarization contributions in the second-order perturbation theory in the Coulomb interaction. The results obtained for the angular dependence of the superconducting gap in different channels are compared with angule-resolved photoemission spectroscopy (ARPES) results. The influence of long-range hops in the phase diagram and critical superconducting transition temperature in different channels is analyzed. The conditions for the appearance of the Kohn-Luttinger superconductivity with the d{sub x{sup 2}-y{sup 2}} symmetry and high critical temperatures T{sub c} {approx} 100 K near the half-filling are determined.

  1. Geometries of low spin states of multi-centre transition metal complexes through extended broken symmetry variational Monte Carlo

    NASA Astrophysics Data System (ADS)

    Barborini, Matteo; Guidoni, Leonardo

    2016-09-01

    The correct description of the ground state electronic and geometrical properties of multi-centre transition metal complexes necessitates of a high-level description of both dynamical and static correlation effects. In di-metallic complexes, the ground state low spin properties can be computed starting from single-determinants High-Spin (HS) and Broken Symmetry (BS) states by reconstructing an approximated low spin potential energy surface through the extended broken symmetry approach, based on the Heisenberg Hamiltonian. In the present work, we first apply this approach within the variational Monte Carlo method to tackle the geometry optimization of a Fe2S2(SH)42- model complex. To describe the HS and BS wavefunctions, we use a fully optimized unrestricted single determinant with a correlated Jastrow factor able to recover a large amount of dynamical correlation. We compared our results with those obtained by density functional theory and other multiconfigurational approaches, discussing the role of the nodal surface on the structural parameters.

  2. Geometries of low spin states of multi-centre transition metal complexes through extended broken symmetry variational Monte Carlo.

    PubMed

    Barborini, Matteo; Guidoni, Leonardo

    2016-09-28

    The correct description of the ground state electronic and geometrical properties of multi-centre transition metal complexes necessitates of a high-level description of both dynamical and static correlation effects. In di-metallic complexes, the ground state low spin properties can be computed starting from single-determinants High-Spin (HS) and Broken Symmetry (BS) states by reconstructing an approximated low spin potential energy surface through the extended broken symmetry approach, based on the Heisenberg Hamiltonian. In the present work, we first apply this approach within the variational Monte Carlo method to tackle the geometry optimization of a Fe2S2(SH)4(2-) model complex. To describe the HS and BS wavefunctions, we use a fully optimized unrestricted single determinant with a correlated Jastrow factor able to recover a large amount of dynamical correlation. We compared our results with those obtained by density functional theory and other multiconfigurational approaches, discussing the role of the nodal surface on the structural parameters.

  3. Embracing the complexity of matricellular proteins: the functional and clinical significance of splice variation.

    PubMed

    Viloria, Katrina; Hill, Natasha J

    2016-05-01

    Matricellular proteins influence wide-ranging fundamental cellular processes including cell adhesion, migration, growth and differentiation. They achieve this both through interactions with cell surface receptors and regulation of the matrix environment. Many matricellular proteins are also associated with diverse clinical disorders including cancer and diabetes. Alternative splicing is a precisely regulated process that can produce multiple isoforms with variable functions from a single gene. To date, the expression of alternate transcripts for the matricellular family has been reported for only a handful of genes. Here we analyse the evidence for alternative splicing across the matricellular family including the secreted protein acidic and rich in cysteine (SPARC), thrombospondin, tenascin and CCN families. We find that matricellular proteins have double the average number of splice variants per gene, and discuss the types of domain affected by splicing in matricellular proteins. We also review the clinical significance of alternative splicing for three specific matricellular proteins that have been relatively well characterised: osteopontin (OPN), tenascin-C (TNC) and periostin. Embracing the complexity of matricellular splice variants will be important for understanding the sometimes contradictory function of these powerful regulatory proteins, and for their effective clinical application as biomarkers and therapeutic targets.

  4. Spatial variation and low diversity in the major histocompatibility complex in walrus (Odobenus rosmarus)

    USGS Publications Warehouse

    Sonsthagen, Sarah A.; Fales, Krystal; Jay, Chadwick V.; Sage, George K.; Talbot, Sandra L.

    2014-01-01

    Increased global temperature and associated changes to Arctic habitats will likely result in the northward advance of species, including an influx of pathogens novel to the Arctic. How species respond to these immunological challenges will depend in part on the adaptive potential of their immune response system. We compared levels of genetic diversity at a gene associated with adaptive immune response [Class II major histocompatibility complex (MHC), DQB exon 2] between populations of walrus (Odobenus rosmarus), a sea ice-dependent Arctic species. Walrus was represented by only five MHC DQB alleles, with frequency differences observed between Pacific and Atlantic populations. MHC DQB alleles appear to be under balancing selection, and most (80 %; n = 4/5) of the alleles were observed in walruses from both oceans, suggesting broad scale differences in the frequency of exposure and diversity of pathogens may be influencing levels of heterozygosity at DQB in walruses. Limited genetic diversity at MHC, however, suggests that walrus may have a reduced capacity to respond to novel immunological challenges associated with shifts in ecological communities and environmental stressors predicted for changing climates. This is particularly pertinent for walrus, since reductions in summer sea ice may facilitate both northward expansion of marine species and associated pathogens from more temperate regions, and exchange of marine mammals and associated pathogens through the recently opened Northwest Passage between the Atlantic and Pacific Oceans in the Canadian high Arctic.

  5. Genetic variation and origin of parthenogenesis in the Aspidoscelis cozumela complex: evidence from mitochondrial genes.

    PubMed

    Manríquez-Morán, Norma L; Cruz, Fausto R Méndez-de la; Murphy, Robert W

    2014-01-01

    Parthenogenesis is a form of clonal reproduction. Eggs develop in the absence of sperm and offspring are genetically identical to their mother. Although common in invertebrates, it occurs in only a few species of squamate reptiles. Parthenogenetic reptiles have their origin in interspecific hybridization, and their populations are exclusively female. Because of its high mutation rate and maternal inheritance, mitochondrial DNA sequence data can evaluate the origin and evolution of all-female vertebrates. Partial sequences from two mitochondrial genes, Cytb and ND4, were analyzed to investigate questions about the origin of parthenogenesis in the Aspidoscelis cozumela complex, which includes A. cozumela, A. maslini and A. rodecki. Low levels of divergence were detected among parthenogenetic species, and between them and A. angusticeps, confirming it as the maternal species of the parthenoforms. A gene tree was constructed using sequences from three populations of A. angusticeps and nine of its unisexual daughter species. The phylogeny suggests that two independent hybridization events between A. angusticeps and A. deppii formed three unisexual species. One hybridization resulted in A. rodecki and the other formed A. maslini and A. cozumela. Although A. cozumela has the haplotype characteristic of A. maslini from Puerto Morelos, it is considered to be a different species based on karyological and morphological characteristics and its geographical isolation.

  6. Complex and multi-allelic copy number variation in human disease.

    PubMed

    Usher, Christina L; McCarroll, Steven A

    2015-09-01

    Hundreds of copy number variants are complex and multi-allelic, in that they have many structural alleles and have rearranged multiple times in the ancestors who contributed chromosomes to current humans. Not only are the relationships of these multi-allelic CNVs (mCNVs) to phenotypes generally unknown, but many mCNVs have not yet been described at the basic levels-alleles, allele frequencies, structural features-that support genetic investigation. To date, most reported disease associations to these variants have been ascertained through candidate gene studies. However, only a few associations have reached the level of acceptance defined by durable replications in many cohorts. This likely stems from longstanding challenges in making precise molecular measurements of the alleles individuals have at these loci. However, approaches for mCNV analysis are improving quickly, and some of the unique characteristics of mCNVs may assist future association studies. Their various structural alleles are likely to have different magnitudes of effect, creating a natural allelic series of growing phenotypic impact and giving investigators a set of natural predictions and testable hypotheses about the extent to which each allele of an mCNV predisposes to a phenotype. Also, mCNVs' low-to-modest correlation to individual single-nucleotide polymorphisms (SNPs) may make it easier to distinguish between mCNVs and nearby SNPs as the drivers of an association signal, and perhaps, make it possible to preliminarily screen candidate loci, or the entire genome, for the many mCNV-disease relationships that remain to be discovered.

  7. Complex and multi-allelic copy number variation in human disease

    PubMed Central

    McCarroll, Steven A.

    2015-01-01

    Hundreds of copy number variants are complex and multi-allelic, in that they have many structural alleles and have rearranged multiple times in the ancestors who contributed chromosomes to current humans. Not only are the relationships of these multi-allelic CNVs (mCNVs) to phenotypes generally unknown, but many mCNVs have not yet been described at the basic levels—alleles, allele frequencies, structural features—that support genetic investigation. To date, most reported disease associations to these variants have been ascertained through candidate gene studies. However, only a few associations have reached the level of acceptance defined by durable replications in many cohorts. This likely stems from longstanding challenges in making precise molecular measurements of the alleles individuals have at these loci. However, approaches for mCNV analysis are improving quickly, and some of the unique characteristics of mCNVs may assist future association studies. Their various structural alleles are likely to have different magnitudes of effect, creating a natural allelic series of growing phenotypic impact and giving investigators a set of natural predictions and testable hypotheses about the extent to which each allele of an mCNV predisposes to a phenotype. Also, mCNVs’ low-to-modest correlation to individual single-nucleotide polymorphisms (SNPs) may make it easier to distinguish between mCNVs and nearby SNPs as the drivers of an association signal, and perhaps, make it possible to preliminarily screen candidate loci, or the entire genome, for the many mCNV–disease relationships that remain to be discovered. PMID:26163405

  8. Energy variational analysis of ions in water and channels: Field theory for primitive models of complex ionic fluids

    PubMed Central

    Eisenberg, Bob; Hyon, YunKyong; Liu, Chun

    2010-01-01

    Ionic solutions are mixtures of interacting anions and cations. They hardly resemble dilute gases of uncharged noninteracting point particles described in elementary textbooks. Biological and electrochemical solutions have many components that interact strongly as they flow in concentrated environments near electrodes, ion channels, or active sites of enzymes. Interactions in concentrated environments help determine the characteristic properties of electrodes, enzymes, and ion channels. Flows are driven by a combination of electrical and chemical potentials that depend on the charges, concentrations, and sizes of all ions, not just the same type of ion. We use a variational method EnVarA (energy variational analysis) that combines Hamilton’s least action and Rayleigh’s dissipation principles to create a variational field theory that includes flow, friction, and complex structure with physical boundary conditions. EnVarA optimizes both the action integral functional of classical mechanics and the dissipation functional. These functionals can include entropy and dissipation as well as potential energy. The stationary point of the action is determined with respect to the trajectory of particles. The stationary point of the dissipation is determined with respect to rate functions (such as velocity). Both variations are written in one Eulerian (laboratory) framework. In variational analysis, an “extra layer” of mathematics is used to derive partial differential equations. Energies and dissipations of different components are combined in EnVarA and Euler–Lagrange equations are then derived. These partial differential equations are the unique consequence of the contributions of individual components. The form and parameters of the partial differential equations are determined by algebra without additional physical content or assumptions. The partial differential equations of mixtures automatically combine physical properties of individual (unmixed) components

  9. Energy variational analysis of ions in water and channels: Field theory for primitive models of complex ionic fluids.

    PubMed

    Eisenberg, Bob; Hyon, Yunkyong; Liu, Chun

    2010-09-14

    Ionic solutions are mixtures of interacting anions and cations. They hardly resemble dilute gases of uncharged noninteracting point particles described in elementary textbooks. Biological and electrochemical solutions have many components that interact strongly as they flow in concentrated environments near electrodes, ion channels, or active sites of enzymes. Interactions in concentrated environments help determine the characteristic properties of electrodes, enzymes, and ion channels. Flows are driven by a combination of electrical and chemical potentials that depend on the charges, concentrations, and sizes of all ions, not just the same type of ion. We use a variational method EnVarA (energy variational analysis) that combines Hamilton's least action and Rayleigh's dissipation principles to create a variational field theory that includes flow, friction, and complex structure with physical boundary conditions. EnVarA optimizes both the action integral functional of classical mechanics and the dissipation functional. These functionals can include entropy and dissipation as well as potential energy. The stationary point of the action is determined with respect to the trajectory of particles. The stationary point of the dissipation is determined with respect to rate functions (such as velocity). Both variations are written in one Eulerian (laboratory) framework. In variational analysis, an "extra layer" of mathematics is used to derive partial differential equations. Energies and dissipations of different components are combined in EnVarA and Euler-Lagrange equations are then derived. These partial differential equations are the unique consequence of the contributions of individual components. The form and parameters of the partial differential equations are determined by algebra without additional physical content or assumptions. The partial differential equations of mixtures automatically combine physical properties of individual (unmixed) components. If a new

  10. Energy variational analysis of ions in water and channels: Field theory for primitive models of complex ionic fluids

    NASA Astrophysics Data System (ADS)

    Eisenberg, Bob; Hyon, YunKyong; Liu, Chun

    2010-09-01

    Ionic solutions are mixtures of interacting anions and cations. They hardly resemble dilute gases of uncharged noninteracting point particles described in elementary textbooks. Biological and electrochemical solutions have many components that interact strongly as they flow in concentrated environments near electrodes, ion channels, or active sites of enzymes. Interactions in concentrated environments help determine the characteristic properties of electrodes, enzymes, and ion channels. Flows are driven by a combination of electrical and chemical potentials that depend on the charges, concentrations, and sizes of all ions, not just the same type of ion. We use a variational method EnVarA (energy variational analysis) that combines Hamilton's least action and Rayleigh's dissipation principles to create a variational field theory that includes flow, friction, and complex structure with physical boundary conditions. EnVarA optimizes both the action integral functional of classical mechanics and the dissipation functional. These functionals can include entropy and dissipation as well as potential energy. The stationary point of the action is determined with respect to the trajectory of particles. The stationary point of the dissipation is determined with respect to rate functions (such as velocity). Both variations are written in one Eulerian (laboratory) framework. In variational analysis, an "extra layer" of mathematics is used to derive partial differential equations. Energies and dissipations of different components are combined in EnVarA and Euler-Lagrange equations are then derived. These partial differential equations are the unique consequence of the contributions of individual components. The form and parameters of the partial differential equations are determined by algebra without additional physical content or assumptions. The partial differential equations of mixtures automatically combine physical properties of individual (unmixed) components. If a new

  11. Saturation sampling for spatial variation in multiple air pollutants across an inversion-prone metropolitan area of complex terrain

    PubMed Central

    2014-01-01

    Background Characterizing intra-urban variation in air quality is important for epidemiological investigation of health outcomes and disparities. To date, however, few studies have been designed to capture spatial variation during select hours of the day, or to examine the roles of meteorology and complex terrain in shaping intra-urban exposure gradients. Methods We designed a spatial saturation monitoring study to target local air pollution sources, and to understand the role of topography and temperature inversions on fine-scale pollution variation by systematically allocating sampling locations across gradients in key local emissions sources (vehicle traffic, industrial facilities) and topography (elevation) in the Pittsburgh area. Street-level integrated samples of fine particulate matter (PM2.5), black carbon (BC), nitrogen dioxide (NO2), sulfur dioxide (SO2), and ozone (O3) were collected during morning rush and probable inversion hours (6-11 AM), during summer and winter. We hypothesized that pollution concentrations would be: 1) higher under inversion conditions, 2) exacerbated in lower-elevation areas, and 3) vary by season. Results During July - August 2011 and January - March 2012, we observed wide spatial and seasonal variability in pollution concentrations, exceeding the range measured at regulatory monitors. We identified elevated concentrations of multiple pollutants at lower-elevation sites, and a positive association between inversion frequency and NO2 concentration. We examined temporal adjustment methods for deriving seasonal concentration estimates, and found that the appropriate reference temporal trend differs between pollutants. Conclusions Our time-stratified spatial saturation approach found some evidence for modification of inversion-concentration relationships by topography, and provided useful insights for refining and interpreting GIS-based pollution source indicators for Land Use Regression modeling. PMID:24735818

  12. Unexpected Actinyl Cation-Directed Structural Variation in Neptunyl(VI) A-Type Tri-lacunary Heteropolyoxotungstate Complexes

    DOE PAGES

    Berg, John M.; Gaunt, Andrew J.; May, Iain; ...

    2015-04-22

    A-type tri-lacunary heteropolyoxotungstate anions (e.g., [PW9O34]9-, [AsW9O34]9-, [SiW9O34]10- and [GeW9O34]10-) are multi-dentate oxygen donor ligands that readily form sandwich complexes with actinyl cations ({UO2}2+, {NpO2}+, {NpO2}2+ & {PuO2}2+) in near neutral/slightly alkaline aqueous solutions. Two or three actinyl cations are sandwiched between two trilacunary anions, with additional cations (Na+, K+ or NH4 +) also often held within the cluster. Studies thus far have indicated that it is these additional +I cations, rather than the specific actinyl cation, that direct the structural variation in the complexes formed. We now report the structural characterization of the neptunyl (VI) cluster complex (NH4)13 [Na(NpO2)2(A-α-more » PW9O34)2]·12H2O. The anion in this complex, [Na(NpO2)2(PW9O34)2]13-, contains one Na+ cation and two {NpO2}2+ cations held between two [PW9O34]9- anions – with an additional partial occupancy NH4 + or {NpO2}2+ cation also present. In the analogous uranium (VI) system, under similar reaction conditions that includes an excess of NH4Cl in the parent solution, it was previously shown that [(NH4)2(UVIO2)2(A-PW9O34)2]12- is the dominant species in both solution and the crystallized salt. Spectroscopic studies provide further proof of differences in the observed chemistry for the {NpO2}2+/[PW9O34]9- and {UO2}2+/[PW9O34]9- systems, both in solution and in solid state complexes crystallized from comparable salt solutions. The work revealed that varying the actinide element (Np vs. U) can indeed measurably impact structure and complex stability in the cluster chemistry of actinyl (VI) cations with A-type tri-lacunary heteropolyoxotungstate anions.« less

  13. Helium Isotope Variations in Peridotite, Gabbro and Basalt from the Kane Oceanic Core Complex

    NASA Astrophysics Data System (ADS)

    Konrad, K.; Graham, D. W.; Dick, H. J.

    2012-12-01

    A fundamental assumption in mapping geochemical variability of the upper mantle is that the isotope composition of mid-ocean ridge basalt is representative of its mantle source region, being largely unmodified during its transport through the crust and eruption on the seafloor. We have begun to test this assumption through measurement of He isotopes in a suite of rocks from the Kane oceanic core complex (OCC) along the Mid-Atlantic Ridge (23oN). The Kane OCC provides a valuable window into crustal architecture and chemical composition of a slow-spreading ridge (Dick et. al. 2008, 2010). A suite of > 30 samples (comprised of whole rocks, mineral separates and basalt glasses) has been analyzed for 3He/4He and He concentrations. Gas extraction experiments included crushing in vacuum, step heating, and fusion in a high-vacuum furnace. We found 3He/4He in the two freshest peridotites (harzburgite and olivine websterite) to be identical to that measured in the most depleted MORB glasses collected from the ridge axis (8.4-8.7 RA). Notably, the freshest and least deformed peridotite (a porphyroclastic harzburgite) has the highest helium content of any of the OCC rocks (~200 ncc/g), and the majority of its helium (>2/3) is only released by melting. In contrast to the results of Kurz et al. (2009), which clearly show increasing helium concentration levels with increasing deformation in abyssal peridotites from other localities, at the Kane OCC we found lower helium contents in three mylonitized peridotites compared to the less deformed peridotites. Troctolites from the Kane OCC experienced very late-stage melt impregnation fed through a conduit represented by a large dunite body near the MOHO. 3He/4He ratios in the troctolites (8.6-9.0 RA) also overlap with values in the fresh peridotites and in the most depleted basalts from the area. Collectively, fresh Kane OCC peridotites and troctolites, having [He] above 10 ncc/g, show a narrow range of 3He/4He ratio (8.4-9.0 RA). This

  14. Complex mountain terrain and disturbance history drive variation in forest aboveground live carbon density in the western Oregon Cascades, USA

    PubMed Central

    Zald, Harold S.J.; Spies, Thomas A.; Seidl, Rupert; Pabst, Robert J.; Olsen, Keith A.; Steel, E. Ashley

    2016-01-01

    Forest carbon (C) density varies tremendously across space due to the inherent heterogeneity of forest ecosystems. Variation of forest C density is especially pronounced in mountainous terrain, where environmental gradients are compressed and vary at multiple spatial scales. Additionally, the influence of environmental gradients may vary with forest age and developmental stage, an important consideration as forest landscapes often have a diversity of stand ages from past management and other disturbance agents. Quantifying forest C density and its underlying environmental determinants in mountain terrain has remained challenging because many available data sources lack the spatial grain and ecological resolution needed at both stand and landscape scales. The objective of this study was to determine if environmental factors influencing aboveground live carbon (ALC) density differed between young versus old forests. We integrated aerial light detection and ranging (lidar) data with 702 field plots to map forest ALC density at a grain of 25 m across the H.J. Andrews Experimental Forest, a 6369 ha watershed in the Cascade Mountains of Oregon, USA. We used linear regressions, random forest ensemble learning (RF) and sequential autoregressive modeling (SAR) to reveal how mapped forest ALC density was related to climate, topography, soils, and past disturbance history (timber harvesting and wildfires). ALC increased with stand age in young managed forests, with much greater variation of ALC in relation to years since wildfire in old unmanaged forests. Timber harvesting was the most important driver of ALC across the entire watershed, despite occurring on only 23% of the landscape. More variation in forest ALC density was explained in models of young managed forests than in models of old unmanaged forests. Besides stand age, ALC density in young managed forests was driven by factors influencing site productivity, whereas variation in ALC density in old unmanaged forests

  15. Complex mountain terrain and disturbance history drive variation in forest aboveground live carbon density in the western Oregon Cascades, USA.

    PubMed

    Zald, Harold S J; Spies, Thomas A; Seidl, Rupert; Pabst, Robert J; Olsen, Keith A; Steel, E Ashley

    2016-04-15

    Forest carbon (C) density varies tremendously across space due to the inherent heterogeneity of forest ecosystems. Variation of forest C density is especially pronounced in mountainous terrain, where environmental gradients are compressed and vary at multiple spatial scales. Additionally, the influence of environmental gradients may vary with forest age and developmental stage, an important consideration as forest landscapes often have a diversity of stand ages from past management and other disturbance agents. Quantifying forest C density and its underlying environmental determinants in mountain terrain has remained challenging because many available data sources lack the spatial grain and ecological resolution needed at both stand and landscape scales. The objective of this study was to determine if environmental factors influencing aboveground live carbon (ALC) density differed between young versus old forests. We integrated aerial light detection and ranging (lidar) data with 702 field plots to map forest ALC density at a grain of 25 m across the H.J. Andrews Experimental Forest, a 6369 ha watershed in the Cascade Mountains of Oregon, USA. We used linear regressions, random forest ensemble learning (RF) and sequential autoregressive modeling (SAR) to reveal how mapped forest ALC density was related to climate, topography, soils, and past disturbance history (timber harvesting and wildfires). ALC increased with stand age in young managed forests, with much greater variation of ALC in relation to years since wildfire in old unmanaged forests. Timber harvesting was the most important driver of ALC across the entire watershed, despite occurring on only 23% of the landscape. More variation in forest ALC density was explained in models of young managed forests than in models of old unmanaged forests. Besides stand age, ALC density in young managed forests was driven by factors influencing site productivity, whereas variation in ALC density in old unmanaged forests

  16. Elliptic Preconditioner for Accelerating the Self-Consistent Field Iteration in Kohn--Sham Density Functional Theory

    SciTech Connect

    Lin, Lin; Yang, Chao

    2013-10-28

    We discuss techniques for accelerating the self consistent field (SCF) iteration for solving the Kohn-Sham equations. These techniques are all based on constructing approximations to the inverse of the Jacobian associated with a fixed point map satisfied by the total potential. They can be viewed as preconditioners for a fixed point iteration. We point out different requirements for constructing preconditioners for insulating and metallic systems respectively, and discuss how to construct preconditioners to keep the convergence rate of the fixed point iteration independent of the size of the atomistic system. We propose a new preconditioner that can treat insulating and metallic system in a unified way. The new preconditioner, which we call an elliptic preconditioner, is constructed by solving an elliptic partial differential equation. The elliptic preconditioner is shown to be more effective in accelerating the convergence of a fixed point iteration than the existing approaches for large inhomogeneous systems at low temperature.

  17. Calculation of negative electron affinity and aqueous anion hardness using kohn-Sham HOMO and LUMO energies.

    PubMed

    De Proft, Frank; Sablon, Nick; Tozer, David J; Geerlings, Paul

    2007-01-01

    An important chemical property emerging from density-functional theory is the hardness, which can be evaluated as half of the difference between the vertical ionisation energy and electron affinity of the system. For many gas phase molecules, however, the electron affinity is negative and standard ways of evaluating this property are troublesome. In this contribution, we investigate an unconventional approximation for the electron affinity, based on the Kohn-Sham orbital energies of the frontier orbitals and the ionisation potential. It is shown that, for a large series of molecules possessing negative electron affinities, this methodology yields reasonable values for this quantity and that the correlation of the computed values with the experimental affinities from electron transmission spectroscopy is superior to other theoretical approaches. In a second part of this contribution, the hardness of a series of stable negative ions is evaluated in aqueous solution.

  18. Power Series Approximation for the Correlation Kernel Leading to Kohn-Sham Methods Combining Accuracy, Computational Efficiency, and General Applicability

    NASA Astrophysics Data System (ADS)

    Erhard, Jannis; Bleiziffer, Patrick; Görling, Andreas

    2016-09-01

    A power series approximation for the correlation kernel of time-dependent density-functional theory is presented. Using this approximation in the adiabatic-connection fluctuation-dissipation (ACFD) theorem leads to a new family of Kohn-Sham methods. The new methods yield reaction energies and barriers of unprecedented accuracy and enable a treatment of static (strong) correlation with an accuracy of high-level multireference configuration interaction methods but are single-reference methods allowing for a black-box-like handling of static correlation. The new methods exhibit a better scaling of the computational effort with the system size than rivaling wave-function-based electronic structure methods. Moreover, the new methods do not suffer from the problem of singularities in response functions plaguing previous ACFD methods and therefore are applicable to any type of electronic system.

  19. Duplication and population dynamics shape historic patterns of selection and genetic variation at the major histocompatibility complex in rodents

    PubMed Central

    Winternitz, Jamie C; Wares, John P

    2013-01-01

    Genetic variation at the major histocompatibility complex (MHC) is vitally important for wildlife populations to respond to pathogen threats. As natural populations can fluctuate greatly in size, a key issue concerns how population cycles and bottlenecks that could reduce genetic diversity will influence MHC genes. Using 454 sequencing, we characterized genetic diversity at the DRB Class II locus in montane voles (Microtus montanus), a North American rodent that regularly undergoes high-amplitude fluctuations in population size. We tested for evidence of historic balancing selection, recombination, and gene duplication to identify mechanisms maintaining allelic diversity. Counter to our expectations, we found strong evidence of purifying selection acting on the DRB locus in montane voles. We speculate that the interplay between population fluctuations and gene duplication might be responsible for the weak evidence of historic balancing selection and strong evidence of purifying selection detected. To further explore this idea, we conducted a phylogenetically controlled comparative analysis across 16 rodent species with varying demographic histories and MHC duplication events (based on the maximum number of alleles detected per individual). On the basis of phylogenetic generalized linear model-averaging, we found evidence that the estimated number of duplicated loci was positively related to allelic diversity and, surprisingly, to the strength of purifying selection at the DRB locus. Our analyses also revealed that species that had undergone population bottlenecks had lower allelic richness than stable species. This study highlights the need to consider demographic history and genetic structure alongside patterns of natural selection to understand resulting patterns of genetic variation at the MHC. PMID:23789067

  20. Diversification in the South American Pampas: the genetic and morphological variation of the widespread Petunia axillaris complex (Solanaceae).

    PubMed

    Turchetto, Caroline; Fagundes, Nelson J R; Segatto, Ana L A; Kuhlemeier, Cris; Solís Neffa, Viviana G; Speranza, Pablo R; Bonatto, Sandro L; Freitas, Loreta B

    2014-02-01

    Understanding the spatiotemporal distribution of genetic variation and the ways in which this distribution is connected to the ecological context of natural populations is fundamental for understanding the nature and mode of intraspecific and, ultimately, interspecific differentiation. The Petunia axillaris complex is endemic to the grasslands of southern South America and includes three subspecies: P. a. axillaris, P. a. parodii and P. a. subandina. These subspecies are traditionally delimited based on both geography and floral morphology, although the latter is highly variable. Here, we determined the patterns of genetic (nuclear and cpDNA), morphological and ecological (bioclimatic) variation of a large number of P. axillaris populations and found that they are mostly coincident with subspecies delimitation. The nuclear data suggest that the subspecies are likely independent evolutionary units, and their morphological differences may be associated with local adaptations to diverse climatic and/or edaphic conditions and population isolation. The demographic dynamics over time estimated by skyline plot analyses showed different patterns for each subspecies in the last 100 000 years, which is compatible with a divergence time between 35 000 and 107 000 years ago between P. a. axillaris and P. a. parodii, as estimated with the IMa program. Coalescent simulation tests using Approximate Bayesian Computation do not support previous suggestions of extensive gene flow between P. a. axillaris and P. a. parodii in their contact zone.

  1. Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus

    PubMed Central

    Sylvester, Kayla; Charron, Guillaume; Leducq, Jean-Baptiste; Landry, Christian R.; Libkind, Diego; Hittinger, Chris Todd

    2016-01-01

    Lager-style beers constitute the vast majority of the beer market, and yet, the genetic origin of the yeast strains that brew them has been shrouded in mystery and controversy. Unlike ale-style beers, which are generally brewed with Saccharomyces cerevisiae, lagers are brewed at colder temperatures with allopolyploid hybrids of Saccharomyces eubayanus x S. cerevisiae. Since the discovery of S. eubayanus in 2011, additional strains have been isolated from South America, North America, Australasia, and Asia, but only interspecies hybrids have been isolated in Europe. Here, using genome sequence data, we examine the relationships of these wild S. eubayanus strains to each other and to domesticated lager strains. Our results support the existence of a relatively low-diversity (π = 0.00197) lineage of S. eubayanus whose distribution stretches across the Holarctic ecozone and includes wild isolates from Tibet, new wild isolates from North America, and the S. eubayanus parents of lager yeasts. This Holarctic lineage is closely related to a population with higher diversity (π = 0.00275) that has been found primarily in South America but includes some widely distributed isolates. A second diverse South American population (π = 0.00354) and two early-diverging Asian subspecies are more distantly related. We further show that no single wild strain from the Holarctic lineage is the sole closest relative of lager yeasts. Instead, different parts of the genome portray different phylogenetic signals and ancestry, likely due to outcrossing and incomplete lineage sorting. Indeed, standing genetic variation within this wild Holarctic lineage of S. eubayanus is responsible for genetic variation still segregating among modern lager-brewing hybrids. We conclude that the relationships among wild strains of S. eubayanus and their domesticated hybrids reflect complex biogeographical and genetic processes. PMID:27385107

  2. Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus.

    PubMed

    Peris, David; Langdon, Quinn K; Moriarty, Ryan V; Sylvester, Kayla; Bontrager, Martin; Charron, Guillaume; Leducq, Jean-Baptiste; Landry, Christian R; Libkind, Diego; Hittinger, Chris Todd

    2016-07-01

    Lager-style beers constitute the vast majority of the beer market, and yet, the genetic origin of the yeast strains that brew them has been shrouded in mystery and controversy. Unlike ale-style beers, which are generally brewed with Saccharomyces cerevisiae, lagers are brewed at colder temperatures with allopolyploid hybrids of Saccharomyces eubayanus x S. cerevisiae. Since the discovery of S. eubayanus in 2011, additional strains have been isolated from South America, North America, Australasia, and Asia, but only interspecies hybrids have been isolated in Europe. Here, using genome sequence data, we examine the relationships of these wild S. eubayanus strains to each other and to domesticated lager strains. Our results support the existence of a relatively low-diversity (π = 0.00197) lineage of S. eubayanus whose distribution stretches across the Holarctic ecozone and includes wild isolates from Tibet, new wild isolates from North America, and the S. eubayanus parents of lager yeasts. This Holarctic lineage is closely related to a population with higher diversity (π = 0.00275) that has been found primarily in South America but includes some widely distributed isolates. A second diverse South American population (π = 0.00354) and two early-diverging Asian subspecies are more distantly related. We further show that no single wild strain from the Holarctic lineage is the sole closest relative of lager yeasts. Instead, different parts of the genome portray different phylogenetic signals and ancestry, likely due to outcrossing and incomplete lineage sorting. Indeed, standing genetic variation within this wild Holarctic lineage of S. eubayanus is responsible for genetic variation still segregating among modern lager-brewing hybrids. We conclude that the relationships among wild strains of S. eubayanus and their domesticated hybrids reflect complex biogeographical and genetic processes.

  3. Complex Control of GABA(A) Receptor Subunit mRNA Expression: Variation, Covariation, and Genetic Regulation

    PubMed Central

    Mulligan, Megan K.; Wang, Xusheng; Adler, Adrienne L.; Mozhui, Khyobeni; Lu, Lu; Williams, Robert W.

    2012-01-01

    GABA type-A receptors are essential for fast inhibitory neurotransmission and are critical in brain function. Surprisingly, expression of receptor subunits is highly variable among individuals, but the cause and impact of this fluctuation remains unknown. We have studied sources of variation for all 19 receptor subunits using massive expression data sets collected across multiple brain regions and platforms in mice and humans. Expression of Gabra1, Gabra2, Gabrb2, Gabrb3, and Gabrg2 is highly variable and heritable among the large cohort of BXD strains derived from crosses of fully sequenced parents—C57BL/6J and DBA/2J. Genetic control of these subunits is complex and highly dependent on tissue and mRNA region. Remarkably, this high variation is generally not linked to phenotypic differences. The single exception is Gabrb3, a locus that is linked to anxiety. We identified upstream genetic loci that influence subunit expression, including three unlinked regions of chromosome 5 that modulate the expression of nine subunits in hippocampus, and that are also associated with multiple phenotypes. Candidate genes within these loci include, Naaa, Nos1, and Zkscan1. We confirmed a high level of coexpression for subunits comprising the major channel—Gabra1, Gabrb2, and Gabrg2—and identified conserved members of this expression network in mice and humans. Gucy1a3, Gucy1b3, and Lis1 are novel and conserved associates of multiple subunits that are involved in inhibitory signaling. Finally, proximal and distal regions of the 3′ UTRs of single subunits have remarkably independent expression patterns in both species. However, corresponding regions of different subunits often show congruent genetic control and coexpression (proximal-to-proximal or distal-to-distal), even in the absence of sequence homology. Our findings identify novel sources of variation that modulate subunit expression and highlight the extraordinary capacity of biological networks to buffer 4–100 fold

  4. Integrative Variation Analysis Reveals that a Complex Genotype May Specify Phenotype in Siblings with Syndromic Autism Spectrum Disorder

    PubMed Central

    Kitajima, João Paulo; Tahira, Ana Carolina; Feio-dos-Santos, Ana Cecília; Fock, Rodrigo Ambrósio; Lisboa, Bianca Cristina Garcia; Simões, Sérgio Nery; Krepischi, Ana C. V.; Rosenberg, Carla; Lourenço, Naila Cristina; Passos-Bueno, Maria Rita; Brentani, Helena

    2017-01-01

    It has been proposed that copy number variations (CNVs) are associated with increased risk of autism spectrum disorder (ASD) and, in conjunction with other genetic changes, contribute to the heterogeneity of ASD phenotypes. Array comparative genomic hybridization (aCGH) and exome sequencing, together with systems genetics and network analyses, are being used as tools for the study of complex disorders of unknown etiology, especially those characterized by significant genetic and phenotypic heterogeneity. Therefore, to characterize the complex genotype-phenotype relationship, we performed aCGH and sequenced the exomes of two affected siblings with ASD symptoms, dysmorphic features, and intellectual disability, searching for de novo CNVs, as well as for de novo and rare inherited point variations—single nucleotide variants (SNVs) or small insertions and deletions (indels)—with probable functional impacts. With aCGH, we identified, in both siblings, a duplication in the 4p16.3 region and a deletion at 8p23.3, inherited by a paternal balanced translocation, t(4, 8) (p16; p23). Exome variant analysis found a total of 316 variants, of which 102 were shared by both siblings, 128 were in the male sibling exome data, and 86 were in the female exome data. Our integrative network analysis showed that the siblings’ shared translocation could explain their similar syndromic phenotype, including overgrowth, macrocephaly, and intellectual disability. However, exome data aggregate genes to those already connected from their translocation, which are important to the robustness of the network and contribute to the understanding of the broader spectrum of psychiatric symptoms. This study shows the importance of using an integrative approach to explore genotype-phenotype variability. PMID:28118382

  5. Unexpected Actinyl Cation-Directed Structural Variation in Neptunyl(VI) A-Type Tri-lacunary Heteropolyoxotungstate Complexes

    SciTech Connect

    Berg, John M.; Gaunt, Andrew J.; May, Iain; Pugmire, Alison L.; Reilly, Sean D.; Scott, Brian L.; Wilkerson, Marianne P.

    2015-04-22

    A-type tri-lacunary heteropolyoxotungstate anions (e.g., [PW9O34]9-, [AsW9O34]9-, [SiW9O34]10- and [GeW9O34]10-) are multi-dentate oxygen donor ligands that readily form sandwich complexes with actinyl cations ({UO2}2+, {NpO2}+, {NpO2}2+ & {PuO2}2+) in near neutral/slightly alkaline aqueous solutions. Two or three actinyl cations are sandwiched between two trilacunary anions, with additional cations (Na+, K+ or NH4 +) also often held within the cluster. Studies thus far have indicated that it is these additional +I cations, rather than the specific actinyl cation, that direct the structural variation in the complexes formed. We now report the structural characterization of the neptunyl (VI) cluster complex (NH4)13 [Na(NpO2)2(A-α- PW9O34)2]·12H2O. The anion in this complex, [Na(NpO2)2(PW9O34)2]13-, contains one Na+ cation and two {NpO2}2+ cations held between two [PW9O34]9- anions – with an additional partial occupancy NH4 + or {NpO2}2+ cation also present. In the analogous uranium (VI) system, under similar reaction conditions that includes an excess of NH4Cl in the parent solution, it was previously shown that [(NH4)2(UVIO2)2(A-PW9O34)2]12- is the dominant species in both solution and the crystallized salt. Spectroscopic studies provide further proof of differences in the observed chemistry for the {NpO2}2+

  6. Genetic variation of the major histocompatibility complex (MHC class II B gene) in the threatened Hume's pheasant, Syrmaticus humiae.

    PubMed

    Chen, Weicai; Bei, Yongjian; Li, Hanhua

    2015-01-01

    Major histocompatibility complex (MHC) genes are the most polymorphic genes in vertebrates and encode molecules that play a crucial role in pathogen resistance. As a result of their diversity, they have received much attention in the fields of evolutionary and conservation biology. Here, we described the genetic variation of MHC class II B (MHCIIB) exon 2 in a wild population of Hume's pheasant (Syrmaticus humiae), which has suffered a dramatic decline in population over the last three decades across its ranges in the face of heavy exploitation and habitat loss. Twenty-four distinct alleles were found in 73 S. humiae specimens. We found seven shared alleles among four geographical groups as well as six rare MHCIIB alleles. Most individuals displayed between one to five alleles, suggesting that there are at least three MHCIIB loci of the Hume's pheasant. The dN ⁄ dS ratio at putative antigen-binding sites (ABS) was significantly greater than one, indicating balancing selection is acting on MHCIIB exon 2. Additionally, recombination and gene conversion contributed to generating MHCIIB diversity in the Hume's pheasant. One to three recombination events and seventy-five significant gene conversion events were observed within the Hume's pheasant MHCIIB loci. The phylogenetic tree and network analysis revealed that the Hume's pheasant alleles do not cluster together, but are scattered through the tree or network indicating a trans-species evolutionary mode. These findings revealed the evolution of the Hume's pheasant MHC after suffering extreme habitat fragmentation.

  7. SOLWEIG 1.0--modelling spatial variations of 3D radiant fluxes and mean radiant temperature in complex urban settings.

    PubMed

    Lindberg, Fredrik; Holmer, Björn; Thorsson, Sofia

    2008-09-01

    The mean radiant temperature, T(mrt), which sums up all shortwave and longwave radiation fluxes (both direct and reflected) to which the human body is exposed is one of the key meteorological parameters governing human energy balance and the thermal comfort of man. In this paper, a new radiation model (SOLWEIG 1.0), which simulates spatial variations of 3D radiation fluxes and T(mrt) in complex urban settings, is presented. The T(mrt) is derived by modelling shortwave and longwave radiation fluxes in six directions (upward, downward and from the four cardinal points) and angular factors. The model requires a limited number of inputs, such as direct, diffuse and global shortwave radiation, air temperature, relative humidity, urban geometry and geographical information (latitude, longitude and elevation). The model was evaluated using 7 days of integral radiation measurements at two sites with different building geometries--a large square and a small courtyard in Göteborg, Sweden (57 degrees N)--across different seasons and in various weather conditions. The evaluation reveals good agreement between modelled and measured values of T(mrt), with an overall good correspondence of R (2) = 0.94, (p < 0.01, RMSE = 4.8 K). SOLWEIG 1.0 is still under development. Future work will incorporate a vegetation scheme, as well as an improvement of the estimation of fluxes from the four cardinal points.

  8. Seasonal and spatial variations of 17Oexcess and dexcess in Antarctic precipitation: Insights from an intermediate complexity isotope model

    NASA Astrophysics Data System (ADS)

    Schoenemann, Spruce W.; Steig, Eric J.

    2016-10-01

    An intermediate complexity model (ICM) is used to investigate the sensitivity of water isotope ratios in precipitation, including 17Oexcess, to climate variations in the Southern Hemisphere. The ICM is forced with boundary conditions from seasonal National Centers for Environmental Prediction/Department of Energy II reanalysis data. Perturbations to the surface temperature and humidity fields are used to investigate the isotopic sensitivity. The response of 17Oexcess to a uniform temperature change is insignificant over the ocean, while there is a large magnitude response over the ice sheet, particularly in East Antarctica. A decrease of ocean surface relative humidity produces increased 17Oexcess and dexcess, with a coherent response over both the ocean and Antarctica. For interior East Antarctica, the model simulates a seasonal cycle in 17Oexcess that is positively correlated with δ18O and of large magnitude ( 50 per meg), consistent with the observations from Vostok. The seasonal cycle in 17Oexcess for interior West Antarctica is predicted to be considerably smaller in magnitude (12 per meg), and is negatively correlated with δ18O, consistent with new data from a firn core near the West Antarctic Ice Sheet Divide site. Over the ocean, the ICM predicts much smaller seasonal cycles in 17Oexcess. Oceanic source changes (i.e., humidity) are insufficient to explain the amplitude of the simulated seasonal cycle over the Antarctic continent. Spatial differences in the seasonal response of 17Oexcess to local temperature reflect the balance of equilibrium and kinetic fractionation during snow formation.

  9. Evolution of reproductive mode variation and host associations in a sexual-asexual complex of aphid parasitoids

    PubMed Central

    2011-01-01

    Background The Lysiphlebus fabarum group is a taxonomically poorly resolved complex of aphid parasitoids, presently split into three described species that comprise sexual (arrhenotokous) and asexual (thelytokous) lineages of unknown relationship. Specifically, it is unclear how asexuals evolved from sexuals in this system, to what extent reproductive modes are still connected by genetic exchange, how much the complex is structured by geography or by host-associated differentiation, and whether species designations are valid. Using a combination of population genetic and phylogenetic approaches, we addressed these issues in a comprehensive sample of parasitoid wasps from across Europe. Results Asexual reproduction predominated in parasitoids of the L. fabarum group, with asexual populations exhibiting high genotypic diversity. Sexual populations were only common in southern France; elsewhere sexual reproduction was restricted to specific aphid hosts. Although reproductive modes were aggregated on the mitochondrial genealogy and significantly differentiated at nuclear microsatellite loci, there was clear evidence for genetic exchange, especially on hosts attacked by sexual and asexual parasitoids. The microsatellite data further revealed that parasitoids collected from certain host aphids were significantly differentiated, yet the mitochondrial sequence variation across the entire L. fabarum group did not exceed 1.32% and exhibited a very shallow topology. Morphological characters used for delineation of described species were found to be phylogenetically non-conservative. Conclusions Our results suggest that the sexual-asexual L. fabarum group represents a young complex of lineages with incomplete isolation between reproductive modes. We propose three mechanisms of genetic exchange that may jointly explain the high genotypic diversity observed in asexual parasitoids: (i) the formation of new asexual lineages via 'contagious parthenogenesis', (ii) introgression from

  10. Quantitative trait loci in hop (Humulus lupulus L.) reveal complex genetic architecture underlying variation in sex, yield and cone chemistry

    PubMed Central

    2013-01-01

    advance our understanding of the genetic control of traits of current economic and breeding significance in hop and demonstrate the complex genetic architecture underlying variation in these traits. The linkage information obtained in this study, based on transferable markers, can be used to facilitate the validation of QTL, crucial to the success of MAS. PMID:23718194

  11. Airflow and sand transport variations within a backshore parabolic dune plain complex: NE Graham Island, British Columbia, Canada

    NASA Astrophysics Data System (ADS)

    Anderson, Jeffrey L.; Walker, Ian J.

    2006-07-01

    Onshore aeolian sand transport beyond the beach and foredune is often overlooked in the morphodynamics and sediment budgets of sandy coastal systems. This study provides detailed measurements of airflow, sand transport (via saltation and modified suspension), vegetation density, and surface elevation changes over an extensive (325 × 30 m) "swath" of a backshore foredune-parabolic dune plain complex. Near-surface (30 cm) wind speeds on the backshore ranged from 4.3 to 7.3 m s - 1 , gusting to 14.0 m s - 1 . Oblique onshore flow is steered alongshore near the incipient foredune then landward into a trough blowout where streamline compression, flow acceleration to 1.8 times the incident speed, and increasing steadiness occur. Highest saltation rates occur in steady, topographically accelerated flow within the blowout. As such, the blowout acts as a conduit to channel flow and sand through the foredune into the foredune plain. Beyond the blowout, flow expands, vegetation roughness increases, and flow decelerates. Over the foredune plain, localized flow steering and acceleration to 1.6 times the incident speed occurs followed by a drop to 40% of incident flow speed in a densely vegetated zone upwind of an active parabolic dune at 250 m from the foredune. Sediment properties reflect variations in near-surface flow and transport processes. Well-sorted, fine skewed backshore sands become more poorly sorted and coarse skewed in the blowout due to winnowing of fines. Sorting improves and sands become fine skewed over the foredune plain toward the parabolic dune due to grainfall of finer sands winnowed from the beach and foredune. During the fall-winter season, significant amounts of sand (up to 110 kg m - 2 ) are transported via modified suspension and deposited as grainfall up to 300 m landward of the foredune. No distinct trend in grainfall was found, although most fell on the depositional lobe of the blowout and at 200 m near an isolated, active parabolic dune. Grainfall

  12. Jackknife Estimation of Sampling Variance of Ratio Estimators in Complex Samples: Bias and the Coefficient of Variation. Research Report. ETS RR-06-19

    ERIC Educational Resources Information Center

    Oranje, Andreas

    2006-01-01

    A multitude of methods has been proposed to estimate the sampling variance of ratio estimates in complex samples (Wolter, 1985). Hansen and Tepping (1985) studied some of those variance estimators and found that a high coefficient of variation (CV) of the denominator of a ratio estimate is indicative of a biased estimate of the standard error of a…

  13. Complexity.

    PubMed

    Gómez-Hernández, J Jaime

    2006-01-01

    It is difficult to define complexity in modeling. Complexity is often associated with uncertainty since modeling uncertainty is an intrinsically difficult task. However, modeling uncertainty does not require, necessarily, complex models, in the sense of a model requiring an unmanageable number of degrees of freedom to characterize the aquifer. The relationship between complexity, uncertainty, heterogeneity, and stochastic modeling is not simple. Aquifer models should be able to quantify the uncertainty of their predictions, which can be done using stochastic models that produce heterogeneous realizations of aquifer parameters. This is the type of complexity addressed in this article.

  14. Response of a hydrothermal system to magmatic heat inferred from temporal variations in the complex frequencies of long-period events at Kusatsu-Shirane Volcano, Japan

    USGS Publications Warehouse

    Nakano, M.; Kumagai, H.

    2005-01-01

    We investigate temporal variations in the complex frequencies (frequency and quality factor Q) of long-period (LP) events that occurred at Kusatsu-Shirane Volcano, central Japan. We analyze LP waveforms observed at this volcano in the period between 1988 and 1995, which covers a seismically active period between 1989 and 1993. Systematic temporal variations in the complex frequencies are observed in October-November 1989, July-October 1991, and September 1992-January 1993. We use acoustic properties of a crack filled with hydrothermal fluids to interpret the observed temporal variations in the complex frequencies. The temporal variations in October-November 1989 can be divided into two periods, which are explained by a gradual decrease and increase of a gas-volume fraction in a water-steam mixture in a crack, respectively. The temporal variations in July-October 1991 can be also divided into two periods. These variations in the first and second periods are similar to those observed in November 1989 and in September-November 1992, respectively, and are interpreted as drying of a water-steam mixture and misty gas in a crack, respectively. The repeated nature of the temporal variations observed in similar seasons between July and November suggests the existence of seasonality in the occurrence of LP events. This may be caused by a seasonally variable meteoritic water supply to a hydrothermal system, which may have been heated by the flux of volcanic gases from magma beneath this volcano. ?? 2005 Elsevier B.V. All rights reserved.

  15. The static response function in Kohn-Sham theory: an appropriate basis for its matrix representation in case of finite AO basis sets.

    PubMed

    Kollmar, Christian; Neese, Frank

    2014-10-07

    The role of the static Kohn-Sham (KS) response function describing the response of the electron density to a change of the local KS potential is discussed in both the theory of the optimized effective potential (OEP) and the so-called inverse Kohn-Sham problem involving the task to find the local KS potential for a given electron density. In a general discussion of the integral equation to be solved in both cases, it is argued that a unique solution of this equation can be found even in case of finite atomic orbital basis sets. It is shown how a matrix representation of the response function can be obtained if the exchange-correlation potential is expanded in terms of a Schmidt-orthogonalized basis comprising orbitals products of occupied and virtual orbitals. The viability of this approach in both OEP theory and the inverse KS problem is illustrated by numerical examples.

  16. Extended application of Kohn-Sham first-principles molecular dynamics method with plane wave approximation at high energy—From cold materials to hot dense plasmas

    NASA Astrophysics Data System (ADS)

    Zhang, Shen; Wang, Hongwei; Kang, Wei; Zhang, Ping; He, X. T.

    2016-04-01

    An extended first-principles molecular dynamics (FPMD) method based on Kohn-Sham scheme is proposed to elevate the temperature limit of the FPMD method in the calculation of dense plasmas. The extended method treats the wave functions of high energy electrons as plane waves analytically and thus expands the application of the FPMD method to the region of hot dense plasmas without suffering from the formidable computational costs. In addition, the extended method inherits the high accuracy of the Kohn-Sham scheme and keeps the information of electronic structures. This gives an edge to the extended method in the calculation of mixtures of plasmas composed of heterogeneous ions, high-Z dense plasmas, lowering of ionization potentials, X-ray absorption/emission spectra, and opacities, which are of particular interest to astrophysics, inertial confinement fusion engineering, and laboratory astrophysics.

  17. Bioassays for TSH Receptor Autoantibodies, from FRTL-5 Cells to TSH Receptor–LH/CG Receptor Chimeras: The Contribution of Leonard D. Kohn

    PubMed Central

    Giuliani, Cesidio; Saji, Motoyasu; Bucci, Ines; Napolitano, Giorgio

    2016-01-01

    Since the discovery 60 years ago of the “long-acting thyroid stimulator” by Adams and Purves, great progress has been made in the detection of thyroid-stimulating hormone (TSH) receptor (TSHR) autoantibodies (TRAbs) in Graves’ disease. Today, commercial assays are available that can detect TRAbs with high accuracy and provide diagnostic and prognostic evaluation of patients with Graves’ disease. The present review focuses on the development of TRAbs bioassays, and particularly on the role that Leonard D. Kohn had in this. Indeed, 30 years ago, the Kohn group developed a bioassay based on the use of FRTL-5 cells that was characterized by high reproducibility, feasibility, and diagnostic accuracy. Using this FRTL-5 bioassay, Kohn and his colleagues were the first to develop monoclonal antibodies (moAbs) against the TSHR. Furthermore, they demonstrated the multifaceted functional nature of TRAbs in patients with Graves’ disease, with the identification of stimulating and blocking TRAbs, and even antibodies that activated pathways other than cAMP. After the cloning of the TSHR, the Kohn laboratory constructed human TSHR–rat luteinizing hormone/chorionic gonadotropin receptor chimeras. This paved the way to a new bioassay based on the use of non-thyroid cells transfected with the Mc4 chimera. The new Mc4 bioassay is characterized by high diagnostic and prognostic accuracy, greater than for other assays. The availability of a commercial kit based on the Mc4 chimera is spreading the use of this assay worldwide, indicating its benefits for these patients with Graves’ disease. This review also describes the main contributions made by other researchers in TSHR molecular biology and TRAbs assay, especially with the development of highly potent moAbs. A comparison of the diagnostic accuracies of the main TRAbs assays, as both immunoassays and bioassays, is also provided. PMID:27504107

  18. Hartree-Fock and Kohn-Sham time-dependent response theory in a second-quantization atomic-orbital formalism suitable for linear scaling.

    PubMed

    Kjaergaard, Thomas; Jørgensen, Poul; Olsen, Jeppe; Coriani, Sonia; Helgaker, Trygve

    2008-08-07

    We present a second-quantization based atomic-orbital method for the computation of time-dependent response functions within Hartree-Fock and Kohn-Sham density-functional theories. The method is suited for linear scaling. Illustrative results are presented for excitation energies, one- and two-photon transition moments, polarizabilities, and hyperpolarizabilities for hexagonal BN sheets with up to 180 atoms.

  19. Breakdown of lung framework and an increase in pores of Kohn as initial events of emphysema and a cause of reduction in diffusing capacity

    PubMed Central

    Yoshikawa, Akira; Sato, Shuntaro; Tanaka, Tomonori; Hashisako, Mikiko; Kashima, Yukio; Tsuchiya, Tomoshi; Yamasaki, Naoya; Nagayasu, Takeshi; Yamamoto, Hiroshi; Fukuoka, Junya

    2016-01-01

    Purpose Pulmonary emphysema is the pathological prototype of chronic obstructive pulmonary disease and is also associated with other lung diseases. We considered that observation with different approaches may provide new insights for the pathogenesis of emphysema. Patients and methods We reviewed tissue blocks of the lungs of 25 cases with/without emphysema and applied a three-dimensional observation method to the blocks. Based on the three-dimensional characteristics of the alveolar structure, we considered one face of the alveolar polyhedron as a structural unit of alveoli and called it a framework unit (FU). We categorized FUs based on their morphological characteristics and counted their number to evaluate the destructive changes in alveoli. We also evaluated the number and the area of pores of Kohn in FUs. We performed linear regression analysis to estimate the effect of these data on pulmonary function tests. Results In multivariable regression analysis, a decrease in the number of FUs without an alveolar wall led to a significant decrease in the diffusing capacity of the lung for carbon monoxide (DLCO) and DLCO per unit alveolar volume, and an increase in the area of pores of Kohn had a significant effect on an increase in residual capacity. Conclusion A breakdown in the lung framework and an increase in pores of Kohn are associated with a decrease in DLCO and DLCO per unit alveolar volume with/without emphysema. PMID:27695315

  20. Configuration interaction singles based on the real-space numerical grid method: Kohn-Sham versus Hartree-Fock orbitals.

    PubMed

    Kim, Jaewook; Hong, Kwangwoo; Choi, Sunghwan; Hwang, Sang-Yeon; Youn Kim, Woo

    2015-12-21

    We developed a program code of configuration interaction singles (CIS) based on a numerical grid method. We used Kohn-Sham (KS) as well as Hartree-Fock (HF) orbitals as a reference configuration and Lagrange-sinc functions as a basis set. Our calculations show that KS-CIS is more cost-effective and more accurate than HF-CIS. The former is due to the fact that the non-local HF exchange potential greatly reduces the sparsity of the Hamiltonian matrix in grid-based methods. The latter is because the energy gaps between KS occupied and virtual orbitals are already closer to vertical excitation energies and thus KS-CIS needs small corrections, whereas HF results in much larger energy gaps and more diffuse virtual orbitals. KS-CIS using the Lagrange-sinc basis set also shows a better or a similar accuracy to smaller orbital space compared to the standard HF-CIS using Gaussian basis sets. In particular, KS orbitals from an exact exchange potential by the Krieger-Li-Iafrate approximation lead to more accurate excitation energies than those from conventional (semi-) local exchange-correlation potentials.

  1. Kohn-Sham Band Structure Benchmark Including Spin-Orbit Coupling for 2D and 3D Solids

    NASA Astrophysics Data System (ADS)

    Huhn, William; Blum, Volker

    2015-03-01

    Accurate electronic band structures serve as a primary indicator of the suitability of a material for a given application, e.g., as electronic or catalytic materials. Computed band structures, however, are subject to a host of approximations, some of which are more obvious (e.g., the treatment of the exchange-correlation of self-energy) and others less obvious (e.g., the treatment of core, semicore, or valence electrons, handling of relativistic effects, or the accuracy of the underlying basis set used). We here provide a set of accurate Kohn-Sham band structure benchmarks, using the numeric atom-centered all-electron electronic structure code FHI-aims combined with the ``traditional'' PBE functional and the hybrid HSE functional, to calculate core, valence, and low-lying conduction bands of a set of 2D and 3D materials. Benchmarks are provided with and without effects of spin-orbit coupling, using quasi-degenerate perturbation theory to predict spin-orbit splittings. This work is funded by Fritz-Haber-Institut der Max-Planck-Gesellschaft.

  2. Inelastic light and electron scattering in parabolic quantum dots in magnetic field: Implications of generalized Kohn's theorem

    NASA Astrophysics Data System (ADS)

    Kushwaha, Manvir S.

    2016-03-01

    We investigate a one-component, quasi-zero-dimensional, quantum plasma exposed to a parabolic potential and an applied magnetic field in the symmetric gauge. If the size of such a system as can be realized in the semiconducting quantum dots is on the order of the de Broglie wavelength, the electronic and optical properties become highly tunable. Then the quantum size effects challenge the observation of many-particle phenomena such as the magneto-optical absorption, Raman intensity, and electron energy loss spectrum. An exact analytical solution of the problem leads us to infer that these many-particle phenomena are, in fact, dictated by the generalized Kohn's theorem in the long-wavelength limit. Maneuvering the confinement and/or the magnetic field furnishes the resonance energy capable of being explored with the FIR, Raman, or electron energy loss spectroscopy. This implies that either of these probes should be competent in observing the localized magnetoplasmons in the system. A deeper insight into the physics of quantum dots is paving the way for their implementation in diverse fields such as quantum computing and medical imaging.

  3. Spatio-temporal variation in the strength and mode of selection acting on major histocompatibility complex diversity in water vole (Arvicola terrestris) metapopulations.

    PubMed

    Oliver, Matthew K; Lambin, Xavier; Cornulier, Thomas; Piertney, Stuart B

    2009-01-01

    Patterns of spatio-temporal genetic variation at a class II major histocompatibility complex (MHC) locus and multiple microsatellite loci were analysed within and between three water vole metapopulations in Scotland, UK. Comparisons of MHC and microsatellite spatial genetic differentiation, based on standardised tests between two demographically asynchronous zones within a metapopulation, suggested that spatial MHC variation was affected by balancing selection, directional selection and random genetic drift, but that the relative effects of these microevolutionary forces vary temporally. At the metapopulation level, between-year differentiation for MHC loci was significantly correlated with that of microsatellites, signifying that neutral factors such as migration and drift were primarily responsible for overall temporal genetic change at the metapopulation scale. Between metapopulations, patterns of genetic differentiation implied that, at large spatial scales, MHC variation was primarily affected by directional selection and drift. Levels of MHC heterozygosity in excess of Hardy-Weinberg expectations were consistent with overdominant balancing selection operating on MHC variation within metapopulations. However, this effect was not constant among all samples, indicating temporal variation in the strength of selection relative to other factors. The results highlight the benefit of contrasting variation at MHC with neutral markers to separate the effects of stochastic and deterministic microevolutionary forces, and add to a growing body of evidence showing that the mode and relative strength of selection acting on MHC diversity varies both spatially and temporally.

  4. Patterns of Molecular Variation. II. Associations of Electrophoretic Mobility and Larval Substrate within Species of the DROSOPHILA MULLERI Complex

    PubMed Central

    Richardson, R. H.; Smouse, Peter E.; Richardson, Martha E.

    1977-01-01

    Electromorphic variation among populations of Drosophila mojavensis, D. arizonensis and D. longicornis was examined for seven genetic loci. The average electrophoretic mobility for a population was used as the metric. D. mojavensis and D. arizonensis use larval substrates in different parts of their geographic ranges, while D. longicornis is more narrowly restricted to different species of the cactus Opuntia in different localities. There is marked electromorphic variation among populations of either D. mojavensis or D. arizonensis, and the bulk of this variation is accounted for by differences in laval substrate. There is somewhat less variation among populations of D. longicornis, and only a moderate portion of this is accounted for by larval substrate differences. There appears to be an association between the taxonomic diversity of the larval substrates and the electromorphic diversity of the Drosophila populations utilizing those substrates. Evidence is reviewed that suggests physiological mechanisms for these possibly adaptive associations. PMID:838268

  5. Parity-time-symmetric solitons in trapped Bose-Einstein condensates and the influence of varying complex potentials: A variational approach.

    PubMed

    Devassy, Lini; Jisha, Chandroth P; Alberucci, Alessandro; Kuriakose, V C

    2015-08-01

    Dynamics and properties of nonlinear matter waves in a trapped BEC subject to a PT-symmetric linear potential, with the trap in the form of a super-Gaussian potential, are investigated via a variational approach accounting for the complex nature of the soliton. In the process, we address how the shape of the imaginary part of the potential, that is, a gain-loss mechanism, affects the self-localization and the stability of the condensate. Variational results are found to be in good agreement with full numerical simulations for predicting the shape, width, and chemical potential of the condensate until the PT breaking point. Variational computation also predicts the existence of solitary solution only above a threshold in the particle number as the gain-loss is increased, in agreement with numerical simulations.

  6. Analytical and numerical validation for solving the fractional Klein-Gordon equation using the fractional complex transform and variational iteration methods

    NASA Astrophysics Data System (ADS)

    Khader, M. M.; Adel, M.

    2016-09-01

    In this paper, we implement the fractional complex transform method to convert the nonlinear fractional Klein-Gordon equation (FKGE) to an ordinary differential equation. We use the variational iteration method (VIM) to solve the resulting ODE. The fractional derivatives are presented in terms of the Caputo sense. Some numerical examples are presented to validate the proposed techniques. Finally, a comparison with the numerical solution using Runge-Kutta of order four is given.

  7. Reproductive biology and variation of nuclear ribosomal ITS and ETS sequences in the Calligonum mongolicum complex (Polygonaceae)

    PubMed Central

    Shi, Wei; Wen, Jun; Zhao, Yanfeng; Johnson, Gabriel; Pan, Borong

    2017-01-01

    Abstract To explore the biosystematics of the Calligonum mongolicum complex (Polygonaceae), the flowering phenological period, breeding and pollination characters and seed set of the complex (Calligonum Mongolicum Turze, Calligonum chinense A. Los., Calligonum gobicum A. Los., Calligonum pumilum A. Los. and Calligonum zaidamense A. Los.) were documented in the Turpan Eremophyte Botanical Garden, China. The sequences of the nuclear ribosomal ITS and ETS region were employed to differentiate the Calligonum mongolicum complex and other species in sect. Medusae. The results showed species of the Calligonum mongolicum complex occupied overlapping flowering periods and had consistent pollination agents. Their breeding systems are all self-compatible, tend to be out-crossing and they interbreed amongst each other (out-crossing index, OCI = 4).The crosses within and amongst species had high seed sets (44 - 65%). Phylogenetic analyses of Calligonum sect. Medusae and the network analysis of nrDNA (ITS and ETS) in the complex suggest interbreeding amongst “species” within the complex and provide evidence for taxonomically merging the five species in the complex. The detected hybridisation, occurring within the complex, suggests the need to improve traditional methods of ex situ plant conservation in botanical gardens for maintaining genetic diversity of Calligonum within and amongst species from different geographic areas. PMID:28228687

  8. Reproductive biology and variation of nuclear ribosomal ITS and ETS sequences in the Calligonum mongolicum complex (Polygonaceae).

    PubMed

    Shi, Wei; Wen, Jun; Zhao, Yanfeng; Johnson, Gabriel; Pan, Borong

    2017-01-01

    To explore the biosystematics of the Calligonum mongolicum complex (Polygonaceae), the flowering phenological period, breeding and pollination characters and seed set of the complex (Calligonum Mongolicum Turze, Calligonum chinense A. Los., Calligonum gobicum A. Los., Calligonum pumilum A. Los. and Calligonum zaidamense A. Los.) were documented in the Turpan Eremophyte Botanical Garden, China. The sequences of the nuclear ribosomal ITS and ETS region were employed to differentiate the Calligonum mongolicum complex and other species in sect. Medusae. The results showed species of the Calligonum mongolicum complex occupied overlapping flowering periods and had consistent pollination agents. Their breeding systems are all self-compatible, tend to be out-crossing and they interbreed amongst each other (out-crossing index, OCI = 4).The crosses within and amongst species had high seed sets (44 - 65%). Phylogenetic analyses of Calligonum sect. Medusae and the network analysis of nrDNA (ITS and ETS) in the complex suggest interbreeding amongst "species" within the complex and provide evidence for taxonomically merging the five species in the complex. The detected hybridisation, occurring within the complex, suggests the need to improve traditional methods of ex situ plant conservation in botanical gardens for maintaining genetic diversity of Calligonum within and amongst species from different geographic areas.

  9. Bioenergetics in human evolution and disease: implications for the origins of biological complexity and the missing genetic variation of common diseases.

    PubMed

    Wallace, Douglas C

    2013-07-19

    Two major inconsistencies exist in the current neo-Darwinian evolutionary theory that random chromosomal mutations acted on by natural selection generate new species. First, natural selection does not require the evolution of ever increasing complexity, yet this is the hallmark of biology. Second, human chromosomal DNA sequence variation is predominantly either neutral or deleterious and is insufficient to provide the variation required for speciation or for predilection to common diseases. Complexity is explained by the continuous flow of energy through the biosphere that drives the accumulation of nucleic acids and information. Information then encodes complex forms. In animals, energy flow is primarily mediated by mitochondria whose maternally inherited mitochondrial DNA (mtDNA) codes for key genes for energy metabolism. In mammals, the mtDNA has a very high mutation rate, but the deleterious mutations are removed by an ovarian selection system. Hence, new mutations that subtly alter energy metabolism are continuously introduced into the species, permitting adaptation to regional differences in energy environments. Therefore, the most phenotypically significant gene variants arise in the mtDNA, are regional, and permit animals to occupy peripheral energy environments where rarer nuclear DNA (nDNA) variants can accumulate, leading to speciation. The neutralist-selectionist debate is then a consequence of mammals having two different evolutionary strategies: a fast mtDNA strategy for intra-specific radiation and a slow nDNA strategy for speciation. Furthermore, the missing genetic variation for common human diseases is primarily mtDNA variation plus regional nDNA variants, both of which have been missed by large, inter-population association studies.

  10. Bioenergetics in human evolution and disease: implications for the origins of biological complexity and the missing genetic variation of common diseases

    PubMed Central

    Wallace, Douglas C.

    2013-01-01

    Two major inconsistencies exist in the current neo-Darwinian evolutionary theory that random chromosomal mutations acted on by natural selection generate new species. First, natural selection does not require the evolution of ever increasing complexity, yet this is the hallmark of biology. Second, human chromosomal DNA sequence variation is predominantly either neutral or deleterious and is insufficient to provide the variation required for speciation or for predilection to common diseases. Complexity is explained by the continuous flow of energy through the biosphere that drives the accumulation of nucleic acids and information. Information then encodes complex forms. In animals, energy flow is primarily mediated by mitochondria whose maternally inherited mitochondrial DNA (mtDNA) codes for key genes for energy metabolism. In mammals, the mtDNA has a very high mutation rate, but the deleterious mutations are removed by an ovarian selection system. Hence, new mutations that subtly alter energy metabolism are continuously introduced into the species, permitting adaptation to regional differences in energy environments. Therefore, the most phenotypically significant gene variants arise in the mtDNA, are regional, and permit animals to occupy peripheral energy environments where rarer nuclear DNA (nDNA) variants can accumulate, leading to speciation. The neutralist–selectionist debate is then a consequence of mammals having two different evolutionary strategies: a fast mtDNA strategy for intra-specific radiation and a slow nDNA strategy for speciation. Furthermore, the missing genetic variation for common human diseases is primarily mtDNA variation plus regional nDNA variants, both of which have been missed by large, inter-population association studies. PMID:23754818

  11. Methodology for the analysis of rare genetic variation in genome-wide association and re-sequencing studies of complex human traits

    PubMed Central

    Moutsianas, Loukas

    2014-01-01

    Genome-wide association studies have been successful in identifying common variants that impact complex human traits and diseases. However, despite this success, the joint effects of these variants explain only a small proportion of the genetic variance in these phenotypes, leading to speculation that rare genetic variation might account for much of the ‘missing heritability’. Consequently, there has been an exciting period of research and development into the methodology for the analysis of rare genetic variants, typically by considering their joint effects on complex traits within the same functional unit or genomic region. In this review, we describe a general framework for modelling the joint effects of rare genetic variants on complex traits in association studies of unrelated individuals. We summarise a range of widely used association tests that have been developed from this model and provide an overview of the relative performance of these approaches from published simulation studies. PMID:24916163

  12. Terrace width variations in complex Mercurian craters and the transient strength of cratered Mercurian and lunar crust

    NASA Technical Reports Server (NTRS)

    Leith, Andrew C.; Mckinnon, William B.

    1991-01-01

    The effective cohesion of the cratered region during crater collapse is determined via the widths of slump terraces of complex craters. Terrace widths are measured for complex craters on Mercury; these generally increase outward toward the rim for a given crater, and the width of the outermost major terrace is generally an increasing function of crater diameter. The terrace widths on Mercury and a gravity-driven slump model are used to estimate the strength of the cratered region immediately after impact (about 1-2 MPa). A comparison with the previous study of lunar complex craters by Pearce and Melosh (1986) indicates that the transient strength of cratered Mercurian crust is no greater than that of the moon. The strength estimates vary only slightly with the geometric model used to restore the outermost major terrace to its precollapse configuration and are consistent with independent strength estimates from the simple-to-complex crater depth/diameter transition.

  13. A role of genomic copy number variation in the complex behavioral phenotype of alcohol dependence: a commentary.

    PubMed

    Urban, Alexander E

    2012-09-01

    In their paper "Copy number variations in 6q14.1 and 5q13.2 are associated with alcohol dependence" Lin and colleagues report on the association between alcohol dependence and 2 duplication CNVs in the genome sequence, one containing 8 genes within its boundaries and another that contains no genes. In this commentary, I point out some of the opportunities and challenges that arise from such a finding.

  14. X-ray absorption resonances near L2,3-edges from real-time propagation of the Dirac-Kohn-Sham density matrix.

    PubMed

    Kadek, Marius; Konecny, Lukas; Gao, Bin; Repisky, Michal; Ruud, Kenneth

    2015-09-21

    The solution of the Liouville-von Neumann equation in the relativistic Dirac-Kohn-Sham density matrix formalism is presented and used to calculate X-ray absorption cross sections. Both dynamical relaxation effects and spin-orbit corrections are included, as demonstrated by calculations of the X-ray absorption of SF6 near the sulfur L2,3-edges. We also propose an analysis facilitating the interpretation of spectral transitions from real-time simulations, and a selective perturbation that eliminates nonphysical excitations that are artifacts of the finite basis representation.

  15. Virial theorem in the Kohn-Sham density-functional theory formalism: accurate calculation of the atomic quantum theory of atoms in molecules energies.

    PubMed

    Rodríguez, Juan I; Ayers, Paul W; Götz, Andreas W; Castillo-Alvarado, F L

    2009-07-14

    A new approach for computing the atom-in-molecule [quantum theory of atoms in molecule (QTAIM)] energies in Kohn-Sham density-functional theory is presented and tested by computing QTAIM energies for a set of representative molecules. In the new approach, the contribution for the correlation-kinetic energy (T(c)) is computed using the density-functional theory virial relation. Based on our calculations, it is shown that the conventional approach where atomic energies are computed using only the noninteracting part of the kinetic energy might be in error by hundreds of kJ/mol.

  16. Ab initio analytical Raman intensities for periodic systems through a coupled perturbed Hartree-Fock/Kohn-Sham method in an atomic orbital basis. I. Theory.

    PubMed

    Maschio, Lorenzo; Kirtman, Bernard; Rérat, Michel; Orlando, Roberto; Dovesi, Roberto

    2013-10-28

    We present a fully analytical formulation for calculating Raman intensities of crystalline periodic systems using a local basis set. Numerical differentiation with respect to atomic coordinates and with respect to wavevectors is entirely avoided as is the determination of crystal orbital coefficient derivatives with respect to nuclear displacements. Instead, our method utilizes the orbital energy-weighted density matrix and is based on the self-consistent solution of first- and second-order Coupled Perturbed Hartree-Fock/Kohn-Sham equations for the electronic response to external electric fields at the equilibrium geometry. This method has also been implemented in the Crystal program, which uses a Gaussian type basis set.

  17. Copy number variation in chemokine superfamily: the complex scene of CCL3L–CCL4L genes in health and disease

    PubMed Central

    Colobran, R; Pedrosa, E; Carretero-Iglesia, L; Juan, M

    2010-01-01

    Genome copy number changes (copy number variations: CNVs) include inherited, de novo and somatically acquired deviations from a diploid state within a particular chromosomal segment. CNVs are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. CNVs are distributed widely in the genomes of apparently healthy individuals and thus constitute significant amounts of population-based genomic variation. Human CNV loci are enriched for immune genes and one of the most striking examples of CNV in humans involves a genomic region containing the chemokine genes CCL3L and CCL4L. The CCL3L–CCL4L copy number variable region (CNVR) shows extensive architectural complexity, with smaller CNVs within the larger ones and with interindividual variation in breakpoints. Furthermore, the individual genes embedded in this CNVR account for an additional level of genetic and mRNA complexity: CCL4L1 and CCL4L2 have identical exonic sequences but produce a different pattern of mRNAs. CCL3L2 was considered previously as a CCL3L1 pseudogene, but is actually transcribed. Since 2005, CCL3L-CCL4L CNV has been associated extensively with various human immunodeficiency virus-related outcomes, but some recent studies called these associations into question. This controversy may be due in part to the differences in alternative methods for quantifying gene copy number and differentiating the individual genes. This review summarizes and discusses the current knowledge about CCL3L–CCL4L CNV and points out that elucidating their complete phenotypic impact requires dissecting the combinatorial genomic complexity posed by various proportions of distinct CCL3L and CCL4L genes among individuals. PMID:20659124

  18. Copy number variation in chemokine superfamily: the complex scene of CCL3L-CCL4L genes in health and disease.

    PubMed

    Colobran, R; Pedrosa, E; Carretero-Iglesia, L; Juan, M

    2010-10-01

    Genome copy number changes (copy number variations: CNVs) include inherited, de novo and somatically acquired deviations from a diploid state within a particular chromosomal segment. CNVs are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. CNVs are distributed widely in the genomes of apparently healthy individuals and thus constitute significant amounts of population-based genomic variation. Human CNV loci are enriched for immune genes and one of the most striking examples of CNV in humans involves a genomic region containing the chemokine genes CCL3L and CCL4L. The CCL3L-CCL4L copy number variable region (CNVR) shows extensive architectural complexity, with smaller CNVs within the larger ones and with interindividual variation in breakpoints. Furthermore, the individual genes embedded in this CNVR account for an additional level of genetic and mRNA complexity: CCL4L1 and CCL4L2 have identical exonic sequences but produce a different pattern of mRNAs. CCL3L2 was considered previously as a CCL3L1 pseudogene, but is actually transcribed. Since 2005, CCL3L-CCL4L CNV has been associated extensively with various human immunodeficiency virus-related outcomes, but some recent studies called these associations into question. This controversy may be due in part to the differences in alternative methods for quantifying gene copy number and differentiating the individual genes. This review summarizes and discusses the current knowledge about CCL3L-CCL4L CNV and points out that elucidating their complete phenotypic impact requires dissecting the combinatorial genomic complexity posed by various proportions of distinct CCL3L and CCL4L genes among individuals.

  19. Comparative patterns of genetic variation among populations of the Zamia pumila L. complex across three islands of the Greater Antilles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Zamia pumila L. complex (Cycadales: Zamiaceae) is a distinctive, monophyletic, diploid (2n =16) assemblage of populations restricted to the West Indies and southeastern U. S. (Florida) that is currently considered to encompass either a single polymorphic, or nine distinct species. We are extensi...

  20. Clinal variation or validation of a subspecies? A case study of the Graptemys nigrinoda complex (Testudines: Emydidae)

    USGS Publications Warehouse

    Ennen, Joshua R.; Kalis, Marley E.; Patterson, Adam L.; Kreiser, Brian R.; Lovich, Jeffrey E.; Godwin, James; Qualls, Carl P.

    2014-01-01

    Widely distributed species often display intraspecific morphological variation due to the abiotic and biotic gradients experienced across their ranges. Historically, in many vertebrate taxa, such as birds and reptiles, these morphological differences within a species were used to delimit subspecies. Graptemys nigrinoda is an aquatic turtle species endemic to the Mobile Bay Basin. Colour pattern and morphological variability were used to describe a subspecies (G. n. delticola) from the lower reaches of the system, although it and the nominate subspecies also reportedly intergrade over a large portion of the range. Other researchers have suggested that these morphological differences merely reflect clinal variation. Our molecular data (mtDNA) did not support the existence of the subspecies, as the haplotypes were differentiated by only a few base pairs and one haplotype was shared between the putative subspecies. While there were significant morphological and pattern differences among putative specimens of G. n. nigrinoda, G. n. delticola and G. n. nigrinoda × delticola, these differences probably represent clinal variation as they were also related to environmental variables [i.e. cumulative drainage area and drainage (categorical)]. Specimens occupying slow-current, high-turbidity river reaches (e.g. the Tensaw River) exhibited greater relative carapace heights and more dark pigmentation, while specimens occupying fast-current, clearer rivers (e.g. the upper Alabama, Cahaba and Tallapoosa rivers) exhibited lower carapace heights and more yellow pigmentation. Given the absence of clear molecular and morphological differences that are related to drainage characteristics, we suggest that there is not sufficient evidence for the recognition of G. n. delticola as a distinct subspecies.

  1. Hydration Differences Explain the Large Variations in the Complexation Thermodynamics of Modified γ-Cyclodextrins with Bile Salts.

    PubMed

    Køhler, Jonatan; Schönbeck, Christian; Westh, Peter; Holm, René

    2016-01-28

    The structure and thermodynamics of inclusion complexes of seven different γ-cyclodextrins (γCDs) and three biologically relevant bile salts (BS) were investigated in the present study. Natural γCD and six modified γCDs [two methyl-γCDs, one sulfobutyl ether-γCD (SBEγCD), and three 2-hydroxypropyl-γCDs (HPγCD)] and their complexes with BS were investigated by isothermal titration calorimetry, NMR, and molecular dynamics simulations. With the exception of the fully methylated γCD, which did not bind the BSs investigated, all of the γCDs formed 1:1 complexes with the BS, and the structures were similar to those with natural γCD; i.e., the modifications of the γCD had limited structural impact on the formation of complexes. Isothermal titration calorimetry was carried out over in the temperature interval 5-55 °C to enable the calculation of the stability constant (K) and the thermodynamic parameters enthalpy (ΔH°), entropy (ΔS°), and heat capacity (ΔCp°). The stability constants decreased with an increased degree of substitution (DS), with methyl substituents having a lower effect on the stability constant than the sulfobutyl ether and hydroxypropyl substituents on the stability constants. Enthalpy-entropy compensation was observed, since both enthalpy and entropy increased with the degree of substitution, which may reflect dehydration of the hydrophobic surface on both CD and BS. Calculations based on ΔCp° data suggested that each of the substituents dehydrated 10-20 (hydroxypropyl), 22-33 (sulfobutyl ether), and 10-15 Å(2) (methyl) of the BS surface area, in reasonable agreement with estimates from the molecular dynamics simulations. Combined with earlier investigations on modified βCDs, these results indicate general trends of the substituents on the thermodynamics of complex formation.

  2. Variation of CH Stretch Frequencies with CH_4 Orientation in the CH_4 - F^- Complex: Multiple Resonances as Vibrational Conical Intersections

    NASA Astrophysics Data System (ADS)

    Thapaliya, Bishnu P.; Perry, David S.

    2016-06-01

    In the CH_4 - F^- complex, an adiabatic separation of the CH stretch frequencies from the CH_4 orientational coordinates allows the calculation of the four adiabatic CH stretch surfaces. These ab initio calculations reveal (i) a large variation of CH stretch frequencies (> 100 wn) in the orientational space and (ii) the existence of four symmetrically equivalent sets of vibrational conical intersections (CIs). Two sets of symmetry-allowed CIs are identified in addition to the symmetry-required CIs at the front- and back-side C3v geometries. These results have implications for the evolution of excited CH vibrations in methane during its approach to a potentially reactive surface.

  3. CO2/ethylene oxide copolymerization and ligand variation for a highly active salen-cobalt(III) complex tethering 4 quaternary ammonium salts.

    PubMed

    Jeon, Jong Yeob; Lee, Jung Jae; Varghese, Jobi Kodiyan; Na, Sung Jae; Sujith, S; Go, Min Jeong; Lee, Junseong; Ok, Myung-Ahn; Lee, Bun Yeoul

    2013-07-07

    A cobalt(III) complex (1) of a salcy-type ligand tethering 4 quaternary ammonium salts, which is thought to act as a highly active catalyst for CO2/propylene oxide (PO) copolymerization, also shows high activity (TOF, 25,900 h(-1); TON, 518,000; 2.72 kg polymer per g cat) and selectivity (>98%) for CO2/ethylene oxide (EO) copolymerization that results in high-molecular-weight polymers (M(n), 200,000-300,000) that have strictly alternating repeating units. The related cobalt(III) complexes 11-14 were prepared through variations of the ligand framework of 1 by replacing the trans-1,2-diaminocyclohexane unit with 2,2-dimethyl-1,3-propanediamine, trans-1,2-diaminocyclopentane, or 1,1'-binaphthyl-2,2'-diamine or by replacing the aldimine bond with ketimine. These ligand frameworks are thought to favour the formation of the cis-β configuration in complexation, and the formation of the cis-β configuration in 11-14 was confirmed through NMR studies or X-ray crystallographic studies of model complexes not bearing the quaternary ammonium salts. Complexes 11, 13, and 14, which adopt the cis-β configuration even in DMSO did not show any activity for CO2/PO copolymerization. Complex 12, which was constructed with trans-1,2-diaminocyclopentane and fluctuated in DMSO between the coordination and de-coordination of the acetate ligand as observed for 1, showed fairly high activity (TOF, 12,400 h(-1)). This fluctuating behaviour may play a role in polymerization. However, complex 12 did not compete with 1 in terms of activity, selectivity, and the catalyst cost.

  4. Dynamical basis sets for algebraic variational calculations in quantum-mechanical scattering theory

    NASA Technical Reports Server (NTRS)

    Sun, Yan; Kouri, Donald J.; Truhlar, Donald G.; Schwenke, David W.

    1990-01-01

    New basis sets are proposed for linear algebraic variational calculations of transition amplitudes in quantum-mechanical scattering problems. These basis sets are hybrids of those that yield the Kohn variational principle (KVP) and those that yield the generalized Newton variational principle (GNVP) when substituted in Schlessinger's stationary expression for the T operator. Trial calculations show that efficiencies almost as great as that of the GNVP and much greater than the KVP can be obtained, even for basis sets with the majority of the members independent of energy.

  5. Quantification of extracellular levels of corticosterone in the basolateral amygdaloid complex of freely-moving rats: a dialysis study of circadian variation and stress-induced modulation.

    PubMed

    Bouchez, Gaëlle; Millan, Mark J; Rivet, Jean-Michel; Billiras, Rodolphe; Boulanger, Raphaël; Gobert, Alain

    2012-05-03

    Corticosterone influences emotion and cognition via actions in a diversity of corticolimbic structures, including the amygdala. Since extracellular levels of corticosterone in brain have rarely been studied, we characterized a specific and sensitive enzymatic immunoassay for microdialysis quantification of corticosterone in the basolateral amygdaloid complex of freely-moving rats. Corticosterone levels showed marked diurnal variation with an evening (dark phase) peak and stable, low levels during the day (light phase). The "anxiogenic agents", FG7142 (20 mg/kg) and yohimbine (10 mg/kg), and an environmental stressor, 15-min forced-swim, induced marked and sustained (1-3 h) increases in dialysis levels of corticosterone in basolateral amygdaloid complex. They likewise increased dialysis levels of dopamine and noradrenaline, but not serotonin and GABA. As compared to basal corticosterone levels of ~200-300 pg/ml, the elevation provoked by forced-swim was ca. 20-fold and this increase was abolished by adrenalectomy. Interestingly, stress-induced rises of corticosterone levels in basolateral amygdaloid complex were abrogated by combined but not separate administration of the corticotrophin releasing factor(1) (CRF(1)) receptor antagonist, CP154,526, and the vasopressin(1b) (V(1b)) receptor antagonist, SSR149,415. Underpinning their specificity, they did not block forced-swim-induced elevations in dopamine and noradrenaline. In conclusion, extracellular levels of corticosterone in the basolateral amygdaloid complex display marked diurnal variation. Further, they are markedly elevated by acute stressors, the effects of which are mediated (in contrast to concomitant elevations in levels of monoamines) by co-joint recruitment of CRF(1) and V(1b) receptors.

  6. 4th International Meeting on Single Nucleotide Polymorphism and Complex Genome Analysis. Various uses for DNA variations.

    PubMed

    Brookes, Anthony J

    2002-02-01

    At the 4th International Meeting on Single Nucleotide Polymorphism and Complex Genome Analysis (Stockholm, Sweden, 10th-14th October 2001), approximately 100 scientists from more than 20 nations undertook a probing review of latest developments in the field. Despite impressive and still ongoing activities towards SNP discovery and validation, plus efforts towards haplotype exploitation, it was clear that supporting technologies for genotyping are way behind where they need to be. Innate complexity and large variances in aspects of genome function together pose immense challenges that are difficult to surmount in the human situation. In contrast, studies in simpler organisms and population/evolutionary genetics studies are yielding important new insights. Breakthroughs that are being made in understanding the genetic etiology of complex disease tend to involve genes of larger effect or extremely well merited candidates. Linkage studies and proximal phenotypes are being recommended, though the best way forward is still hotly debated. Consequently, many diverse and ambitious projects are underway, from which the data itself will eventually show what is and is not possible.

  7. Spatial Variation in Host Feeding Patterns of Culex tarsalis and the Culex pipiens complex (Diptera: Culicidae) in California

    PubMed Central

    THIEMANN, T. C.; LEMENAGER, D. A.; KLUH, S.; CARROLL, B. D.; LOTHROP, H. D.; REISEN, W. K.

    2012-01-01

    West Nile virus (family Flaviviridae, genus Flavivirus, WNV) is now endemic in California across a variety of ecological regions that support a wide diversity of potential avian and mammalian host species. Because different avian hosts have varying competence for WNV, determining the blood-feeding patterns of Culex (Diptera: Culicidae) vectors is a key component in understanding the maintenance and amplification of the virus as well as tangential transmission to humans and horses. We investigated the blood-feeding patterns of Culex tarsalis Coquillett and members of the Culex pipiens L. complex from southern to northern California. Nearly 100 different host species were identified from 1,487 bloodmeals, by using the mitochondrial gene cytochrome c oxidase I (COI). Cx. tarsalis fed on a higher diversity of hosts and more frequently on nonhuman mammals than did the Cx. pipiens complex. Several WNV-competent host species, including house finch and house sparrow, were common bloodmeal sources for both vector species across several biomes and could account for WNV maintenance and amplification in these areas. Highly competent American crow, western scrub-jay and yellow-billed magpie also were fed upon often when available and are likely important as amplifying hosts for WNV in some areas. Neither species fed frequently on humans (Cx. pipiens complex [0.4%], Cx. tarsalis [0.2%]), but with high abundance, both species could serve as both enzootic and bridge vectors for WNV. PMID:22897051

  8. Role of adaptive and non-adaptive mechanisms forming complex patterns of genome size variation in six cytotypes of polyploid Allium oleraceum (Amaryllidaceae) on a continental scale

    PubMed Central

    Duchoslav, Martin; Šafářová, Lenka; Jandová, Michaela

    2013-01-01

    Background and Aims Although the large variation in genome size among different species is widely acknowledged, the occurrence and extent of variation below the species level are still controversial and have not yet been satisfactorily analysed. The aim of this study was to assess genome size variation in six ploidy levels (2n = 3x–8x) of the polyploid Allium oleraceum over a large geographical gradient and to search for potential interpretations of the size variation. Methods The genome sizes of 407 individuals of A. oleraceum collected from 114 populations across Europe were determined by flow cytometry using propidium iodide staining. The genome size variation was correlated with spatial, climatic and habitat variables. Key Results The mean holoploid genome size (2C DNA) was 42·49, 52·14, 63·34, 71·94, 85·51 and 92·12 pg at the tri-, tetra-, penta-, hexa-, hepta- and octoploid levels, respectively. Genome size varied from a minimum of 2·3 % in the octoploids to a maximum of 18·3 % in the tetraploids. Spatial structuring of genome size was observed within the tetra- and pentaploids, where 2C DNA significantly increased with both latitude and longitude, and correlated with several climatic variables, suggesting a gradient of continentality. Genome size in hexaploids showed low variation, weak correlation with climatic variables and no spatial structuring. Downsizing in monoploid genome size was observed between all cytotypes except for heptaploids. Splitting populations into western and eastern European groups resulted in strong differences in monoploid genome size between groups in tetra- and pentaploids but not in hexaploids. The monoploid genome sizes of the cytotypes were similar in the western group but diverged in the eastern group. Conclusions Complex patterns of holoploid and monoploid genome size variation found both within and between A. oleraceum cytotypes are most likely the result of several interacting factors, including different

  9. Variational theory of complex rays applied to shell structures: in-plane inertia, quasi-symmetric ray distribution, and orthotropic materials

    NASA Astrophysics Data System (ADS)

    Cattabiani, Alessandro; Barbarulo, Andrea; Riou, Hervé; Ladevèze, Pierre

    2015-12-01

    Recently, interest of aerospace and automotive industries on medium-frequency vibrational behavior of composite shell structures has grown due to their high specific stiffness and fatigue resistance. Conventional methods such as the finite element method and the statistical energy analysis are not suitable for the medium-frequency bandwidth. Conversely, the variational theory of complex rays (VTCR) is taking place as an ad-hoc technique to tackle such frequency band. It is a Trefftz method based on a weak variational formulation. Equilibrium equations are met using exact solutions as shape functions. The variational problem imposes boundary conditions in weak form. The present paper extends VTCR to orthotropic shell structures. Moreover, several new enhancements are introduced. Now, we use a quasi-symmetric ray distribution which can greatly reduce computational costs, and addresses in-plane inertia which was neglected in previous works. Some relevant numerical examples are presented to show the strategy and results are compared with a FEM reference to study performances.

  10. Genetic analysis of TOR complex gene variation with human longevity: a nested case-control study of American men of Japanese ancestry.

    PubMed

    Morris, Brian J; Donlon, Timothy A; He, Qimei; Grove, John S; Masaki, Kamal H; Elliott, Ayako; Willcox, D Craig; Allsopp, Richard; Willcox, Bradley J

    2015-02-01

    The mechanistic target of rapamycin (mTOR) pathway is crucial for life span determination in model organisms. The aim of the present study was to test tagging single-nucleotide polymorphisms that captured most of the genetic variation across key TOR complex 1 (TORC1) and TOR complex 2 (TORC2) genes MTOR, RPTOR, and RICTOR and the important downstream effector gene RPS6KA1 for association with human longevity (defined as attainment of at least 95 years of age) as well as health span phenotypes. Subjects comprised a homogeneous population of American men of Japanese ancestry, well characterized for aging phenotypes and who have been followed for 48 years. The study used a nested case-control design involving 440 subjects aged 95 years and older and 374 controls. It found no association of 6 tagging single-nucleotide polymorphisms for MTOR, 61 for RPTOR, 7 for RICTOR, or 5 for RPS6KA1 with longevity. Of 40 aging-related phenotypes, no significant association with genotype was seen. Thus common genetic variation (minor allele frequency ≥10%) in MTOR, RPTOR, RICTOR, and RPS6KA1 is not associated with extreme old age or aging phenotypes in this population. Further research is needed to assess the potential genetic contribution of other mTOR pathway genes to human longevity, gene expression, upstream and downstream targets, and clinically relevant aging phenotypes.

  11. Because difficulty is not the same for everyone: the impact of complexity in working memory is associated with cannabinoid 1 receptor genetic variation in young adults.

    PubMed

    Ruiz-Contreras, Alejandra E; Román-López, Talía V; Caballero-Sánchez, Ulises; Rosas-Escobar, Cintia B; Ortega-Mora, E Ivett; Barrera-Tlapa, Miguel A; Romero-Hidalgo, Sandra; Carrillo-Sánchez, Karol; Hernández-Morales, Salvador; Vadillo-Ortega, Felipe; González-Barrios, Juan Antonio; Méndez-Díaz, Mónica; Prospéro-García, Oscar

    2017-03-01

    Individual differences in working memory ability are mainly revealed when a demanding challenge is imposed. Here, we have associated cannabinoid 1 (CB1) receptor genetic variation rs2180619 (AA, AG, GG), which is located in a potential CNR1 regulatory sequence, with performance in working memory. Two-hundred and nine Mexican-mestizo healthy young participants (89 women, 120 men, mean age: 23.26 years, SD = 2.85) were challenged to solve a medium (2-back) vs. a high (3-back) difficulty N-back tasks. All subjects responded as expected, performance was better with the medium than the high demand task version, but no differences were found among genotypes while performing each working memory (WM) task. However, the cost of the level of complexity in N-back paradigm was double for GG subjects than for AA subjects. It is noteworthy that an additive-dosage allele relation was found for G allele in terms of cost of level of complexity. These genetic variation results support that the endocannabinoid system, evaluated by rs2180619 polymorphism, is involved in WM ability in humans.

  12. Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

    PubMed Central

    Pearse, Devon E.; Miller, Michael R.; Abadía-Cardoso, Alicia; Garza, John Carlos

    2014-01-01

    Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) life-history strategies of Oncorhynchus mykiss. Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats. PMID:24671976

  13. Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout.

    PubMed

    Pearse, Devon E; Miller, Michael R; Abadía-Cardoso, Alicia; Garza, John Carlos

    2014-05-22

    Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) life-history strategies of Oncorhynchus mykiss. Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats.

  14. Structural variations in terbium(III) complexes with 1,3-adamantanedicarboxylate and diverse co-ligands

    NASA Astrophysics Data System (ADS)

    Thuéry, Pierre

    2015-07-01

    Terbium nitrate was reacted with 1,3-adamantanedicarboxylic acid (LH2) under solvo-hydrothermal conditions with either N,N-dimethylformamide (DMF) or N,N-dimethylacetamide (DMA) as organic solvents. Hydrolysation of the latter co-solvents resulted in the formation of formate or acetate ions, which are present as co-ligands in the 1D coordination polymer [Tb(L)(HCOO)(H2O)2] (1) and the 2D assembly [Tb(L)(CH3COO)(H2O)] (2). The increase in dimensionality in the latter arises from the higher connectivity provided by acetate versus formate, the L2- ligand being bis-chelating in both cases. The complex [Tb2(L)3(H2O)5][Tb2(L)3(H2O)4]·3H2O (3), another 1D species, crystallizes alongside crystals of 2. Further addition of cucurbit[6]uril (CB6), with DMF as co-solvent, gave the two complexes [Tb2(L)2(CB6)(H2O)6](NO3)2·6H2O (4) and [H2NMe2]2[Tb(L)(HCOO)2]2·CB6·3H2O (5). Complex 4 crystallizes as a 3D framework in which Tb(L)+ chains are connected by tetradentate CB6 molecules, while 5 unites a carboxylate-bridged anionic 2D planar assembly and layers of CB6 molecules with counter-cations held at both portals.

  15. Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex (Phrynosoma).

    PubMed

    Leaché, Adam D; Koo, Michelle S; Spencer, Carol L; Papenfuss, Theodore J; Fisher, Robert N; McGuire, Jimmy A

    2009-07-28

    Lineage separation and divergence form a temporally extended process whereby populations may diverge genetically, morphologically, or ecologically, and these contingent properties of species provide the operational criteria necessary for species delimitation. We inferred the historical process of lineage formation in the coast horned lizard (Phrynosoma coronatum) species complex by evaluating a diversity of operational species criteria, including divergence in mtDNA (98 specimens; 2,781 bp) and nuclear loci (RAG-1, 1,054 bp; BDNF 529 bp), ecological niches (11 bioclimatic variables; 285 unique localities), and cranial horn shapes (493 specimens; 16 landmarks). A phylogenetic analysis of mtDNA recovers 5 phylogeographic groups arranged latitudinally along the Baja California Peninsula and in California. The 2 southern phylogeographic groups exhibit concordance between genetic, morphological, and ecological divergence; however, differentiation is weak or absent at more recent levels defined by phylogeographic breaks in California. Interpreting these operational species criteria together suggests that there are 3 ecologically divergent and morphologically diagnosable species within the P. coronatum complex. Our 3-species taxonomic hypothesis invokes a deep coalescence event when fitting the mtDNA genealogy into the species tree, which is not unexpected for populations that have diverged recently. Although the hypothesis that the 3 phylogeographic groups distributed across California each represent distinctive species is not supported by all of the operational species criteria evaluated in this study, the conservation status of the imperiled populations represented by these genealogical units remains critical.

  16. Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex (Phrynosoma)

    PubMed Central

    Leaché, Adam D.; Koo, Michelle S.; Spencer, Carol L.; Papenfuss, Theodore J.; Fisher, Robert N.; McGuire, Jimmy A.

    2009-01-01

    Lineage separation and divergence form a temporally extended process whereby populations may diverge genetically, morphologically, or ecologically, and these contingent properties of species provide the operational criteria necessary for species delimitation. We inferred the historical process of lineage formation in the coast horned lizard (Phrynosoma coronatum) species complex by evaluating a diversity of operational species criteria, including divergence in mtDNA (98 specimens; 2,781 bp) and nuclear loci (RAG−1, 1,054 bp; BDNF 529 bp), ecological niches (11 bioclimatic variables; 285 unique localities), and cranial horn shapes (493 specimens; 16 landmarks). A phylogenetic analysis of mtDNA recovers 5 phylogeographic groups arranged latitudinally along the Baja California Peninsula and in California. The 2 southern phylogeographic groups exhibit concordance between genetic, morphological, and ecological divergence; however, differentiation is weak or absent at more recent levels defined by phylogeographic breaks in California. Interpreting these operational species criteria together suggests that there are 3 ecologically divergent and morphologically diagnosable species within the P. coronatum complex. Our 3-species taxonomic hypothesis invokes a deep coalescence event when fitting the mtDNA genealogy into the species tree, which is not unexpected for populations that have diverged recently. Although the hypothesis that the 3 phylogeographic groups distributed across California each represent distinctive species is not supported by all of the operational species criteria evaluated in this study, the conservation status of the imperiled populations represented by these genealogical units remains critical. PMID:19625623

  17. Variations in the radiation sensitivity of foodborne pathogens associated with complex ready-to-eat food products

    NASA Astrophysics Data System (ADS)

    Sommers, Christopher H.; Boyd, Glenn

    2006-07-01

    Foodborne illness outbreaks and product recalls are occasionally associated with ready-to-eat (RTE) sandwiches and other "heat and eat" multi-component RTE products. Ionizing radiation can inactivate foodborne pathogens on meat and poultry, fruits and vegetables, seafood, and RTE meat products. However, less data are available on the ability of low-dose ionizing radiation, doses under 5 kGy typically used for pasteurization purposes, to inactivate pathogenic bacteria on complex multi-component food products. In this study, the efficacy of ionizing radiation to inactivate Salmonella spp., Listeria monocytogenes, Staphylococcus aureus, Escherichia coli O157:H7, and Yersinia enterocolitica on RTE foods including a "frankfurter on a roll", a "beef cheeseburger on a bun" and a "vegetarian cheeseburger on a bun" was investigated. The average D-10 values, the radiation dose needed to inactivate 1 log 10 of pathogen, by bacterium species, were 0.61, 0.54, 0.47, 0.36 and 0.15 kGy for Salmonella spp., S. aureus, L. monocytogenes, E. coli O157:H7, and Y. enterocolitica, respectively when inoculated onto the three product types. These results indicate that irradiation may be an effective means for inactivating common foodborne pathogens including Salmonella spp, S. aureus, L. monocytogenes, E. coli O157:H7 and Y. enterocolitica in complex RTE food products such as 'heat and eat" sandwich products.

  18. Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex (Phrynosoma)

    USGS Publications Warehouse

    Leache, A.D.; Koo, M.S.; Spencer, C.L.; Papenfuss, T.J.; Fisher, R.N.; McGuire, J.A.

    2009-01-01

    Lineage separation and divergence form a temporally extended process whereby populations may diverge genetically, morphologically, or ecologically, and these contingent properties of species provide the operational criteria necessary for species delimitation.We inferred the historical process of lineage formation in the coast horned lizard (Phrynosoma coronatum) species complex by evaluating a diversity of operational species criteria, including divergence in mtDNA (98 specimens; 2,781 bp) and nuclear loci (RAG-1, 1,054 bp; BDNF 529 bp), ecological niches (11 bioclimatic variables; 285 unique localities), and cranial horn shapes (493 specimens; 16 landmarks). A phylogenetic analysis of mtDNA recovers 5 phylogeographic groups arranged latitudinally along the Baja California Peninsula and in California. The 2 southern phylogeographic groups exhibit concordance between genetic, morphological, and ecological divergence; however, differentiation is weak or absent at more recent levels defined by phylogeographic breaks in California. Interpreting these operational species criteria together suggests that there are 3 ecologically divergent and morphologically diagnosable species within the P. coronatum complex. Our 3-species taxonomic hypothesis invokes a deep coalescence event when fitting the mtDNA genealogy into the species tree, which is not unexpected for populations that have diverged recently. Although the hypothesis that the 3 phylogeographic groups distributed across California each represent distinctive species is not supported by all of the operational species criteria evaluated in this study, the conservation status of the imperiled populations represented by these genealogical units remains critical.

  19. Examining the complexity and variation of health care system distrust across neighborhoods: Implications for preventive health care1

    PubMed Central

    Yang, Tse-Chuan; Chen, I-Chien; Noah, Aggie J.

    2015-01-01

    Purpose Recently, the institutional performance model has been used to explain the increased distrust of health care system by arguing that distrust is a function of individuals’ perceptions on the quality of life in neighborhood and social institutions. We examined (1) whether individuals assess two dimensions of distrust consistently, (2) if the multilevel institutional performance model explains the variation of distrust, and (3) how distrust patterns affect preventive health care behaviors. Methodology Using data from 9,497 respondents in 914 census tracts (neighborhoods) in Philadelphia, we examined the patterns of how individuals evaluate the competence and values distrust using the Multilevel Latent Class Analysis (MLCA), and then investigated how neighborhood environment factors are associated with distrust patterns. Finally, we used regression to examine the relationships between distrust patterns and preventive health care. Findings The MLCA identified four distrust patterns: Believers, Doubters, Competence Skeptics, and Values Skeptics. We found that 55 % of the individuals evaluated competence and values distrust coherently, with Believers reporting low levels and Doubters having high levels of distrust. Competence and Values Skeptics assessed distrust inconsistently. Believers were the least likely to reside in socioeconomically disadvantaged and racially segregated neighborhoods than other patterns. In contrast to Doubters, Believers were more likely to use preventive health care, even after controlling for other socioeconomic factors including insurance coverage. Practical implications Our findings suggest that distrust patterns are function of neighborhood conditions and distrust patterns are associated with preventive health care. This study provides important policy implications for health care and future interventions. PMID:26435564

  20. Surface temperature patterns in complex terrain: Daily variations and long-term change in the central Sierra Nevada, California

    USGS Publications Warehouse

    Lundquist, J.D.; Cayan, D.R.

    2007-01-01

    A realistic description of how temperatures vary with elevation is crucial for ecosystem studies and for models of basin-scale snowmelt and spring streamflow. This paper explores surface temperature variability using temperature data from an array of 37 sensors, called the Yosemite network, which traverses both slopes of the Sierra Nevada in the vicinity of Yosemite National Park, California. These data indicate that a simple lapse rate is often a poor description of the spatial temperature structure. Rather, the spatial pattern of temperature over the Yosemite network varies considerably with synoptic conditions. Empirical orthogonal functions (EOFs) were used to identify the dominant spatial temperature patterns and how they vary in time. Temporal variations of these surface temperature patterns were correlated with large-scale weather conditions, as described by National Centers for Environmental Prediction-National Center for Atmospheric Research Reanalysis data. Regression equations were used to downscale larger-scale weather parameters, such as Reanalysis winds and pressure, to the surface temperature structure over the Yosemite network. These relationships demonstrate that strong westerly winds are associated with relatively warmer temperatures on the east slope and cooler temperatures on the west slope of the Sierra, and weaker westerly winds are associated with the opposite pattern. Reanalysis data from 1948 to 2005 indicate weakening westerlies over this time period, a trend leading to relatively cooler temperatures on the east slope over decadal timescale's. This trend also appears in long-term observations and demonstrates the need to consider topographic effects when examining long-term changes in mountain regions. Copyright 2007 by the American Geophysical Union.

  1. Structure of the Pauli and Correlation-Kinetic Components of the Kohn-Sham Exchange Potential at a Metal Surface

    NASA Astrophysics Data System (ADS)

    Solomatin, Alexander; Sahni, Viraht

    1998-09-01

    According to the rigorous physical interpretation of Kohn-Sham (KS) density-functional theory in terms of the components of the true wavefunction, the KS exchange potentialνKSx(r)=δEKSx[ρ]/δρ(r), whereEKSx[ρ] is the exchange energy functional, is the work done to move an electron in a conservative fieldR(r). This field comprises a component EKSx(r) representative of Pauli correlations and anotherZ(1)tc(r) that constitutespartof the correlation contribution to the kinetic energy. The field EKSx(r) is derived via Coulomb's law from the KS Fermi hole charge, and the fieldZ(1)tc(r) from the kinetic-energy-density tensor involving the first-order correction to the KS single-particle density matrix. For systems in which the curls of these component fields separately vanish, the potentialvKSx(r) is the sum of the work doneWKSx(r) andW(1)tc(r) in the fields EKSx(r) andZ(1)tc(r), respectively. In this paper we study the structure of the workWKSx(r) andW(1)tc(r) at a simple-metal surface as represented by the jellium and structureless-pseudopotential models for which the workWKSx(r) andW(1)tc(r) are separately path-independent. A general expression for the field EKSx(r) is derived in terms of momentum-space integrals of the electron orbitals. This enables its easy determination, and thereby determination of the potentialWKSx(r). The field expression further allows for the derivation of theexact analyticalasymptotic structure of the potentialWKSx(r) in the vacuum region, a result valid for thefully self-consistentlydetermined orbitals of both models. With the exact analytical asymptotic structure ofvKSx(r) in the vacuum known, that of the potentialW(1)tc(r) in this region is then determinedanalytically. As is the case forvKSx(r) which decays asymptotically in the vacuum as -αKS/x, the potentialsWKSx(r) andW(1)tc(r) also decay as -αW/xandα(1)tc/x, respectively, the decay coefficients depending upon the metal Fermi energy and barrier height. It is further shown that

  2. Seasonal variation and spatial distribution of atmospheric mercury and its gas-particulate partition in the vicinity of a semiconductor manufacturing complex.

    PubMed

    Jen, Yi-Hsiu; Chen, Wei-Hsiang; Yuan, Chung-Shin; Ie, Iau-Ren; Hung, Chung-Hsuang

    2014-04-01

    This study investigated the tempospatial variation of atmospheric mercury and its gas-particulate partition in the vicinity of a semiconductor manufacturing complex, where a plenty of flat-monitor manufacturing plants using elemental mercury as a light-initiating medium to produce backlight fluorescence tubes and may fugitively emit mercury-containing air pollutants to the atmosphere. Atmospheric mercury speciation, concentration, and the partition of total gaseous mercury (TGM) and particulate mercury (Hgp) were measured at four sites surrounding the semiconductor manufacturing intensive district/complex. One-year field measurement showed that the seasonal averaged concentrations of TGM and Hgp were in the range of 3.30-6.89 and 0.06-0.14 ng/m(3), respectively, whereas the highest 24-h TGM and Hgp concentrations were 10.33 and 0.26 ng/m(3), respectively. Atmospheric mercury apportioned as 92.59-99.01 % TGM and 0.99-7.41 % Hgp. As a whole, the highest and lowest concentrations of TGM were observed in the winter and summer sampling periods, respectively, whereas the concentration of Hgp did not vary much seasonally. The highest TGM concentrations were always observed at the downwind sites, indicating that the semiconductor manufacturing complex was a hot spot of mercury emission source, which caused severe atmospheric mercury contamination over the investigation region.

  3. Major histocompatibility complex variation and evolution at a single, expressed DQA locus in two genera of elephants.

    PubMed

    Archie, Elizabeth A; Henry, Tammy; Maldonado, Jesus E; Moss, Cynthia J; Poole, Joyce H; Pearson, Virginia R; Murray, Suzan; Alberts, Susan C; Fleischer, Robert C

    2010-02-01

    Genes of the vertebrate major histocompatibility complex (MHC) are crucial to defense against infectious disease, provide an important measure of functional genetic diversity, and have been implicated in mate choice and kin recognition. As a result, MHC loci have been characterized for a number of vertebrate species, especially mammals;however, elephants are a notable exception. Our study is the first to characterize patterns of genetic diversity and natural selection in the elephant MHC. We did so using DNA sequences from a single, expressed DQA locus in elephants.We characterized six alleles in 30 African elephants(Loxodonta africana) and four alleles in three Asian elephants (Elephas maximus). In addition, for two of the African alleles and three of the Asian alleles, we characterized complete coding sequences (exons 1-5) and nearly complete non-coding sequences (introns 2-4) for the class II DQA loci. Compared to DQA in other wild mammals, we found moderate polymorphism and allelic diversity and similar patterns of selection; patterns of non-synonymous and synonymous substitutions were consistent with balancing selection acting on the peptides involved in antigen binding in the second exon. In addition, balancing selection has led to strong trans-species allelism that has maintained multiple allelic lineages across both genera of extant elephants for at least 6 million years. We discuss our results in the context of MHC diversity in other mammals and patterns of evolution in elephants.

  4. Variation of bulk Lorentz factor in AGN jets due to Compton rocket in a complex photon field

    NASA Astrophysics Data System (ADS)

    Vuillaume, T.; Henri, G.; Petrucci, P.-O.

    2015-09-01

    Radio-loud active galactic nuclei are among the most powerful objects in the universe. In these objects, most of the emission comes from relativistic jets getting their power from the accretion of matter ontosupermassive black holes. However, despite the number of studies, a jet's acceleration to relativistic speeds is still poorly understood. It is widely known that jets contain relativistic particles that emit radiation through several physical processes, one of them being the inverse Compton scattering of photons coming from external sources. In the case of a plasma composed of electrons and positrons continuously heated by the turbulence, inverse Compton scattering can lead to relativistic bulk motions through the Compton rocket effect. We investigate this process and compute the resulting bulk Lorentz factor in the complex photon field of an AGN composed of several external photon sources. We consider various sources:the accretion disk, the dusty torus, and the broad line region. We take their geometry and anisotropy carefully into account in order to numerically compute the bulk Lorentz factor of the jet at every altitude. The study, made for a broad range of parameters, shows interesting and unexpected behaviors of the bulk Lorentz factor, exhibiting acceleration and deceleration zones in the jet. We investigate the patterns of the bulk Lorentz factor along the jet depending on the source sizes and on the observation angle and we finally show that these patterns can induce variability in the AGN emission with timescales going from hours to months.

  5. Genetic variation in the major histocompatibility complex of the European brown hare (Lepus europaeus) across distinct phylogeographic areas.

    PubMed

    Koutsogiannouli, Evagelia A; Moutou, Katerina A; Stamatis, Costas; Walter, Lutz; Mamuris, Zissis

    2014-06-01

    The major histocompatibility complex is one of the best studied systems in vertebrates providing evidence for the long-term action of selection. Here, we examined the intra- and inter-population genetic diversity of the MHC class II DRB locus in European brown hare (Lepus europaeus) and correlated the results with genetic variability already estimated from the MHC DQA locus and from maternally (mitochondrial DNA (mtDNA)) and biparentally (allozymes, microsatellites) inherited loci. L. europaeus showed remarkable genetic polymorphism in both DQA and DRB1 loci. The Anatolian populations exhibited the highest genetic polymorphism for both loci. Balancing selection has established increased variability in the European populations despite the founder effects after the last glaciation. Different evolutionary rates were traced for DRB1 and DQA loci, as evidenced by the higher number of common DRB1 than DQA alleles and the greater differences between DRB1 alleles with common origin in comparison with DQA alleles. The high number of rare alleles with low frequencies detected implies that frequency-dependent selection drives MHC evolution in the brown hare through the advantage of rare alleles. Both loci were under the influence of positive selection within the peptide-binding region. The functional polymorphism, recorded as amino acid substitutions within the binding pockets, fell also within distinct geographic patterns, yet it was much narrower than the genetic polymorphism. We hypothesize that certain structural and functional characteristics of the binding pockets set limitations to the actual shape of genetic polymorphism in MHC.

  6. Genetic Variation on the BAT1-NFKBIL1-LTA Region of Major Histocompatibility Complex Class III Associates with Periodontitis

    PubMed Central

    Marchesani, Marja; Vlachopoulou, Efthymia; Mäntylä, Päivi; Paju, Susanna; Buhlin, Kåre; Suominen, Anna L.; Contreras, Johanna; Knuuttila, Matti; Hernandez, Marcela; Huumonen, Sisko; Nieminen, Markku S.; Perola, Markus; Sinisalo, Juha; Lokki, Marja-Liisa; Pussinen, Pirkko J.

    2014-01-01

    Periodontitis is a chronic inflammatory disease with a multifactorial etiology. We investigated whether human major histocompatibility complex (MHC) polymorphisms (6p21.3) are associated with periodontal parameters. Parogene 1 population samples (n = 169) were analyzed with 13,245 single nucleotide polymorphisms (SNPs) of the MHC region. Eighteen selected SNPs (P ≤ 0.001) were replicated in Parogene 2 population samples (n = 339) and the Health 2000 Survey (n = 1,420). All subjects had a detailed clinical and radiographic oral health examination. Serum lymphotoxin-α (LTA) concentrations were measured in the Parogene populations, and the protein was detected in inflamed periodontal tissue. In the Parogene 1 population, 10 SNPs were associated with periodontal parameters. The strongest associations emerged from the parameters bleeding on probing (BOP) and a probing pocket depth (PPD) of ≥6 mm with the genes BAT1, NFKBIL1, and LTA. Six SNPs, rs11796, rs3130059, rs2239527, rs2071591, rs909253, and rs1041981 (r2, ≥0.92), constituted a risk haplotype. In the Parogene 1 population, the haplotype had the strongest association with the parameter BOP, a PPD of ≥6 mm, and severe periodontitis with odds ratios (95% confidence intervals) of 2.63 (2.21 to 3.20), 2.90 (2.37 to 3.52), and 3.10 (1.63 to 5.98), respectively. These results were replicated in the other two populations. High serum LTA concentrations in the Parogene population were associated with the periodontitis risk alleles of the LTA SNPs (rs909253 and rs1041981) of the haplotype. In addition, the protein was expressed in inflamed gingival connective tissue. We identified a novel BAT1-NFKBIL1-LTA haplotype as a significant contributor to the risk of periodontitis. The genetic polymorphisms in the MHC class III region may be functionally important in periodontitis susceptibility. PMID:24566624

  7. Complex, Dynamic Combination of Physical, Chemical and Nutritional Variables Controls Spatio-Temporal Variation of Sandy Beach Community Structure

    PubMed Central

    Ortega Cisneros, Kelly; Smit, Albertus J.; Laudien, Jürgen; Schoeman, David S.

    2011-01-01

    Sandy beach ecological theory states that physical features of the beach control macrobenthic community structure on all but the most dissipative beaches. However, few studies have simultaneously evaluated the relative importance of physical, chemical and biological factors as potential explanatory variables for meso-scale spatio-temporal patterns of intertidal community structure in these systems. Here, we investigate macroinfaunal community structure of a micro-tidal sandy beach that is located on an oligotrophic subtropical coast and is influenced by seasonal estuarine input. We repeatedly sampled biological and environmental variables at a series of beach transects arranged at increasing distances from the estuary mouth. Sampling took place over a period of five months, corresponding with the transition between the dry and wet season. This allowed assessment of biological-physical relationships across chemical and nutritional gradients associated with a range of estuarine inputs. Physical, chemical, and biological response variables, as well as measures of community structure, showed significant spatio-temporal patterns. In general, bivariate relationships between biological and environmental variables were rare and weak. However, multivariate correlation approaches identified a variety of environmental variables (i.e., sampling session, the C∶N ratio of particulate organic matter, dissolved inorganic nutrient concentrations, various size fractions of photopigment concentrations, salinity and, to a lesser extent, beach width and sediment kurtosis) that either alone or combined provided significant explanatory power for spatio-temporal patterns of macroinfaunal community structure. Overall, these results showed that the macrobenthic community on Mtunzini Beach was not structured primarily by physical factors, but instead by a complex and dynamic blend of nutritional, chemical and physical drivers. This emphasises the need to recognise ocean-exposed sandy

  8. The power of gene-based rare variant methods to detect disease-associated variation and test hypotheses about complex disease.

    PubMed

    Moutsianas, Loukas; Agarwala, Vineeta; Fuchsberger, Christian; Flannick, Jason; Rivas, Manuel A; Gaulton, Kyle J; Albers, Patrick K; McVean, Gil; Boehnke, Michael; Altshuler, David; McCarthy, Mark I

    2015-04-01

    Genome and exome sequencing in large cohorts enables characterization of the role of rare variation in complex diseases. Success in this endeavor, however, requires investigators to test a diverse array of genetic hypotheses which differ in the number, frequency and effect sizes of underlying causal variants. In this study, we evaluated the power of gene-based association methods to interrogate such hypotheses, and examined the implications for study design. We developed a flexible simulation approach, using 1000 Genomes data, to (a) generate sequence variation at human genes in up to 10K case-control samples, and (b) quantify the statistical power of a panel of widely used gene-based association tests under a variety of allelic architectures, locus effect sizes, and significance thresholds. For loci explaining ~1% of phenotypic variance underlying a common dichotomous trait, we find that all methods have low absolute power to achieve exome-wide significance (~5-20% power at α = 2.5 × 10(-6)) in 3K individuals; even in 10K samples, power is modest (~60%). The combined application of multiple methods increases sensitivity, but does so at the expense of a higher false positive rate. MiST, SKAT-O, and KBAC have the highest individual mean power across simulated datasets, but we observe wide architecture-dependent variability in the individual loci detected by each test, suggesting that inferences about disease architecture from analysis of sequencing studies can differ depending on which methods are used. Our results imply that tens of thousands of individuals, extensive functional annotation, or highly targeted hypothesis testing will be required to confidently detect or exclude rare variant signals at complex disease loci.

  9. The Power of Gene-Based Rare Variant Methods to Detect Disease-Associated Variation and Test Hypotheses About Complex Disease

    PubMed Central

    Fuchsberger, Christian; Flannick, Jason; Rivas, Manuel A.; Gaulton, Kyle J.; Albers, Patrick K.; McVean, Gil; Boehnke, Michael; Altshuler, David; McCarthy, Mark I.

    2015-01-01

    Genome and exome sequencing in large cohorts enables characterization of the role of rare variation in complex diseases. Success in this endeavor, however, requires investigators to test a diverse array of genetic hypotheses which differ in the number, frequency and effect sizes of underlying causal variants. In this study, we evaluated the power of gene-based association methods to interrogate such hypotheses, and examined the implications for study design. We developed a flexible simulation approach, using 1000 Genomes data, to (a) generate sequence variation at human genes in up to 10K case-control samples, and (b) quantify the statistical power of a panel of widely used gene-based association tests under a variety of allelic architectures, locus effect sizes, and significance thresholds. For loci explaining ~1% of phenotypic variance underlying a common dichotomous trait, we find that all methods have low absolute power to achieve exome-wide significance (~5-20% power at α=2.5×10-6) in 3K individuals; even in 10K samples, power is modest (~60%). The combined application of multiple methods increases sensitivity, but does so at the expense of a higher false positive rate. MiST, SKAT-O, and KBAC have the highest individual mean power across simulated datasets, but we observe wide architecture-dependent variability in the individual loci detected by each test, suggesting that inferences about disease architecture from analysis of sequencing studies can differ depending on which methods are used. Our results imply that tens of thousands of individuals, extensive functional annotation, or highly targeted hypothesis testing will be required to confidently detect or exclude rare variant signals at complex disease loci. PMID:25906071

  10. How complexity science can inform scale-up and spread in health care: understanding the role of self-organization in variation across local contexts.

    PubMed

    Lanham, Holly Jordan; Leykum, Luci K; Taylor, Barbara S; McCannon, C Joseph; Lindberg, Curt; Lester, Richard T

    2013-09-01

    Health care systems struggle to scale-up and spread effective practices across diverse settings. Failures in scale-up and spread (SUS) are often attributed to a lack of consideration for variation in local contexts among different health care delivery settings. We argue that SUS occurs within complex systems and that self-organization plays an important role in the success, or failure, of SUS. Self-organization is a process whereby local interactions give rise to patterns of organizing. These patterns may be stable or unstable, and they evolve over time. Self-organization is a major contributor to local variations across health care delivery settings. Thus, better understanding of self-organization in the context of SUS is needed. We re-examine two cases of successful SUS: 1) the application of a mobile phone short message service intervention to improve adherence to medications during HIV treatment scale up in resource-limited settings, and 2) MRSA prevention in hospital inpatient settings in the United States. Based on insights from these cases, we discuss the role of interdependencies and sensemaking in leveraging self-organization in SUS initiatives. We argue that self-organization, while not completely controllable, can be influenced, and that improving interdependencies and sensemaking among SUS stakeholders is a strategy for facilitating self-organization processes that increase the probability of spreading effective practices across diverse settings.

  11. Samarkand complex setup for investigation of cosmic ray variation in the energy range of 7 10 (9) - 10 (15) eV

    NASA Technical Reports Server (NTRS)

    Dorman, L. I.

    1985-01-01

    The Samarkand complex setup is aimed at the study of cosmic ray variations in a wide energy range from 7 billion eV (which corresponds to the geomagnetic threshold in the region of Samarkand) up to approx 10 to the 15th power to 10 to the 16th power eV. The setup consists of four 6-counter sections of neutron supermonitor with counters SNM-15 and 48 scintillator detectors (1 sq m each) placed under and above the supermonitor. The effective area of the setup for recording neutrons and muons is 24 sq m. The setup can register time variations of the following cosmic ray components: (1) the total neutron counting rate, (2) counting rates for neutrons of different multiplicity, (3) soft-muon fluxes, (4) hard-muon fluxes at various zenith and azimuth angles, (5) electron-photon component, (6) extensive air showers (EAS) induced by primary particles in a wide energy range and accompanied or not accompanied by muons and neutrons.

  12. From genome-wide to candidate gene: an investigation of variation at the major histocompatibility complex in common bottlenose dolphins exposed to harmful algal blooms.

    PubMed

    Cammen, Kristina M; Wilcox, Lynsey A; Rosel, Patricia E; Wells, Randall S; Read, Andrew J

    2015-02-01

    The role the major histocompatibility complex (MHC) plays in response to exposure to environmental toxins is relatively poorly understood, particularly in comparison to its well-described role in pathogen immunity. We investigated associations between MHC diversity and resistance to brevetoxins in common bottlenose dolphins (Tursiops truncatus). A previous genome-wide association study investigating an apparent difference in harmful algal bloom (HAB) resistance among dolphin populations in the Gulf of Mexico identified genetic variation associated with survival in close genomic proximity to multiple MHC class II loci. Here, we characterized genetic variation at DQA, DQB, DRA, and DRB loci in dolphins from central-west Florida and the Florida Panhandle, including dolphins that died during HABs and dolphins presumed to have survived HAB exposure. We found that DRB and DQB exhibited patterns of genetic differentiation among geographic regions that differed from neutral microsatellite loci. In addition, genetic differentiation at DRB across multiple pairwise comparisons of live and dead dolphins was greater than differentiation observed at neutral loci. Our findings at these MHC loci did not approach the strength of association with survival previously described for a nearby genetic variant. However, the results provide evidence that selective pressures at the MHC vary among dolphin populations that differ in the frequency of HAB exposure and that the overall composition of DRB variants differs between dolphin survivors and non-survivors of HABs. These results may suggest a potential role of MHC diversity in variable survival of bottlenose dolphins exposed to HABs.

  13. A new multi-frequency approach based on Padé approximants for the treatment of transient dynamics problems with the variational theory of complex rays

    NASA Astrophysics Data System (ADS)

    Rouzaud, C.; Gatuingt, F.; Hervé, G.; Dorival, O.

    2017-03-01

    Frequency-based methods were set up in order to circumvent the limits of classical finite element methods in fast dynamic simulations due to discretizations. In this approach the dynamic loading was shifted in the frequency domain by FFT, then treated by the Variational Theory of Complex Rays, and then the time response was reconstructed through an IFFT. This strategy proved to be very efficient due to the CPU VTCR very low cost. However in the case of a large loading spectrum this frequency-by-frequency approach could seriously degrade the computational performances of the strategy. This paper addresses this point by proposing the use of Padé approximants in order to limit the number of frequencies at which the response should be calculated. Padé approximation is applied to the overall VTCR system based on its frequency dependency. Finally, as simulations on a simple academic case and on a civil engineering structure show, this method is found to be very efficient for interpolating the frequency response functions of a complex structure. This is a key point to preserve the efficiency of the complete VTCR strategy for transient dynamic problems.

  14. Density functional resonance theory: complex density functions, convergence, orbital energies, and functionals.

    PubMed

    Whitenack, Daniel L; Wasserman, Adam

    2012-04-28

    Aspects of density functional resonance theory (DFRT) [D. L. Whitenack and A. Wasserman, Phys. Rev. Lett. 107, 163002 (2011)], a recently developed complex-scaled version of ground-state density functional theory (DFT), are studied in detail. The asymptotic behavior of the complex density function is related to the complex resonance energy and system's threshold energy, and the function's local oscillatory behavior is connected with preferential directions of electron decay. Practical considerations for implementation of the theory are addressed including sensitivity to the complex-scaling parameter, θ. In Kohn-Sham DFRT, it is shown that almost all θ-dependence in the calculated energies and lifetimes can be extinguished via use of a proper basis set or fine grid. The highest occupied Kohn-Sham orbital energy and lifetime are related to physical affinity and width, and the threshold energy of the Kohn-Sham system is shown to be equal to the threshold energy of the interacting system shifted by a well-defined functional. Finally, various complex-scaling conditions are derived which relate the functionals of ground-state DFT to those of DFRT via proper scaling factors and a non-Hermitian coupling-constant system.

  15. Simultaneous identification of the low-field-induced tiny variation of complex refractive index for anisotropic and opaque magnetic-fluid thin film by a stable heterodyne Mach-Zehnder interferometer.

    PubMed

    Hong, Chin-Yih; Chieh, Jen-Jie; Yang, Shieh-Yueh; Yang, Hong-Chang; Horng, Herng-Er

    2009-10-10

    We use a heterodyne Mach-Zehnder interferometer to simultaneously and simply measure the complex refractive index by only normal incidence on the specimen, instead of using a complicated measurement procedure or instrument that only measures the real or imaginary part of the complex refractive index. To study the tiny variation of the complex refractive index, the small complex refractive-index variation of a rare-concentration magnetic-fluid thin film, due to a weak field of less than 200 Oe, was processed by this interferometer. We also present the wavelength trend of the complex refractive index of magnetic fluids to verify the appearance of the slight change in a small wavelength range.

  16. Of mice and the 'Age of Discovery': the complex history of colonization of the Azorean archipelago by the house mouse (Mus musculus) as revealed by mitochondrial DNA variation.

    PubMed

    Gabriel, S I; Mathias, M L; Searle, J B

    2015-01-01

    Humans have introduced many species onto remote oceanic islands. The house mouse (Mus musculus) is a human commensal and has consequently been transported to oceanic islands around the globe as an accidental stowaway. The history of these introductions can tell us not only about the mice themselves but also about the people that transported them. Following a phylogeographic approach, we used mitochondrial D-loop sequence variation (within an 849- to 864-bp fragment) to study house mouse colonization of the Azores. A total of 239 sequences were obtained from all nine islands, and interpretation was helped by previously published Iberian sequences and 66 newly generated Spanish sequences. A Bayesian analysis revealed presence in the Azores of most of the D-loop clades previously described in the domesticus subspecies of the house mouse, suggesting a complex colonization history of the archipelago as a whole from multiple geographical origins, but much less heterogeneity (often single colonization?) within islands. The expected historical link with mainland Portugal was reflected in the pattern of D-loop variation of some of the islands but not all. A more unexpected association with a distant North European source area was also detected in three islands, possibly reflecting human contact with the Azores prior to the 15th century discovery by Portuguese mariners. Widening the scope to colonization of the Macaronesian islands as a whole, human linkages between the Azores, Madeira, the Canaries, Portugal and Spain were revealed through the sharing of mouse sequences between these areas. From these and other data, we suggest mouse studies may help resolve historical uncertainties relating to the 'Age of Discovery'.

  17. A Multiple Interaction Analysis Reveals ADRB3 as a Potential Candidate for Gallbladder Cancer Predisposition via a Complex Interaction with Other Candidate Gene Variations.

    PubMed

    Rai, Rajani; Kim, Jong Joo; Misra, Sanjeev; Kumar, Ashok; Mittal, Balraj

    2015-11-25

    Gallbladder cancer is the most common and a highly aggressive biliary tract malignancy with a dismal outcome. The pathogenesis of the disease is multifactorial, comprising the combined effect of multiple genetic variations of mild consequence along with numerous dietary and environmental risk factors. Previously, we demonstrated the association of several candidate gene variations with GBC risk. In this study, we aimed to identify the combination of gene variants and their possible interactions contributing towards genetic susceptibility of GBC. Here, we performed Multifactor-Dimensionality Reduction (MDR) and Classification and Regression Tree Analysis (CRT) to investigate the gene-gene interactions and the combined effect of 14 SNPs in nine genes (DR4 (rs20576, rs6557634); FAS (rs2234767); FASL (rs763110); DCC (rs2229080, rs4078288, rs7504990, rs714); PSCA (rs2294008, rs2978974); ADRA2A (rs1801253); ADRB1 (rs1800544); ADRB3 (rs4994); CYP17 (rs2486758)) involved in various signaling pathways. Genotyping was accomplished by PCR-RFLP or Taqman allelic discrimination assays. SPSS software version 16.0 and MDR software version 2.0 were used for all the statistical analysis. Single locus investigation demonstrated significant association of DR4 (rs20576, rs6557634), DCC (rs714, rs2229080, rs4078288) and ADRB3 (rs4994) polymorphisms with GBC risk. MDR analysis revealed ADRB3 (rs4994) to be crucial candidate in GBC susceptibility that may act either alone (p < 0.0001, CVC = 10/10) or in combination with DCC (rs714 and rs2229080, p < 0.0001, CVC = 9/10). Our CRT results are in agreement with the above findings. Further, in-silico results of studied SNPs advocated their role in splicing, transcriptional and/or protein coding regulation. Overall, our result suggested complex interactions amongst the studied SNPs and ADRB3 rs4994 as candidate influencing GBC susceptibility.

  18. A Multiple Interaction Analysis Reveals ADRB3 as a Potential Candidate for Gallbladder Cancer Predisposition via a Complex Interaction with Other Candidate Gene Variations

    PubMed Central

    Rai, Rajani; Kim, Jong Joo; Misra, Sanjeev; Kumar, Ashok; Mittal, Balraj

    2015-01-01

    Gallbladder cancer is the most common and a highly aggressive biliary tract malignancy with a dismal outcome. The pathogenesis of the disease is multifactorial, comprising the combined effect of multiple genetic variations of mild consequence along with numerous dietary and environmental risk factors. Previously, we demonstrated the association of several candidate gene variations with GBC risk. In this study, we aimed to identify the combination of gene variants and their possible interactions contributing towards genetic susceptibility of GBC. Here, we performed Multifactor-Dimensionality Reduction (MDR) and Classification and Regression Tree Analysis (CRT) to investigate the gene–gene interactions and the combined effect of 14 SNPs in nine genes (DR4 (rs20576, rs6557634); FAS (rs2234767); FASL (rs763110); DCC (rs2229080, rs4078288, rs7504990, rs714); PSCA (rs2294008, rs2978974); ADRA2A (rs1801253); ADRB1 (rs1800544); ADRB3 (rs4994); CYP17 (rs2486758)) involved in various signaling pathways. Genotyping was accomplished by PCR-RFLP or Taqman allelic discrimination assays. SPSS software version 16.0 and MDR software version 2.0 were used for all the statistical analysis. Single locus investigation demonstrated significant association of DR4 (rs20576, rs6557634), DCC (rs714, rs2229080, rs4078288) and ADRB3 (rs4994) polymorphisms with GBC risk. MDR analysis revealed ADRB3 (rs4994) to be crucial candidate in GBC susceptibility that may act either alone (p < 0.0001, CVC = 10/10) or in combination with DCC (rs714 and rs2229080, p < 0.0001, CVC = 9/10). Our CRT results are in agreement with the above findings. Further, in-silico results of studied SNPs advocated their role in splicing, transcriptional and/or protein coding regulation. Overall, our result suggested complex interactions amongst the studied SNPs and ADRB3 rs4994 as candidate influencing GBC susceptibility. PMID:26602921

  19. Magnesium retention on the soil exchange complex controlling Mg isotope variations in soils, soil solutions and vegetation in volcanic soils, Iceland

    NASA Astrophysics Data System (ADS)

    Opfergelt, S.; Burton, K. W.; Georg, R. B.; West, A. J.; Guicharnaud, R. A.; Sigfusson, B.; Siebert, C.; Gislason, S. R.; Halliday, A. N.

    2014-01-01

    Understanding the biogeochemical cycle of magnesium (Mg) is not only crucial for terrestrial ecology, as this element is a key nutrient for plants, but also for quantifying chemical weathering fluxes of Mg and associated atmospheric CO2 consumption, requiring distinction of biotic from abiotic contributions to Mg fluxes exported to the hydrosphere. Here, Mg isotope compositions are reported for parent basalt, bulk soils, clay fractions, exchangeable Mg, seasonal soil solutions, and vegetation for five types of volcanic soils in Iceland in order to improve the understanding of sources and processes controlling Mg supply to vegetation and export to the hydrosphere. Bulk soils (δ26Mg = -0.40 ± 0.11‰) are isotopically similar to the parent basalt (δ26Mg = -0.31‰), whereas clay fractions (δ26Mg = -0.62 ± 0.12‰), exchangeable Mg (δ26Mg = -0.75 ± 0.14‰), and soil solutions (δ26Mg = -0.89 ± 0.16‰) are all isotopically lighter than the basalt. These compositions can be explained by a combination of mixing and isotope fractionation processes on the soil exchange complex. Successive adsorption-desorption of heavy Mg isotopes leads to the preferential loss of heavy Mg from the soil profile, leaving soils with light Mg isotope compositions relative to the parent basalt. Additionally, external contributions from sea spray and organic matter decomposition result in a mixture of Mg sources on the soil exchange complex. Vegetation preferentially takes up heavy Mg from the soil exchange complex (Δ26Mgplant-exch = +0.50 ± 0.09‰), and changes in δ26Mg in vegetation reflect changes in bioavailable Mg sources in soils. This study highlights the major role of Mg retention on the soil exchange complex amongst the factors controlling Mg isotope variations in soils and soil solutions, and demonstrates that Mg isotopes provide a valuable tool for monitoring biotic and abiotic contributions of Mg that is bioavailable for plants and is exported to the hydrosphere.

  20. The Saccharomyces cerevisiae transcriptome as a mirror of phytochemical variation in complex extracts of Equisetum arvense from America, China, Europe and India

    PubMed Central

    2013-01-01

    Background Pattern-oriented chemical profiling is increasingly being used to characterize the phytochemical composition of herbal medicines for quality control purposes. Ideally, a fingerprint of the biological effects should complement the chemical fingerprint. For ethical and practical reasons it is not possible to test each herbal extract in laboratory animals or humans. What is needed is a test system consisting of an organism with relevant biology and complexity that can serve as a surrogate in vitro system. The purpose of this study was to test the hypothesis that the Saccharomyces cerevisiae transcriptome might be used as an indicator of phytochemical variation of closely-related yet distinctly different extracts prepared from a single species of a phytogeographically widely distributed medicinal plant. We combined phytochemical profiling using chromatographic methods (HPTLC, HPLC-PDA-MS/MS) and gene expression studies using Affymetrix Yeast 2.0 gene chip with principal component analysis and k-nearest neighbor clustering analysis to test this hypothesis using extracts prepared from the phytogeographically widely distributed medicinal plant Equisetum arvense as a test case. Results We found that the Equisetum arvense extracts exhibited qualitative and quantitative differences in their phytochemical composition grouped along their phytogeographical origin. Exposure of yeast to the extracts led to changes in gene expression that reflected both the similarities and differences in the phytochemical composition of the extracts. The Equisetum arvense extracts elicited changes in the expression of genes involved in mRNA translation, drug transport, metabolism of energy reserves, phospholipid metabolism, and the cellular stress response. Conclusions Our data show that functional genomics in S. cerevisiae may be developed as a sensitive bioassay for the scientific investigation of the interplay between phytochemical composition and transcriptional effects of complex

  1. Low Major Histocompatibility Complex Class II Variation in the Endangered Indo-Pacific Humpback Dolphin (Sousa chinensis): Inferences About the Role of Balancing Selection.

    PubMed

    Zhang, Xiyang; Lin, Wenzhi; Zhou, Ruilian; Gui, Duan; Yu, Xinjian; Wu, Yuping

    2016-03-01

    It has been widely reported that the major histocompatibility complex (MHC) is under balancing selection due to its immune function across terrestrial and aquatic mammals. The comprehensive studies at MHC and other neutral loci could give us a synthetic evaluation about the major force determining genetic diversity of species. Previously, a low level of genetic diversity has been reported among the Indo-Pacific humpback dolphin (Sousa chinensis) in the Pearl River Estuary (PRE) using both mitochondrial marker and microsatellite loci. Here, the expression and sequence polymorphism of 2 MHC class II genes (DQB and DRB) in 32 S. chinensis from PRE collected between 2003 and 2011 were investigated. High ratios of non-synonymous to synonymous substitution rates, codon-based selection analysis, and trans-species polymorphism (TSP) support the hypothesis that balancing selection acted on S. chinensis MHC sequences. However, only 2 haplotypes were detected at either DQB or DRB loci. Moreover, the lack of deviation from the Hardy-Weinberg expectation at DRB locus combined with the relatively low heterozygosity at both DQB locus and microsatellite loci suggested that balancing selection might not be sufficient, which further suggested that genetic drift associated with historical bottlenecks was not mitigated by balancing selection in terms of the loss of MHC and neutral variation in S. chinensis. The combined results highlighted the importance of maintaining the genetic diversity of the endangered S. chinensis.

  2. Predicting the structure and vibrational frequencies of ethylene using harmonic and anharmonic approaches at the Kohn-Sham complete basis set limit.

    PubMed

    Buczek, Aneta; Kupka, Teobald; Broda, Małgorzata A; Żyła, Adriana

    2016-01-01

    In this work, regular convergence patterns of the structural, harmonic, and VPT2-calculated anharmonic vibrational parameters of ethylene towards the Kohn-Sham complete basis set (KS CBS) limit are demonstrated for the first time. The performance of the VPT2 scheme implemented using density functional theory (DFT-BLYP and DFT-B3LYP) in combination with two Pople basis sets (6-311++G** and 6-311++G(3df,2pd)), the polarization-consistent basis sets pc-n, aug-pc-n, and pcseg-n (n = 0, 1, 2, 3, 4), and the correlation-consistent basis sets cc-pVXZ and aug-cc-pVXZ (X = D, T, Q, 5, 6) was tested.The BLYP-calculated harmonic frequencies were found to be markedly closer than the B3LYP-calculated harmonic frequencies to the experimentally derived values, while the calculated anharmonic frequencies consistently underestimated the observed wavenumbers. The different basis set families gave very similar estimated values for the CBS parameters. The anharmonic frequencies calculated with B3LYP/aug-pc-3 were consistently significantly higher than those obtained with the pc-3 basis set; applying the aug-pcseg-n basis set family alleviated this problem. Utilization of B3LYP/aug-pcseg-n basis sets instead of B3LYP/aug-cc-pVXZ, which is computationally less expensive, is suggested for medium-sized molecules. Harmonic BLYP/pc-2 calculations produced fairly accurate ethylene frequencies. Graphical Abstract In this study, the performance of the VPT2 scheme implemented using density functional theory (DFT-BLYP and DFT-B3LYP) in combination with the polarization-consistent basis sets pc-n, aug-pc-n, and pcseg-n (n = 0, 1, 2, 3, 4), and the correlation-consistent basis sets cc-pVXZ and aug-cc-pVXZ (X = D, T, Q, 5, and 6) was tested. For the first time, we demonstrated regular convergence patterns of the structural, harmonic, and VPT2-calculated anharmonic vibrational parameters of ethylene towards the Kohn-Sham complete basis set (KS CBS) limit.

  3. Kohn-Sham calculations with self-interaction-corrected local-spin-density exchange-correlation energy functional for atomic systems

    NASA Astrophysics Data System (ADS)

    Chen, Jiqiang; Krieger, J. B.; Li, Yan; Iafrate, G. J.

    1996-11-01

    We have investigated the accuracy of the local-spin-density approximation with orbital-density-dependent self-interaction correction (LSDSIC) as proposed by Perdew and Zunger within a Kohn-Sham approach in which electrons with a given spin projection all move in a single optimized effective potential (OEP). We have also studied the accuracy of the Krieger-Li-Iafrate (KLI) approximation to the OEP for the same energy functional in order to assess its applicability to systems in which the integral equation for the OEP cannot be reduced to a one-dimensional problem, e.g., molecules. Self-consistent Kohn-Sham LSDSIC calculations have been performed for atoms with atomic number Z=1-20 in the exchange-only case for the total energy, the highest-occupied orbital energy ɛm, and the expectation value of r2. In addition, the structure of the resulting exchange potential is examined and compared with the exact exchange-only density-functional theory (OEP method with Hartree-Fock exchange-energy functional) results. Furthermore, we display ɛm, the ionization potential I, and the electron affinity A when both exchange and correlation energy effects are included. Finally, we also consider the results of evaluating the LSDSIC energy functional by employing the exact (in the central-field approximation) single particle orbitals as proposed by Harrison. We find that the LSDSIC energy functional generally leads to calculated values that are superior to those provided by the LSD approximation and that the KLI approximation yields results in excellent agreement with the corresponding exact OEP results for this energy functional. In particular, quantities strongly related to the behavior of the valence electrons are nearly identical in both the OEP and KLI calculations, i.e., the difference between the and ɛm is less than 0.2% on average, while the difference between the calculated I is less than 0.2 millihartree on average with the corresponding difference of only 0

  4. A Complex Structural Variation on Chromosome 27 Leads to the Ectopic Expression of HOXB8 and the Muffs and Beard Phenotype in Chickens

    PubMed Central

    Wang, Yanqiang; Luo, Chenglong; Liu, Ranran; Qu, Hao; Shu, Dingming; Wen, Jie; Crooijmans, Richard P. M. A.; Zhao, Yiqiang; Hu, Xiaoxiang; Li, Ning

    2016-01-01

    Muffs and beard (Mb) is a phenotype in chickens where groups of elongated feathers gather from both sides of the face (muffs) and below the beak (beard). It is an autosomal, incomplete dominant phenotype encoded by the Muffs and beard (Mb) locus. Here we use genome-wide association (GWA) analysis, linkage analysis, Identity-by-Descent (IBD) mapping, array-CGH, genome re-sequencing and expression analysis to show that the Mb allele causing the Mb phenotype is a derived allele where a complex structural variation (SV) on GGA27 leads to an altered expression of the gene HOXB8. This Mb allele was shown to be completely associated with the Mb phenotype in nine other independent Mb chicken breeds. The Mb allele differs from the wild-type mb allele by three duplications, one in tandem and two that are translocated to that of the tandem repeat around 1.70 Mb on GGA27. The duplications contain total seven annotated genes and their expression was tested during distinct stages of Mb morphogenesis. A continuous high ectopic expression of HOXB8 was found in the facial skin of Mb chickens, strongly suggesting that HOXB8 directs this regional feather-development. In conclusion, our results provide an interesting example of how genomic structural rearrangements alter the regulation of genes leading to novel phenotypes. Further, it again illustrates the value of utilizing derived phenotypes in domestic animals to dissect the genetic basis of developmental traits, herein providing novel insights into the likely role of HOXB8 in feather development and differentiation. PMID:27253709

  5. Symmetry-adapted perturbation theory with Kohn-Sham orbitals using non-empirically tuned, long-range-corrected density functionals

    NASA Astrophysics Data System (ADS)

    Lao, Ka Un; Herbert, John M.

    2014-01-01

    The performance of second-order symmetry-adapted perturbation theory (SAPT) calculations using Kohn-Sham (KS) orbitals is evaluated against benchmark results for intermolecular interactions. Unlike previous studies of this "SAPT(KS)" methodology, the present study uses non-empirically tuned long-range corrected (LRC) functionals for the monomers. The proper {v{}_xc}(r)rArr 0 asymptotic limit is achieved by tuning the range separation parameter in order to satisfy the condition that the highest occupied KS energy level equals minus the molecule's ionization energy, for each monomer unit. Tests for He2, Ne2, and the S22 and S66 data sets reveal that this condition is important for accurate prediction of the non-dispersion components of the energy, although errors in SAPT(KS) dispersion energies remain unacceptably large. In conjunction with an empirical dispersion potential, however, the SAPT(KS) method affords good results for S22 and S66, and also accurately predicts the whole potential energy curve for the sandwich isomer of the benzene dimer. Tuned LRC functionals represent an attractive alternative to other asymptotic corrections that have been employed in density-functional-based SAPT calculations, and we recommend the use of tuned LRC functionals in both coupled-perturbed SAPT(DFT) calculations and dispersion-corrected SAPT(KS) calculations.

  6. Outstanding performance of configuration interaction singles and doubles using exact exchange Kohn-Sham orbitals in real-space numerical grid method.

    PubMed

    Lim, Jaechang; Choi, Sunghwan; Kim, Jaewook; Kim, Woo Youn

    2016-12-14

    To assess the performance of multi-configuration methods using exact exchange Kohn-Sham (KS) orbitals, we implemented configuration interaction singles and doubles (CISD) in a real-space numerical grid code. We obtained KS orbitals with the exchange-only optimized effective potential under the Krieger-Li-Iafrate (KLI) approximation. Thanks to the distinctive features of KLI orbitals against Hartree-Fock (HF), such as bound virtual orbitals with compact shapes and orbital energy gaps similar to excitation energies; KLI-CISD for small molecules shows much faster convergence as a function of simulation box size and active space (i.e., the number of virtual orbitals) than HF-CISD. The former also gives more accurate excitation energies with a few dominant configurations than the latter, even with many more configurations. The systematic control of basis set errors is straightforward in grid bases. Therefore, grid-based multi-configuration methods using exact exchange KS orbitals provide a promising new way to make accurate electronic structure calculations.

  7. Band-structure calculations of noble-gas and alkali halide solids using accurate Kohn-Sham potentials with self-interaction correction

    SciTech Connect

    Li, Y.; Krieger, J.B. ); Norman, M.R. ); Iafrate, G.J. )

    1991-11-15

    The optimized-effective-potential (OEP) method and a method developed recently by Krieger, Li, and Iafrate (KLI) are applied to the band-structure calculations of noble-gas and alkali halide solids employing the self-interaction-corrected (SIC) local-spin-density (LSD) approximation for the exchange-correlation energy functional. The resulting band gaps from both calculations are found to be in fair agreement with the experimental values. The discrepancies are typically within a few percent with results that are nearly the same as those of previously published orbital-dependent multipotential SIC calculations, whereas the LSD results underestimate the band gaps by as much as 40%. As in the LSD---and it is believed to be the case even for the exact Kohn-Sham potential---both the OEP and KLI predict valence-band widths which are narrower than those of experiment. In all cases, the KLI method yields essentially the same results as the OEP.

  8. A simple scheme for magnetic balance in four-component relativistic Kohn-Sham calculations of nuclear magnetic resonance shielding constants in a Gaussian basis.

    PubMed

    Olejniczak, Małgorzata; Bast, Radovan; Saue, Trond; Pecul, Magdalena

    2012-01-07

    We report the implementation of nuclear magnetic resonance (NMR) shielding tensors within the four-component relativistic Kohn-Sham density functional theory including non-collinear spin magnetization and employing London atomic orbitals to ensure gauge origin independent results, together with a new and efficient scheme for assuring correct balance between the large and small components of a molecular four-component spinor in the presence of an external magnetic field (simple magnetic balance). To test our formalism we have carried out calculations of NMR shielding tensors for the HX series (X = F, Cl, Br, I, At), the Xe atom, and the Xe dimer. The advantage of simple magnetic balance scheme combined with the use of London atomic orbitals is the fast convergence of results (when compared with restricted kinetic balance) and elimination of linear dependencies in the basis set (when compared to unrestricted kinetic balance). The effect of including spin magnetization in the description of NMR shielding tensor has been found important for hydrogen atoms in heavy HX molecules, causing an increase of isotropic values of 10%, but negligible for heavy atoms.

  9. Outstanding performance of configuration interaction singles and doubles using exact exchange Kohn-Sham orbitals in real-space numerical grid method

    NASA Astrophysics Data System (ADS)

    Lim, Jaechang; Choi, Sunghwan; Kim, Jaewook; Kim, Woo Youn

    2016-12-01

    To assess the performance of multi-configuration methods using exact exchange Kohn-Sham (KS) orbitals, we implemented configuration interaction singles and doubles (CISD) in a real-space numerical grid code. We obtained KS orbitals with the exchange-only optimized effective potential under the Krieger-Li-Iafrate (KLI) approximation. Thanks to the distinctive features of KLI orbitals against Hartree-Fock (HF), such as bound virtual orbitals with compact shapes and orbital energy gaps similar to excitation energies; KLI-CISD for small molecules shows much faster convergence as a function of simulation box size and active space (i.e., the number of virtual orbitals) than HF-CISD. The former also gives more accurate excitation energies with a few dominant configurations than the latter, even with many more configurations. The systematic control of basis set errors is straightforward in grid bases. Therefore, grid-based multi-configuration methods using exact exchange KS orbitals provide a promising new way to make accurate electronic structure calculations.

  10. How amino and nitro substituents direct electrophilic aromatic substitution in benzene: an explanation with Kohn-Sham molecular orbital theory and Voronoi deformation density analysis.

    PubMed

    Stasyuk, O A; Szatylowicz, H; Krygowski, T M; Fonseca Guerra, C

    2016-04-28

    The substituent effect of the amino and nitro groups on the electronic system of benzene has been investigated quantum chemically using quantitative Kohn-Sham molecular orbital theory and a corresponding energy decomposition analysis (EDA). The directionality of electrophilic substitution in aniline can accurately be explained with the amount of contribution of the 2pz orbitals on the unsubstituted carbon atoms to the highest occupied π orbital. For nitrobenzene, the molecular π orbitals cannot explain the regioselectivity of electrophilic substitution as there are two almost degenerate π orbitals with nearly the same 2pz contributions on the unsubstituted carbon atoms. The Voronoi deformation density analysis has been applied to aniline and nitrobenzene to obtain an insight into the charge rearrangements due to the substituent. This analysis method identified the orbitals involved in the C-N bond formation of the π system as the cause for the π charge accumulation at the ortho and para positions in the case of the NH2 group and the largest charge depletion at these same positions for the NO2 substituent. Furthermore, we showed that it is the repulsive interaction between the πHOMO of the phenyl radical and the πHOMO of the NH2 radical that is responsible for pushing up the πHOMO of aniline and therefore activating this π orbital of the phenyl ring towards electrophilic substitution.

  11. Multiconfiguration Pair-Density Functional Theory Outperforms Kohn-Sham Density Functional Theory and Multireference Perturbation Theory for Ground-State and Excited-State Charge Transfer.

    PubMed

    Ghosh, Soumen; Sonnenberger, Andrew L; Hoyer, Chad E; Truhlar, Donald G; Gagliardi, Laura

    2015-08-11

    The correct description of charge transfer in ground and excited states is very important for molecular interactions, photochemistry, electrochemistry, and charge transport, but it is very challenging for Kohn-Sham (KS) density functional theory (DFT). KS-DFT exchange-correlation functionals without nonlocal exchange fail to describe both ground- and excited-state charge transfer properly. We have recently proposed a theory called multiconfiguration pair-density functional theory (MC-PDFT), which is based on a combination of multiconfiguration wave function theory with a new type of density functional called an on-top density functional. Here we have used MC-PDFT to study challenging ground- and excited-state charge-transfer processes by using on-top density functionals obtained by translating KS exchange-correlation functionals. For ground-state charge transfer, MC-PDFT performs better than either the PBE exchange-correlation functional or CASPT2 wave function theory. For excited-state charge transfer, MC-PDFT (unlike KS-DFT) shows qualitatively correct behavior at long-range with great improvement in predicted excitation energies.

  12. A low-complexity 2-point step size gradient projection method with selective function evaluations for smoothed total variation based CBCT reconstructions

    NASA Astrophysics Data System (ADS)

    Song, Bongyong; Park, Justin C.; Song, William Y.

    2014-11-01

    The Barzilai-Borwein (BB) 2-point step size gradient method is receiving attention for accelerating Total Variation (TV) based CBCT reconstructions. In order to become truly viable for clinical applications, however, its convergence property needs to be properly addressed. We propose a novel fast converging gradient projection BB method that requires ‘at most one function evaluation’ in each iterative step. This Selective Function Evaluation method, referred to as GPBB-SFE in this paper, exhibits the desired convergence property when it is combined with a ‘smoothed TV’ or any other differentiable prior. This way, the proposed GPBB-SFE algorithm offers fast and guaranteed convergence to the desired 3DCBCT image with minimal computational complexity. We first applied this algorithm to a Shepp-Logan numerical phantom. We then applied to a CatPhan 600 physical phantom (The Phantom Laboratory, Salem, NY) and a clinically-treated head-and-neck patient, both acquired from the TrueBeam™ system (Varian Medical Systems, Palo Alto, CA). Furthermore, we accelerated the reconstruction by implementing the algorithm on NVIDIA GTX 480 GPU card. We first compared GPBB-SFE with three recently proposed BB-based CBCT reconstruction methods available in the literature using Shepp-Logan numerical phantom with 40 projections. It is found that GPBB-SFE shows either faster convergence speed/time or superior convergence property compared to existing BB-based algorithms. With the CatPhan 600 physical phantom, the GPBB-SFE algorithm requires only 3 function evaluations in 30 iterations and reconstructs the standard, 364-projection FDK reconstruction quality image using only 60 projections. We then applied the algorithm to a clinically-treated head-and-neck patient. It was observed that the GPBB-SFE algorithm requires only 18 function evaluations in 30 iterations. Compared with the FDK algorithm with 364 projections, the GPBB-SFE algorithm produces visibly equivalent quality CBCT

  13. The ecological complexity of the Thai-Laos Mekong River: I. Geology, seasonal variation and human impact assessment on river quality.

    PubMed

    Udomchoke, Veerasak; Sunthornranun, Patcharee; Songsasen, Apisit; Phanwichien, Kantimanee; Jiwapornkupt, Pongsakorn; Homchan, Unop; Lauhachinda, Nitaya; Sakultantimetha, Arthit; Bangkedphol, Sornnarin; Torrance, Keith; Gibson, Mark D; Gaines, Alec F; Booth, Peter H; Keenan, Helen E

    2010-11-01

    The objective of this study is to assess the variation of pollution in the Thai-Laos Mekong associated with seasonal dynamics concomitant with the natural geological features and human activities that impact on the adverse quality of the river. The complex ecology of the 1500 km stretch of the Thai-Laos Mekong River has been studied in this paper to understand the relationship with the geomorphology, with the sub-tropical monsoonal climate and the impact of human activity. Sub-surface geology controls the nature and extent of the drainage basin and of the river channel. The volume flow of the river varies naturally and dynamically in phase with the rainfall; traditional models based on steady state hydraulics are inappropriate. Continuous erosion of the river banks and bed generates a sediment load of impure silt, mica, quartz and clay minerals that inhibits light penetration and limits the primary productivity of the river. The river separates two countries at different stages of development; it flows through or close to eight non-industrial conurbations (Populations 350,000-2,000,000) but is otherwise sparsely populated. The river is used for subsistence agriculture, village transport, fishing including aquaculture and as a source of domestic water. Hydroelectricity is generated from the Laos tributaries. The river is a depository for partially treated urban waste and untreated village waste, hence populations of E.coli bacteria sometimes render the water unsuitable for drinking unless treated with the highest value of 240/100 ml found at station 7 during the summer season of 2003. Furthermore the river is polluted by trace metals, notably cadmium and mercury, and by Polycyclic Aromatic Hydrocarbons (PAHs), which are particularly concentrated in the sediments. Previous work has shown that cadmium and mercury exceed the Probable Effect Level (PEL) values of Canadian Environmental Quality Guidelines and that the PAH concentrations were also greater than the Interim

  14. A low-complexity 2-point step size gradient projection method with selective function evaluations for smoothed total variation based CBCT reconstructions.

    PubMed

    Song, Bongyong; Park, Justin C; Song, William Y

    2014-11-07

    The Barzilai-Borwein (BB) 2-point step size gradient method is receiving attention for accelerating Total Variation (TV) based CBCT reconstructions. In order to become truly viable for clinical applications, however, its convergence property needs to be properly addressed. We propose a novel fast converging gradient projection BB method that requires 'at most one function evaluation' in each iterative step. This Selective Function Evaluation method, referred to as GPBB-SFE in this paper, exhibits the desired convergence property when it is combined with a 'smoothed TV' or any other differentiable prior. This way, the proposed GPBB-SFE algorithm offers fast and guaranteed convergence to the desired 3DCBCT image with minimal computational complexity. We first applied this algorithm to a Shepp-Logan numerical phantom. We then applied to a CatPhan 600 physical phantom (The Phantom Laboratory, Salem, NY) and a clinically-treated head-and-neck patient, both acquired from the TrueBeam™ system (Varian Medical Systems, Palo Alto, CA). Furthermore, we accelerated the reconstruction by implementing the algorithm on NVIDIA GTX 480 GPU card. We first compared GPBB-SFE with three recently proposed BB-based CBCT reconstruction methods available in the literature using Shepp-Logan numerical phantom with 40 projections. It is found that GPBB-SFE shows either faster convergence speed/time or superior convergence property compared to existing BB-based algorithms. With the CatPhan 600 physical phantom, the GPBB-SFE algorithm requires only 3 function evaluations in 30 iterations and reconstructs the standard, 364-projection FDK reconstruction quality image using only 60 projections. We then applied the algorithm to a clinically-treated head-and-neck patient. It was observed that the GPBB-SFE algorithm requires only 18 function evaluations in 30 iterations. Compared with the FDK algorithm with 364 projections, the GPBB-SFE algorithm produces visibly equivalent quality CBCT image for

  15. Estimating variation in stomatal frequency at intra-individual, intra-site, and inter-taxonomic levels in populations of the Leonardoxa africana (Fabaceae) complex over environmental gradients in Cameroon

    NASA Astrophysics Data System (ADS)

    Finsinger, Walter; Dos Santos, Thibaut; McKey, Doyle

    2013-07-01

    Variation of stomatal frequency (stomatal density and stomatal index) includes genetically-based, potentially-adaptive variation, and variation due to phenotypic plasticity, the degree of which may be fundamental to the ability to maintain high water-use efficiency and thus to deal with environmental change. We analysed stomatal frequency and morphology (pore length, pore width) in leaves from several individuals from nine populations of four sub-species of the Leonardoxa africana complex. The dataset represents a hierarchical sampling wherein factors are nested within each level (leaves in individuals, individuals in sites, etc.), allowing estimation of the contribution of different levels to overall variation, using variance-component analysis. SI showed significant variation among sites ("site" is largely confounded with "sub-species"), being highest in the sub-species localized in the highest-elevation site. However, most of the observed variance was accounted for at intra-site and intra-individual levels. This variance could reflect great phenotypic plasticity, presumably in response to highly local variation in micro-environmental conditions.

  16. Subquadratic-scaling subspace projection method for large-scale Kohn-Sham density functional theory calculations using spectral finite-element discretization

    NASA Astrophysics Data System (ADS)

    Motamarri, Phani; Gavini, Vikram

    2014-09-01

    We present a subspace projection technique to conduct large-scale Kohn-Sham density functional theory calculations using higher-order spectral finite-element discretization. The proposed method treats both metallic and insulating materials in a single framework and is applicable to both pseudopotential as well as all-electron calculations. The key ideas involved in the development of this method include: (i) employing a higher-order spectral finite-element basis that is amenable to mesh adaption; (ii) using a Chebyshev filter to construct a subspace, which is an approximation to the occupied eigenspace in a given self-consistent field iteration; (iii) using a localization procedure to construct a nonorthogonal localized basis spanning the Chebyshev filtered subspace; and (iv) using a Fermi-operator expansion in terms of the subspace-projected Hamiltonian represented in the nonorthogonal localized basis to compute relevant quantities like the density matrix, electron density, and band energy. We demonstrate the accuracy and efficiency of the proposed approach on benchmark systems involving pseudopotential calculations on aluminum nanoclusters up to 3430 atoms and on alkane chains up to 7052 atoms, as well as all-electron calculations on silicon nanoclusters up to 3920 electrons. The benchmark studies revealed that accuracies commensurate with chemical accuracy can be obtained with the proposed method, and a subquadratic-scaling with system size was observed for the range of materials systems studied. In particular, for the alkane chains—representing an insulating material—close to linear scaling is observed, whereas, for aluminum nanoclusters—representing a metallic material—the scaling is observed to be O (N1.46). For all-electron calculations on silicon nanoclusters, the scaling with the number of electrons is computed to be O (N1.75). In all the benchmark systems, significant computational savings have been realized with the proposed approach, with

  17. MN15-L and MN-15: New Kohn-Sham Density Functionals with Board Accuracy for Main-Group and Transition Metal Chemistry and Noncovalent Interactions

    NASA Astrophysics Data System (ADS)

    Yu, Haoyu; He, Xiao; Truhlar, Donald G.; Donald G. Truhlar Team

    The accuracy of Kohn-Sham density functional theory depends on the exchange-correlation functional. Local functionals depending on only the density (ρ) , density gradient (grad), and possibly kinetic energy density (τ) have been popular because of their low cost and simplicity, but the most successful functionals for chemistry have involved nonlocal Hartree-Fock exchange (hybrid functionals). We have designed a new meta gradient approximation called MN15-L and a new hybrid meta gradient approximation called MN15 and tested them systematically for 17 absolute atomic energies, 51 noncovalent interaction energies, 56 data on transition metal atoms and molecules, and for 298 other atomic and molecular energetic data, including main-group and transition metal bond energies, ionization potentials, proton affinities, reaction barrier heights, hydrocarbon thermochemistry, excitation energies, and isomerization energies. When compared with 84 previous density MN15 and MN15-L give respectively the smallest and second smallest mean unsigned errors (MUEs, in kcal/mol) on all 422 data with errors for the 4 subsets above being: MN15: 6, 0.26, 4.4, 1.6; MN15-L: 7, 0.45, 4.3, 2.0. Third best: M06: 4, 0.35, 7.7, 2.2. Best previous local functional: M06-L: 7, 0.42, 6.0, 3.5. Other popular functionals: B3LYP: 18, 0.82, 8.2, 4.3; HSE06: 33, 0.58, 8.8, 3.6; TPSS: 18, 0.89, 7.25, 5.0; PBE, 47, 0.88, 9.1, 6.0. MN15-L also performs well for solid-state cohesive energies. This research is supported by the U.S. Department of Energy and inorganic catalyst design center from university of Minnesota.

  18. Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

    NASA Astrophysics Data System (ADS)

    Zhang, Gaigong; Lin, Lin; Hu, Wei; Yang, Chao; Pask, John E.

    2017-04-01

    Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn-Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann-Feynman forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann-Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H2 and liquid Al-Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.

  19. Role of noncollinear magnetization for the first-order electric-dipole hyperpolarizability at the four-component Kohn-Sham density functional theory level.

    PubMed

    Bast, Radovan; Saue, Trond; Henriksson, Johan; Norman, Patrick

    2009-01-14

    The quadratic response function has been derived and implemented at the adiabatic four-component Kohn-Sham density functional theory level with inclusion of noncollinear spin magnetization and gradient corrections in the exchange-correlation functional-a work that is an extension of our previous report where magnetization dependencies in the exchange-correlation functional were ignored [J. Henriksson, T. Saue, and P. Norman, J. Chem. Phys. 128, 024105 (2008)]. The electric-field induced second-harmonic generation experiments on CF(3)Cl and CF(3)Br are addressed by a determination of beta(-2omega;omega, omega) for a wavelength of 694.3 nm, and the same property is also determined for CF(3)I. The relativistic effects on the static hyperpolarizability for the series of molecules amount to 1%, 5%, and 9%, respectively. At the experimental wavelength, the contributions to beta due to the magnetization dependence in the exchange-correlation functional are negligible for CF(3)Cl and CF(3)Br and small for CF(3)I. The noticeable effect of magnetization in the latter case is attributed to a near two-photon resonance with the excited state 1 (3)E (nonrelativistic notation). It is emphasized, however, that the effect of magnetization on beta for CF(3)I is negligible both in comparison to the total relativistic correction as well as to the effects of electron correlation. It is concluded that, in calculations of hyperpolarizabilities under nonresonant conditions, the magnetization dependence in the exchange-correlation functional may be ignored.

  20. Variation in DNA binding constants with a change in geometry of ternary copper(II) complexes with N2O donor Schiff base and cyanate or dicyanamide

    NASA Astrophysics Data System (ADS)

    Jana, Subrata; Santra, Ramesh Chandra; Das, Saurabh; Chattopadhyay, Shouvik

    2014-09-01

    Two new copper(II) complexes, [Cu(L)(OCN)] (1) and [CuL(dca)]n (2), where HL = 2-(-(2-(diethylamino)ethylimino)methyl)naphthalen-1-ol, dca = N(CN)2-, have been synthesized and characterized by elemental analysis, IR, UV-VIS spectroscopy and single crystal X-ray diffraction studies. Complex 1 has square planar and complex 2 square pyramidal geometries in solid state around metal centre. Interactions of the complexes with calf thymus DNA (CT DNA) were studied by UV-VIS spectroscopy. Binding constant and site size of interaction were determined. Binding site size and intrinsic binding constant K revealed complex 1 interacted with calf thymus DNA better than complex 2.

  1. Prediction of electron paramagnetic resonance g values using coupled perturbed Hartree-Fock and Kohn-Sham theory

    NASA Astrophysics Data System (ADS)

    Neese, Frank

    2001-12-01

    A method for calculating the EPR g-tensor based on coupled perturbed Hartree-Fock (HF) and density functional theory (DFT) is presented. The one-electron molecular orbitals of a spin- unrestricted Slater determinant are calculated up to first order in the applied magnetic field. The g-tensor is evaluated as a mixed second derivative property with respect to the applied field and the electron magnetic moment. Thus, spin-polarization and spin-orbit coupling are simultaneously included in the calculation. The treatment focuses on orbitally nondegenerate molecules but is valid for a general ground state spin S and, for the first time, it is possible to include hybrid density functionals in the treatment. The relativistic mass and diamagnetic gauge corrections are also considered. An implementation of the theory is described. Extensive numerical calculations for a series of small molecules are reported with the Hartree-Fock (HF) method, the local density approximation (LSD), the generalized gradient approximation (GGA) and hybrid density functionals such as B3LYP and PBE0 and large Gaussian basis sets. Detailed comparison with available ab initio and DFT calculations are made. The results indicate that the hybrid functionals offer little or no improvement over the GGA functionals for small radicals made of light atoms. For transition metal complexes the situation is different. The hybrid functionals give, on average, better results than the GGA functionals but significant disagreement between theoretical and experimental g-shifts still remain. Overall, the results indicate that the present method is among the most accurate so far developed models for the prediction of g values.

  2. Enabling Predictive Simulation and UQ of Complex Multiphysics PDE Systems by the Development of Goal-Oriented Variational Sensitivity Analysis and a-Posteriori Error Estimation Methods

    SciTech Connect

    Estep, Donald

    2015-11-30

    This project addressed the challenge of predictive computational analysis of strongly coupled, highly nonlinear multiphysics systems characterized by multiple physical phenomena that span a large range of length- and time-scales. Specifically, the project was focused on computational estimation of numerical error and sensitivity analysis of computational solutions with respect to variations in parameters and data. In addition, the project investigated the use of accurate computational estimates to guide efficient adaptive discretization. The project developed, analyzed and evaluated new variational adjoint-based techniques for integration, model, and data error estimation/control and sensitivity analysis, in evolutionary multiphysics multiscale simulations.

  3. Structural variation in copper(I) complexes with pyridylmethylamide ligands: structural analysis with a new four-coordinate geometry index, tau4.

    PubMed

    Yang, Lei; Powell, Douglas R; Houser, Robert P

    2007-03-07

    Four Cu(I) complexes were synthesized with a family of pyridylmethylamide ligands, HL(R) [HL(R) = N-(2-pyridylmethyl)acetamide, R = null; 2,2-dimethyl-N-(2-pyridylmethyl)propionamide, R = Me(3); 2,2,2-triphenyl-N-(2-pyridylmethyl)acetamide, R = Ph(3))]. Complexes 1-3 were synthesized from the respective ligand and [Cu(CH(3)CN)(4)]PF(6) in a 2 : 1 molar ratio: [Cu(HL)(2)]PF(6) (1), [Cu(2)(HL(Me3))(4)](PF(6))(2) (2), [Cu(HL(Ph3))(2)]PF(6) (3). Complex 4, [Cu(HL)(CH(3)CN)(PPh(3))]PF(6), was synthesized from the reaction of HL with [Cu(CH(3)CN)(4)]PF(6) and PPh(3) in a 1 : 1 : 1 molar ratio. X-Ray crystal structures reveal that complexes 1, 3 and 4 are mononuclear Cu(I) species, while complex 2 is a Cu(I) dimer. The copper ions are four-coordinate with geometries ranging from distorted tetrahedral to seesaw in 1, 2, and 4. Complexes 1 and 2 are very air sensitive and they display similar electrochemical properties. The coordination geometry of complex 3 is nearly linear, two-coordinate. Complex 3 is exceptionally stable with respect to oxidation in the air, and its cyclic voltammetry shows no oxidation wave in the range of 0-1.5 V. The unusual inertness of complex 3 towards oxidation is attributed to the protection from bulky triphenyl substituent of the HL(Ph3) ligand. A new geometric parameter for four-coordinate compounds, tau(4), is proposed as an improved, simple metric for quantitatively evaluating the geometry of four-coordinate complexes and compounds.

  4. Photoluminescent mixed ligand complexes of CuX (X = Cl, Br, I) with PPh3 and a polydentate imino-pyridyl ligand - Syntheses, structural variations and catalytic property

    NASA Astrophysics Data System (ADS)

    Ghorai, Anupam; Mondal, Jahangir; Patra, Goutam K.

    2015-10-01

    Three ternary copper(I) complexes [CuI2Cl2(L1)(PPh3)4] (1), [CuI2Br2(L1) (PPh3)4] (2) and [CuI2(μ-I)2 (μ-L1) (PPh3)2]n (3) have been prepared by reactions of CuX (X = Cl, Br and I) with PPh3 and the polydentate imino-pyridyl ligand L1. These complexes have been characterized by elemental analysis, IR, UV-Vis, NMR and X-ray crystallography. From single crystal structural analysis it has been found that complexes 1 and 2 are homo-dinuclear having non-bridging halide ions whereas complex 3 is a 1-D zig-zag co-ordination polymer containing bridged iodide ions. Complexes 1, 2 and 3 are photoluminescent at room temperature in chloroform whereas ligand L1 is non-emissive. The E½ values of the CuIsbnd CuII couple of 1, 2 and 3 are 0.98 V, 0.92 V and 0.42 V respectively (vs Ag/AgCl in 1 M KCl, scan rate 100 mV s-1). All three complexes function as effective catalysts for the synthesis of 2-substituted benzoxazoles.

  5. Merging Kohn-Sham and Orbital-Free DFT Calculations to Extend the LiH Hugoniot to Very High Pressures

    NASA Astrophysics Data System (ADS)

    Kress, Joel

    2013-06-01

    Large-scale hydrodynamic simulations of fluids and plasmas under extreme conditions require knowledge of various properties such as the equation of state (EOS), mass diffusion, and shear viscosity. While many approaches exist for the determination of these properties, one of the most accurate employs quantum molecular dynamics (QMD) simulations on large samples of atoms of the various species. Examples include the shock compression of metal hydrides and the mixing of deuterium/tritium (DT) fuel with ablator materials (such as C/H plastics and Be) in inertial confinement fusion capsules. The quantum nature of the electrons is described with two flavors of finite-temperature density functional theory (DFT), namely orbital-based Kohn-Sham (KS) and Orbital Free (OF). EOSs for Lithium Hydride and Lithium 6 Deuteride (Li6D) have been calculated with both KSMD and with OFMD. The shock Hugoniot for Li6D has been determined for temperatures up to 25 eV (5000 GPa) using a KSMD based EOS, and for T = 5 eV and above (up to 10,000 GPa) using an OFMD based EOS. KSMD simulations here have a practical upper limit of T = 25 eV due to the scaling of the computational work. The OFMD simulations have a lower limit of T = 5 eV since the OF DFT yields a poor description at low temperatures. The KSMD and OFMD Hugoniots agree well in the region of overlap (T = 5 to 25 eV). Comparisons will be presented with experimental data and with shock Hugoniots constructed from both existing EOS tables and from a new, improved SESAME table. By utilizing the KSMD and OFMD results to guide the parameter choices, the new EOS overall is a better match to melt and shock experimental data. This work was performed in collaboration with L. A. Collins, S. Crockett, M. P. Desjarlais, and F. Lambert and under the auspices of an agreement between CEA/DAM and NNSA/DP on cooperation on fundamental science. LANL is operated by LANS, LLC for the NNSA of the USDoE under contract no. DE-AC52-06NA25396.

  6. Effect of environmental conditions on variation in the sediment-water interface created by complex macrofaunal burrows on a tidal flat

    NASA Astrophysics Data System (ADS)

    Koo, Bon Joo; Kwon, Kae Kyoung; Hyun, Jung-Ho

    2007-11-01

    We quantified the increase in the sediment-water interface created by the burrowing activities of the resident macrofaunal community and its variation with respect to the physical conditions of the habitat on a tidal fat. We investigated environmental factors and dimensions of macrofaunal burrows with respect to tidal height and vegetation during spring and summer at three sites. A resin-casting method was used to quantify the dimensions of all burrows at each site. The dimensions of macrofaunal burrows varied both temporally and spatially and the increase in the sediment-water interface reached a maximum of 311%, ranging from 20 to 255% under different habitat conditions. The sediment-water interface depended on the duration of exposure resulting from tidal height, increased temperatures resulting from seasonality, and marsh plant density. Burrows were deeper and more expansive at both higher tidal levels and higher temperatures in summer. Burrow dimensions were sharply reduced with the disappearance of adult macrofauna in areas where the roots of the marsh plant Suaeda japonica were dense. The significance of this study lies in quantifying the burrow dimensions of the entire macrofaunal community, rather than just a single population, and confirming their spatial and temporal variation with respect to physical conditions of the habitat. Environmental factors responsible for variation in burrow dimensions are discussed.

  7. Natural Crossbreeding between Sympatric Species of the Phyllosoma Complex (Insecta: Hemiptera: Reduviidae) Indicate the Existence of Only One Species with Morphologic and Genetic Variations

    PubMed Central

    Martínez-Hernandez, Fernando; Martínez-Ibarra, Jose A.; Catalá, Silvia; Villalobos, Guiehdani; de la Torre, Patricia; Laclette, Juan P.; Alejandre-Aguilar, Ricardo; Espinoza, Bertha

    2010-01-01

    The nucleotide sequences of the cytochrome B gene and the antennal phenotypes were analyzed for the following triatomine species: Triatoma longipennis, Triatoma pallidipennis, and Triatoma picturata, which belong to the Phyllosoma complex. These species inhabit sympatric areas from Talpa de Allende, Autlan de Navarro, and Teocuitatlan de Corona in Jalisco, Mexico. Molecular marker analysis showed that the sympatric individuals are the natural crossbred descendents of different individuals living in close proximity in these natural areas that resulted in mixed populations. The antennal phenotype results are coincident with these genetic findings, which point to the high similitude between all Phyllosoma complex populations analyzed. These data support the hypothesis that these species are morphotypes with chromatic and genetic varieties, which preserves the possibility of natural breeding with fertile descent. In conclusion, our results strongly support the hypothesis that T. pallidipennis, T. longipennis, and T. picturata are subspecies of the Phyllosoma complex. PMID:20064999

  8. A density matrix-based method for the linear-scaling calculation of dynamic second- and third-order properties at the Hartree-Fock and Kohn-Sham density functional theory levels.

    PubMed

    Kussmann, Jörg; Ochsenfeld, Christian

    2007-11-28

    A density matrix-based time-dependent self-consistent field (D-TDSCF) method for the calculation of dynamic polarizabilities and first hyperpolarizabilities using the Hartree-Fock and Kohn-Sham density functional theory approaches is presented. The D-TDSCF method allows us to reduce the asymptotic scaling behavior of the computational effort from cubic to linear for systems with a nonvanishing band gap. The linear scaling is achieved by combining a density matrix-based reformulation of the TDSCF equations with linear-scaling schemes for the formation of Fock- or Kohn-Sham-type matrices. In our reformulation only potentially linear-scaling matrices enter the formulation and efficient sparse algebra routines can be employed. Furthermore, the corresponding formulas for the first hyperpolarizabilities are given in terms of zeroth- and first-order one-particle reduced density matrices according to Wigner's (2n+1) rule. The scaling behavior of our method is illustrated for first exemplary calculations with systems of up to 1011 atoms and 8899 basis functions.

  9. Variation of the coordination environment and its effect on the white light emission properties in a Mn-doped ZnO-ZnS complex structure.

    PubMed

    Cheng, Yan; Chen, Rui; Feng, Haifeng; Hao, Weichang; Xu, Huaizhe; Wang, Yu; Li, Jiong

    2014-03-14

    Mn-doped ZnO-ZnS complex nanocrystals were fabricated through coating of dodecanethiol on Mn-doped ZnO nanocrystals. The relationship between the component of white light emission and the coordination environments of Mn-dopants were experimentally investigated. It was shown that Mn ions mainly formed Mn(3+)O6 octahedra in as prepared Mn-doped ZnO, while the Mn(3+) ions on the surface of ZnO transferred into Mn(2+) ions at the interface between ZnO and ZnS after dodecanethiol coating. The Mn(2+)S4 tetrahedron density and the orange emission intensity increased upon enhancing the dodecanethiol content. These results provide an alternative way to optimize the white emission spectrum from nanocrystals of Mn-doped ZnS-ZnO complex structures through modulation of the coordination environment of Mn ions.

  10. Phenotypic Variation among Culex pipiens Complex (Diptera: Culicidae) Populations from the Sacramento Valley, California: Horizontal and Vertical Transmission of West Nile Virus, Diapause Potential, Autogeny, and Host Selection

    PubMed Central

    Nelms, Brittany M.; Kothera, Linda; Thiemann, Tara; Macedo, Paula A.; Savage, Harry M.; Reisen, William K.

    2013-01-01

    The vector competence and bionomics of Culex pipiens form pipiens L. and Cx. pipiens f. molestus Forskäl were evaluated for populations from the Sacramento Valley. Both f. pipiens and f. molestus females became infected, produced disseminated infections, and were able to transmit West Nile virus. Form molestus females also transmitted West Nile virus vertically to egg rafts and F1 progeny, whereas f. pipiens females only transmitted to egg rafts. Culex pipiens complex from urban Sacramento blood-fed on seven different avian species and two mammalian species. Structure analysis of blood-fed mosquitoes identified K = 4 genetic clusters: f. molestus, f. pipiens, a group of genetically similar hybrids (Cluster X), and admixed individuals. When females were exposed as larvae to midwinter conditions in bioenvironmental chambers, 85% (N = 79) of aboveground Cx. pipiens complex females and 100% (N = 34) of underground f. molestus females did not enter reproductive diapause. PMID:24043690

  11. Phenotypic variation among Culex pipiens complex (Diptera: Culicidae) populations from the Sacramento Valley, California: horizontal and vertical transmission of West Nile virus, diapause potential, autogeny, and host selection.

    PubMed

    Nelms, Brittany M; Kothera, Linda; Thiemann, Tara; Macedo, Paula A; Savage, Harry M; Reisen, William K

    2013-12-01

    The vector competence and bionomics of Culex pipiens form pipiens L. and Cx. pipiens f. molestus Forskäl were evaluated for populations from the Sacramento Valley. Both f. pipiens and f. molestus females became infected, produced disseminated infections, and were able to transmit West Nile virus. Form molestus females also transmitted West Nile virus vertically to egg rafts and F1 progeny, whereas f. pipiens females only transmitted to egg rafts. Culex pipiens complex from urban Sacramento blood-fed on seven different avian species and two mammalian species. Structure analysis of blood-fed mosquitoes identified K = 4 genetic clusters: f. molestus, f. pipiens, a group of genetically similar hybrids (Cluster X), and admixed individuals. When females were exposed as larvae to midwinter conditions in bioenvironmental chambers, 85% (N = 79) of aboveground Cx. pipiens complex females and 100% (N = 34) of underground f. molestus females did not enter reproductive diapause.

  12. Density functional theory of complex transition densities.

    PubMed

    Ernzerhof, Matthias

    2006-09-28

    We present an extension of Hohenberg-Kohn-Sham density functional theory to the domain of complex local potentials and complex electron densities. The approach is applicable to resonance (Siegert) [Phys. Rev. 56, 750 (1939)] states and other scattering and transport problems that can be described by a normalized state of a Hamiltonian containing a complex local potential. Such Hamiltonians are non-Hermitian and their eigenvalues are in general complex, the imaginary part being inversely proportional to the lifetime of the system. The one-to-one correspondence between complex local potentials nu and complex electron densities rho is established provided that the complex variables are sufficiently close to real local potentials and densities of nondegenerate ground states. We show that the exchange-correlation functionals, contributing to the complex energy, are determined through analytic continuation of their ground-state-theory counterparts. This implies that the exchange-correlation effects on the lifetime of a resonance are, under appropriate conditions, already determined by the functionals of the ground-state theory.

  13. Variational filtering.

    PubMed

    Friston, K J

    2008-07-01

    This note presents a simple Bayesian filtering scheme, using variational calculus, for inference on the hidden states of dynamic systems. Variational filtering is a stochastic scheme that propagates particles over a changing variational energy landscape, such that their sample density approximates the conditional density of hidden and states and inputs. The key innovation, on which variational filtering rests, is a formulation in generalised coordinates of motion. This renders the scheme much simpler and more versatile than existing approaches, such as those based on particle filtering. We demonstrate variational filtering using simulated and real data from hemodynamic systems studied in neuroimaging and provide comparative evaluations using particle filtering and the fixed-form homologue of variational filtering, namely dynamic expectation maximisation.

  14. Theoretical studies for the rates and kinetic isotope effects of the excited-state double proton transfer in the 1:1 7-azaindole:H2O complex using variational transition state theory including multidimensional tunneling.

    PubMed

    Duong, My Phu Thi; Kim, Yongho

    2010-03-18

    Variational transition state theory calculations including multidimensional tunneling (VTST/MT) for excited-state tautomerization in the 1:1 7-azaindole:H(2)O complex were performed. Electronic structures and energies for reactant, product, transition state, and potential energy curves along the reaction coordinate were computed at the CASSCF(10,9)/6-31G(d,p) level of theory. The potential energies were corrected by second-order multireference perturbation theory to take the dynamic electron correlation into consideration. The final potential energy curves along the reaction coordinate were generated at the MRPT2//CASSCF(10,9)/6-31G(d,p) level. Two protons in the excited-state tautomerization are transferred concertedly, albeit asynchronously. The position of the variational transition state is very different from the conventional transition state, and is highly dependent on isotopic substitution. Rate constants were calculated using VTST/MT, and were on the order of 10(-6) s(-1) at room temperature. The HH/DD kinetic isotope effects are consistent with experimental observations; consideration of both tunneling and variational effects was essential to predict the experimental values correctly.

  15. Self-consistent Kohn-Sham method based on the adiabatic-connection fluctuation-dissipation theorem and the exact-exchange kernel

    SciTech Connect

    Bleiziffer, Patrick Krug, Marcel; Görling, Andreas

    2015-06-28

    A self-consistent Kohn-Sham method based on the adiabatic-connection fluctuation-dissipation (ACFD) theorem, employing the frequency-dependent exact exchange kernel f{sub x} is presented. The resulting SC-exact-exchange-only (EXX)-ACFD method leads to even more accurate correlation potentials than those obtained within the direct random phase approximation (dRPA). In contrast to dRPA methods, not only the Coulomb kernel but also the exact exchange kernel f{sub x} is taken into account in the EXX-ACFD correlation which results in a method that, unlike dRPA methods, is free of self-correlations, i.e., a method that treats exactly all one-electron systems, like, e.g., the hydrogen atom. The self-consistent evaluation of EXX-ACFD total energies improves the accuracy compared to EXX-ACFD total energies evaluated non-self-consistently with EXX or dRPA orbitals and eigenvalues. Reaction energies of a set of small molecules, for which highly accurate experimental reference data are available, are calculated and compared to quantum chemistry methods like Møller-Plesset perturbation theory of second order (MP2) or coupled cluster methods [CCSD, coupled cluster singles, doubles, and perturbative triples (CCSD(T))]. Moreover, we compare our methods to other ACFD variants like dRPA combined with perturbative corrections such as the second order screened exchange corrections or a renormalized singles correction. Similarly, the performance of our EXX-ACFD methods is investigated for the non-covalently bonded dimers of the S22 reference set and for potential energy curves of noble gas, water, and benzene dimers. The computational effort of the SC-EXX-ACFD method exhibits the same scaling of N{sup 5} with respect to the system size N as the non-self-consistent evaluation of only the EXX-ACFD correlation energy; however, the prefactor increases significantly. Reaction energies from the SC-EXX-ACFD method deviate quite little from EXX-ACFD energies obtained non

  16. The effects of structural variations of thiophene-containing Ru(II) complexes on the acid-base and DNA binding properties.

    PubMed

    Yuan, Cui-Li; Zhang, An-Guo; Zheng, Ze-Bo; Wang, Ke-Zhi

    2013-03-01

    A phenylthiophenyl-bearing Ru(II) complex of [Ru(bpy)₂(Hbptip)](PF₆)₂ {bpy = 2,2'-bipyridine, Hbptip = 2-(4-phenylthiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline} was synthesized and characterized by elemental analysis, ¹H NMR spectroscopy, and electrospray ionization mass spectrometry. The ground- and excited-state acid-base properties of the complex were studied by UV-visible absorption and photoluminescence spectrophotometric pH titrations and the negative logarithm values of the ground-state acid ionization constants were derived to be pK(a1) = 1.31 ± 0.09 and pK(a2) = 5.71 ± 0.11 with the pK(a2) associated deprotonation/protonation process occurring over 3 pK(a) units more acidic than thiophenyl-free parent complex of [Ru(bpy)₂(Hpip)]²⁺ {Hpip = 2-phenyl-1H-imidazo[4,5-f][1,10]phenanthroline}. The calf thymus DNA-binding properties of [Ru(bpy)₂(Hbptip)]²⁺ in Tris-HCl buffer (pH 7.1 and 50 mM NaCl) were investigated by DNA viscosities and density functional theoretical calculations as well as UV-visible and emission spectroscopy techniques of UV-visible and luminescence titrations, steady-state emission quenching by [Fe(CN)₆]⁴⁻, DNA competitive binding with ethidium bromide, DNA melting experiments, and reverse salt effects. The complex was evidenced to bind to the DNA intercalatively with binding affinity being greater than those for previously reported analogs of [Ru(bpy)₂(Hip)]²⁺, [Ru(bpy)₂(Htip)]²⁺, and [Ru(bpy)₂(Haptip)]²⁺ {Hip = 1H-imidazo[4,5-f][1,10]phenanthroline, Htip = 2-thiophenimidazo[4,5-f][1,10]phenanthroline, Haptip = 2-(5-phenylthiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline}.

  17. Complex genetics controls natural variation among seed quality phenotypes in a recombinant inbred population of an interspecific cross between Solanum lycopersicum × Solanum pimpinellifolium.

    PubMed

    Kazmi, Rashid H; Khan, Noorullah; Willems, Leo A J; VAN Heusden, Adriaan W; Ligterink, Wilco; Hilhorst, Henk W M

    2012-05-01

    Seed quality in tomato is associated with many complex physiological and genetic traits. While plant processes are frequently controlled by the action of small- to large-effect genes that follow classic Mendelian inheritance, our study suggests that seed quality is primarily quantitative and genetically complex. Using a recombinant inbred line population of Solanum lycopersicum × Solanum pimpinellifolium, we identified quantitative trait loci (QTLs) influencing seed quality phenotypes under non-stress, as well as salt, osmotic, cold, high-temperature and oxidative stress conditions. In total, 42 seed quality traits were analysed and 120 QTLs were identified for germination traits under different conditions. Significant phenotypic correlations were observed between germination traits under optimal conditions, as well as under different stress conditions. In conclusion, one or more QTLs were identified for each trait with some of these QTLs co-locating. Co-location of QTLs for different traits can be an indication that a locus has pleiotropic effects on multiple traits due to a common mechanistic basis. However, several QTLs also dissected seed quality in its separate components, suggesting different physiological mechanisms and signalling pathways for different seed quality attributes.

  18. Control over the Self-Assembly Modes of Pt(II) Complexes by Alkyl Chain Variation: From Slipped to Parallel π-Stacks.

    PubMed

    Allampally, Naveen Kumar; Mayoral, María José; Chansai, Sarayute; Lagunas, María Cristina; Hardacre, Christopher; Stepanenko, Vladimir; Albuquerque, Rodrigo Q; Fernández, Gustavo

    2016-06-01

    We report the self-assembly of a new family of hydrophobic, bis(pyridyl) Pt(II) complexes featuring an extended oligophenyleneethynylene-derived π-surface appended with six long (dodecyloxy (2)) or short (methoxy (3)) side groups. Complex 2, containing dodecyloxy chains, forms fibrous assemblies with a slipped arrangement of the monomer units (dPt⋅⋅⋅Pt ≈14 Å) in both nonpolar solvents and the solid state. Dispersion-corrected PM6 calculations suggest that this organization is driven by cooperative π-π, C-H⋅⋅⋅Cl and π-Pt interactions, which is supported by EXAFS and 2D NMR spectroscopic analysis. In contrast, nearly parallel π-stacks (dPt⋅⋅⋅Pt ≈4.4 Å) stabilized by multiple π-π and C-H⋅⋅⋅Cl contacts are obtained in the crystalline state for 3 lacking long side chains, as shown by X-ray analysis and PM6 calculations. Our results reveal not only the key role of alkyl chain length in controlling self-assembly modes but also show the relevance of Pt-bound chlorine ligands as new supramolecular synthons.

  19. Variational first hyperpolarizabilities of 2,3-naphtho-15-crown-5 ether derivatives with cation-complexing: a potential and selective cation detector.

    PubMed

    Yu, Hai-Ling; Wang, Wen-Yong; Hong, Bo; Zong, Ying; Si, Yan-Ling; Hu, Zhong-Qiang

    2016-09-29

    Crown ethers, as a kind of heterocycle, have been the subject of great interest over recent decades due to their selective capability to bind to metal cations. The use of a constant crown ether, such as naphtho-15-crown-5 (N15C5), and varied metal cations (Li(+), Na(+), K(+), Be(2+), Mg(2+), Ca(2+), Co(2+), Ni(2+), Cu(2+)) makes it possible to determine the contributions of the metal cations to nonlinear optical (NLO) responses and to design an appropriate NLO-based cation detector. N15C5 and its metal cation derivatives have been systematically investigated by density functional theory. It is found that the dependency of the first hyperpolarizability relies on the metal cation, especially for transition metals. The decrease of the first hyperpolarizabilities for alkali metal cation derivatives is due to their relatively low oscillator strengths, whereas the significant increase of the first hyperpolarizabilities for transition metal cation derivatives can be further illustrated by their low transition energies, large amplitudes and separate distributions of first hyperpolarizability density. Thus, the alkali metal and transition metal cations are distinguishable and the transition metal cations are easier to detect by utilizing the variations in NLO responses.

  20. Evaluation of the behavior of clouds in a region of severe acid rain pollution in southern China: species, complexes, and variations.

    PubMed

    Sun, Lei; Wang, Yan; Yue, Taixing; Yang, Xueqiao; Xue, Likun; Wang, Wenxing

    2015-09-01

    Cloud samples were collected during the summer of 2011 and the spring of 2012 at a high-elevation site in southern China in an effort to examine the chemical characteristics of acid clouds. In total, 141 cloud samples were collected during 44 cloud events over the observation period. The dominant ionic species were SO4(2-), NH4(+), and NO3(-), contributing approximately 75% of the total inorganic ion concentration. The primary acidifying factors were sulfate and nitrate, and the primary neutralizing factors were ammonium and calcium. The volume-weighted mean (VWM) pH of the cloud water was 3.79, indicating an acidic nature. In these cloud samples, Zn and Al exhibited the highest trace metal concentrations, contributing approximately 60% of the total trace element concentration. Toxic metals, such as Pb, Ba, As, and Cr, were detected at high concentrations, indicating potential hazards for human health, vegetation, and waters in this region. Visual MINTEQ 3.0 results revealed that the majority of Zn(II) and Pb(II) existed in the form of free ions. The behavior of Al, however, differed from the behaviors of zinc and lead. The temporal variation in cloud chemistry indicated that temperature, sandstorms, and long-range transport could affect the concentrations of species. During the lifetime of a cloud event, the concentrations of the chemical species were controlled by the transfer of gases or particles to liquid droplets.

  1. Chromosomal variation in the tropical armoured catfish Callichthys callichthys (Siluriformes, Callichthyidae): implications for conservation and taxonomy in a species complex from a Brazilian hotspot.

    PubMed

    Almeida, Josivanda Santos; Affonso, Paulo Roberto Antunes de Mello; Diniz, Débora; Carneiro, Paulo Luiz Souza; Dias, Ana Lúcia

    2013-12-01

    The Neotropical catfish family Callichthyidae is characterized by wide karyotype variation, although reports are restricted to a few species/populations. This work provides new chromosomal information in two populations of armoured catfish (Callichthys callichthys) within the Atlantic forest boundaries in northeastern Brazil. Both populations of C. callichthys presented 2n=54 (16 metacentric, 24 submetacentric, 6 subtelocentric, and 8 acrocentric chromosomes) with occurrence of a metacentric B macrochromosome, reported for the first time in "2n=54" karyomorph. The lack of heterochromatin in the supernumerary chromosome suggests a recent origin of Bs with a significant difference in their frequency (p<0.05) between localities. Contrasting to the predominance of single nucleolus organizer regions (NORs) in other populations from South America, a remarkable polymorphism of 18S rDNA and GC-rich sites was detected, inasmuch as NOR phenotypes were unique for each individual, comprising up to 13 NOR-bearing chromosomes. The 5S rDNA was also mapped onto multiple chromosomes nonsyntenic to NORs. Such divergence in a number of NORs and occurrence of an euchromatic B chromosome in relation to other karyomorphs reinforces the divergent evolution of C. callichthys populations. Furthermore, these results also support central and drier Atlantic forest areas in northeastern Brazil as a biodiversity hotspot.

  2. Single-Molecule Sequencing Reveals Complex Genome Variation of Hepatitis B Virus during 15 Years of Chronic Infection following Liver Transplantation

    PubMed Central

    Betz-Stablein, B. D.; Töpfer, A.; Littlejohn, M.; Yuen, L.; Colledge, D.; Sozzi, V.; Angus, P.; Thompson, A.; Revill, P.; Beerenwinkel, N.; Warner, N.

    2016-01-01

    ABSTRACT Chronic hepatitis B (CHB) is prevalent worldwide. The infectious agent, hepatitis B virus (HBV), replicates via an RNA intermediate and is error prone, leading to the rapid generation of closely related but not identical viral variants, including those that can escape host immune responses and antiviral treatments. The complexity of CHB can be further enhanced by the presence of HBV variants with large deletions in the genome generated via splicing (spHBV variants). Although spHBV variants are incapable of autonomous replication, their replication is rescued by wild-type HBV. spHBV variants have been shown to enhance wild-type virus replication, and their prevalence increases with liver disease progression. Single-molecule deep sequencing was performed on whole HBV genomes extracted from samples, including the liver explant, longitudinally collected from a subject with CHB over a 15-year period after liver transplantation. By employing novel bioinformatics methods, this analysis showed that the dynamics of the viral population across a period of changing treatment regimens was complex. The spHBV variants detected in the liver explant remained present posttransplantation, and a highly diverse novel spHBV population as well as variants with multiple deletions in the pre-S genes emerged. The identification of novel mutations outside the HBV reverse transcriptase gene that co-occurred with known drug resistance-associated mutations highlights the relevance of using full-genome deep sequencing and supports the hypothesis that drug resistance involves interactions across the full length of the HBV genome. IMPORTANCE Single-molecule sequencing allowed the characterization, in unprecedented detail, of the evolution of HBV populations and offered unique insights into the dynamics of defective and spHBV variants following liver transplantation and complex treatment regimens. This analysis also showed the rapid adaptation of HBV populations to treatment regimens with

  3. Variation of exciton-vibrational coupling in photosystem II core complexes from Thermosynechococcus elongatus as revealed by single-molecule spectroscopy.

    PubMed

    Skandary, Sepideh; Hussels, Martin; Konrad, Alexander; Renger, Thomas; Müh, Frank; Bommer, Martin; Zouni, Athina; Meixner, Alfred J; Brecht, Marc

    2015-03-19

    The spectral properties and dynamics of the fluorescence emission of photosystem II core complexes are investigated by single-molecule spectroscopy at 1.6 K. The emission spectra are dominated by sharp zero-phonon lines (ZPLs). The sharp ZPLs are the result of weak to intermediate exciton-vibrational coupling and slow spectral diffusion. For several data sets, it is possible to surpass the effect of spectral diffusion by applying a shifting algorithm. The increased signal-to-noise ratio enables us to determine the exciton-vibrational coupling strength (Huang-Rhys factor) with high precision. The Huang-Rhys factors vary between 0.03 and 0.8. The values of the Huang-Rhys factors show no obvious correlation between coupling strength and wavelength position. From this result, we conclude that electrostatic rather than exchange or dispersive interactions are the main contributors to the exciton-vibrational coupling in this system.

  4. Variations in clique and community patterns in protein structures during allosteric communication: investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes.

    PubMed

    Ghosh, Amit; Vishveshwara, Saraswathi

    2008-11-04

    The allosteric concept has played a key role in understanding the biological functions of proteins. The rigidity or plasticity and the conformational population are the two important ideas invoked in explaining the allosteric effect. Although molecular insights have been gained from a large number of structures, a precise assessment of the ligand-induced conformational changes in proteins at different levels, ranging from gross topology to intricate details, remains a challenge. In this study, we have explored the conformational changes in the complexes of methionyl tRNA synthetase (MetRS) through novel network parameters such as cliques and communities, which identify the rigid regions in the protein structure networks (PSNs) constructed from the noncovalent interactions of amino acid side chains. MetRS belongs to the aminoacyl tRNA synthetase (aaRS) family that plays a crucial role in the translation of genetic code. These enzymes are modular with distinct domains from which extensive genetic, kinetic, and structural data are available, highlighting the role of interdomain communication. The network parameters evaluated here on the conformational ensembles of MetRS complexes, generated from molecular dynamics simulations, have enabled us to understand the interdomain communication in detail. Additionally, the characterization of conformational changes in terms of cliques and communities has also become possible, which had eluded conventional analyses. Furthermore, we find that most of the residues participating in cliques and communities are strikingly different from those that take part in long-range communication. The cliques and communities evaluated here for the first time on PSNs have beautifully captured the local geometries in detail within the framework of global topology. Here the allosteric effect is revealed at the residue level via identification of the important residues specific for structural rigidity and functional flexibility in MetRS. This ought

  5. Categorical complexities of Plasmodium falciparum malaria in individuals is associated with genetic variations in ADORA2A and GRK5 genes.

    PubMed

    Gupta, Himanshu; Jain, Aditya; Saadi, Abdul Vahab; Vasudevan, Thanvanthri G; Hande, Manjunath H; D'Souza, Sydney C; Ghosh, Susanta K; Umakanth, Shashikiran; Satyamoorthy, Kapaettu

    2015-08-01

    In the erythrocytes, malaria parasite entry and infection is mediated through complex membrane sorting and signaling processes. We investigated the effects of single-locus and multilocus interactions to test the hypothesis that the members of the GPCR family genes, adenosine A2a receptor (ADORA2A) and G-protein coupled receptor kinase5 (GRK5), may contribute to the pathogenesis of malaria caused by Plasmodium falciparum (Pf) independently or through complex interactions. In a case-control study of adults, individuals affected by Pf malaria (complicated n=168; uncomplicated n=282) and healthy controls (n=450) were tested for their association to four known SNPs in GRK5 (rs2230345, rs2275036, rs4752307 and rs11198918) and two in ADORA2A (rs9624472 and rs5751876) genes with malaria susceptibility, using techniques of polymerase chain reaction-restriction fragment length polymorphisms and direct DNA sequencing. Single-locus analysis showed significant association of 2 SNPs; rs5751876 (OR=3.2(2.0-5.2); p=0.0006) of ADORA2A and rs2230345 (OR=0.3(0.2-0.5); p=0.0006) of GRK5 with malaria. The mean of the serum creatinine levels were significantly higher in patients with variant GG (p=0.006) of rs9624472 in ADORA2A gene compared to AA and AG genotypes in complicated Pf malaria cases, with the G allele also showing increased risk for malaria (OR=1.3(1.1-1.6); p=0.017). Analyses of predicted haplotypes of the two ADORA2A and the four GRK5 SNPs have identified the haplotypes that conferred risk as well as resistance to malaria with statistical significance. Molecular docking analysis of evolutionary rs2230345 SNP indicated a stable activity of GRK5 for the mutant allele compared to the wild type. Further, generalized multifactor dimensionality reduction to test the contribution of individual effects of the six polymorphisms and higher-order interactions to risk of symptoms/clinical complications of malaria suggested a best six-locus model showing statistical significance. The

  6. Influence of Halogen Variation on Structure and Interactions in Vinyl Halide (H_2C=CHX)\\cdotsCO_2 (x = F, Cl, Br) Complexes

    NASA Astrophysics Data System (ADS)

    Anderton, Ashley M.; Christenholz, Cori L.; Dorris, Rachel E.; Peebles, Rebecca A.; Peebles, Sean A.

    2016-06-01

    Chirped-pulse and resonant cavity Fourier-transform microwave spectroscopy have been used to investigate dimers of CO_2 with vinyl fluoride (VF), vinyl chloride (VCl) and vinyl bromide (VBr). For all three complexes, CO_2 is aligned adjacent to the X-C-H end (X = F, Cl, Br) of the ethylene subunit, with C-X\\cdotsC and C-H\\cdotsO contacts. For VF\\cdotsCO_2, a second isomer is also observed, with CO_2 roughly parallel to the H-C=C-F side of VF; however, there is no spectroscopic indication that similar structures are present for VCl\\cdotsCO_2 or VBr\\cdotsCO_2. For vinyl fluoride\\cdotsCO_2, a full structural analysis has previously been published, while for the Cl- and Br-containing species, insufficient data are presently available for complete structure determinations. However, structural information from ab initio calculations, 35Cl/37Cl and 79B/81Br isotopic substitution, and analysis of chlorine and bromine nuclear quadrupole coupling constants will be presented. In addition, for this series of dimers containing C-H\\cdotsO contacts, further insight into the nature of the weak interactions may be obtained from Quantum Theory of Atoms in Molecules (QTAIM) and other ab initio} analyses that are presently in progress. C. L. Christenholz, R. E. Dorris, R. A. Peebles, S. A. Peebles, J. Phys. Chem. A, 118, (2014), 8765-8772.

  7. Different crystal morphologies lead to slightly different conformations of light-harvesting complex II as monitored by variations of the intrinsic fluorescence lifetime.

    PubMed

    van Oort, Bart; Maréchal, Amandine; Ruban, Alexander V; Robert, Bruno; Pascal, Andrew A; de Ruijter, Norbert C A; van Grondelle, Rienk; van Amerongen, Herbert

    2011-07-21

    In 2005, it was found that the fluorescence of crystals of the major light-harvesting complex LHCII of green plants is significantly quenched when compared to the fluorescence of isolated LHCII (A. A. Pascal et al., Nature, 2005, 436, 134-137). The Raman spectrum of crystallized LHCII was also found to be different from that of isolated LHCII but very similar to that of aggregated LHCII, which has often been considered a good model system for studying nonphotochemical quenching (NPQ), the major protection mechanism of plants against photodamage in high light. It was proposed that in the crystal LHCII adopts a similar (quenching) conformation as during NPQ and indeed similar changes in the Raman spectrum were observed during NPQ in vivo (A. V. Ruban et al., Nature, 2007, 450, 575-579). We now compared the fluorescence of various types of crystals, differing in morphology and age. Each type gave rise to its own characteristic mono-exponential fluorescence lifetime, which was 5 to 10 times shorter than that of isolated LHCII. This indicates that fluorescence is not quenched by random impurities and packing defects (as proposed recently by T. Barros et al., EMBO Journal, 2009, 28, 298-306), but that LHCII adopts a particular structure in each crystal type, that leads to fluorescence quenching. Most interestingly, the extent of quenching appears to depend on the crystal morphology, indicating that also the crystal structure depends on this crystal morphology but at the moment no data are available to correlate the crystals' structural changes to changes in fluorescence lifetime.

  8. Changes in the Plasma Proteome of Manduca sexta Larvae in Relation to the Transcriptome Variations after an Immune Challenge: Evidence for High Molecular Weight Immune Complex Formation*

    PubMed Central

    He, Yan; Cao, Xiaolong; Zhang, Shuguang; Rogers, Janet; Hartson, Steve; Jiang, Haobo

    2016-01-01

    Manduca sexta is a lepidopteran model widely used to study insect physiological processes, including innate immunity. In this study, we explored the proteomes of cell-free hemolymph from larvae injected with a sterile buffer (C for control) or a mixture of bacteria (I for induced). Of the 654 proteins identified, 70 showed 1.67 to >200-fold abundance increases after the immune challenge; 51 decreased to 0–60% of the control levels. While there was no strong parallel between plasma protein levels and their transcript levels in hemocytes or fat body, the mRNA level changes (i.e. I/C ratios of normalized read numbers) in the tissues concurred with their protein level changes (i.e. I/C ratios of normalized spectral counts) with correlation coefficients of 0.44 and 0.57, respectively. Better correlations support that fat body contributes a more significant portion of the plasma proteins involved in various aspects of innate immunity. Consistently, ratios of mRNA and protein levels were better correlated for immunity-related proteins than unrelated ones. There is a set of proteins whose apparent molecular masses differ considerably from the calculated Mr's, suggestive of posttranslational modifications. In addition, some low Mr proteins were detected in the range of 80 to >300 kDa on a reducing SDS-polyacrylamide gel, indicating the existence of high Mr covalent complexes. We identified 30 serine proteases and their homologs, 11 of which are known members of an extracellular immune signaling network. Along with our quantitative transcriptome data, the protein identification, inducibility, and association provide leads toward a focused exploration of humoral immunity in M. sexta. PMID:26811355

  9. Long-Term Colonization of the Cystic Fibrosis Lung by Burkholderia cepacia Complex Bacteria: Epidemiology, Clonal Variation, and Genome-Wide Expression Alterations

    PubMed Central

    Coutinho, Carla P.; dos Santos, Sandra C.; Madeira, Andreia; Mira, Nuno P.; Moreira, Ana S.; Sá-Correia, Isabel

    2011-01-01

    Long-term respiratory infections with Burkholderia cepacia complex (Bcc) bacteria in cystic fibrosis (CF) patients generally lead to a more rapid decline in lung function and, in some cases, to a fatal necrotizing pneumonia known as the “cepacia syndrome.” Bcc bacteria are ubiquitous in the environment and are recognized as serious opportunistic pathogens that are virtually impossible to eradicate from the CF lung, posing a serious clinical threat. The epidemiological survey of Bcc bacteria involved in respiratory infections at the major Portuguese CF Treatment Center at Santa Maria Hospital, in Lisbon, has been carried out by our research group for the past 16 years, covering over 500 clinical isolates where B. cepacia and B. cenocepacia are the predominant species, with B. stabilis, B. contaminans, B. dolosa, and B. multivorans also represented. The systematic and longitudinal study of this CF population during such an extended period of time represents a unique case–study, comprehending 41 Bcc-infected patients (29 pediatric and 12 adult) of whom around 70% have been persistently colonized between 7 months and 9 years. During chronic infection, the CF airways represent an evolving ecosystem, with multiple phenotypic variants emerging from the clonal population and becoming established in the patients’ airways as the result of genetic adaptation. Understanding the evolutionary mechanisms involved is crucial for an improved therapeutic outcome of chronic infections in CF. This review focuses on our contribution to the understanding of these adaptive mechanisms based on extensive phenotypic, genotypic, and genome-wide expression approaches of selected Bcc clonal variants obtained during long-term colonization of the CF airways. PMID:22919578

  10. Changes in the Plasma Proteome of Manduca sexta Larvae in Relation to the Transcriptome Variations after an Immune Challenge: Evidence for High Molecular Weight Immune Complex Formation.

    PubMed

    He, Yan; Cao, Xiaolong; Zhang, Shuguang; Rogers, Janet; Hartson, Steve; Jiang, Haobo

    2016-04-01

    Manduca sextais a lepidopteran model widely used to study insect physiological processes, including innate immunity. In this study, we explored the proteomes of cell-free hemolymph from larvae injected with a sterile buffer (C for control) or a mixture of bacteria (I for induced). Of the 654 proteins identified, 70 showed 1.67 to >200-fold abundance increases after the immune challenge; 51 decreased to 0-60% of the control levels. While there was no strong parallel between plasma protein levels and their transcript levels in hemocytes or fat body, the mRNA level changes (i.e.I/C ratios of normalized read numbers) in the tissues concurred with their protein level changes (i.e.I/C ratios of normalized spectral counts) with correlation coefficients of 0.44 and 0.57, respectively. Better correlations support that fat body contributes a more significant portion of the plasma proteins involved in various aspects of innate immunity. Consistently, ratios of mRNA and protein levels were better correlated for immunity-related proteins than unrelated ones. There is a set of proteins whose apparent molecular masses differ considerably from the calculatedMr's, suggestive of posttranslational modifications. In addition, some lowMrproteins were detected in the range of 80 to >300 kDa on a reducing SDS-polyacrylamide gel, indicating the existence of highMrcovalent complexes. We identified 30 serine proteases and their homologs, 11 of which are known members of an extracellular immune signaling network. Along with our quantitative transcriptome data, the protein identification, inducibility, and association provide leads toward a focused exploration of humoral immunity inM. sexta.

  11. Variation in the composition of corals, fishes, sponges, echinoderms, ascidians, molluscs, foraminifera and macroalgae across a pronounced in-to-offshore environmental gradient in the Jakarta Bay-Thousand Islands coral reef complex.

    PubMed

    Cleary, D F R; Polónia, A R M; Renema, W; Hoeksema, B W; Rachello-Dolmen, P G; Moolenbeek, R G; Budiyanto, A; Yahmantoro; Tuti, Y; Giyanto; Draisma, S G A; Prud'homme van Reine, W F; Hariyanto, R; Gittenberger, A; Rikoh, M S; de Voogd, N J

    2016-09-30

    Substrate cover, water quality parameters and assemblages of corals, fishes, sponges, echinoderms, ascidians, molluscs, benthic foraminifera and macroalgae were sampled across a pronounced environmental gradient in the Jakarta Bay-Thousand Islands reef complex. Inshore sites mainly consisted of sand, rubble and turf algae with elevated temperature, dissolved oxygen, pH and chlorophyll concentrations and depauperate assemblages of all taxa. Live coral cover was very low inshore and mainly consisted of sparse massive coral heads and a few encrusting species. Faunal assemblages were more speciose and compositionally distinct mid- and offshore compared to inshore. There were, however, small-scale differences among taxa. Certain midshore sites, for example, housed assemblages resembling those typical of the inshore environment but this differed depending on the taxon. Substrate, water quality and spatial variables together explained from 31% (molluscs) to 72% (foraminifera) of the variation in composition. In general, satellite-derived parameters outperformed locally measured parameters.

  12. Robust Understanding of Statistical Variation

    ERIC Educational Resources Information Center

    Peters, Susan A.

    2011-01-01

    This paper presents a framework that captures the complexity of reasoning about variation in ways that are indicative of robust understanding and describes reasoning as a blend of design, data-centric, and modeling perspectives. Robust understanding is indicated by integrated reasoning about variation within each perspective and across…

  13. Theoretical study of the structural properties of plutonium(IV) and (VI) complexes.

    PubMed

    Odoh, Samuel O; Schreckenbach, Georg

    2011-12-08

    The structural properties of several plutonium(IV) and (VI) complexes have been examined in the gaseous and aqueous phases using Kohn-Sham density functional theory calculations with scalar relativistic effective core potentials and the polarizable continuum solvation model. The aquo and nitrate complexes of PuO(2)(2+) and Pu(4+) were considered in addition to the aquo-chloro complexes of PuO(2)(2+). The nitrate and chloro- complexes formed with triphenylphosphine oxide (TPPO) and tributylphosphate (TBP) respectively were also studied. The structural parameters of the plutonyl complexes were compared to their uranyl and neptunyl analogues. The bond lengths and vibrational frequencies of the plutonyl complexes can generally be computed with sufficient accuracy with the pure PBE density functional with shorter bond lengths being predicted by the B3LYP functional. The structural parameters of the [PuO(2)Cl(2)L(2)] systems formed with TPPO and TBP as well as the aqueous [PuO(2)Cl(2)(H(2)O)(3)] complex are matched to previous experimental results. Overall, the inclusion of ligands in the equatorial region results in significant changes in the stretching frequency of the plutonyl group. The structural features of the plutonyl (VI) systems are rather similar to those of their 5f(0) uranyl and 5f(1) neptunyl counterparts. For the Pu(IV) aquo and nitrate complexes, the average of the calculated Pu-OH(2) and Pu-O(nitrate) bond lengths are generally within 0.04 Å of the reported experimental values. Overall Kohn-Sham DFT can be used successfully in predicting the structures of this diverse set of Pu(VI) and Pu(IV) complexes.

  14. FROG - Fingerprinting Genomic Variation Ontology.

    PubMed

    Abinaya, E; Narang, Pankaj; Bhardwaj, Anshu

    2015-01-01

    Genetic variations play a crucial role in differential phenotypic outcomes. Given the complexity in establishing this correlation and the enormous data available today, it is imperative to design machine-readable, efficient methods to store, label, search and analyze this data. A semantic approach, FROG: "FingeRprinting Ontology of Genomic variations" is implemented to label variation data, based on its location, function and interactions. FROG has six levels to describe the variation annotation, namely, chromosome, DNA, RNA, protein, variations and interactions. Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant. For example, in chromosome level, one of the attributes is location of variation and which has two properties, allosomes or autosomes. Another attribute is variation kind which has four properties, namely, indel, deletion, insertion, substitution. Likewise, there are 48 attributes and 278 properties to capture the variation annotation across six levels. Each property is then assigned a bit score which in turn leads to generation of a binary fingerprint based on the combination of these properties (mostly taken from existing variation ontologies). FROG is a novel and unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis. A web-based platform is designed as a test case for users to navigate sample datasets and generate fingerprints. The platform is available at http://ab-openlab.csir.res.in/frog.

  15. (Genomic variation in maize)

    SciTech Connect

    Rivin, C.J.

    1991-01-01

    These studies have sought to learn how different DNA sequences and sequence arrangements contribute to genome plasticity in maize. We describe quantitative variation among maize inbred lines for tandemly arrayed and dispersed repeated DNA sequences and gene families, and qualitative variation for sequences homologous to the Mutator family of transposons. The potential of these sequences to undergo unequal crossing over, non-allelic (ectopic) recombination and transposition makes them a source of genome instability. We have found examples of rapid genomic change involving these sequences in Fl hybrids, tissue culture cells and regenerated plants. We describe the repetitive portion of the maize genome as composed primarily of sequences that vary markedly in copy number among different genetic stocks. The most highly variable is the 185 bp repeat associated with the heterochromatic chromosome knobs. Even in lines without visible knobs, there is a considerable quantity of tandemly arrayed repeats. We also found a high degree of variability for the tandemly arrayed 5S and ribosomal DNA repeats. While such variation might be expected as the result of unequal cross-over, we were surprised to find considerable variation among lower copy number, dispersed repeats as well. One highly repeated sequence that showed a complex tandem and dispersed arrangement stood out as showing no detectable variability among the maize lines. In striking contrast to the variability seen between the inbred stocks, individuals within a stock were indistinguishable with regard to their repeated sequence multiplicities.

  16. FROG - Fingerprinting Genomic Variation Ontology

    PubMed Central

    Bhardwaj, Anshu

    2015-01-01

    Genetic variations play a crucial role in differential phenotypic outcomes. Given the complexity in establishing this correlation and the enormous data available today, it is imperative to design machine-readable, efficient methods to store, label, search and analyze this data. A semantic approach, FROG: “FingeRprinting Ontology of Genomic variations” is implemented to label variation data, based on its location, function and interactions. FROG has six levels to describe the variation annotation, namely, chromosome, DNA, RNA, protein, variations and interactions. Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant. For example, in chromosome level, one of the attributes is location of variation and which has two properties, allosomes or autosomes. Another attribute is variation kind which has four properties, namely, indel, deletion, insertion, substitution. Likewise, there are 48 attributes and 278 properties to capture the variation annotation across six levels. Each property is then assigned a bit score which in turn leads to generation of a binary fingerprint based on the combination of these properties (mostly taken from existing variation ontologies). FROG is a novel and unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis. A web-based platform is designed as a test case for users to navigate sample datasets and generate fingerprints. The platform is available at http://ab-openlab.csir.res.in/frog. PMID:26244889

  17. Natural Variation in Small Molecule–Induced TIR-NB-LRR Signaling Induces Root Growth Arrest via EDS1- and PAD4-Complexed R Protein VICTR in Arabidopsis[C][W

    PubMed Central

    Kim, Tae-Houn; Kunz, Hans-Henning; Bhattacharjee, Saikat; Hauser, Felix; Park, Jiyoung; Engineer, Cawas; Liu, Amy; Ha, Tracy; Parker, Jane E.; Gassmann, Walter; Schroeder, Julian I.

    2012-01-01

    In a chemical genetics screen we identified the small-molecule [5-(3,4-dichlorophenyl)furan-2-yl]-piperidine-1-ylmethanethione (DFPM) that triggers rapid inhibition of early abscisic acid signal transduction via PHYTOALEXIN DEFICIENT4 (PAD4)- and ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1)-dependent immune signaling mechanisms. However, mechanisms upstream of EDS1 and PAD4 in DFPM-mediated signaling remain unknown. Here, we report that DFPM generates an Arabidopsis thaliana accession-specific root growth arrest in Columbia-0 (Col-0) plants. The genetic locus responsible for this natural variant, VICTR (VARIATION IN COMPOUND TRIGGERED ROOT growth response), encodes a TIR-NB-LRR (for Toll-Interleukin1 Receptor–nucleotide binding–Leucine-rich repeat) protein. Analyses of T-DNA insertion victr alleles showed that VICTR is necessary for DFPM-induced root growth arrest and inhibition of abscisic acid–induced stomatal closing. Transgenic expression of the Col-0 VICTR allele in DFPM-insensitive Arabidopsis accessions recapitulated the DFPM-induced root growth arrest. EDS1 and PAD4, both central regulators of basal resistance and effector-triggered immunity, as well as HSP90 chaperones and their cochaperones RAR1 and SGT1B, are required for the DFPM-induced root growth arrest. Salicylic acid and jasmonic acid signaling pathway components are dispensable. We further demonstrate that VICTR associates with EDS1 and PAD4 in a nuclear protein complex. These findings show a previously unexplored association between a TIR-NB-LRR protein and PAD4 and identify functions of plant immune signaling components in the regulation of root meristematic zone-targeted growth arrest. PMID:23275581

  18. Communication: Physical origins of ionization potential shifts in mixed carboxylic acids and water complexes

    NASA Astrophysics Data System (ADS)

    Gu, Quanli; Tang, Zhen; Su, Peifeng; Wu, Wei; Yang, Zhijun; Trindle, Carl O.; Knee, Joseph L.

    2016-08-01

    The ionization potential (IP) of the aromatic alpha hydroxy carboxylic acid, 9-hydroxy-9-fluorene carboxylic acid (9HFCA), is shifted by complexation with hydrogen bonding ligands such as water and formic acid. Generalized Kohn-Sham energy decomposition analysis decomposes the intermolecular binding energies into a frozen energy term, polarization, correlation, and/or dispersion energy terms, as well as terms of geometric relaxation and zero point energy. We observe that in each dimer the attractive polarization always increases upon ionization, enhancing binding in the cation and shifting the IP toward the red. For 9HFCA—H2O, a substantial decrease of the repulsive frozen energy in cation further shifts the IP toward red. For 9HFCA—HCOOH, the increase of the frozen energy actually occurs in the cation and shifts the IP toward blue. Consistent with the experimental measurements, our analysis provides new, non-intuitive perspectives on multiple hydrogen bonds interactions in carboxylic acids and water complexes.

  19. Anatomic Variations in Head and Neck Reconstruction

    PubMed Central

    Tan, Bien-Keem; Wong, Chin-Ho; Chen, Hung-Chi

    2010-01-01

    Head and neck reconstruction is a technically challenging procedure. Variations encountered in the recipient vessels and commonly used flaps add to the complexity of surgery. This article reviews the commonly encountered variations in the recipient vessels in the neck with emphasis on alternatives and techniques to circumvent these variations. Flaps commonly used in head and neck reconstruction are also reviewed in detail. Furthermore, safety, potential pitfalls, and technical pearls are highlighted. PMID:22550436

  20. Velocity resolved [C ii], [C i], and CO observations of the N159 star-forming region in the Large Magellanic Cloud: a complex velocity structure and variation of the column densities

    NASA Astrophysics Data System (ADS)

    Okada, Yoko; Requena-Torres, Miguel Angel; Güsten, Rolf; Stutzki, Jürgen; Wiesemeyer, Helmut; Pütz, Patrick; Ricken, Oliver

    2015-08-01

    Context. The [C ii] 158 μm fine structure line is one of the dominant cooling lines in star-forming active regions. Together with models of photon-dominated regions, the data is used to constrain the physical properties of the emitting regions, such as the density and the radiation field strength. According to the modeling, the [C ii] 158 μm line integrated intensity compared to the CO emission is expected to be stronger in lower metallicity environments owing to lower dust shielding of the UV radiation, a trend that is also shown by spectral-unresolved observations. In the commonly assumed clumpy UV-penetrated cloud scenario, the models predict a [C ii] line profile similar to that of CO. However, recent spectral-resolved observations by Herschel/HIFI and SOFIA/GREAT (as well as the observations presented here) show that the velocity resolved line profile of the [C ii] emission is often very different from that of CO lines, indicating a more complex origin of the line emission including the dynamics of the source region. Aims: The Large Magellanic Cloud (LMC) provides an excellent opportunity to study in great detail the physics of the interstellar medium (ISM) in a low-metallicity environment by spatially resolving individual star-forming regions. The aim of our study is to investigate the physical properties of the star-forming ISM in the LMC by separating the origin of the emission lines spatially and spectrally. In this paper, we focus on the spectral characteristics and the origin of the emission lines, and the phases of carbon-bearing species in the N159 star-forming region in the LMC. Methods: We mapped a 4' × (3'-4') region in N159 in [C ii] 158 μm and [N ii] 205 μm with the GREAT instrument on board SOFIA. We also observed CO(3-2), (4-3), (6-5), 13CO(3-2), and [C i] 3P1-3P0 and 3P2-3P1 with APEX. All spectra are velocity resolved. Results: The emission of all transitions observed shows a large variation in the line profiles across the map and in

  1. Calculation of longitudinal polarizability and second hyperpolarizability of polyacetylene with the coupled perturbed Hartree-Fock/Kohn-Sham scheme: where it is shown how finite oligomer chains tend to the infinite periodic polymer.

    PubMed

    Lacivita, Valentina; Rèrat, Michel; Orlando, Roberto; Ferrero, Mauro; Dovesi, Roberto

    2012-03-21

    The longitudinal polarizability, α(xx), and second hyperpolarizability, γ(xxxx), of polyacetylene are evaluated by using the coupled perturbed Hartree-Fock/Kohn-Sham (HF/KS) scheme as implemented in the periodic CRYSTAL code and a split valence type basis set. Four different density functionals, namely local density approximation (LDA) (pure local), Perdew-Becke-Ernzerhof (PBE) (gradient corrected), PBE0, and B3LYP (hybrid), and the Hartree-Fock Hamiltonian are compared. It is shown that very tight computational conditions must be used to obtain well converged results, especially for γ(xxxx), that is, very sensitive to the number of k(->) points in reciprocal space when the band gap is small (as for LDA and PBE), and to the extension of summations of the exact exchange series (HF and hybrids). The band gap in LDA is only 0.01 eV: at least 300 k(->) points are required to obtain well converged total energy and equilibrium geometry, and 1200 for well converged optical properties. Also, the exchange series convergence is related to the band gap. The PBE0 band gap is as small as 1.4 eV and the exchange summation must extend to about 130 Å from the origin cell. Total energy, band gap, equilibrium geometry, polarizability, and second hyperpolarizability of oligomers -(C(2)H(2))(m)-, with m up to 50 (202 atoms), and of the polymer have been compared. It turns out that oligomers of that length provide an extremely poor representation of the infinite chain polarizability and hyperpolarizability when the gap is smaller than 0.2 eV (that is, for LDA and PBE). Huge differences are observed on α(xx) and γ(xxxx) of the polymer when different functionals are used, that is in connection to the well-known density functional theory (DFT) overshoot, reported in the literature about short oligomers: for the infinite model the ratio between LDA (or PBE) and HF becomes even more dramatic (about 500 for α(xx) and 10(10) for γ(xxxx)). On the basis of previous systematic

  2. A theoretical characterization of covalency in rare earth complexes through their absorption electronic properties: f-f transitions.

    PubMed

    Petit, Laurence; Borel, Alain; Daul, Claude; Maldivi, Pascale; Adamo, Carlo

    2006-09-04

    Experimental uncertainties concerning the coordination mode of trivalent plutonium in concentrated LiCl have led us to theoretically evaluate the f-f transitions of a series of rare earth aquo and chloro complexes. The calculation of Pr(III), U(III), Np(III), and Pu(III) systems' spectra was undertaken using the LFDFT (ligand field density functional theory) route that combines the backgrounds of ligand field (LF) theory with Kohn-Sham orbitals. LF parameters are fitted to previous DFT calculations, thus preventing the use of empirical data. The f-f transitions values are globally well predicted, but the lack of accurate experimental references can sometimes hinder reliable comparisons. Despite this, the nephelauxetic effect from aquo to chloro complexes is clearly observed through both spectral red shifts and the decrease in F2, the Slater-Condon parameter. Accordingly, this work provides the first theoretical characterization of covalency in trivalent f elements through their electronic spectra.

  3. Tooth Size Variation in Pinniped Dentitions.

    PubMed

    Wolsan, Mieczyslaw; Suzuki, Satoshi; Asahara, Masakazu; Motokawa, Masaharu

    2015-01-01

    It is contentious whether size variation among mammalian teeth is heterogeneous or homogeneous, whether the coefficient of variation is reliable, and whether the standard deviation of log-transformed data and the residual of standard deviation on mean variable size are useful replacements for the coefficient of variation. Most studies of tooth size variation have been on mammals with complex-crowned teeth, with relatively little attention paid to taxa with simple-crowned teeth, such as Pinnipedia. To fill this gap in knowledge and to resolve the existing controversies, we explored the variation of linear size variables (length and width) for all teeth from complete permanent dentitions of four pinniped species, two phocids (Histriophoca fasciata, Phoca largha) and two otariids (Callorhinus ursinus, Eumetopias jubatus). Size variation among these teeth was mostly heterogeneous both along the toothrow and among species. The incisors, canines, and mesial and distal postcanines were often relatively highly variable. The levels of overall dental size variation ranged from relatively low as in land carnivorans (Phoca largha and both otariids) to high (Histriophoca fasciata). Sexual size dimorphism varied among teeth and among species, with teeth being, on average, larger in males than in females. This dimorphism was more pronounced, and the canines were larger and more dimorphic relative to other teeth in the otariids than in the phocids. The coefficient of variation quantified variation reliably in most cases. The standard deviation of log-transformed data was redundant with the coefficient of variation. The residual of standard deviation on mean variable size was inaccurate when size variation was considerably heterogeneous among the compared variables, and was incomparable between species and between sexes. The existing hypotheses invoking developmental fields, occlusal complexity, and the relative timing of tooth formation and sexually dimorphic hormonal activity do

  4. Tooth Size Variation in Pinniped Dentitions

    PubMed Central

    Wolsan, Mieczyslaw; Suzuki, Satoshi; Asahara, Masakazu; Motokawa, Masaharu

    2015-01-01

    It is contentious whether size variation among mammalian teeth is heterogeneous or homogeneous, whether the coefficient of variation is reliable, and whether the standard deviation of log-transformed data and the residual of standard deviation on mean variable size are useful replacements for the coefficient of variation. Most studies of tooth size variation have been on mammals with complex-crowned teeth, with relatively little attention paid to taxa with simple-crowned teeth, such as Pinnipedia. To fill this gap in knowledge and to resolve the existing controversies, we explored the variation of linear size variables (length and width) for all teeth from complete permanent dentitions of four pinniped species, two phocids (Histriophoca fasciata, Phoca largha) and two otariids (Callorhinus ursinus, Eumetopias jubatus). Size variation among these teeth was mostly heterogeneous both along the toothrow and among species. The incisors, canines, and mesial and distal postcanines were often relatively highly variable. The levels of overall dental size variation ranged from relatively low as in land carnivorans (Phoca largha and both otariids) to high (Histriophoca fasciata). Sexual size dimorphism varied among teeth and among species, with teeth being, on average, larger in males than in females. This dimorphism was more pronounced, and the canines were larger and more dimorphic relative to other teeth in the otariids than in the phocids. The coefficient of variation quantified variation reliably in most cases. The standard deviation of log-transformed data was redundant with the coefficient of variation. The residual of standard deviation on mean variable size was inaccurate when size variation was considerably heterogeneous among the compared variables, and was incomparable between species and between sexes. The existing hypotheses invoking developmental fields, occlusal complexity, and the relative timing of tooth formation and sexually dimorphic hormonal activity do

  5. Taxonomic variation in the Mycobacterium fortuitum third biovariant complex: description of Mycobacterium boenickei sp. nov., Mycobacterium houstonense sp. nov., Mycobacterium neworleansense sp. nov. and Mycobacterium brisbanense sp. nov. and recognition of Mycobacterium porcinum from human clinical isolates.

    PubMed

    Schinsky, Mark F; Morey, Roger E; Steigerwalt, Arnold G; Douglas, Michael P; Wilson, Rebecca W; Floyd, Margaret M; Butler, W Ray; Daneshvar, Maryam I; Brown-Elliott, Barbara A; Wallace, Richard J; McNeil, Michael M; Brenner, Don J; Brown, June M

    2004-09-01

    The Mycobacterium fortuitum third biovariant complex (sorbitol-negative and sorbitol-positive) contains unnamed taxa first characterized in 1991. These organisms can cause respiratory infections, a spectrum of soft tissue and skeletal infections, bacteraemia and disseminated disease. To evaluate this group of organisms, clinical reference isolates and the type strains of M. fortuitum third biovariant complex sorbitol-negative (n = 21), M. fortuitum third biovariant complex sorbitol-positive (n = 3), M. fortuitum (n = 3), Mycobacterium peregrinum (pipemidic acid-susceptible) (n = 1), Mycobacterium porcinum (n = 1), Mycobacterium senegalense (n = 2) and Mycobacterium septicum (n = 1) were characterized by using conventional phenotypic (morphological, physiological and antimicrobial susceptibilities), chemotaxonomic (HPLC and cellular fatty acids) and genotypic [RFLP of the rRNA gene (ribotyping), PCR-RFLP of a 439 bp segment of the 65 kDa hsp gene (PCR restriction analysis) and 16S rRNA gene sequence] analysis, DNA G + C content and DNA-DNA relatedness analyses. The results of these studies indicated that the strains comprised M. porcinum (n = 13), M. septicum (n = 1) and four novel closely related genetic groups within the M. fortuitum third biovariant complex: Mycobacterium boenickei sp. nov. (n = 6), Mycobacterium houstonense sp. nov. (n = 2), Mycobacterium neworleansense sp. nov. (n = 1) and Mycobacterium brisbanense sp. nov. (n = 1), with type strains ATCC 49935T (= W5998T = DSM 44677T), ATCC 49403T (= W5198T = DSM 44676T) ATCC 49404T (= W6705T = DSM 44679T) and ATCC 49938T (= W6743T = DSM 44680T), respectively.

  6. Complex polarization propagator calculations of magnetic circular dichroism spectra

    NASA Astrophysics Data System (ADS)

    Solheim, Harald; Ruud, Kenneth; Coriani, Sonia; Norman, Patrick

    2008-03-01

    It is demonstrated that the employment of the nonlinear complex polarization propagator enables the calculation of the complete magnetic circular dichroism spectra of closed-shell molecules, including at the same time both the so-called Faraday A and B terms. In this approach, the differential absorption of right and left circularly polarized light in the presence of a static magnetic field is determined from the real part of the magnetic field-perturbed electric dipole polarizability. The introduction of the finite lifetimes of the electronically excited states into the theory results in response functions that are well behaved in the entire spectral region, i.e., the divergencies that are found in conventional response theory approaches at the transition energies of the system are not present. The applicability of the approach is demonstrated by calculations of the ultraviolet magnetic circular dichroism spectra of para-benzoquinone, tetrachloro-para-benzoquinone, and cyclopropane. The present results are obtained with the complex polarization propagator approach in conjunction with Kohn-Sham density functional theory and the standard adiabatic density functionals B3LYP, CAM-B3LYP, and BHLYP.

  7. Studies of a Series of [Ni(PR2NPh2)2(CH3CN)]2+ Complexes as Electrocatalysts for H2 Production: Substituent Variation at the Phosphorus Atom of the P2N2 Ligand

    SciTech Connect

    Kilgore, Uriah J.; Stewart, Michael P.; Helm, Monte L.; Dougherty, William G.; Kassel, W. S.; Rakowski DuBois, Mary; DuBois, Daniel L.; Bullock, R. Morris

    2011-11-07

    A series of [Ni(PR2NPh2)2(CH3CN)](BF4)2 complexes containing the cyclic diphosphine ligands (PR2NPh2 = 1,5-diaza-3,7-diphosphacyclooctane; R = benzyl (Bn), n-butyl (n-Bu), 2-phenylethyl (PE), 2,4,4-trimethylpentyl (TP), and cyclohexyl (Cy)) have been synthesized and characterized. X-ray diffraction studies reveal that the cations of [Ni(PBn2NPh2)2(CH3CN)](BF4)2 and [Ni(Pn-Bu2NPh2)2(CH3CN)](BF4)2 have distorted trigonal bipyramidal geometries. The Ni(0) complex [Ni(PBn2NPh2)2 (CH3CN)] was also synthesized and characterized by X-ray diffraction studies and shown to have a distorted tetrahedral structure. These complexes, with the exception of [Ni(PCy2NPh2)2(CH3CN)](BF4)2, all exhibit reversible electron transfer processes for both the Ni(II/I) and Ni(I/0) couples and are electrocatalysts for the production of H2 in acidic acetonitrile solutions. The heterolytic cleavage of H2 by [Ni(PR2NPh2)2(CH3CN)](BF4)2 complexes in the presence of p-anisidine or p-bromoaniline was used to determine the hydride donor abilities of the corresponding [HNi(PR2NPh2)2](BF4) complexes. However, the failure to observe a strong correlation between the turnover frequencies for H2 production and the hydride donor abilities, along with structural features of [Ni(PBn2NPh2)2(CH3CN)], suggest that steric interactions between the alkyl substituents on phosphorus and the nitrogen atom of the pendant amines play an important role in determining the overall catalytic rate. This material is based upon work supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences.

  8. Complex virial theorem and complex scaling

    SciTech Connect

    Junker, B.R.

    1983-06-01

    We present the simple generalization to complex energies of the normal global real scaling used for bound-state calculations to produce a variational energy which satisfies the virial theorem. We show that in two limiting cases, one or the other of which is almost always p satisfied in all calculations, the virially stabilized complex energy is sensitive to only the real part or the imaginary part of the complex virial expression. We then compute the virial expression for a number of wave functions for the 1s2s/sup 2/ /sup 2/S He/sup -/, 1s2s2p /sup 2/P/sup o/ He/sup -/, and 1s/sup 2/2s/sup 2/kp /sup 2/P/sup o/ Be/sup -/ resonances and the corresponding virially stabilized resonance energies. In all calculations one of the limiting cases was applicable.

  9. Adaptive major histocompatibility complex (MHC) and neutral genetic variation in two native Baltic Sea fishes (perch Perca fluviatilis and zander Sander lucioperca) with comparisons to an introduced and disease susceptible population in Australia (P. fluviatilis): assessing the risk of disease epidemics.

    PubMed

    Faulks, L K; Östman, Ö

    2016-04-01

    This study assessed the major histocompatibility complex (MHC) and neutral genetic variation and structure in two percid species, perch Perca fluviatilis and zander Sander lucioperca, in a unique brackish ecosystem, the Baltic Sea. In addition, to assess the importance of MHC diversity to disease susceptibility in these populations, comparisons were made to an introduced, disease susceptible, P. fluviatilis population in Australia. Eighty-three MHC class II B exon 2 variants were amplified: 71 variants from 92 P. fluviatilis samples, and 12 variants from 82 S. lucioperca samples. Microsatellite and MHC data revealed strong spatial genetic structure in S. lucioperca, but not P. fluviatilis, across the Baltic Sea. Both microsatellite and MHC data showed higher levels of genetic diversity in P. fluviatilis from the Baltic Sea compared to Australia, which may have facilitated the spread of an endemic virus, EHNV in the Australian population. The relatively high levels of genetic variation in the Baltic Sea populations, together with spatial genetic structure, however, suggest that there currently seems to be little risk of disease epidemics in this system. To ensure this remains the case in the face of ongoing environmental changes, fisheries and habitat disturbance, the conservation of local-scale genetic variation is recommended.

  10. Effects of soluble organic complexants and their degradation products on the removal of selected radionuclides from high-level waste. Part 3, Distributions of Sr, Cs, Tc, Pu, and Am onto 33 absorbers from four variations of a 3:1 dilution of Hanford complexant concentrate (CC) simulant: Part 4, The effects of varying dilution ratios on the distributions of Sr, Cs, Tc, Pu, and Am onto 12 absorbers

    SciTech Connect

    Marsh, S.F.; Svitra, Z.V.; Bowen, S.M.

    1995-09-01

    Many of the radioactive waste storage tanks at USDOE facilities contain organic compounds that have been degraded by radiolysis and chemical reactions during decades of storage. Objective of this study was to measure effects of soluble organic complexants and their degradation products on sorption of Sr, Cs, Tc, Pu and Am onto 33 absorbers that in the absence of these organic compounds offer high sorption of these elements. The elements were in a generic simulant for Hanford complexant concentrate supernate that initially contained six organic complexants: EDTA, HEDTA, NTA, citrate, gluconate, and iminodiacetate. This simulant was tested as prepared and after gamma-irradiation to approximately 34 Mrads. Two other variations consisted of the unirradiated and irradiated simulants after treatment at 450C and 15,000 psi in a hydrothermal organic-destruction process. These experiments were conducted with a 3:1 water-to-simulant dilution of each of the four simulant variations. To determine effects of varying dilution ratios on the sorption of these five elements from the unirradiated and gamma-irradiated simulants that were not treated with the hydrothermal process, we measured their distribution from a 1:1 dilution, using 1 M NaOH as the diluent, onto the 12 best-performing absorbers. We then measured the sorption of these five elements from solutions having diluent-simulant ratios of 0, 0.5, 2.0, and 3.0 onto the three absorbers that performed best for sorbing Sr, Pu and Am from the 1:1 dilution. For each of 900 element/absorber/solution combinations, we measured distribution coefficients (Kd values) twice for each period for dynamic contact periods of 30 min, 2 h, and 6 h to obtain information about absorber stability and sorption kinetics. The 5400 measured Kd values indicate that the sorption of Sr, Pu, and Am is significantly decreased by the organic complexants in these simulant solutions, whereas the sorption of Cs and Tc is much less affected.

  11. Cis-trans isomerism in diphenoxido bridged dicopper complexes: role of crystallized water to stabilize the cis isomer, variation in magnetic properties and conversion of both into a trinuclear species.

    PubMed

    Biswas, Apurba; Drew, Michael G B; Diaz, Carmen; Bauzá, Antonio; Frontera, Antonio; Ghosh, Ashutosh

    2012-10-21

    The trans-[Cu(2)L(2)Cl(2)] (1), and cis-[Cu(2)L(2)Cl(2)]·H(2)O (2) isomers of a diphenoxido bridged Cu(2)O(2) core have been synthesized using a tridentate reduced Schiff base ligand 2-[(2-dimethylamino-ethylamino)-methyl]-phenol. The geometry around Cu(II) is intermediate between square pyramid and trigonal bipyramid (Addison parameter, τ = 0.463) in 1 but nearly square pyramidal (τ = 0.049) in 2. The chloride ions are coordinated to Cu(II) and are trans oriented in 1 but cis oriented in 2. Both isomers have been optimized using density functional theory (DFT) calculations and it is found that the trans isomer is 7.2 kcal mol(-1) more favorable than the cis isomer. However, the hydrogen bonding interaction of crystallized water molecule with chloride ions compensates for the energy difference and stabilizes the cis isomer. Both complexes have been converted to a very rare phenoxido-azido bridged trinuclear species, [Cu(3)L(2)(μ(1,1)-N(3))(2)(H(2)O)(2)(ClO(4))(2)] (3) which has also been characterized structurally. All the complexes are antiferromagnetically coupled but the magnitude of the coupling constants are significantly different (J = -156.60, -652.31, and -31.54 cm(-1) for 1, 2, 3 and respectively). Density functional theory (DFT) calculations have also been performed to gain further insight into the qualitative theoretical interpretation on the overall magnetic behavior of the complexes.

  12. Clinical Interpretation of Genomic Variations

    PubMed Central

    Sayitoğlu, Müge

    2016-01-01

    Novel high-throughput sequencing technologies generate large-scale genomic data and are used extensively for disease mapping of monogenic and/or complex disorders, personalized treatment, and pharmacogenomics. Next-generation sequencing is rapidly becoming routine tool for diagnosis and molecular monitoring of patients to evaluate therapeutic efficiency. The next-generation sequencing platforms generate huge amounts of genetic variation data and it remains a challenge to interpret the variations that are identified. Such data interpretation needs close collaboration among bioinformaticians, clinicians, and geneticists. There are several problems that must be addressed, such as the generation of new algorithms for mapping and annotation, harmonization of the terminology, correct use of nomenclature, reference genomes for different populations, rare disease variant databases, and clinical reports. PMID:27507302

  13. Clinical Interpretation of Genomic Variations.

    PubMed

    Sayitoğlu, Müge

    2016-09-05

    Novel high-throughput sequencing technologies generate large-scale genomic data and are used extensively for disease mapping of monogenic and/or complex disorders, personalized treatment, and pharmacogenomics. Next-generation sequencing is rapidly becoming routine tool for diagnosis and molecular monitoring of patients to evaluate therapeutic efficiency. The next-generation sequencing platforms generate huge amounts of genetic variation data and it remains a challenge to interpret the variations that are identified. Such data interpretation needs close collaboration among bioinformaticians, clinicians, and geneticists. There are several problems that must be addressed, such as the generation of new algorithms for mapping and annotation, harmonization of the terminology, correct use of nomenclature, reference genomes for different populations, rare disease variant databases, and clinical reports.

  14. Association between common variation at the FTO locus and changes in body mass index from infancy to late childhood: the complex nature of genetic association through growth and development.

    PubMed

    Sovio, Ulla; Mook-Kanamori, Dennis O; Warrington, Nicole M; Lawrence, Robert; Briollais, Laurent; Palmer, Colin N A; Cecil, Joanne; Sandling, Johanna K; Syvänen, Ann-Christine; Kaakinen, Marika; Beilin, Lawrie J; Millwood, Iona Y; Bennett, Amanda J; Laitinen, Jaana; Pouta, Anneli; Molitor, John; Davey Smith, George; Ben-Shlomo, Yoav; Jaddoe, Vincent W V; Palmer, Lyle J; Pennell, Craig E; Cole, Tim J; McCarthy, Mark I; Järvelin, Marjo-Riitta; Timpson, Nicholas J

    2011-02-01

    An age-dependent association between variation at the FTO locus and BMI in children has been suggested. We meta-analyzed associations between the FTO locus (rs9939609) and BMI in samples, aged from early infancy to 13 years, from 8 cohorts of European ancestry. We found a positive association between additional minor (A) alleles and BMI from 5.5 years onwards, but an inverse association below age 2.5 years. Modelling median BMI curves for each genotype using the LMS method, we found that carriers of minor alleles showed lower BMI in infancy, earlier adiposity rebound (AR), and higher BMI later in childhood. Differences by allele were consistent with two independent processes: earlier AR equivalent to accelerating developmental age by 2.37% (95% CI 1.87, 2.87, p = 10(-20)) per A allele and a positive age by genotype interaction such that BMI increased faster with age (p = 10(-23)). We also fitted a linear mixed effects model to relate genotype to the BMI curve inflection points adiposity peak (AP) in infancy and AR. Carriage of two minor alleles at rs9939609 was associated with lower BMI at AP (-0.40% (95% CI: -0.74, -0.06), p = 0.02), higher BMI at AR (0.93% (95% CI: 0.22, 1.64), p = 0.01), and earlier AR (-4.72% (-5.81, -3.63), p = 10(-17)), supporting cross-sectional results. Overall, we confirm the expected association between variation at rs9939609 and BMI in childhood, but only after an inverse association between the same variant and BMI in infancy. Patterns are consistent with a shift on the developmental scale, which is reflected in association with the timing of AR rather than just a global increase in BMI. Results provide important information about longitudinal gene effects and about the role of FTO in adiposity. The associated shifts in developmental timing have clinical importance with respect to known relationships between AR and both later-life BMI and metabolic disease risk.

  15. Anatomic variation and orgasm: Could variations in anatomy explain differences in orgasmic success?

    PubMed

    Emhardt, E; Siegel, J; Hoffman, L

    2016-07-01

    Though the public consciousness is typically focused on factors such as psychology, penis size, and the presence of the "G-spot," there are other anatomical and neuro-anatomic differences that could play an equal, or more important, role in the frequency and intensity of orgasms. Discovering these variations could direct further medical or procedural management to improve sexual satisfaction. The aim of this study is to review the available literature of anatomical sexual variation and to explain why this variation may predispose some patients toward a particular sexual experience. In this review, we explored the available literature on sexual anatomy and neuro-anatomy. We used PubMed and OVID Medline for search terms, including orgasm, penile size variation, clitoral variation, Grafenberg spot, and benefits of orgasm. First we review the basic anatomy and innervation of the reproductive organs. Then we describe several anatomical variations that likely play a superior role to popular known variation (penis size, presence of g-spot, etc). For males, the delicate play between the parasympathetic and sympathetic nervous systems is vital to achieve orgasm. For females, the autonomic component is more complex. The clitoris is the primary anatomical feature for female orgasm, including its migration toward the anterior vaginal wall. In conclusions, orgasms are complex phenomena involving psychological, physiological, and anatomic variation. While these variations predispose people to certain sexual function, future research should explore how to surgically or medically alter these. Clin. Anat. 29:665-672, 2016. © 2016 Wiley Periodicals, Inc.

  16. Bovine leukocyte antigen major histocompatibility complex class II DRB3*2703 and DRB3*1501 alleles are associated with variation in levels of protection against Theileria parva challenge following immunization with the sporozoite p67 antigen.

    PubMed

    Ballingall, Keith T; Luyai, Anthony; Rowlands, G John; Sales, Jill; Musoke, Anthony J; Morzaria, Subash P; McKeever, Declan J

    2004-05-01

    Initial laboratory trials of an experimental subunit vaccine against Theileria parva based on the 67-kDa major sporozoite surface antigen revealed a range of responses to challenge. We have analyzed convergence in seven sets of monozygotic twins which suggests that genetic factors may have an influence in determining the degree of protection provided by p67 immunization. In addition, we have examined whether allelic diversity at major histocompatibility complex class II loci influences protection. Analysis of bovine leukocyte antigen DRB3 diversity in 201 animals identified significant associations with vaccine success (DRB3*2703; P = 0.027) and vaccine failure (DRB3*1501; P = 0.013). Furthermore, DRB3*2703 was associated with the likelihood of immunized animals showing little to no clinical signs of disease following challenge. We discuss the acquired and innate immune mechanisms that may be behind the associations described here.

  17. Broken symmetry approach to density functional calculation of magnetic anisotropy or zero field splittings for multinuclear complexes with antiferromagnetic coupling.

    PubMed

    van Wüllen, Christoph

    2009-10-29

    Antiferromagnetic coupling in multinuclear transition metal complexes usually leads to electronic ground states that cannot be described by a single Slater determinant and that are therefore difficult to describe by Kohn-Sham density functional methods. Density functional calculations in such cases are usually converged to broken symmetry solutions which break spin and, in many cases, also spatial symmetry. While a procedure exists to extract isotropic Heisenberg (exchange) coupling constants from such calculations, no such approach is yet established for the calculation of magnetic anisotropy energies or zero field splitting parameters. This work proposes such a procedure. The broken symmetry solutions are not only used to extract the exchange couplings but also single-ion D tensors which are then used to construct a (phenomenological) spin Hamiltonian, from which the magnetic anisotropy and the zero-field energy levels can be computed. The procedure is demonstrated for a bi- and a trinuclear Mn(III) model compound.

  18. Quantum mechanical/molecular mechanical/continuum style solvation model: Linear response theory, variational treatment, and nuclear gradients

    NASA Astrophysics Data System (ADS)

    Li, Hui

    2009-11-01

    Linear response and variational treatment are formulated for Hartree-Fock (HF) and Kohn-Sham density functional theory (DFT) methods and combined discrete-continuum solvation models that incorporate self-consistently induced dipoles and charges. Due to the variational treatment, analytic nuclear gradients can be evaluated efficiently for these discrete and continuum solvation models. The forces and torques on the induced point dipoles and point charges can be evaluated using simple electrostatic formulas as for permanent point dipoles and point charges, in accordance with the electrostatic nature of these methods. Implementation and tests using the effective fragment potential (EFP, a polarizable force field) method and the conductorlike polarizable continuum model (CPCM) show that the nuclear gradients are as accurate as those in the gas phase HF and DFT methods. Using B3LYP/EFP/CPCM and time-dependent-B3LYP/EFP/CPCM methods, acetone S0→S1 excitation in aqueous solution is studied. The results are close to those from full B3LYP/CPCM calculations.

  19. Genetic Variation in Cardiomyopathy and Cardiovascular Disorders.

    PubMed

    McNally, Elizabeth M; Puckelwartz, Megan J

    2015-01-01

    With the wider deployment of massively-parallel, next-generation sequencing, it is now possible to survey human genome data for research and clinical purposes. The reduced cost of producing short-read sequencing has now shifted the burden to data analysis. Analysis of genome sequencing remains challenged by the complexity of the human genome, including redundancy and the repetitive nature of genome elements and the large amount of variation in individual genomes. Public databases of human genome sequences greatly facilitate interpretation of common and rare genetic variation, although linking database sequence information to detailed clinical information is limited by privacy and practical issues. Genetic variation is a rich source of knowledge for cardiovascular disease because many, if not all, cardiovascular disorders are highly heritable. The role of rare genetic variation in predicting risk and complications of cardiovascular diseases has been well established for hypertrophic and dilated cardiomyopathy, where the number of genes that are linked to these disorders is growing. Bolstered by family data, where genetic variants segregate with disease, rare variation can be linked to specific genetic variation that offers profound diagnostic information. Understanding genetic variation in cardiomyopathy is likely to help stratify forms of heart failure and guide therapy. Ultimately, genetic variation may be amenable to gene correction and gene editing strategies.

  20. Variation of the ground spin state in homo- and hetero-octanuclear copper(II) and nickel(II) double-star complexes with a meso-helicate-type metallacryptand core.

    PubMed

    Pardo, Emilio; Dul, Marie-Claire; Lescouëzec, Rodrigue; Chamoreau, Lise-Marie; Journaux, Yves; Pasán, Jorge; Ruiz-Pérez, Catalina; Julve, Miguel; Lloret, Francesc; Ruiz-García, Rafael; Cano, Joan

    2010-05-28

    Homo- and heterometallic octanuclear complexes of formula Na₂{[Cu₂(mpba)₃][Cu(Me₅dien)]₆}-(ClO₄)₆·12H₂O (1), Na₂{[Cu₂(Mempba)₃][Cu(Me₅dien)]₆}(ClO₄)₆·12H₂O (2), Na₂{[Ni₂(mpba)₃]-[Cu(Me₅dien)]₆}(ClO₄)₆·12H₂O (3), Na₂{[Ni₂(Mempba)₃][Cu(Me₅dien)]₆}(ClO₄)₆·9H₂O (4), {[Ni₂(mpba)₃][Ni(dipn)(H₂O)]₆}(ClO₄)₄·12.5H₂O (5), and {[Ni₂(Mempba)₃][Ni(dipn)-(H₂O)]₆}(ClO₄)₄·12H₂O (6) [mpba = 1,3-phenylenebis(oxamate), Mempba = 4-methyl-1,3-phenylenebis(oxamate), Me₅dien = N,N,N',N'',N''-pentamethyldiethylenetriamine, and dipn = dipropylenetriamine] have been synthesized through the "complex-as-ligand/complex-as-metal" strategy. Single-crystal X-ray diffraction analyses of 1, 3, and 5 show cationic M(II)₂M'(II)₆ entities (M, M' = Cu and Ni) with an overall double-star architecture, which is made up of two oxamato-bridged M(II)M'(II)₃ star units connected through three meta-phenylenediamidate bridges between the two central metal atoms leading to a binuclear metallacryptand core of the meso-helicate-type. Dc magnetic susceptibility data for 1-6 in the temperature range 2-300 K have been analyzed through a "dimer-of-tetramers" model [H = - J(S(1A)·S(3A) + S(1A)·S(4A) + S(1A)·S(5A) + S(2B)·S(6B) + S(2B)·S(7B) + S(2B)·S(8B)) - J'S(1A)·S(2B), with S(1A) = S(2B) = S(M) and S(3A) = S(4A) = S(5A) = S(6B) = S(7B) = S(8B) = S(M')]. The moderate to strong antiferromagnetic coupling between the M(II) and M'(II) ions through the oxamate bridge in 1-6 (-J(Cu-Cu) = 52.0-57.0 cm⁻¹, -J(Ni-Cu) = 39.1-44.7 cm⁻¹, and -J(Ni-Ni) = 26.3-26.6 cm⁻¹) leads to a non-compensation of the ground spin state for the tetranuclear M(II)M'(II)₃ star units [S(A) = S(B) = 3S(M') - S(M) = 1 (1 and 2), 1/2 (3 and 4), and 2 (5 and 6)]. Within the binuclear M(II)₂ meso-helicate cores of 1-4, a moderate to weak antiferromagnetic coupling between the M(II) ions (-J'(Cu-Cu) = 28.0-48.0 cm⁻¹ and -J

  1. Complexity Survey.

    ERIC Educational Resources Information Center

    Gordon, Sandra L.; Anderson, Beth C.

    To determine whether consensus existed among teachers about the complexity of common classroom materials, a survey was administered to 66 pre-service and in-service kindergarten and prekindergarten teachers. Participants were asked to rate 14 common classroom materials as simple, complex, or super-complex. Simple materials have one obvious part,…

  2. Nd, Sr, and O isotopic variations in metaluminous ash-flow tuffs and related volcanic rocks at the Timber Mountain/Oasis Valley Caldera, Complex, SW Nevada: implications for the origin and evolution of large-volume silicic magma bodies

    USGS Publications Warehouse

    Farmer, G.L.; Broxton, D.E.; Warren, R.G.; Pickthorn, W.

    1991-01-01

    Nd, Sr and O isotopic data were obtained from silicic ash-flow tuffs and lavas at the Tertiary age (16-9 Ma) Timber (Mountain/Oasis Valley volcanic center (TMOV) in southern Nevada, to assess models for the origin and evolution of the large-volume silicic magma bodies generated in this region. The large-volume (>900 km3), chemically-zoned, Topopah Spring (TS) and Tiva Canyon (TC) members of the Paintbrush Tuff, and the Rainier Mesa (RM) and Ammonia Tanks (AT) members of the younger Timber Mountain Tuff all have internal Nd and Sr isotopic zonations. In each tuff, high-silica rhyolites have lower initial e{open}Nd values (???1 e{open}Nd unit), higher87Sr/86Sr, and lower Nd and Sr contents, than cocrupted trachytes. The TS, TC, and RM members have similar e{open}Nd values for high-silica rhyolites (-11.7 to -11.2) and trachytes (-10.5 to -10.7), but the younger AT member has a higher e{open}Nd for both compositional types (-10.3 and -9.4). Oxygen isotope data confirm that the TC and AT members were derived from low e{open}Nd magmas. The internal Sr and Nd isotopic variations in each tuff are interpreted to be the result of the incorporation of 20-40% (by mass) wall-rock into magmas that were injected into the upper crust. The low e{open}Nd magmas most likely formed via the incorporation of low ??18O, hydrothermally-altered, wall-rock. Small-volume rhyolite lavas and ash-flow tuffs have similar isotopic characteristics to the large-volume ash-flow tuffs, but lavas erupted from extracaldera vents may have interacted with higher ??18O crustal rocks peripheral to the main magma chamber(s). Andesitic lavas from the 13-14 Ma Wahmonie/Salyer volcanic center southeast of the TMOV have low e{open}Nd (-13.2 to -13.8) and are considered on the basis of textural evidence to be mixtures of basaltic composition magmas and large proportions (70-80%) of anatectic crustal melts. A similar process may have occurred early in the magmatic history of the TMOV. The large-volume rhyolites

  3. Variations in Sexual Behavior.

    ERIC Educational Resources Information Center

    Juhasz, Anne McCreary

    1983-01-01

    Questions are raised about the difficulty of defining normal and atypical sexual behavior. Variations from normalcy that students, parents, and educators are most likely to encounter are discussed. The importance of dealing with variations in ways that are best for the individual and the group is emphasized. (PP)

  4. Total variation regularization with bounded linear variations

    NASA Astrophysics Data System (ADS)

    Makovetskii, Artyom; Voronin, Sergei; Kober, Vitaly

    2016-09-01

    One of the most known techniques for signal denoising is based on total variation regularization (TV regularization). A better understanding of TV regularization is necessary to provide a stronger mathematical justification for using TV minimization in signal processing. In this work, we deal with an intermediate case between one- and two-dimensional cases; that is, a discrete function to be processed is two-dimensional radially symmetric piecewise constant. For this case, the exact solution to the problem can be obtained as follows: first, calculate the average values over rings of the noisy function; second, calculate the shift values and their directions using closed formulae depending on a regularization parameter and structure of rings. Despite the TV regularization is effective for noise removal; it often destroys fine details and thin structures of images. In order to overcome this drawback, we use the TV regularization for signal denoising subject to linear signal variations are bounded.

  5. Complex variations during a caldera-forming Plinian eruption, including precursor deposits, thick pumice fallout, co-ignimbrite breccias and climactic lag breccias: The 184 ka Lower Pumice 1 eruption sequence, Santorini, Greece

    NASA Astrophysics Data System (ADS)

    Simmons, J. M.; Cas, R. A. F.; Druitt, T. H.; Folkes, C. B.

    2016-09-01

    The 184 ka Lower Pumice 1 eruption sequence records a complex history of eruption behaviours denoted by two significant eruptive phases: (1) a minor precursor (LP1-Pc) and (2) a major Plinian phase (LP1-A, B, C). The precursor phase produced 13 small-volume pyroclastic fallout, surge and flow deposits, which record the transition from a dominantly magmatic to a phreatomagmatic eruptive style, and exhibit a normal (dacite to andesitic-dacite) to reverse (andesitic-dacite to dacite) compositional zonation of juvenile pyroclasts in the stratigraphy. Incipient bioturbation and variability in unit thickness and lithology reflect multiple time breaks and highlight the episodic nature of volcanism prior to the main Plinian eruption phase. The Plinian magmatic eruption phase is defined by three major stratigraphic divisions, including a basal pumice fallout deposit (LP1-A), an overlying valley-confined ignimbrite (LP1-B) and a compositionally zoned (rhyodacite to basaltic andesite) lithic-rich lag breccia (LP1-C), which caps the sequence. This sequence records the initial development of a buoyant convective eruption column and the transition to eruption column and catastrophic late-stage caldera collapse events. Similarities in pyroclast properties (i.e., chemistry, density), between the Plinian fallout (LP1-A) and pyroclastic flow (LP1-B) deposits, indicate that changes in magma properties exerted no influence on the dynamics and temporal evolution of the LP1 eruption. Conversely, lithic breccias at the base of the LP1-B ignimbrite suggest that the transition from a buoyant convective column to column collapse was facilitated by mechanical erosion of the conduit system and/or the initiation of caldera collapse, leading to vent widening, an increase in magma discharge rate and the increased incorporation of lithics into the eruption column, causing mass overload. Lithic-rich lag breccia deposits (LP1-C), which cap the eruption sequence, record incremental, high

  6. Density Functional Theory: Toward Better Understanding of Complex Systems in Chemistry and Physics

    NASA Astrophysics Data System (ADS)

    Luo, Sijie

    Density functional theory (DFT) has become the workhorse of computational chemistry and physics in the past two decades. The continuous developments of high-quality exchange-correlation functionals (xcFs) have enabled chemists and physicists to study complex as well as large systems with high accuracy at low-to-moderate computational expense. Although a wide range of normal systems have been well understood by DFT, there are still complex ones presenting particular challenges where most commonly used xcFs have failed due to the complex nature of the system, lack of or difficulty to obtain reliable reference data, or the practical limitations of the Kohn-Sham DFT (KS-DFT) formulation. This thesis presents studies with various exchange-correlation functionals on a wide selection of complex systems in chemistry and solid-state physics, including large organic molecules, adsorption on metallic surfaces, transition states, as well as transition metal atoms, ions, and compounds, to (i) draw conclusions upon recommendations of xcFs for important practical applications; (ii) understand the root of errors to help design better xcFs or propose new theoretical schemes of DFT; (iii) explore the utility of noncollinear spin orbitals in KS-DFT for better description of multi-reference systems.

  7. Atomic dipole polarization in charge-transfer complexes with halogen bonding.

    PubMed

    Bartashevich, E V; Tsirelson, V G

    2013-02-21

    The polarization effects associated with halogen bonding for the series of charge-transfer complexes D(m)···X-Y, where donor molecules D(m) = NH(3), H(2)O, H(2)S, C(2)H(4), CO and X-Y = Cl(2), ClF, Br(2), BrCl, ICl, I(2), are characterized in terms of the quantum theory of atoms in molecules using the B3LYP/6-311** Kohn-Sham wave functions. We study the electrostatic potential features of separate donor and acceptor molecules, the change in atomic charges as well as the atomic electric dipole moments and their components, and the intra-atomic electron density dipole polarization and the bonding dipole moments resulting from the electron density redistribution between the molecules in the charge-transfer complexes. The equation linking the most negative electrostatic potential values in the donor molecules and the most positive values in dihalogen molecules with the stretching force constants was found using two-factor regression. It is demonstrated that the dipole polarization of the acceptor atom mirrors the strength of halogen bonding in complexes in a series of different donors and acceptors. An exponential relationship between the magnitude of the total atomic electric dipole moment of the acceptor atom and the intermolecular stretching force constant is established for weakly bounded complexes.

  8. Multi-objective optimization shapes ecological variation.

    PubMed

    Kaitaniemi, Pekka; Scheiner, Annette; Klemola, Tero; Ruohomäki, Kai

    2012-02-22

    Ecological systems contain a huge amount of quantitative variation between and within species and locations, which makes it difficult to obtain unambiguous verification of theoretical predictions. Ordinary experiments consider just a few explanatory factors and are prone to providing oversimplified answers because they ignore the complexity of the factors that underlie variation. We used multi-objective optimization (MO) for a mechanistic analysis of the potential ecological and evolutionary causes and consequences of variation in the life-history traits of a species of moth. Optimal life-history solutions were sought for environmental conditions where different life stages of the moth were subject to predation and other known fitness-reducing factors in a manner that was dependent on the duration of these life stages and on variable mortality rates. We found that multi-objective optimal solutions to these conditions that the moths regularly experience explained most of the life-history variation within this species. Our results demonstrate that variation can have a causal interpretation even for organisms under steady conditions. The results suggest that weather and species interactions can act as underlying causes of variation, and MO acts as a corresponding adaptive mechanism that maintains variation in the traits of organisms.

  9. Variational Transition State Theory

    SciTech Connect

    Truhlar, Donald G.

    2016-09-29

    This is the final report on a project involving the development and applications of variational transition state theory. This project involved the development of variational transition state theory for gas-phase reactions, including optimized multidimensional tunneling contributions and the application of this theory to gas-phase reactions with a special emphasis on developing reaction rate theory in directions that are important for applications to combustion. The development of variational transition state theory with optimized multidimensional tunneling as a useful computational tool for combustion kinetics involved eight objectives.

  10. Masks: Interpretations and Variations.

    ERIC Educational Resources Information Center

    Basso, Robert

    1990-01-01

    Presents a high school art teacher's views of and experiences with masks. Outlines a maskmaking activity in which students were required to create variations on existing masks. Emphasizes use of experimental materials. Displays examples of student-created masks. (DB)

  11. Human genomic variation

    PubMed Central

    Disotell, Todd R

    2000-01-01

    The recent completion and assembly of the first draft of the human genome, which combines samples from several ethnically diverse males and females, provides preliminary data on the extent of human genetic variation. PMID:11178257

  12. Generalized quasi variational inequalities

    SciTech Connect

    Noor, M.A.

    1996-12-31

    In this paper, we establish the equivalence between the generalized quasi variational inequalities and the generalized implicit Wiener-Hopf equations using essentially the projection technique. This equivalence is used to suggest and analyze a number of new iterative algorithms for solving generalized quasi variational inequalities and the related complementarity problems. The convergence criteria is also considered. The results proved in this paper represent a significant improvement and refinement of the previously known results.

  13. The Schwinger Variational Method

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.

    1995-01-01

    Variational methods have proven invaluable in theoretical physics and chemistry, both for bound state problems and for the study of collision phenomena. For collisional problems they can be grouped into two types: those based on the Schroedinger equation and those based on the Lippmann-Schwinger equation. The application of the Schwinger variational (SV) method to e-molecule collisions and photoionization has been reviewed previously. The present chapter discusses the implementation of the SV method as applied to e-molecule collisions.

  14. Crystallization of macromolecular complexes: combinatorial complex crystallization

    NASA Astrophysics Data System (ADS)

    Stura, Enrico A.; Graille, Marc; Charbonnier, Jean-Baptiste

    2001-11-01

    antigens. We find that such binding involves only the well conserved framework region of the variable domain of the antibody heavy chain (VH) and does not affect the conformation of the hypervariable loops that define the antigen recognition site. Thus this domain could be used to complex to Fab or Fv fragments derived from a wide variety of antibodies. While protein A complexes with the VH domain, protein L recognizes the VL region of immunoglobulins. Our recent study of the interaction between an Fab and a domain of protein L shows that the situation is very similar. Indeed this domain binds to the VL framework region outside the antigen binding site. Since individual domains from each of these three multi-domain proteins bind to well separated and independent locations on immunoglobulins, they can be combined to search for a suitable crystalline lattice. This allows us to propose a combinatorial method as a rational way to exploit antibody complexation for the crystallographic structure determination of proteins that are otherwise difficult to crystallize. The overall method has strong parallels with other combinatorial methods used elsewhere in biology and chemistry, and we propose that together with stoichiometry variation screening (SVS), it may further enhance the probability of crystallization.

  15. Complex derivatives

    NASA Astrophysics Data System (ADS)

    Battiston, Stefano; Caldarelli, Guido; Georg, Co-Pierre; May, Robert; Stiglitz, Joseph

    2013-03-01

    The intrinsic complexity of the financial derivatives market has emerged as both an incentive to engage in it, and a key source of its inherent instability. Regulators now faced with the challenge of taming this beast may find inspiration in the budding science of complex systems.

  16. Designing Complexity

    ERIC Educational Resources Information Center

    Glanville, Ranulph

    2007-01-01

    This article considers the nature of complexity and design, as well as relationships between the two, and suggests that design may have much potential as an approach to improving human performance in situations seen as complex. It is developed against two backgrounds. The first is a world view that derives from second order cybernetics and radical…

  17. Complex odontoma.

    PubMed

    Preetha, A; Balikai, Bharati S; Sujatha, D; Pai, Anuradha; Ganapathy, K S

    2010-01-01

    Odontomas are hamartomatous lesions or malformations composed of mature enamel, dentin, and pulp. They may be compound or complex, depending on the extent of morphodifferentiation or their resemblance to normal teeth. The etiology of odontoma is unknown, although several theories have been proposed. This article describes a case of a large infected complex odontoma in the residual mandibular ridge, resulting in considerable mandibular expansion.

  18. Emerging patterns of epigenomic variation

    PubMed Central

    Milosavljevic, Aleksandar

    2011-01-01

    Fuelled by new sequencing technologies, epigenome mapping projects are revealing epigenomic variation at all levels of biological complexity, from species to cells. Comparisons of methylation profiles among species reveal evolutionary conservation of gene body methylation patterns, pointing to the fundamental role of epigenomes in gene regulation. At the human population level, epigenomic changes provide footprints of the effects of genomic variants within the vast non-protein coding fraction of the genome while comparisons of the epigenomes of parents and their offspring point to quantitative epigenomic parent-of-origin effects confounding classical Mendelian genetics. At the organismal level, comparisons of epigenomes from diverse cell types provide insights into cellular differentiation. Finally, comparisons of epigenomes from monozygotic twins help dissect genetic and environmental influences on human phenotypes and longitudinal comparisons reveal aging-associated epigenomic drift. The development of new bioinformatic frameworks for comparative epigenome analysis is putting epigenome maps within reach of researchers across a wide spectrum of biological disciplines. PMID:21507501

  19. Complexity and synchronization in stochastic chaotic systems

    NASA Astrophysics Data System (ADS)

    Dang, Thai Son; Palit, Sanjay Kumar; Mukherjee, Sayan; Hoang, Thang Manh; Banerjee, Santo

    2016-02-01

    We investigate the complexity of a hyperchaotic dynamical system perturbed by noise and various nonlinear speech and music signals. The complexity is measured by the weighted recurrence entropy of the hyperchaotic and stochastic systems. The synchronization phenomenon between two stochastic systems with complex coupling is also investigated. These criteria are tested on chaotic and perturbed systems by mean conditional recurrence and normalized synchronization error. Numerical results including surface plots, normalized synchronization errors, complexity variations etc show the effectiveness of the proposed analysis.

  20. Variations in Recollection: The Effects of Complexity on Source Recognition

    ERIC Educational Resources Information Center

    Parks, Colleen M.; Murray, Linda J.; Elfman, Kane; Yonelinas, Andrew P.

    2011-01-01

    Whether recollection is a threshold or signal detection process is highly controversial, and the controversy has centered in part on the shape of receiver operating characteristics (ROCs) and z-transformed ROCs (zROCs). U-shaped zROCs observed in tests thought to rely heavily on recollection, such as source memory tests, have provided evidence in…

  1. Variations in cell morphology in the canine cruciate ligament complex.

    PubMed

    Smith, K D; Vaughan-Thomas, A; Spiller, D G; Clegg, P D; Innes, J F; Comerford, E J

    2012-08-01

    Cell morphology may reflect the mechanical environment of tissues and influence tissue physiology and response to injury. Normal cruciate ligaments (CLs) from disease-free stifle joints were harvested from dog breeds with a high (Labrador retriever) and low (Greyhound) risk of cranial cruciate ligament (CCL) rupture. Antibodies against the cytoskeletal components vimentin and alpha tubulin were used to analyse cell morphology; nuclei were stained with 4',6-diamidino-2-phenylindole, and images were collected using conventional and confocal microscopy. Both cranial and caudal CLs contained cells of heterogenous morphologies. Cells were arranged between collagen bundles and frequently had cytoplasmic processes. Some of these processes were long (type A cells), others were shorter, thicker and more branched (type B cells), and some had no processes (type C cells). Processes were frequently shown to contact other cells, extending longitudinally and transversely through the CLs. Cells with longer processes had fusiform nuclei, and those with no processes had rounded nuclei and were more frequent in the mid-substance of both CLs. Cells with long processes were more commonly noted in the CLs of the Greyhound. As contact between cells may facilitate direct communication, variances in cell morphology between breeds at a differing risk of CCL rupture may reflect differences in CL physiology.

  2. Discrete Variational Optimal Control

    NASA Astrophysics Data System (ADS)

    Jiménez, Fernando; Kobilarov, Marin; Martín de Diego, David

    2013-06-01

    This paper develops numerical methods for optimal control of mechanical systems in the Lagrangian setting. It extends the theory of discrete mechanics to enable the solutions of optimal control problems through the discretization of variational principles. The key point is to solve the optimal control problem as a variational integrator of a specially constructed higher dimensional system. The developed framework applies to systems on tangent bundles, Lie groups, and underactuated and nonholonomic systems with symmetries, and can approximate either smooth or discontinuous control inputs. The resulting methods inherit the preservation properties of variational integrators and result in numerically robust and easily implementable algorithms. Several theoretical examples and a practical one, the control of an underwater vehicle, illustrate the application of the proposed approach.

  3. Variation tolerant SoC design

    NASA Astrophysics Data System (ADS)

    Kozhikkottu, Vivek J.

    performance distribution. This task is particularly complex and challenging due to the inter-dependencies between components' execution, indirect effects of shared resources, and interactions between multiple system-level "execution paths". We argue that accurate variation-aware performance analysis requires Monte-Carlo based repeated system execution. Our proposed analysis framework leverages emulation to significantly speedup performance analysis without sacrificing the generality and accuracy achieved by Monte-Carlo based simulations. Our experiments show performance improvements of around 60x compared to state-of-the-art hardware-software co-simulation tools and also underscore the framework's potential to enable variation-aware design and exploration at the system level. Our second contribution addresses the problem of designing variation-tolerant SoCs using recovery based design, a popular circuit design paradigm that addresses variations by eliminating guard-bands and operating circuits at close to "zero margins" while detecting and recovering from timing errors. While previous efforts have demonstrated the potential benefits of recovery based design, we identify several challenges that need to be addressed in order to apply this technique to SoCs. We present a systematic design framework to apply recovery based design at the system level. We propose to partition SoCs into "recovery islands", wherein each recovery island consists of one or more SoC components that can recover independent of the rest of the SoC. We present a variation-aware design methodology that partitions a given SoC into recovery islands and computes the optimal operating points for each island, taking into account the various trade-offs involved. Our experiments demonstrate that the proposed design framework achieves an average of 32% energy savings over conventional worst-case designs, with negligible losses in performance. The third contribution of this thesis introduces disproportionate

  4. Medically Complex Home Care and Caregiver Strain

    ERIC Educational Resources Information Center

    Moorman, Sara M.; Macdonald, Cameron

    2013-01-01

    Purpose of the study: To examine (a) whether the content of caregiving tasks (i.e., nursing vs. personal care) contributes to variation in caregivers' strain and (b) whether the level of complexity of nursing tasks contributes to variation in strain among caregivers providing help with such tasks. Design and methods: The data came from the Cash…

  5. Genomic variation in maize

    SciTech Connect

    Rivin, C.J.

    1990-01-01

    We have endeavored to learn to learn how different DNA sequences and sequence arrangements contribute to genome plasticity in maize. We describe quantitative variation among maize inbred lines for tandemly arrayed and dispersed repeated DNA sequences and gene families, and qualitative variation for sequences homologous to the Mutator family of transposons. The potential of these sequences to undergo unequal crossing over, non-allelic (ectopic) recombination and transposition makes them a source of genome instability. We have found examples of rapid genomic change involving these sequences in F1 hybrids, tissue culture cells and regenerated plants.

  6. Non-differentiable variational principles

    NASA Astrophysics Data System (ADS)

    Cresson, Jacky

    2005-07-01

    We develop a calculus of variations for functionals which are defined on a set of non-differentiable curves. We first extend the classical differential calculus in a quantum calculus, which allows us to define a complex operator, called the scale derivative, which is the non-differentiable analogue of the classical derivative. We then define the notion of extremals for our functionals and obtain a characterization in term of a generalized Euler-Lagrange equation. We finally prove that solutions of the Schrödinger equation can be obtained as extremals of a non-differentiable variational principle, leading to an extended Hamilton's principle of least action for quantum mechanics. We compare this approach with the scale relativity theory of Nottale, which assumes a fractal structure of space-time.Résumé (Principes variationnels non différentiable). Nous développons un calcul des variations pour des fonctionnelles définies sur un ensemble de courbes non différentiables. Pour cela, nous étendons le calcul différentiel classique, en calcul appelé calcul quantique, qui nous permet de définir un opérateur à valeur complexes, appelé dérivée d'échelle, qui est l'analogue non différentiable de la dérivée usuelle. On définit alors la notion d'extremale pour ces fonctionnelles pour lesquelles nous obtenons une caractérisation via une équation d'Euler-Lagrange généralisée. On prouve enfin que les solutions de l'équation de Schrödinger peuvent s'obtenir comme solution d'un problème variationnel non différentiable, étendant ainsi le principe de moindre action de Hamilton au cadre de la mécanique quantique. On discute enfin la connexion entre ce travail et la théorie de la relativité d'échelle développée par Nottale, et qui suppose une structure fractale de l'espace-temps.

  7. Reducing GWAS Complexity

    PubMed Central

    Hazelett, Dennis J.; Conti, David V.; Han, Ying; Al Olama, Ali Amin; Easton, Doug; Eeles, Rosalind A.; Kote-Jarai, Zsofia; Haiman, Christopher A.; Coetzee, Gerhard A.

    2016-01-01

    ABSTRACT Genome-wide association studies (GWAS) have revealed numerous genomic 'hits' associated with complex phenotypes. In most cases these hits, along with surrogate genetic variation as measure by numerous single nucleotide polymorphisms (SNPs) that are in linkage disequilibrium, are not in coding genes making assignment of functionality or causality intractable. Here we propose that fine-mapping along with the matching of risk SNPs at chromatin biofeatures lessen this complexity by reducing the number of candidate functional/causal SNPs. For example, we show here that only on average 2 SNPs per prostate cancer risk locus are likely candidates for functionality/causality; we further propose that this manageable number should be taken forward in mechanistic studies. The candidate SNPs can be looked up for each prostate cancer risk region in 2 recent publications in 20151,2 from our groups. PMID:26771711

  8. Variational transition state theory

    SciTech Connect

    Truhlar, D.G.

    1993-12-01

    This research program involves the development of variational transition state theory (VTST) and semiclassical tunneling methods for the calculation of gas-phase reaction rates and selected applications. The applications are selected for their fundamental interest and/or their relevance to combustion.

  9. Sociolinguistic Variation and Change.

    ERIC Educational Resources Information Center

    Trudgill, Peter

    This book examines linguistic variation and change. Section 1, "Sociohistorical Linguistics," includes: (1) "British Vernacular Dialects in the Formation of American English: The Case of East Anglian 'Do'"; (2) "'Short o' in East Anglia and New England"; and (3) "Sociohistorical Linguistics and Dialect Survival:…

  10. Situational Variation in English.

    ERIC Educational Resources Information Center

    Littlewood, William T.

    1981-01-01

    Presents data which shows, in a systematic and objective way, how the same speaker can express the same meaning in a variety of ways depending upon the social situation. Such data offer the teacher of English a basis for discussing some of the linguistic features involved in this variation. (Author/PJM)

  11. Seasonal Variation in Epidemiology

    ERIC Educational Resources Information Center

    Marrero, Osvaldo

    2013-01-01

    Seasonality analyses are important in medical research. If the incidence of a disease shows a seasonal pattern, then an environmental factor must be considered in its etiology. We discuss a method for the simultaneous analysis of seasonal variation in multiple groups. The nuts and bolts are explained using simple trigonometry, an elementary…

  12. Modeling Behavior and Variation for Crowd Animation

    DTIC Science & Technology

    2009-08-01

    navigation strategies in complex environments. In Proceedings of the 2003 Intl. Confer- ence on Humanoid Robots , October 2003. 4.7.3 [15] Wallace Ching and...generate spatial and temporal variants from a small amount of data. We think of our work as one step towards the problem of motion variation; we...Treuille and his colleagues [102] generate crowd motions by thinking of crowds of agents as particles in a fluid. They model a potential field in

  13. [Circadian variations of performances and basic rhythms].

    PubMed

    Querrioux-Coulombier, G; Rossi, J P

    1995-12-01

    Difficulties with chronopsychology studies include a masking effect of variables, the combination of different rhythms and variations of strategies. An experiment is conducted to analyze the role of circadian variations of elementary processes in the variations of performance for a complex task. Twenty-four subjects solved anagrams and tried to find the rule of anagram construction, during two sessions, at 10 am and 5 pm. Responses were classified in three groups: (a) discovery of the anagram construction rule (R2 responses); (b) resolution of anagram without discovery of rule (R1 responses); (c) failure, no resolution of anagram (R0 responses). During the second session, R2 performances were better at 10 am than at 5 pm. In contrast, R1 performances were better at 5 pm than at 10 am. Rule application was faster at 10 am than at 5 pm. Results are discussed in terms of variations of short-term memory capacity (Folkard and Monk, 1980). Using chronopsychology to analyze the role of elementary processes in a complex task is discussed.

  14. Quantum dynamics in continuum for proton transport II: Variational solvent-solute interface.

    PubMed

    Chen, Duan; Chen, Zhan; Wei, Guo-Wei

    2012-01-01

    Proton transport plays an important role in biological energy transduction and sensory systems. Therefore, it has attracted much attention in biological science and biomedical engineering in the past few decades. The present work proposes a multiscale/multiphysics model for the understanding of the molecular mechanism of proton transport in transmembrane proteins involving continuum, atomic, and quantum descriptions, assisted with the evolution, formation, and visualization of membrane channel surfaces. We describe proton dynamics quantum mechanically via a new density functional theory based on the Boltzmann statistics, while implicitly model numerous solvent molecules as a dielectric continuum to reduce the number of degrees of freedom. The density of all other ions in the solvent is assumed to obey the Boltzmann distribution in a dynamic manner. The impact of protein molecular structure and its charge polarization on the proton transport is considered explicitly at the atomic scale. A variational solute-solvent interface is designed to separate the explicit molecule and implicit solvent regions. We formulate a total free-energy functional to put proton kinetic and potential energies, the free energy of all other ions, and the polar and nonpolar energies of the whole system on an equal footing. The variational principle is employed to derive coupled governing equations for the proton transport system. Generalized Laplace-Beltrami equation, generalized Poisson-Boltzmann equation, and generalized Kohn-Sham equation are obtained from the present variational framework. The variational solvent-solute interface is generated and visualized to facilitate the multiscale discrete/continuum/quantum descriptions. Theoretical formulations for the proton density and conductance are constructed based on fundamental laws of physics. A number of mathematical algorithms, including the Dirichlet-to-Neumann mapping, matched interface and boundary method, Gummel iteration, and Krylov

  15. Human immune system variation

    PubMed Central

    Brodin, Petter; Davis, Mark M.

    2017-01-01

    The human immune system is highly variable between individuals but relatively stable over time within a given person. Recent conceptual and technological advances have enabled systems immunology analyses, which reveal the composition of immune cells and proteins in populations of healthy individuals. The range of variation and some specific influences that shape an individual’s immune system is now becoming clearer. Human immune systems vary as a consequence of heritable and non-heritable influences, but symbiotic and pathogenic microbes and other non-heritable influences explain most of this variation. Understanding when and how such influences shape the human immune system is key for defining metrics of immunological health and understanding the risk of immune-mediated and infectious diseases. PMID:27916977

  16. The Schwinger Variational Method

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.

    1995-01-01

    Variational methods have proven invaluable in theoretical physics and chemistry, both for bound state problems and for the study of collision phenomena. The application of the Schwinger variational (SV) method to e-molecule collisions and molecular photoionization has been reviewed previously. The present chapter discusses the implementation of the SV method as applied to e-molecule collisions. Since this is not a review of cross section data, cross sections are presented only to server as illustrative examples. In the SV method, the correct boundary condition is automatically incorporated through the use of Green's function. Thus SV calculations can employ basis functions with arbitrary boundary conditions. The iterative Schwinger method has been used extensively to study molecular photoionization. For e-molecule collisions, it is used at the static exchange level to study elastic scattering and coupled with the distorted wave approximation to study electronically inelastic scattering.

  17. Amorphic complexity

    NASA Astrophysics Data System (ADS)

    Fuhrmann, G.; Gröger, M.; Jäger, T.

    2016-02-01

    We introduce amorphic complexity as a new topological invariant that measures the complexity of dynamical systems in the regime of zero entropy. Its main purpose is to detect the very onset of disorder in the asymptotic behaviour. For instance, it gives positive value to Denjoy examples on the circle and Sturmian subshifts, while being zero for all isometries and Morse-Smale systems. After discussing basic properties and examples, we show that amorphic complexity and the underlying asymptotic separation numbers can be used to distinguish almost automorphic minimal systems from equicontinuous ones. For symbolic systems, amorphic complexity equals the box dimension of the associated Besicovitch space. In this context, we concentrate on regular Toeplitz flows and give a detailed description of the relation to the scaling behaviour of the densities of the p-skeletons. Finally, we take a look at strange non-chaotic attractors appearing in so-called pinched skew product systems. Continuous-time systems, more general group actions and the application to cut and project quasicrystals will be treated in subsequent work.

  18. Complex interactions

    NASA Astrophysics Data System (ADS)

    de Régules, Sergio

    2016-04-01

    Complexity science - which describes phenomena such as collective and emergent behaviour - is the focus of a new centre where researchers are examining everything from the spread of influenza to what a healthy heartbeat looks like. Sergio de Régules reports.

  19. Complex Clouds

    Atmospheric Science Data Center

    2013-04-16

    ...     View Larger Image The complex structure and beauty of polar clouds are highlighted by these images acquired ... corner, the edge of the Antarctic coastline and some sea ice can be seen through some thin, high cirrus clouds. The right-hand panel ...

  20. Researching Complexity.

    ERIC Educational Resources Information Center

    Sumara, Dennis J.

    2000-01-01

    Discusses what Complexity Theory (presented as a rubric that collects theoretical understandings from a number of domains such as ecology, biology, neurology, and education) suggests about mind, selfhood, intelligence, and practices of reading, and the import of these reconceptualizations to reader-response researchers. Concludes that developing…

  1. The Complexity of One-Step Equations

    ERIC Educational Resources Information Center

    Ngu, Bing

    2014-01-01

    An analysis of one-step equations from a cognitive load theory perspective uncovers variation within one-step equations. The complexity of one-step equations arises from the element interactivity across the operational and relational lines. The higher the number of operational and relational lines, the greater the complexity of the equations.…

  2. Variation, Repetition, And Choice

    PubMed Central

    Abreu-Rodrigues, Josele; Lattal, Kennon A; dos Santos, Cristiano V; Matos, Ricardo A

    2005-01-01

    Experiment 1 investigated the controlling properties of variability contingencies on choice between repeated and variable responding. Pigeons were exposed to concurrent-chains schedules with two alternatives. In the REPEAT alternative, reinforcers in the terminal link depended on a single sequence of four responses. In the VARY alternative, a response sequence in the terminal link was reinforced only if it differed from the n previous sequences (lag criterion). The REPEAT contingency generated low, constant levels of sequence variation whereas the VARY contingency produced levels of sequence variation that increased with the lag criterion. Preference for the REPEAT alternative tended to increase directly with the degree of variation required for reinforcement. Experiment 2 examined the potential confounding effects in Experiment 1 of immediacy of reinforcement by yoking the interreinforcer intervals in the REPEAT alternative to those in the VARY alternative. Again, preference for REPEAT was a function of the lag criterion. Choice between varying and repeating behavior is discussed with respect to obtained behavioral variability, probability of reinforcement, delay of reinforcement, and switching within a sequence. PMID:15828592

  3. Complex chemistry with complex compounds

    NASA Astrophysics Data System (ADS)

    Eichler, Robert; Asai, M.; Brand, H.; Chiera, N. M.; Di Nitto, A.; Dressler, R.; Düllmann, Ch. E.; Even, J.; Fangli, F.; Goetz, M.; Haba, H.; Hartmann, W.; Jäger, E.; Kaji, D.; Kanaya, J.; Kaneya, Y.; Khuyagbaatar, J.; Kindler, B.; Komori, Y.; Kraus, B.; Kratz, J. V.; Krier, J.; Kudou, Y.; Kurz, N.; Miyashita, S.; Morimoto, K.; Morita, K.; Murakami, M.; Nagame, Y.; Ooe, K.; Piguet, D.; Sato, N.; Sato, T. K.; Steiner, J.; Steinegger, P.; Sumita, T.; Takeyama, M.; Tanaka, K.; Tomitsuka, T.; Toyoshima, A.; Tsukada, K.; Türler, A.; Usoltsev, I.; Wakabayashi, Y.; Wang, Y.; Wiehl, N.; Wittwer, Y.; Yakushev, A.; Yamaki, S.; Yano, S.; Yamaki, S.; Qin, Z.

    2016-12-01

    In recent years gas-phase chemical studies assisted by physical pre-separation allowed for the investigation of fragile single molecular species by gas-phase chromatography. The latest success with the heaviest group 6 transactinide seaborgium is highlighted. The formation of a very volatile hexacarbonyl compound Sg(CO)6 was observed similarly to its lighter homologues molybdenum and tungsten. The interactions of these gaseous carbonyl complex compounds with quartz surfaces were investigated by thermochromatography. Second-generation experiments are under way to investigate the intramolecular bond between the central metal atom of the complexes and the ligands addressing the influence of relativistic effects in the heaviest compounds. Our contribution comprises some aspects of the ongoing challenging experiments as well as an outlook towards other interesting compounds related to volatile complex compounds in the gas phase.

  4. Managing Complexity

    SciTech Connect

    Chassin, David P.; Posse, Christian; Malard, Joel M.

    2004-08-01

    Physical analogs have shown considerable promise for understanding the behavior of complex adaptive systems, including macroeconomics, biological systems, social networks, and electric power markets. Many of today’s most challenging technical and policy questions can be reduced to a distributed economic control problem. Indeed, economically-based control of large-scale systems is founded on the conjecture that the price-based regulation (e.g., auctions, markets) results in an optimal allocation of resources and emergent optimal system control. This paper explores the state of the art in the use physical analogs for understanding the behavior of some econophysical systems and to deriving stable and robust control strategies for them. In particular we review and discussion applications of some analytic methods based on the thermodynamic metaphor according to which the interplay between system entropy and conservation laws gives rise to intuitive and governing global properties of complex systems that cannot be otherwise understood.

  5. Seasonal Variation in Human Gut Microbiome Composition

    PubMed Central

    Davenport, Emily R.; Mizrahi-Man, Orna; Michelini, Katelyn; Barreiro, Luis B.; Ober, Carole; Gilad, Yoav

    2014-01-01

    The composition of the human gut microbiome is influenced by many environmental factors. Diet is thought to be one of the most important determinants, though we have limited understanding of the extent to which dietary fluctuations alter variation in the gut microbiome between individuals. In this study, we examined variation in gut microbiome composition between winter and summer over the course of one year in 60 members of a founder population, the Hutterites. Because of their communal lifestyle, Hutterite diets are similar across individuals and remarkably stable throughout the year, with the exception that fresh produce is primarily served during the summer and autumn months. Our data indicate that despite overall gut microbiome stability within individuals over time, there are consistent and significant population-wide shifts in microbiome composition across seasons. We found seasonal differences in both (i) the abundance of particular taxa (false discovery rate <0.05), including highly abundant phyla Bacteroidetes and Firmicutes, and (ii) overall gut microbiome diversity (by Shannon diversity; P = 0.001). It is likely that the dietary fluctuations between seasons with respect to produce availability explain, at least in part, these differences in microbiome composition. For example, high levels of produce containing complex carbohydrates consumed during the summer months might explain increased abundance of Bacteroidetes, which contain complex carbohydrate digesters, and decreased levels of Actinobacteria, which have been negatively correlated to fiber content in food questionnaires. Our observations demonstrate the plastic nature of the human gut microbiome in response to variation in diet. PMID:24618913

  6. Cryptic Genetic Variation in Evolutionary Developmental Genetics.

    PubMed

    Paaby, Annalise B; Gibson, Greg

    2016-06-13

    Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes-processes that cannot be fully observed in continuously varying visible traits.

  7. Cryptic Genetic Variation in Evolutionary Developmental Genetics

    PubMed Central

    Paaby, Annalise B.; Gibson, Greg

    2016-01-01

    Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes—processes that cannot be fully observed in continuously varying visible traits. PMID:27304973

  8. Anisotropic Total Variation Filtering

    SciTech Connect

    Grasmair, Markus; Lenzen, Frank

    2010-12-15

    Total variation regularization and anisotropic filtering have been established as standard methods for image denoising because of their ability to detect and keep prominent edges in the data. Both methods, however, introduce artifacts: In the case of anisotropic filtering, the preservation of edges comes at the cost of the creation of additional structures out of noise; total variation regularization, on the other hand, suffers from the stair-casing effect, which leads to gradual contrast changes in homogeneous objects, especially near curved edges and corners. In order to circumvent these drawbacks, we propose to combine the two regularization techniques. To that end we replace the isotropic TV semi-norm by an anisotropic term that mirrors the directional structure of either the noisy original data or the smoothed image. We provide a detailed existence theory for our regularization method by using the concept of relaxation. The numerical examples concluding the paper show that the proposed introduction of an anisotropy to TV regularization indeed leads to improved denoising: the stair-casing effect is reduced while at the same time the creation of artifacts is suppressed.

  9. Variations in brain DNA

    PubMed Central

    Avila, Jesús; Gómez-Ramos, Alberto; Soriano, Eduardo

    2014-01-01

    It is assumed that DNA sequences are conserved in the diverse cell types present in a multicellular organism like the human being. Thus, in order to compare the sequences in the genome of DNA from different individuals, nucleic acid is commonly isolated from a single tissue. In this regard, blood cells are widely used for this purpose because of their availability. Thus blood DNA has been used to study genetic familiar diseases that affect other tissues and organs, such as the liver, heart, and brain. While this approach is valid for the identification of familial diseases in which mutations are present in parental germinal cells and, therefore, in all the cells of a given organism, it is not suitable to identify sporadic diseases in which mutations might occur in specific somatic cells. This review addresses somatic DNA variations in different tissues or cells (mainly in the brain) of single individuals and discusses whether the dogma of DNA invariance between cell types is indeed correct. We will also discuss how single nucleotide somatic variations arise, focusing on the presence of specific DNA mutations in the brain. PMID:25505410

  10. Harmonically excited orbital variations

    SciTech Connect

    Morgan, T.

    1985-08-06

    Rephrasing the equations of motion for orbital maneuvers in terms of Lagrangian generalized coordinates instead of Newtonian rectangular cartesian coordinates can make certain harmonic terms in the orbital angular momentum vector more readily apparent. In this formulation the equations of motion adopt the form of a damped harmonic oscillator when torques are applied to the orbit in a variationally prescribed manner. The frequencies of the oscillator equation are in some ways unexpected but can nonetheless be exploited through resonant forcing functions to achieve large secular variations in the orbital elements. Two cases are discussed using a circular orbit as the control case: (1) large changes in orbital inclination achieved by harmonic excitation rather than one impulsive velocity change, and (2) periodic and secular changes to the longitude of the ascending node using both stable and unstable excitation strategies. The implications of these equations are also discussed for both artificial satellites and natural satellites. For the former, two utilitarian orbits are suggested, each exploiting a form of harmonic excitation. 5 refs.

  11. Multifunctions of bounded variation

    NASA Astrophysics Data System (ADS)

    Vinter, R. B.

    2016-02-01

    Consider control systems described by a differential equation with a control term or, more generally, by a differential inclusion with velocity set F (t , x). Certain properties of state trajectories can be derived when it is assumed that F (t , x) is merely measurable w.r.t. the time variable t. But sometimes a refined analysis requires the imposition of stronger hypotheses regarding the time dependence. Stronger forms of necessary conditions for minimizing state trajectories can be derived, for example, when F (t , x) is Lipschitz continuous w.r.t. time. It has recently become apparent that significant addition properties of state trajectories can still be derived, when the Lipschitz continuity hypothesis is replaced by the weaker requirement that F (t , x) has bounded variation w.r.t. time. This paper introduces a new concept of multifunctions F (t , x) that have bounded variation w.r.t. time near a given state trajectory, of special relevance to control. We provide an application to sensitivity analysis.

  12. Complex Systems

    PubMed Central

    Goldberger, Ary L.

    2006-01-01

    Physiologic systems in health and disease display an extraordinary range of temporal behaviors and structural patterns that defy understanding based on linear constructs, reductionist strategies, and classical homeostasis. Application of concepts and computational tools derived from the contemporary study of complex systems, including nonlinear dynamics, fractals and “chaos theory,” is having an increasing impact on biology and medicine. This presentation provides a brief overview of an emerging area of biomedical research, including recent applications to cardiopulmonary medicine and chronic obstructive lung disease. PMID:16921107

  13. Toward a computational description of nitrile hydratase: studies of the ground state bonding and spin-dependent energetics of mononuclear, non-heme Fe(III) complexes.

    PubMed

    Chang, Christopher H; Boone, Amy J; Bartlett, Rodney J; Richards, Nigel G J

    2004-01-26

    The metal coordination and spin state of the Fe(III) center in nitrile hydratase (NHase) has stimulated the synthesis of model complexes in efforts to understand the reactivity and spectroscopic properties of the enzyme. We report density functional theory (DFT) calculations on a number of Fe(III) complexes that have been prepared as models of the NHase metal center, together with others having similar ligands but different ground state spin multiplicities. Our results suggest that a DFT description of specific spin configurations in these systems does not suffer from significant amounts of spin contamination. In particular, B3LYP calculations not only reproduce the observed spin state preferences of these Fe(III) complexes but also predict spin-dependent structural properties consistent with those expected on the basis of ligand field models. An analysis of the natural bond orbital (NBO) transformation of the Kohn-Sham wave functions has enabled quantitation of the overall contribution to covalency of ligand-to-metal sigma-donation and pi-donation, and metal-to-ligand pi-back-bonding in these Fe(III) complexes at their BLYP-optimized geometries. Although sulfur ligands are the primary source of covalency in the Fe(III) complexes, our quantitative analysis suggests that hyperbonding between metal-bound nitrogens and an Fe-S bond represents a mechanism by which Fe-N covalency may arise. These studies establish the computational methodology for future theoretical investigations of the NHase Fe(III) center.

  14. [Genomic variation in maize]. Final project report

    SciTech Connect

    Rivin, C.J.

    1991-12-31

    These studies have sought to learn how different DNA sequences and sequence arrangements contribute to genome plasticity in maize. We describe quantitative variation among maize inbred lines for tandemly arrayed and dispersed repeated DNA sequences and gene families, and qualitative variation for sequences homologous to the Mutator family of transposons. The potential of these sequences to undergo unequal crossing over, non-allelic (ectopic) recombination and transposition makes them a source of genome instability. We have found examples of rapid genomic change involving these sequences in Fl hybrids, tissue culture cells and regenerated plants. We describe the repetitive portion of the maize genome as composed primarily of sequences that vary markedly in copy number among different genetic stocks. The most highly variable is the 185 bp repeat associated with the heterochromatic chromosome knobs. Even in lines without visible knobs, there is a considerable quantity of tandemly arrayed repeats. We also found a high degree of variability for the tandemly arrayed 5S and ribosomal DNA repeats. While such variation might be expected as the result of unequal cross-over, we were surprised to find considerable variation among lower copy number, dispersed repeats as well. One highly repeated sequence that showed a complex tandem and dispersed arrangement stood out as showing no detectable variability among the maize lines. In striking contrast to the variability seen between the inbred stocks, individuals within a stock were indistinguishable with regard to their repeated sequence multiplicities.

  15. Meiosis-Driven Genome Variation in Plants

    PubMed Central

    Cai, Xiwen; Xu, Steven S

    2007-01-01

    Meiosis includes two successive divisions of the nucleus with one round of DNA replication and leads to the formation of gametes with half of the chromosomes of the mother cell during sexual reproduction. It provides a cytological basis for gametogenesis and nheritance in eukaryotes. Meiotic cell division is a complex and dynamic process that involves a number of molecular and cellular events, such as DNA and chromosome replication, chromosome pairing, synapsis and recombination, chromosome segregation, and cytokinesis. Meiosis maintains genome stability and integrity over sexual life cycles. On the other hand, meiosis generates genome variations in several ways. Variant meiotic recombination resulting from specific genome structures induces deletions, duplications, and other rearrangements within the genic and non-genic genomic regions and has been considered a major driving force for gene and genome evolution in nature. Meiotic abnormalities in chromosome segregation lead to chromosomally imbalanced gametes and aneuploidy. Meiotic restitution due to failure of the first or second meiotic division gives rise to unreduced gametes, which triggers polyploidization and genome expansion. This paper reviews research regarding meiosis-driven genome variation, including deletion and duplication of genomic regions, aneuploidy, and polyploidization, and discusses the effect of related meiotic events on genome variation and evolution in plants. Knowledge of various meiosis-driven genome variations provides insight into genome evolution and genetic variability in plants and facilitates plant genome research. PMID:18645601

  16. Cosmic Complexity

    NASA Technical Reports Server (NTRS)

    Mather, John C.

    2012-01-01

    What explains the extraordinary complexity of the observed universe, on all scales from quarks to the accelerating universe? My favorite explanation (which I certainty did not invent) ls that the fundamental laws of physics produce natural instability, energy flows, and chaos. Some call the result the Life Force, some note that the Earth is a living system itself (Gaia, a "tough bitch" according to Margulis), and some conclude that the observed complexity requires a supernatural explanation (of which we have many). But my dad was a statistician (of dairy cows) and he told me about cells and genes and evolution and chance when I was very small. So a scientist must look for me explanation of how nature's laws and statistics brought us into conscious existence. And how is that seemll"!gly Improbable events are actually happening a!1 the time? Well, the physicists have countless examples of natural instability, in which energy is released to power change from simplicity to complexity. One of the most common to see is that cooling water vapor below the freezing point produces snowflakes, no two alike, and all complex and beautiful. We see it often so we are not amazed. But physlc!sts have observed so many kinds of these changes from one structure to another (we call them phase transitions) that the Nobel Prize in 1992 could be awarded for understanding the mathematics of their common features. Now for a few examples of how the laws of nature produce the instabilities that lead to our own existence. First, the Big Bang (what an insufficient name!) apparently came from an instability, in which the "false vacuum" eventually decayed into the ordinary vacuum we have today, plus the most fundamental particles we know, the quarks and leptons. So the universe as a whole started with an instability. Then, a great expansion and cooling happened, and the loose quarks, finding themselves unstable too, bound themselves together into today's less elementary particles like protons and

  17. Cosmic Complexity

    NASA Technical Reports Server (NTRS)

    Mather, John C.

    2012-01-01

    What explains the extraordinary complexity of the observed universe, on all scales from quarks to the accelerating universe? My favorite explanation (which I certainty did not invent) ls that the fundamental laws of physics produce natural instability, energy flows, and chaos. Some call the result the Life Force, some note that the Earth is a living system itself (Gaia, a "tough bitch" according to Margulis), and some conclude that the observed complexity requires a supernatural explanation (of which we have many). But my dad was a statistician (of dairy cows) and he told me about cells and genes and evolution and chance when I was very small. So a scientist must look for me explanation of how nature's laws and statistics brought us into conscious existence. And how is that seemll"!gly Improbable events are actually happening a!1 the time? Well, the physicists have countless examples of natural instability, in which energy is released to power change from simplicity to complexity. One of the most common to see is that cooling water vapor below the freezing point produces snowflakes, no two alike, and all complex and beautiful. We see it often so we are not amazed. But physlc!sts have observed so many kinds of these changes from one structure to another (we call them phase transitions) that the Nobel Prize in 1992 could be awarded for understanding the mathematics of their common features. Now for a few examples of how the laws of nature produce the instabilities that lead to our own existence. First, the Big Bang (what an insufficient name!) apparently came from an instability, in which the "false vacuum" eventually decayed into the ordinary vacuum we have today, plus the most fundamental particles we know, the quarks and leptons. So the universe as a whole started with an instability. Then, a great expansion and cooling happened, and the loose quarks, finding themselves unstable too, bound themselves together into today's less elementary particles like protons and

  18. Variations of hybrid damping

    NASA Astrophysics Data System (ADS)

    Lam, Margaretha J.; Inman, Daniel J.; Saunders, William R.

    1998-06-01

    Damping is important to structures and can be achieved through the addition of viscoelastic materials (VEM). The damping of the VEM is enhanced if a constraining layer is attached to the VEM. If this constraining layer is active, the treatment is called active constrained layer damping (ACLD). In the last few years, ACLD has proven to be superior in vibration control to active or passive damping. The active element makes ACLD more effective than passive constrained layer damping. It also provides a fail-safe in case of breakdown of the active element that is not present for purely active control. It is shown that the control effort needed to damp vibration using ACLD can be significantly higher than purely active control. In order to combine the inherent damping of passive control with the effectiveness of the active element, this paper will explore different variations of active, passive and hybrid damping. Some of the variations include: passive constrained layer damping (PCLD) separate from active element but on the same side of beam, PCLD separate from active on the opposite side of the beam, and active element underneath PCLD. The discretized system equations will be obtained using assumed modes method and Lagrange's equation. The damping will be modeled using the Golla-Hughes-McTavish (GHM) method. The optimal placement and size of the active, passive, ACLD and hybrid treatments will be found using different schemes. The issue of overshoot and settling time of the output and control force using LQR will be addressed, as well as the control effort, passive and active vibration suppression, and LQR cost function. It will be shown that the hybrid treatments are capable of greater vibration control for lower control effort for different optimization schemes. 31

  19. An index of floodplain surface complexity

    NASA Astrophysics Data System (ADS)

    Scown, M. W.; Thoms, M. C.; De Jager, N. R.

    2015-04-01

    Floodplain surface topography is an important component of floodplain ecosystems. It is the primary physical template upon which ecosystem processes are acted out. There has been a limited appreciation of floodplain surface complexity because of the traditional focus on temporal variability in floodplains as well as limitations to quantifying spatial complexity. An index of floodplain surface complexity (FSC) is developed in this paper and applied to eight floodplains from different geographic settings. The index is based on the two key indicators of complexity; variability in surface geometry (VSG) and the spatial organization of surface conditions (SOC) and was determined at three sampling scales. Relationships between these measures of spatial complexity and environmental drivers, namely; flow variability (mean daily discharge [Q], the coefficient of variation of daily discharge [QCV], the coefficient of variation of mean annual discharge [QCVAnn], the coefficient of variation of maximum annual discharge [QCVMax]), sediment yield (SY), valley slope (Vs), and floodplain width (Fpw) were examined. FSC, VSG, and SOC varied between the eight floodplains and this was dependent upon sampling scale. All complexity values declined with increasing Fpw in either a power, logarithmic, or exponential function. There was little change in surface complexity with floodplain widths greater than 10 km. VSG was significantly related to SY and no significant relationships were determined between any of the hydrological variables and floodplain surface complexity.

  20. The Power of Natural Variation for Model Organism Biology.

    PubMed

    Gasch, Audrey P; Payseur, Bret A; Pool, John E

    2016-03-01

    Genetic background effects have long been recognized and, in some cases studied, but they are often viewed as a nuisance by molecular biologists. We suggest that genetic variation currently represents a critical frontier for molecular studies. Human genetics has seen a surge of interest in genetic variation and its contributions to disease, but insights into disease mechanisms are difficult since information about gene function is lacking. By contrast, model organism genetics has excelled at revealing molecular mechanisms of cellular processes, but often de-emphasizes genetic variation and its functional consequences. We argue that model organism biology would benefit from incorporating natural variation, both to capture how well laboratory lines exemplify the species they represent and to inform on molecular processes and their variability. Such a synthesis would also greatly expand the relevance of model systems for studies of complex trait variation, including disease.

  1. Ionization and fragmentation of complex molecules studied with a density functional theory based approach

    NASA Astrophysics Data System (ADS)

    Kirchner, Tom

    2013-05-01

    Ion-impact induced ionization and fragmentation of complex molecules have important applications in many branches of science. If the molecule is H2O an obvious topic to address is the radiobiological relevance of these processes, e.g. in the context of hadron therapy, to name just one example. From a more fundamental physics viewpoint ion-molecule collision systems constitute interesting many-body systems, whose analysis poses challenges to both experimentalists and theorists. This talk will describe a theoretical approach to ion-molecule collisions, which is based on density functional theory to describe the nonperturbative electron dynamics. The basis generator method applied in the past successfully to ion-atom collisions is adapted to deal with the multi-center problem one faces when one considers molecular targets. Cross sections for single- and multiple-electron processes (capture and transfer to the continuum) are obtained directly from solving time-dependent Kohn-Sham-type orbital equations and using a Slater determinant based analysis. Fragmentation yields are predicted on the basis of a semi-phenomenological model which uses the calculated cross sections as input. Results will be presented for various ions impacting on water molecules in the energy range of 10-5000 keV/amu and compared with experimental data and previous theoretical calculations where available. First applications of the model to collisions involving CH4 molecules will also be discussed. This work has been supported by SHARCNET and NSERC Canada.

  2. Gene Transposition Causing Natural Variation for Growth in Arabidopsis thaliana

    PubMed Central

    Vlad, Daniela; Rappaport, Fabrice; Simon, Matthieu; Loudet, Olivier

    2010-01-01

    A major challenge in biology is to identify molecular polymorphisms responsible for variation in complex traits of evolutionary and agricultural interest. Using the advantages of Arabidopsis thaliana as a model species, we sought to identify new genes and genetic mechanisms underlying natural variation for shoot growth using quantitative genetic strategies. More quantitative trait loci (QTL) still need be resolved to draw a general picture as to how and where in the pathways adaptation is shaping natural variation and the type of molecular variation involved. Phenotypic variation for shoot growth in the Bur-0 × Col-0 recombinant inbred line set was decomposed into several QTLs. Nearly-isogenic lines generated from the residual heterozygosity segregating among lines revealed an even more complex picture, with major variation controlled by opposite linked loci and masked by the segregation bias due to the defective phenotype of SG3 (Shoot Growth-3), as well as epistasis with SG3i (SG3-interactor). Using principally a fine-mapping strategy, we have identified the underlying gene causing phenotypic variation at SG3: At4g30720 codes for a new chloroplast-located protein essential to ensure a correct electron flow through the photosynthetic chain and, hence, photosynthesis efficiency and normal growth. The SG3/SG3i interaction is the result of a structural polymorphism originating from the duplication of the gene followed by divergent paralogue's loss between parental accessions. Species-wide, our results illustrate the very dynamic rate of duplication/transposition, even over short periods of time, resulting in several divergent—but still functional—combinations of alleles fixed in different backgrounds. In predominantly selfing species like Arabidopsis, this variation remains hidden in wild populations but is potentially revealed when divergent individuals outcross. This work highlights the need for improved tools and algorithms to resolve structural variation

  3. Geometric constrained variational calculus. II: The second variation (Part I)

    NASA Astrophysics Data System (ADS)

    Massa, Enrico; Bruno, Danilo; Luria, Gianvittorio; Pagani, Enrico

    2016-10-01

    Within the geometrical framework developed in [Geometric constrained variational calculus. I: Piecewise smooth extremals, Int. J. Geom. Methods Mod. Phys. 12 (2015) 1550061], the problem of minimality for constrained calculus of variations is analyzed among the class of differentiable curves. A fully covariant representation of the second variation of the action functional, based on a suitable gauge transformation of the Lagrangian, is explicitly worked out. Both necessary and sufficient conditions for minimality are proved, and reinterpreted in terms of Jacobi fields.

  4. Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation.

    PubMed

    Hedrick, Philip W

    2013-09-01

    Adaptive genetic variation has been thought to originate primarily from either new mutation or standing variation. Another potential source of adaptive variation is adaptive variants from other (donor) species that are introgressed into the (recipient) species, termed adaptive introgression. Here, the various attributes of these three potential sources of adaptive variation are compared. For example, the rate of adaptive change is generally thought to be faster from standing variation, slower from mutation and potentially intermediate from adaptive introgression. Additionally, the higher initial frequency of adaptive variation from standing variation and lower initial frequency from mutation might result in a higher probability of fixation of the adaptive variants for standing variation. Adaptive variation from introgression might have higher initial frequency than new adaptive mutations but lower than that from standing variation, again making the impact of adaptive introgression variation potentially intermediate. Adaptive introgressive variants might have multiple changes within a gene and affect multiple loci, an advantage also potentially found for adaptive standing variation but not for new adaptive mutants. The processes that might produce a common variant in two taxa, convergence, trans-species polymorphism from incomplete lineage sorting or from balancing selection and adaptive introgression, are also compared. Finally, potential examples of adaptive introgression in animals, including balancing selection for multiple alleles for major histocompatibility complex (MHC), S and csd genes, pesticide resistance in mice, black colour in wolves and white colour in coyotes, Neanderthal or Denisovan ancestry in humans, mimicry genes in Heliconius butterflies, beak traits in Darwin's finches, yellow skin in chickens and non-native ancestry in an endangered native salamander, are examined.

  5. Spectral-collocation variational integrators

    NASA Astrophysics Data System (ADS)

    Li, Yiqun; Wu, Boying; Leok, Melvin

    2017-03-01

    Spectral methods are a popular choice for constructing numerical approximations for smooth problems, as they can achieve geometric rates of convergence and have a relatively small memory footprint. In this paper, we introduce a general framework to convert a spectral-collocation method into a shooting-based variational integrator for Hamiltonian systems. We also compare the proposed spectral-collocation variational integrators to spectral-collocation methods and Galerkin spectral variational integrators in terms of their ability to reproduce accurate trajectories in configuration and phase space, their ability to conserve momentum and energy, as well as the relative computational efficiency of these methods when applied to some classical Hamiltonian systems. In particular, we note that spectrally-accurate variational integrators, such as the Galerkin spectral variational integrators and the spectral-collocation variational integrators, combine the computational efficiency of spectral methods together with the geometric structure-preserving and long-time structural stability properties of symplectic integrators.

  6. Structure of complexes between aluminum chloride and other chlorides, 2: Alkali-(chloroaluminates). Gaseous complexes

    NASA Technical Reports Server (NTRS)

    Hargittai, M.

    1980-01-01

    The structural chemistry of complexes between aluminum chloride and other metal chlorides is important both for practice and theory. Condensed-phase as well as vapor-phase complexes are of interest. Structural information on such complexes is reviewed. The first emphasis is given to the molten state because of its practical importance. Aluminum chloride forms volatile complexes with other metal chlorides and these vapor-phase complexes are dealt with in the second part. Finally, the variations in molecular shape and geometrical parameters are summarized.

  7. Tailoring the physical properties of Ni-based single-phase equiatomic alloys by modifying the chemical complexity.

    PubMed

    Jin, K; Sales, B C; Stocks, G M; Samolyuk, G D; Daene, M; Weber, W J; Zhang, Y; Bei, H

    2016-02-01

    Equiatomic alloys (e.g. high entropy alloys) have recently attracted considerable interest due to their exceptional properties, which might be closely related to their extreme disorder induced by the chemical complexity. In order to understand the effects of chemical complexity on their fundamental physical properties, a family of (eight) Ni-based, face-center-cubic (FCC), equiatomic alloys, extending from elemental Ni to quinary high entropy alloys, has been synthesized, and their electrical, thermal, and magnetic properties are systematically investigated in the range of 4-300 K by combining experiments with ab initio Korring-Kohn-Rostoker coherent-potential-approximation (KKR-CPA) calculations. The scattering of electrons is significantly increased due to the chemical (especially magnetic) disorder. It has weak correlation with the number of elements but strongly depends on the type of elements. Thermal conductivities of the alloys are largely lower than pure metals, primarily because the high electrical resistivity suppresses the electronic thermal conductivity. The temperature dependence of the electrical and thermal transport properties is further discussed, and the magnetization of five alloys containing three or more elements is measured in magnetic fields up to 4 T.

  8. Tailoring the physical properties of Ni-based single-phase equiatomic alloys by modifying the chemical complexity

    SciTech Connect

    Jin, Ke; Sales, Brian C.; Stocks, George Malcolm; Samolyuk, German D.; Daene, Markus; Weber, William J.; Zhang, Yanwen; Bei, Hongbin

    2016-02-01

    We discovered that equiatomic alloys (e.g. high entropy alloys) have recently attracted considerable interest due to their exceptional properties, which might be closely related to their extreme disorder induced by the chemical complexity. To understand the effects of chemical complexity on their fundamental physical properties, a family of (eight) Ni-based, face-center-cubic (FCC), equiatomic alloys, extending from elemental Ni to quinary high entropy alloys, has been synthesized, and their electrical, thermal, and magnetic properties are systematically investigated in the range of 4–300 K by combining experiments with ab initio Korring-Kohn-Rostoker coherent-potential-approximation (KKR-CPA) calculations. The scattering of electrons is significantly increased due to the chemical (especially magnetic) disorder. It has weak correlation with the number of elements but strongly depends on the type of elements. Thermal conductivities of the alloys are largely lower than pure metals, primarily because the high electrical resistivity suppresses the electronic thermal conductivity. Moreover, the temperature dependence of the electrical and thermal transport properties is further discussed, and the magnetization of five alloys containing three or more elements is measured in magnetic fields up to 4 T.

  9. Tailoring the physical properties of Ni-based single-phase equiatomic alloys by modifying the chemical complexity

    DOE PAGES

    Jin, Ke; Sales, Brian C.; Stocks, George Malcolm; ...

    2016-02-01

    We discovered that equiatomic alloys (e.g. high entropy alloys) have recently attracted considerable interest due to their exceptional properties, which might be closely related to their extreme disorder induced by the chemical complexity. To understand the effects of chemical complexity on their fundamental physical properties, a family of (eight) Ni-based, face-center-cubic (FCC), equiatomic alloys, extending from elemental Ni to quinary high entropy alloys, has been synthesized, and their electrical, thermal, and magnetic properties are systematically investigated in the range of 4–300 K by combining experiments with ab initio Korring-Kohn-Rostoker coherent-potential-approximation (KKR-CPA) calculations. The scattering of electrons is significantly increased duemore » to the chemical (especially magnetic) disorder. It has weak correlation with the number of elements but strongly depends on the type of elements. Thermal conductivities of the alloys are largely lower than pure metals, primarily because the high electrical resistivity suppresses the electronic thermal conductivity. Moreover, the temperature dependence of the electrical and thermal transport properties is further discussed, and the magnetization of five alloys containing three or more elements is measured in magnetic fields up to 4 T.« less

  10. Tailoring the physical properties of Ni-based single-phase equiatomic alloys by modifying the chemical complexity

    NASA Astrophysics Data System (ADS)

    Jin, K.; Sales, B. C.; Stocks, G. M.; Samolyuk, G. D.; Daene, M.; Weber, W. J.; Zhang, Y.; Bei, H.

    2016-02-01

    Equiatomic alloys (e.g. high entropy alloys) have recently attracted considerable interest due to their exceptional properties, which might be closely related to their extreme disorder induced by the chemical complexity. In order to understand the effects of chemical complexity on their fundamental physical properties, a family of (eight) Ni-based, face-center-cubic (FCC), equiatomic alloys, extending from elemental Ni to quinary high entropy alloys, has been synthesized, and their electrical, thermal, and magnetic properties are systematically investigated in the range of 4–300 K by combining experiments with ab initio Korring-Kohn-Rostoker coherent-potential-approximation (KKR-CPA) calculations. The scattering of electrons is significantly increased due to the chemical (especially magnetic) disorder. It has weak correlation with the number of elements but strongly depends on the type of elements. Thermal conductivities of the alloys are largely lower than pure metals, primarily because the high electrical resistivity suppresses the electronic thermal conductivity. The temperature dependence of the electrical and thermal transport properties is further discussed, and the magnetization of five alloys containing three or more elements is measured in magnetic fields up to 4 T.

  11. Electrical properties of complex tungsten bronze ceramics

    NASA Astrophysics Data System (ADS)

    Padhee, R.; Das, Piyush R.

    2014-09-01

    This paper highlights the electrical properties of two new complex tungsten bronze ceramics (K2Pb2Eu2W2Ti4Nb4O30 and K2Pb2Pr2W2Ti4Nb4O30) which were prepared by high temperature mixed oxide method. Variation of impedance parameters with temperature (27-500 °C) and frequency (1 kHz to 5 MHz) shows the grain and grain boundary effects in the samples. The variation of dielectric parameters with frequency is also studied. The ac conductivity variation with temperature clearly exhibits that the materials have thermally activated transport properties of Arrhenius type.

  12. Developmental and Genetic Origins of Murine Long Bone Length Variation

    PubMed Central

    Sanger, Thomas J.; Norgard, Elizabeth A.; Pletscher, L. Susan; Bevilacqua, Michael; Brooks, Victoria R.; Sandell, Linda M.; Cheverud, James M.

    2011-01-01

    If we wish to understand whether development influences the rate or direction of morphological evolution, we must first understand the developmental bases of morphological variation within species. However, quantitative variation in adult morphology is the product of molecular and cellular processes unfolding from embryonic development through juvenile growth to maturity. The Atchley-Hall model provides a useful framework for dissecting complex morphologies into their component parts as a way of determining which developmental processes contribute to variation in adult form. We have examined differences in postnatal allometry and the patterns of genetic correlation between age-specific traits for 10 recombinant inbred strains of mice generated from an intercross of LG/J and SM/J. Long bone length is closely tied to body size, but variation in adult morphology is more closely tied to differences in growth rate between 3 and 5 weeks of age. These analyses show that variation generated during early development is overridden by variation generated later in life. To more precisely determine the cellular processes generating this variation we then examined the cellular dynamics of long bone growth plates at the time of maximum elongation rate differences in the parent strains. Our analyses revealed that variation in long bone length is the result of faster elongation rates of the LG/J stain. The developmental bases for these differences in growth rate involve the rate of cell division and chondrocyte hypertrophy in the growth plate. PMID:21328530

  13. Explorations in Regional Variation: A Variational Pragmatic Perspective

    ERIC Educational Resources Information Center

    Barron, Anne

    2015-01-01

    The present article introduces the Special Issue entitled "A Variational Pragmatic Approach to Regional Variation in Language," a collection of papers which celebrates the work of Klaus P. Schneider (Rheinische Friedrich-Wilhelms-Universität Bonn, Germany) on the occasion of his 60th birthday.

  14. Complexation of Sr in aqueous fluids equilibrated with silicate melts: effect of melt and fluid composition

    NASA Astrophysics Data System (ADS)

    Borchert, Manuela; Wilke, Max; Schmidt, Christian; Kvashnina, Kristina

    2010-05-01

    At crustal conditions, the fluid-melt partitioning of Sr is mainly controlled by the salinity of the fluid and the composition of the melt (Borchert et al., 2010). The data show a sharp increase in the Sr partition coefficient with the alumina saturation index (ASI) to a maximum of 0.3 at an ASI of 1.05. Because fluid-melt partitioning of a given element depends on its complexation in the fluid and its incorporation in the melt, these data imply a change in the Sr speciation at least one of the two phases. For silicate melts, Kohn et al. (1990) found only small changes in the first coordination shell of Sr in a suite of melts with various degrees of polymerization, and argued that incorporation of Sr in the melt should not play a major role in controlling Sr partitioning. For the aqueous fluid, Bai and Koster van Groos (1999) and Webster et al. (1989) suggested a control of the Sr partition coefficient by SrCl2 complexes based on the correlation between partition coefficient and Cl concentration in the fluid after quenching. Both hypotheses cannot explain our partitioning data. Thus, new information on Sr complexation is required. Here, we studied the complexation of Sr in peraluminous or peralkaline melt dissolved in aqueous fluids in-situ at elevated PT conditions using hydrothermal diamond-anvil cells (HDAC) and X-ray absorption near edge structure (XANES) spectroscopy. The starting materials were peraluminous or peralkaline glass and H2O or a chloridic solution. The glass was doped with high concentrations of 5000 or 10000 ppm Sr. We used bulk compositions with 10 to 15 wt.% glass to ensure that the melt was completely dissolved in the fluid at high PT conditions. For qualitative evaluation, we analyzed the starting glasses and various crystalline compounds and standard solutions. The experiments were performed at beamline ID26 at ESRF (Grenoble, France) using a high resolution emission spectrometer and Si(311) monochromator crystals for high resolution and Si

  15. Discovery of rare variants for complex phenotypes.

    PubMed

    Kosmicki, Jack A; Churchhouse, Claire L; Rivas, Manuel A; Neale, Benjamin M

    2016-06-01

    With the rise of sequencing technologies, it is now feasible to assess the role rare variants play in the genetic contribution to complex trait variation. While some of the earlier targeted sequencing studies successfully identified rare variants of large effect, unbiased gene discovery using exome sequencing has experienced limited success for complex traits. Nevertheless, rare variant association studies have demonstrated that rare variants do contribute to phenotypic variability, but sample sizes will likely have to be even larger than those of common variant association studies to be powered for the detection of genes and loci. Large-scale sequencing efforts of tens of thousands of individuals, such as the UK10K Project and aggregation efforts such as the Exome Aggregation Consortium, have made great strides in advancing our knowledge of the landscape of rare variation, but there remain many considerations when studying rare variation in the context of complex traits. We discuss these considerations in this review, presenting a broad range of topics at a high level as an introduction to rare variant analysis in complex traits including the issues of power, study design, sample ascertainment, de novo variation, and statistical testing approaches. Ultimately, as sequencing costs continue to decline, larger sequencing studies will yield clearer insights into the biological consequence of rare mutations and may reveal which genes play a role in the etiology of complex traits.

  16. Anomalous paleointensity variation in the Late Cretaceous

    NASA Astrophysics Data System (ADS)

    Chang, B.; Doh, S.; Yu, Y.; Kim, W.

    2010-12-01

    A successive paleointensity variation of the Late Cretaceous (~73.1 Ma) was obtained from the six consecutive lava flows at Jeon-gok Volcanic Complex (JVC) in Korea. A total of 283 samples were collected vertically from the bottom of the flow exposures. For the paleointensity determination, over 200 samples were subjected to the Thellier-type IZZI method with systematic alteration checks. Seventy-nine samples passed conventional reliable criteria, yielding a success rate of 38.7%. The paleofield carrier was found as a magnetite, based on the thermomagnetic analysis. Additional rock magnetic experiments revealed a predominance of single-domain magnetite with partial contribution from superparamagnetic grains. Temporally, the estimated paleointensities (2.7-51.1 μT) displayed distinctive half-sinusoidal fluctuation. The corresponding virtual axial dipole moments range from 4.7 to 90.1 ZAm2 (Z = 1021). Such enormous paleointensity variation with extremely low to high intensity might indicate the period of the geomagnetic field transition or excursion in the Late Cretaceous. Perhaps this ancient geomagnetic field intensity fluctuation reflects the geomagnetic secular variation in late Cretaceous.

  17. Human structural variation: mechanisms of chromosome rearrangements

    PubMed Central

    Weckselblatt, Brooke; Rudd, M. Katharine

    2015-01-01

    Chromosome structural variation (SV) is a normal part of variation in the human genome, but some classes of SV can cause neurodevelopmental disorders. Analysis of the DNA sequence at SV breakpoints can reveal mutational mechanisms and risk factors for chromosome rearrangement. Large-scale SV breakpoint studies have become possible recently owing to advances in next-generation sequencing (NGS) including whole-genome sequencing (WGS). These findings have shed light on complex forms of SV such as triplications, inverted duplications, insertional translocations, and chromothripsis. Sequence-level breakpoint data resolve SV structure and determine how genes are disrupted, fused, and/or misregulated by breakpoints. Recent improvements in breakpoint sequencing have also revealed non-allelic homologous recombination (NAHR) between paralogous long interspersed nuclear element (LINE) or human endogenous retrovirus (HERV) repeats as a cause of deletions, duplications, and translocations. This review covers the genomic organization of simple and complex constitutional SVs, as well as the molecular mechanisms of their formation. PMID:26209074

  18. Variational extensions of the mean spherical approximation

    NASA Astrophysics Data System (ADS)

    Blum, L.; Ubriaco, M.

    2000-04-01

    In a previous work we have proposed a method to study complex systems with objects of arbitrary size. For certain specific forms of the atomic and molecular interactions, surprisingly simple and accurate theories (The Variational Mean Spherical Scaling Approximation, VMSSA) [(Velazquez, Blum J. Chem. Phys. 110 (1990) 10 931; Blum, Velazquez, J. Quantum Chem. (Theochem), in press)] can be obtained. The basic idea is that if the interactions can be expressed in a rapidly converging sum of (complex) exponentials, then the Ornstein-Zernike equation (OZ) has an analytical solution. This analytical solution is used to construct a robust interpolation scheme, the variation mean spherical scaling approximation (VMSSA). The Helmholtz excess free energy Δ A=Δ E- TΔ S is then written as a function of a scaling matrix Γ. Both the excess energy Δ E( Γ) and the excess entropy Δ S( Γ) will be functionals of Γ. In previous work of this series the form of this functional was found for the two- (Blum, Herrera, Mol. Phys. 96 (1999) 821) and three-exponential closures of the OZ equation (Blum, J. Stat. Phys., submitted for publication). In this paper we extend this to M Yukawas, a complete basis set: We obtain a solution for the one-component case and give a closed-form expression for the MSA excess entropy, which is also the VMSSA entropy.

  19. Variational multiscale models for charge transport

    PubMed Central

    Wei, Guo-Wei; Zheng, Qiong; Chen, Zhan; Xia, Kelin

    2012-01-01

    This work presents a few variational multiscale models for charge transport in complex physical, chemical and biological systems and engineering devices, such as fuel cells, solar cells, battery cells, nanofluidics, transistors and ion channels. An essential ingredient of the present models, introduced in an earlier paper (Bulletin of Mathematical Biology, 72, 1562-1622, 2010), is the use of differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain from the microscopic domain, meanwhile, dynamically couple discrete and continuum descriptions. Our main strategy is to construct the total energy functional of a charge transport system to encompass the polar and nonpolar free energies of solvation, and chemical potential related energy. By using the Euler-Lagrange variation, coupled Laplace-Beltrami and Poisson-Nernst-Planck (LB-PNP) equations are derived. The solution of the LB-PNP equations leads to the minimization of the total free energy, and explicit profiles of electrostatic potential and densities of charge species. To further reduce the computational complexity, the Boltzmann distribution obtained from the Poisson-Boltzmann (PB) equation is utilized to represent the densities of certain charge species so as to avoid the computationally expensive solution of some Nernst-Planck (NP) equations. Consequently, the coupled Laplace-Beltrami and Poisson-Boltzmann-Nernst-Planck (LB-PBNP) equations are proposed for charge transport in heterogeneous systems. A major emphasis of the present formulation is the consistency between equilibrium LB-PB theory and non-equilibrium LB-PNP theory at equilibrium. Another major emphasis is the capability of the reduced LB-PBNP model to fully recover the prediction of the LB-PNP model at non-equilibrium settings. To account for the fluid impact on the charge transport, we derive coupled Laplace-Beltrami, Poisson-Nernst-Planck and Navier-Stokes equations from the variational principle

  20. Stratospheric condensation nuclei variations may relate to solar activity

    NASA Technical Reports Server (NTRS)

    Hofmann, D. J.; Rosen, J. M.

    1982-01-01

    Observations of increases of stratospheric condensation nuclei suggest a photo-initiated sulphuric acid vapour formation process in spring in polar regions. It is proposed that the sulphuric acid rapidly forms condensation nuclei through attachment to negatively charged multi-ion complexes and that the process may be modulated through variations in solar activity.

  1. Higher Education Earnings Premium: Value, Variation, and Trends

    ERIC Educational Resources Information Center

    Baum, Sandy

    2014-01-01

    Much of the current skepticism about the financial payoff of higher education emerges from recent media focus on young college graduates struggling to enter a weak labor market. This brief highlights some of the complexities underlying discussions of the return to the investment in postsecondary education and describes some of the variation in…

  2. Sea level variation

    NASA Technical Reports Server (NTRS)

    Douglas, Bruce C.

    1992-01-01

    Published values for the long-term, global mean sea level rise determined from tide gauge records range from about one to three mm per year. The scatter of the estimates appears to arise largely from the use of data from gauges located at convergent tectonic plate boundaries where changes of land elevation give fictitious sea level trends, and the effects of large interdecadal and longer sea level variations on short (less than 50+ years) or sappy records. In addition, virtually all gauges undergo subsidence or uplift due to isostatic rebound from the last deglaciation at a rate comparable to or greater than the secular rise of sea level. Modeling rebound by the ICE-3G model of Tushingham and Peltier (1990) and avoiding tide gauge records in areas of converging tectonic plates produces a highly consistent set of long sea level records. A global set of 21 such stations in nine oceanic regions with an average record length of 76 years during the period 1880-1980 yields the global sea level rise value 1.8 mm/year +/- 0.1. Greenhouse warming scenarios commonly forecast an additional acceleration of global sea level in the next 5 or 6+ decades in the range 0.1-0.2 mm/yr2. Because of the large power at low frequencies in the sea level spectrum, very long tide gauge records (75 years minimum) have been examined for past apparent sea level acceleration. For the 80-year period 1905-1985, 23 essentially complete tide gauge records in 10 geographic groups are available for analysis. These yielded the apparent global acceleration -0.011 (+/- 0.012) mm/yr2. A larger, less uniform set of 37 records in the same 10 groups with 92 years average length covering the 141 years from 1850-1991 gave 0.001 (+/- 0.008) mm/yr2. Thus there is no evidence for an apparent acceleration in the past 100+ years that is significant either statistically, or in comparison to values associated with global warming. Unfortunately, the large interdecadal fluctuations of sea level severely affect

  3. Variational Derivation of Dissipative Equations

    NASA Astrophysics Data System (ADS)

    Sogo, Kiyoshi

    2017-03-01

    A new variational principle is formulated to derive various dissipative equations. Model equations considered are the damping equation, Bloch equation, diffusion equation, Fokker-Planck equation, Kramers equation and Smoluchowski equation. Each equation and its time reversal equation are simultaneously obtained in our variational principle.

  4. Variational Bounds for Creeping Composites

    NASA Astrophysics Data System (ADS)

    Procházka, Petr

    2010-05-01

    In the paper time dependent variational bounds are derived based on Extended Hashin-Shtrikman variational principles. Direct calculation leads to explicit formulas to be presented in the text. For various mechanical properties easy coding in Excel, say, can be used and verification of accuracy for numerical procedures is available using the derived formulas.

  5. Kohn's localization in disordered fermionic systems with and without interactions

    NASA Astrophysics Data System (ADS)

    Kerala Varma, Vipin; Pilati, Sebastiano

    2015-10-01

    Understanding the metal-insulator transition in disordered many-fermion systems, both with and without interactions, is one of the most challenging and consequential problems in condensed matter physics. In this paper, we address this issue from the perspective of the modern theory of the insulating state (MTIS), which has already proven to be effective for band and Mott insulators in clean systems. First, we consider noninteracting systems with different types of aperiodic external potentials: uncorrelated disorder (one-dimensional Anderson model), deterministic disorder (Aubry-André Hamiltonian and its modification including next-nearest-neighbor hopping), and disorder with long-range correlations (self-affine potential). We show how the many-body localization tensor defined within the MTIS may be used as a powerful probe to discriminate the insulating and the metallic phases, and to locate the transition point. Then, we investigate the effect of weak repulsive interactions in the Aubry-André Hamiltonian, a model which describes a recent cold-atoms experiment. By treating the weak interactions within a mean-field approximation we obtain a linear shift of the transition point towards stronger disorder, providing evidence for delocalization induced by interactions.

  6. Genetics of the dentofacial variation in human malocclusion.

    PubMed

    Moreno Uribe, L M; Miller, S F

    2015-04-01

    Malocclusions affect individuals worldwide, resulting in compromised function and esthetics. Understanding the etiological factors contributing to the variation in dentofacial morphology associated with malocclusions is the key to develop novel treatment approaches. Advances in dentofacial phenotyping, which is the comprehensive characterization of hard and soft tissue variation in the craniofacial complex, together with the acquisition of large-scale genomic data have started to unravel genetic mechanisms underlying facial variation. Knowledge on the genetics of human malocclusion is limited even though results attained thus far are encouraging, with promising opportunities for future research. This review summarizes the most common dentofacial variations associated with malocclusions and reviews the current knowledge of the roles of genes in the development of malocclusions. Lastly, this review will describe ways to advance malocclusion research, following examples from the expanding fields of phenomics and genomic medicine, which aim to better patient outcomes.

  7. Genetics of the dentofacial variation in human malocclusion

    PubMed Central

    Moreno Uribe, L. M.; Miller, S. F.

    2015-01-01

    Malocclusions affect individuals worldwide, resulting in compromised function and esthetics. Understanding the etiological factors contributing to the variation in dentofacial morphology associated with malocclusions is the key to develop novel treatment approaches. Advances in dentofacial phenotyping, which is the comprehensive characterization of hard and soft tissue variation in the craniofacial complex, together with the acquisition of large-scale genomic data have started to unravel genetic mechanisms underlying facial variation. Knowledge on the genetics of human malocclusion is limited even though results attained thus far are encouraging, with promising opportunities for future research. This review summarizes the most common dentofacial variations associated with malocclusions and reviews the current knowledge of the roles of genes in the development of malocclusions. Lastly, this review will describe ways to advance malocclusion research, following examples from the expanding fields of phenomics and genomic medicine, which aim to better patient outcomes. PMID:25865537

  8. Landscape-scale variation in an anthropogenic factor shapes immune gene variation within a wild population.

    PubMed

    Gonzalez-Quevedo, Catalina; Davies, Richard G; Phillips, Karl P; Spurgin, Lewis G; Richardson, David S

    2016-09-01

    Understanding the spatial scale at which selection acts upon adaptive genetic variation in natural populations is fundamental to our understanding of evolutionary ecology, and has important ramifications for conservation. The environmental factors to which individuals of a population are exposed can vary at fine spatial scales, potentially generating localized patterns of adaptation. Here, we compared patterns of neutral and major histocompatibility complex (MHC) variation within an island population of Berthelot's pipit (Anthus berthelotii) to assess whether landscape-level differences in pathogen-mediated selection generate fine-scale spatial structuring in these immune genes. Specifically, we tested for spatial associations between the distribution of avian malaria, and the factors previously shown to influence that distribution, and MHC variation within resident individuals. Although we found no overall genetic structure across the population for either neutral or MHC loci, we did find localized associations between environmental factors and MHC variation. One MHC class I allele (ANBE48) was directly associated with malaria infection risk, while the presence of the ANBE48 and ANBE38 alleles within individuals correlated (positively and negatively, respectively) with distance to the nearest poultry farm, an anthropogenic factor previously shown to be an important determinant of disease distribution in the study population. Our findings highlight the importance of considering small spatial scales when studying the patterns and processes involved in evolution at adaptive loci.

  9. Population genetic variation in gene expression is associated withphenotypic variation in Saccharomyces cerevisiae

    SciTech Connect

    Fay, Justin C.; McCullough, Heather L.; Sniegowski, Paul D.; Eisen, Michael B.

    2004-02-25

    The relationship between genetic variation in gene expression and phenotypic variation observable in nature is not well understood. Identifying how many phenotypes are associated with differences in gene expression and how many gene-expression differences are associated with a phenotype is important to understanding the molecular basis and evolution of complex traits. Results: We compared levels of gene expression among nine natural isolates of Saccharomyces cerevisiae grown either in the presence or absence of copper sulfate. Of the nine strains, two show a reduced growth rate and two others are rust colored in the presence of copper sulfate. We identified 633 genes that show significant differences in expression among strains. Of these genes,20 were correlated with resistance to copper sulfate and 24 were correlated with rust coloration. The function of these genes in combination with their expression pattern suggests the presence of both correlative and causative expression differences. But the majority of differentially expressed genes were not correlated with either phenotype and showed the same expression pattern both in the presence and absence of copper sulfate. To determine whether these expression differences may contribute to phenotypic variation under other environmental conditions, we examined one phenotype, freeze tolerance, predicted by the differential expression of the aquaporin gene AQY2. We found freeze tolerance is associated with the expression of AQY2. Conclusions: Gene expression differences provide substantial insight into the molecular basis of naturally occurring traits and can be used to predict environment dependent phenotypic variation.

  10. Beyond Punnett Squares: Student Word Association and Explanations of Phenotypic Variation through an Integrative Quantitative Genetics Unit Investigating Anthocyanin Inheritance and Expression in "Brassica rapa" Fast Plants

    ERIC Educational Resources Information Center

    Batzli, Janet M.; Smith, Amber R.; Williams, Paul H.; McGee, Seth A.; Dosa, Katalin; Pfammatter, Jesse

    2014-01-01

    Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question "What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev)," we developed a 4-wk unit for an inquiry-based laboratory…

  11. Anatomical Variation of Human Collector Channel Orifices

    PubMed Central

    Bentley, Michael D.; Hann, Cheryl R.; Fautsch, Michael P.

    2016-01-01

    Purpose To examine the anatomical variation of normal human collector channel orifices and their relationship with Schlemm's canal. Methods Ten human anterior segments fixed by immersion or perfusion were dissected radially and further divided by fine dissection into corresponding inner and outer wall segments. The tissues were dehydrated, critical-point dried, sputter coated, and examined by scanning electron microscopy. Images were obtained at magnifications from ×200 to ×10,000. Selected radial collector channel regions were processed for plastic embedding. Results Two classes of collector channel orifices were identified. Simple oval orifices (54.7 ± 4.6–μm diameter) were lined with endothelial cells and most often occurred on a planar region of Schlemm's canal outer wall. Complex orifices (62.7 ± 3.4–μm diameter) were often found associated with septal columns and bridges, and typically covered with flap-like structures (10–40 μm) that extended between the inner and outer wall and over the collector channel orifices. Both simple and complex orifices had complete or partial lip-like rims. In orifices with partial rims, a trough-like groove was often visible on the outer wall surface opposite the lip. Transected septa and inner and outer wall adhesion sites were often found in association with complex collector channel orifices. Conclusions Collector channel orifice structure varied from simple ovals to complex tethered flaps and bridges. Collector channel orifices with complex flaps connect the inner and outer walls of Schlemm's canal, and may serve to enhance and regulate aqueous outflow in these regions. PMID:26975026

  12. Variational formulation of high performance finite elements: Parametrized variational principles

    NASA Technical Reports Server (NTRS)

    Felippa, Carlos A.; Militello, Carmello

    1991-01-01

    High performance elements are simple finite elements constructed to deliver engineering accuracy with coarse arbitrary grids. This is part of a series on the variational basis of high-performance elements, with emphasis on those constructed with the free formulation (FF) and assumed natural strain (ANS) methods. Parametrized variational principles that provide a foundation for the FF and ANS methods, as well as for a combination of both are presented.

  13. Statistical Analysis of Variation in the Human Plasma Proteome

    DOE PAGES

    Corzett, Todd H.; Fodor, Imola K.; Choi, Megan W.; ...

    2010-01-01

    Quantifying the variation in the human plasma proteome is an essential prerequisite for disease-specific biomarker detection. We report here on the longitudinal and individual variation in human plasma characterized by two-dimensional difference gel electrophoresis (2-D DIGE) using plasma samples from eleven healthy subjects collected three times over a two week period. Fixed-effects modeling was used to remove dye and gel variability. Mixed-effects modeling was then used to quantitate the sources of proteomic variation. The subject-to-subject variation represented the largest variance component, while the time-within-subject variation was comparable to the experimental variation found in a previous technical variability study where onemore » human plasma sample was processed eight times in parallel and each was then analyzed by 2-D DIGE in triplicate. Here, 21 protein spots had larger than 50% CV, suggesting that these proteins may not be appropriate as biomarkers and should be carefully scrutinized in future studies. Seventy-eight protein spots showing differential protein levels between different individuals or individual collections were identified by mass spectrometry and further characterized using hierarchical clustering. The results present a first step toward understanding the complexity of longitudinal and individual variation in the human plasma proteome, and provide a baseline for improved biomarker discovery.« less

  14. Chemical Variations Affect Seismic Velocities Less Than Grain Size Variations

    NASA Astrophysics Data System (ADS)

    de Jong, B. H.; Jacobs, M. H.

    2001-12-01

    It is well known that mantle velocities depend on the ``Magnesium number'' of constituent minerals. According to our recently developed equation of state (Jacobs & Oonk, Calphad 24, 133--147, 2000) this speed varies almost linearly between 6.7422 (Mg2SiO4) and 6.0113 (Fe2SiO4) km/sec at 10 GPa and 1500 K, i.e. a velocity contrast of 730 m/sec, the canonical mantle composition at 400 km depth being 52% Mg2SiO4 in accordance with the estimates by Lee et al. (1998). We have shown experimentally elsewhere that grain size variations of isochemical, equal density, holocrystalline alkali disilicates affect acoustic velocities. These vary at room temperature and ambient pressure between 6.6 km/sec (coarse grained) and 7.7 km/sec (fine grained), a difference of 1100 m/sec, i.e. substantially larger than the above mentioned 730 m/sec for chemical variations. Such differences in grain size occur because of variations in time, temperature, transformation (TTT) conditions to which a material is subjected. Thus velocity variations as observed in the mantle do not necessarily reflect current hottter or colder localities or compositional variations. They more likely reflect different TTT conditions with concomitant fabric variation during subduction.

  15. Statistics, Uncertainty, and Transmitted Variation

    SciTech Connect

    Wendelberger, Joanne Roth

    2014-11-05

    The field of Statistics provides methods for modeling and understanding data and making decisions in the presence of uncertainty. When examining response functions, variation present in the input variables will be transmitted via the response function to the output variables. This phenomenon can potentially have significant impacts on the uncertainty associated with results from subsequent analysis. This presentation will examine the concept of transmitted variation, its impact on designed experiments, and a method for identifying and estimating sources of transmitted variation in certain settings.

  16. Elastic electron scattering from formic acid

    SciTech Connect

    Trevisan, Cynthia S.; Orel, Ann E.; Rescigno, Thomas N.

    2006-07-31

    Following our earlier study on the dynamics of low energy electron attachment to formic acid, we report the results of elastic low-energy electron collisions with formic acid. Momentum transfer and angular differential cross sections were obtained by performing fixed-nuclei calculations employing the complex Kohn variational method. We make a brief description of the technique used to account for the polar nature of this polyatomic target and compare our results with available experimental data.

  17. Holding the Words in Our Mouths: Responses to Dialect Variations in Oral Reading

    ERIC Educational Resources Information Center

    Van Duinen, Deborah Vriend; Wilson, Marilyn J.

    2008-01-01

    Deborah Vriend Van Duinen and Marilyn J. Wilson confront normalized notions of "correct" English. They offer suggestions for teaching about marginalized voices and introducing students to the complexities of English dialect variations. (Contains 1 figure.)

  18. FUNCTIONAL IMPLICATION OF MAJOR HISTOCOMPATIBILITY (MH) VARIATION USING AN ESTUARINE FISH POPULATION

    EPA Science Inventory

    Recently, there has been a dramatic expansion of studies of major histocompatibility complex (MHC) variation aimed at discovering functional differences in immunity across wild populations of diverse vertebrate species. Some species with relatively low genetic diversity or under ...

  19. Variational Approach to Molecular Kinetics.

    PubMed

    Nüske, Feliks; Keller, Bettina G; Pérez-Hernández, Guillermo; Mey, Antonia S J S; Noé, Frank

    2014-04-08

    The eigenvalues and eigenvectors of the molecular dynamics propagator (or transfer operator) contain the essential information about the molecular thermodynamics and kinetics. This includes the stationary distribution, the metastable states, and state-to-state transition rates. Here, we present a variational approach for computing these dominant eigenvalues and eigenvectors. This approach is analogous to the variational approach used for computing stationary states in quantum mechanics. A corresponding method of linear variation is formulated. It is shown that the matrices needed for the linear variation method are correlation matrices that can be estimated from simple MD simulations for a given basis set. The method proposed here is thus to first define a basis set able to capture the relevant conformational transitions, then compute the respective correlation matrices, and then to compute their dominant eigenvalues and eigenvectors, thus obtaining the key ingredients of the slow kinetics.

  20. Extensions to total variation denoising

    NASA Astrophysics Data System (ADS)

    Blomgren, Peter; Chan, Tony F.; Mulet, Pep

    1997-10-01

    The total variation denoising method, proposed by Rudin, Osher and Fatermi, 92, is a PDE-based algorithm for edge-preserving noise removal. The images resulting from its application are usually piecewise constant, possibly with a staircase effect at smooth transitions and may contain significantly less fine details than the original non-degraded image. In this paper we present some extensions to this technique that aim to improve the above drawbacks, through redefining the total variation functional or the noise constraints.

  1. Variational integrators for electric circuits

    SciTech Connect

    Ober-Blöbaum, Sina; Tao, Molei; Cheng, Mulin; Owhadi, Houman; Marsden, Jerrold E.

    2013-06-01

    In this contribution, we develop a variational integrator for the simulation of (stochastic and multiscale) electric circuits. When considering the dynamics of an electric circuit, one is faced with three special situations: 1. The system involves external (control) forcing through external (controlled) voltage sources and resistors. 2. The system is constrained via the Kirchhoff current (KCL) and voltage laws (KVL). 3. The Lagrangian is degenerate. Based on a geometric setting, an appropriate variational formulation is presented to model the circuit from which the equations of motion are derived. A time-discrete variational formulation provides an iteration scheme for the simulation of the electric circuit. Dependent on the discretization, the intrinsic degeneracy of the system can be canceled for the discrete variational scheme. In this way, a variational integrator is constructed that gains several advantages compared to standard integration tools for circuits; in particular, a comparison to BDF methods (which are usually the method of choice for the simulation of electric circuits) shows that even for simple LCR circuits, a better energy behavior and frequency spectrum preservation can be observed using the developed variational integrator.

  2. Modified stochastic variational approach to non-Hermitian quantum systems

    NASA Astrophysics Data System (ADS)

    Kraft, Daniel; Plessas, Willibald

    2016-08-01

    The stochastic variational method has proven to be a very efficient and accurate tool to calculate especially bound states of quantum-mechanical few-body systems. It relies on the Rayleigh-Ritz variational principle for minimizing real eigenenergies of Hermitian Hamiltonians. From molecular to atomic, nuclear, and particle physics there is actually a great demand of describing also resonant states to a high degree of reliance. This is especially true with regard to hadron resonances, which have to be treated in a relativistic framework. So far standard methods of dealing with quantum chromodynamics have not yet succeeded in describing hadron resonances in a realistic manner. Resonant states can be handled by non-Hermitian quantum Hamiltonians. These states correspond to poles in the lower half of the unphysical sheet of the complex energy plane and are therefore intimately connected with complex eigenvalues. Consequently the Rayleigh-Ritz variational principle cannot be employed in the usual manner. We have studied alternative selection principles for the choice of test functions to treat resonances along the stochastic variational method. We have found that a stationarity principle for the complex energy eigenvalues provides a viable method for selecting test functions for resonant states in a constructive manner. We discuss several variants thereof and exemplify their practical efficiencies.

  3. Spatial Variation as a Tool for Inferring Temporal Variation and Diagnosing Types of Mechanisms in Ecosystems

    PubMed Central

    Hammond, Matthew P.; Kolasa, Jurek

    2014-01-01

    Ecological processes, like the rise and fall of populations, leave an imprint of their dynamics as a pattern in space. Mining this spatial record for insight into temporal change underlies many applications, including using spatial snapshots to infer trends in communities, rates of species spread across boundaries, likelihood of chaotic dynamics, and proximity to regime shifts. However, these approaches rely on an inherent but undefined link between spatial and temporal variation. We present a quantitative link between a variable’s spatial and temporal variation based on established variance-partitioning techniques, and test it for predictive and diagnostic applications. A strong link existed between spatial and regional temporal variation (estimated as Coefficients of Variation or CV’s) in 136 variables from three aquatic ecosystems. This association suggests a basis for substituting one for the other, either quantitatively or qualitatively, when long time series are lacking. We further show that weak substitution of temporal for spatial CV results from distortion by specific spatiotemporal patterns (e.g., inter-patch synchrony). Where spatial and temporal CV’s do not match, we pinpoint the spatiotemporal causes of deviation in the dynamics of variables and suggest ways that may control for them. In turn, we demonstrate the use of this framework for describing spatiotemporal patterns in multiple ecosystem variables and attributing them to types of mechanisms. Linking spatial and temporal variability makes quantitative the hitherto inexact practice of space-for-time substitution and may thus point to new opportunities for navigating the complex variation of ecosystems. PMID:24586627

  4. Structural and functional impacts of copy number variations on the cattle genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although there have been significant advances in resolving the pattern and nature of single nucleotide polymorphisms (SNPs), similar realizations for larger, more complex forms of genetic variation have just emerged. Several recent publications reveal that copy number variations (CNVs) are common an...

  5. A variational principle for compressible fluid mechanics: Discussion of the multi-dimensional theory

    NASA Technical Reports Server (NTRS)

    Prozan, R. J.

    1982-01-01

    The variational principle for compressible fluid mechanics previously introduced is extended to two dimensional flow. The analysis is stable, exactly conservative, adaptable to coarse or fine grids, and very fast. Solutions for two dimensional problems are included. The excellent behavior and results lend further credence to the variational concept and its applicability to the numerical analysis of complex flow fields.

  6. On State Complexes and Special Cube Complexes

    ERIC Educational Resources Information Center

    Peterson, Valerie J.

    2009-01-01

    This thesis presents the first steps toward a classification of non-positively curved cube complexes called state complexes. A "state complex" is a configuration space for a "reconfigurable system," i.e., an abstract system in which local movements occur in some discrete manner. Reconfigurable systems can be used to describe, for example,…

  7. Diffusion and thermodynamic equilibrium under pressure variations

    NASA Astrophysics Data System (ADS)

    Moulas, Evangelos; Tajčmanová, Lucie; Vrijmoed, Johannes; Podladchikov, Yuri

    2015-04-01

    Pressure is one of the most fundamental variables in mineral thermodynamics. In that respect, pressure-sensitive mineral reactions provide an important constraint on pressure under which the rock was developed. One implicit assumption when interpreting such pressure estimates is that the state-of-stress is close to hydrostatic, homogeneous and that the differential stress is negligible. Recent spectroscopic data from the mineral scale documenting pressure variations do not support this assumption. In addition to observations, mechanical models (numerical and analytical) suggest that rocks can develop and maintain heterogeneous pressure distributions at geological time scales. The recently developed unconventional barometry explains chemical zoning in minerals as a result of a pressure variation. We focus to apply the unconventional barometry in cases where chemical zoning in minerals cannot be explained by sluggish kinetics. In that respect, the unconventional barometry offers an alternative view of the chemical zoning which is consistent with thermodynamic equilibrium. However, to distinguish between a pressure-controlled chemical zoning and a zoning reflecting an incomplete chemical reaction is still challenging, especially for multicomponent systems. In this contribution, different types of chemical zoning are discussed. We investigate plagioclase rims around kyanite from an amphibolitized eclogite from Rhodope Metamorphic Complex (Greece-Bulgaria) as a case study and compare them with similar published textures from the Bohemian Massif. Mineral microstructures and phase equilibrium suggest that both rocks experienced near-isothermal decompression at high (>700C) temperatures. However, several distinct microstructural features suggest the development and/or the decay of mechanically maintained heterogeneous pressure distributions. We discuss our results and interpretations based on phase-equilibrium modeling, unconventional barometry and diffusion modeling under

  8. Copy Number Variation in Schizophrenia in Sweden

    PubMed Central

    Szatkiewicz, Jin P.; O’Dushlaine, Colm; Chen, Guanhua; Chambert, Kimberly; Moran, Jennifer L.; Neale, Benjamin M; Fromer, Menachem; Ruderfer, Douglas; Akterin, Susanne; Bergen, Sarah E; Kähler, Anna; Magnusson, Patrik KE; Kim, Yunjung; Crowley, James J; Rees, Elliott; Kirov, George; O’Donovan, Michael C.; Owen, Michael J.; Walters, James; Scolnick, Edward; Sklar, Pamela; Purcell, Shaun; Hultman, Christina M.; McCarroll, Steven A.; Sullivan, Patrick F.

    2014-01-01

    Schizophrenia is a highly heritable neuropsychiatric disorder of complex genetic etiology. Previous genome-wide surveys have revealed a greater burden of large, rare CNVs in schizophrenia cases and identified multiple rare recurrent CNVs that increase risk of schizophrenia although with incomplete penetrance and pleiotropic effects. Identification of additional recurrent CNVs and biological pathways enriched for schizophrenia CNVs requires greater sample sizes. We conducted a genome-wide survey for CNVs associated with schizophrenia using a Swedish national sample (4,719 cases and 5,917 controls). High-confidence CNV calls were generated using genotyping array intensity data and their effect on risk of schizophrenia was measured. Our data confirm increased burden of large, rare CNVs in schizophrenia cases as well as significant associations for recurrent 16p11.2 duplications, 22q11.2 deletions and 3q29 deletions. We report a novel association for 17q12 duplications (odds ratio=4.16, P=0.018), previously associated with autism and mental retardation but not schizophrenia. Intriguingly, gene set association analyses implicate biological pathways previously associated with schizophrenia through common variation and exome sequencing (calcium channel signaling and binding partners of the fragile X mental retardation protein). We found significantly increased burden of the largest CNVs (>500Kb) in genes present in the post-synaptic density, in genomic regions implicated via schizophrenia genome-wide association studies, and in gene products localized to mitochondria and cytoplasm. Our findings suggest that multiple lines of genomic inquiry – genome-wide screens for CNVs, common variation, and exonic variation – are converging on similar sets of pathways and/or genes. PMID:24776740

  9. Heat transfer variations of bicycle helmets.

    PubMed

    Brühwiler, P A; Buyan, M; Huber, R; Bogerd, C P; Sznitman, J; Graf, S F; Rösgen, T

    2006-09-01

    Bicycle helmets exhibit complex structures so as to combine impact protection with ventilation. A quantitative experimental measure of the state of the art and variations therein is a first step towards establishing principles of bicycle helmet ventilation. A thermal headform mounted in a climate-regulated wind tunnel was used to study the ventilation efficiency of 24 bicycle helmets at two wind speeds. Flow visualization in a water tunnel with a second headform demonstrated the flow patterns involved. The influence of design details such as channel length and vent placement was studied, as well as the impact of hair. Differences in heat transfer among the helmets of up to 30% (scalp) and 10% (face) were observed, with the nude headform showing the highest values. On occasion, a negative role of some vents for forced convection was demonstrated. A weak correlation was found between the projected vent cross-section and heat transfer variations when changing the head tilt angle. A simple analytical model is introduced that facilitates the understanding of forced convection phenomena. A weak correlation between exposed scalp area and heat transfer was deduced. Adding a wig reduces the heat transfer by approximately a factor of 8 in the scalp region and up to one-third for the rest of the head for a selection of the best ventilated helmets. The results suggest that there is significant optimization potential within the basic helmet structure represented in modern bicycle helmets.

  10. Accurate Variational Description of Adiabatic Quantum Optimization

    NASA Astrophysics Data System (ADS)

    Carleo, Giuseppe; Bauer, Bela; Troyer, Matthias

    Adiabatic quantum optimization (AQO) is a quantum computing protocol where a system is driven by a time-dependent Hamiltonian. The initial Hamiltonian has an easily prepared ground-state and the final Hamiltonian encodes some desired optimization problem. An adiabatic time evolution then yields a solution to the optimization problem. Several challenges emerge in the theoretical description of this protocol: on one hand, the exact simulation of quantum dynamics is exponentially complex in the size of the optimization problem. On the other hand, approximate approaches such as tensor network states (TNS) are limited to small instances by the amount of entanglement that can be encoded. I will present here an extension of the time-dependent Variational Monte Carlo approach to problems in AQO. This approach is based on a general class of (Jastrow-Feenberg) entangled states, whose parameters are evolved in time according to a stochastic variational principle. We demonstrate this approach for optimization problems of the Ising spin-glass type. A very good accuracy is achieved when compared to exact time-dependent TNS on small instances. We then apply this approach to larger problems, and discuss the efficiency of the quantum annealing scheme in comparison with its classical counterpart.

  11. Algorithms, complexity, and the sciences

    PubMed Central

    Papadimitriou, Christos

    2014-01-01

    Algorithms, perhaps together with Moore’s law, compose the engine of the information technology revolution, whereas complexity—the antithesis of algorithms—is one of the deepest realms of mathematical investigation. After introducing the basic concepts of algorithms and complexity, and the fundamental complexity classes P (polynomial time) and NP (nondeterministic polynomial time, or search problems), we discuss briefly the P vs. NP problem. We then focus on certain classes between P and NP which capture important phenomena in the social and life sciences, namely the Nash equlibrium and other equilibria in economics and game theory, and certain processes in population genetics and evolution. Finally, an algorithm known as multiplicative weights update (MWU) provides an algorithmic interpretation of the evolution of allele frequencies in a population under sex and weak selection. All three of these equivalences are rife with domain-specific implications: The concept of Nash equilibrium may be less universal—and therefore less compelling—than has been presumed; selection on gene interactions may entail the maintenance of genetic variation for longer periods than selection on single alleles predicts; whereas MWU can be shown to maximize, for each gene, a convex combination of the gene’s cumulative fitness in the population and the entropy of the allele distribution, an insight that may be pertinent to the maintenance of variation in evolution. PMID:25349382

  12. Vocalic Variations in Spanish Verbs

    ERIC Educational Resources Information Center

    Norman, Linda Schwartz; Sanders, Gerald A.

    1977-01-01

    Roots of Spanish verbs exhibit systematic vowel alternations. In traditional accounts of these alternations, the mid simplex nuclei are assumed to be basic, with complex nuclei being derived from them by rule. This paper suggests an alternative analysis assuming that the complex nuclei are more basic than the simplex ones. (CHK)

  13. Visual Complexity and Pictorial Memory: A Fifteen Year Research Perspective.

    ERIC Educational Resources Information Center

    Berry, Louis H.

    For 15 years an ongoing research project at the University of Pittsburgh has focused on the effects of variations in visual complexity and color on the storage and retrieval of visual information by learners. Research has shown that visual materials facilitate instruction, but has not fully delineated the interactions of visual complexity and…

  14. Magma rheology variation in sheet intrusions (Invited)

    NASA Astrophysics Data System (ADS)

    Magee, C.; O'Driscoll, B.; Petronis, M. S.; Stevenson, C.

    2013-12-01

    The rheology of magma fundamentally controls igneous intrusion style as well as the explosivity and type of volcanic eruptions. Importantly, the dynamic interplay between the viscosity of magma and other processes active during intrusion (e.g., crystallisation, magma mixing, assimilation of crystal mushes and/or xenolith entrainment) will likely bear an influence on the temporal variation of magma rheology. Constraining the timing of rheological changes during magma transit therefore plays an important role in understanding the nuances of volcanic systems. However, the rheological evolution of actively emplacing igneous intrusions cannot be directly studied. While significant advances have been made via experimental modelling and analysis of lava flows, how these findings relate to intruding magma remains unclear. This has led to an increasing number of studies that analyse various characteristics of fully crystallised intrusions in an attempt to ';back-out' the rheological conditions governing emplacement. For example, it has long been known that crystallinity affects the rheology and, consequently, the velocity of intruding magma. This means that quantitative textural analysis of crystal populations (e.g., crystal size distribution; CSD) used to elucidate crystallinity at different stages of emplacement can provide insights into magma rheology. Similarly, methods that measure flow-related fabrics (e.g., anisotropy of magnetic susceptibility; AMS) can be used to discern velocity profiles, a potential proxy for the magma rheology. To illustrate these ideas, we present an integrated AMS and petrological study of several sheet intrusions located within the Ardnamurchan Central Complex, NW Scotland. We focus on the entrainment and transport dynamics of gabbroic inclusions that were infiltrated by the host magma upon entrainment. Importantly, groundmass magnetic fabrics within and external to these inclusions are coaxial. This implies that a deviatoric stress was

  15. Complexity and dynamics of topological and community structure in complex networks

    NASA Astrophysics Data System (ADS)

    Berec, Vesna

    2017-01-01

    Complexity is highly susceptible to variations in the network dynamics, reflected on its underlying architecture where topological organization of cohesive subsets into clusters, system's modular structure and resulting hierarchical patterns, are cross-linked with functional dynamics of the system. Here we study connection between hierarchical topological scales of the simplicial complexes and the organization of functional clusters - communities in complex networks. The analysis reveals the full dynamics of different combinatorial structures of q-th-dimensional simplicial complexes and their Laplacian spectra, presenting spectral properties of resulting symmetric and positive semidefinite matrices. The emergence of system's collective behavior from inhomogeneous statistical distribution is induced by hierarchically ordered topological structure, which is mapped to simplicial complex where local interactions between the nodes clustered into subcomplexes generate flow of information that characterizes complexity and dynamics of the full system.

  16. Natural complexity, computational complexity and depth.

    PubMed

    Machta, J

    2011-09-01

    Depth is a complexity measure for natural systems of the kind studied in statistical physics and is defined in terms of computational complexity. Depth quantifies the length of the shortest parallel computation required to construct a typical system state or history starting from simple initial conditions. The properties of depth are discussed and it is compared with other complexity measures. Depth can only be large for systems with embedded computation.

  17. Hotspots for copy number variation in chimpanzees and humans

    PubMed Central

    Perry, George H.; Tchinda, Joelle; McGrath, Sean D.; Zhang, Junjun; Picker, Simon R.; Cáceres, Angela M.; Iafrate, A. John; Tyler-Smith, Chris; Scherer, Stephen W.; Eichler, Evan E.; Stone, Anne C.; Lee, Charles

    2006-01-01

    Copy number variation is surprisingly common among humans and can be involved in phenotypic diversity and variable susceptibility to complex diseases, but little is known of the extent of copy number variation in nonhuman primates. We have used two array-based comparative genomic hybridization platforms to identify a total of 355 copy number variants (CNVs) in the genomes of 20 wild-born chimpanzees (Pan troglodytes) and have compared the identified chimpanzee CNVs to known human CNVs from previous studies. Many CNVs were observed in the corresponding regions in both chimpanzees and humans; especially those CNVs of higher frequency. Strikingly, these loci are enriched 20-fold for ancestral segmental duplications, which may facilitate CNV formation through nonallelic homologous recombination mechanisms. Therefore, some of these regions may be unstable “hotspots” for the genesis of copy number variation, with recurrent duplications and deletions occurring across and within species. PMID:16702545

  18. Molecular Darwinism: the contingency of spontaneous genetic variation.

    PubMed

    Arber, Werner

    2011-01-01

    The availability of spontaneously occurring genetic variants is an important driving force of biological evolution. Largely thanks to experimental investigations by microbial geneticists, we know today that several different molecular mechanisms contribute to the overall genetic variations. These mechanisms can be assigned to three natural strategies to generate genetic variants: 1) local sequence changes, 2) intragenomic reshuffling of DNA segments, and 3) acquisition of a segment of foreign DNA. In these processes, specific gene products are involved in cooperation with different nongenetic elements. Some genetic variations occur fully at random along the DNA filaments, others rather with a statistical reproducibility, although at many possible sites. We have to be aware that evolution in natural ecosystems is of higher complexity than under most laboratory conditions, not at least in view of symbiotic associations and the occurrence of horizontal gene transfer. The encountered contingency of genetic variation can possibly best ensure a long-term persistence of life under steadily changing living conditions.

  19. Ecologically relevant genetic variation from a non-Arabidopsis perspective.

    PubMed

    Karrenberg, Sophie; Widmer, Alex

    2008-04-01

    Ecologically relevant genetic variation occurs in genes harbouring alleles that are adaptive in some environments but not in others. Analysis of this type of genetic variation in model organisms has made substantial progress, and is now being expanded to other species in order to better cover the diversity of plant life. Recent advances in connecting ecological and molecular studies in non-model species have been made with regard to edaphic and climatic adaptation, plant reproduction, life-history parameters and biotic interactions. New research avenues that increase biological complexity and ecological relevance by integrating ecological experiments with population genetic and functional genomic approaches provide new insights into the genetic basis of ecologically relevant variation.

  20. Energy conservation and constants variation.

    NASA Astrophysics Data System (ADS)

    Kraiselburd, L.; Miller Bertolami, M. M.; Sisterna, P.; Vucetich, H.

    If fundamental constants vary, the internal energy of macroscopic bodies should change. This should produce observable effects. It is shown that those effects can produce upper bounds on the variation of much lower than those coming from Eötvös experiments.

  1. Tense Variation in Indirect Speech.

    ERIC Educational Resources Information Center

    Pufahl, Ingrid

    A study of the extent to which the sequence-of-tenses rule (STR) is used in television news reporting in the United States is presented. The study examines which tenses are shifted most frequently and explains the uses and functions of tense variation. It is argued that STR is not always a semantically and pragmatically unmarked form as proposed…

  2. ACS PSF Variations with Temperatures

    NASA Astrophysics Data System (ADS)

    Sahu, Kailash C.; Lallo, Matt; Makidon, Russ

    2007-09-01

    We have used the HST ACS/WFC observations of a Galactic bulge field taken over a continuous interval of 7 days (Prop 9750) to investigate the possible dependence of the ACS focus with the external temperatures. This dataset allows us to investigate possible focus variations over timescales of a few hours to a few days. The engineering data related to the external temperatures for this duration show that the maximum temperature change occurred over the first 1.5 days. Among all the different temperatures recorded, the truss diametric differential and the truss axial temperatures are the only two temperatures which have the same timescale of variation as the PSFwidth variations. The PSF-widths also strongly correlate with these two temperatures during this time interval. We empirically fit the PSF-width variations with these 2 temperature sensor values. This suggests that the focus has a similar dependence, and we recommend that this finding be followed up with the determination of actual focus values to check if the focus values indeed have the same correlation. If so, the temperature data can be useful in estimating the focus values, which can then be used to predict the PSFs to a first order.

  3. Sociocultural Variation in Literacy Achievement

    ERIC Educational Resources Information Center

    Verhoeven, Ludo

    2006-01-01

    The purpose of this study was to describe the variations in literacy achievement among native and non-native upper primary school children (grades three to six) in the Netherlands. Various measures of word decoding, reading literacy and writing skill were collected from 1091 native Dutch children, 753 children with a former Dutch colonial…

  4. Variations of the solar constant

    SciTech Connect

    Sofia, S.

    1981-12-01

    The variations in data received from rocket-borne and balloon-borne instruments are discussed. Indirect techniques to measure and monitor the solar constant are presented. Emphasis is placed on the correlation of data from the Solar Maximum Mission and the Nimbus 7 satellites. Abstracts of individual items from the workshop were prepared separately for the data base.

  5. The Dimensionality of Grammatical Variation

    ERIC Educational Resources Information Center

    Sankoff, David; Cedergren, Henrietta J.

    1976-01-01

    Computer-based multidimensional scaling techniques are used to determine the dimensionality of grammatical variation in three large sets of data: Ross' (1973) Noun Phrase and fake Noun Phrase data; Sankoff's (1974) complementizer "que"-deletion (Montreal French) data; and Cedergren's (1973) syllable-final S-reduction (Panamanian Spanish) data. (DB)

  6. Modeling Natural Variation through Distribution

    ERIC Educational Resources Information Center

    Lehrer, Richard; Schauble, Leona

    2004-01-01

    This design study tracks the development of student thinking about natural variation as late elementary grade students learned about distribution in the context of modeling plant growth at the population level. The data-modeling approach assisted children in coordinating their understanding of particular cases with an evolving notion of data as an…

  7. Head Start Planned Variation Program.

    ERIC Educational Resources Information Center

    Klein, Jenny

    There is little agreement concerning which methods of preschool intervention are most effective. In order to evaluate several approaches to early childhood education, Project Head Start, in conjunction with Project Follow Through, has initiated the Planned Variation program. This year only a pilot project is underway with eight schools…

  8. Mitochondrial Dysfunction may explain symptom variation in Phelan-McDermid Syndrome

    PubMed Central

    Frye, Richard E.; Cox, Devin; Slattery, John; Tippett, Marie; Kahler, Stephen; Granpeesheh, Doreen; Damle, Shirish; Legido, Agustin; Goldenthal, Michael J.

    2016-01-01

    Phelan-McDermid Syndrome (PMS), which is defined by a deletion within 22q13, demonstrates significant phenotypic variation. Given that six mitochondrial genes are located within 22q13, including complex I and IV genes, we hypothesize that mitochondrial complex activity abnormalities may explain phenotypic variation in PMS symptoms. Complex I, II, II + III and IV activity was measured in 51 PMS participants. Caretakers completed questionnaires and provided genetic information through the PMS foundation registry. Complex activity was abnormal in 59% of PMS participants. Abnormalities were found in complex I and IV but not complex II + III and II activity, consistent with disruption of genes within the 22q13 region. However, complex activity abnormalities were not related to specific gene deletions suggesting a “neighboring effect” of regional deletions on adjacent gene expression. A specific combination of symptoms (autism spectrum disorder, developmental regression, failure-to-thrive, exercise intolerance/fatigue) was associated with complex activity abnormalities. 64% of 106 individuals in the PMS foundation registry who did not have complex activity measured also endorsed this pattern of symptoms. These data suggest that mitochondrial abnormalities, specifically abnormalities in complex I and IV activity, may explain some phenotypic variation in PMS individuals. These results point to novel pathophysiology mechanisms and treatment targets for PMS patients. PMID:26822410

  9. Mitochondrial DNA variations associated with recurrent pregnancy loss among Indian women.

    PubMed

    Vanniarajan, Ayyasamy; Govindaraj, Periyasamy; Carlus, S Justin; Aruna, Meka; Aruna, P; Kumar, Ajay; Jayakar, Richard Issac; Lionel, Anath C; Gupta, Sandeep; Rao, Lakshmi; Gupta, Nalini J; Chakravarthy, Baidyanath; Deenadayal, Mamatha; Selvaraj, Kamala; Andal, Sadaranga; Reddy, B Mohan; Singh, Lalji; Thangaraj, Kumarasamy

    2011-05-01

    Several genetic factors have been found to be associated with recurrent pregnancy loss (RPL). However, not many attempts have been made to associate the mitochondrial DNA (mtDNA) variations with RPL. Therefore, we have analyzed the complete mtDNA of 100 women with RPL and 12 aborted fetal tissues. Our analysis revealed a total of 681 variations, most of which were in NADH Dehydrogenase (ND) genes that encode mitochondrial enzyme Complex I. Presence of T4216C variation (ND1 gene) in 9% of the RPL women and several pathogenic, and novel mutations suggest the role of mtDNA variations in RPL.

  10. [Complexity of land ecosystem].

    PubMed

    Wu, Cifang; Chen, Meiqiu

    2002-06-01

    In recent years, complexity studies has become a new research region and been widely applied in engineering, biology, economy, management, military, police and sociology. In this paper, from the view of complex science, the main complexity characteristics of land ecosystem were described, furthermore, the application of fractal, chaos, and artificial neural network on the complexity of land ecosystem were also discussed.

  11. Mössbauer and positron annihilation studies of pharmaceutically important iron-dextran complexes

    NASA Astrophysics Data System (ADS)

    Oshtrakh, M. I.; Kopelyan, E. A.; Semionkin, V. A.; Livshits, A. B.; Krylova, V. E.; Kozlov, A. A.

    1993-04-01

    Iron-dextran complexes are pharmaceutically important models of iron-storage protein ferritin. These complexes are used for treatment of iron-deficiency anemias. In this work we present the results of the study of various iron-dextran complexes by Mössbauer spectroscopy and the positron annihilation technique. Mössbauer spectroscopy indicated the differences between the electronic and magnetic structures of iron cores in iron-dextran complexes while positron annihilation showed variations of dextran shells in those complexes. Both techniques appeared to be useful to study microstructural variations in iron-dextran complexes.

  12. Geometric constrained variational calculus. III: The second variation (Part II)

    NASA Astrophysics Data System (ADS)

    Massa, Enrico; Luria, Gianvittorio; Pagani, Enrico

    2016-03-01

    The problem of minimality for constrained variational calculus is analyzed within the class of piecewise differentiable extremaloids. A fully covariant representation of the second variation of the action functional based on a family of local gauge transformations of the original Lagrangian is proposed. The necessity of pursuing a local adaptation process, rather than the global one described in [1] is seen to depend on the value of certain scalar attributes of the extremaloid, here called the corners’ strengths. On this basis, both the necessary and the sufficient conditions for minimality are worked out. In the discussion, a crucial role is played by an analysis of the prolongability of the Jacobi fields across the corners. Eventually, in the appendix, an alternative approach to the concept of strength of a corner, more closely related to Pontryagin’s maximum principle, is presented.

  13. alpha-Lactalbumin species variation, HAMLET formation, and tumor cell death.

    PubMed

    Pettersson, Jenny; Mossberg, Ann-Kristin; Svanborg, Catharina

    2006-06-23

    HAMLET (human alpha-lactalbumin made lethal to tumor cells) is a tumoricidal complex of apo alpha-lactalbumin and oleic acid, formed in casein after low pH treatment of human milk. This study examined if HAMLET-like complexes are present in casein from different species and if isolated alpha-lactalbumin from those species can form such complexes with oleic acid. Casein from human, bovine, equine, and porcine milk was separated by ion exchange chromatography and active complexes were only found in human casein. This was not explained by alpha-lactalbumin sequence variation, as purified bovine, equine, porcine, and caprine alpha-lactalbumins formed complexes with oleic acid with biological activity similar to HAMLET. We conclude that structural variation of alpha-lactalbumins does not preclude the formation of HAMLET-like complexes and that natural HAMLET formation in casein was unique to human milk, which also showed the highest oleic acid content.

  14. Genetic variation and its maintenance

    SciTech Connect

    Roberts, D.F.; De Stefano, G.F.

    1986-01-01

    This book contains several papers divided among three sections. The section titles are: Genetic Diversity--Its Dimensions; Genetic Diversity--Its Origin and Maintenance; and Genetic Diversity--Applications and Problems of Complex Characters.

  15. Reduction of Subjective and Objective System Complexity

    NASA Technical Reports Server (NTRS)

    Watson, Michael D.

    2015-01-01

    in finding the optimal or 'best balance' of the system functions and interrelationships. This is achievable following von Bertalanffy's approach of describing