Sample records for complex kohn variational

  1. Equivalence of the generalized and complex Kohn variational methods

    E-print Network

    J. N. Cooper; M. Plummer; E. A. G. Armour

    2010-03-11

    For Kohn variational calculations on low energy positron hydrogen molecule elastic scattering, we prove that the phase shift approximation obtained using the complex Kohn method is precisely equal to a value which can be obtained immediately via the real-generalized Kohn method. Our treatment is sufficiently general to be applied directly to arbitrary potential scattering or single open channel scattering problems, with exchange if required. In the course of our analysis, we develop a framework formally to describe the anomalous behaviour of our generalized Kohn calculations in the regions of the well known Schwartz singularities. This framework also explains the mathematical origin of the anomaly-free singularities we reported in a previous article. Moreover, we demonstrate a novelty, that explicit solutions of the Kohn equations are not required in order to calculate optimal phase shift approximations. We relate our rigorous framework to earlier descriptions of the Kohn-type methods.

  2. Nonexistence of a Hohenberg-Kohn variational principle in total current-density-functional theory

    NASA Astrophysics Data System (ADS)

    Laestadius, Andre; Benedicks, Michael

    2015-03-01

    For a many-electron system, whether the particle density ? (r ) and the total current density j (r ) are sufficent to determine the one-body potential V (r ) and vector potential A (r ) is still an open question. For the one-electron case, a Hohenberg-Kohn theorem exists formulated with the total current density. Here we show that the generalized Hohenberg-Kohn energy functional EV0,A0(? ,j ) = can be minimal for densities that are not the ground-state densities of the fixed potentials V0 and A0. Furthermore, for an arbitrary number of electrons and under the assumption that a Hohenberg-Kohn theorem exists formulated with ? and j , we discuss the possibility of a variational principle in total current-density-functional theory such as that of Hohenberg-Kohn.

  3. Non-existence of a Hohenberg-Kohn Variational Principle in Total Current Density Functional Theory

    E-print Network

    Andre Laestadius; Michael Benedicks

    2014-04-12

    For a many-electron system, whether the particle density $\\rho(\\mathbf{r})$ and the total current density $\\mathbf{j}(\\mathbf{r})$ are sufficient to determine the one-body potential $V(\\mathbf{r})$ and vector potential $\\mathbf{A}(\\mathbf{r})$, is still an open question. For the one-electron case, a Hohenberg-Kohn theorem exists formulated with the total current density. Here we show that the generalized Hohenberg-Kohn energy functional $\\mathord{\\cal E}_{V_0,\\mathbf{A}_0}(\\rho,\\mathbf{j}) = \\langle \\psi(\\rho,\\mathbf{j}),H(V_0,\\mathbf{A}_0)\\psi(\\rho,\\mathbf{j})\\rangle$ can be minimal for densities that are not the ground-state densities of the fixed potentials $V_0$ and $\\mathbf{A}_0$. Furthermore, for an arbitrary number of electrons and under the assumption that a Hohenberg-Kohn theorem exists formulated with $\\rho$ and $\\mathbf{j}$, we show that a variational principle for Total Current Density Functional Theory as that of Hohenberg-Kohn for Density Functional Theory does not exist. The reason is that the assumed map from densities to the vector potential, written $(\\rho,\\mathbf{j})\\mapsto \\mathbf{A}(\\rho,\\mathbf{j};\\mathbf{r})$, enters explicitly in $\\mathord{\\cal E}_{V_0,\\mathbf{A}_0}(\\rho,\\mathbf{j})$.

  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. 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…

  6. Symmetry-adapted perturbation theory based on unrestricted Kohn-Sham orbitals for high-spin open-shell van der Waals complexes

    NASA Astrophysics Data System (ADS)

    Hapka, Micha?; ?uchowski, Piotr S.; Szcze?niak, Ma?gorzata M.; Cha?asi?ski, Grzegorz

    2012-10-01

    Two open-shell formulations of the symmetry-adapted perturbation theory are presented. They are based on the spin-unrestricted Kohn-Sham (SAPT(UKS)) and unrestricted Hartree-Fock (SAPT(UHF)) descriptions of the monomers, respectively. The key reason behind development of SAPT(UKS) is that it is more compatible with density functional theory (DFT) compared to the previous formulation of open-shell SAPT based on spin-restricted Kohn-Sham method of ?uchowski et al. [J. Chem. Phys. 129, 084101 (2008), 10.1063/1.2968556]. The performance of SAPT(UKS) and SAPT(UHF) is tested for the following open-shell van der Waals complexes: He⋯NH, H2O⋯HO2, He⋯OH, Ar⋯OH, Ar⋯NO. The results show an excellent agreement between SAPT(UKS) and SAPT(ROKS). Furthermore, for the first time SAPT based on DFT is shown to be suitable for the treatment of interactions involving ?-state radicals (He⋯OH, Ar⋯OH, Ar⋯NO). In the interactions of transition metal dimers (^3? _u^+)Au2 and (^{13}? _g^+)Cr2 we show that SAPT is incompatible with the use of effective core potentials. The interaction energies of both systems expressed instead as supermolecular UHF interaction plus dispersion from SAPT(UKS) result in reasonably accurate potential curves.

  7. Elise C. Kohn, MD

    Cancer.gov

    Dr. Elise Kohn is a graduate of the University of Michigan Medical School where she also completed residency training in Internal Medicine; she came to the NCI for Medical Oncology training in the Medicine Branch. Dr. Kohn then joined the Laboratory of Pathology to investigate signal transduction molecular targets in invasion and angiogenesis, and ovarian cancer and maintained her clinical focus in the translational clinical studies of ovarian cancer. Recently, Dr.

  8. Kohn anomalies in graphene nanoribbons

    E-print Network

    Dresselhaus, Mildred

    The quantum corrections to the energies of the ? point optical phonon modes (Kohn anomalies) in graphene nanoribbons (NRs) are investigated. We show theoretically that the longitudinal optical (LO) modes undergo a Kohn ...

  9. Hohenberg-Kohn redux

    E-print Network

    Paul E. Lammert

    2015-02-08

    The Hohenberg-Kohn theorem is a cornerstone of electronic density functional theory, yet completing its proof in the traditional way requires the {\\em assumption} that ground state wavefunctions never vanish on sets of nonzero Lebesgue measure. This is an unsatisfactory situation, since DFT is supposed to obviate knowledge of many-body wavefunctions. We approach the issue from a more density-centric direction, allowing mild hypotheses on the density which can be regarded as checkable in a DFT context. By ordinary Hilbert space analysis, the following is proved: If the density $\\rho$ is continuous and everywhere nonzero, then there can be at most one potential (modulo constants) expressible as a sum of a square-integrable and a bounded function (i.e., Kato-Rellich) with $\\rho$ as a ground state density. In case $\\rho$ is not nonzero everywhere, the theorem allows an independent constant on each connected component of the set where the density is positive, a weakening which can be reversed by requiring locally weak-$L^3$ potentials and calling on a unique continuation result of Schechter and Simon.

  10. Variational principles for complex conductivity, viscoelasticity and

    E-print Network

    Cherkaev, Andrej

    Variational principles for complex conductivity, viscoelasticity and similar problems in media : : : : : : : : : : : : : : : : : : 16 4 Viscoelasticity problem 17 5 Application to composites. The problem of bounds. 22 Abstract We consider linear processes in media with dissipation arising in conductiv­ ity, optics, viscoelasticity, etc

  11. Chromosome Variation in the Heleocharis palustris-uniglumis Complex

    Microsoft Academic Search

    Lise H. Saunte

    1958-01-01

    THE Heleocharis (Eleocharis) palustris-uniglumis complex shows a considerable variation in chromosome number, the following figures being recorded in the literature: 2n = 10, 16, 32, 36, 38, 46, c. 69, 921. The taxonomical implications of this variation is under discussion2-4, but no definite conclusions have been reached. It was felt that more information about the chromosome variation was needed before

  12. Human genetic variation and its contribution to complex traits

    Microsoft Academic Search

    Sarah S. Murray; Nicholas J. Schork; Eric J. Topol; Kelly A. Frazer

    2009-01-01

    The last few years have seen extensive efforts to catalogue human genetic variation and correlate it with phenotypic differences. Most common SNPs have now been assessed in genome-wide studies for statistical associations with many complex traits, including many important common diseases. Although these studies have provided new biological insights, only a limited amount of the heritable component of any complex

  13. 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.

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

    SciTech Connect

    Hinckley, C.M. [Sandia National Labs., Livermore, CA (United States); Barkan, P. [Stanford Univ., CA (United States)

    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.

  15. Epigenetic variation in the Egfr gene generates quantitative variation in a complex trait in ants.

    PubMed

    Alvarado, Sebastian; Rajakumar, Rajendhran; Abouheif, Ehab; Szyf, Moshe

    2015-01-01

    Complex quantitative traits, like size and behaviour, are a pervasive feature of natural populations. Quantitative trait variation is the product of both genetic and environmental factors, yet little is known about the mechanisms through which their interaction generates this variation. Epigenetic processes, such as DNA methylation, can mediate gene-by-environment interactions during development to generate discrete phenotypic variation. We therefore investigated the developmental role of DNA methylation in generating continuous size variation of workers in an ant colony, a key trait associated with division of labour. Here we show that, in the carpenter ant Camponotus floridanus, global (genome-wide) DNA methylation indirectly regulates quantitative methylation of the conserved cell-signalling gene Epidermal growth factor receptor to generate continuous size variation of workers. DNA methylation can therefore generate quantitative variation in a complex trait by quantitatively regulating the transcription of a gene. This mechanism, alongside genetic variation, may determine the phenotypic possibilities of loci for generating quantitative trait variation in natural populations. PMID:25758336

  16. Epistasis and balanced polymorphism influencing complex trait variation

    Microsoft Academic Search

    Juergen Kroymann; Thomas Mitchell-Olds

    2005-01-01

    Complex traits such as human disease, growth rate, or crop yield are polygenic, or determined by the contributions from numerous genes in a quantitative manner. Although progress has been made in identifying major quantitative trait loci (QTL), experimental constraints have limited our knowledge of small-effect QTL, which may be responsible for a large proportion of trait variation. Here, we identified

  17. Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits

    PubMed Central

    Saliba-Colombani, Vera; Simon, Matthieu; Agier, Nicolas; Bulski, Agnès; Albuisson, Juliette; Heredia, Fabiana; Audigier, Pascal; Bouchez, David; Dillmann, Christine; Guerche, Philippe; Hospital, Frédéric; Colot, Vincent

    2009-01-01

    Loss or gain of DNA methylation can affect gene expression and is sometimes transmitted across generations. Such epigenetic alterations are thus a possible source of heritable phenotypic variation in the absence of DNA sequence change. However, attempts to assess the prevalence of stable epigenetic variation in natural and experimental populations and to quantify its impact on complex traits have been hampered by the confounding effects of DNA sequence polymorphisms. To overcome this problem as much as possible, two parents with little DNA sequence differences, but contrasting DNA methylation profiles, were used to derive a panel of epigenetic Recombinant Inbred Lines (epiRILs) in the reference plant Arabidopsis thaliana. The epiRILs showed variation and high heritability for flowering time and plant height (?30%), as well as stable inheritance of multiple parental DNA methylation variants (epialleles) over at least eight generations. These findings provide a first rationale to identify epiallelic variants that contribute to heritable variation in complex traits using linkage or association studies. More generally, the demonstration that numerous epialleles across the genome can be stable over many generations in the absence of selection or extensive DNA sequence variation highlights the need to integrate epigenetic information into population genetics studies. PMID:19557164

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

    SciTech Connect

    De Sole, Alberto [Dipartimento di Matematica, Universita di Roma ''La Sapienza'', 00185 Roma (Italy); Hekmati, Pedram [School of Mathematical Sciences, University of Adelaide, Adelaide, SA 5005 (Australia); Kac, Victor G. [Department of Mathematics, MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States)

    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.

  19. Individual Variation in the Late Positive Complex to Semantic Anomalies

    PubMed Central

    Kos, Miriam; van den Brink, Danielle; Hagoort, Peter

    2012-01-01

    It is well-known that, within ERP paradigms of sentence processing, semantically anomalous words elicit N400 effects. Less clear, however, is what happens after the N400. In some cases N400 effects are followed by Late Positive Complexes (LPC), whereas in other cases such effects are lacking. We investigated several factors which could affect the LPC, such as contextual constraint, inter-individual variation, and working memory. Seventy-two participants read sentences containing a semantic manipulation (Whipped cream tastes sweet/anxious and creamy). Neither contextual constraint nor working memory correlated with the LPC. Inter-individual variation played a substantial role in the elicitation of the LPC with about half of the participants showing a negative response and the other half showing an LPC. This individual variation correlated with a syntactic ERP as well as an alternative semantic manipulation. In conclusion, our results show that inter-individual variation plays a large role in the elicitation of the LPC and this may account for the diversity in LPC findings in language research. PMID:22973249

  20. 60 : DVD (9.1) 1998, Walter Kohn

    E-print Network

    Zexian, Cao

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  1. On the Kohn-Luttinger conundrum

    SciTech Connect

    Hirata, So [Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 (United States); CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 (Japan); He Xiao [Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 (United States)

    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.

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

    E-print Network

    M. Ruggenthaler; F. Mackenroth; D. Bauer

    2011-10-10

    We prove a generalization of the van Leeuwen theorem towards quantum electrodynamics, providing the formal foundations of a time-dependent Kohn-Sham construction for coupled quantized matter and electromagnetic fields. Thereby 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.

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

    SciTech Connect

    Ruggenthaler, M. [Institut fuer Physik, Universitaet Rostock, DE-18051 Rostock (Germany); Department of Physics, Nanoscience Center, University of Jyvaeskylae, FI-40014 Jyvaeskylae (Finland); Mackenroth, F. [Max-Planck-Institut fuer Kernphysik, Postfach 103980, DE-69029 Heidelberg (Germany); Bauer, D. [Institut fuer Physik, Universitaet Rostock, DE-18051 Rostock (Germany)

    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.

  4. 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 progenitor. 6. Our findings support the hypothesis that increased tolerance to severe environmental conditions is a plausible mechanism of polyploid establishment.

  5. Variation at the major histocompatibility complex in Savannah sparrows.

    PubMed

    Freeman-Gallant, Corey R; Johnson, Elizabeth M; Saponara, Fiorella; Stanger, Matthew

    2002-06-01

    The class I and class II genes of the major histocompatibility complex (Mhc) encode dimeric glycoproteins responsible for eliciting the adaptive immune response of vertebrates. Recent work with birds suggests that the number, size, and arrangement of these genes can differ markedly across species, although the extent of this variation, and its causes and consequences, are poorly understood. We have used a 157-base-pair (bp) portion of the second exon of a class II B gene to probe the Mhc in a free-living population of Savannah sparrows (Passerculus sandwichensis). Segregation analysis of Mhc bands suggests that class II B genes can be found in two independently assorting clusters, as previously described for domestic chickens (Gallus gallus) and ring-necked pheasants (Phasianus colchicus) but unlike gene organization in mammals. The Mhc in Savannah sparrows appears large (with many class II B genes) and variable; we found 42 unique genotypes among 48 adults breeding on Kent Island, New Brunswick, Canada in 1995. Savannah sparrows are long-distance migrants, and these results support recent predictions that migratory birds should show higher levels of Mhc polymorphism and/or a greater number of genes than sedentary species. Savannah sparrows are also socially polygynous with high levels of extra-pair paternity, suggesting that a history of sexual selection might also influence the size and/or structure of the avian Mhc. PMID:12030987

  6. Mapping Kohn-Sham eigenenergies onto vertical ionization energies and electron affinities

    NASA Astrophysics Data System (ADS)

    Joubert, Daniel P.

    2012-06-01

    Each Kohn-Sham eigenenergy can be mapped onto a difference between the interacting ground-state energies of successive integer-electron systems via a coupling-constant integration. Occupied Kohn-Sham energies can be mapped onto vertical ionization energies and virtual Kohn-Sham energies can be mapped onto vertical electron affinities. This mapping is unique for nondegenerate Kohn-Sham energies, but degenerate Kohn-Sham levels can be mapped onto multiple ionization energies or electron affinities. Exact expressions for the first ionization and electron affinity energies lead to exact formal expressions for the difference between the Kohn-Sham gap and the fundamental gap.

  7. Kohn-Sham Theory in the Presence of Magnetic Field

    E-print Network

    Andre Laestadius

    2014-04-11

    In the well-known Kohn-Sham theory in Density Functional Theory, a fictitious non-interacting system is introduced that has the same particle density as a system of $N$ electrons subjected to mutual Coulomb repulsion and an external electric field. For a long time, the treatment of the kinetic energy was not correct and the theory was not well-defined for $N$-representable particle densities. In the work of [Hadjisavvas and Theophilou, Phys. Rev. A, 1984, 30, 2183], a rigorous Kohn-Sham theory for $N$-representable particle densities was developed using the Levy-Lieb functional. Since a Levy-Lieb-type functional can be defined for Current Density Functional Theory formulated with the paramagnetic current density, we here develop a rigorous $N$-representable Kohn-Sham approach for interacting electrons in magnetic field. Furthermore, in the one-electron case, criteria for $N$-representable particle densities to be $v$-representable are given.

  8. Global Properties and Functional Complexity of Human Gene Regulatory Variation

    PubMed Central

    Gaffney, Daniel J.

    2013-01-01

    Identification and functional interpretation of gene regulatory variants is a major focus of modern genomics. The application of genetic mapping to molecular and cellular traits has enabled the detection of regulatory variation on genome-wide scales and revealed an enormous diversity of regulatory architecture in humans and other species. In this review I summarise the insights gained and questions raised by a decade of genetic mapping of gene expression variation. I discuss recent extensions of this approach using alternative molecular phenotypes that have revealed some of the biological mechanisms that drive gene expression variation between individuals. Finally, I highlight outstanding problems and future directions for development. PMID:23737752

  9. Standing and flowing: the complex origins of adaptive variation.

    PubMed

    Welch, John J; Jiggins, Chris D

    2014-08-01

    A population faced with a new selection pressure can only adapt if appropriate genetic variation is available. This genetic variation might come from new mutations or from gene exchange with other populations or species, or it might already segregate in the population as standing genetic variation (which might itself have arisen from either mutation or gene flow). Understanding the relative importance of these sources of adaptive variation is a fundamental issue in evolutionary genetics (Orr & Betancourt ; Barrett & Schluter ; Gladyshev et al. ) and has practical implications for conservation, plant and animal breeding, biological control and infectious disease prevention (e.g. Robertson ; Soulé & Wilcox ; Prentis et al. ; Pennings ). In this issue of Molecular Ecology, Roesti et al. () make an important contribution to this longstanding debate. PMID:25088550

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

    SciTech Connect

    Yang Zenghui; Burke, Kieron [Department of Chemistry, University of California, Irvine, California 92697 (United States); Faassen, Meta van [Department of Theoretical Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, NL-1081 HV Amsterdam (Netherlands)

    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.

  11. Kohn's theorem and Newton-Hooke symmetry for Hill's equations

    NASA Astrophysics Data System (ADS)

    Zhang, P. M.; Gibbons, G. W.; Horvathy, P. A.

    2012-02-01

    Hill’s equations, which first arose in the study of the Earth-Moon-Sun system, admit the two-parameter centrally extended Newton-Hooke symmetry without rotations. This symmetry allows us to extend Kohn’s theorem about the center-of-mass decomposition. Particular light is shed on the problem using Duval’s “Bargmann” framework. The separation of the center-of-mass motion into that of a guiding center and relative motion is derived by a generalized chiral decomposition.

  12. A Kohn-Sham system at zero temperature

    E-print Network

    Horia Cornean; Kurt Hoke; Hagen Neidhardt; Paul N. Racec; Joachim Rehberg

    2008-01-17

    An one-dimensional Kohn-Sham system for spin particles is considered which effectively describes semiconductor {nano}structures and which is investigated at zero temperature. We prove the existence of solutions and derive a priori estimates. For this purpose we find estimates for eigenvalues of the Schr\\"odinger operator with effective Kohn-Sham potential and obtain $W^{1,2}$-bounds of the associated particle density operator. Afterwards, compactness and continuity results allow to apply Schauder's fixed point theorem. In case of vanishing exchange-correlation potential uniqueness is shown by monotonicity arguments. Finally, we investigate the behavior of the system if the temperature approaches zero.

  13. Determination of the ionic radii by means of the Kohn-Sham potential: Identification of the chemical potential

    NASA Astrophysics Data System (ADS)

    Barrera, Mauricio; Zuloaga, Fernando

    Under the Kohn-Sham theory, we examine solutions for the equations ?TS/??(r) = 0 and ?TS/??(r) = ?KS(r) that link the chemical potential of the electronic system with the effective Kohn-Sham potential through ? = ?KS(r) + ?TS/??. For single ions, we identify the chemical potential with the eigenvalue of the frontier orbital when the atom is in the limit of full ionization. For the case of cations, the chemical potential is found above -(I + A)/2 and has the property of grouping ions with the same chemical characteristics. For the anion instead, the chemical potential is fixed at the ionization energy. By solving the above equations numerically, two radial points called r- and r+ are obtained and compared with the Shannon-Prewitt ionic radius. Moreover, we found for the halide series, that r- is numerically equivalent to rm, the radii where the electrostatic potential has its minimum, but shows different behavior upon charge variation.

  14. Superconducting vortices in ac fields: does the Kohn theorem work?

    PubMed

    Kopnin, N B; Vinokur, V M

    2001-07-01

    Electrodynamics of clean pinning-free type II superconductors in the mixed state is derived using the Boltzmann kinetic equations for excitations. The condition of the vortex cyclotron resonance is found. The reason why this resonance does not comply with the Kohn theorem is discussed. PMID:11461487

  15. Second-order Kohn-Sham perturbation theory: correlation potential for atoms in a cavity.

    PubMed

    Jiang, Hong; Engel, Eberhard

    2005-12-01

    Second-order perturbation theory based on the Kohn-Sham Hamiltonian leads to an implicit density functional for the correlation energy E(c) (MP2), which is explicitly dependent on both occupied and unoccupied Kohn-Sham single-particle orbitals and energies. The corresponding correlation potential v(c) (MP2), which has to be evaluated by the optimized potential method, was found to be divergent in the asymptotic region of atoms, if positive-energy continuum states are included in the calculation [Facco Bonetti et al., Phys. Rev. Lett. 86, 2241 (2001)]. On the other hand, Niquet et al., [J. Chem. Phys. 118, 9504 (2003)] showed that v(c) (MP2) has the same asymptotic -alpha(2r(4)) behavior as the exact correlation potential, if the system under study has a discrete spectrum only. In this work we study v(c) (MP2) for atoms in a spherical cavity within a basis-set-free finite differences approach, ensuring a completely discrete spectrum by requiring hard-wall boundary conditions at the cavity radius. Choosing this radius sufficiently large, one can devise a numerical continuation procedure which allows to normalize v(c) (MP2) consistent with the standard choice v(c)(r-->infinity)=0 for free atoms, without modifying the potential in the chemically relevant region. An important prerequisite for the success of this scheme is the inclusion of very high-energy virtual states. Using this technique, we have calculated v(c) (MP2) for all closed-shell and spherical open-shell atoms up to argon. One finds that v(c) (MP2) reproduces the shell structure of the exact correlation potential very well but consistently overestimates the corresponding shell oscillations. In the case of spin-polarized atoms one observes a strong interrelation between the correlation potentials of the two spin channels, which is completely absent for standard density functionals. However, our results also demonstrate that E(c) (MP2) can only serve as a first step towards the construction of a suitable implicit correlation functional: The fundamental variational instability of this functional is recovered for beryllium, for which a breakdown of the self-consistent Kohn-Sham iteration is observed. Moreover, even for those atoms for which the self-consistent iteration is stable, the results indicate that the inclusion of v(c) (MP2) in the total Kohn-Sham potential does not lead to an improvement compared to the complete neglect of the correlation potential. PMID:16375465

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

    SciTech Connect

    Gonis, A. [Lawrence Livermore National Lab., CA (United States); Butler, W.H. [Oak Ridge National Lab., TN (United States); Zhang, X.-G. [Kentucky Univ., Lexington, KY (United States). Center for Computational Sciences

    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.

  17. 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 sequencing of these uniquely informative cohorts. PMID:24349040

  18. Kohn-Sham orbitals and potentials from quantum Monte Carlo molecular densities

    SciTech Connect

    Varsano, Daniele, E-mail: daniele.varsano@nano.cnr.it [Dipartimento di Fisica, Sapienza-Università di Roma, P.le Aldo Moro 5, 00185 Roma (Italy)] [Dipartimento di Fisica, Sapienza-Università di Roma, P.le Aldo Moro 5, 00185 Roma (Italy); Barborini, Matteo [Dipartimento di ingegneria e scienze dell'informazione e matematica, Università degli studi dell'Aquila, Via Vetoio, Coppito, 67100 L'Aquila (Italy) [Dipartimento di ingegneria e scienze dell'informazione e matematica, Università degli studi dell'Aquila, Via Vetoio, Coppito, 67100 L'Aquila (Italy); Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell'Aquila, Via Vetoio, Coppito, 67100 L'Aquila (Italy); Guidoni, Leonardo, E-mail: leonardo.guidoni@univaq.it [Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell'Aquila, Via Vetoio, Coppito, 67100 L'Aquila (Italy)] [Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell'Aquila, Via Vetoio, Coppito, 67100 L'Aquila (Italy)

    2014-02-07

    In this work we show the possibility to extract Kohn-Sham orbitals, orbital energies, and exchange correlation potentials from accurate Quantum Monte Carlo (QMC) densities for atoms (He, Be, Ne) and molecules (H{sub 2}, Be{sub 2}, H{sub 2}O, and C{sub 2}H{sub 4}). The Variational Monte Carlo (VMC) densities based on accurate Jastrow Antisymmetrised Geminal Power wave functions are calculated through different estimators. Using these reference densities, we extract the Kohn-Sham quantities with the method developed by Zhao, Morrison, and Parr (ZMP) [Phys. Rev. A 50, 2138 (1994)]. We compare these extracted quantities with those obtained form CISD densities and with other data reported in the literature, finding a good agreement between VMC and other high-level quantum chemistry methods. Our results demonstrate the applicability of the ZMP procedure to QMC molecular densities, that can be used for the testing and development of improved functionals and for the implementation of embedding schemes based on QMC and Density Functional Theory.

  19. Variation in child health care utilization by medical complexity.

    PubMed

    Kuo, Dennis Z; Melguizo-Castro, Maria; Goudie, Anthony; Nick, Todd G; Robbins, James M; Casey, Patrick H

    2015-01-01

    Children with medical complexity (CMC) have multiple specialty need, technology dependence, and high health care utilization. The objective of this study is to profile types of pediatric health care utilization and costs by increasing levels of medical complexity. This is a cross-sectional study of the 2007, 2008 and 2009 Full-Year Data Sets from the Medical Expenditure Panel Survey. Medical complexity was defined by a higher number of positive items from the five question children with special health care needs (CSHCN) Screener. CMC were defined by ? 4 positive screener items. Outcomes included the number of inpatient, outpatient, and emergency department visits, associated costs and diagnoses, and reported satisfaction. ICD-9 codes were grouped by Clinical Classifications Software. Of 27,755 total study subjects ? 17 years, 4,851 had special needs and 541 were CMC. Older age, male gender, white/non-Hispanic race/ethnicity, and public insurance were all associated with medical complexity (all p < 0.001). CMC had an annual mean of 19 annual outpatient visits ($616) and 0.26 inpatient visits ($3,308), with other significant cost drivers including home health ($2,957) and prescriptions ($2,182). The most common reasons for non-CSHCN and less-complex CSHCN outpatient visits were viral illnesses, while the main reasons for CMC visits were for mental health. Compared to families without CSHCN, those with CMC have, on average, lower satisfaction with health care (8.4 vs. 8.9 out of 10, p < 0.001). Health care models for CMC should account for mental health conditions that may be driving high numbers of outpatient encounters. PMID:24740726

  20. Syntheses of Variations of Stereogenic-at-Metal Imido Alkylidene Complexes of Molybdenum

    E-print Network

    Müller, Peter

    Syntheses of Variations of Stereogenic-at-Metal Imido Alkylidene Complexes of Molybdenum Smaranda C of several new stereogenic-at-metal imido alkylidene complexes of molybdenum, Mo(NR)(CHR)(X)(Y), many to the alkylidene and imido ligands. INTRODUCTION Recent advances in olefin metathesis by molybdenum,1 tungsten,2

  1. Real-time adaptive finite element solution of time-dependent Kohn-Sham equation

    NASA Astrophysics Data System (ADS)

    Bao, Gang; Hu, Guanghui; Liu, Di

    2015-01-01

    In our previous paper (Bao et al., 2012 [1]), a general framework of using adaptive finite element methods to solve the Kohn-Sham equation has been presented. This work is concerned with solving the time-dependent Kohn-Sham equations. The numerical methods are studied in the time domain, which can be employed to explain both the linear and the nonlinear effects. A Crank-Nicolson scheme and linear finite element space are employed for the temporal and spatial discretizations, respectively. To resolve the trouble regions in the time-dependent simulations, a heuristic error indicator is introduced for the mesh adaptive methods. An algebraic multigrid solver is developed to efficiently solve the complex-valued system derived from the semi-implicit scheme. A mask function is employed to remove or reduce the boundary reflection of the wavefunction. The effectiveness of our method is verified by numerical simulations for both linear and nonlinear phenomena, in which the effectiveness of the mesh adaptive methods is clearly demonstrated.

  2. Complexity and variation in loggerhead sea turtle life history.

    PubMed

    McClellan, Catherine M; Read, Andrew J

    2007-12-22

    Juvenile loggerhead sea turtles spend more than a decade in the open ocean before returning to neritic waters to mature and reproduce. It has been assumed that this transition from an oceanic to neritic existence is a discrete ontogenetic niche shift. We tested this hypothesis by tracking the movements of large juveniles collected in a neritic foraging ground in North Carolina, USA. Our work shows that the shift from the oceanic to neritic waters is both complex and reversible; some individuals move back into coastal waters and then return to the open ocean for reasons that are still unclear, sometimes for multiple years. These findings have important consequences for efforts to protect these threatened marine reptiles from mortality in both coastal and open-ocean fisheries. PMID:17698451

  3. Guaranteed Convergence of the Kohn-Sham Equations

    NASA Astrophysics Data System (ADS)

    Wagner, Lucas O.; Stoudenmire, E. M.; Burke, Kieron; White, Steven R.

    2013-08-01

    A sufficiently damped iteration of the Kohn-Sham (KS) equations with the exact functional is proven to always converge to the true ground-state density, regardless of the initial density or the strength of electron correlation, for finite Coulomb systems. We numerically implement the exact functional for one-dimensional continuum systems and demonstrate convergence of the damped KS algorithm. More strongly correlated systems converge more slowly.

  4. Interpreting non-coding variation in complex disease genetics

    PubMed Central

    Ward, Lucas D.; Kellis, Manolis

    2012-01-01

    Association studies provide genome-wide information about the genetic basis of complex disease, but medical research has primarily focused on protein-coding variants, due to the difficulty of interpreting non-coding mutations. This picture has changed with advances in the systematic annotation of functional non-coding elements. Evolutionary conservation, functional genomics, chromatin state, sequence motifs, and molecular quantitative trait loci all provide complementary information about non-coding function. These functional maps can help prioritize variants on risk haplotypes, filter mutations encountered in the clinic, and perform systems-level analyses to reveal processes underlying disease associations. Advances in predictive modeling can enable dataset integration to reveal pathways shared across loci and alleles, and richer regulatory models can guide the search for epistatic interactions. Lastly, new massively parallel reporter experiments can systematically validate regulatory predictions. Ultimately, advances in regulatory and systems genomics can help unleash the value of whole-genome sequencing for personalized genomic risk assessment, diagnosis, and treatment. PMID:23138309

  5. Morphological variation of "complex vertebral malformation" in Holstein calves.

    PubMed

    Agerholm, Jorgen S; Bendixen, Christian; Arnbjerg, Jens; Andersen, Ole

    2004-11-01

    A study was performed to investigate the morphological expression of the inherited syndrome "complex vertebral malformation" (CVM) in Holstein calves. A total of 107 late-term aborted, premature, or neonatal calves suspected of having CVM were necropsied and retrospectively analyzed for the causal mutation in the gene SLC35A3. Sixty-two calves were homozygous affected, 16 were heterozygous, and 29 were homozygous normal. Calves affected by CVM were growth retarded. Vertebral lesions identified by radiography were present in 61 cases, of which 58 also had costal malformation. Malformation of the head, primarily in the form of dysplasia or palatoschisis, was present in 15 cases. Bilateral symmetric flexion of the carpal and metacarpophalangeal joints was present in all cases, whereas posterior arthrogryposis was found in 54 cases. Interventricular septal defects occurred in 33 calves, often in combination with other cardiac malformations. A wide spectrum of additional malformations was found. Other congenital syndromes were in most cases distinguishable from CVM on a morphological basis. However, a calf with a prenatal infection with bovine virus diarrhea virus constituted a phenocopy. The study demonstrated that the morphological expression of CVM is wide, but certain aspects, i.e., growth retardation, vertebral malformation, and symmetric arthrogryposis, are almost constant findings. However, cases without vertebral defects and phenocopies constitute a diagnostic problem. A presumptive diagnosis of CVM can in most cases be based on necropsy findings combined with information on descent and paternal CVM genotype, whereas a definitive diagnosis requires genotyping. PMID:15586570

  6. Anatomical Variations of Ostiomeatal Complex in CBCT of Patients Seeking Rhinoplasty

    PubMed Central

    Khojastepour, Leila; Mirhadi, Sabah; Mesbahi, Seyed Alireza

    2015-01-01

    Statement of the Problem Anatomic variation can potentially impact the surgical safety. Purpose The purpose of this cross-sectional study was to assess the prevalence of ostiomeatal complex variations based on cone beam computed tomography (CBCT) images of the patients seeking rhinoplasty. Materials and Method In this cross-sectional study, CBCT images of 281 patients including 153 female and 128 male with Mean±SD age of 26.97±7.38 were retrieved and analyzed for presence of variations of ostiomeatal complex and mucosal thickening. All CBCT images were acquired by NewTom VGi scanner with 15×15 field of view, as a part of preoperative recording of patients seeking rhinoplasty in an otolaryngology clinic. Chi- square test and Odds ratio were used for statistical analysis of the obtained data and p< 0.05 was considered to be statistically significant. Results Agger nasi cells which were seen in 93.2% of the cases were the most common anatomic variation. It was followed by Haller cells (68%), concha bullosa (67.3%), uncinate process variations (54.8%), nasal sepal deviation (49.5%) and paradoxical curvature of middle turbinate (10%). Mucosal thickening were detected in 60.7% of the studied cases. Conclusion Ostiomeatal complex variations and mucosal thickening are considerably prevalent among the patients seeking rhinoplasty. This study also revealed that CBCT evaluation of paranasal sinuses has comparable result in delineation of the sinonasal anatomy. PMID:25759857

  7. Diurnal variation of horizontal wind direction fluctuations in complex terrain at Geysers, Cal

    Microsoft Academic Search

    Steven R. Hanna

    1981-01-01

    Horizontal diffusion in the surface layer is dependent on the standard deviation of wind direction fluctuations ??. Diurnal variation of this parameter in complex terrain was studied for the July 1979 Geysers, Cal., experiment using data from a network of 11 short meteorological towers in the 25 km2 Anderson Creek watershed Valley side slopes are roughly 20 ° and maximum

  8. Asymptotic form of the Kohn-Sham correlation potential

    SciTech Connect

    Joubert, D. P. [School of Physics, University of the Witwatersrand, P.O. Wits 2050, Johannesburg (South Africa)

    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)].

  9. Functional and architectural complexity within and between muscles: regional variation and intermuscular force transmission

    PubMed Central

    Higham, Timothy E.; Biewener, Andrew A.

    2011-01-01

    Over the past 30 years, studies of single muscles have revealed complex patterns of regional variation in muscle architecture, activation, strain and force. In addition, muscles are often functionally integrated with other muscles in parallel or in series. Understanding the extent of this complexity and the interactions between muscles will profoundly influence how we think of muscles in relation to organismal function, and will allow us to address questions regarding the functional benefits (or lack thereof) and dynamics of this complexity under in vivo conditions. This paper has two main objectives. First, we present a cohesive and integrative review of regional variation in function within muscles, and discuss the functional ramifications that can stem from this variation. This involves splitting regional variation into passive and active components. Second, we assess the functional integration of muscles between different limb segments by presenting new data involving in vivo measurements of activation and strain from the medial gastrocnemius, iliotibialis cranialis and iliotibialis lateralis pars preacetabularis of the helmeted guinea fowl (Numida meleagris) during level running on a motorized treadmill. Future research directions for both of these objectives are presented. PMID:21502119

  10. Dominance genetic variation contributes little to the missing heritability for human complex traits.

    PubMed

    Zhu, Zhihong; Bakshi, Andrew; Vinkhuyzen, Anna A E; Hemani, Gibran; Lee, Sang Hong; Nolte, Ilja M; van Vliet-Ostaptchouk, Jana V; Snieder, Harold; Esko, Tonu; Milani, Lili; Mägi, Reedik; Metspalu, Andres; Hill, William G; Weir, Bruce S; Goddard, Michael E; Visscher, Peter M; Yang, Jian

    2015-03-01

    For human complex traits, non-additive genetic variation has been invoked to explain "missing heritability," but its discovery is often neglected in genome-wide association studies. Here we propose a method of using SNP data to partition and estimate the proportion of phenotypic variance attributed to additive and dominance genetic variation at all SNPs (hSNP(2) and ?SNP(2)) in unrelated individuals based on an orthogonal model where the estimate of hSNP(2) is independent of that of ?SNP(2). With this method, we analyzed 79 quantitative traits in 6,715 unrelated European Americans. The estimate of ?SNP(2) averaged across all the 79 quantitative traits was 0.03, approximately a fifth of that for additive variation (average hSNP(2) = 0.15). There were a few traits that showed substantial estimates of ?SNP(2), none of which were replicated in a larger sample of 11,965 individuals. We further performed genome-wide association analyses of the 79 quantitative traits and detected SNPs with genome-wide significant dominance effects only at the ABO locus for factor VIII and von Willebrand factor. All these results suggest that dominance variation at common SNPs explains only a small fraction of phenotypic variation for human complex traits and contributes little to the missing narrow-sense heritability problem. PMID:25683123

  11. 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

  12. Structure of nylon 6\\/iodine complex. 5: variation of intercalation in complexes induced by humidification

    Microsoft Academic Search

    Akio Kawaguchi; Naoki Tsurutani

    2011-01-01

    A nylon 6\\/iodine complex prepared with nylon 6 (polyamide-6, PA6) and provided by immersion in aqueous solutions of polyiodide, In?, showed intercalated structures composed of iodine in which polyiodide ions are coordinated between hydrogen-bonded sheets of nylon 6. This work reports that these intercalated structures can be modified by aging under their swollen condition. After iodine doping with an I2–KI

  13. 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.

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

    SciTech Connect

    Heller, William T [ORNL; Mo, Yiming [ORNL

    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.

  15. Genetic divergence and geographic variation in the deep-water Conus orbignyi complex (Mollusca: Conoidea)

    PubMed Central

    Puillandre, Nicolas; Meyer, Christopher P.; Bouchet, Philippe; Olivera, Baldomero M.

    2011-01-01

    Puillandre, N. et al. (2010) Genetic divergence and geographic variation in a deep-water cone lineage: molecular and morphological analyses of the Conus orbignyi complex (Mollusca: Conoidea). The cone snails (family Conidae) are a hyperdiverse lineage of venomous gastropods. Two standard markers, COI and ITS2, were used to define six genetically-divergent groups within a subclade of Conidae that includes Conus orbignyi; each of these was then evaluated based on their shell morphology. We conclude that three forms, previously regarded as subspecies of Conus orbignyi are distinct species, now recognized as Conus orbignyi, Conus elokismenos and Conus coriolisi. In addition, three additional species (Conus pseudorbignyi, Conus joliveti and Conus comatosa) belong to this clade. Some of the proposed species (e.g., Conus elokismenos) are possibly in turn complexes comprising multiple species. Groups such as Conidae illustrate the challenges generally faced in species delimitation in biodiverse lineages. In the case of the Conus orbignyi complex, not only are there definable, genetically divergent lineages, but also considerable geographic variation within each group. Our study suggests that an intensive analysis of multiple specimens within a single locality helps to minimize the confounding effects of geographic variation and can be a useful starting point for circumscribing different species within such a confusing complex. PMID:21712968

  16. A Study of Anatomical Variations of Osteomeatal Complex in Chronic Rhinosinusitis Patients-CT Findings

    PubMed Central

    Karadi, R.N.; Kumar, Saurabh

    2014-01-01

    Background: Chronic rhino sinusitis (CRS) is the most common disease for which consultation of otorhinolaryngologist is sought. The approach to patients with chronic rhino sinusitis is endoscopic surgery which aims at removing the obstruction of the main drainage pathway. The osteomeatal complex based essentially on the concept that such obstruction perpetuates the sinus disease. This in turn requires the surgeons to have detailed knowledge of the anatomy of the lateral nasal wall, paranasal sinuses and surrounding vital structures and of the large number of anatomical variants in the region. Aim: To study anatomical variations of osteomeatal complex in chronic sinusitis patients. Materials and Methods: Descriptive cross-sectional study design in which 54 consecutive cases of chronic rhino sinusitis patients attending the ENT outpatient department, who had chronic sinusitis for more than three months duration not responding to the medical line of treatment and who were willing to undergo Functional Endoscopic Sinus Surgery satisfying the inclusion criteria were studied. The results were expressed in percentage and proportions. Results: In our study it was observed that 53.7% of the chronic sinusitis cases had two or more anatomical variations and 33.3% of the cases had single anatomical variation. Deviated nasal septum was found to be the most common amongst the anatomical variations in chronic sinusitis cases in the present study which was followed by unilateral concha bullosa and paradoxically bent middle turbinate. Agger nasi cell and Haller cell were seen in one case each. Conclusion: Prevalence of multiple anatomical variations was more in our study in comparison to single anatomical variation. Deviated nasal septum was the most common anatomical variation encountered in our study followed by concha bullosa. PMID:25478374

  17. Natural genetic variation in complex mating behaviors of male Drosophila melanogaster.

    PubMed

    Ruedi, Elizabeth A; Hughes, Kimberly A

    2008-07-01

    Mating behavior, including courtship and copulation, is a main component of male fitness, especially in species with no parental care. Variation in this behavior can thus be a target for mate choice and sexual selection, and can lead to evolution. The fruit fly, Drosophila melanogaster, has well-documented complex male courtship comprised of a sequence behaviors, and is an ideal model for behavior-genetic analysis. In order to evaluate genetic differences in the temporal pattern of mating behavior, we developed a high-throughput method that allows us to document the progression of male courtship and copulation using an ordinal scale (male mating progression scale, MMP). Using this method, we document natural genetic variation in the temporal pattern of behavior that was not detected using other metrics. This method was robust enough to detect genetic variation in this trait for males placed with both virgin and mated female targets. PMID:18369720

  18. Mitochondrial DNA sequence variation in a sea star (Leptasterias spp.) species complex.

    PubMed

    Hrincevich, A W; Foltz, D W

    1996-12-01

    A 551-bp region of a PCR product containing the putative mitochondrial control region and flanking sequences was analyzed for sequence variation among 19 sea stars representing 10 previously described PCR-RFLP haplotypes within a cryptic species complex (Leptasterias spp.). Most (97%) of the sequence variation was interhaplotypic rather than intrahaplotypic, which greatly reduced the utility of sequence polymorphisms in this mtDNA region as markers of intrahaplotypic population structure and gene flow. The estimated number of transition and transversion substitutions per nucleotide site, corrected for multiple hits, was 0.0364 and 0.0158, respectively. Most of the sequence variation occurred in the first half of the putative control region. Phylogenetic analysis (both maximum parsimony and maximum likelihood) revealed three well-supported clades, but the position of two PCR-RFLP haplotypes was not completely resolved. Low intraspecific mtDNA sequence divergence over large geographic distances may be a general pattern for echinoderm species. PMID:8975695

  19. 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…

  20. Natural Genetic Variation in Complex Mating Behaviors of Male Drosophila melanogaster

    Microsoft Academic Search

    Elizabeth A. Ruedi; Kimberly A. Hughes

    2008-01-01

    Mating behavior, including courtship and copulation, is a main component of male fitness, especially in species with no parental\\u000a care. Variation in this behavior can thus be a target for mate choice and sexual selection, and can lead to evolution. The\\u000a fruit fly, Drosophila melanogaster, has well-documented complex male courtship comprised of a sequence behaviors, and is an ideal model

  1. Age-related variation in EEG complexity to photic stimulation: A multiscale entropy analysis

    PubMed Central

    Takahashi, Tetsuya; Cho, Raymond Y.; Murata, Tetsuhito; Mizuno, Tomoyuki; Kikuchi, Mitsuru; Mizukami, Kimiko; Kosaka, Hirotaka; Takahashi, Koichi; Wada, Yuji

    2010-01-01

    Objective This study was intended to examine variations in electroencephalographic (EEG) complexity in response to photic stimulation (PS) during aging to test the hypothesis that the aging process reduces physiologic complexity and functional responsiveness. Methods Multiscale entropy (MSE), an estimate of time-series signal complexity associated with long-range temporal correlation, is used as a recently proposed method for quantifying EEG complexity with multiple coarse-grained sequences. We recorded EEG in 13 healthy elderly subjects and 12 healthy young subjects during pre-PS and post-PS conditions and estimated their respective MSE values. Results For the pre-PS condition, no significant complexity difference was found between the groups. However, a significant MSE change (complexity increase) was found post-PS only in young subjects, thereby revealing a power-law scaling property, which means long-range temporal correlation. Conclusions Enhancement of long-range temporal correlation in young subjects after PS might reflect a cortical response to stimuli, which was absent in elderly subjects. These results are consistent with the general “loss of complexity/diminished functional response to stimuli” theory of aging. Significance Our findings demonstrate that application of MSE analysis to EEG is a powerful approach for studying age-related changes in brain function. PMID:19231279

  2. Self-optimizing Kohn-Sham hybrid functional

    NASA Astrophysics Data System (ADS)

    Tamblyn, Isaac; Baer, Roi; Kronik, Leeor; Neaton, Jeffrey

    2011-03-01

    Recent work using range-separated hybrid functionals has confirmed the importance of including long-range exchange in treatments of phenomena such as charge transfer reactions. Using a self-optimizing [1,2] form of the BNL [3] functional, we present results for structural, electronic, and thermochemical properties of a large set of molecules (including the G2 and G3 test sets). The success of this approach, as well as its ability to describe reaction barriers, will be discussed. [4pt] [1] T. Stein, L. Kronik, and R. Baer, JACS, 131 (8), 2818, 2009 [2] T. Stein, H. Eisenberg, L. Kronik, and R. Baer, "Fundamental gaps of finite systems from the eigenvalues of a generalized Kohn-Sham method", Phys. Rev. Lett., in press. [3] E. Livshits and R. Baer, PCCP, 9, 2932 , 2007

  3. Time-dependent Internal DFT formalism and Kohn-Sham scheme

    E-print Network

    J. Messud

    2009-11-05

    We generalize to the time-dependent case the stationary Internal DFT / Kohn-Sham formalism presented in Ref. [14]. We prove that, in the time-dependent case, the internal properties of a self-bound system (as an atomic nuclei) are all defined by the internal one-body density and the initial state. We set-up a time-dependent Internal Kohn-Sham scheme as a practical way to compute the internal density. The main difference with the traditional DFT / Kohn-Sham formalism is the inclusion of the center-of-mass correlations in the functional.

  4. 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

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

    SciTech Connect

    Yuhki, Naoya; O'Brien, S.J. (National Cancer Institute, Frederick, MD (USA))

    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. The authors 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.

  6. Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations.

    PubMed

    Trotter, Meredith V; Weissman, Daniel B; Peterson, Grant I; Peck, Kayla M; Masel, Joanna

    2014-12-01

    The existence of complex (multiple-step) genetic adaptations that are "irreducible" (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here, we demonstrate, using a simple model, that evolution can cross wide valleys to produce "irreducibly complex" adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley-crossing saddle in allele frequency space. Moreover, simple combinatorics implies an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations. PMID:25178652

  7. Cell-to-Cell Stochastic Variation in Gene Expression Is a Complex Genetic Trait

    PubMed Central

    Ansel, Juliet; Bottin, Hélène; Rodriguez-Beltran, Camilo; Damon, Christelle; Nagarajan, Muniyandi; Fehrmann, Steffen; François, Jean; Yvert, Gaël

    2008-01-01

    The genetic control of common traits is rarely deterministic, with many genes contributing only to the chance of developing a given phenotype. This incomplete penetrance is poorly understood and is usually attributed to interactions between genes or interactions between genes and environmental conditions. Because many traits such as cancer can emerge from rare events happening in one or very few cells, we speculate an alternative and complementary possibility where some genotypes could facilitate these events by increasing stochastic cell-to-cell variations (or ‘noise’). As a very first step towards investigating this possibility, we studied how natural genetic variation influences the level of noise in the expression of a single gene using the yeast S. cerevisiae as a model system. Reproducible differences in noise were observed between divergent genetic backgrounds. We found that noise was highly heritable and placed under a complex genetic control. Scanning the genome, we mapped three Quantitative Trait Loci (QTL) of noise, one locus being explained by an increase in noise when transcriptional elongation was impaired. Our results suggest that the level of stochasticity in particular molecular regulations may differ between multicellular individuals depending on their genotypic background. The complex genetic architecture of noise buffering couples genetic to non-genetic robustness and provides a molecular basis to the probabilistic nature of complex traits. PMID:18404214

  8. Stochastic Variational Method as Quantization Scheme I: Field Quantization of Complex Klein-Gordan Equation

    E-print Network

    T. Koide; T. Kodama

    2014-06-24

    Stochastic Variational Method (SVM) is the generalization of the variation method to the case with stochastic variables. In the series of papers, we investigate the applicability of SVM as an alternative field quantization scheme. Here, we discuss the complex Klein-Gordon equation. In this scheme, the Euler-Lagrangian equation for the stochastic fields leads to the functional Schroedinger equation, which in turn can be interpreted as the ideal fluid equation in the functional space. We show that the Fock state vector is given by the stationary solution of these differential equations and various results in the usual canonical quantization can be reproduced, including the effect of anti-particles. The present formulation is a quantization scheme based on commutable variables, so that there appears no ambiguity associated with the ordering of operators, for example, in the definition of Noether charges.

  9. Genic Heterozygosity and Variation in Permanent Translocation Heterozygotes of the OENOTHERA BIENNIS Complex

    PubMed Central

    Levy, Morris; Levin, Donald A.

    1975-01-01

    Genic heterozygosity and variation were studied in the permanent translocation heterozygotes Oenothera biennis I, Oe. biennis II, Oe. biennis III, Oe. strigosa, Oe. parviflora I, Oe. parviflora II, and in the related bivalent formers Oe. argillicola and Oe. hookeri. From variation at 20 enzyme loci, we find that translocation heterozygosity for the entire chromosome complex is accompanied by only moderate levels of genic heterozygosity: 2.8% in Oe. strigosa, 9.5% in Oe. biennis and 14.9% in Oe. parviflora. Inbred garden strains of Oe. argillicola exhibited 8% heterozygosity; neither garden nor wild strains of Oe. hookeri displayed heterozygosity and only a single allozyme genotype was found. The mean number of alleles per locus is only 1.30 in Oe. strigosa, 1.40 in Oe. biennis, and 1.55 in Oe. parviflora, compared to 1.40 in Oe. argillicola. Clearly, the ability to accumulate and/or retain heterozygosity and variability has not been accompanied by extraordinary levels of either. Clinal variation is evident at some loci in each ring-former. A given translocation complex may vary geographically in its allozymic constitution. From gene frequencies, Oe. biennis I, II, and III, Oe. strigosa and Oe. hookeri are judged to be very closely related, whereas Oe. argillicola seems quite remote; Oe. parviflora is intermediate to the two phylads. Gene frequencies also suggest that Oe. argillicola diverged from the Euoenothera progenitor about 1,000,000 years ago, whereas most of the remaining evolution in the complex has occurred within the last 150,000 years. PMID:17248680

  10. Fractional Kohn-Sham Occupancies from a Strong-Correlation Density Functional.

    PubMed

    Becke, Axel D

    2014-12-01

    It is not always possible in Kohn-Sham density-functional theory for the non-interacting reference state to have integer-only occupancies. Cases of "strong" correlation, with very small HOMO-LUMO gaps, involve fractional occupancies. At the transition states of symmetric avoided-crossing reactions, for example, representation of the correct density requires a 50/50 mixing of degenerate HOMOs. In a recent paper (Becke, J Chem Phys 139:021104, 2013) the "B13" strong-correlation density functional of Becke (J Chem Phys 138:074109, 2013 and 138:161101, 2013) was shown to give excellent barrier heights in symmetric avoided-crossing reactions. However, the calculations were performed only at reactant and transition-state geometries, where the fractional HOMO-LUMO occupancies in the latter are 50/50 by symmetry. In the present chapter, we compute full reaction curves for avoided crossings in H2?+?H2, ethylene (twisting around the double bond), and cyclobutadiene (double-bond automerization) by determining fractional occupancies variationally. We adopt a practical strategy for doing so which does not involve self-consistent B13 computations (not yet possible) and involves minimal cost. Single-bond dissociation curves for H2 and LiH are also presented. PMID:25467535

  11. 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

  12. Evaluation of somaclonal variation during somatic embryogenesis of interior spruce ( Picea glauca engelmannii complex) using culture morphology and isozyme analysis

    Microsoft Academic Search

    P. Ann K. Eastman; Fiona B. Webster; Jack A. Pitel; Dane R. Roberts

    1991-01-01

    Somaclonal variation during interior spruce (Picea glauca engelmannii complex) somatic embryogenesis was evaluated using culture morphology and isozyme analysis. Genotype-specific abscisic acid-dependent developmental profiles and isozyme patterns were similar for subclone and parent line embryogenic cultures and cotyledonary somatic embryos. Extensive analysis of fifteen hundred subclone embryos of one genotype revealed no isozyme pattern variation. Initiation of embryogenic cultures was

  13. Social and extra-pair mating in relation to major histocompatibility complex variation in common yellowthroats

    PubMed Central

    Bollmer, Jennifer L.; Dunn, Peter O.; Freeman-Gallant, Corey R.; Whittingham, Linda A.

    2012-01-01

    Females are thought to gain better-quality genes for their offspring by mating with particular males. Genes of the major histocompatibility complex (MHC) play a critical role in adaptive immunity, and several studies have examined female mate choice in relation to MHC variation. In common yellowthroats, females prefer males that have larger black facial masks, an ornament associated with MHC variation, immune function and condition. Here we also tested whether mating patterns are directly correlated with MHC diversity or similarity. Using pyrosequencing, we found that the presence of extra-pair young in the brood was not related to male MHC diversity or similarity between the female and her within-pair mate. Furthermore, extra-pair sires did not differ in overall diversity from males they cuckolded, or in their similarity to the female. MHC diversity is extremely high in this species, and it may limit the ability of females to assess MHC variation in males. Thus, mating may be based on ornaments, such as mask size, which are better indicators of overall male health and genetic quality. PMID:23055067

  14. Emergence of complex haplotypes from microevolutionary variation in sequence and structure of Colias phosphoglucose isomerase.

    PubMed

    Wang, Baiqing; Watt, Ward B; Aakre, Christopher; Hawthorne, Noah

    2009-05-01

    A molecular evolutionary explanation of natural genetic variation requires analysis of specific variants' evolutionary dynamics. To pursue this for phosphoglucose isomerase (PGI) of Colias butterflies, whose polymorphism is maintained by strong natural selection, we assembled a large data set of wild haplotypes, highly variable at the amino acid and DNA levels. The most common electrophoretic, i.e., charge macrostate, allele class, 3, is conserved in its pattern of charged amino acid residues. The next most common macrostate, 4, has multiple patterns of charge, i.e., microstates, while less common (1, 2, 5, 6) macrostates are very diverse. Macrostate 4 shows significant linkage disequilibrium (LD) among its variants, especially for two groups of five haplotypes each. We find extensive intragenic recombination among all haplotypes except the two high-LD groups of macrostate 4, which display none. Phyletic relations among haplotypes are largely reticulate, again except for the high-LD groups of macrostate 4, which form clades with strong bootstrap support. Charge-changing and linked charge-neutral amino acid variants occur in diverse parts of PGI's sequence. Homology-based modeling of PGI's structure shows that these regions are related spatially in ways suggesting functional interaction. The high-LD groups of macrostate 4 display parallel amino acid variation in these regions. This pattern of haplotype clades with high LD among multiple varying sites, emerging from chaotically recombining variation, may be a "signature" of refinement of complex adaptive sequences by recombination and selection. It should be tested further in this study system and others as a possibly general feature of the evolution of living complexity. PMID:19424742

  15. Evolutionary factors affecting Lactate dehydrogenase A and B variation in the Daphnia pulex species complex

    PubMed Central

    2011-01-01

    Background Evidence for historical, demographic and selective factors affecting enzyme evolution can be obtained by examining nucleotide sequence variation in candidate genes such as Lactate dehydrogenase (Ldh). Two closely related Daphnia species can be distinguished by their electrophoretic Ldh genotype and habitat. Daphnia pulex populations are fixed for the S allele and inhabit temporary ponds, while D. pulicaria populations are fixed for the F allele and inhabit large stratified lakes. One locus is detected in most allozyme surveys, but genome sequencing has revealed two genes, LdhA and LdhB. Results We sequenced both Ldh genes from 70 isolates of these two species from North America to determine if the association between Ldh genotype and habitat shows evidence for selection, and to elucidate the evolutionary history of the two genes. We found that alleles in the pond-dwelling D. pulex and in the lake-dwelling D. pulicaria form distinct groups at both loci, and the substitution of Glutamine (S) for Glutamic acid (F) at amino acid 229 likely causes the electrophoretic mobility shift in the LDHA protein. Nucleotide diversity in both Ldh genes is much lower in D. pulicaria than in D. pulex. Moreover, the lack of spatial structuring of the variation in both genes over a wide geographic area is consistent with a recent demographic expansion of lake populations. Neutrality tests indicate that both genes are under purifying selection, but the intensity is much stronger on LdhA. Conclusions Although lake-dwelling D. pulicaria hybridizes with the other lineages in the pulex species complex, it remains distinct ecologically and genetically. This ecological divergence, coupled with the intensity of purifying selection on LdhA and the strong association between its genotype and habitat, suggests that experimental studies would be useful to determine if variation in molecular function provides evidence that LDHA variants are adaptive. PMID:21767386

  16. DNA Sequence Variation at the Period Locus within and among Species of the Drosophila Melanogaster Complex

    PubMed Central

    Kliman, R. M.; Hey, J.

    1993-01-01

    A 1.9-kilobase region of the period locus was sequenced in six individuals of Drosophila melanogaster and from six individuals of each of three sibling species: Drosophila simulans, Drosophila sechellia and Drosophila mauritiana. Extensive genealogical analysis of 174 polymorphic sites reveals a complex history. It appears that D. simulans, as a large population still segregating very old lineages, gave rise to the island species D. mauritiana and D. sechellia. Rather than considering these speciation events as having produced ``sister'' taxa, it seems more appropriate to consider D. simulans a parent species to D. sechellia and D. mauritiana. The order, in time, of these two phylogenetic events remains unclear. D. mauritiana supports a large number of polymorphisms, many of which are shared with D. simulans, and so appears to have begun and persisted as a large population. In contrast, D. sechellia has very little variation and seems to have experienced a severe population bottleneck. Alternatively, the low variation in D. sechellia could be due to recent directional selection and genetic hitchhiking at or near the per locus. PMID:8436278

  17. Variations in the identity and complexity of endosymbiont combinations in whitefly hosts

    PubMed Central

    Zchori-Fein, Einat; Lahav, Tamar; Freilich, Shiri

    2014-01-01

    The target of natural selection is suggested to be the holobiont - the organism together with its associated symbiotic microorganisms. The well-defined endosymbiotic communities of insects make them a useful model for exploring the role of symbiotic interactions in shaping the functional repertoire of plants and animals. Here, we studied the variations in the symbiotic communities of the sweet potato whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) by compiling a dataset of over 2000 individuals derived from several independent screenings. The secondary endosymbionts harbored by each individual were clustered into entities termed Facultative Endosymbiont Combinations (FECs), each representing a natural assemblage of co-occurring bacterial genera. The association of FECs with whitefly individuals stratified the otherwise homogeneous population into holobiont units. We both identified bacterial assemblages that are specific to whitefly groups sharing unique genetic backgrounds, and characterized the FEC variations within these groups. The analysis revealed that FEC complexity is positively correlated with both distance from the equator and specificity of the genetic clade of the host insect. These findings highlight the importance of symbiotic combinations in shaping the distribution patterns of B. tabaci and possibly other insect species. PMID:25071729

  18. Kohn anomalies and non-adiabaticity in doped carbon nanotubes

    E-print Network

    Nicolas Caudal; A. Marco Saitta; Michele Lazzeri; Francesco Mauri

    2007-02-21

    The high-frequency Raman-active phonon modes of metallic single-walled carbon nanotubes (SWNTs) are thought to be characterized by Kohn anomalies (KAs), which are expected to be modified by the doping-induced tuning of the Fermi energy level $\\epsilon_F$, obtained through the intercalation of SWNTs with alkali atoms or by the application of a gate potential. We present a Density-Functional Theory (DFT) study of the phonon properties of a (9,9) metallic SWNT as a function of electronic doping. For such study, we use, as in standard DFT calculations of vibrational properties, the Born-Oppenheimer (BO) approximation. We also develop an analytical model capable of reproducing and interpreting our DFT results. Both DFT calculations and this model predict, for increasing doping levels, a series of EPC-induced KAs in the vibrational mode parallel to the tube axis at the $\\mathbf\\Gamma$ point of the Brillouin zone, usually indicated in Raman spectroscopy as the $G^-$ peak. Such KAs would arise each time a new conduction band is populated. However, we show that they are an artifact of the BO approximation. The inclusion of non-adiabatic (NA) effects dramatically affects the results, predicting KAs at $\\mathbf\\Gamma$ only when $\\epsilon_F$ is close to a band crossing $E_{X}$. For each band crossing a double KA occurs for $\\epsilon_F=E_{X}\\pm \\hbar\\omega/2$, where $\\hbar\\omega$ is the phonon energy. In particular, for a 1.2 $nm$ metallic nanotube, we predict a KA to occur in the so-called $G^-$ peak at a doping level of about $N_{el}/C=\\pm 0.0015$ atom ($\\epsilon_F\\approx \\pm 0.1 ~eV$). Furthermore, we predict that the Raman linewidth of the $G^-$ peak significantly decreases for $|\\epsilon_F| \\geq \\hbar\\omega/2$.

  19. Relating variation in species composition to environmental variables: a multi-taxon study in an Indonesian coral reef complex

    Microsoft Academic Search

    Daniel F. R. Cleary; Lyndon De Vantier; Giyanto; Lyle Vail; Philip Manto; Nicole J. de Voogd; Paola G. Rachello-Dolmen; Yosephine Tuti; Agus Budiyanto; Jackie Wolstenholme; Bert W. Hoeksema; Suharsono

    2008-01-01

    .  In order to manage and conserve coral reefs it is essential to understand the factors that structure reef communities. In\\u000a Indonesia’s Jakarta Bay – Pulau Seribu reef complex, pronounced on-to-offshore variation in a number of variables was observed.\\u000a Live coral cover, and echinoderm and fish species richness were higher in midshore sites than either in- or offshore sites.\\u000a Variation in

  20. Sulfide saturation history of the Stillwater Complex, Montana: chemostratigraphic variation in platinum group elements

    NASA Astrophysics Data System (ADS)

    Keays, Reid R.; Lightfoot, Peter C.; Hamlyn, Paul R.

    2012-01-01

    A platinum group element (PGE) investigation of a 5.3 km-thick stratigraphic section of the Stillwater Complex, Montana was undertaken to refine and test a geochemical technique to explore for platiniferous horizons in layered mafic/ultramafic complexes. PGE, Au, major, and trace elements were determined in 92 samples from outcrops along traverses in the Chrome Mountain and Contact Mountain areas in the western part of the Stillwater Complex where the J-M reef occurs ˜1,460 m above the floor of the intrusion. A further 29 samples from a drill hole cored in the immediate vicinity of the J-M reef were analyzed to detail compositional variations directly above and below the J-M reef. Below the J-M reef, background concentrations of Pt (10 ppb) and Pd (7 ppb) are features of peridotites with intermediate S concentrations (mostly 100-200 ppm) and rocks from the Bronzitite, Norite I, and Gabbronorite I zones (mostly <100 ppm S). A sustained increase in S abundance commences at the J-M reef and continues to increase and peaks in the center of the 600 m-thick middle banded series. Over this same interval, Pt, Pd, and Au are initially elevated and then decrease in the order Pd > Pt > Au. Within the middle and upper banded series, S abundances fluctuate considerably, but exhibit an overall upward increase. The behavior of these elements records periodic sulfide saturation during deposition of the Peridotite zone, followed by crystallization under sulfide-undersaturated conditions until saturation is achieved at the base of the J-M reef. Following formation of the reef, sulfide-saturated conditions persisted throughout the deposition of most of the remaining Lower Layered Series. This resulted in a pronounced impoverishment in PGE abundance in the remaining magma, a condition that continued throughout deposition of the remainder of a succession, which is characterized by very low Pt (1.5 ppb) and Pd (0.7 ppb) abundances. Because only unmineralized rock was selected for study in the 5.3 km-thick section, the results provide an unbiased picture of the variation in background PGE levels during crystallization of the Stillwater Complex. In contrast, the variations in the drill core samples through the reef provide a detailed record of ore formation. Plots of Pt, Pd, Pd/S, and Pt + Pd as a function of stratigraphic height in the intrusion show that the location of the J-M reef is defined by an abrupt change in these concentrations and ratios. Although this is the most abrupt change, three other anomalies in PGE abundance and ratios are apparent in the profiles and coincide with known laterally extensive sub-economic sulfide concentrations above the J-M reef. The uppermost of these is the PGE-bearing Picket Pin sulfide horizon. The relative ease with which mineralized horizons can be pinpointed in these diagrams indicates that a similar approach could be used in exploration programs in other ultramafic/mafic intrusions. Our observations exclude the possibilities of either magma mixing within the Stillwater chamber or the fluxing of a volatile-rich fluid as the mechanisms responsible for the genesis of the J-M reef. Rather, our data indicate that the J-M reef formed from a parental magma that was strongly enriched in PGE; this magma likely formed at depth below the Stillwater magma chamber by the interaction of the parental magma with S-rich meta-sedimentary rocks, followed by the re-dissolution of these sulfides in the Stillwater magma.

  1. Corrections to the Kohn-Luttinger wave function for donors in silicon

    NASA Astrophysics Data System (ADS)

    Castner, T. G., Jr.

    2008-05-01

    Corrections to the Kohn-Luttinger ground state wave function from subsidiary minima are calculated using first order perturbation theory and a variational approach. The very precise Fermi contact constants ahpf(Rnmm) of the Hale-Mieher data determine a set of linear equations based on donor-dependent ratios such as ??d(333&barbelow;)?/??d(115)?=Kd=[ahpf(333&barbelow;)/ahpf(115)]1/2 . The minima considered [ L1(cb1) , ?2'(cb4) , ?(cb5) , ?W(cb2) , ?2'(cb5) , and XU(cb2) ] are each characterized by an A(k-kj) , a phase eikj?r and envelope functions F?j (?=x,y,z) . The ?d employed contains four terms not included in the comprehensive Ivey-Mieher (IM) calculation with pseudopotential Bloch functions for eight bands. Two terms arise from the crucial tetrahedral potential Ut?xyzf(r) ignored in most earlier work. The admixture coefficients are varied subject to the three constraint equations to minimize the mean-squared deviations of the calculated and experimental ahpf(nnm) of the 11 odd sites identified by IM. The results are not only vastly improved (compared to IM) for site (111) but also reverse the IM assignments for (331) and (551). Some of the inverted donor anomalies are explained. The average root-mean-squared deviation ?rmsd? for the 11 sites is better than the IM results for these odd sites. The results suggest that additional changes in the zeroth order ?KL may be required to improve the overall agreement. The uniaxial stress parameters id and 2f/a(0) are also reconsidered with some of the new corrections and compared with experimental values.

  2. Superconductivityand absence of a Kohn anomaly in the quasi-one-dimensional organic conductor : (TMTSF)2AsF6 (+)

    E-print Network

    Paris-Sud XI, Université de

    L-607 Superconductivityand absence of a Kohn anomaly in the quasi-one-dimensional organic conductor Kohn à 2 kF à basse température et à pression atmosphérique. Abstract. 2014 Superconductivity has been under 12 kbar. The establishment of the superconducting state is apparently not related to the existence

  3. Fluid flow in subduction zones: evidence from Nd and Sr-isotope variations in metabasalts of the Franciscan complex, California

    Microsoft Academic Search

    Bruce K. Nelson

    1995-01-01

    Greenstone, blueschist and eclogite metabasaltic blocks from the Franciscan complex of California preserve extensive petrographic and chemical evidence for interaction with hydrous fluids at high- P, low- T metamorphic conditions. The Nd and Sr isotope variations within and among the blocks constrain the origin of the basaltic protoliths, the nature of the fluid metasomatism that occurred within the upper levels

  4. Natural variation for carbohydrate content in Arabidopsis. Interaction with complex traits dissected by quantitative genetics.

    PubMed

    Calenge, Fanny; Saliba-Colombani, Véra; Mahieu, Stéphanie; Loudet, Olivier; Daniel-Vedele, Françoise; Krapp, Anne

    2006-08-01

    Besides being a metabolic fuel, carbohydrates play important roles in plant growth and development, in stress responses, and as signal molecules. We exploited natural variation in Arabidopsis (Arabidopsis thaliana) to decipher the genetic architecture determining carbohydrate content. A quantitative trait locus (QTL) approach in the Bay-0 x Shahdara progeny grown in two contrasting nitrogen environments led to the identification of 39 QTLs for starch, glucose, fructose, and sucrose contents representing at least 14 distinct polymorphic loci. A major QTL for fructose content (FR3.4) and a QTL for starch content (ST3.4) were confirmed in heterogeneous inbred families. Several genes associated with carbon (C) metabolism colocalize with the identified QTL. QTLs for senescence-related traits, and for flowering time, water status, and nitrogen-related traits, previously detected with the same genetic material, colocalize with C-related QTLs. These colocalizations reflect the complex interactions of C metabolism with other physiological processes. QTL fine-mapping and cloning could thus lead soon to the identification of genes potentially involved in the control of different connected physiological processes. PMID:16798941

  5. Variation in genes of the epidermal differentiation complex in German atopic dermatitis patients.

    PubMed

    Stemmler, S; Nothnagel, M; Parwez, Q; Petrasch-Parwez, E; Epplen, J T; Hoffjan, S

    2009-08-01

    The filaggrin (FLG) gene is one of the most widely replicated susceptibility genes for atopic dermatitis (AD) so far. Yet, FLG mutations cannot fully account for the original linkage peak on chromosome 1q21, a region comprising the so-called epidermal differentiation complex (EDC). Since the EDC contains numerous genes relevant for epidermal differentiation, we sought to evaluate variation in other genes located in this region in a German AD case-control cohort. Thirty-two single nucleotide polymorphisms (SNPs) in 21 genes across the EDC were genotyped in 402 unrelated AD patients and 325 non-atopic controls by means of restriction enzyme digestion or TaqMan assays. Allele and genotype frequencies were tested for differences between patients and controls by logistic regression. Haplotype frequencies were evaluated using the famhap software. Except for the already known association with FLG, we did not identify any additional significant associations of EDC genes with AD. Thus, in this German cohort, there is no evidence that additional genes in the EDC region apart from FLG contribute substantially to AD pathogenesis. PMID:19601998

  6. Genetic variation of the mitochondrial Complex I subunit NDUFV2 and Parkinson disease

    PubMed Central

    Nishioka, Kenya; Vilariño-Güell, Carles; Cobb, Stephanie A.; Kachergus, Jennifer M.; Ross, Owen A.; Hentati, Emna; Hentati, Faycal; Farrer, Matthew J.

    2010-01-01

    NADH dehydrogenase ubiquinone flavoprotein 2 (NDUFV2), encoding a subunit of mitochondrial complex I, is a candidate gene for several neuronal diseases; schizophrenia, bipolar disorder and Parkinson disease (PD). We screened the entire coding region of NDUFV2 in 33 familial PD patients of North African Arab-Berber ethnicity in which all known genetic forms of PD had been excluded. We detected one novel substitution p.K209R (c.626A>G) in one PD. Segregation analysis within the family is inconclusive due to small sample size, but consistent with autosomal dominant mode of inheritance. Subsequent screening of this mutation in ethnically-matched sporadic PD patients (n=238) and controls (n=371) identified p.K209R in one additional patient. The clinical features of the mutation carriers revealed a mild form of parkinsonism with a prognosis similar to idiopathic PD. Our findings suggest further studies addressing the role of NDUFV2 variation in PD may be warranted. PMID:20971673

  7. Sexual selection explains more functional variation in the mammalian major histocompatibility complex than parasitism

    PubMed Central

    Winternitz, J. C.; Minchey, S. G.; Garamszegi, L. Z.; Huang, S.; Stephens, P. R.; Altizer, S.

    2013-01-01

    Understanding drivers of genetic diversity at the major histocompatibility complex (MHC) is vitally important for predicting how vertebrate immune defence might respond to future selection pressures and for preserving immunogenetic diversity in declining populations. Parasite-mediated selection is believed to be the major selective force generating MHC polymorphism, and while MHC-based mating preferences also exist for multiple species including humans, the general importance of mate choice is debated. To investigate the contributions of parasitism and sexual selection in explaining among-species variation in MHC diversity, we applied comparative methods and meta-analysis across 112 mammal species, including carnivores, bats, primates, rodents and ungulates. We tested whether MHC diversity increased with parasite richness and relative testes size (as an indicator of the potential for mate choice), while controlling for phylogenetic autocorrelation, neutral mutation rate and confounding ecological variables. We found that MHC nucleotide diversity increased with parasite richness for bats and ungulates but decreased with parasite richness for carnivores. By contrast, nucleotide diversity increased with relative testes size for all taxa. This study provides support for both parasite-mediated and sexual selection in shaping functional MHC polymorphism across mammals, and importantly, suggests that sexual selection could have a more general role than previously thought. PMID:23966643

  8. Sexual selection explains more functional variation in the mammalian major histocompatibility complex than parasitism.

    PubMed

    Winternitz, J C; Minchey, S G; Garamszegi, L Z; Huang, S; Stephens, P R; Altizer, S

    2013-10-22

    Understanding drivers of genetic diversity at the major histocompatibility complex (MHC) is vitally important for predicting how vertebrate immune defence might respond to future selection pressures and for preserving immunogenetic diversity in declining populations. Parasite-mediated selection is believed to be the major selective force generating MHC polymorphism, and while MHC-based mating preferences also exist for multiple species including humans, the general importance of mate choice is debated. To investigate the contributions of parasitism and sexual selection in explaining among-species variation in MHC diversity, we applied comparative methods and meta-analysis across 112 mammal species, including carnivores, bats, primates, rodents and ungulates. We tested whether MHC diversity increased with parasite richness and relative testes size (as an indicator of the potential for mate choice), while controlling for phylogenetic autocorrelation, neutral mutation rate and confounding ecological variables. We found that MHC nucleotide diversity increased with parasite richness for bats and ungulates but decreased with parasite richness for carnivores. By contrast, nucleotide diversity increased with relative testes size for all taxa. This study provides support for both parasite-mediated and sexual selection in shaping functional MHC polymorphism across mammals, and importantly, suggests that sexual selection could have a more general role than previously thought. PMID:23966643

  9. 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

  10. A Constitution for Israel: The Design of the Leo Kohn Proposal, 1948

    Microsoft Academic Search

    Amihai Radzyner

    2010-01-01

    :UN General Assembly Resolution 181 declared that the states which will be established in the Land of Israel should accept a constitution. Dr. Leo Kohn was chosen to write the constitution proposal for the Jewish State. The article describes his constitutional project, which was carried out in three stages between the end of 1947 and October 1948. It identifies the

  11. A Constitution for Israel: The Design of the Leo Kohn Proposal, 1948

    Microsoft Academic Search

    Amihai Radzyner

    2010-01-01

    UN General Assembly Resolution 181 declared that the states which will be established in the Land of Israel should accept a constitution. Dr. Leo Kohn was chosen to write the constitution proposal for the Jewish State. The article describes his constitutional project, which was carried out in three stages between the end of 1947 and October 1948. It identifies the

  12. 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

  13. Robin M. Kohn University of Central Florida School of Social Work

    E-print Network

    Van Stryland, Eric

    Robin M. Kohn University of Central Florida School of Social Work P.O. Box 163358 Orlando, FL 32816-3358 (407) 823-2967 EDUCATION Masters in Clinical Social Work (1979) Florida State University Tallahassee/Facilitator of ALS Support Group August 2002-Present Bachelors in Social Work (BSW) Program Coordinator August 2001

  14. Describing static correlation in bond dissociation by KohnSham density functional theory

    E-print Network

    dissociation in H2 in a spin-restricted Kohn­Sham formalism, i.e., without artificial symmetry breaking. We, as exemplified by the H2 + molecule, where 100% exact exchange mixing and zero correlation en- ergy would wave function. A famous example is the dissoci- ating H2 molecule. The proper singlet KS ground state

  15. 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 thought. Our data suggest that the symbiont, but not the host, is restricted by biogeographical boundaries. PMID:25275632

  16. 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 data suggest that the symbiont, but not the host, is restricted by biogeographical boundaries. PMID:25275632

  17. Fluid flow in subduction zones: evidence from Nd and Sr-isotope variations in metabasalts of the Franciscan complex, California

    Microsoft Academic Search

    Bruce K. Nelson

    1995-01-01

    Greenstone, blueschist and eclogite metabasaltic blocks from the Franciscan complex of California preserve extensive petrographic and chemical evidence for interaction with hydrous fluids at high-P, low-T metamorphic conditions. The Nd and Sr isotope variations within and among the blocks constrain the origin of the basaltic protoliths, the nature of the fluid metasomatism that occurred within the upper levels (15–45 km)

  18. Ploidy variation in the cultivated yams ( Dioscorea cayenensis-Dioscorea rotundata complex) from Cameroon as determined by flow cytometry

    Microsoft Academic Search

    A. Dansi; H. D. Mignouna; M. Pillay; S. Zok

    2001-01-01

    The ploidy levels of the twenty-two yam (Dioscorea cayenensis-D. rotundata complex) cultivars within germplasm Cameroon Guinea yam were determined by flow cytometry. Three different ploidy levels\\u000a (4x,6x, 8x) were detected within the samples analysed. Fifteen cultivars were tetraploids, five were hexaploids, and two were\\u000a octoploids. The cultivar group EKOTO showed a high level of ploidy variation with tetraploid, hexaploid and

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

    SciTech Connect

    Hinckley, C.M.

    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.

  20. Genetic drift outweighs balancing selection in shaping post-bottleneck major histocompatibility complex variation in New Zealand robins (Petroicidae).

    PubMed

    Miller, Hilary C; Lambert, David M

    2004-12-01

    The Chatham Island black robin, Petroica traversi, is a highly inbred, endangered passerine with extremely low levels of variation at hypervariable neutral DNA markers. In this study we investigated variation in major histocompatibility complex (MHC) class II genes in both the black robin and its nonendangered relative, the South Island robin Petroica australis australis. Previous studies have shown that Petroica have at least four expressed class II B MHC genes. In this study, the sequences of introns flanking exon 2 of these loci were characterized to design primers for peptide-binding region (PBR) sequence analysis. Intron sequences were comprised of varying numbers of repeated units, with highly conserved regions immediately flanking exon 2. Polymerase chain reaction primers designed to this region amplified three or four sequences per black robin individual, and eight to 14 sequences per South Island robin individual. MHC genes are fitness-related genes thought to be under balancing selection, so they may be more likely to retain variation in bottlenecked populations. To test this, we compared MHC variation in the black robin with artificially bottlenecked populations of South Island robin, and with their respective source populations, using restriction fragment length polymorphism analyses and DNA sequencing of the PBR. Our results indicate that the black robin is monomorphic at class II B MHC loci, while both source and bottlenecked populations of South Island robin have retained moderate levels of variation. Comparison of MHC variation with minisatellite DNA variation indicates that genetic drift outweighs balancing selection in determining MHC diversity in the bottlenecked populations. However, balancing selection appears to influence MHC diversity over evolutionary timescales, and the effects of gene conversion are evident. PMID:15548285

  1. Physics of transformation from Schrödinger theory to Kohn-Sham density-functional theory: Application to an exactly solvable model

    Microsoft Academic Search

    Zhixin Qian; Viraht Sahni

    1998-01-01

    According to Hohenberg-Kohn-Sham density-functional theory (DFT), and its constrained search formulation, the Schrödinger ground-state wave function Psi is a functional of the ground-state electronic density rho(r). But the explicit functional dependence of Psi on rho is unknown. It is, however, possible to describe Kohn-Sham (KS) DFT and its electron-interaction energy functional and functional derivative rigorously in terms of the wave

  2. Determination of Kohn-Sham effective potentials from electron densities using the differential virial theorem.

    PubMed

    Ryabinkin, Ilya G; Staroverov, Viktor N

    2012-10-28

    We present an accurate method for constructing the Kohn-Sham effective potential corresponding to a given electron density in one-dimensional and spherically symmetric systems. The method is based on the differential virial theorem--an exact relation between the effective potential, the electron density, and the kinetic energy density. A distinctive feature of the proposed technique is that it employs a size-consistent bosonic reference potential to ensure the correct asymptotic behavior of the resulting Kohn-Sham potential. We describe a practical implementation of our method and use it to obtain high-quality exchange-correlation and correlation potentials of the neon and argon atoms from ab initio densities generated in large Slater- and Gaussian-type basis sets. PMID:23126701

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

    E-print Network

    Mott, Richard

    implicated in complex disease such as asthma, diabetes, heart disease or cancer. Recent and more of complex diseases in humans has been slow. This is despite the fact that genetic effects frequently account limited successes with asthma (Van Eerdewegh et al. 2002; Allen et al. 2003; Zhang et al. 2003; Laitinen

  4. Periodicity of the time-dependent Kohn-Sham equation and the Floquet theorem

    E-print Network

    V. Kapoor; M. Ruggenthaler; D. Bauer

    2013-02-25

    The Floquet theorem allows to reformulate periodic time-dependent problems such as the interaction of a many-body system with a laser field in terms of time-independent, field-dressed states, also known as Floquet states. If this was possible for density functional theory as well, one could reduce in such cases time-dependent density functional theory to a time-independent Floquet density functional theory. We analyze under which conditions the Floquet theorem is applicable in a density-functional framework. By employing numerical {\\em ab initio} solutions of the interacting time-dependent Schr\\"odinger equation with time-periodic external potentials we show that the exact effective potential in the corresponding Kohn-Sham equation is {\\em not} unconditionally periodic. Whenever several Floquet states in the interacting system are involved in a physical process the corresponding Hartree-exchange-correlation potential is not periodic with the external frequency only. Using an analytically solvable example we demonstrate that, in general, the periodicity of the time-dependent Kohn-Sham Hamiltonian cannot be restored by choosing a different initial state. Only if the external periodic potential is sufficiently weak such that the initial state of the interacting system evolves adiabatically to a single, field-dressed state, the resulting Kohn-Sham system admits the application of the Floquet theorem.

  5. 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.

  6. 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

  7. Quantitative Statistical Analysis of Atomic Scale Structural and Chemical Variations in Complex Oxides Interfaces

    NASA Astrophysics Data System (ADS)

    Yang, Hao

    Grain boundaries (GBs) are known to have far-reaching effects on the electrical and mechanical properties of materials. Understanding the atomic scale mechanisms behind these effects requires an accurate determination of the interplay between GB structure and composition. Based on the analysis of a range of grain boundaries using aberration corrected scanning transmission electron microscopy (STEM), a general structural units model has been derived for the structure of grain boundaries in various dense packing cubic materials including FCC metals, perovskites and fluorites. The similarities in the observed grain boundary structures of these materials originate from related space (and point) group symmetries of the parent structures. The presence of structural variations away from the general structural units model may be caused by frustrations of certain symmetry operations that result from the incorporation of point defects (vacancies and impurities). A clear understanding of the similarity and variation in grain boundary atomic structures will not only provide a means to infer the structure-property relationships in broad classes of materials, but also enables us eventually to effectively manipulate the GB structures to achieve better materials properties. To understand these chemical induced variations, and further quantify exactly how atomic scale variations at the boundary plane extend to the practical mesoscale operating length of the system, statistical analysis has been applied to the aberration corrected STEM Z-contrast images acquired from a series of undoped and doped SrTiO3 GBs. In order to understand the effects of oxygen vacancies incorporation, in-situ characterization of GB atomic structures were performed using the Environmental TEM under the reduced gas and heating environment. This analysis of GB similarity and variation provides insights into the structure-composition relationship in GBs to understand the influence of nonstoichiometry and dopant segregations. It also helps to determine experimentally the energetics behind the formation of grain boundary structures to predict GB formation in various materials.

  8. Syntheses of Variations of Stereogenic-at-Metal Imido Alkylidene Complexes of Molybdenum

    E-print Network

    Marinescu, Smaranda C.

    In this paper we describe the syntheses of several new stereogenic-at-metal imido alkylidene complexes of molybdenum, Mo(NR)(CHR?)(X)(Y), many of which had to be prepared through selective nucleophilic displacement reactions ...

  9. Morphologic variation and classification of the North American Aristida purpurea complex (Gramineae)

    Microsoft Academic Search

    Kelly W. Allred

    1984-01-01

    The morphology of the Purpureae Group of North AmericanAristida is assessed by principal components and statistical analyses. Long considered a complex of about eight species, a mosaic\\u000a of intergrading phenetic forms is revealed and the complex is reduced to one species with seven varieties. The taxa that are\\u000a recognized areAristida purpurea var.purpurea, var.nealleyi (comb. nov.), var.curvifolia (comb. nov.), var.parishii (comb.

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

    SciTech Connect

    NONE

    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.

  11. 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, C.

    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 moisture, since t-test's among adjacent plots with different LULCs showed significant differences. These results confirm that a remote sensing approach that considers homogeneous LULC landscape fragments can be used to identify landscape units of similar soil moisture behavior under heterogeneous landscapes. In addition, the in situ USDA-ARS network will serve better in remote sensing studies in which sensors with fine spatial resolution are evaluated. This study is a first step towards identifying landscape units that can be monitored using the single point reading of the USDA-ARS stations network. ?? 2008 Elsevier B.V.

  12. Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads.

    PubMed

    Moncunill, Valentí; Gonzalez, Santi; Beà, Sílvia; Andrieux, Lise O; Salaverria, Itziar; Royo, Cristina; Martinez, Laura; Puiggròs, Montserrat; Segura-Wang, Maia; Stütz, Adrian M; Navarro, Alba; Royo, Romina; Gelpí, Josep L; Gut, Ivo G; López-Otín, Carlos; Orozco, Modesto; Korbel, Jan O; Campo, Elias; Puente, Xose S; Torrents, David

    2014-11-01

    The development of high-throughput sequencing technologies has advanced our understanding of cancer. However, characterizing somatic structural variants in tumor genomes is still challenging because current strategies depend on the initial alignment of reads to a reference genome. Here, we describe SMUFIN (somatic mutation finder), a single program that directly compares sequence reads from normal and tumor genomes to accurately identify and characterize a range of somatic sequence variation, from single-nucleotide variants (SNV) to large structural variants at base pair resolution. Performance tests on modeled tumor genomes showed average sensitivity of 92% and 74% for SNVs and structural variants, with specificities of 95% and 91%, respectively. Analyses of aggressive forms of solid and hematological tumors revealed that SMUFIN identifies breakpoints associated with chromothripsis and chromoplexy with high specificity. SMUFIN provides an integrated solution for the accurate, fast and comprehensive characterization of somatic sequence variation in cancer. PMID:25344728

  13. 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

  14. Emergence of Complex Haplotypes from Microevolutionary Variation in Sequence and Structure of Colias Phosphoglucose Isomerase

    Microsoft Academic Search

    Baiqing Wang; Ward B. Watt; Christopher Aakre; Noah Hawthorne

    2009-01-01

    A molecular evolutionary explanation of natural genetic variation requires analysis of specific variants’ evolutionary dynamics.\\u000a To pursue this for phosphoglucose isomerase (PGI) of Colias butterflies, whose polymorphism is maintained by strong natural selection, we assembled a large data set of wild haplotypes,\\u000a highly variable at the amino acid and DNA levels. The most common electrophoretic, i.e., charge macrostate, allele class,

  15. A review of the compositional variation of amphiboles in alkaline plutonic complexes

    NASA Astrophysics Data System (ADS)

    Mitchell, Roger H.

    1990-12-01

    Compositional data for amphiboles occurring in alkaline plutonic complexes are reviewed and a standard procedure for plotting these data in an isometric prism is proposed. The main compositional trend found in both oversaturated and undersaturated complexes of either miascitic or peralkaline affinity is referred to as the primary magmatic trend. Amphiboles range in composition from magnesian hastingsitic hornblende and ferro-edenitic hornblende through katophorite to ferro-richterite and arfvedsonite. Individual complexes differ with respect to the amphibole {Mg}/{Fe} and {Si}/{Al} ratio and the extent of Na-enrichment. Extensive or limited ranges in the composition of amphiboles may occur in a given complex. A subtrend found only in oversaturated complexes is from ferro-edenitic hornblende to ferro-actinolite. This trend termed the ferro-actinolitic subtrend is found only in low temperature non-peralkaline residua. Some aluminous nepheline syenites and associated alkali gabbros contain amphiboles which range in composition from kaersutite through ferroan pargasitic hornblende to hastingsite. This trend termed the primary miascitic magmatic trend is is one of decreasing {Mg}/{Fe}, at essentially constant {Si}/{Al} and Ca content. Na-enrichment does not occur. Amphiboles formed by reactions of preexisting phases with hydrothermal or deuteric fluids are termed the late stage reaction assemblage. Amphibole compositional trends from calcic through sodic-calcic to sodic amphiboles reflect decreasing temperature and oxygen fugacity at or below the QFM oxygen buffer. The compositional trends are of use in determining petrogenetic relationships between apparently consanguineous syenites.

  16. Genetic variation in the DAOA gene complex: Impact on susceptibility for schizophrenia and on cognitive performance

    PubMed Central

    Opgen-Rhein, Carolin; Lencz, Todd; Burdick, Katherine E.; Neuhaus, Andres H; DeRosse, Pamela; Goldberg, Terry E.; Malhotra, Anil K.

    2008-01-01

    Introduction The genetic region coding for D-amino acid oxidase activator (DAOA) is considered an intriguing susceptibility locus for schizophrenia. However, association studies have often resulted in conflicting findings, and the risk conferring variants and their biological impact remain elusive. Our aim in this study was to investigate the relationship between DAOA variation and schizophrenia, and the influence of DAOA on cognitive performance. Methods We analyzed block structure and association patterns of a ~173 kb region on chromosome 13q33, applying genotype data of 55 SNPs derived from Caucasian North American sample (178 cases, 144 healthy controls). Haplotypes were assigned using the program PHASE and frequencies compared between cases and controls. We applied MANOVA to investigate the relationship between the identified risk haplotype on cognitive performance. Results We identified multiple haplotypes within the region containing the DAOA gene. Of these, one was significantly associated with schizophrenia, being over-represented in schizophrenia versus healthy controls. This haplotype was also associated with one aspect of cognitive performance, semantic fluency. Carriers of the risk haplotype showed better semantic fluency than non-carriers. Conclusions We report a significant effect of DAOA variation on risk for schizophrenia. Moreover, we identified a relationship between DAOA genetic variation and specific aspects of neurocognitive function. As the identified DAOA risk haplotype was associated with better performance on a semantic fluency measure, further work is required to identify the mechanism of DAOA action on CNS function, including the possibility of a role for balanced selection at this locus. PMID:18541412

  17. 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.

  18. 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.

  19. Variations of trends of indicators describing complex systems: Change of scaling precursory to extreme events

    NASA Astrophysics Data System (ADS)

    Keilis-Borok, V. I.; Soloviev, A. A.

    2010-09-01

    Socioeconomic and natural complex systems persistently generate extreme events also known as disasters, crises, or critical transitions. Here we analyze patterns of background activity preceding extreme events in four complex systems: economic recessions, surges in homicides in a megacity, magnetic storms, and strong earthquakes. We use as a starting point the indicators describing the system's behavior and identify changes in an indicator's trend. Those changes constitute our background events (BEs). We demonstrate a premonitory pattern common to all four systems considered: relatively large magnitude BEs become more frequent before extreme event. A premonitory change of scaling has been found in various models and observations. Here we demonstrate this change in scaling of uniformly defined BEs in four real complex systems, their enormous differences notwithstanding.

  20. Variation of stability constants of thorium and uranium oxalate complexes with ionic strength

    SciTech Connect

    Erten, H.N; Mohammed, A.K.; Choppin, G.R. [Florida State Univ., Tallahassee, FL (United States). Dept. of Chemistry

    1993-12-31

    Extraction of Th(IV) and UO{sub 2}{sup 2+} by a solution of TTA and HDEHP, respectively, in toluene was used to obtain stability constants of their oxalate complexes in 1, 3, 5, 7 and 9 M ionic strength (NaClO{sub 2}) solutions. The complexes formed were the MOx, MHOx, MOx{sub 2} and M(HOx){sub 2} (M = Th, UO{sub 2}) species. The values were analyzed by the Specific Interaction Theory and agreed to I {le} 3 M but required an additional term for fitting at I > 3 M.

  1. 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

  2. Structure, histochemistry, ultrastructure and seasonal variations of the male prostatic complex in the black Myotis bat, Myotis nigricans (Chiroptera: Vespertilionidae).

    PubMed

    Negrin, Ana C; Beguelini, Mateus R; Puga, Cintia C I; Christante, Caroline M; Bueno, Larissa M; Morielle-Versute, Eliana; Vilamaior, Patrícia S L; Taboga, Sebastião R

    2014-10-01

    Chiroptera are one of the most diverse orders of mammals and a unique group within Mammalia that posses a wide geographic distribution and considerable variability in reproductive strategies. The aims of the present study were to characterise the male prostatic complex of the bat Myotis nigricans (Vespertilionidae) and evaluate seasonal variations in the prostatic complex of M. nigricans specifically. Twenty-three sexually mature specimens (four sample groups: winter, spring, summer and autumn) were subjected to macroscopic, microscopic, morphometric and ultrastructural analyses. The reproductive accessory glands of M. nigricans were found to be composed of a multilobed complex associated with the urethra and a pair of inguinal bulbourethral glands. The complex was composed of three bilobed prostatic regions (ventral, dorsolateral and dorsal) with no ampullary gland and seminal vesicles. This pattern of lobulation is very similar to that described for the prostate of rodents; however, it differs from that of other mammals and even other families of bats (e.g. Phyllostomidae and Molossidae). Each prostatic region in M. nigricans has unique and distinctive characteristics, which synchronise to establish the main reproductive peak of the species in summer. The data also indicated an asynchrony in the activity of primary and secondary reproductive organs in the annual reproductive cycle of M. nigricans in São Paulo State, Brazil. PMID:25294361

  3. Variation in the Festuca brachyphylla (Poaceae) complex in Svalbard, elucidated by chromosome numbers and isozymes

    Microsoft Academic Search

    ANE S. GULDAHL; LIV BORGEN; INGER NORDAL

    2001-01-01

    Contrasting with former taxonomic treatments, chromosome numbers and isozyme data support the delimitation of the seminiferous representatives of the Festuca brachyphylla complex in Svalbard into four species F. baffinensis, F. brachyphylla, F. hyperborea and F. edlundiae. Unique enzyme markers were found for all species. Festuca brachyphylla proved hexaploid, and the others, tetraploid. The chromosome numbers of F. hyperborea and F.

  4. Genetic Variation and Evolutionary Origin of the Direct Repeat Locus of Mycobacterium tuberculosis Complex Bacteria

    Microsoft Academic Search

    J. D. A. van Embden; T. van Gorkom; K. Kremer; R. Jansen; B. A. M. van der Zeijst; L. M. Schouls

    2000-01-01

    The direct repeat region in Mycobacterium tuberculosis complex strains is composed of multiple direct variant repeats (DVRs), each of which is composed of a 36-bp direct repeat (DR) plus a nonrepetitive spacer sequence of similar size. It has been shown previously that clinical isolates show extensive polymorphism in the DR region by the variable presence of DVRs, and this polymorphism

  5. Song complexity, song rate, and variation in the adrenocortical stress response in song sparrows (Melospiza melodia).

    PubMed

    Grunst, Melissa L; Grunst, Andrea S

    2014-05-01

    Physiological mechanisms that pleiotropically affect condition, life-history decisions, and fitness may covary with the expression of sexually selected ornaments. The adrenocortical stress response regulates energy balance, controls vertebrate responses to survival threats, and may divert energy expenditure away from investment in costly sexual displays. Further, developmental stress may induce correlations between the stress response during adulthood and sexual signals that develop early in life, such as song in oscine birds. We examined the relationship between the adrenocortical stress response (measured by plasma corticosterone concentrations) and the sexually selected traits of song complexity and song rate in song sparrows (Melospiza melodia). Additionally, we explored whether the stress response, song complexity, or song rate predict other male quality and fitness metrics. In contrast to prior research, which reports negative relationships between song complexity and the stress response in this species, males with larger song repertoires had larger stress responses. Song rate was unrelated to the stress response, but positively correlated with male body mass and nestling mass. In addition, males with higher syllable diversity had longer wingchords and lower hematocrit, males with larger song repertoires had heavier nestlings and higher hematocrit, and males with larger stress responses and baseline corticosterone had higher hematocrit. Results suggest that the relationship between the stress response and song complexity is context-dependent, and that song repertoire size, syllable diversity, and song rate serve distinct signaling functions. PMID:24650781

  6. Complex Genetics Control Natural Variation in Arabidopsis thaliana Resistance to Botrytis cinerea

    Microsoft Academic Search

    Heather C. Rowe; Daniel J. Kliebenstein

    2008-01-01

    The genetic architecture of plant defense against microbial pathogens may be influenced by pathogen lifestyle. While plant interactions with biotrophic pathogens are frequently controlled by the action of large-effect resistance genes that follow classic Mendelian inheritance, our study suggests that plant defense against the necrotrophic pathogen Botrytis cinerea is primarily quantitative and genetically complex. Few studies of quantitative resistance to

  7. The transient variation of the complexes of the low latitude ionosphere within the equatorial ionization anomaly region of Nigeria

    NASA Astrophysics Data System (ADS)

    Rabiu, A. B.; Ogunsua, B. O.; Fuwape, I. A.; Laoye, J. A.

    2014-12-01

    The quest to find an index for proper characterization and description of the dynamical response of the ionosphere to external influences and its various internal irregularities has led to the study of the day to day variations of the chaoticity and dynamical complexity of the ionosphere. This study was conducted using Global Positioning System (GPS) Total Electron Content (TEC) time series, measured in the year 2011, from 5 GPS receiver stations in Nigeria which lies within the Equatorial Ionization Anomaly region. The nonlinear aspect of the TEC time series were obtained by detrending the data. The detrended TEC time series were subjected to various analyses for phase space reconstruction and to obtain the values of chaotic quantifiers which are Lyapunov exponents LE, correlation dimension, and Tsallis entropy for the study of dynamical complexity. The results show positive Lyapunov exponents for all days which indicate chaoticity of the ionosphere with no definite pattern for both quiet and disturbed days. However values of LE were lower for the storm period compared to its nearest relative quiet periods for all the stations. Considering all the days of the year the daily/transient variations show no definite pattern for each month but day to day values of Lyapunov exponent for the entire year show a wavelike semiannual variation pattern with lower values around March, April, September and October, a change in pattern which demonstrates the self-organized critical phenomenon of the system. This can be seen from the correlation dimension with values between 2.7 and 3.2 with lower values occurring mostly during storm periods demonstrating a phase transition from higher dimension during the quiet periods to lower dimension during storms for most of the stations. The values of Tsallis entropy show similar variation pattern with that of Lyapunov exponent with a lot of agreement in their comparison, with all computed values of Lyapunov exponent correlating with values of Tsallis entropy within the range of 0.79 to 0.82. These results show that Lyapunov quantifiers can be used together as indices in the study of the variations of the dynamical complexity of the ionosphere. The presence of chaos and high variations in the dynamical complexity, even at quiet periods in the ionosphere may be due to the internal dynamics and inherent irregularities of the ionosphere which exhibit non-linear properties. However, this inherent dynamics may be complicated by external factors like geomagnetic storms. This may be the main reason for the drop in the values of Lyapunov exponent and Tsallis entropy during storms. The results also show a strong interplay between determinism and stochasticity, as the ionosphere shows its response to changes in solar activities and in its internal dynamics. The dynamical behavior of the ionosphere throughout the year as described by these quantifiers, were discussed in this work.

  8. THERMOMECHANICAL STRESS ANALYSIS OF LAMINATES WITH A CUTOUT VIA A COMPLEX POTENTIAL-VARIATIONAL METHOD

    Microsoft Academic Search

    A. Barut; E. Madenci

    2004-01-01

    This study presents a new semianalytical method for the thermoelastic bending analysis of laminated plates with an elliptical hole under a nonuniform through-the-thickness temperature distribution. This new method employs the principle of stationary potential energy in conjunction with the complex variable approach for approximating displacement and stress resultants that automatically satisfy both in-plane and bending equilibrium equations. The numerical results

  9. Regulation of major histocompatibility complex class II gene expression, genetic variation and disease

    Microsoft Academic Search

    L Handunnetthi; S V Ramagopalan; G C Ebers; J C Knight

    2010-01-01

    Major histocompatibility complex (MHC) class II molecules are central to adaptive immune responses and maintenance of self-tolerance. Since the early 1970s, the MHC class II region at chromosome 6p21 has been shown to be associated with a remarkable number of autoimmune, inflammatory and infectious diseases. Given that a full explanation for most MHC class II disease associations has not been

  10. 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. PMID:22506273

  11. Sperm displacement in the Drosophila bipectinata species complex: Evidence for interspecific variations.

    PubMed

    Singh, Akanksha; Singh, Bashisth N

    2015-04-01

    We studied sperm displacement in two members of the Drosophila bipectinata species complex i.e., Drosophila parabipectinata and Drosophila malerkotliana by employing mutant and wild type strains. We found a significant increase in the productivity of remated females than that of once mated ones in all the crosses of the two species. The P2' values range from 0.67 to 0.70 in D. malerkotliana and 0.52 to 0.56 in D. parabipectinata. These results were compared with that of our earlier finding in D. bipectinata belonging to the same complex. We found that though the three species exhibit differences in the degree of sperm displacement, the pattern is somewhat similar in the three species. However, as far as its genetic variability and population size maintenance is considered, D. malerkotliana and D. bipectinata (P2' is 0.60-0.67) are at the forefront. Our finding is also supported by the fact that D. parabipectinata is derived from D. bipectinata and has not diverged much since its emergence as a separate species. The differences in the pattern of sperm displacement may be attributed to differences in remating latency, duration of copulation in first mating and sperm usage pattern among the members of this complex. PMID:25556898

  12. Phase effects on the masking of speech by harmonic complexes: Variations with level

    PubMed Central

    Green, Tim; Rosen, Stuart

    2013-01-01

    Speech reception thresholds were obtained in normally hearing listeners for sentence targets masked by harmonic complexes constructed with different phase relationships. Maskers had either a constant fundamental frequency (F0), or had F0 changing over time, following a pitch contour extracted from natural speech. The median F0 of the target speech was very similar to that of the maskers. In experiment 1 differences in the masking produced by Schroeder positive and Schroeder negative phase complexes were small (around 1.5 dB) for moderate levels [60 dB sound pressure level (SPL)], but increased to around 6 dB for maskers at 80 dB SPL. Phase effects were typically around 1.5 dB larger for maskers that had naturally varying F0 contours than for maskers with constant F0. Experiment 2 showed that shaping the long-term spectrum of the maskers to match the target speech had no effect. Experiment 3 included additional phase relationships at moderate levels and found no effect of phase. Therefore, the phase relationship within harmonic complexes appears to have only minor effects on masking effectiveness, at least at moderate levels, and when targets and maskers are in the same F0 range. PMID:24116424

  13. 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. PMID:21535276

  14. Variational Methods in Charged-Particle Collision Theory

    Microsoft Academic Search

    Leonard Rosenberg

    1973-01-01

    A variational principle of the Kohn type is formulated for the scattering of three charged particles, with particular attention given to the breakup process. In addition, an effective-potential theory, which also allows for variational formulation, is derived for the three-body system with long-ranged Coulomb interactions properly accounted for. These results generalize previous work done for systems with short-ranged interactions; the

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

    SciTech Connect

    Motamarri, P. [Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States)] [Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Nowak, M.R. [Department of Electrical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States)] [Department of Electrical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Leiter, K.; Knap, J. [U.S. Army Research Labs, Aberdeen Proving Ground, Aberdeen, MD 21001 (United States)] [U.S. Army Research Labs, Aberdeen Proving Ground, Aberdeen, MD 21001 (United States); Gavini, V., E-mail: vikramg@umich.edu [Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States)

    2013-11-15

    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 modest computational resources, and good scalability of the present implementation up to 192 processors.

  16. Kohn condition and exotic Newton-Hooke symmetry in the non-commutative Landau problem

    E-print Network

    Zhang, P-M

    2011-01-01

    $N$ "exotic" [alias non-commutative] particles with masses $m_a$, charges $e_a$ and non-commutative parameters $\\theta_a$, moving in a uniform magnetic field $B$, separate into center-of-mass and internal motions if Kohn's condition $e_a/m_a=\\const$ is supplemented with $e_a\\theta_a=\\const.$ Then the center-of-mass behaves as a single exotic particle carrying the total mass and charge of the system, $M$ and $e$, and a suitably defined non-commutative parameter $\\Theta$. For vanishing electric field off the critical case $e\\Theta B\

  17. Recent Advances in the Korringa-Kohn-Rostoker Green Function Method

    NASA Astrophysics Data System (ADS)

    Zeller, Rudolf

    2014-09-01

    The Korringa-Kohn-Rostoker (KKR) Green function (GF) method is a technique for all-electron full-potential density-functional calculations. Similar to the historical Wigner-Seitz cellular method, the KKR-GF method uses a partitioning of space into atomic Wigner-Seitz cells. However, the numerically demanding wave-function matching at the cell boundaries is avoided by use of an integral equation formalism based on the concept of reference Green functions. The advantage of this formalism will be illustrated by the recent progress made for very large systems with thousands of inequivalent atoms and for very accurate calculations of atomic forces and total energies.

  18. Genome size variation in the Artemisia arborescens complex (Asteraceae, Anthemideae) and its cultivars.

    PubMed

    Garcia, Sònia; Garnatje, Teresa; Twibell, John D; Vallès, Joan

    2006-03-01

    Different wild Mediterranean populations of Artemisia arborescens from diverse locations representing its geographical distribution, as well as some of its well-known cultivars and some specimens cultivated as ornamentals in gardens, streets, roads and nurseries, were analysed for genome size. Other closely related species endemic to Macaronesia, Artemisia canariensis, Artemisia argentea, and Artemisia gorgonum, were also analysed, and their nuclear DNA amount has been related to the biogeography of this group of species. Additionally, 5 populations of the closely related Artemisia absinthium were analysed to establish comparisons. Measurements acquired by flow cytometry ranged from 8.29 to 11.61 pg for 2C values. Statistically significant differences of 2C nuclear DNA amounts with respect to factors such as insularity or domestication have been detected. However, quite a low intraspecific genome size variation has been found in these species. Furthermore, the study also addressed the possible hybrid origins and possible misidentifications of some of the supposed cultivars of A. arborescens. PMID:16604107

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

    PubMed Central

    Robson, Paul R.H.

    2013-01-01

    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. PMID:23599277

  20. Assessing Spatial, Temporal, and Analytical Variation of Groundwater Chemistry in a Large Nuclear Complex, USA

    SciTech Connect

    Chou, Charissa J.

    2006-08-01

    Statistical analyses were applied at the Hanford Site, USA to assess groundwater contamination problems that included (1) determining local backgrounds to ascertain whether a facility is affecting the groundwater quality; and (2) determining a ‘pre-Hanford’ groundwater background to allow formulation of background-based cleanup standards. The primary purpose of this paper is to extend the random effects models for (1) assessing the spatial, temporal, and analytical variability of groundwater background measurements; (2) demonstrating that the usual variance estimate s-squared, which ignores the variance components, is a biased estimator; (3) providing formulas for calculating the amount of bias; and (4) recommending monitoring strategies to reduce the uncertainty in estimating the average background concentrations. A case study is provided. Results indicate that (1) without considering spatial and temporal variability, there is a high probability of false positives, resulting in unnecessary remediation and/or monitoring expenses; (2) the most effective way to reduce the uncertainty in estimating the average background, and enhance the power of the statistical tests in general, is to increase the number of background wells; and (3) background for a specific constituent should be considered as a statistical distribution, not as a single value or threshold. The methods and the related analysis of variance tables discussed in this paper can be used as diagnostic tools in documenting the extent of inherent spatial and/or temporal variation and to help select an appropriate statistical method for testing purposes.

  1. Assessing spatial, temporal, and analytical variation of groundwater chemistry in a large nuclear complex, USA.

    PubMed

    Chou, Charissa J

    2006-08-01

    Statistical analyses were applied at the Hanford Site, USA, to assess groundwater contamination problems that included (1) determining local backgrounds to ascertain whether a facility is affecting the groundwater quality and (2) determining a 'pre-Hanford' groundwater background to allow formulation of background-based cleanup standards. The primary purpose of this paper is to extend the random effects models for (1) assessing the spatial, temporal, and analytical variability of groundwater background measurements; (2) demonstrating that the usual variance estimate s2, which ignores the variance components, is a biased estimator; (3) providing formulas for calculating the amount of bias; and (4) recommending monitoring strategies to reduce the uncertainty in estimating the average background concentrations. A case study is provided. Results indicate that (1) without considering spatial and temporal variability, there is a high probability of false positives, resulting in unnecessary remediation and/or monitoring expenses; (2) the most effective way to reduce the uncertainty in estimating the average background, and enhance the power of the statistical tests in general, is to increase the number of background wells; and (3) background for a specific constituent should be considered as a statistical distribution, not as a single value or threshold. The methods and the related analysis of variance tables discussed in this paper can be used as diagnostic tools in documenting the extent of inherent spatial and/or temporal variation and to help select an appropriate statistical method for testing purposes. PMID:16758293

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

    PubMed

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

    2015-03-01

    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

  3. 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

  4. 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 component is added to the energy or dissipation, the Euler-Lagrange equations change form and interaction terms appear without additional adjustable parameters. EnVarA has previously been used to compute properties of liquid crystals, polymer fluids, and electrorheological fluids containing solid balls and charged oil droplets that fission and fuse. Here we apply EnVarA to the primitive model of electrolytes in which ions are spheres in a frictional dielectric. The resulting Euler-Lagrange equations include electrostatics and diffusion and friction. They are a time dependent generalization of the Poisson-Nernst-Planck equations of semiconductors, electrochemistry, and molecular biophysics. They include the finite diameter of ions. The EnVarA treatment is applied to ions next to a charged wall, where layering is observed. Applied to an ion channel, EnVarA calculates a quick transient pile-up of electric charge, transient and steady flow through the channel, stationary "binding" in the channel, and the eventual accumulation of salts in "unstirred layers" near channels. EnVarA treats electrolytes in a unified way as complex rather than simple fluids. Ad hoc descriptions of interactions and flow have been used in many areas of science to deal with the nonideal properties of electrolytes. It seems likely that the variational treatment can simplify, unify, and perhaps derive and improve those descriptions.

  5. 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. If a new component is added to the energy or dissipation, the Euler–Lagrange equations change form and interaction terms appear without additional adjustable parameters. EnVarA has previously been used to compute properties of liquid crystals, polymer fluids, and electrorheological fluids containing solid balls and charged oil droplets that fission and fuse. Here we apply EnVarA to the primitive model of electrolytes in which ions are spheres in a frictional dielectric. The resulting Euler–Lagrange equations include electrostatics and diffusion and friction. They are a time dependent generalization of the Poisson–Nernst–Planck equations of semiconductors, electrochemistry, and molecular biophysics. They include the finite diameter of ions. The EnVarA treatment is applied to ions next to a charged wall, where layering is observed. Applied to an ion channel, EnVarA calculates a quick transient pile-up of electric charge, transient and steady flow through the channel, stationary “binding” in the channel, and the eventual accumulation of salts in “unstirred layers” near channels. EnVarA treats electrolytes in a unified way as complex rather than simple fluids. Ad hoc descriptions of interactions and flow have been used in many areas of science to deal with the nonideal properties of electrolytes. It seems likely that the variational treatment can simplify, unify, and perhaps derive and improve those descriptions. PMID:20849161

  6. 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 component is added to the energy or dissipation, the Euler-Lagrange equations change form and interaction terms appear without additional adjustable parameters. EnVarA has previously been used to compute properties of liquid crystals, polymer fluids, and electrorheological fluids containing solid balls and charged oil droplets that fission and fuse. Here we apply EnVarA to the primitive model of electrolytes in which ions are spheres in a frictional dielectric. The resulting Euler-Lagrange equations include electrostatics and diffusion and friction. They are a time dependent generalization of the Poisson-Nernst-Planck equations of semiconductors, electrochemistry, and molecular biophysics. They include the finite diameter of ions. The EnVarA treatment is applied to ions next to a charged wall, where layering is observed. Applied to an ion channel, EnVarA calculates a quick transient pile-up of electric charge, transient and steady flow through the channel, stationary "binding" in the channel, and the eventual accumulation of salts in "unstirred layers" near channels. EnVarA treats electrolytes in a unified way as complex rather than simple fluids. Ad hoc descriptions of interactions and flow have been used in many areas of science to deal with the nonideal properties of electrolytes. It seems likely that the variational treatment can simplify, unify, and perhaps derive and improve those descriptions. PMID:20849161

  7. 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

  8. Seasonal variations in erodibility and sediment transport potential in a mesotidal channel-flat complex, Willapa Bay, WA

    NASA Astrophysics Data System (ADS)

    Wiberg, Patricia L.; Law, Brent A.; Wheatcroft, Robert A.; Milligan, Timothy G.; Hill, Paul S.

    2013-06-01

    Measurements of erodibility, porosity and sediment size were made three times over the course of a year at sites within a muddy, mesotidal flat-channel complex in southern Willapa Bay, WA, to examine spatial and seasonal variations in sediment properties and transport potential. Average critical shear stress profiles, the metric we used for erodibility, were quantified using a power-law fit to cumulative eroded mass vs. shear stress for the flats and channel. Laboratory erosion measurements of deposits made from slurries of flat and channel sediment were used to quantify erodibility over consolidation time scales ranging from 6 to 96h. Erodibility of the tidal flats was consistently low, with spatial variability comparable to seasonal variability despite seasonal changes in biological activity. In contrast, channel-bed erodibility underwent large seasonal variations, with mobile sediment present in the channel thalweg during winter that was absent in the spring and summer, when channel-bed erodibility was low and comparable to that of the tidal flats. Sediment on the northern (left) channel flank was mobile in summer and winter, whereas sediment on the southern flank was not. Seasonal changes in channel-bed erodibility are sufficient to produce order-of-magnitude changes in suspended sediment concentrations during peak tidal flows. Porosity just below the sediment surface was the best predictor of erodibility in our study area.

  9. Seasonal variations in erodibility and sediment transport potential in a mesotidal channel-flat complex, Willapa Bay, WA

    NASA Astrophysics Data System (ADS)

    Wiberg, Patricia L.; Law, Brent A.; Wheatcroft, Robert A.; Milligan, Timothy G.; Hill, Paul S.

    2013-06-01

    Measurements of erodibility, porosity and sediment size were made three times over the course of a year at sites within a muddy, mesotidal flat-channel complex in southern Willapa Bay, WA, to examine spatial and seasonal variations in sediment properties and transport potential. Average critical shear stress profiles, the metric we used for erodibility, were quantified using a power-law fit to cumulative eroded mass vs. shear stress for the flats and channel. Laboratory erosion measurements of deposits made from slurries of flat and channel sediment were used to quantify erodibility over consolidation time scales ranging from 6 to 96 h. Erodibility of the tidal flats was consistently low, with spatial variability comparable to seasonal variability despite seasonal changes in biological activity. In contrast, channel-bed erodibility underwent large seasonal variations, with mobile sediment present in the channel thalweg during winter that was absent in the spring and summer, when channel-bed erodibility was low and comparable to that of the tidal flats. Sediment on the northern (left) channel flank was mobile in summer and winter, whereas sediment on the southern flank was not. Seasonal changes in channel-bed erodibility are sufficient to produce order-of-magnitude changes in suspended sediment concentrations during peak tidal flows. Porosity just below the sediment surface was the best predictor of erodibility in our study area.

  10. Seasonal Variations in Sediment Transport Potential in a Tidal Channel-Flat Complex in Willapa Bay, WA

    NASA Astrophysics Data System (ADS)

    Wiberg, P. L.; Law, B.; Wheatcroft, R. A.; Milligan, T.; Hill, P. S.

    2010-12-01

    Field measurements of sediment size, porosity and erodibility were collected 3 times over the course of a year within a flat-channel complex in Willapa Bay to examine seasonal and spatial variations in sediment properties and transport potential. Grain size measurements of the sediment surface and eroded sediment and measurements of sediment strength were carried out in conjunction with erosion tests made using a 10.5-cm diameter Gust erosion chamber; porosity was measured for a subset of the samples. Laboratory erosion measurements of deposits made from slurries of flat and channel sediment were used to quantify consolidation time scales ranging from 6 hrs to 4 days. Results support a conceptual model in which sediment on the flats always has relatively low mobility while sediment on the channel flanks is always relatively mobile. In contrast, sediment properties at the channel bed undergo large seasonal variations, with mobile sediment accumulating in the channel thalweg during winter which is subsequently evacuated by summer, leaving a coarse, low mobility lag deposit at the bed surface. Comparison of measured erodibility with tidal and wave forcing indicates that suspended sediment concentrations in the channel could be 10 times greater in winter than summer during peak tidal currents, whereas waves, which play a secondary role to tidal currents in this mesotidal setting, are mostly important on the flats.

  11. A complexity analysis of 222Rn concentration variation: A case study for Domica cave, Slovakia for the period June 2010-June 2011

    NASA Astrophysics Data System (ADS)

    Mihailovi?, D. T.; Krmar, M.; Mimi?, G.; Nikoli?-?ori?, E.; Smetanová, I.; Holý, K.; Zelinka, J.; Omelka, J.

    2015-01-01

    In this paper we have analyzed 222Rn concentration variation in Domica cave (Slovakia) for the period June 2010-June 2011. In that sense we have applied a complexity analysis on 222Rn concentration time series. We have considered possible existence of a periodical component in the variation of 222Rn concentration and some environmental parameters, as well as possible correlation between them. In addition we have offered novel complexity measures based on the Kolmogorov complexity (KC), i.e. the Kolmogorov complexity spectrum, its highest value (KCM) and the integral Kolmogorov complexity (KCI). These measures have been applied on 222Rn concentration time series: (i) to establish the dependence of 222Rn concentration on cave environmental parameters (wind speed inside the cave, external wind speed, air temperature, atmospheric pressure and CO2 concentration) and (ii) to see whether influence of some parameters make the distribution of measured quantity less or more stochastic.

  12. Systems-Based Approaches to Probing Metabolic Variation within the Mycobacterium tuberculosis Complex

    PubMed Central

    Lofthouse, Emma K.; Wheeler, Paul R.; Beste, Dany J. V.; Khatri, Bhagwati L.; Wu, Huihai; Mendum, Tom A.; Kierzek, Andrzej M.; McFadden, Johnjoe

    2013-01-01

    The Mycobacterium tuberculosis complex includes bovine and human strains of the tuberculosis bacillus, including Mycobacterium tuberculosis, Mycobacterium bovis and the Mycobacterium bovis BCG vaccine strain. M. bovis has evolved from a M. tuberculosis-like ancestor and is the ancestor of the BCG vaccine. The pathogens demonstrate distinct differences in virulence, host range and metabolism, but the role of metabolic differences in pathogenicity is poorly understood. Systems biology approaches have been used to investigate the metabolism of M. tuberculosis, but not to probe differences between tuberculosis strains. In this study genome scale metabolic networks of M. bovis and M. bovis BCG were constructed and interrogated, along with a M. tuberculosis network, to predict substrate utilisation, gene essentiality and growth rates. The models correctly predicted 87-88% of high-throughput phenotype data, 75-76% of gene essentiality data and in silico-predicted growth rates matched measured rates. However, analysis of the metabolic networks identified discrepancies between in silico predictions and in vitro data, highlighting areas of incomplete metabolic knowledge. Additional experimental studies carried out to probe these inconsistencies revealed novel insights into the metabolism of these strains. For instance, that the reduction in metabolic capability observed in bovine tuberculosis strains, as compared to M. tuberculosis, is not reflected by current genetic or enzymatic knowledge. Hence, the in silico networks not only successfully simulate many aspects of the growth and physiology of these mycobacteria, but also provide an invaluable tool for future metabolic studies. PMID:24098743

  13. 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. PMID:24410491

  14. Influence of Gene Interaction on Complex Trait Variation with Multilocus Models

    PubMed Central

    Mäki-Tanila, Asko; Hill, William G.

    2014-01-01

    Although research effort is being expended into determining the importance of epistasis and epistatic variance for complex traits, there is considerable controversy about their importance. Here we undertake an analysis for quantitative traits utilizing a range of multilocus quantitative genetic models and gene frequency distributions, focusing on the potential magnitude of the epistatic variance. All the epistatic terms involving a particular locus appear in its average effect, with the number of two-locus interaction terms increasing in proportion to the square of the number of loci and that of third order as the cube and so on. Hence multilocus epistasis makes substantial contributions to the additive variance and does not, per se, lead to large increases in the nonadditive part of the genotypic variance. Even though this proportion can be high where epistasis is antagonistic to direct effects, it reduces with multiple loci. As the magnitude of the epistatic variance depends critically on the heterozygosity, for models where frequencies are widely dispersed, such as for selectively neutral mutations, contributions of epistatic variance are always small. Epistasis may be important in understanding the genetic architecture, for example, of function or human disease, but that does not imply that loci exhibiting it will contribute much genetic variance. Overall we conclude that theoretical predictions and experimental observations of low amounts of epistatic variance in outbred populations are concordant. It is not a likely source of missing heritability, for example, or major influence on predictions of rates of evolution. PMID:24990992

  15. 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.

  16. Variation in the Complex Carbohydrate Biosynthesis Loci of Acinetobacter baumannii Genomes

    PubMed Central

    Kenyon, Johanna J.; Hall, Ruth M.

    2013-01-01

    Extracellular polysaccharides are major immunogenic components of the bacterial cell envelope. However, little is known about their biosynthesis in the genus Acinetobacter, which includes A. baumannii, an important nosocomial pathogen. Whether Acinetobacter sp. produce a capsule or a lipopolysaccharide carrying an O antigen or both is not resolved. To explore these issues, genes involved in the synthesis of complex polysaccharides were located in 10 complete A. baumannii genome sequences, and the function of each of their products was predicted via comparison to enzymes with a known function. The absence of a gene encoding a WaaL ligase, required to link the carbohydrate polymer to the lipid A-core oligosaccharide (lipooligosaccharide) forming lipopolysaccharide, suggests that only a capsule is produced. Nine distinct arrangements of a large capsule biosynthesis locus, designated KL1 to KL9, were found in the genomes. Three forms of a second, smaller variable locus, likely to be required for synthesis of the outer core of the lipid A-core moiety, were designated OCL1 to OCL3 and also annotated. Each K locus includes genes for capsule export as well as genes for synthesis of activated sugar precursors, and for glycosyltransfer, glycan modification and oligosaccharide repeat-unit processing. The K loci all include the export genes at one end and genes for synthesis of common sugar precursors at the other, with a highly variable region that includes the remaining genes in between. Five different capsule loci, KL2, KL6, KL7, KL8 and KL9 were detected in multiply antibiotic resistant isolates belonging to global clone 2, and two other loci, KL1 and KL4, in global clone 1. This indicates that this region is being substituted repeatedly in multiply antibiotic resistant isolates from these clones. PMID:23614028

  17. A Candidate Complex Approach to Study Functional Mitochondrial DNA Changes: Sequence Variation and Quaternary Structure Modeling of Drosophila simulans Cytochrome c Oxidase

    Microsoft Academic Search

    Richard G. Melvin; Subhash D. Katewa; J. William O. Ballard

    2008-01-01

    A problem with studying evolutionary dynamics of mitochondrial (mt) DNA is that classical population genetic techniques cannot\\u000a identify selected substitutions because of genetic hitchhiking. We circumvented this problem by employing a candidate complex\\u000a approach to study sequence variation in cytochrome c oxidase (COX) genes within and among three distinct Drosophila simulans mtDNA haplogroups. First, we determined sequence variation in complete

  18. Stability of titanium oxide phases in Kohn-Sham density functional A well known problem in practical Kohn-Sham (KS) density functional theory (DFT) calculations is that it yields the wrong order of

    E-print Network

    Bjørnstad, Ottar Nordal

    Stability of titanium oxide phases in Kohn-Sham density functional theory A well known problem of stability of titanium oxide phases at room temperature. That is, anatase instead of rutile is predicted as the room temperature phase for titanium oxide. In this work we try to establish the reasons

  19. 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 value is elevated compared to the median value for MORBs (8 RA). Our observations suggest that domains of highly depleted MORB mantle tend to have higher 3He/4He ratios, approaching 9 RA, consistent with what is observed in depleted MORB glasses globally. Kane gabbroic rocks are more variable, and typically show lower 3He/4He ratios, often accompanied by lower He concentrations. This likely reflects an increased importance of atmospheric and radiogenic components. Lower initial 3He/4He ratios (<8 RA) may also be present in some of the gabbros, perhaps from partial meting of a lithologically heterogeneous mantle source.

  20. File DR1. Garnet dissolution calculations following Kohn and Spear (2000) Measurements and calculations for sample GP-5

    E-print Network

    Kidd, William S. F.

    2000-01-01

    File DR1. Garnet dissolution calculations following Kohn and Spear (2000) Measurements and calculations for sample GP-5 Garnet mode = 10% Biotite mode = 20% Biotite Fe/(Fe + Mg) (matrix) = 1 of analyzed garnet: 3.8 mm2 Present volume of analyzed garnet (assuming spherical geometry): 5.6 mm3 Radius

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

    PubMed

    Winternitz, Jamie C; Wares, John P

    2013-06-01

    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

  2. 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

  3. Genome-wide SNP and microsatellite variation illuminate population-level epidemiology in the Leishmania donovani species complex

    PubMed Central

    Downing, Tim; Stark, Olivia; Vanaerschot, Manu; Imamura, Hideo; Sanders, Mandy; Decuypere, Saskia; de Doncker, Simonne; Maes, Ilse; Rijal, Suman; Sundar, Shyam; Dujardin, Jean-Claude; Berriman, Matthew; Schönian, Gabriele

    2012-01-01

    The species of the Leishmania donovani species complex cause visceral leishmaniasis, a debilitating infectious disease transmitted by sandflies. Understanding molecular changes associated with population structure in these parasites can help unravel their epidemiology and spread in humans. In this study, we used a panel of standard microsatellite loci and genome-wide SNPs to investigate population-level diversity in L. donovani strains recently isolated from a small geographic area spanning India, Bihar and Nepal, and compared their variation to that found in diverse strains of the L. donovani complex isolates from Europe, Africa and Asia. Microsatellites and SNPs could clearly resolve the phylogenetic relationships of the strains between continents, and microsatellite phylogenies indicated that certain older Indian strains were closely related to African strains. In the context of the anti-malaria spraying campaigns in the 1960s, this was consistent with a pattern of episodic population size contractions and clonal expansions in these parasites that was supported by population history simulations. In sharp contrast to the low resolution provided by microsatellites, SNPs retained a much more fine-scale resolution of population-level variability to the extent that they identified four different lineages from the same region one of which was more closely related to African and European strains than to Indian or Nepalese ones. Joining results of in vitro testing the antimonial drug sensitivity with the phylogenetic signals from the SNP data highlighted protein-level mutations revealing a distinct drug-resistant group of Nepalese and Indian L. donovani. This study demonstrates the power of genomic data for exploring parasite population structure. Furthermore, markers defining different genetic groups have been discovered that could potentially be applied to investigate drug resistance in clinical Leishmania strains. PMID:22119748

  4. Coupled perturbed Kohn-Sham calculation of static polarizabilities of periodic compounds

    NASA Astrophysics Data System (ADS)

    Ferrero, M.; Rérat, M.; Orlando, R.; Dovesi, R.; Bush, I. J.

    2008-06-01

    The Coupled Perturbed Hartree-Fock (CPHF) scheme recently implemented in the CRYSTAL06 code for systems periodic in 1-3 dimensions has been generalized to Density Functional Hamiltonians (CPKS, Coupled Perturbed Kohn-Sham). The dielectric tensor of Magnesium Oxide, Diamond, and Silicon is calculated with four different Hamiltonians, ranging from DFT, in the local density and gradient corrected approximations, to 'hybrid' functional B3LYP and Hartree-Fock. The effect of the computational parameters (Pack-Monkhorst net and basis set) is explored. DFT is shown to perform generally better than HF, as it is the case for other properties such as band gaps (which influence the CPHF and CPKS equations via the energy difference between occupied and virtual states) and vibration frequencies.

  5. Adiabatic and local approximations for the Kohn-Sham potential in time-dependent Hubbard chains

    NASA Astrophysics Data System (ADS)

    Mancini, L.; Ramsden, J. D.; Hodgson, M. J. P.; Godby, R. W.

    2014-05-01

    We obtain the exact Kohn-Sham potentials VKS of time-dependent density-functional theory for one-dimensional Hubbard chains, driven by a dc external field, using the time-dependent electron density and current density obtained from exact many-body time evolution. The exact Vxc is compared to the adiabatically exact Vxcad and the "instantaneous ground state" Vxcigs. The latter is shown to work effectively in some cases when the former fails. Approximations for the exchange-correlation potential Vxc and its gradient, based on the local density and on the local current density, are also considered and both physical quantities are observed to be far outside the reach of any possible local approximation. Insight into the respective roles of ground-state and excited-state correlation in the time-dependent system, as reflected in the potentials, is provided by the pair correlation function.

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

    SciTech Connect

    Gaiduk, Alex P.; Staroverov, Viktor N. [Department of Chemistry, University of Western Ontario, London, Ontario N6A 5B7 (Canada)

    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.

  7. Variation in postfire organic layer thickness in a black spruce forest complex in interior Alaska and its effects on soil temperature and moisture

    Microsoft Academic Search

    Eric S. Kasischke; Jill F. Johnstone

    2005-01-01

    This study investigated the relationship between climate and landscape characteristics and surface fuel con- sumption as well as the effects of variations in postfire organic layer depth on soil temperature and moisture in a black spruce (Picea mariana (Mill.) BSP) forest complex in interior Alaska. Mineral soil moisture and temperature at the end of the growing season and organic layer

  8. Alkaloid polymorphism and ITS sequence variation in the Spiraea japonica complex (Rosaceae) in China: traces of the biological effects of the Himalaya-Tibet Plateau uplift

    Microsoft Academic Search

    ZHAOYANG ZHANG; L IMING FAN; J UNBO YANG; X. Hao; Z. Gu

    2006-01-01

    Spiraea japonica, a diverse, perennial shrubby species complex widespread across E Asia, was a useful model in a first attempt to link specific phylogeny, floristic evolution, and historical environmental changes in E Asia. DNA-based phylogenetic reconstruction served as a framework to investigate whether the patterns of variation in alkaloids and nrITS from varieties of S. japonica reflect the geological history

  9. The Use of Trust Regions in Kohn-Sham Total EnergyMinimization

    SciTech Connect

    Yang, Chao; Meza, Juan C.; Wang, Lin-wang

    2006-05-30

    The Self Consistent Field (SCF) iteration, widely used forcomputing the ground state energy and the corresponding single particlewave functions associated with a many-electronatomistic system, is viewedin this paper as an optimization procedure that minimizes the Kohn-Shamtotal energy indirectly by minimizing a sequence of quadratic surrogatefunctions. We point out the similarity and difference between the totalenergy and the surrogate, and show how the SCF iteration can fail whenthe minimizer of the surrogate produces an increase in the KS totalenergy. A trust region technique is introduced as a way to restrict theupdate of the wave functions within a small neighborhood of anapproximate solution at which the gradient of the total energy agreeswith that of the surrogate. The use of trust region in SCF is not new.However, it has been observed that directly applying a trust region basedSCF(TRSCF) to the Kohn-Sham total energy often leads to slowconvergence.We propose to use TRSCF within a direct constrainedminimization(DCM) algorithm we developed in \\cite dcm. The keyingredients of theDCM algorithm involve projecting the total energyfunction into a sequence of subspaces of small dimensions and seeking theminimizerof the total energy function within each subspace. Theminimizer of a subspace energy function, which is computed by TRSCF, notonly provides a search direction along which the KS total energy functiondecreases but also gives an optimal "step-length" that yields asufficient decrease in total energy. A numerical example is provided todemonstrate that the combination of TRSCF and DCM is more efficient thanSCF.

  10. 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. PMID:25629763

  11. Variation of the ultraviolet extinction law across the Taurus-Auriga star forming complex. A GALEX based study

    E-print Network

    de Castro, Ana I Gomez; Lopez-Martinez, Fatima; Sanchez, Nestor; de Castro, Elisa; Cornide, Manuel

    2015-01-01

    The Taurus-Auriga molecular complex (TMC) is the main laboratory for the study of low mass star formation. The density and properties of interstellar dust are expected to vary across the TMC. These variations trace important processes such as dust nucleation or the magnetic field coupling with the cloud. In this article, we show how the combination of near ultraviolet (NUV) and infrared (IR) photometry can be used to derive the strength of the 2175 \\AA\\ bump and thus any enhancement in the abundance of small dust grains and PAHs in the dust grains size distribution. This technique is applied to the envelope of the TMC, mapped by the GALEX All Sky Survey (AIS). UV and IR photometric data have been retrieved from the GALEX-AIS and the 2MASS catalogues. NUV and K-band star counts have been used to identify the areas in the cloud envelope where the 2175 \\AA\\ bump is weaker than in the diffuse ISM namely, the low column density extensions of L1495, L1498 and L1524 in Taurus, L1545, L1548, L1519, L1513 in Auriga an...

  12. Morphological variation in Echinorhynchustruttae Schrank, 1788 and the Echinorhynchusbothniensis Zdzitowiecki & Valtonen, 1987 species complex from freshwater fishes of northern Europe.

    PubMed

    Wayland, Matthew T

    2013-01-01

    Echinorhynchustruttae and the Echinorhynchusbothniensis species complex are common parasites of salmoniform and other fishes in northern Europe. Echinorhynchusbothniensis and its sibling species Echinorhynchus 'bothniensis' are thought to be closely related to the Nearctic Echinorhynchusleidyi Van Cleave, 1924 based on morphological similarity and common usage of a mysid intermediate host. This study provides the first analysis of morphological and meristic variation in Echinorhynchustruttae and expands our knowledge of anatomical variability in the Echinorhynchusbothniensis group. Morphological variability in Echinorhynchustruttae was found to be far greater than previously reported, with part of the variance attributable to sexual dimorphism. Echinorhynchustruttae, the two species of the Echinorhynchusbothniensis group and Echinorhynchusleidyi displayed considerable interspecific overlap in the ranges of all conventional morphological characters. However, Proboscis profiler, a tool for detecting acanthocephalan morphotypes using multivariate analysis of hook morphometrics, successfully separated Echinorhynchustruttae from the other taxa. The Echinorhynchusbothniensis species group could not be reliably distinguished from Echinorhynchusleidyi (or each other), providing further evidence of the affinity of these taxa. Observations on the distribution of Echinorhynchustruttae in its definitive host population are also reported. PMID:24723769

  13. 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. PMID:18523814

  14. Geographic variation in size and coloration in the Turdus poliocephalus complex: A first review of species limits

    E-print Network

    Peterson, A. Townsend

    2007-09-12

    allopatric populations, and document patterns of geographic variation in plumage coloration and sexual dimorphism. Overall patterns of variation indicate 12 distinct plumage types, with 31 geographically contiguous populations that present one of the 12...

  15. 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 sexual lineages through matings between sexual males and thelytokous females, and (iii) 'cryptic sex' within asexuals, mediated by rare males that thelytokous lines are known to produce spontaneously. The partially strong differentiation among wasps collected from different aphids suggests that host specialization can evolve readily in these parasitoids. Finally, we conclude that in the light of our data, the current taxonomic division of the L. fabarum group into three species cannot be upheld. PMID:22132834

  16. 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.

  17. 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 amounts may reflect several transporting events over the measurement period and the transport process is likely via localized, modified suspension from the crest of the foredune and other compound dune features in the foredune plain. This evidence suggests that the process of grainfall delivery, though often overlooked in coastal research, may be a key process in maintaining active dunes hundreds of metres from the shoreline in a densely vegetated foredune plain. The effectiveness of this process is controlled by seasonal changes in vegetation cover and wind strength as well as shorter term (e.g., tidally controlled) variations in sand availability from the beach.

  18. 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

    Background Hop (Humulus lupulus L.) is cultivated for its cones, the secondary metabolites of which contribute bitterness, flavour and aroma to beer. Molecular breeding methods, such as marker assisted selection (MAS), have great potential for improving the efficiency of hop breeding. The success of MAS is reliant on the identification of reliable marker-trait associations. This study used quantitative trait loci (QTL) analysis to identify marker-trait associations for hop, focusing on traits related to expediting plant sex identification, increasing yield capacity and improving bittering, flavour and aroma chemistry. Results QTL analysis was performed on two new linkage maps incorporating transferable Diversity Arrays Technology (DArT) markers. Sixty-three QTL were identified, influencing 36 of the 50 traits examined. A putative sex-linked marker was validated in a different pedigree, confirming the potential of this marker as a screening tool in hop breeding programs. An ontogenetically stable QTL was identified for the yield trait dry cone weight; and a QTL was identified for essential oil content, which verified the genetic basis for variation in secondary metabolite accumulation in hop cones. A total of 60 QTL were identified for 33 secondary metabolite traits. Of these, 51 were pleiotropic/linked, affecting a substantial number of secondary metabolites; nine were specific to individual secondary metabolites. Conclusions Pleiotropy and linkage, found for the first time to influence multiple hop secondary metabolites, have important implications for molecular selection methods. The selection of particular secondary metabolite profiles using pleiotropic/linked QTL will be challenging because of the difficulty of selecting for specific traits without adversely changing others. QTL specific to individual secondary metabolites, however, offer unequalled value to selection programs. In addition to their potential for selection, the QTL identified in this study 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

  19. Clonal variations in complement activation and deposition of C3b and C4b on model immune complexes.

    PubMed Central

    Yokoyama, I; Waxman, F

    1993-01-01

    This study examined the relationship between complement activation and the deposition of C3b and C4b on a panel of model immune complexes (IC). IC were constructed by combining murine monoclonal IgM, IgA, IgG1, IgG2a or IgG3 anti-dinitrophenyl (DNP) antibodies with DNP-bovine serum albumin (DNP-BSA). The IC were incubated with human plasma as a complement source and the formation of C4a and C3a, as well as the deposition of C4b and C3b on the IC, measured by radioimmunoassay. The results indicate that there were isotype-independent variations in the capacity of different types of IC to activate the classical pathway, especially for isotype-matched pairs of IC containing IgG1, IgG2a and IgG3 antibodies. In most cases, there was a direct relationship between classical pathway activation and the cleavage of C3. There was, for most of the IC, a direct correlation between cleavage of C4 and C3 and the subsequent deposition of C4b and C3b on the IC. However, a pair of IC constructed with independently derived IgG1 antibodies was virtually identical with respect to C3 cleavage and yet differed in the number of C3b molecules deposited on the IC. Collectively, these data suggest that the immunoglobulin variable region can play a significant role in both complement activation and the deposition of C3b and C4b on IC. PMID:8262546

  20. Unraveling the complexities of variation in female mate preference for vertical bars in the swordtail, Xiphophorus cortezi

    Microsoft Academic Search

    Donelle M. Robinson; Molly R. Morris

    2010-01-01

    Investigations into the nature of mate choice suggest that variation in female mate preferences is often context dependent,\\u000a varying in response to genetic and environmental influences on female condition as well as to external environmental stimuli.\\u000a Determining whether variation in female mate preference is adaptive requires understanding the variables involved that produce\\u000a this variation and how they interact. Comparative, multivariate

  1. Allozyme Variation and Population Differentiation of the Aconitum delavayi Complex (Ranunculaceae) in the Hengduan Mountains of China

    Microsoft Academic Search

    Fumin Zhang; Hongzhi Kong; Song Ge

    2003-01-01

    The Aconitum delavayi complex is a group of four climbing species with trisect- leaves occurring in the Hengduan Mountains. The species of this complex are highly localized on very narrow regions with quite small population sizes. Be- cause of rapid environmental changes recently in the Hengduan Mountains, this complex shows complicated morphological variability, which makes it difficult to delimit species.

  2. Allozyme Variation and Population Differentiation of the Aconitum delavayi Complex (Ranunculaceae) in the Hengduan Mountains of China

    Microsoft Academic Search

    Fumin Zhang; Hongzhi Kong; Song Ge

    2003-01-01

    The Aconitum delavayi complex is a group of four climbing species with trisect-leaves occurring in the Hengduan Mountains. The species of this complex are highly localized on very narrow regions with quite small population sizes. Because of rapid environmental changes recently in the Hengduan Mountains, this complex shows complicated morphological variability, which makes it difficult to delimit species. In the

  3. From Spherical to Leaf-Like Morphologies: Tunable Supramolecular Assembly of Alkynylgold(I) Complexes through Variations of the Alkyl Chain Length.

    PubMed

    Hong, Eugene Yau-Hin; Wong, Hok-Lai; Yam, Vivian Wing-Wah

    2015-04-01

    A series of luminescent polynuclear alkynylgold(I) complexes with different lengths of alkyl chains attached at the N-heterocyclic carbene moieties has been synthesised and demonstrated to display intriguing self-assembly behaviours through a cooperative growth mechanism. Variation of the alkyl chain length was found to cause drastic morphological differences in the aggregates and to strongly affect the thermodynamic parameters as revealed by the nucleation-elongation model. PMID:25707360

  4. Inter-individual variation in brain phenylalanine concentration in patients with PKU is not caused by genetic variation in the 4F2hc/LAT1 complex.

    PubMed

    Møller, Lisbeth Birk; Paulsen, Marianne; Koch, Richard; Moats, Rex; Guldberg, Per; Güttler, Flemming

    2005-12-01

    It remains a question why some patients with phenylketonuria (PKU) have high IQ and low brain phenylalanine (Phe) concentrations in spite of high blood Phe levels. One possible explanation for the low brain Phe concentrations in these patients would be a reduced transport of Phe across the blood-brain barrier. The 4F2hc/LAT1 complex has been suggested to be the most important molecular component responsible for this transport. To test the hypothesis that structural variant(s) in the genes encoding 4F2hc and LAT1 might result in a complex with reduced affinity for Phe, we have screened the two genes for sequence variants in a group of 13 PKU patients with a low ratio of brain to blood Phe concentrations. Several common sequence variants were identified, but none of these is predicted to affect the resulting protein product. Our data suggest that individual vulnerability to Phe in patients with PKU is not due to structural variants in the 4F2hc/LAT1 complex. PMID:16176881

  5. 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.

  6. Self-Averaging Stochastic Kohn-Sham Density-Functional Theory

    NASA Astrophysics Data System (ADS)

    Baer, Roi; Neuhauser, Daniel; Rabani, Eran

    2013-09-01

    We formulate the Kohn-Sham density functional theory (KS-DFT) as a statistical theory in which the electron density is determined from an average of correlated stochastic densities in a trace formula. The key idea is that it is sufficient to converge the total energy per electron to within a predefined statistical error in order to obtain reliable estimates of the electronic band structure, the forces on nuclei, the density and its moments, etc. The fluctuations in the total energy per electron are guaranteed to decay to zero as the system size increases. This facilitates “self-averaging” which leads to the first ever report of sublinear scaling KS-DFT electronic structure. The approach sidesteps calculation of the density matrix and thus, is insensitive to its evasive sparseness, as demonstrated here for silicon nanocrystals. The formalism is not only appealing in terms of its promise to far push the limits of application of KS-DFT, but also represents a cognitive change in the way we think of electronic structure calculations as this stochastic theory seamlessly converges to the thermodynamic limit.

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

    SciTech Connect

    Schauer, Volker [Institute of Applied Mechanics (CE) Chair I, University of Stuttgart, 70550 Stuttgart, Pfaffenwaldring 7 (Germany)] [Institute of Applied Mechanics (CE) Chair I, University of Stuttgart, 70550 Stuttgart, Pfaffenwaldring 7 (Germany); Linder, Christian, E-mail: linder@stanford.edu [Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305 (United States)] [Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305 (United States)

    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. Kohn's Theorem, Larmor's Equivalence Principle and the Newton-Hooke Group

    E-print Network

    G. W. Gibbons; C. N. Pope

    2010-11-10

    We consider non-relativistic electrons, each of the same charge to mass ratio, moving in an external magnetic field with an interaction potential depending only on the mutual separations, possibly confined by a harmonic trapping potential. We show that the system admits a "relativity group" which is a one-parameter family of deformations of the standard Galilei group to the Newton-Hooke group which is a Wigner-Inonu contraction of the de Sitter group. This allows a group-theoretic interpretation of Kohn's theorem and related results. Larmor's Theorem is used to show that the one-parameter family of deformations are all isomorphic. We study the "Eisenhart" or "lightlike" lift of the system, exhibiting it as a pp-wave. In the planar case, the Eisenhart lift is the Brdicka-Eardley-Nappi-Witten pp-wave solution of Einstein-Maxwell theory, which may also be regarded as a bi-invariant metric on the Cangemi-Jackiw group.

  9. Kinetic Formulation of the Kohn-Sham Equations for ab initio Electronic Structure Calculations

    NASA Astrophysics Data System (ADS)

    Mendoza, M.; Succi, S.; Herrmann, H. J.

    2014-08-01

    We introduce a new connection between density functional theory and kinetic theory. In particular, we show that the Kohn-Sham equations can be reformulated as a macroscopic limit of the steady-state solution of a suitable single-particle kinetic equation. We derive a Boltzmann-like equation for a gas of quasiparticles, where the potential plays the role of an external source that generates and destroys particles, so as to drive the system towards its ground state. The ions are treated as classical particles by using either the Born-Oppenheimer dynamics or by imposing concurrent evolution with the electronic orbitals. In order to provide quantitative support to our approach, we implement a discrete (lattice) kinetic model and compute the exchange and correlation energies of simple atoms and the geometrical configuration of the methane molecule. Moreover, we also compute the first vibrational mode of the hydrogen molecule, with both Born-Oppenheimer and concurrent dynamics. Excellent agreement with values in the literature is found in all cases.

  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. Interpretation of the Kohn-Sham orbital energies as approximate vertical ionization potentials

    NASA Astrophysics Data System (ADS)

    Chong, D. P.; Gritsenko, O. V.; Baerends, E. J.

    2002-02-01

    Theoretical analysis and results of calculations are put forward to interpret the energies -?k of the occupied Kohn-Sham (KS) orbitals as approximate but rather accurate relaxed vertical ionization potentials (VIPs) Ik. Exact relations between ?k and Ik are established with a set of linear equations for the ?k, which are expressed through Ik and the matrix elements ?kresp of a component of the KS exchange-correlation (xc) potential vxc, the response potential vresp. Although -Ik will be a leading contribution to ?k, other Ij?k do enter through coupling terms which are determined by the overlaps between the densities of the KS orbitals as well as by overlaps between the KS and Dyson orbital densities. The orbital energies obtained with "exact" KS potentials are compared with the experimental VIPs of the molecules N2, CO, HF, and H2O. Very good agreement between the accurate -?k of the outer valence KS orbitals and the corresponding VIPs is established. The average difference, approaching 0.1 eV, is about an order of magnitude smaller than for HF orbital energies. The lower valence KS levels are a few eV higher than the corresponding -Ik, and the core levels some 20 eV, in agreement with the theoretically deduced upshift of the KS levels compared to -Ik by the response potential matrix elements. Calculations of 64 molecules are performed with the approximate vxc obtained with the statistical averaging of (model) orbitals potentials (SAOP) and the calculated ?k are compared with 406 experimental VIPs. Reasonable agreement between the SAOP -?k and the outer valence VIPs is found with an average deviation of about 0.4 eV.

  12. SOURCES OF VARIATION IN THE MUTAGENIC POTENCY OF COMPLEX CHEMICAL MIXTURES BASED ON THE SALMONELLA/MICROSOME ASSAY

    EPA Science Inventory

    Twenty laboratories worldwide participated in a collaborative trial sponsored by the International Programme on Chemical Safety on the mutagenicity of complex mixtures as expressed in the Salmonella/ microsome assay. he U.S. National Institute of Standards and Technology provided...

  13. 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

  14. Relationship between singlet triplet excitation energies and the Kohn Sham orbitals obtained with potentials that exhibit a wrong asymptotic behavior

    NASA Astrophysics Data System (ADS)

    Vázquez-Mayagoitia, Álvaro; Vargas, Rubicelia; Nichols, Jeffrey A.; Fuentealba, Patricio; Garza, Jorge

    2006-02-01

    A linear relationship was found between the singlet-triplet excitation energy and the energy difference presented by the Kohn-Sham frontier molecular orbitals, independently of the used exchange-correlation functional and of the basis set functions quality. The relationship was explored in three different situations: (a) when the number of carbons is increased in an all- trans acetylene family; (b) rotation of the trans-butadiene around the single bond; (c) dissociation process of the molecules H 2 and FH. Additionally, it was found a strong relationship between the vertical singlet-triplet excitation energy obtained with the B3LYP and the multiconfiguration-self consistent methods.

  15. Detecting single DNA copy number variations in complex genomes using one nanogram of starting DNA and BAC-array CGH

    Microsoft Academic Search

    Marine Guillaud-Bataille; Alexander Valent; Pascal Soularue; Christine Perot; Maria-del-Mar Inda; Aline Receveur; Sadek Smaili; Hugues Roest Crollius; Jean Benard; Alain Bernheim; Xavier Gidrol; Gisele Danglot

    2004-01-01

    Comparative genomic hybridization to bacterial artificial chromosome (BAC)-arrays (array-CGH) is a highly efficient technique, allowing the simultaneous measurement of genomic DNA copy number at hundreds or thousands of loci, and the reliable detec- tion of local one-copy-level variations. We report a genome-wide amplification method allowing the same measurement sensitivity, using 1 ng of starting genomic DNA, instead of the classical

  16. Kohn's pores are not responsible for collateral ventilation between inflated and deflated segments: a microscopic study of pulmonary intersegmental septa in the human lung.

    PubMed

    Zuo, Yizhi; Li, Lin; Liu, Shuwei

    2015-04-01

    The composition of the pulmonary intersegmental septum has not been clearly identified by thoracic surgeons who regard Kohn's pores as the main channel that causes air leakage when determining the intersegmental septum by segmental ventilation. In this study, we aimed to examine this possible misinterpretation by focusing on a detailed description of the microscopic anatomy of the intersegmental septum. To accomplish this aim, 50 lung samples of the intersegmental septum from fresh cadavers without emphysema were studied by histological and electron microscopy. The findings of light microscopy and electron microscopy showed that the intersegmental septum is composed of three layers. The alveolar walls of adjacent segments serve as the superficial layer. They are integral, and no Kohn's pores were identified. The deep layer contains collagen fibres. As shown by our findings, Kohn's pores are absent within the intersegmental septum. Therefore, they could not be the main channel for the collateral ventilation between inflated and deflated lung segments during a pulmonary segmentectomy. PMID:25832125

  17. Copy Number Variations Burden on miRNA Genes Reveals Layers of Complexities Involved in the Regulation of Pathways and Phenotypic Expression

    PubMed Central

    Veerappa, Avinash M.; Nachappa, Somanna Ajjamada; Prashali, Nelchi; Yadav, Sangeetha Nuggehalli; Srikanta, Manjula Arsikere; Manjegowda, Dinesh S.; Seshachalam, Keshava B.; Ramachandra, Nallur B.

    2014-01-01

    MicroRNAs are involved in post-transcriptional down-regulation of gene expression. Variations in miRNA genes can severely affect downstream-regulated genes and their pathways. However, population-specific burden of CNVs on miRNA genes and the complexities created towards the phenotype is not known. From a total of 44109 CNVs investigated from 1715 individuals across 12 populations using high-throughput arrays, 4007 miRNA-CNVs (?9%) consisting 6542 (?5%) miRNA genes with a total of 333 (?5%) singleton miRNA genes were identified. We found miRNA-CNVs across the genomes of individuals showing multiple hits in many targets, co-regulated under the same pathway. This study proposes four mechanisms unraveling the many complexities in miRNA genes, targets and co-regulated miRNA genes towards establishment of phenotypic diversity. PMID:24587348

  18. Structure variation and luminescence properties of lanthanide complexes with 1,9-bis [2-(2'-picolylaminoformyl)-1,4,7,9-tetraoxadecane

    SciTech Connect

    Song Xueqin [College of Chemistry and Chemical Engineering and State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000 (China); School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou 730070 (China); Zang Zhipeng [College of Chemistry and Chemical Engineering and State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000 (China); Liu Weisheng, E-mail: liuws@lzu.edu.c [College of Chemistry and Chemical Engineering and State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000 (China); Zhang Yujie [School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou 730070 (China)

    2009-04-15

    Using 1,9-salicylamide bissubstituted oxadecane ligand, 1,9-bis [2-(2'-picolylaminoformyl)-1,4,7,9-tetraoxadecane (L), two novel lanthanide complexes have been prepared and well characterized by means of elemental analysis, IR spectroscopy, UV-vis spectroscopy, TGA analysis and single-crystal X-ray diffraction. {l_brace}[PrL(NO{sub 3}){sub 3}(H{sub 2}O){sub 2}].CH{sub 3}OH{r_brace}{sub n} is a 1D zigzag polymer with three-dimensional supramolecular structure formed by hydrogen bonds, while [EuL(NO{sub 3}){sub 3}(H{sub 2}O)]{sub n} is a linear coordination polymer and present an interesting supramolecular double chain, which are very different from the structure of terbium complex reported before. The result reported herein demonstrated that steric crowding associated with the decreasing lanthanide ion radius causes changes of the conformation of the ligand as well as structures. Luminescence studies for the Eu(III) complexes demonstrated that the salicylamide ligand also exhibits a good antennae effect for the Eu(III) ion due to efficient intersystem crossing and ligand-to-metal energy transfer and the Eu(III) ion is well shielded from the surrounding environment. - Graphical abstract: Structure variation and luminescence properties of lanthanide complexes with 1,9-bis [2-(2'-picolylaminoformyl)-1,4,7,9-tetraoxadecane.

  19. The Nature of Genetic Variation in Sex and Reproduction-related Genes Among Sibling Species of the Drosophila melanogaster Complex

    Microsoft Academic Search

    Rob J. Kulathinal; Rama S. Singh

    2004-01-01

    Much is known about the biology of Drosophila melanogaster. As a model organism, a comprehensive understanding of its development, physiology and reproduction has been acquired. As a result, a broad variety of transferable genetic tools and information has allowed sibling species of the D. melanogaster complex to emerge as an important speciation model system. By comparing D. melanogaster with its

  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. 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 ?-conjugated molecules, it is shown how the DE manifests itself either in too strong or too weak delocalization of localized molecular orbitals (LMOs). Optical rotation is an electric-magnetic linear response property that is calculated in a similar fashion as the electric polarizability, but it is more sensitive to approximations and can benefit greatly from tuning and small DE. Hyperpolarizabilities of ?-conjugated "push-pull" systems are examples of NLO properties that can be greatly improved by tuning of range-separated exchange (RSE) functionals, in part due to improved charge-transfer excitation energies. On-going work on band gap predictions is also mentioned. The findings may provide clues for future improvements of KST because different molecular properties exhibit varying sensitivity to approximations in the electronic structure model. The utility of analyzing molecular properties and the impact of the DE in terms of LMOs, representing "chemist's orbitals" such as individual lone pairs and bonds, is highlighted. PMID:24968277

  2. 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. PMID:24589862

  3. An assessment indicator for air ventilation and pollutant dispersion potential in an urban canopy with complex natural terrain and significant wind variations

    NASA Astrophysics Data System (ADS)

    Yim, S. H. L.; Fung, J. C. H.; Ng, E. Y. Y.

    2014-09-01

    In an urban planning context, an assessment indicator for evaluating a city's dispersion potential is beneficial, especially if the city has a complex natural terrain and significant wind variations. A study was conducted to implement an urban canopy drag indicator, taking site wind variation into account by involving both wind speed and direction in the calculations. Hong Kong (HK) was taken as an example due to its complicated natural topography and wind characteristics. A spatial distribution of an urban canopy drag over HK was determined based on wind data from 2004. The urban canopy drag values in three highly urbanized areas in HK, including Kowloon West, Kowloon East and Hong Kong Island North, were obtained and are discussed in detail. A fluid particle tracking program was developed and applied to identify the major wind paths in Kowloon West, with an area of approximately 5.5 × 6 km as an example. We analyzed the diurnal variation in the dispersion times and the major wind paths in the region during both summer and winter. Our results estimated that the horizontal dispersion times of Kowloon West during both winter and summer were approximately 20 min. By combining the wind paths from both seasons, we identified several major wind paths and critical ventilation areas in Kowloon West. This paper demonstrates the potential use of an urban canopy drag indicator for assessing air ventilation and pollutant dispersion in a city planning context.

  4. Electronic structures in coupled two quantum dots by 3D-mesh Hartree-Fock-Kohn-Sham calculation

    NASA Astrophysics Data System (ADS)

    Matsuse, T.; Hama, T.; Kaihatsu, H.; Toyoda, N.; Takizawa, T.

    To study the electronic structures of quantum dots in the framework of self-interaction-free including three dimensional effects, we adopt the theory of nonlocal effective potential introduced by Kohn and Sham [#!ks65!#]. For utilizing the advantageous point of the real space (3D) mesh method to solve the original nonlinear and nonlocal Hartree-Fock-Kohn-Sham (HFKS)-equation, we introduce a linearization of the equation in the local form by introducing the local Coulomb potentials which depend on explicitly the two single particle states. In practice, for solving the local form HFKS-equation, we use the Car-Parrinello-like relaxation method and the Coulomb potentials are obtained by solving the Poisson equation under proper boundary conditions. Firstly the observed energy gap between triplet- and singlet-states of N = 4 in DBS [#!tarucha96!#] is discussed to reproduce the addition energies and chemical potentials depending the magnetic field. Next the coupling between two-quantum dots in TBS [#!aht97!#] is studied by adding the square barrier between two dots. The spin-degeneracy [#!aht97!#] measured in gate-voltage depending on magnetic field is well reproduced in the limit of small mismatch. Finally, the electronic states in the ring structure are calculated and discussed how the ring size and magnetic field affect to the structures.

  5. The pole expansion and selected inversion technique for solving Kohn-Sham density functional theory at large scale

    NASA Astrophysics Data System (ADS)

    Lin, Lin; Chen, Mohan; E, Weinan; He, Lixin; Lu, Jianfeng; Yang, Chao; Ying, Lexing

    2013-03-01

    The standard diagonalization based method for solving Kohn-Sham density functional theory (KSDFT) requires N eigenvectors for an O(N) * O(N) Kohn-Sham Hamiltonian matrix, with N being the number of electrons in the system. The computational cost for such procedure is expensive and scales as O(N^3). We have developed a novel pole expansion plus selected inversion (PEXSI) method, in which KSDFT is solved by evaluating the selected elements of the inverse of a series of sparse symmetric matrices, and the overall algorithm scales at most O(N^2) for all materials including metallic and insulating systems without any truncation. The PEXSI method can be used with orthogonal or nonorthogonal basis set, and the electron density, total energy, Helmholtz free energy and atomic force are calculated simultaneously and accurately without using the eigenvalues and eigenvectors. Combined with atomic orbital basis functions, the PEXSI method can be applied to study the electronic structure of boron nitride nanotube and carbon nanotube with more than 10,000 atoms on a single processor.

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

    SciTech Connect

    Kagan, M. Yu., E-mail: kagan@kapitza.ras.ru [Russian Academy of Sciences, Kapitza Institute for Physical Problems (Russian Federation); Val'kov, V. V.; Mitskan, V. A.; Korovuskin, M. M. [Russian Academy of Sciences, Kirenskii Physics Institute, Siberian Branch (Russian Federation)] [Russian Academy of Sciences, Kirenskii Physics Institute, Siberian Branch (Russian Federation)

    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.

  7. The nature of genetic variation in sex and reproduction-related genes among sibling species of the Drosophila melanogaster complex

    Microsoft Academic Search

    Rob J. Kulathinal; Rama S. Singh

    \\u000a Much is known about the biology of Drosophila melanogaster. As a model organism, a comprehensive understanding of its development, physiology and reproduction has been acquired. As\\u000a a result, a broad variety of transferable genetic tools and information has allowed sibling species of the D. melanogaster complex to emerge as an important speciation model system. By comparing D. melanogaster with its

  8. Using qualitative evidence on patients’ views to help understand variation in effectiveness of complex interventions: a qualitative comparative analysis

    PubMed Central

    2013-01-01

    Background Complex healthcare interventions consist of multiple components which may vary in trials conducted in different populations and contexts. Pooling evidence from trials in a systematic review is challenging because it is unclear which components are needed for effectiveness. The potential is recognised for using recipients’ views to explore why some complex interventions are effective and others are not. Methods to maximise this potential are poorly developed. Methods We used a novel approach to explore how patients’ views may explain the disparity in effectiveness of complex interventions. We used qualitative comparative analysis to explore agreement between qualitative syntheses of data on patients’ views and evidence from trialed interventions to increase adherence to treatments. We first populated data matrices to reflect whether the content of each trialed intervention could be matched with suggestions arising from patients’ views. We then used qualitative comparative analysis software to identify, by a process of elimination, the smallest number of configurations (patterns) of components that corresponded with patients’ suggestions and accounted for whether each intervention was effective or ineffective. Results We found suggestions by patients were poorly represented in interventions. Qualitative comparative analysis identified particular combinations of components corresponding with patients’ suggestions and with whether an intervention was effective or ineffective. Six patterns were identified for an effective and four for an ineffective intervention. Two types of patterns arose for the effective interventions, one being didactic (providing clear information or instruction) and the other interactive (focusing on personal risk factors). Conclusions Our analysis highlights how data on patients’ views has the potential to identify key components across trials of complex interventions or inform the content of new interventions to be trialed. PMID:23777465

  9. Temporal and spatial variations in the parasitoid complex of the horse chestnut leafminer during its invasion of Europe

    Microsoft Academic Search

    Giselher Grabenweger; Patrik Kehrli; Irene Zweimüller; Sylvie Augustin; Nikolaos Avtzis; Sven Bacher; Jona Freise; Sandrine Girardoz; Sylvain Guichard; Werner Heitland; Christa Lethmayer; Michaela Stolz; Rumen Tomov; Lubomir Volter; Marc Kenis

    2010-01-01

    The enemy release hypothesis posits that the initial success of invasive species depends on the scarcity and poor adaptation\\u000a of native natural enemies such as predators and parasitoids. As for parasitoids, invading hosts are first attacked at low\\u000a rates by a species-poor complex of mainly generalist species. Over the years, however, parasitoid richness may increase either\\u000a because the invading host

  10. Spatial variation in host feeding patterns of Culex tarsalis and the Culex pipiens complex (Diptera: Culicidae) in California.

    PubMed

    Thiemann, T C; Lemenager, D A; Kluh, S; Carroll, B D; Lothrop, H D; Reisen, W K

    2012-07-01

    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

  11. 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

  12. 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

  13. 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.

  14. 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. PMID:19625623

  15. 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.

  16. 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.

  17. The spin-unrestricted molecular Kohn-Sham solution and the analogue of Koopmans's theorem for open-shell molecules

    NASA Astrophysics Data System (ADS)

    Gritsenko, O. V.; Baerends, E. J.

    2004-05-01

    Spin-unrestricted Kohn-Sham (KS) solutions are constructed from accurate ab initio spin densities for the prototype doublet molecules NO2, ClO2, and NF2 with the iterative local updating procedure of van Leeuwen and Baerends (LB). A qualitative justification of the LB procedure is given with a "strong" form of the Hohenberg-Kohn theorem. The calculated energies ?i? of the occupied KS spin orbitals provide numerical support to the analogue of Koopmans' theorem in spin-density functional theory. In particular, the energies -?i? of the minor spin (?) valence orbitals of the considered doublet molecules correspond fairly well to the experimental vertical ionization potentials (VIPs) Ii1 to the triplet cationic states. The energy -?H? of the highest occupied (spin-unpaired) ? orbital is equal to the first VIP IH0 to the singlet cationic state. In turn, the energies -?i? of the major spin (?) valence orbitals of the closed subshells correspond to a fifty-fifty average of the experimental VIPs Ii1 and Ii0 to the triplet and singlet states. For the Li atom we find that the exact spin densities are represented by a spin-polarized Kohn-Sham system which is not in its ground state, i.e., the orbital energy of the lowest unoccupied ? spin orbital is lower than that of the highest occupied ? spin orbital ("a hole below the Fermi level"). The addition of a magnetic field in the -z direction will shift the ? levels up so as to restore the Aufbau principle. This is an example of the nonuniqueness of the mapping of the spin density on the KS spin-dependent potentials discussed recently in the literature. The KS potentials may no longer go to zero at infinity, and it is in general the differences ?s?(?)-?i? that can be interpreted as (averages of) ionization energies. In total, the present results suggest the spin-unrestricted KS theory as a natural one-electron independent-particle model for interpretation and assignment of the experimental photoelectron spectra of open-shell molecules.

  18. 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 (?26Mg = -0.40 ± 0.11‰) are isotopically similar to the parent basalt (?26Mg = -0.31‰), whereas clay fractions (?26Mg = -0.62 ± 0.12‰), exchangeable Mg (?26Mg = -0.75 ± 0.14‰), and soil solutions (?26Mg = -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 (?26Mgplant-exch = +0.50 ± 0.09‰), and changes in ?26Mg 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.

  19. Variations in atmospheric PM trace metal content in Spanish towns: Illustrating the chemical complexity of the inorganic urban aerosol cocktail

    NASA Astrophysics Data System (ADS)

    Moreno, Teresa; Querol, Xavier; Alastuey, Andrés; Viana, Mar; Salvador, Pedro; Sánchez de la Campa, Ana; Artiñano, Begoña; de la Rosa, Jesús; Gibbons, Wes

    The majority of the Spanish urban population breathe air containing inhalable ambient airborne particles at average concentrations of 30-46 ?g m -3 (PM 10) and 20-30 ?g m -3 (PM 2.5). Even though the average weight of inhaled urban aerosol is commonly similar, however, there can be large chemical differences between the ambient dusts from different towns, including the more bioreactive elements such as some metals. In this context, we compare the source-apportioned trace metal content of airborne PM 10 and PM 2.5 collected daily over a 1-year period from six population centres in Spain: Barcelona, Alcobendas, Llodio, Huelva, Tarragona and Las Palmas de Gran Canaria. Total average trace metal (?TM) PM 10 and PM 2.5 contents vary by up to a factor of around 3, reaching a maximum of ?TM 10 811 ng m -3 and ?TM 2.5 503 ng m -3 at Llodio, an industrial but humid site with the lowest PM 10 mass levels but high contamination by Zn, Pb, Mn, Sn, Ni and Cr. In contrast, pollution at Huelva, although another industrially influenced site, instead emphasises Cu and As, whereas Barcelona, where traffic emissions and resuspension contribute to some of the highest average PM 10 levels in Spain, has unusually raised levels of Ti, V and Ba. Such variations in both daily and annual average PM bulk chemistry, particularly in potentially toxic trace metals concentrated in the finer aerosols (such as Cd, As, Pb, Hg and Ni), predict that PM health effects on resident populations from different towns are unlikely to be the same.

  20. Disentangling the effects of recombination, selection, and demography on the genetic variation at a major histocompatibility complex class II gene in the alpine chamois.

    PubMed

    Mona, S; Crestanello, B; Bankhead-Dronnet, S; Pecchioli, E; Ingrosso, S; D'Amelio, S; Rossi, L; Meneguz, P G; Bertorelle, G

    2008-09-01

    The major histocompatibility complex (MHC) harbours some of the most polymorphic loci in vertebrate genomes. MHC genes are thought to be subject to some form of balancing selection, most likely pathogen-mediated selection. Hence, MHC genes are excellent candidates for exploring adaptive processes. In this study, we investigated the genetic variation at exon 2 of the DRB class II MHC locus in 191 alpine chamois (Rupicapra rupicapra) from 10 populations in the eastern Alps of Italy. In particular, we were interested in distinguishing and estimating the relative impact of selective and demographic factors, while taking into account the confounding effect of recombination. The extremely high d(n)/d(s) ratio and the presence of trans-species polymorphisms suggest that a strong long-term balancing selection effect has been operating at this locus throughout the evolutionary history of this species. We analysed patterns of genetic variation within and between populations, and the mitochondrial D-loop polymorphism patterns were analysed to provide a baseline indicator of the effects of demographic processes. These analyses showed that (i) the chamois experienced a demographic decline in the last 5000-30 000 years, most likely related to the postglacial elevation in temperature; (ii) this demographic process can explain the results of neutrality tests applied to MHC variation within populations, but cannot justify the much weaker divergence between populations implied by MHC as opposed to mitochondrial DNA; (iii) similar sets of divergent alleles are probably maintained with similar frequencies by balancing selection in different populations, and this mechanism is also operating in small isolated populations, which are strongly affected by drift. PMID:19238706

  1. 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. PMID:22819737

  2. 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. PMID:25475909

  3. Synthesis of binucleating macrocycles and their nickel(II) hydroxo- and cyano-bridged complexes with divalent ions: anatomical variation of ligand features.

    PubMed

    Zhang, Xiaofeng; Huang, Deguang; Chen, Yu-Sheng; Holm, R H

    2012-10-15

    The planar NNN-pincer complexes [M(II)(pyN(2)(Me2))(OH)](1-) (M(II) = Ni, Cu) fix CO(2) in ?(1)-OCO(2)H complexes; results for the copper system are described. Mn(II), Fe(II), Co(II), and Zn(II) behave differently, forming [M(II)(pyN(2)(Me2))(2)](2-) with N(4)O(2) coordination. Incorporation of the Ni(II) pincer into binucleating macrocycle 2 containing a triamino M(II) locus connected by two 1,3-biphenylene groups affords proximal Ni(II) and M(II) sites for investigation of the synthesis, structure, and reactivity of Ni-X-M bridge units. This ligand structure is taken as a reference for variations in M(II) atoms and binding sites and bridges X = OH(-) and CN(-) to produce additional members of the macrocyclic family with improved properties. Macrocycle 2 with a 22-membered ring is shown to bind M(II) = Mn, Fe, and Cu with hydroxo bridges. Introduction of the 4-Bu(i)O group (macrocycle 3) improves the solubility of neutral complexes such as those with Ni(II)-OH-Cu(II) and Ni(II)-CN-Fe(II) bridges. Syntheses of macrocycle 5 with a 7-Me-[12]aneSN(3) and macrocycle 6 with a 1,8-Me(2)-[14]aneN(4) M(II) binding site are described together with hydoxo-bridged Ni/Cu and cyano-bridged Ni/Fe complexes. This work was motivated by the presence of a Ni···(HO)-Fe bridge grouping in a reactive state of carbon monoxide dehydrogenase. Attempted decrease in Ni-(OH)-M distances (3.70-3.87 Å) to smaller values observed in the enzyme by use of macrocycle 4 having 1,2-biphenylene connectors led to a mononuclear octahedral Ni(II) complex. Bridge structural units are summarized, and the structures of 14 macrocyclic complexes including 8 with bridges are described. PMID:23030366

  4. Ab initio analytical infrared intensities for periodic systems through a coupled perturbed Hartree-Fock/Kohn-Sham method

    NASA Astrophysics Data System (ADS)

    Maschio, Lorenzo; Kirtman, Bernard; Orlando, Roberto; Rèrat, Michel

    2012-11-01

    A fully analytical method for calculating Born charges and, hence, infrared intensities of periodic systems, is formulated and implemented in the CRYSTAL program, which uses a local Gaussian type basis set. Our efficient formalism combines integral gradients with first-order coupled perturbed Hartree-Fock/Kohn Sham electronic response to an electric field. It avoids numerical differentiation with respect to wave vectors, as in some Berry phase approaches, and with respect to atomic coordinates. No perturbation equations for the atomic displacements need to be solved. Several tests are carried out to verify numerical stability, consistency in one, two, and three dimensions, and applicability to large unit cells. Future extensions to piezoelectricity and Raman intensities are noted.

  5. Complex, dynamic combination of physical, chemical and nutritional variables controls spatio-temporal variation of sandy beach community structure.

    PubMed

    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 beaches as functional ecosystems in their own right. PMID:21858213

  6. 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 beaches as functional ecosystems in their own right. PMID:21858213

  7. Basis set convergence of indirect spin-spin coupling constants in the Kohn-Sham limit for several small molecules.

    PubMed

    Kupka, Teobald; Nieradka, Marzena; Stachów, Micha?; Pluta, Tadeusz; Nowak, Piotr; Kjær, Hanna; Kongsted, Jacob; Kaminsky, Jakub

    2012-04-12

    The performance of more than 40 density functionals in predicting indirect spin-spin coupling constants (SSCCs) in the Kohn-Sham basis set limit was tested. For comparison, similar calculations were performed using the RHF, SOPPA, SOPPA(CC2), and SOPPA(CCSD) methods, and the results were estimated toward the complete basis set (CBS) limit. The SSCCs of nine small molecules (N(2), CO, CO(2), NH(3), CH(4), C(2)H(2), C(2)H(4), C(2)H(6), and C(6)H(6)) were calculated using the dedicated Jensen pcJ-n polarization-consistent basis sets and used for the CBS limit estimations within the Kohn-Sham limit. These CBS results were compared with calculations using the aug-cc-pVTZ-J basis set. Among the 41 studied DFT methods, the tHCTHhyb, HSEh1PBE, HSE2PBE, wB97XD, wB97, and wB97X functionals reproduced accurately the experimental (1)J(XH) SSCCs and (3)J(HH60) and (2)J(HH(gem)) in ethane. Similarly, the functionals HSEh1PBE, HSE2PBE, wB97XD, wB97, and wB97X predicted accurately (1)J(CC), and B98, B97-1, B97-2, PBE1PBE, B1LYP, and O3LYP provided accurate (1)J(CO) results in the CO molecule. A very good performance for the calculation of the SSCCs based on the use of the relatively small basis set aug-cc-pVTZ-J was observed. PMID:22401301

  8. Alkaloid polymorphism and ITS sequence variation in the Spiraea japonica complex (Rosaceae) in China: traces of the biological effects of the Himalaya-Tibet Plateau uplift.

    PubMed

    Zhang, Zhaoyang; Fan, Liming; Yang, Junbo; Hao, Xiaojiang; Gu, Zhijian

    2006-05-01

    Spiraea japonica, a diverse, perennial shrubby species complex widespread across E Asia, was a useful model in a first attempt to link specific phylogeny, floristic evolution, and historical environmental changes in E Asia. DNA-based phylogenetic reconstruction served as a framework to investigate whether the patterns of variation in alkaloids and nrITS from varieties of S. japonica reflect the geological history of China and the uplifting of the Himalaya-Tibet plateau, the most significant geological event in E Asia since the late Paleocene. The high geographical structure found in the phylogenetic trees was corroborated by the distribution of alkaloids. All populations from E China, with mainly hetisine-type alkaloids, formed a single clade, sister to a clade of all populations from SW China, with mainly atisine-type alkaloids. The distribution boundary between the two clades roughly matched the floristic division between the Sino-Japanese Forest and the Sino-Himalayan Forest subkingdoms, as well as the environmental division between SW and E China, suggesting a close link between specific phylogeny, floristic evolution, and geographical changes in E Asia. The divergence between lineages at variety and population level within the eastern clade was slightly older than those within the southwestern clade, supporting the hypothesis of a northeast-southwest migration of Spiraea since the Eocene. The uplift of the Himalaya-Tibet plateau and subsequent increase in geographical complexity in SW China, could facilitate divergence maintenance, thus accelerating the evolutionary rate. PMID:21642139

  9. 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'. PMID:25394749

  10. 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 mixtures of chemical compounds. S. cerevisiae transcriptomics may also be developed for testing of mixtures of conventional drugs (“polypills”) to discover novel antagonistic or synergistic effects of those drug combinations. PMID:23826764

  11. Plane-wave pseudopotential implementation of explicit integrators for time-dependent Kohn-Sham equations in large-scale simulations.

    PubMed

    Schleife, André; Draeger, Erik W; Kanai, Yosuke; Correa, Alfredo A

    2012-12-14

    Explicit integrators for real-time propagation of time-dependent Kohn-Sham equations are compared regarding their suitability for performing large-scale simulations. Four algorithms are implemented and assessed for both stability and accuracy within a plane-wave pseudopotential framework, employing the adiabatic approximation to the exchange-correlation functional. Simulation results for a single sodium atom and a sodium atom embedded in bulk magnesium oxide are discussed. While the first-order Euler scheme and the second-order finite-difference scheme are unstable, the fourth-order Runge-Kutta scheme is found to be conditionally stable and accurate within this framework. Excellent parallel scalability of the algorithm up to more than a thousand processors is demonstrated for a system containing hundreds of electrons, evidencing the suitability for large-scale simulations based on real-time propagation of time-dependent Kohn-Sham equations. PMID:23249083

  12. Mixed-Methods Research in a Complex Multisite VA Health Services Study: Variations in the Implementation and Characteristics of Chiropractic Services in VA

    PubMed Central

    Cohen, Angela B.; Lisi, Anthony J.; Smith, Monica M.; Delevan, Deborah; Armstrong, Courtney; Mittman, Brian S.

    2013-01-01

    Maximizing the quality and benefits of newly established chiropractic services represents an important policy and practice goal for the US Department of Veterans Affairs' healthcare system. Understanding the implementation process and characteristics of new chiropractic clinics and the determinants and consequences of these processes and characteristics is a critical first step in guiding quality improvement. This paper reports insights and lessons learned regarding the successful application of mixed methods research approaches—insights derived from a study of chiropractic clinic implementation and characteristics, Variations in the Implementation and Characteristics of Chiropractic Services in VA (VICCS). Challenges and solutions are presented in areas ranging from selection and recruitment of sites and participants to the collection and analysis of varied data sources. The VICCS study illustrates the importance of several factors in successful mixed-methods approaches, including (1) the importance of a formal, fully developed logic model to identify and link data sources, variables, and outcomes of interest to the study's analysis plan and its data collection instruments and codebook and (2) ensuring that data collection methods, including mixed-methods, match study aims. Overall, successful application of a mixed-methods approach requires careful planning, frequent trade-offs, and complex coding and analysis. PMID:24489589

  13. Morphological variation in Echinorhynchus truttae Schrank, 1788 and the Echinorhynchus bothniensis Zdzitowiecki & Valtonen, 1987 species complex from freshwater fishes of northern Europe

    PubMed Central

    2013-01-01

    Abstract Echinorhynchus truttae and the Echinorhynchus bothniensis species complex are common parasites of salmoniform and other fishes in northern Europe. Echinorhynchus bothniensis and its sibling species Echinorhynchus 'bothniensis' are thought to be closely related to the Nearctic Echinorhynchus leidyi Van Cleave, 1924 based on morphological similarity and common usage of a mysid intermediate host. This study provides the first analysis of morphological and meristic variation in Echinorhynchus truttae and expands our knowledge of anatomical variability in the Echinorhynchus bothniensis group. Morphological variability in Echinorhynchus truttae was found to be far greater than previously reported, with part of the variance attributable to sexual dimorphism. Echinorhynchus truttae, the two species of the Echinorhynchus bothniensis group and Echinorhynchus leidyi displayed considerable interspecific overlap in the ranges of all conventional morphological characters. However, Proboscis profiler, a tool for detecting acanthocephalan morphotypes using multivariate analysis of hook morphometrics, successfully separated Echinorhynchus truttae from the other taxa. The Echinorhynchus bothniensis species group could not be reliably distinguished from Echinorhynchus leidyi (or each other), providing further evidence of the affinity of these taxa. Observations on the distribution of Echinorhynchus truttae in its definitive host population are also reported. PMID:24723769

  14. The chromosomal polymorphism linked to variation in social behavior in the white-throated sparrow (Zonotrichia albicollis) is a complex rearrangement and suppressor of recombination.

    PubMed

    Thomas, James W; Cáceres, Mario; Lowman, Joshua J; Morehouse, Caroline B; Short, Meghan E; Baldwin, Erin L; Maney, Donna L; Martin, Christa L

    2008-07-01

    Variation in social behavior and plumage in the white-throated sparrow (Zonotrichia albicollis) is linked to an inversion polymorphism on chromosome 2. Here we report the results of our comparative cytogenetic mapping efforts and population genetics studies focused on the genomic characterization of this balanced chromosomal polymorphism. Comparative chromosome painting and cytogenetic mapping of 15 zebra finch BAC clones to the standard (ZAL2) and alternative (ZAL2(m)) arrangements revealed that this chromosome is orthologous to chicken chromosome 3, and that at a minimum, ZAL2 and ZAL2(m) differ by a pair of included pericentric inversions that we estimate span at least 98 Mb. Population-based sequencing and genotyping of multiple loci demonstrated that ZAL2(m) suppresses recombination in the heterokaryotype and is evolving as a rare nonrecombining autosomal segment of the genome. In addition, we estimate that the first inversion within the ZAL2(m) arrangement originated 2.2+/-0.3 million years ago. Finally, while previously recognized as a genetic model for the evolution of social behavior, we found that the ZAL2/ZAL2(m) polymorphism also shares genetic and phenotypic features with the mouse t complex and we further suggest that the ZAL2/ZAL2(m) polymorphism is a heretofore unrecognized model for the early stages of sex chromosome evolution. PMID:18562641

  15. The Chromosomal Polymorphism Linked to Variation in Social Behavior in the White-Throated Sparrow (Zonotrichia albicollis) Is a Complex Rearrangement and Suppressor of Recombination

    PubMed Central

    Thomas, James W.; Cáceres, Mario; Lowman, Joshua J.; Morehouse, Caroline B.; Short, Meghan E.; Baldwin, Erin L.; Maney, Donna L.; Martin, Christa L.

    2008-01-01

    Variation in social behavior and plumage in the white-throated sparrow (Zonotrichia albicollis) is linked to an inversion polymorphism on chromosome 2. Here we report the results of our comparative cytogenetic mapping efforts and population genetics studies focused on the genomic characterization of this balanced chromosomal polymorphism. Comparative chromosome painting and cytogenetic mapping of 15 zebra finch BAC clones to the standard (ZAL2) and alternative (ZAL2m) arrangements revealed that this chromosome is orthologous to chicken chromosome 3, and that at a minimum, ZAL2 and ZAL2m differ by a pair of included pericentric inversions that we estimate span at least 98 Mb. Population-based sequencing and genotyping of multiple loci demonstrated that ZAL2m suppresses recombination in the heterokaryotype and is evolving as a rare nonrecombining autosomal segment of the genome. In addition, we estimate that the first inversion within the ZAL2m arrangement originated 2.2 ± 0.3 million years ago. Finally, while previously recognized as a genetic model for the evolution of social behavior, we found that the ZAL2/ZAL2m polymorphism also shares genetic and phenotypic features with the mouse t complex and we further suggest that the ZAL2/ZAL2m polymorphism is a heretofore unrecognized model for the early stages of sex chromosome evolution. PMID:18562641

  16. Stability conditions for exact-exchange Kohn-Sham methods and their relation to correlation energies from the adiabatic-connection fluctuation-dissipation theorem

    NASA Astrophysics Data System (ADS)

    Bleiziffer, Patrick; Schmidtel, Daniel; Görling, Andreas

    2014-11-01

    The occurrence of instabilities, in particular singlet-triplet and singlet-singlet instabilities, in the exact-exchange (EXX) Kohn-Sham method is investigated. Hessian matrices of the EXX electronic energy with respect to the expansion coefficients of the EXX effective Kohn-Sham potential in an auxiliary basis set are derived. The eigenvalues of these Hessian matrices determine whether or not instabilities are present. Similar as in the corresponding Hartree-Fock case instabilities in the EXX method are related to symmetry breaking of the Hamiltonian operator for the EXX orbitals. In the EXX methods symmetry breaking can easily be visualized by displaying the local multiplicative exchange potential. Examples (N2, O2, and the polyyne C10H2) for instabilities and symmetry breaking are discussed. The relation of the stability conditions for EXX methods to approaches calculating the Kohn-Sham correlation energy via the adiabatic-connection fluctuation-dissipation (ACFD) theorem is discussed. The existence or nonexistence of singlet-singlet instabilities in an EXX calculation is shown to indicate whether or not the frequency-integration in the evaluation of the correlation energy is singular in the EXX-ACFD method. This method calculates the Kohn-Sham correlation energy through the ACFD theorem theorem employing besides the Coulomb kernel also the full frequency-dependent exchange kernel and yields highly accurate electronic energies. For the case of singular frequency-integrands in the EXX-ACFD method a regularization is suggested. Finally, we present examples of molecular systems for which the self-consistent field procedure of the EXX as well as the Hartree-Fock method can converge to more than one local minimum depending on the initial conditions.

  17. On the N-Representability and Universality of F[rho] in the Hohenberg-Kohn Version of Density Functional Theory

    Microsoft Academic Search

    Eduardo V. Ludeña; Francesc Illas; Alejandro Ramirez-Solis

    2009-01-01

    We discuss two basic problems in the Hohenberg-Kohn-Sham version of density functional theory, HKS-DFT: the first, the N-representability of the functional F[rho] and, the second, the universality of F[rho]. In relation to the first, we show that F[rho] must satisfy N-representability conditions that follow from those on the 2-matrix D2(r1, r2; r', r'2). In the case of the second, we

  18. On the N-Representability and Universality of F[rho] in the Hohenberg-Kohn Version of Density Functional Theory

    Microsoft Academic Search

    Eduardo V. Ludeña; Francesc Illas; Alejandro Ramirez-Solis

    2008-01-01

    We discuss two basic problems in the Hohenberg-Kohn-Sham version of density functional theory, HKS-DFT: the first, the N-representability of the functional F[rho] and, the second, the universality of F[rho]. In relation to the first, we show that F[rho] must satisfy N-representability conditions that follow from those on the 2-matrix D2(r1, r2; r', r'2). In the case of the second, we

  19. Performance of a new hybrid Hartree–Fock\\/Kohn–Sham model (B98) in predicting vibrational frequencies, polarisabilities and NMR chemical shifts

    Microsoft Academic Search

    Massimiliano Bienati; Carlo Adamo; Vincenzo Barone

    1999-01-01

    We have implemented a new hybrid Hartree–Fock\\/Kohn–Sham model recently introduced by Becke (B98) in a fully self-consistent approach including analytical first and second derivatives with respect to both geometric and electromagnetic field parameters. Since this functional was originally optimized with respect to formation enthalpies only, we analyze in this Letter its performance for other properties including geometric structures, vibrational frequencies,

  20. A self-interaction-free local hybrid functional: Accurate binding energies vis-à-vis accurate ionization potentials from Kohn-Sham eigenvalues

    SciTech Connect

    Schmidt, Tobias; Kümmel, Stephan [Theoretical Physics IV, University of Bayreuth, 95440 Bayreuth (Germany)] [Theoretical Physics IV, University of Bayreuth, 95440 Bayreuth (Germany); Kraisler, Eli; Makmal, Adi; Kronik, Leeor [Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth 76100 (Israel)] [Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth 76100 (Israel)

    2014-05-14

    We present and test a new approximation for the exchange-correlation (xc) energy of Kohn-Sham density functional theory. It combines exact exchange with a compatible non-local correlation functional. The functional is by construction free of one-electron self-interaction, respects constraints derived from uniform coordinate scaling, and has the correct asymptotic behavior of the xc energy density. It contains one parameter that is not determined ab initio. We investigate whether it is possible to construct a functional that yields accurate binding energies and affords other advantages, specifically Kohn-Sham eigenvalues that reliably reflect ionization potentials. Tests for a set of atoms and small molecules show that within our local-hybrid form accurate binding energies can be achieved by proper optimization of the free parameter in our functional, along with an improvement in dissociation energy curves and in Kohn-Sham eigenvalues. However, the correspondence of the latter to experimental ionization potentials is not yet satisfactory, and if we choose to optimize their prediction, a rather different value of the functional's parameter is obtained. We put this finding in a larger context by discussing similar observations for other functionals and possible directions for further functional development that our findings suggest.

  1. The Hartree product and the description of local and global quantities in atomic systems: A study within Kohn-Sham theory

    SciTech Connect

    Garza, Jorge [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352 (United States)] [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352 (United States); Nichols, Jeffrey A. [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352 (United States)] [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352 (United States); Dixon, David A. [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352 (United States)] [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352 (United States)

    2000-01-15

    The Hartree product is analyzed in the context of Kohn-Sham theory. The differential equations that emerge from this theory are solved with the optimized effective potential using the Krieger, Li, and Iafrate approximation, in order to get a local potential as required by the ordinary Kohn-Sham procedure. Because the diagonal terms of the exact exchange energy are included in Hartree theory, it is self-interaction free and the exchange potential has the proper asymptotic behavior. We have examined the impact of this correct asymptotic behavior on local and global properties using this simple model to approximate the exchange energy. Local quantities, such as the exchange potential and the average local electrostatic potential are used to examine whether the shell structure in an atom is revealed by this theory. Global quantities, such as the highest occupied orbital energy (related to the ionization potential) and the exchange energy are also calculated. These quantities are contrasted with those obtained from calculations with the local density approximation, the generalized gradient approximation, and the self-interaction correction approach proposed by Perdew and Zunger. We conclude that the main characteristics in an atomic system are preserved with the Hartree theory. In particular, the behavior of the exchange potential obtained in this theory is similar to those obtained within other Kohn-Sham approximations. (c) 2000 American Institute of Physics.

  2. Dissociation of diatomic molecules and the exact-exchange Kohn-Sham potential: The case of LiF

    SciTech Connect

    Makmal, Adi; Kronik, Leeor [Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth 76100 (Israel); Kuemmel, Stephan [Physikalisches Institut, Universitaet Bayreuth, D-95440 Bayreuth (Germany)

    2011-06-15

    We examine the role of the exact-exchange (EXX) Kohn-Sham potential in curing the problem of fractional molecular dissociation. This is achieved by performing EXX calculations for the illustrative case of the LiF molecule. We show that by choosing the lowest-energy electronic configuration for each interatomic distance, a qualitatively correct binding energy curve, reflecting integer dissociation, is obtained. Surprisingly, for LiF this comes at the cost of violating the Aufbau principle, a phenomenon we discuss at length. Furthermore, we numerically confirm that in the EXX potential of the diatomic molecule, one of the atomic potentials is shifted by a constant while the other one is not, depending on where the highest occupied molecular orbital is localized. This changes the relative positions of the energies of each atom and enforces the integer configuration by preventing spurious charge transfer. The size of the constant shift becomes increasingly unstable numerically the larger the interatomic separation is, reflecting the increasing absence of coupling between the atoms.

  3. Restoration of the derivative discontinuity in Kohn-Sham density functional theory: an efficient scheme for energy gap correction.

    PubMed

    Chai, Jeng-Da; Chen, Po-Ta

    2013-01-18

    From the perspective of perturbation theory, we propose a systematic procedure for the evaluation of the derivative discontinuity (DD) of the exchange-correlation energy functional in Kohn-Sham (KS) density functional theory, wherein the exact DD can in principle be obtained by summing up all the perturbation corrections to infinite order. Truncation of the perturbation series at low order yields an efficient scheme for obtaining the approximate DD. While the zeroth-order theory yields a vanishing DD, the first-order correction to the DD can be expressed as an explicit universal functional of the ground-state density and the KS lowest unoccupied molecular orbital density, allowing the direct evaluation of the DD in the standard KS method without extra computational cost. The fundamental gap can be predicted by adding the estimated DD to the KS gap. This scheme is shown to be accurate in the prediction of the fundamental gaps for a wide variety of atoms and molecules. PMID:23373919

  4. Combining Kohn-Sham and orbital-free density-functional theory for Hugoniot calculations to extreme pressures

    NASA Astrophysics Data System (ADS)

    Sheppard, Daniel; Kress, Joel D.; Crockett, Scott; Collins, Lee A.; Desjarlais, Michael P.

    2014-12-01

    The shock Hugoniot for lithium 6 deuteride (6LiD) was calculated via first principles using Kohn-Sham density-functional theory molecular dynamics (KSMD) for temperatures of 0.5-25 eV. The upper limit of 25 eV represents a practical limit where KSMD is no longer computationally feasible due to the number of electronic bands which are required to be populated. To push the Hugoniot calculations to higher temperatures we make use of orbital-free density-functional theory molecular dynamics (OFMD). Thomas-Fermi-Dirac-based OFMD gives a poor description of the electronic structure at low temperatures so the initial state is not well defined. We propose a method of bootstrapping the Hugoniot from OFMD to the Hugoniot from KSMD between 10 and 20 eV, where the two methods are in agreement. The combination of KSMD and OFMD allows construction of a first-principles Hugoniot from the initial state to 1000 eV. Theoretical shock-compression results are in good agreement with available experimental data and exhibit the appropriate high-temperature limits. We show that a unified KSMD-OFMD Hugoniot can be used to assess the quality of the existing equation-of-state (EOS) models and inform better EOS models based on justifiable physics.

  5. Combining Kohn-Sham and orbital-free density-functional theory for Hugoniot calculations to extreme pressures.

    PubMed

    Sheppard, Daniel; Kress, Joel D; Crockett, Scott; Collins, Lee A; Desjarlais, Michael P

    2014-12-01

    The shock Hugoniot for lithium 6 deuteride ((6)LiD) was calculated via first principles using Kohn-Sham density-functional theory molecular dynamics (KSMD) for temperatures of 0.5-25 eV. The upper limit of 25 eV represents a practical limit where KSMD is no longer computationally feasible due to the number of electronic bands which are required to be populated. To push the Hugoniot calculations to higher temperatures we make use of orbital-free density-functional theory molecular dynamics (OFMD). Thomas-Fermi-Dirac-based OFMD gives a poor description of the electronic structure at low temperatures so the initial state is not well defined. We propose a method of bootstrapping the Hugoniot from OFMD to the Hugoniot from KSMD between 10 and 20 eV, where the two methods are in agreement. The combination of KSMD and OFMD allows construction of a first-principles Hugoniot from the initial state to 1000 eV. Theoretical shock-compression results are in good agreement with available experimental data and exhibit the appropriate high-temperature limits. We show that a unified KSMD-OFMD Hugoniot can be used to assess the quality of the existing equation-of-state (EOS) models and inform better EOS models based on justifiable physics. PMID:25615229

  6. Computational complexity of time-dependent density functional theory

    E-print Network

    J. D. Whitfield; M. -H. Yung; D. G. Tempel; S. Boixo; A. Aspuru-Guzik

    2014-08-21

    Time-dependent density functional theory (TDDFT) is rapidly emerging as a premier method for solving dynamical many-body problems in physics and chemistry. The mathematical foundations of TDDFT are established through the formal existence of a fictitious non-interacting system (known as the Kohn-Sham system), which can reproduce the one-electron reduced probability density of the actual system. We build upon these works and show that on the interior of the domain of existence, the Kohn-Sham system can be efficiently obtained given the time-dependent density. Since a quantum computer can efficiently produce such time-dependent densities, we present a polynomial time quantum algorithm to generate the time-dependent Kohn-Sham potential with controllable error bounds. As a consequence, in contrast to the known intractability result for ground state density functional theory (DFT), the computation of the necessary time-dependent potentials given the initial state is in the complexity class described by bounded error quantum computation in polynomial time (BQP).

  7. 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.

  8. 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. PMID:19603962

  9. 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.

  10. The trust-region self-consistent field method: Towards a black-box optimization in Hartree-Fock and Kohn-Sham theories

    NASA Astrophysics Data System (ADS)

    Thøgersen, Lea; Olsen, Jeppe; Yeager, Danny; Jørgensen, Poul; Sa?ek, Pawe?; Helgaker, Trygve

    2004-07-01

    The trust-region self-consistent field (TRSCF) method is presented for optimizing the total energy ESCF of Hartree-Fock theory and Kohn-Sham density-functional theory. In the TRSCF method, both the Fock/Kohn-Sham matrix diagonalization step to obtain a new density matrix and the step to determine the optimal density matrix in the subspace of the density matrices of the preceding diagonalization steps have been improved. The improvements follow from the recognition that local models to ESCF may be introduced by carrying out a Taylor expansion of the energy about the current density matrix. At the point of expansion, the local models have the same gradient as ESCF but only an approximate Hessian. The local models are therefore valid only in a restricted region—the trust region—and steps can only be taken with confidence within this region. By restricting the steps of the TRSCF model to be inside the trust region, a monotonic and significant reduction of the total energy is ensured in each iteration of the TRSCF method. Examples are given where the TRSCF method converges monotonically and smoothly, but where the standard DIIS method diverges.

  11. Elimination of the asymptotic fractional dissociation problem in Kohn-Sham density-functional theory using the ensemble-generalization approach

    NASA Astrophysics Data System (ADS)

    Kraisler, Eli; Kronik, Leeor

    2015-03-01

    Many approximations within density-functional theory spuriously predict that a many-electron system can dissociate into fractionally charged fragments. Here, we revisit the case of dissociated diatomic molecules, known to exhibit this problem when studied within standard approaches, including the local spin-density approximation (LSDA). By employing our recently proposed [E. Kraisler and L. Kronik, Phys. Rev. Lett. 110, 126403 (2013), 10.1103/PhysRevLett.110.126403] ensemble generalization we find that asymptotic fractional dissociation is eliminated in all systems examined, even if the underlying exchange correlation (xc) is still the LSDA. Furthermore, as a result of the ensemble-generalization procedure, the Kohn-Sham potential develops a spatial step between the dissociated atoms, reflecting the emergence of the derivative discontinuity in the xc energy functional. This step, predicted in the past for the exact Kohn-Sham potential and observed in some of its more advanced approximate forms, is a desired feature that prevents any fractional charge transfer between the system's fragments. It is usually believed that simple xc approximations such as the LSDA cannot develop this step. Our findings show, however, that ensemble generalization to fractional electron densities automatically introduces the desired step even to the most simple approximate xc functionals and correctly predicts asymptotic integer dissociation.

  12. Fabric anisotropy induced by primary depositional variations in the silt: clay ratio in two fine-grained slope fan complexes: Texas Gulf Coast and northern North Sea

    E-print Network

    Fabric anisotropy induced by primary depositional variations in the silt: clay ratio in two fine March 2010 Communicated by G.J. Weltje Keywords: Mudstone Phyllosilicate Fabric Textural goniometry­smectite fabric intensity (phyllosi- licate alignments) ranges from low alignment values of 2.42 m.r.d. (multiples

  13. The Chromosomal Polymorphism Linked to Variation in Social Behavior in the White-Throated Sparrow (Zonotrichia albicollis) Is a Complex Rearrangement and Suppressor of Recombination

    Microsoft Academic Search

    James W. Thomas; Mario Caceres; Joshua J. Lowman; Caroline B. Morehouse; Meghan E. Short; Erin L. Baldwin; Donna L. Maney; Christa L. Martin

    2008-01-01

    Variation in social behavior and plumage in the white-throated sparrow (Zonotrichia albicollis) is linked to an inversion polymorphism on chromosome 2. Here we report the results of our comparative cytogenetic mapping efforts and population genetics studies focused on the genomic characterization of this balanced chromosomal polymorphism. Comparative chromosome painting and cytogenetic mapping of 15 zebra finch BAC clones to the

  14. Contrast between extensive variation of 28S rDNA and stability of 5S rDNA and telomeric repeats in the diploid-polyploid Squalius alburnoides complex and in its maternal ancestor Squalius pyrenaicus (Teleostei, Cyprinidae).

    PubMed

    Gromicho, Marta; Coutanceau, Jean-Pierre; Ozouf-Costaz, Catherine; Collares-Pereira, Maria João

    2006-01-01

    The diploid-polyploid Squalius alburnoides complex resulted from interspecific hybridization. The chromosomal mapping of 28S and 5S ribosomal genes and of (TTAGGG)n telomeric repeats was performed on specimens from the complex and from the sympatric bisexual species S. pyrenaicus (the complex maternal ancestor) as part of an investigation of the evolutionary relationships between genomic constitutions and the consequences of the ongoing polyploidization process in terms of chromosome reshaping. Contrasting results were obtained. While results with 5S rDNA and telomeric probes gave an impression of genomic stability, the variability detected with 28S rDNA probe suggested quite the opposite. The 5S rDNA probe mapped constantly to three chromosomes per haploid genome with apparently conserved locations in morphologically similar chromosomes; conversely, prominent intra- and inter-individual variations of 28S rDNA and of syntenic sites with 5S rDNA were detected with regard to number, size and location. Hypotheses for the causes of such polymorphisms are discussed. The terminal position of most 28S rDNA sites and the absence of detectable interstitial telomeric sequences suggest a mechanism that does not involve major chromosomal rearrangements. These fishes share similar patterns for the studied cytogenetic markers which may be taken as evidence of an apparent stability that may be hiding extensive and subtle genome variations that are possibly related to an ongoing evolutionary process of genome tetraploidization and speciation. PMID:16628500

  15. Direct Variation

    NSDL National Science Digital Library

    2012-01-01

    This learning unit from Regents Prep Exam Center introduces the topic of direct variation equations. The material includes a lesson plan, practice problems and a teacher's guide. Students will learn the basics of what a direct variation equation is and the formula for direct variation.

  16. Age variation in the source of the diapiric mud breccia along and across the axis of the Mediterranean Ridge Accretionary Complex

    Microsoft Academic Search

    Isabella Premoli Silva; Elisabetta Erba; Silvia Spezzaferri; Maria Bianca Cita

    1996-01-01

    Pleistocene, or younger, mud diapirism is recorded along the arcuated crest of the Mediterranean Ridge Accretionary Complex over a distance of more than 450 km. The extruded mud-supported breccia, named mud breccia, is poorly fossiliferous, but the matrix may be dated as Late Aptian to Albian and Late Burdigalian to Langhian in age based on the calcareous plankton content.Calcareous nannofossils

  17. Kohn-Sham kinetic energy density in the nuclear and asymptotic regions: Deviations from the von Weizsäcker behavior and applications to density functionals

    NASA Astrophysics Data System (ADS)

    Della Sala, Fabio; Fabiano, Eduardo; Constantin, Lucian A.

    2015-01-01

    We show that the Kohn-Sham positive-definite kinetic energy (KE) density significantly differs from the von Weizsäcker (VW) one at the nuclear cusp as well as in the asymptotic region. At the nuclear cusp, the VW functional is shown to be linear, and the contribution of p -type orbitals to the KE density is theoretically derived and numerically demonstrated in the limit of infinite nuclear charge as well in the semiclassical limit of neutral large atoms. In the latter case, it reaches 12% of the KE density. In the asymptotic region we find new exact constraints for meta-generalized gradient approximation (meta-GGA) exchange functionals: with an exchange enhancement factor proportional to ?{? }, where ? is the common meta-GGA ingredient, both the exchange energy density and the potential are proportional to the exact ones. In addition, this describes exactly the large-gradient limit of quasi-two-dimensional systems.

  18. Ground-state energy as a simple sum of orbital energies in Kohn-Sham theory: a shift in perspective through a shift in potential.

    PubMed

    Levy, Mel; Zahariev, Federico

    2014-09-12

    It is observed that the exact interacting ground-state electronic energy of interest may be obtained directly, in principle, as a simple sum of orbital energies when a universal density-dependent term is added to w([?];r), the familiar Hartree plus exchange-correlation component in the Kohn-Sham effective potential. The resultant shifted potential, w[over ¯]([?];r), actually changes less on average than w([?];r) when the density changes, including the fact that w[over ¯]([?];r) does not undergo a discontinuity when the number of electrons increases through an integer. Thus, the approximation of w[over ¯]([?];r) represents an alternative direct approach for the approximation of the ground-state energy and density. PMID:25259974

  19. Ground-State Energy as a Simple Sum of Orbital Energies in Kohn-Sham Theory: A Shift in Perspective through a Shift in Potential

    NASA Astrophysics Data System (ADS)

    Levy, Mel; Zahariev, Federico

    2014-09-01

    It is observed that the exact interacting ground-state electronic energy of interest may be obtained directly, in principle, as a simple sum of orbital energies when a universal density-dependent term is added to w([?];r), the familiar Hartree plus exchange-correlation component in the Kohn-Sham effective potential. The resultant shifted potential, w¯([?];r), actually changes less on average than w([?];r) when the density changes, including the fact that w¯([?];r) does not undergo a discontinuity when the number of electrons increases through an integer. Thus, the approximation of w¯([?];r) represents an alternative direct approach for the approximation of the ground-state energy and density.

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

    E-print Network

    Motamarri, Phani

    2014-01-01

    We present a subspace projection technique to conduct large-scale Kohn-Sham density functional theory calculations using 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 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 non-orthogonal localized basis spanning the Chebyshev filtered subspace; (iv) using a Fermi-operator expansion in terms of the subspace-projected Hamiltonian represented in the non-orthogonal localized basis to compute relevant quantities like the density matrix, electron density and band energy. We demonstrate the accuracy and efficiency of the app...

  1. 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

  2. Chinook salmon NADP + -dependent cytosolic isocitrate dehydrogenase: Electrophoretic and genetic dissection of a complex isozyme system and geographic patterns of variation

    Microsoft Academic Search

    James B. Shaklee; Stevan R. Phelps

    1992-01-01

    Species in the genusOncorhynchus express complicated isocitrate dehydrogenase (IDHP) isozyme patterns in many tissues. Subcellular localization experiments show that the electrophoretically distinct isozymes of low anodal mobility expressed predominantly in skeletal and heart muscle are mitochondrial forms (mIDHP), while the more anodal, complex isolocus isozyme system predominant in liver and eye is cytosolic (sIDHP). The two loci encoding sIDHP isozymes

  3. Adaptation at specific loci. VII. Natural selection, dispersal and the diversity of molecular-functional variation patterns among butterfly species complexes (Colias: Lepidoptera, Pieridae).

    PubMed

    Watt, W B; Wheat, C W; Meyer, E H; Martin, J-F

    2003-05-01

    Natural genetic variants at the phosphoglucose isomerase, PGI, gene differ in spatial patterning of their polymorphism among species complexes of Colias butterflies in North America. In both lowland and alpine complexes, molecular-functional properties of the polymorphic genotypes can be used to predict genotype-specific adult flight performances and resulting large genotypic differences in adult fitness components. In the lowland species complex, there is striking uniformity of PGI polymorph frequencies at a number of sites across the American West; this fits with earlier findings of strong, similar differences in fitness components over this range. In an alpine complex, Colias meadii shows similar uniformity of PGI frequencies within habitat types, either montane steppe or alpine tundra, over several hundred kilometres in the absence of dispersal. At the same time, large shifts (10-20%) in frequency of the most common alleles occur between steppe and tundra populations, whether these are isolated or, as in some cases, are in contact and exchange many dispersing adults each generation. Data on male mating success of common C. meadii PGI genotypes in steppe and tundra show heterozygote advantage in both habitat types, with shifts in relative homozygote disadvantage between habitats which are consistent with observed frequency differences. Nonadaptive explanations for this situation are rejected, and alternative, thermal-ecology-based adaptive hypotheses are proposed for later experimental test. These findings show that strong local selection may dominate dispersal as an evolutionary agent, whether or not dispersal is present, and that selection may often be the major force promoting 'cohesion' of species over long distances. This case offers new opportunities for integrating studies of molecular structure and function with ecological aspects of natural selection in the wild, both within and among species. PMID:12694289

  4. Regularity Underlying Complexity: A Redshift-independent Description of the Continuous Variation of Galaxy-scale Molecular Gas Properties in the Mass-star Formation Rate Plane

    NASA Astrophysics Data System (ADS)

    Sargent, M. T.; Daddi, E.; Béthermin, M.; Aussel, H.; Magdis, G.; Hwang, H. S.; Juneau, S.; Elbaz, D.; da Cunha, E.

    2014-09-01

    Star-forming galaxies (SFGs) display a continuous specific star formation rate (sSFR) distribution, which can be approximated by two log-normal functions: one encompassing the galaxy main sequence (MS), and the other a rarer, starbursting population. Starburst (SB) sSFRs can be regarded as the outcome of a physical process (plausibly merging) taking the mathematical form of a log-normal boosting kernel that enhances star formation activity. We explore the utility of splitting the star-forming population into MS and SB galaxies—an approach we term the "2-Star Formation Mode" framework—for understanding their molecular gas properties. Star formation efficiency (SFE) and gas fraction variations among SFGs take a simple redshift-independent form, once these quantities are normalized to the corresponding values for average MS galaxies. SFE enhancements during SB episodes scale supra-linearly with the SFR increase, as expected for mergers. Consequently, galaxies separate more clearly into loci for SBs and normal galaxies in the Schmidt-Kennicutt plane than in (s)SFR versus M sstarf space. SBs with large deviations (>10 fold) from the MS, e.g., local ULIRGs, are not average SBs, but are much rarer events whose progenitors had larger gas fractions than typical MS galaxies. Statistically, gas fractions in SBs are reduced two- to threefold compared to their direct MS progenitors, as expected for short-lived SFR boosts where internal gas reservoirs are depleted more quickly than gas is re-accreted from the cosmic web. We predict variations of the conversion factor ?CO in the SFR-M sstarf plane and we show that the higher sSFR of distant galaxies is directly related to their larger gas fractions.

  5. Ecological Variation in Response to Mass-Flowering Oilseed Rape and Surrounding Landscape Composition by Members of a Cryptic Bumblebee Complex.

    PubMed

    Stanley, Dara A; Knight, Mairi E; Stout, Jane C

    2013-01-01

    The Bombus sensu stricto species complex is a widespread group of cryptic bumblebee species which are important pollinators of many crops and wild plants. These cryptic species have, until now, largely been grouped together in ecological studies, and so little is known about their individual colony densities, foraging ranges or habitat requirements, which can be influenced by land use at a landscape scale. We used mass-flowering oilseed rape fields as locations to sample bees of this complex, as well as the second most common visitor to oilseed rape B. lapidarius, and molecular RFLP methods to distinguish between the cryptic species. We then used microsatellite genotyping to identify sisters and estimate colony densities, and related both proportions of cryptic species and their colony densities to the composition of the landscape surrounding the fields. We found B. lucorum was the most common member of the complex present in oilseed rape followed by B. terrestris. B. cryptarum was also present in all but one site, with higher proportions found in the east of the study area. High numbers of bumblebee colonies were estimated to be using oilseed rape fields as a forage resource, with B. terrestris colony numbers higher than previous estimates from non-mass-flowering fields. We also found that the cryptic species responded differently to surrounding landscape composition: both relative proportions of B. cryptarum in samples and colony densities of B. lucorum were negatively associated with the amount of arable land in the landscape, while proportions and colony densities of other species did not respond to landscape variables at the scale measured. This suggests that the cryptic species have different ecological requirements (which may be scale-dependent) and that oilseed rape can be an important forage resource for many colonies of bumblebees. Given this, we recommend sustainable management of this crop to benefit bumblebees. PMID:23840338

  6. Ecological Variation in Response to Mass-Flowering Oilseed Rape and Surrounding Landscape Composition by Members of a Cryptic Bumblebee Complex

    PubMed Central

    Stanley, Dara A.; Knight, Mairi E.; Stout, Jane C.

    2013-01-01

    The Bombus sensu stricto species complex is a widespread group of cryptic bumblebee species which are important pollinators of many crops and wild plants. These cryptic species have, until now, largely been grouped together in ecological studies, and so little is known about their individual colony densities, foraging ranges or habitat requirements, which can be influenced by land use at a landscape scale. We used mass-flowering oilseed rape fields as locations to sample bees of this complex, as well as the second most common visitor to oilseed rape B. lapidarius, and molecular RFLP methods to distinguish between the cryptic species. We then used microsatellite genotyping to identify sisters and estimate colony densities, and related both proportions of cryptic species and their colony densities to the composition of the landscape surrounding the fields. We found B. lucorum was the most common member of the complex present in oilseed rape followed by B. terrestris. B. cryptarum was also present in all but one site, with higher proportions found in the east of the study area. High numbers of bumblebee colonies were estimated to be using oilseed rape fields as a forage resource, with B. terrestris colony numbers higher than previous estimates from non-mass-flowering fields. We also found that the cryptic species responded differently to surrounding landscape composition: both relative proportions of B. cryptarum in samples and colony densities of B. lucorum were negatively associated with the amount of arable land in the landscape, while proportions and colony densities of other species did not respond to landscape variables at the scale measured. This suggests that the cryptic species have different ecological requirements (which may be scale-dependent) and that oilseed rape can be an important forage resource for many colonies of bumblebees. Given this, we recommend sustainable management of this crop to benefit bumblebees. PMID:23840338

  7. Protein Folding as a Complex Reaction: A Two-Component Potential for the Driving Force of Folding and Its Variation with Folding Scenario

    PubMed Central

    Chekmarev, Sergei F.

    2015-01-01

    The Helmholtz decomposition of the vector field of probability fluxes in a two-dimensional space of collective variables makes it possible to introduce a potential for the driving force of protein folding [Chekmarev, J. Chem. Phys. 139 (2013) 145103]. The potential has two components: one component (?) is responsible for the source and sink of the folding flow, which represent, respectively, the unfolded and native state of the protein, and the other (?) accounts for the flow vorticity inherently generated at the periphery of the flow field and provides the canalization of the flow between the source and sink. Both components obey Poisson’s equations with the corresponding source/sink terms. In the present paper, we consider how the shape of the potential changes depending on the scenario of protein folding. To mimic protein folding dynamics projected onto a two-dimensional space of collective variables, the two-dimensional Müller and Brown potential is employed. Three characteristic scenarios are considered: a single pathway from the unfolded to the native state without intermediates, two parallel pathways without intermediates, and a single pathway with an off-pathway intermediate. To determine the probability fluxes, the hydrodynamic description of the folding reaction is used, in which the first-passage folding is viewed as a steady flow of the representative points of the protein from the unfolded to the native state. We show that despite the possible complexity of the folding process, the ?-component is simple and universal in shape. The ?-component is more complex and reveals characteristic features of the process of folding. The present approach is potentially applicable to other complex reactions, for which the transition from the reactant to the product can be described in a space of two (collective) variables. PMID:25848943

  8. Variations in Os isotope ratios of pyrrhotite as a result of water-rock and magma-rock interaction: Constraints from Virginia Formation-Duluth Complex contact zones

    NASA Astrophysics Data System (ADS)

    Williams, Curtis D.; Ripley, Edward M.; Li, Chusi

    2010-08-01

    Os isotope ratios in pyrrhotite-bearing pelitic rocks of the ˜1.85 Ga Virginia Formation are variable, with perturbations linked to the emplacement of the ˜1.1 Ga Duluth Complex. Pyrrhotite in footwall rocks of the contact aureole show evidence for a mixing event at 1.1 Ga involving a low 187Os/ 188Os fluid. However, because rocks with perturbed pyrrhotite Os isotope ratios occur 1½ km or more from the Duluth Complex, the fluid is unlikely to have been of magmatic origin. Fluid inclusions in layer-parallel quartz veins provide evidence of the involvement of a boiling fluid at temperatures between ˜300 and 400 °C. Analyses of fluid inclusions via LA-ICP-MS show that the fluids contain up to 1.7 wt% Na, 1.1 wt% K, 4330 ppm Fe, 2275 ppm Zn, and 415 ppm Mg. The veins also contain pyrite or pyrrhotite, plus minor amounts of chalcopyrite, bornite, pentlandite, and sphalerite. The Re-Os isotopic ratios of pyrite from the veins indicate that they crystallized from low 187Os/ 188Os fluids (<0.2). ? 18O values of vein quartz range from 7.7‰ to 9.5‰, consistent with an origin involving fluid with a relatively low ? 18O value between 2‰ and 5‰. Meteoric water with such a low ? 18O value could have interacted with the igneous rocks of the Complex and would have acquired Os with a low 187Os/ 188Os ratio. Strongly serpentinized olivine-rich rocks of the Complex are commonly characterized by such low ? 18O values and we propose that the fluid involved in serpentinization was also responsible for the perturbation of the Os isotopic system recorded by pyrrhotite in the Virginia Formation. Two important observations are that only pyrrhotite-bearing assemblages in the contact aureole show isotopic perturbation and that intervals showing Os exchange are spatially restricted, and not uniformly distributed. Os exchange and mixing has occurred only where temperatures were sufficient to convert pyrite to pyrrhotite, and where time-integrated water-rock ratios in the aureole were high enough to provide a supply of Os. Troctolitic and gabbroic rocks of the Partridge River Intrusion, Duluth Complex, are characterized by Os isotope ratios that are indicative of variable degrees of crustal contamination ( ?Os values of ˜0-543). Xenoliths of carbonaceous and sulfidic pelitic rocks of the Virginia Formation found in the igneous rocks provide evidence that Os was released by organic matter and pyrite in the sedimentary rocks and assimilated by mantle-derived magma. However, residual pyrrhotite produced as a result of pyrite breakdown in the xenoliths is characterized by 187Os/ 188Os ratios that are much lower than anticipated and similar to those of pyrrhotite in the contact aureole. The Os exchange and addition shown by pyrrhotite in the xenoliths highlight an unusual cycle of Re-Os liberation during devolatilization, kerogen maturation, and pyrite to pyrrhotite conversion (processes that contribute to magma contamination), followed by Os uptake by pyrrhotite during back reaction involving magma and/or fluid characterized by a relatively low 187Os/ 188Os ratio. The extreme Os uptake recorded by pyrrhotite in the xenoliths, as well as the lesser degree of uptake recorded by pyrrhotite in the contact aureole, is in line with the high Os diffusivity in pyrrhotite experimentally determined by Brenan et al. (2000). Our data confirm that Os isotope ratios in pyrrhotite-bearing rocks may be readily perturbed. For this reason caution should be exercised in the interpretation of Os isotope ratios in rocks where pyrrhotite may be the primary host of Os.

  9. 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. PMID:25708355

  10. Variation of Exciton-Vibrational Coupling in Photosystem II Core Complexes from Thermosynechococcus elongatus As Revealed by Single-Molecule Spectroscopy

    PubMed Central

    2015-01-01

    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. PMID:25708355

  11. Unprecedented structural variations in trinuclear mixed valence Co(ii/iii) complexes: theoretical studies, pnicogen bonding interactions and catecholase-like activities.

    PubMed

    Hazari, Alokesh; Kanta Das, Lakshmi; Kadam, Ramakant M; Bauzá, Antonio; Frontera, Antonio; Ghosh, Ashutosh

    2015-02-10

    Three new mixed valence trinuclear Co(ii/iii) compounds cis-[Co3L2(MeOH)2(N3)2(?1,1-N3)2] (), trans-[Co3L2(H2O)2(N3)2(?1,1-N3)2]·(H2O)2 () and [Co3L(R)2(N3)3(?1,3-N3)] () have been synthesized by reacting a di-Schiff base ligand () or its reduced form [] (where = N,N'-bis(salicylidene)-1,3-propanediamine and = N,N'-bis(2-hydroxybenzyl)-1,3-propanediamine) with cobalt perchlorate hexahydrate and sodium azide. All three products have been characterized by IR, UV-Vis and EPR spectroscopies, ESI-MS, elemental, powder and single crystal X-ray diffraction analyses. Complex is an angular trinuclear species in which two terminal octahedral Co(iii)N2O4 centers coordinate to the central octahedral cobalt(ii) ion through ?2-phenoxido oxygen and ?1,1-azido nitrogen atoms along with two mutually cis-oxygen atoms of methanol molecules. On the other hand, in linear trinuclear complex , in addition to the ?2-phenoxido and ?1,1-azido bridges with terminal octahedral Co(iii) centres, the central Co(ii) is bonded with two mutually trans-oxygen atoms of water molecules. Thus the cis-trans configuration of the central Co(ii) is solvent dependent. In complex , the two terminal octahedral Co(iii)N2O4 centers coordinate to the central penta-coordinated Co(ii) ion through double phenoxido bridges along with the nitrogen atom of a terminal azido ligand. In addition, the two terminal Co(iii) are connected through a ?1,3-azido bridge that participates in pnicogen bonding interactions (intermolecular N-N interaction) as an acceptor. Both the cis and trans isomeric forms of and have been optimized using density functional theory (DFT) calculations and it is found that the cis configuration is energetically more favorable than the trans one. However, the trans configuration of is stabilized by the hydrogen bonding network involving a water dimer. The pnicogen bonding interactions have been demonstrated using MEP surfaces and CSD search which support the counter intuitive electron acceptor ability of the ?1,3-azido ligand. Complexes exhibit catecholase-like activities in the aerial oxidation of 3,5-di-tert-butylcatechol to the corresponding o-quinone. Kinetic data analyses of this oxidation reaction in acetonitrile reveal that the catecholase-like activity follows the order: (kcat = 142 h(-1)) > (kcat = 99 h(-1)) > (kcat = 85 h(-1)). Mechanistic investigations of the catalytic behaviors by X-band EPR spectroscopy and estimation of hydrogen peroxide formation indicate that the oxidation reaction proceeds through the reduction of Co(iii) to Co(ii). PMID:25611163

  12. Reliable Modeling of Complex Organic/Metal Interfaces

    NASA Astrophysics Data System (ADS)

    Liu, Wei; Filimonov, Sergey; Ruiz, Victor G.; Scheffler, Matthias; Tkatchenko, Alexandre

    2013-03-01

    The understanding of electronic properties of complex organic/metal interfaces requires a reliable method for the prediction of their structure and stability. The bonding at complex interfaces arises from delicate balance between covalent bonds, van der Waals (vdW) forces, charge transfer, and Pauli repulsion. We developed a method based on density-functional theory with vdW interactions (PBE+vdW^surf [1]) to accurately model adsorbates on surfaces, by a synergetic linkage of the PBE+vdW [2] for intermolecular interactions with the Lifshitz-Zaremba-Kohn theory [3] for the dielectric screening within the substrate surface. This method is demonstrated to reliably model a multitude of molecules on metal surfaces [1,4], leading to an accuracy of 0.1 å in adsorption heights and 0.1 eV in binding energies wrt experiments. To demonstrate the predictive power of the PBE+vdW^surf, we design a novel type of single-molecule push button switch, by carefully controlling the stability and activation barrier between a chemically bound state and a physically bound state for benzene derivatives adsorbed on metal surfaces.[4pt] [1] Ruiz, et al., PRL (2012).[0pt] [2] Tkatchenko and Scheffler, PRL (2009).[0pt] [3] Zaremba and Kohn, PRB (1976).[0pt] [4] Wagner, et al., PRL (2012).

  13. A comprehensive survey of copy number variation in 18 diverse pig populations and identification of candidate copy number variable genes associated with complex traits

    PubMed Central

    2012-01-01

    Background Copy number variation (CNV) is a major source of structural variants and has been commonly identified in mammalian genome. It is associated with gene expression and may present a major genetic component of phenotypic diversity. Unlike many other mammalian genomes where CNVs have been well annotated, studies of porcine CNV in diverse breeds are still limited. Result Here we used Porcine SNP60 BeadChip and PennCNV algorithm to identify 1,315 putative CNVs belonging to 565 CNV regions (CNVRs) in 1,693 pigs from 18 diverse populations. Total 538 out of 683 CNVs identified in a White Duroc?×?Erhualian F2 population fit Mendelian transmission and 6 out of 7 randomly selected CNVRs were confirmed by quantitative real time PCR. CNVRs were non-randomly distributed in the pig genome. Several CNV hotspots were found on pig chromosomes 6, 11, 13, 14 and 17. CNV numbers differ greatly among different pig populations. The Duroc pigs were identified to have the most number of CNVs per individual. Among 1,765 transcripts located within the CNVRs, 634 genes have been reported to be copy number variable genes in the human genome. By integrating analysis of QTL mapping, CNVRs and the description of phenotypes in knockout mice, we identified 7 copy number variable genes as candidate genes for phenotypes related to carcass length, backfat thickness, abdominal fat weight, length of scapular, intermuscle fat content of logissimus muscle, body weight at 240 day, glycolytic potential of logissimus muscle, mean corpuscular hemoglobin, mean corpuscular volume and humerus diameter. Conclusion We revealed the distribution of the unprecedented number of 565 CNVRs in pig genome and investigated copy number variable genes as the possible candidate genes for phenotypic traits. These findings give novel insights into porcine CNVs and provide resources to facilitate the identification of trait-related CNVs. PMID:23270433

  14. Evolution of plastid gene rps2 in a lineage of hemiparasitic and holoparasitic plants: Many losses of photosynthesis and complex patterns of rate?variation

    PubMed Central

    dePamphilis, Claude W.; Young, Nelson D.; Wolfe, Andrea D.

    1997-01-01

    The plastid genomes of some nonphotosynthetic parasitic plants have experienced an extreme reduction in gene content and an increase in evolutionary rate of remaining genes. Nothing is known of the dynamics of these events or whether either is a direct outcome of the loss of photosynthesis. The parasitic Scrophulariaceae and Orobanchaceae, representing a continuum of heterotrophic ability ranging from photosynthetic hemiparasites to nonphotosynthetic holoparasites, are used to investigate these issues. We present a phylogenetic hypothesis for parasitic Scrophulariaceae and Orobanchaceae based on sequences of the plastid gene rps2, encoding the S2 subunit of the plastid ribosome. Parasitic Scrophulariaceae and Orobanchaceae form a monophyletic group in which parasitism can be inferred to have evolved once. Holoparasitism has evolved independently at least five times, with certain holoparasitic lineages representing single species, genera, and collections of nonphotosynthetic genera. Evolutionary loss of the photosynthetic gene rbcL is limited to a subset of holoparasitic lineages, with several holoparasites retaining a full length rbcL sequence. In contrast, the translational gene rps2 is retained in all plants investigated but has experienced rate accelerations in several hemi- as well as holoparasitic lineages, suggesting that there may be substantial molecular evolutionary changes to the plastid genome of parasites before the loss of photosynthesis. Independent patterns of synonymous and nonsynonymous rate acceleration in rps2 point to distinct mechanisms underlying rate variation in different lineages. Parasitic Scrophulariaceae (including the traditional Orobanchaceae) provide a rich platform for the investigation of molecular evolutionary process, gene function, and the evolution of parasitism. PMID:9207097

  15. Calculation of elastic constants in complex oxides by Self-Consistent Atomic Deformation (SCAD) method

    NASA Astrophysics Data System (ADS)

    Ossowski, M. M.; Boyer, L. L.; Mehl, M. J.; Stokes, H. T.

    2002-03-01

    The SCAD method(L.L. Boyer, H.T. Stokes and M.J. Mehl, Phys.Rev.Lett. 84), 709 (2000) expresses the charge density of a system of atoms as a sum over localized densities derived from potentials defined variationally from the total energy expression which includes contributions from overlapping densities treated in the Thomas-Fermi approximation. The resulting self-consistent procedure, analogous to the Kohn-Sham approach, allows the densities of the "atoms" to relax both radially and nonspherically. The total energies produced by SCAD can be used to determine elastic properties of a given system. We show the results for corundum to illustrate this procedure.

  16. Major-histocompatibility-complex-associated variation in secondary sexual traits of white-tailed deer (Odocoileus virginianus): evidence for good-genes advertisement.

    PubMed

    Ditchkoff, S S; Lochmiller, R L; Masters, R E; Hoofer, S R; Van Den Bussche, R A

    2001-03-01

    Good-genes hypotheses predict that development of secondary sexual characters can be an honest advertisement of heritable male quality. We explored this hypothesis using a cervid model (adult, male white-tailed deer, Odocoileus virginianus) to determine whether antler development could provide an honest signal of a male's genetic quality and condition to adversaries. We compared antler, morphometric, hormonal, and parasitic data collected from hunter-harvested deer to characteristics of the Mhc-DRB (Odvi), the most widely studied gene of the major histocompatibility complex (MHC) in Artiodactyla. We detected associations between genetic characteristics at Odvi-DRB and antler development and body mass, suggesting that antler development and body mass may be associated with pathogen resistance in deer and thus may be an honest signal of genetic quality. We also detected associations between Odvi-DRB characteristics and serum testosterone during the breeding season, suggesting that certain MHC characteristics may help deer cope with stresses related to breeding activity. In addition, we observed a negative relationship between degree of antler development and overall abundance of abomasal helminths. Our observations provide support for the hypothesis that antler development in white-tailed deer is an honest signal of quality. PMID:11327168

  17. Variation Game

    NSDL National Science Digital Library

    Lawrence Hall of Science

    1980-01-01

    In this set of outdoor games, learners play the role of monkeys that are trying to get enough resources (food, shelter, and space) to survive. They play several simple games which involve strength, quickness, coordination, intuition, and luck in order to acquire these resources. The games focus attention on the participants’ individual variations in these areas. There are three “rounds” which represent three different changing environments, each of which requires different skills for survival. After the games, learners compare who got enough resources and what variations among the players may have affected how the game went.

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

    SciTech Connect

    Lao, Ka Un; Herbert, John M., E-mail: herbert@chemistry.ohio-state.edu [Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210 (United States)

    2014-01-28

    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{sub xc} (r)?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 He{sub 2}, Ne{sub 2}, 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.

  19. 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. (Department of Physics, Brooklyn College, City University of New York, Brooklyn, New York 11210 (United States)); Norman, M.R. (Material Sciences Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)); Iafrate, G.J. (U.S. Army Research Office, Research Triangle Park, North Carolina 27709-2211 (United States))

    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.

  20. Space Complexity Algorithms & Complexity

    E-print Network

    Way, Andy

    Space Complexity Algorithms & Complexity Space Complexity Nicolas Stroppa Patrik Lambert - plambert@computing.dcu.ie CA313@Dublin City University. 2008-2009. December 4, 2008 #12;Space Complexity Hierarchy of problems #12;Space Complexity NP-intermediate Languages If P = NP, then are there languages which neither in P

  1. Profile variations in AGN spectra

    E-print Network

    W. Kollatschny; K. Bischoff

    1998-10-07

    We present results of optical long-term variability campaigns (10 - 20 years) of the two Seyfert galaxies NGC 7603 and Mrk 110. The variations of the continuum, of the individual broad line intensities and of their line profiles are investigated in detail and compared to line profile variations in NGC 5548 and NGC 4593. Individual emission line profiles vary differently from line to line and from outburst to outburst indicating a complex and structured broad emission line region.

  2. 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 approximately tenfold speedups observed for the largest systems with respect to reference calculations.

  3. Theoretical study of the structural properties of plutonium(IV) and (VI) complexes.

    PubMed

    Odoh, Samuel O; Schreckenbach, Georg

    2011-12-01

    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. PMID:22040181

  4. Worm variation made accessible

    PubMed Central

    Snoek, L Basten; Joeri van der Velde, K; Li, Yang; Jansen, Ritsert C; Swertz, Morris A; Kammenga, Jan E

    2014-01-01

    In Caenorhabditis elegans, the recent advances in high-throughput quantitative analyses of natural genetic and phenotypic variation have led to a wealth of data on genotype phenotype relations. This data has resulted in the discovery of genes with major allelic effects and insights in the effect of natural genetic variation on a whole range of complex traits as well as how this variation is distributed across the genome. Regardless of the advances presented in specific studies, the majority of the data generated in these studies had yet to be made easily accessible, allowing for meta-analysis. Not only data in figures or tables but meta-data should be accessible for further investigation and comparison between studies. A platform was created where all the data, phenotypic measurements, genotypes, and mappings can be stored, compared, and new linkages within and between published studies can be discovered. WormQTL focuses on quantitative genetics in Caenorhabditis and other nematode species, whereas WormQTLHD quantitatively links gene expression quantitative trait loci (eQTL) in C. elegans to gene–disease associations in humans. PMID:24843834

  5. Jovimagnetic Secular Variation

    NASA Astrophysics Data System (ADS)

    Ridley, V. A.; Holme, R.

    2010-12-01

    Planetary dynamos, resulting from fluid flow in electrically conductive parts of their interior, are thought to be highly time dependent. Currently, our understanding of time variation (secular variation) of these fields is limited because we only have observations for one example - the Earth. To overcome this, data acquired by 5 NASA space missions, from Pioneer 10 (1973) to Galileo (1995-2003), are being used to investigate possible time variation of Jupiter’s magnetic field. The internal field of Jupiter is solved as a potential field expanded in spherical harmonics using a regularized minimum norm approach, placing additional physical constraints on the system to create a model which fits the data with minimal complexity. This differs from previous efforts to model jovimagnetic secular variation (e.g. [1]), as modelling can be implemented to a higher harmonic degree without the elimination of poorly determined Gauss coefficients, resulting in a loss of small scale structure. Additionally, unlike previous studies, estimation of the magnetodisc field is performed for each individual flyby using the 6 parameter model of Connerney et al (1981) [2], allowing for effective removal of this field from the data and a more robust determination of the internal planetary field. The corrected data from all flybys are then used to determine a time-averaged model of the field; this model is of higher resolution than previous models restricted to only a few flybys because of the much better geographical coverage achieved by combining all of the data. Exploration of the parameter space allows further inferences to be made about the internal structure of Jupiter. This includes investigating the depth to the dynamo source (between 0.7-0.9 Jovian radii) and inferring the drop-off in conductivity outside this region. The procedure has been extended to consider linear time variation of the internal field. Through comparison of this model with the time-averaged model, secular variation would be indicated by a substantial improvement to the data fit or a decrease in model spatial complexity. As expected, there is a tendency for the models to preferentially fit the Pioneer 11 data, being the only close approach and high latitude pass of the planet. Time-averaged results show dipole orientation consistent with previous studies of Jupiter’s magnetic field but a dipole magnetic moment of 4.115 G, slightly less than that quoted by the majority of previous modelling attempts (e.g. 4.300 G [3]). Modelling which accounts for temporal variation, indicates a change in dipole magnetic moment of between 0.03-0.14% per year. References: [1] Yu, Z. J., H. K. Leinweber, and C. T. Russell (2010), Galileo constraints on the secular variation of the Jovian magnetic field, J. Geophys. Res., 115, E03002, doi:10.1029/2009JE003492 [2] Connerney, J. E. P., M. H. Acuna, and N. F. Ness (1981), Modelling the Jovian Current Sheet and Inner Magnetosphere, J. Geophys. Res., 86, 8370-8384. [3] Connerney, J. E. P. (1992), Doing more with Jupiter’s magnetic field. In Rucker, H.O., Bauer, S.J. and Kaiser, M.L. (eds.), Planetary Radio Emissions III, pp. 13-33. Vienna: Austrian Academy of Science.

  6. Discrete genetic variation in mate choice and a condition-dependent preference function in the side-blotched lizard: implications for the formation and maintenance of coadapted gene complexes

    Microsoft Academic Search

    Colin Bleay; Barry Sinervo

    2006-01-01

    Variation in female preference functions, both genotypic and phenotypic, has been largely ignored in the literature, despite its implications to the maintenance of genetic variation in populations and the resolution of the ''Lek paradox.'' Polymorphic populations, such as in the side-blotched lizard, provide ideal study systems for its investigation, especially in the context of incipient processes of sympatric speciation. Females

  7. Intermittency and local Reynolds number in Navier-Stokes turbulence: A cross-over scale in the Caffarelli-Kohn-Nirenberg integral

    NASA Astrophysics Data System (ADS)

    Dowker, Mark; Ohkitani, Koji

    2012-11-01

    We study space-time integrals, which appear in the Caffarelli-Kohn-Nirenberg (CKN) theory for the Navier-Stokes equations analytically and numerically. The key quantity is written in standard notations ? (r)=1/(? r)int _{Q_r}left|nabla {u}right|^2 d{{x}} dt, which can be regarded as a local Reynolds number over a parabolic cylinder Qr. First, by re-examining the CKN integral, we identify a cross-over scale r_* ? Lleft( overline{Vert nabla {u} Vert ^2_{L^2}} /Vert nabla {u Vert ^2_{L^infty }} right)^{1/3}, at which the CKN Reynolds number ?(r) changes its scaling behavior. This reproduces a result on the minimum scale rmin in turbulence: r_min^2 Vert nabla {u}Vert _infty ? ? , consistent with a result of Henshaw et al. ["On the smallest scale for the incompressible Navier-Stokes equations," Theor. Comput. Fluid Dyn. 1, 65 (1989), 10.1007/BF00272138]. For the energy spectrum E(k) ? k-q (1 < q < 3), we show that r* ? ?a with a=4/3(3-q)-1. Parametric representations are then obtained as Vert nabla {u}Vert _infty ? ? ^{-(1+3a)/2} and rmin ? ?3(a+1)/4. By the assumptions of the regularity and finite energy dissipation rate in the inviscid limit, we derive lim _{p rArr infty }? _p/p=1 - ? _2 for any phenomenological models on intermittency, where ?p is the exponent of pth order (longitudinal) velocity structure function. It follows that ?p ? (1 - ?2)(p - 3) + 1 for any p ? 3 without invoking fractal energy cascade. Second, we determine the scaling behavior of ?(r) in direct numerical simulations of the Navier-Stokes equations. In isotropic turbulence around R? ? 100 starting from random initial conditions, we have found that ?(r) ? r4throughout the inertial range. This can be explained by the smallness of a ? 0.26,with a result that r* is in the energy-containing range. If the ?-model is perfectly correct, the intermittency parameter a must be related to the dissipation correlation exponent ? as ? =4a/1+a ? 0.8, which is larger than the observed ? ? 0.20. Furthermore, corresponding integrals are studied using the Burgers vortex and the Burgers equation. In those single-scale phenomena, the cross-over scale lies in the dissipative range. The scale r* offers a practical method of quantifying intermittency. This paper also sorts out a number of existing mathematical bounds and phenomenological models on the basis of the CKN Reynolds number.

  8. Architecting complex systems for robustness

    E-print Network

    Slagle, Jason C

    2007-01-01

    Robust design methodologies are frequently utilized by organizations to develop robust and reliable complex systems. The intent of robust design is to create systems that are insensitive to variations from production, the ...

  9. Heritable Epigenetic Variation among Maize Inbreds

    PubMed Central

    Schnable, James C.; Waters, Amanda J.; Hermanson, Peter J.; Liu, Sanzhen; Yeh, Cheng-Ting; Jia, Yi; Gendler, Karla; Freeling, Michael; Schnable, Patrick S.; Vaughn, Matthew W.; Springer, Nathan M.

    2011-01-01

    Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. There is the potential for pure epigenetic variation that occurs in the absence of any genetic change or for more complex situations that involve both genetic and epigenetic differences. Methylation of cytosine residues provides one mechanism for the inheritance of epigenetic information. A genome-wide profiling of DNA methylation in two different genotypes of Zea mays (ssp. mays), an organism with a complex genome of interspersed genes and repetitive elements, allowed the identification and characterization of examples of natural epigenetic variation. The distribution of DNA methylation was profiled using immunoprecipitation of methylated DNA followed by hybridization to a high-density tiling microarray. The comparison of the DNA methylation levels in the two genotypes, B73 and Mo17, allowed for the identification of approximately 700 differentially methylated regions (DMRs). Several of these DMRs occur in genomic regions that are apparently identical by descent in B73 and Mo17 suggesting that they may be examples of pure epigenetic variation. The methylation levels of the DMRs were further studied in a panel of near-isogenic lines to evaluate the stable inheritance of the methylation levels and to assess the contribution of cis- and trans- acting information to natural epigenetic variation. The majority of DMRs that occur in genomic regions without genetic variation are controlled by cis-acting differences and exhibit relatively stable inheritance. This study provides evidence for naturally occurring epigenetic variation in maize, including examples of pure epigenetic variation that is not conditioned by genetic differences. The epigenetic differences are variable within maize populations and exhibit relatively stable trans-generational inheritance. The detected examples of epigenetic variation, including some without tightly linked genetic variation, may contribute to complex trait variation. PMID:22125494

  10. Nonlinear d10-ML2 Transition-Metal Complexes

    PubMed Central

    Wolters, Lando P; Bickelhaupt, F Matthias

    2013-01-01

    We have investigated the molecular geometries of a series of dicoordinated d10-transition-metal complexes ML2 (M=Co?, Rh?, Ir?, Ni, Pd, Pt, Cu+, Ag+, Au+; L=NH3, PH3, CO) using relativistic density functional theory (DFT) at ZORA-BLYP/TZ2P. Not all complexes have the expected linear ligand–metal–ligand (L–M–L) angle: this angle varies from 180° to 128.6° as a function of the metal as well as the ligands. Our main objective is to present a detailed explanation why ML2 complexes can become bent. To this end, we have analyzed the bonding mechanism in ML2 as a function of the L–M–L angle using quantitative Kohn–Sham molecular orbital (MO) theory in combination with an energy decomposition analysis (EDA) scheme. The origin of bent L–M–L structures is ? backdonation. In situations of strong ? backdonation, smaller angles increase the overlap of the ligand’s acceptor orbital with a higher-energy donor orbital on the metal-ligand fragment, and therefore favor ? backdonation, resulting in additional stabilization. The angle of the complexes thus depends on the balance between this additional stabilization and increased steric repulsion that occurs as the complexes are bent. PMID:24551547

  11. Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae

    Microsoft Academic Search

    Justin C. Fay; Heather L. McCullough; Paul D. Sniegowski; Michael B. Eisen

    2004-01-01

    Background: 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

  12. Irreducible Complexity Revisited

    Microsoft Academic Search

    William A. Dembski

    2004-01-01

    Michael Behe's concept of irreducible complexity, and in particular his use of this concept to critique Darwinism, continues to come under heavy fire from the biological community. The problem with Behe, so Darwinists inform us, is that he has created a problem where there is no problem. Far from constituting an obstacle to the Darwinian mechanism of random variation and

  13. Lesson 21: Variation

    NSDL National Science Digital Library

    2011-01-01

    The lesson begins with a comparison of data tables and graphs of two functions, one directly proportional (cost of gas) and the other exponential (population), before a definition for direct variation is introduced. Direct variation is then linked to linear function (f(x)= kx)and the scaling property of direct variation is examined (i.e. a multiple of the independent variable will always correspond to that same multiple of the dependent variable). Direct variation with a power of x follows with a test for direct variation before indirect variation and indirect variation with a power of x are introduced.

  14. Innovation et variation en didactique des langues etrangeres (Innovation and Variation in Foreign Language Instruction).

    ERIC Educational Resources Information Center

    Puren, Christian

    1991-01-01

    A model of foreign language education is presented that takes into account the complexity of instruction itself and the dimensions added by interaction of teacher, learner, institution, materials, and environment. Uncertainty is seen as a by-product of complexity, and innovation and variation in instructional practice are ways of dealing with…

  15. Stratigraphic variation of complex impurities in platform limestones and possible significance of atmospheric dust: a study with emphasis on gamma-ray spectrometry and magnetic susceptibility outcrop logging (Eifelian-Frasnian, Moravia, Czech Republic)

    Microsoft Academic Search

    J. Hladil; M. Gersl; L. Strnad; J. Frana; A. Langrova; J. Spisiak

    2006-01-01

    Mineral dust and other constituents of Devonian atmospheric aerosols together with certain amounts of aquatic suspensions of riverine detrital origin, colloidal particle dispersions and seawater solutes were embedded in ~95–98% (or purer) limestones on a consistently subsiding isolated carbonate platform where they formed very complex impurity systems. Very low Th\\/U values, relative abundance of Fe but a slight excess of

  16. Studies of a series of [Ni(P(R)2N(Ph)2)2(CH3CN)]2+ complexes as electrocatalysts for H2 production: substituent variation at the phosphorus atom of the P2N2 ligand.

    PubMed

    Kilgore, Uriah J; Stewart, Michael P; Helm, Monte L; Dougherty, William G; Kassel, W Scott; DuBois, Mary Rakowski; DuBois, Daniel L; Bullock, R Morris

    2011-11-01

    A series of [Ni(P(R)(2)N(Ph)(2))(2)(CH(3)CN)](BF(4))(2) complexes containing the cyclic diphosphine ligands [P(R)(2)N(Ph)(2) = 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(P(Bn)(2)N(Ph)(2))(2)(CH(3)CN)](BF(4))(2) and [Ni(P(n-Bu)(2)N(Ph)(2))(2)(CH(3)CN)](BF(4))(2) have distorted trigonal bipyramidal geometries. The Ni(0) complex [Ni(P(Bn)(2)N(Ph)(2))(2)] 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(P(Cy)(2)N(Ph)(2))(2)(CH(3)CN)](BF(4))(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 H(2) in acidic acetonitrile solutions. The heterolytic cleavage of H(2) by [Ni(P(R)(2)N(Ph)(2))(2)(CH(3)CN)](BF(4))(2) complexes in the presence of p-anisidine or p-bromoaniline was used to determine the hydride donor abilities of the corresponding [HNi(P(R)(2)N(Ph)(2))(2)](BF(4)) complexes. However, for the catalysts with the most bulky R groups, the turnover frequencies do not parallel the driving force for elimination of H(2), suggesting 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. PMID:21999814

  17. 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. [Sandia National Labs., Albuquerque, NM (United States); Svitra, Z.V.; Bowen, S.M. [Los Alamos National Lab., NM (United States)

    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.

  18. 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.

  19. Modeling Earth's magnetic field variation

    NASA Astrophysics Data System (ADS)

    Wardinski, I.

    2012-12-01

    Observations of the Earth's magnetic field taken at the Earth's surface and at satellite altitude have been combined to construct models of the geomagnetic field and its variation. Lesur et al. (2010) developed a kinematic reconstruction of core field changes that satisfied the frozen-flux constraint. By constraining the field evolution to be entirely due to advection of the magnetic field at the core surface it maintained the spatial complexity of the field morphology imposed by a satellite field model backward in time [Wardinski & Lesur,2012]. In this study we attempt a kinematic construction of future variation in Earth's magnetic field variation. Our approach, first seeks to identify typical time scales of the magnetic field and core surface flows present in decadal and millennial field and flow models. Therefore, the individual spherical harmonic coefficients are treated by methods of time series analysis. The second step employs stochastic modelling of the temporal variability of such spherical harmonic coefficients that represent the field and core surface flow. Difficulties arise due to the non-stationary behavior of the field and core surface flow. However, the broad behavior may consist of some homogeneity, which could be captured by a generalized stochastic model that calls for the d'th difference of the time series to be stationary (ARIMA-Model), or by detrending the coefficient time series. By computing stochastic models, we obtain two sets of field-forecasts, the first set is obtained from stochastic models of the Gauss coefficients. Here, first results suggest that secular variation on time scales shorter than 5 years behaves rather randomly and cannot be described sufficiently well by stochastic models. The second set is derived from forward modeling the secular variation using the diffusion-less induction equation (kinematic construction). This approach has not provide consistent results.

  20. Non-uniform random variate generation

    Microsoft Academic Search

    L. Devroye

    1986-01-01

    Abstract. This chapter provides a survey of the main methods in non-uniform random variate generation, and highlights recent research on the subject. Classical paradigms such as inversion, rejection, guide tables, and transformations are reviewed. We provide information on the expected time complexity of various algorithms, before addressing modern topics such as indirectly specied distributions, random processes, and Markov chain methods.

  1. Accessing genetic variation: genotyping single nucleotide polymorphisms

    Microsoft Academic Search

    Ann-Christine Syvänen

    2001-01-01

    Understanding the relationship between genetic variation and biological function on a genomic scale is expected to provide fundamental new insights into the biology, evolution and pathophysiology of humans and other species. The hope that single nucleotide polymorphisms (SNPs) will allow genes that underlie complex disease to be identified, together with progress in identifying large sets of SNPs, are the driving

  2. 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 Central

    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.

    2011-01-01

    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. PMID:21379325

  3. DFT description of the electronic structure and spectromagnetic properties of strongly correlated electronic systems: NiII, CuII and ZnII o-dioxolene complexes.

    PubMed

    Bencini, Alessandro; Carbonera, Chiara; Totti, Federico

    2004-03-19

    The spectroscopic and magnetic properties of dioxolene complexes of zinc, copper and nickel were studied by DFT calculations on model complexes of formulas [(NH(3))(4)M(II)(SQ)](+) (M=Zn, Ni; SQ=semiquinonato) and [(NH(3))(2)Cu(II)(SQ)](+). Standard approaches such as time-dependent DFT (TDDFT), the Slater transition state (STS), and broken symmetry (BS) were found to be unable to completely account for the physical properties of the systems, and complete active space-configuration interaction (CAS-CI) calculations based on the Kohn-Sham (KS) orbitals was applied. The CAS-CI energies, properly corrected with multireference perturbation theory (MR-PT), were found to be in good agreement with experimental data. We present here a calculation protocol that has a low CPU cost/accuracy ratio and seems to be very promising for interpreting the properties of strongly correlated electronic systems in complexes of real chemical size. PMID:15034891

  4. Pair-distribution functions of two-temperature two-mass systems: comparison of molecular dynamics, classical-map hypernetted chain, quantum Monte Carlo, and Kohn-Sham calculations for dense hydrogen.

    PubMed

    Dharma-wardana, M W C; Murillo, Michael S

    2008-02-01

    Two-temperature, two-mass quasiequilibrium plasmas may occur in electron-ion plasmas, nuclear-matter, as well as in electron-hole condensed-matter systems. Dense two-temperature hydrogen plasmas straddle the difficult partially degenerate regime of electron densities and temperatures which are important in astrophysics, in inertial-confinement fusion research, and other areas of warm dense-matter physics. Results from quantum Monte Carlo (QMC) are used to benchmark the procedures used in classical molecular-dynamics simulations and hypernetted chain (HNC) and classical-map HNC (CHNC) methods to derive electron-electron and electron-proton pair-distribution functions. Where QMC is not available, we used Kohn-Sham results as the reference calculation. Then, nonequilibrium molecular dynamics for two-temperature, two-mass plasmas are used to obtain pair distribution functions without specifying the interspecies cross temperature. Using these results, the correct HNC and CHNC procedures for the evaluation of pair-distribution functions in two-temperature two-mass two-component charged fluids are established and results for a mass ratio of 1:5, typical of electron-hole fluids, are presented. PMID:18352127

  5. Sequence-dependent variation in DNA minor groove width dictates orientational preference of Hoechst 33258 in A-tract recognition: solution NMR structure of the 2:1 complex with d(CTTTTGCAAAAG)2

    PubMed Central

    Gavathiotis, Evripidis; Sharman, Gary J.; Searle, Mark S.

    2000-01-01

    The solution structure of the dodecamer duplex d(CTTTTGCAAAAG)2 and its 2:1 complex with the bis-benzimidazole Hoechst 33258 has been investigated by NMR and NOE-restrained molecular dynamics (rMD) simulations. Drug molecules are bound in each of the two A-tracts with the bulky N-methylpiperazine ring of each drug located close to the central TG (CA) step, binding essentially to the narrow minor groove of each A-tract. MD simulations over 1 ns, using an explicit solvation model, reveal time-averaged sequence-dependent narrowing of the minor groove from the 3?-end towards the 5?-end of each TTTT sequence. Distinct junctions at the TpG (CpA) steps, characterised by large positive roll, low helical and propeller twists and rapid AT base pair opening rates, add to the widening of the groove at these sites and appear to account for the bound orientation of the two drug molecules with the N-methylpiperazine ring binding in the wider part of the groove close to the junctions. Comparisons between the free DNA structure and the 2:1 complex (heavy atom RMSD 1.55 Å) reveal that these sequence-dependent features persist in both structures. NMR studies of the sequence d(GAAAAGCTTTTC)2, in which the A-tracts have been inverted with the elimination of the TpG junctions, results in loss of orientational specificity of Hoechst 33258 and formation of multiple bound species in solution, consistent with the drug binding in a number of different orientations. PMID:10637324

  6. Multi-objective optimization shapes ecological variation

    PubMed Central

    Kaitaniemi, Pekka; Scheiner, Annette; Klemola, Tero; Ruohomäki, Kai

    2012-01-01

    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. PMID:21849318

  7. Variation and linkage disequilibrium between a structurally polymorphic Alu located near the OR12D2 gene of the extended major histocompatibility complex class I region and HLA-A alleles.

    PubMed

    Kulski, J K; Shigenari, A; Inoko, H

    2014-06-01

    We investigated the genetic structure and population frequency of an Alu repeat dimorphism (absence or presence) located near the OR12D2 gene within the olfactory receptor gene region telomeric of the alpha HLA class I region (HLA-J, -A, -G, -F). The structurally polymorphic Alu insertion (POALIN) locus rs33972478 that we designated as AluOR and its allele and haplotype frequencies and association with HLA-A and six other structurally polymorphic retroelements (3 Alu, 2 SVA and an HERVK9) were determined in 100 Japanese, 174 Caucasians and 100 African American DNA samples. The AluOR insertion varied in population frequency between 14.4% and 31.5% with significant differences between the Japanese and Caucasians, but not between the Caucasian and African Americans. Although AluOR is located 600 kb from the HLA-A gene, there was a significant linkage disequilibrium between the two loci and a high percentage association of the AluOR insertion with HLA-A29 (79%) in Caucasians and HLA-A31 (69.4%) in Japanese. Inferred haplotypes among three-locus to eight-locus haplotype structures showed maximum differences between the populations with the eight-locus haplotypes. The most frequent multilocus haplotype shared between the populations was the HLA-A2 allele in combination with the AluHG insertion. The AluOR whether investigated alone or together with the HLA class I alleles and other dimorphic retroelements is an informative ancestral marker for the identification of lineages and variations within the same and/or different populations and for examining the linkage and crossing-over between the HLA and OR genomic regions in the extended MHC. PMID:24305111

  8. Complex Numbers

    NSDL National Science Digital Library

    2010-04-01

    This is a short study guide from the University of Maryland's Physics Education Research Group on introducing, interpreting, and using complex numbers. Mathematical equations are included to help students understand the nature of complex numbers.

  9. A simplified recurrent neural network for solving nonlinear variational inequalities

    Microsoft Academic Search

    Long Cheng; Zeng-guang Hou; Min Tan; Xiuqing Wang

    2008-01-01

    A recurrent neural network is proposed to deal with the nonlinear variational inequalities with linear equality and nonlinear inequality constraints. By exploiting the equality constraints, the original variational inequality problem can be transformed into a simplified one with only inequality constraints. Therefore, by solving this simplified problem, the neural network architecture complexity is reduced dramatically. In addition, the proposed neural

  10. First evidence for heritable variation in cooperative breeding behaviour

    Microsoft Academic Search

    Anne Charmantier; Amber J. Keyser; Daniel E. L. Promislow

    2007-01-01

    Understanding the evolution of complex social behaviours, such as cooperative breeding, is a fundamental problem in evolutionary biology, which has attracted much theoretical and empirical interest. Variation within and between species in the frequency of helping behaviour has been typically associated with variation in direct costs and benefits due to ecological constraints, or with indirect fitness payoffs (i.e. kin selection).

  11. Computational complexity of time-dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Whitfield, J. D.; Yung, M.-H.; Tempel, D. G.; Boixo, S.; Aspuru-Guzik, A.

    2014-08-01

    Time-dependent density functional theory (TDDFT) is rapidly emerging as a premier method for solving dynamical many-body problems in physics and chemistry. The mathematical foundations of TDDFT are established through the formal existence of a fictitious non-interacting system (known as the Kohn-Sham system), which can reproduce the one-electron reduced probability density of the actual system. We build upon these works and show that on the interior of the domain of existence, the Kohn-Sham system can be efficiently obtained given the time-dependent density. We introduce a V-representability parameter which diverges at the boundary of the existence domain and serves to quantify the numerical difficulty of constructing the Kohn-Sham potential. For bounded values of V-representability, we present a polynomial time quantum algorithm to generate the time-dependent Kohn-Sham potential with controllable error bounds.

  12. Ab initio calculations on collisions of low energy electrons with polyatomic molecules

    SciTech Connect

    Rescigno, T.N.

    1991-08-01

    The Kohn variational method is one of simplest, and oldest, techniques for performing scattering calculations. Nevertheless, a number of formal problems, as well as practical difficulties associated with the computation of certain required matrix elements, delayed its application to electron--molecule scattering problems for many years. This paper will describe the recent theoretical and computational developments that have made the complex'' Kohn variational method a practical tool for carrying out calculations of low energy electron--molecule scattering. Recent calculations on a number of target molecules will also be summarized. 41 refs., 7 figs.

  13. Analysis of biomarkers for complex human diseases 

    E-print Network

    Ansari, Morad

    2009-01-01

    The aims of this study were to analyse known and potential biomarkers of common and genetically complex human disorders and to identify genetic and environmental variation associated with plasma biomarker concentrations. ...

  14. Separation of the geomagnetic variation of cosmic rays

    NASA Astrophysics Data System (ADS)

    Zhumabaev, B. T.; Kozin, I. D.

    The contributions of geomagnetic variations and complex variations in cosmic ray intensities to measured variations in the neutron component of cosmic ray flux are separated by a study of normalized neutron intensities recorded at three stations with different cut-off rigidities. The correlation between Dst variations and temporal variations in normalized intensity differences is calculated for stations with rigidities of 0.0, 4.0 and 13 GV during the large magnetic storm (300 nT) of March 5-13, 1970. Results show the increase in cosmic ray intensities observed during the storm to be due to a decrease in cosmic ray cut-off rigidities. The maximum Dst decrease of 280 nT is found to lead to a 3.2 percent variation in the intensity difference between Dallas and Churchill stations, and a 4.2 percent variation in the difference between Chacataya and Churchill, in agreement with theoretical calculations.

  15. Complex topology rather than complex membership is a determinant of protein dosage sensitivity

    Microsoft Academic Search

    Richard Oberdorf; Tanja Kortemme

    2009-01-01

    The ‘balance hypothesis’ predicts that non-stoichiometric variations in concentrations of proteins participating in complexes should be deleterious. As a corollary, heterozygous deletions and overexpression of protein complex members should have measurable fitness effects. However, genome-wide studies of heterozygous deletions in Saccharomyces cerevisiae and overexpression have been unable to unambiguously relate complex membership to dosage sensitivity. We test the hypothesis that

  16. Parametrization and performance appraisal of the analytic and variational X? method

    NASA Astrophysics Data System (ADS)

    Zope, Rajendra; Dunlap, Brett

    2005-03-01

    The linear combination of atomic orbitals, analytic and variational implementation of Slater's X? method that allows arbitrary scaling of the exchange-correlation potential around each atom has been formulated. The method is numerical integration free, and thus delivers machine-precision energies that are stationary in all respects. One choice of scaling uses the ?s that give exact atomic energies. We present the results of a performance assessment of this method by calculating the atomization energies and total energies of the G2 and extended G2 sets of molecules. Similar calculations for uniform ? are also appraised. Minimizing the mean absolute error in both the X? energies and the Hartree-Fock energies shows that Slater's exchange functional with ? = 0.7091 performs significantly better than the G'asp'ar-Kohn-Sham exchange functional for these molecules and for equally weighted atoms H-Kr. The Office of Naval Research, directly and through the Naval Research Laboratory, and the DoD's High Performance Computing Modernization Program, through the Common High Performance Computing Software Support Initiative, Project MBD-5, supported this work. The calculations were performed at the Army Research Laboratory Major Shared Resource Center (ARL MSRC).

  17. Ensembl variation resources

    PubMed Central

    2010-01-01

    Background The maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics. Description The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl. Conclusions Variation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org. PMID:20459805

  18. 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…

  19. Complex Numbers

    NSDL National Science Digital Library

    Mrs. Pierce

    2010-11-16

    The objective of this lesson is to gain a better understanding of complex numbers and their graphs Situation: The Swiss Mathemation, Jean Robert Argand developed a means to graphically represent complex numbers. This led to solving problems related to altenating electrical current, which provides current day luxuries. Could you do the same? Current Knowledge: Use your knowledge of complex number and the coordinate system and with your partner, ...

  20. Cellular genomics for complex traits

    Microsoft Academic Search

    Emmanouil T. Dermitzakis

    2012-01-01

    Recent developments in the collection and analysis of cellular multilayered data in large cohorts with extensive organismal phenotyping promise to reveal links between genetic variation and biological processes. The use of these cellular resources as models for human biology — known as 'cellular phenotyping' — is likely to transform our understanding of the genetic and long-term environmental influences on complex

  1. Epistasis correlates to genomic complexity

    Microsoft Academic Search

    Rafael Sanjuán; Santiago F. Elena

    2006-01-01

    Whether systematic genetic interactions (epistasis) occur at the genomic scale remains a challenging topic in evolutionary biology. Epistasis should make a significant contribution to variation in complex traits and influence the evolution of genetic systems as sex, diploidy, dominance, or the contamination of genomes with deleterious mutations. We have collected data from widely different organisms and quantified epistasis in a

  2. Controlling complexity

    SciTech Connect

    Poon, L.; Grebogi, C. [Institute for Plasma Research, University of Maryland, College Park, Maryland 20742 (United States)] [Institute for Plasma Research, University of Maryland, College Park, Maryland 20742 (United States)

    1995-11-27

    Complex systems have the property that many competing behaviors are possible, and the system tends to alternate among them. In fact, the ability of a complex system to access many different states, combined with its sensitivity, offers great flexibility in manipulating the system`s dynamics to select a desired behavior. By understanding dynamically how some of the complex features arise, we show that it is indeed possible to control a complex system`s behavior. This is illustrated by using the noisy double rotor map as a paradigm. {copyright} {ital 1995} {ital The} {ital American} {ital Physical} {ital Society}.

  3. Livestock Seasonal Price Variation

    E-print Network

    Davis, Ernest E.; Sartwelle III, James D.; Mintert, James R.

    1999-09-21

    Livestock Seasonal Price Variation Ernest E. Davis, James D. Sartwelle, III and James Mintert* Nature dictates many of the production and supply patterns in the livestock industry. For example, a majority of the annual calf, lamb and kid crops...

  4. Variation tolerant SoC design

    NASA Astrophysics Data System (ADS)

    Kozhikkottu, Vivek J.

    The scaling of integrated circuits into the nanometer regime has led to variations emerging as a primary concern for designers of integrated circuits. Variations are an inevitable consequence of the semiconductor manufacturing process, and also arise due to the side-effects of operation of integrated circuits (voltage, temperature, and aging). Conventional design approaches, which are based on design corners or worst-case scenarios, leave designers with an undesirable choice between the considerable overheads associated with over-design and significantly reduced manufacturing yield. Techniques for variation-tolerant design at the logic, circuit and layout levels of the design process have been developed and are in commercial use. However, with the incessant increase in variations due to technology scaling and design trends such as near-threshold computing, these techniques are no longer sufficient to contain the effects of variations, and there is a need to address variations at all stages of design. This thesis addresses the problem of variation-tolerant design at the earliest stages of the design process, where the system-level design decisions that are made can have a very significant impact. There are two key aspects to making system-level design variation-aware. First, analysis techniques must be developed to project the impact of variations on system-level metrics such as application performance and energy. Second, variation-tolerant design techniques need to be developed to absorb the residual impact of variations (that cannot be contained through lower-level techniques). In this thesis, we address both these facets by developing robust and scalable variation-aware analysis and variation mitigation techniques at the system level. The first contribution of this thesis is a variation-aware system-level performance analysis framework. We address the key challenge of translating the per-component clock frequency distributions into a system-level application 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 allocation of shared system resources as a means to combat the advers

  5. Emerging patterns of epigenomic variation.

    PubMed

    Milosavljevic, Aleksandar

    2011-06-01

    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 nonprotein-coding fraction of the genome, and 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 the reach of researchers across a wide spectrum of biological disciplines. PMID:21507501

  6. Phenotypic Variation in Plants

    NSDL National Science Digital Library

    Lawrence Blumer (Morehouse College; )

    1997-01-01

    This resource is a detailed manual of protocols and instructional information for carrying out an undergraduate laboratory exercise in ecology and evolutionary biolog. Students examine the causes of phenotypic variation in Brassica rapa. This exercise provides an excellent example of potential factors associated with the causes of phenotypic variation for lower division undergraduates, but could also be expanded upon to allow unique scientific inquiry in labs for upper-division undergrads. It includes student outlines, instructor's notes, and suggested questions for laboratory reports.

  7. Inverse Total Variation Flow

    Microsoft Academic Search

    M. Burger; K. Frick; S. Osher; O. Scherzer

    2007-01-01

    In this paper we analyze iterative regularization with the Breg- man distance of the total variation semi norm. Moreover, we prove existence of a solution of the corresponding flow equation as introduced in (8) in a func- tional analytical setting using methods from convex analysis. The results are generalized to variational denoising methods with Lp-norm fit-to-data terms and Bregman distance

  8. 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.

  9. Direct and Inverse Variation

    NSDL National Science Digital Library

    Annenberg Media

    2009-12-23

    "Lesson 1 of two lessons teaches students about direct variation by allowing them to explore a simulated oil spill using toilet paper tissues (to represent land) and drops of vegetable oil (to simulate a volume of oil). Lesson 2 teaches students about inverse variation by exploring the relationship between the heights of a fixed amount of water poured into cylindrical containers of different sizes as compared to the area of the containers' bases." from Insights into Algebra 1 - Annenberg Foundation.

  10. 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…

  11. Structural genomic variation in ischemic stroke

    Microsoft Academic Search

    Mar Matarin; Javier Simon-Sanchez; Hon-Chung Fung; Sonja Scholz; J. Raphael Gibbs; Dena G. Hernandez; Cynthia Crews; Angela Britton; Fabienne Wavrant De Vrieze; Thomas G. Brott; Robert D. Brown Jr; Bradford B. Worrall; Scott Silliman; L. Douglas Case; John A. Hardy; Stephen S. Rich; James F. Meschia; Andrew B. Singleton

    2008-01-01

    Technological advances in molecular genetics allow rapid and sensitive identification of genomic copy number variants (CNVs).\\u000a This, in turn, has sparked interest in the function such variation may play in disease. While a role for copy number mutations\\u000a as a cause of Mendelian disorders is well established, it is unclear whether CNVs may affect risk for common complex disorders.\\u000a We

  12. 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.

  13. Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping

    Microsoft Academic Search

    Christoph Bock; Jörn Walter; Martina Paulsen; Thomas Lengauer

    2008-01-01

    Genomic DNA methylation profiles exhibit substan- tial variation within the human population, with important functional implications for gene regula- tion. So far little is known about the characteristics and determinants of DNA methylation variation among healthy individuals. We performed bioinfor- matic analysis of high-resolution methylation pro- files from multiple individuals, uncovering complex patterns of inter-individual variation that are strongly correlated

  14. Complexity International

    NSDL National Science Digital Library

    Complexity International (CI) is an electronic journal devoted to "the field of complex systems, the generation of complex behaviour from the interaction of multiple parallel processes." The journal covers a wide variety of topics, including genetic algorithms, neural networks, and chaos theory. Because much of the focus is based on technological imitation of biological processes, some of the papers are closely tied to the life sciences. Volumes are added to on a continual basis as papers are accepted. Due to the lengthy acceptance process, it is especially useful that the CI Web site offers drafts of current submissions.

  15. Carney Complex

    MedlinePLUS

    ... a complex procedure with financial, physical, and emotional factors for couples to consider before starting. For more information, talk with an assisted reproduction specialist at a fertility clinic. How common is ...

  16. Complex Networks

    NASA Astrophysics Data System (ADS)

    Cohen, Reuven; Havlin, Shlomo

    2010-07-01

    1. Introduction; Part I. Random Network Models: 2. The Erdos-Renyi models; 3. Observations in real-world networks; 4. Models for complex networks; 5. Growing network models; Part II. Structure and Robustness of Complex Networks: 6. Distances in scale-free networks - the ultra small world; 7. Self-similarity in complex networks; 8. Distances in geographically embedded networks; 9. The network's structure - the generating function method; 10. Percolation on complex networks; 11. Structure of random directed networks - the bow tie; 12. Introducing weights - bandwidth allocation and multimedia broadcasting; Part III. Network Function - Dynamics and Applications: 13. Optimization of the network structure; 14. Epidemiological models; 15. Immunization; 16. Thermodynamic models on networks; 17. Spectral properties, transport, diffusion and dynamics; 18. Searching in networks; 19. Biological networks and network motifs; Part IV. Appendices; References; Index.

  17. Complex Numbers

    NSDL National Science Digital Library

    Kuphaldt, Tony R.

    Written by Tony R. Kuphaldt and Jason Starck, this chapter of All About Circuit's second volume on Alternating Current describes complex numbers: "In order to successfully analyze AC circuits, we need to work with mathematical objects and techniques capable of representing these multi-dimensional quantities. Here is where we need to abandon scalar numbers for something better suited: complex numbers." In addition to the introduction and credits to contributors, the chapter has seven sections: Vectors and AC waveforms, Simple vector addition, Complex vector addition, Polar and rectangular notation, Complex number arithmetic, More on AC "polarity," and Some examples with AC circuits. Each section has clear illustrations and a concise, bulleted review of what was covered at the end.

  18. Measuring temporal gravitational variations using SLR data

    NASA Technical Reports Server (NTRS)

    Nerem, Robert S.

    1994-01-01

    Redistribution of mass within the Earth system changes its gravitational field, and thus changes the orbits of Earth satellites. While these variations are small, Satellite Laser Ranging (SLR) to precise geodetic satellites such as Lageos-1, Lageos-2, Starlette, Ajisai, and Stella can detect these changes at their broadest spatial scales (currently greater than 10,000 km). The satellites sense only the combined variation in the solid Earth-ocean-atmosphere system; however, modeling of these different components has led to detection of long-wavelength variations in the distribution of atmospheric mass, changes in the amplitudes of atmospheric and oceanic tides, and secular variations caused by the post-glacial adjustment of the Earth's crust. The unambiguous detection of ocean mass redistribution by SLR has not been verified due largely to inadequacies in current ocean models. Great progress has been made in recent years in the determination of luni-solar tides and the braking they induce in the Earth-Moon-Sun system (leading to secular changes in the length-to-day and lengthening of the lunar orbit period) using a wide variety of techniques including ocean tide gauges, satellite altimetry, Lunar Laser Ranging, and near-Earth satellite orbit modeling. Recent investigations of the more complex and less predictable non-tidal temporal variations in the gravity field have generally proceeded along two fronts: 1) the determination of long-wavelength variations in the gravity field through the changing perturbations seen in the orbits of near-Earth satellites, and 2) the prediction of temporal variations in gravity using geophysical, atmospheric, and oceanic models. A convergence of these efforts is sought to better understand the source of observed changes in the Earth's gravitational field.

  19. 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…

  20. Complex Ploidy Level Variation in Guayule Breeding Programs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Guayule (Parthenium argentatum Gray) is a potential source of natural rubber, but attempts to domesticate and cultivate this perennial crop for large-scale commercial production in the southwestern United States have been intermittent over the past century. Genetic improvement through modern plant b...

  1. Complexation of Sr in aqueous fluids equilibrated with silicate melts: effect of melt and fluid composition

    NASA Astrophysics Data System (ADS)

    Borchert, M.; Wilke, M.; Schmidt, C.; Kvashnina, K.

    2009-12-01

    Experimental data show that fluid-melt partitioning of Sr is controlled by the bulk chemistry of the system. For chloridic fluids, there is 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) suggested formation of SrCl2 complexes based on the correlation between partition coefficient and Cl concentration in the fluid after quenching. 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 to facilitate in-situ analyses of the aqueous fluids. We used bulk compositions of 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. We applied different monochromator crystals, Si311 for high resolution and Si111 for low resolution measurements. An overall resolution of 1.98 eV (Si311) and 3 eV (Si111) was achieved using a beamsize of 120x400 ?m, Si(777) analyzer crystals and a Rowland circle diameter of 1 m. In contrast to the study by Kohn et al. (1990), XANES spectra of peraluminous and peralkaline starting glasses show distinct differences in pre-edge, main edge and position of the first EXAFS maximum. The latter is directly correlated to the distance of Sr and its nearest neighbor. The spectra of SrCl2 and Sr(OH)2 standard solutions at various PT conditions indicate very small temperature-dependent changes of the complexation. The XANES spectra of solutions after dissolution of peraluminous or peralkaline melt in chloridic fluids vary significantly from each other. The latter are similar to the one of the peralkaline starting glass, while this is not the case for solutions with peraluminous melt. The spectra of water with dissolved peralkaline melt distinctly differ from those using chloridic fluids. In conclusion, the first direct information on Sr complexation at elevated PT condition indicates significant speciation changes in both fluid and melt. Bai and Koster van Groos (1999), GCA 63, 1117-1131. Kohn et. Al. (1990), CMP 105, 359-368.

  2. Variations in sending Morse code

    Microsoft Academic Search

    Charles Windle

    1955-01-01

    Studied the deviations from the theoretical Morse code sequence (dot: dash: space ratios) in inexperienced and experienced Ss. Found evidence of variations due to different contextual occurrences of the signals (heterotaxic variation). Confirmed the finding that variations due to repetition of a signal decrease with expertness but did not confirm that heterotaxic variation increases with expertness. 16 references.

  3. A Variational Formulation of

    E-print Network

    Nagurney, Anna

    Constraints Patrizia Daniele, F. Toyasaki, T. Wakolbinger Outline A Variational Inequality Formulation of Equilibrium Models for End-of-Life Products with Nonlinear Constraints Patrizia Daniele F. Toyasaki T with Nonlinear Constraints Patrizia Daniele, F. Toyasaki, T. Wakolbinger Outline Outline 1 A few examples

  4. Variational transition state theory

    SciTech Connect

    Truhlar, D.G. [Univ. of Minnesota, Minneapolis (United States)

    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.

  5. Algebra Lab: Inverse Variation

    NSDL National Science Digital Library

    2012-08-29

    This lesson from Algebra Lab demonstrates "how to write equations of quantities which vary inversely." The lesson includes an example of a graph of this type of equation, and several example problems. This supporting material would be best used following some in-class instruction explaining how to solve inverse variation equations.

  6. Observer variation in ophthalmology

    Microsoft Academic Search

    R A Gibson; H F Sanderson

    1980-01-01

    Data collected by clinicians and nurses from patients with clinically diagnosed lens opacities revealed that there was poor repeatability of the description of the position of lens opacities, statistically significant observer variation in determining visual acuity, and good repeatability as to what visual tasks the patient can perform. It is suggested that clinicans should give more weight to the visual

  7. Fluency Variation in Adolescents

    ERIC Educational Resources Information Center

    De Andrade, Claudia Regina Furquim; Martins, Vanessa De Oliveira

    2007-01-01

    The Speech Fluency Profile of fluent adolescent speakers of Brazilian Portuguese, were examined with respect to gender and neurolinguistic variations. Speech samples of 130 male and female adolescents, aged between 12;0 and 17;11 years were gathered. They were analysed according to type of speech disruption; speech rate; and frequency of speech…

  8. 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…

  9. Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae

    Microsoft Academic Search

    Justin C Fay; Heather L McCullough; Paul D Sniegowski; Michael B Eisen

    2004-01-01

    Background  The relationship between genetic variation in gene expression and phenotypic variation observable in nature is not well understood.\\u000a Identifying how many phenotypes are associated with differences in gene expression and how many gene-expression differences\\u000a are associated with a phenotype is important to understanding the molecular basis and evolution of complex traits.\\u000a \\u000a \\u000a \\u000a \\u000a Results  We compared levels of gene expression among nine natural

  10. Nested biological variation and speciation

    PubMed Central

    Foster, S. A.

    1998-01-01

    The modes of speciation that are thought to have contributed most to the generation of biodiversity require population differentiation as the initial stage in the speciation process. Consequently, a complete understanding of the mechanisms of speciation requires that the process be examined not just after speciation is complete, or nearly so, but also much earlier. Because reproductive isolation defines biological species, and it evolves slowly, study of the process may require a prohibitive span of time. Even if speciation could be observed directly, selection of populations in the process of speciation is typically difficult or impossible, because those that will ultimately undergo speciation cannot be distinguished from those that will differentiate but never assume the status of new biological species. One means of circumventing this problem is to study speciation in taxa comprising several sibling species, at least one of which exhibits extensive population differentiation. We illustrate this approach by exploring patterns of population variation in the post-glacial radiation of the threespine stickleback, Gasterosteus aculeatus. We focus on lacustrine populations and species within this complex, demonstrating parallel axes of divergence within populations, among populations and among species. The pattern that emerges is one of parallel relationships between phenotype and fitness at all three hierarchical levels, a pattern that facilitates exploration of the causes and consequences of speciation and secondary contact. A second outcome of this exploration is the observation that speciation can be the consequence of a cascade of effects, beginning with selection on trophic or other characteristics that in turn force the evolution of other population characteristics that precipitate speciation. Neither of these conclusions could have been reached without comparative studies of wild populations at several hierarchical levels, a conclusion reinforced by a brief survey of similar efforts to elucidate the process of speciation. We address the issues most likely to be resolved using this approach, and suggest that comparisons of natural variation within taxa at several hierarchical levels may substantially increase our understanding of the speciation process.

  11. What makes a champion? Explaining variation in human athletic performance

    Microsoft Academic Search

    Tom D. Brutsaert; Esteban J. Parra

    2006-01-01

    Variation in human athletic performance is determined by a complex interaction of socio-cultural, psychological, and proximate physiological factors. Human physiological trait variance has both an environmental and genetic basis, although the classic gene-environment dichotomy is clearly too simplistic to understand the full range of variation for most proximate determinants of athletic performance, e.g., body composition. In other words, gene and

  12. 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.

  13. Total variation blind deconvolution

    Microsoft Academic Search

    Tony F. Chan; Chiu-Kwong Wong

    1998-01-01

    We present a blind deconvolution algorithm based on the total variational (TV) minimization method proposed by Acar and Vogel (1994). The motivation for regularizing with the TV norm is that it is extremely effective for recovering edges of images as well as some blurring functions, e.g., motion blur and out-of-focus blur. An alternating minimization (AM) implicit iterative scheme is devised

  14. Variations and Adaptations

    NSDL National Science Digital Library

    The Concord Consortium

    2011-12-11

    Students discover that variation in plants allows some varieties to survive in near-drought conditions. Next, students learn that different types of rabbits prefer to eat different varieties of plants. Students make the connection between rainfall amount and the rabbit population?s ability to survive by thinking first about rainfall and plants, then about plants and rabbits. Students discover that when certain plants cannot grow and reproduce, the rabbits that eat those plants will not have enough food to survive.

  15. 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 by the Multi-angle ... cyclonic circulation over the Southern Indian Ocean, to the north of Enderbyland, East Antarctica. The image at left was created by ...

  16. The implementation of a self-consistent constricted variational density functional theory for the description of excited states

    NASA Astrophysics Data System (ADS)

    Ziegler, Tom; Krykunov, Mykhaylo; Cullen, John

    2012-03-01

    We present here the implementation of a self-consistent approach to the calculation of excitation energies within regular Kohn-Sham density functional theory. The method is based on the n-order constricted variational density functional theory (CV(n)-DFT) [T. Ziegler, M. Seth, M. Krykunov, J. Autschbach, and F. Wang, J. Chem. Phys. 130, 154102 (2009)], 10.1063/1.3114988 and its self-consistent formulation (SCF-CV(?)-DFT) [J. Cullen, M. Krykunov, and T. Ziegler, Chem. Phys. 391, 11 (2011)], 10.1016/j.chemphys.2011.05.021. A full account is given of the way in which SCF-CV(?)-DFT is implemented. The SCF-CV(?)-DFT scheme is further applied to transitions from occupied ? orbitals to virtual ?* orbitals. The same series of transitions has been studied previously by high-level ab initio methods. We compare here the performance of SCF-CV(?)-DFT to that of time dependent density functional theory (TD-DFT), CV(n)-DFT and ?SCF-DFT, with the ab initio results as a benchmark standard. It is finally demonstrated how adiabatic TD-DFT and ?SCF-DFT are related through different approximations to SCF-CV(?)-DFT.

  17. December, 2012. CURRICULUM VITAE: Melvin L. Kohn

    E-print Network

    on Family Relations, for the research reported in "Social Class and the Exercise of Parental Authority-52 Cornell University, Ph.D. in sociology, with minors in social psychology and industrial relations. Positions held: 1948-51 Teaching and research assistant, Cornell University. 1951-52 Research Fellow, Social

  18. Geometrically Constrained Walls Robert V. Kohn

    E-print Network

    Slastikov, Valeriy V.

    . The analysis is motivated by recent investigations of magnetic domain walls trapped by sharp thin necks and electrical resistance [5]. To explain the basic phenomenon let us briefly summarize Bruno's discussion. He the neck has trapped a wall, i.e. the magnetization is m (0, 0, -1) to the left of the neck and m (0, 0

  19. Epistasis: too often neglected in complex trait studies?

    Microsoft Academic Search

    Chris S. Haley; Örjan Carlborg

    2004-01-01

    Interactions among loci or between genes and environmental factors make a substantial contribution to variation in complex traits such as disease susceptibility. Nonetheless, many studies that attempt to identify the genetic basis of complex traits ignore the possibility that loci interact. We argue that epistasis should be accounted for in complex trait studies; we critically assess current study designs for

  20. COMPLEX NUMBERS 1. Definition of complex numbers

    E-print Network

    La Rosa, Andres H.

    COMPLEX NUMBERS 1. Definition of complex numbers Complex conjugate, Magnitude Operations Addition, multiplication, reciprocal number 2. Representation of complex numbers in polar complex variable #12;2.2.A Complex numbers #12;#12;3 #12;4 #12;In short, Anytime we write Ae j we

  1. Pavane for a pulse pressure variation defunct

    PubMed Central

    2013-01-01

    Hemodynamic management of critically ill patients in the ICU or high-risk patients in the operating room has paradoxically shown progress in terms of outcome after the systematic application of volume responsiveness/flow optimization based on pulse pressure variation and/or stroke volume variation during controlled, positive-pressure ventilation in patients without spontaneous respiratory efforts. This assessment of circulatory optimization should ideally be based on an exhaustive, predictive and coherent physiological understanding of the cardiovascular system model. This paper sketches the extremely complex physiological background of the concept of volume responsiveness, concluding that it is not a reliable means of guiding hemodynamic optimization because it is based on a nonexhaustive, nonpredictive and incoherent physiological model. PMID:24229428

  2. Comprehensive variation discovery in single human genomes.

    PubMed

    Weisenfeld, Neil I; Yin, Shuangye; Sharpe, Ted; Lau, Bayo; Hegarty, Ryan; Holmes, Laurie; Sogoloff, Brian; Tabbaa, Diana; Williams, Louise; Russ, Carsten; Nusbaum, Chad; Lander, Eric S; MacCallum, Iain; Jaffe, David B

    2014-12-01

    Complete knowledge of the genetic variation in individual human genomes is a crucial foundation for understanding the etiology of disease. Genetic variation is typically characterized by sequencing individual genomes and comparing reads to a reference. Existing methods do an excellent job of detecting variants in approximately 90% of the human genome; however, calling variants in the remaining 10% of the genome (largely low-complexity sequence and segmental duplications) is challenging. To improve variant calling, we developed a new algorithm, DISCOVAR, and examined its performance on improved, low-cost sequence data. Using a newly created reference set of variants from the finished sequence of 103 randomly chosen fosmids, we find that some standard variant call sets miss up to 25% of variants. We show that the combination of new methods and improved data increases sensitivity by several fold, with the greatest impact in challenging regions of the human genome. PMID:25326702

  3. Time complexity and gate complexity

    NASA Astrophysics Data System (ADS)

    Koike, Tatsuhiko; Okudaira, Yosuke

    2010-10-01

    We formulate and investigate the simplest version of time-optimal quantum computation theory (TO-QCT), where the computation time is defined by the physical one and the Hamiltonian contains only one- and two-qubit interactions. This version of TO-QCT is also considered as optimality by sub-Riemannian geodesic length. The work has two aims: One is to develop a TO-QCT itself based on a physically natural concept of time, and the other is to pursue the possibility of using TO-QCT as a tool to estimate the complexity in conventional gate-optimal quantum computation theory (GO-QCT). In particular, we investigate to what extent is true the following statement: Time complexity is polynomial in the number of qubits if and only if gate complexity is also. In the analysis, we relate TO-QCT and optimal control theory (OCT) through fidelity-optimal computation theory (FO-QCT); FO-QCT is equivalent to TO-QCT in the limit of unit optimal fidelity, while it is formally similar to OCT. We then develop an efficient numerical scheme for FO-QCT by modifying Krotov’s method in OCT, which has a monotonic convergence property. We implemented the scheme and obtained solutions of FO-QCT and of TO-QCT for the quantum Fourier transform and a unitary operator that does not have an apparent symmetry. The former has a polynomial gate complexity and the latter is expected to have an exponential one which is based on the fact that a series of generic unitary operators has an exponential gate complexity. The time complexity for the former is found to be linear in the number of qubits, which is understood naturally by the existence of an upper bound. The time complexity for the latter is exponential in the number of qubits. Thus, both the targets seem to be examples satisfyng the preceding statement. The typical characteristics of the optimal Hamiltonians are symmetry under time reversal and constancy of one-qubit operation, which are mathematically shown to hold in fairly general situations.

  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. Quantum dynamics in continuum for proton transport II: Variational solvent-solute interface

    PubMed Central

    Chen, Duan; Chen, Zhan; Wei, Guo-Wei

    2011-01-01

    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, 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 (DNM), matched interface and boundary (MIB) method, Gummel iteration, and Krylov space techniques are utilized to implement the proposed model in a computationally efficient manner. The Gramicidin A (GA) channel is used to validate the performance of the proposed proton transport model and demonstrate the efficiency of the proposed mathematical algorithms. The proton channel conductances are studied over a number of applied voltages and reference concentrations. A comparison with experimental data verifies the present model predictions and confirms the proposed model. PMID:22328970

  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. Spatial variation of microstructure and

    E-print Network

    Fossen, Haakon

    Spatial variation of microstructure and petrophysical properties along deformation bands and petrophysical variations. In many of the examples explored, the internal microstruc- ture, porosity% and permeability by up to two orders of magnitude. Such petrophysical variations are found along different types

  8. Crystalline variational methods

    PubMed Central

    Taylor, Jean E.

    2002-01-01

    A surface free energy function is defined to be crystalline if its Wulff shape (the equilibrium crystal shape) is a polyhedron. All the questions that one considers for the area functional, where the surface free energy per unit area is 1 for all normal directions, can be considered for crystalline surface free energies. Such questions are interesting for both mathematical and physical reasons. Methods from the geometric calculus of variations are useful for studying a number of such questions; a survey of some of the results is given. PMID:12427965

  9. 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. PMID:23906376

  10. Spatial variation as a tool for inferring temporal variation and diagnosing types of mechanisms in ecosystems.

    PubMed

    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

  11. Power variations of wireless communication systems.

    PubMed

    Andersen, J B; Mogensen, P E; Pedersen, G F

    2010-05-01

    The use of wireless digital communication devices like GSM, WCDMA, HSPA, DECT, and WiFi changes the exposure of electromagnetic waves toward the user. Concentrating on the power variations on a slow and fast time scale, these new systems are discussed. Experimental results for both uplink and downlink are included for a sample of systems. The spectrum of the power fluctuations is seen as a convenient and compact way of describing very complex system behavior. The results are of interest for scientific studies of epidemiology and biological effects, and for general electromagnetic compatibility (EMC) aspects. PMID:20112260

  12. 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.

  13. Variational Principle for the Pareto Power Law

    NASA Astrophysics Data System (ADS)

    Chakraborti, Anirban; Patriarca, Marco

    2009-11-01

    A mechanism is proposed for the appearance of power-law distributions in various complex systems. It is shown that in a conservative mechanical system composed of subsystems with different numbers of degrees of freedom a robust power-law tail can appear in the equilibrium distribution of energy as a result of certain superpositions of the canonical equilibrium energy densities of the subsystems. The derivation only uses a variational principle based on the Boltzmann entropy, without assumptions outside the framework of canonical equilibrium statistical mechanics. Two examples are discussed, free diffusion on a complex network and a kinetic model of wealth exchange. The mechanism is illustrated in the general case through an exactly solvable mechanical model of a dimensionally heterogeneous system.

  14. Genetic variation in social influence on mate preferences

    PubMed Central

    Rebar, Darren; Rodríguez, Rafael L.

    2013-01-01

    Patterns of phenotypic variation arise in part from plasticity owing to social interactions, and these patterns contribute, in turn, to the form of selection that shapes the variation we observe in natural populations. This proximate–ultimate dynamic brings genetic variation in social environments to the forefront of evolutionary theory. However, the extent of this variation remains largely unknown. Here, we use a member of the Enchenopa binotata species complex of treehoppers (Hemiptera: Membracidae) to assess how mate preferences are influenced by genetic variation in the social environment. We used full-sibling split-families as ‘treatment’ social environments, and reared focal females alongside each treatment family, describing the mate preferences of the focal females. With this method, we detected substantial genetic variation in social influence on mate preferences. The mate preferences of focal females varied according to the treatment families along with which they grew up. We discuss the evolutionary implications of the presence of such genetic variation in social influence on mate preferences, including potential contributions to the maintenance of genetic variation, the promotion of divergence, and the adaptive evolution of social effects on fitness-related traits. PMID:23698010

  15. 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…

  16. 3. Complex Numbers 17 3 Complex Numbers

    E-print Network

    Givental, Alexander

    3. Complex Numbers 17 3 Complex Numbers Law and Order Life is unfair: The quadratic equation x2 - 1 solutions to the equation. This is how complex numbers could have been invented. More formally, complex numbers a and b are called respectively the real part and imagi- nary part of the complex number z

  17. Variation and evolution of biomolecular systems: Searching for functional relevance

    Microsoft Academic Search

    Martijn A. Huynen; Toni Gabaldón; Berend Snel

    2005-01-01

    The availability of genome sequences and functional genomics data from multiple species enables us to compare the composition of biomolecular systems like biochemical pathways and protein complexes between species. Here, we review small- and large-scale, “genomics-based” approaches to biomolecular systems variation. In general, caution is required when comparing the results of bioinformatics analyses of genomes or of functional genomics data

  18. Variational Structure of Inverse Problems in Wave Propagation and Vibration

    E-print Network

    Variational Structure of Inverse Problems in Wave Propagation and Vibration James G. Berryman in wave propagation (traveltime tomography) and two examples in vibration (the plucked string and free.'' For vibrating systems, the apparently very complex behavior of an excited string, drumhead, or the Earth can

  19. The influence of variation in litter habitats on spider communities

    Microsoft Academic Search

    George W. Uetz

    1979-01-01

    Spider communities were sampled over an artificial gradient of litter depth (created by raking) and compared to those of two other forests exhibiting natural variation in litter depth. More species of spiders were present in areas of greater depth and\\/or complexity in all sites. Relative abundance of Lycosidae decreased, while relative abundance of Clubionidae, Thomisidae and Gnaphosidae increased over gradients

  20. 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…

  1. Nuthatches eavesdrop on variations in heterospecific chickadee mobbing alarm calls

    Microsoft Academic Search

    C. N. Templeton; Erick Greene

    2007-01-01

    Many animals recognize the alarm calls produced by other species, but the amount of information they glean from these eaves- dropped signals is unknown. We previously showed that black- capped chickadees (Poecile atricapillus) have a sophisticated alarm call system in which they encode complex information about the size and risk of potential predators in variations of a single type of

  2. Methods of attenuating wind turbine ac generator output variations

    NASA Technical Reports Server (NTRS)

    Gold, H.

    1978-01-01

    Wind speed variation, tower blockage and structural and inertial factors produce unsteady torque in wind turbines. Methods for modifying the turbine torque so that steady torque is delivered to the coupled ac generator are discussed. The method that may evolve will be influenced by the power use that develops and the trade-offs of cost, weight and complexity.

  3. Testing the spectral variation hypothesis by using satellite multispectral images

    Microsoft Academic Search

    Duccio Rocchini; Alessandro Chiarucci; Steven A. Loiselle

    2004-01-01

    In the present paper, a test of the spectral variation hypothesis (SVH) was performed using multispectral high resolution satellite data. The SVH was tested by comparing the relationship between the spectral heterogeneity and species richness in plots of different size (100–10000 m2) in a complex wetland ecosystem, the “Montepulciano Lake”, Central Italy. The nature reserve of the Montepulciano Lake is centered

  4. CLIMATE VARIATIONS, CLIMATE CHANGE, AND WATER RESOUCES ENGINEERING

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Complex water resources systems are developed to ensure a continued safe and reliable water supply for our society. Climate variability, one among several factors, can stress these systems and lead to water shortages and related problems. While many aspects of climate variations and their impact o...

  5. Visualizing patterns of craniofacial shape variation in Homo sapiens.

    PubMed Central

    Zollikofer, Christoph P E; Ponce De León, Marcia S

    2002-01-01

    The geometric morphometric analysis of shape variation in complex biological structures such as the human skull poses a number of specific challenges: the registration of homologous morphologies, the treatment of bilateral symmetry, the graphical representation of form variability in three dimensions and the interpretation of the results in terms of differential growth processes. To visualize complex patterns of shape change, we propose an alternative to classical Cartesian deformation grids in the style of D'Arcy W. Thompson. Reference to the surface structures of the organism under investigation permits a comprehensive visual grasp of shape change and its tentative interpretation in terms of differential growth. The application of this method to the analysis of human craniofacial shape variation reveals distinct modes of growth and development of the neurocranial and viscerocranial regions of the skull. Our data further indicate that variations in the orientation of the viscerocranium relative to the neurocranium impinge on the shapes of the face and the cranial vault. PMID:11958711

  6. 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 neutrons, liberating a little energy and creating complexity. Then, the expanding universe cooled some more, and neutrons and protons, no longer kept apart by immense temperatures, found themselves unstable and formed helium nuclei. Then, a little more cooling, and atomic nuclei and electrons were no longer kept apart, and the universe became transparent. Then a little more cooling, and the next instability began: gravitation pulled matter together across cosmic distances to form stars and galaxies. This instability is described as a "negative heat capadty" in which extracting energy from a gravitating system makes it hotter -- clearly the 2nd law of thermodynamics does not apply here! (This is the physicist's part of the answer to e e cummings' question: what is the wonder that's keeping the stars apart?) Then, the next instability is that hydrogen and helium nuclei can fuse together to release energy and make stars burn for billions of years. And then at the end of the fuel source, stars become unstable and explode and liberate the chemical elements back into space. And because of that, on planets like Earth, sustained energy flows support the development of additional instabilities and all kinds of complex patterns. Gravitational instability pulls the densest materials into the core of the Earth, leaving a thin skin of water and air, and makes the interior churn incessantly as heat flows outwards. And the heat from the sun, received mostly near the equator and flowing towards the poles, supports the complex atmospheric and oceanic circulations. And because or that, the physical Earth is full of natural chemical laboratories, concentrating elements here, mixing them there, raising and lowering temperatures, ceaselessly experimenting with uncountable events where new instabilities can arise. At least one of them was the new experiment called life. Now that we know that there are at least as many planets as there are stars, it is hard to imagine that nature's ceasess experimentation would not be able to produce life elsewhere

  7. Observations on the Screened Korringa-Kohn-Rostoker Method (Work supported by Office of Basic Energy Sciences, Division of Materials Science and Mathematical, Information, and Computational Sciences Division, US-DOE, under subcontract DEAC05-960R22464 with Lockheed-Martin Energy Research Corporation.)

    NASA Astrophysics Data System (ADS)

    Moghadam, Nassrin Y.; Stocks, G. Malcolm; Újfalussy, B.; Faulkner, J. S.

    1997-03-01

    We point out that the screened Korringa-Kohn-Rostoker method recently proposed by Zeller et al.(R. Zeller et. al. , Physical Review B, 52), 8807 (1995) can be viewed as a special case of the embedded cluster method previously used in alloy theory. In addition, we present results of total energy calculations for elemental metals based on this method that demonstrate that unphysical results (total energy, densities of states) can be obtained unless considerable care is taken in choosing the cut off parameters. Finally, we indicate how these paramaters can be chosen such that the method yields accurate total energies while preserving the (near) tight binding character of the screened structure constants.

  8. Conservation genetics of the species complex Cochlearia officinalis L. s.l. in Britain 

    E-print Network

    Gill, Estelle

    2008-01-01

    The genus Cochlearia is a taxonomically complex genus with a circumpolar distribution. In common with many other post-glacial colonisers it exhibits complex patterns of morphological and ecological variation. The genus ...

  9. RESULTS OF IPCS COLLABORATIVE STUDY ON COMPLEX MIXTURES

    EPA Science Inventory

    The International Programme on Chemical Safety (IPCS) sponsored a collaborative study to examine the intra- and interlaboratory variation associated with the preparation and bioassay of complex chemical mixtures. The mixtures selected were National Institute of Standards and Tech...

  10. [Module for analyzing physiological processes of the OMIS software complex].

    PubMed

    Genkin, A A

    2002-01-01

    The informational technology designed for systems analysis of changes in the characteristics of single variations in physiological process is outlined. This technology has been used in the module of analysis of the physiological processes of an software complex. PMID:12224251

  11. What constrains directional selection on complex traits in the wild?

    E-print Network

    Mojica, Julius Penalba

    2011-08-31

    The fact that abundant genetic variation persists within populations despite strong directional selection on complex traits is one of the unresolved conundrums in evolutionary biology. In this dissertation, I employed a ...

  12. Variational multiscale models for charge transport.

    PubMed

    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 for chemo-electro-fluid systems. A number of computational algorithms is developed to implement the proposed new variational multiscale models in an efficient manner. A set of ten protein molecules and a realistic ion channel, Gramicidin A, are employed to confirm the consistency and verify the capability. Extensive numerical experiment is designed to validate the proposed variational multiscale models. A good quantitative agreement between our model prediction and the experimental measurement of current-voltage curves is observed for the Gramicidin A channel transport. This paper also provides a brief review of the field. PMID:23172978

  13. 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 for chemo-electro-fluid systems. A number of computational algorithms is developed to implement the proposed new variational multiscale models in an efficient manner. A set of ten protein molecules and a realistic ion channel, Gramicidin A, are employed to confirm the consistency and verify the capability. Extensive numerical experiment is designed to validate the proposed variational multiscale models. A good quantitative agreement between our model prediction and the experimental measurement of current-voltage curves is observed for the Gramicidin A channel transport. This paper also provides a brief review of the field. PMID:23172978

  14. Mean photon number dependent variational method to the Rabi model

    NASA Astrophysics Data System (ADS)

    Liu, Maoxin; Ying, Zu-Jian; An, Jun-Hong; Luo, Hong-Gang

    2015-04-01

    We present a mean photon number dependent variational method, which works well in the whole coupling regime if the photon energy is dominant over the spin-flipping, to evaluate the properties of the Rabi model for both the ground state and excited states. For the ground state, it is shown that the previous approximate methods, the generalized rotating-wave approximation (only working well in the strong coupling limit) and the generalized variational method (only working well in the weak coupling limit), can be recovered in the corresponding coupling limits. The key point of our method is to tailor the merits of these two existing methods by introducing a mean photon number dependent variational parameter. For the excited states, our method yields considerable improvements over the generalized rotating-wave approximation. The variational method proposed could be readily applied to more complex models, for which it is difficult to formulate an analytic formula.

  15. 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 ...

  16. Quantifying Cell-to-Cell Variation in Power-Law Rheology

    E-print Network

    Cai, PingGen

    Among individual cells of the same source and type, the complex shear modulus G[subscript ?] exhibits a large log-normal distribution that is the result of spatial, temporal, and intrinsic variations. Such large distributions ...

  17. CCMR: New Iridium Complexes for the Dehydrogenation of Alkanes

    NSDL National Science Digital Library

    Wang, David

    2004-08-17

    To introduce small variations on the previously investigated iridium P-C-P pincer complexes. The variations include substitution of cyclohexyl groups for the tert-butyl and the iso-propyl groups found on the phosphines.Thus, synthesis of these new iridium P-C-P pincer complexes was performed with the aim of improved catalytic dehydrogenation activity as well as a better understand of the influence that ligand sterics and electronics have on the active species.

  18. Seasonal Variations in Soudan 2

    NASA Astrophysics Data System (ADS)

    Goodman, Maury

    1999-08-01

    Seasonal Variations in an underground detector may be a signature for Dark Matter. 1 The Soudan 2 detector searches for nucleon decay and atmospheric neutrinos. The trigger rate is about 0.5 Hertz. It is dominated by approximately equal numbers of atmospheric muons and low level radioactivity. The muon rate has a seasonal variation of +-2°, which is consistent with a similar e ect at MACRO. The MACRO e ect has been correlated with temperature in the upper atmosphere. Our trigger rate has a seasonal variation of +-15° which we believe is due to radon in the mine, and variations in air ow with outside temperature.

  19. Getting a Handle on Variation

    NSDL National Science Digital Library

    The Wisconsin Fast Plants Program

    This is an article explaining about variation in a population in general, using height as a specific example. The article is designed to help students and teachers think about the nature of various determinants underlying biological variation.Variation in height is easily observed and measured by learners, and quantifying height observations over time is a rich context for all ages to make key mathematics and science connections."Fast Plants, rapid cycling Brassica rapa are ideally suited for getting a handle on variation."

  20. Temperature Variations and Habitability

    NSDL National Science Digital Library

    These are the student pages for a two part lesson plan that will teach students about observing, describing, and adapting to temperature variations and relating factors that influence planetary temperature and habitability. The class will decide upon a plan for describing indoor and outdoor environments and compare them with the data on environmental conditions at other Earth locales and planets in our solar system. These will be used to discuss temperature ranges, their relation to habitability, and ways to adapt to these conditions. In the second activity, students will give three examples of how humans modify the environment to improve livability, identify three factors that may determine the average temperature of a planet, identify a minimum of five factors that may determine the habitability of a planet, state the importance of maintaining habitable temperature on a planet, and briefly describe the links between two sets of factors of their choosing. The site provides a list of materials, objectives, and worksheets. Teachers' notes are also included.

  1. Variational bayesian super resolution.

    PubMed

    Babacan, S Derin; Molina, Rafael; Katsaggelos, Aggelos K

    2011-04-01

    In this paper, we address the super resolution (SR) problem from a set of degraded low resolution (LR) images to obtain a high resolution (HR) image. Accurate estimation of the sub-pixel motion between the LR images significantly affects the performance of the reconstructed HR image. In this paper, we propose novel super resolution methods where the HR image and the motion parameters are estimated simultaneously. Utilizing a bayesian formulation, we model the unknown HR image, the acquisition process, the motion parameters and the unknown model parameters in a stochastic sense. Employing a variational bayesian analysis, we develop two novel algorithms which jointly estimate the distributions of all unknowns. The proposed framework has the following advantages: 1) Through the incorporation of uncertainty of the estimates, the algorithms prevent the propagation of errors between the estimates of the various unknowns; 2) the algorithms are robust to errors in the estimation of the motion parameters; and 3) using a fully bayesian formulation, the developed algorithms simultaneously estimate all algorithmic parameters along with the HR image and motion parameters, and therefore they are fully-automated and do not require parameter tuning. We also show that the proposed motion estimation method is a stochastic generalization of the classical Lucas-Kanade registration algorithm. Experimental results demonstrate that the proposed approaches are very effective and compare favorably to state-of-the-art SR algorithms. PMID:20876021

  2. In Silico Detection of Sequence Variations Modifying Transcriptional Regulation

    PubMed Central

    Andersen, Malin C; Engström, Pär G; Lithwick, Stuart; Arenillas, David; Eriksson, Per; Lenhard, Boris; Wasserman, Wyeth W; Odeberg, Jacob

    2008-01-01

    Identification of functional genetic variation associated with increased susceptibility to complex diseases can elucidate genes and underlying biochemical mechanisms linked to disease onset and progression. For genes linked to genetic diseases, most identified causal mutations alter an encoded protein sequence. Technological advances for measuring RNA abundance suggest that a significant number of undiscovered causal mutations may alter the regulation of gene transcription. However, it remains a challenge to separate causal genetic variations from linked neutral variations. Here we present an in silico driven approach to identify possible genetic variation in regulatory sequences. The approach combines phylogenetic footprinting and transcription factor binding site prediction to identify variation in candidate cis-regulatory elements. The bioinformatics approach has been tested on a set of SNPs that are reported to have a regulatory function, as well as background SNPs. In the absence of additional information about an analyzed gene, the poor specificity of binding site prediction is prohibitive to its application. However, when additional data is available that can give guidance on which transcription factor is involved in the regulation of the gene, the in silico binding site prediction improves the selection of candidate regulatory polymorphisms for further analyses. The bioinformatics software generated for the analysis has been implemented as a Web-based application system entitled RAVEN (regulatory analysis of variation in enhancers). The RAVEN system is available at http://www.cisreg.ca for all researchers interested in the detection and characterization of regulatory sequence variation. PMID:18208319

  3. Propagation of genetic variation in gene regulatory networks

    NASA Astrophysics Data System (ADS)

    Plahte, Erik; Gjuvsland, Arne B.; Omholt, Stig W.

    2013-08-01

    A future quantitative genetics theory should link genetic variation to phenotypic variation in a causally cohesive way based on how genes actually work and interact. We provide a theoretical framework for predicting and understanding the manifestation of genetic variation in haploid and diploid regulatory networks with arbitrary feedback structures and intra-locus and inter-locus functional dependencies. Using results from network and graph theory, we define propagation functions describing how genetic variation in a locus is propagated through the network, and show how their derivatives are related to the network’s feedback structure. Similarly, feedback functions describe the effect of genotypic variation of a locus on itself, either directly or mediated by the network. A simple sign rule relates the sign of the derivative of the feedback function of any locus to the feedback loops involving that particular locus. We show that the sign of the phenotypically manifested interaction between alleles at a diploid locus is equal to the sign of the dominant feedback loop involving that particular locus, in accordance with recent results for a single locus system. Our results provide tools by which one can use observable equilibrium concentrations of gene products to disclose structural properties of the network architecture. Our work is a step towards a theory capable of explaining the pleiotropy and epistasis features of genetic variation in complex regulatory networks as functions of regulatory anatomy and functional location of the genetic variation.

  4. Genetic architecture of regulatory variation in Arabidopsis thaliana.

    PubMed

    Zhang, Xu; Cal, Andrew J; Borevitz, Justin O

    2011-05-01

    Studying the genetic regulation of expression variation is a key method to dissect complex phenotypic traits. To examine the genetic architecture of regulatory variation in Arabidopsis thaliana, we performed genome-wide association (GWA) mapping of gene expression in an F(1) hybrid diversity panel. At a genome-wide false discovery rate (FDR) of 0.2, an associated single nucleotide polymorphism (SNP) explains >38% of trait variation. In comparison with SNPs that are distant from the genes to which they were associated, locally associated SNPs are preferentially found in regions with extended linkage disequilibrium (LD) and have distinct population frequencies of the derived alleles (where Arabidopsis lyrata has the ancestral allele), suggesting that different selective forces are acting. Locally associated SNPs tend to have additive inheritance, whereas distantly associated SNPs are primarily dominant. In contrast to results from mapping of expression quantitative trait loci (eQTL) in linkage studies, we observe extensive allelic heterogeneity for local regulatory loci in our diversity panel. By association mapping of allele-specific expression (ASE), we detect a significant enrichment for cis-acting variation in local regulatory variation. In addition to gene expression variation, association mapping of splicing variation reveals both local and distant genetic regulation for intron and exon level traits. Finally, we identify candidate genes for 59 diverse phenotypic traits that were mapped to eQTL. PMID:21467266

  5. 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.

  6. What controls chemical variation in granitic magmas?

    NASA Astrophysics Data System (ADS)

    Clemens, J. D.; Stevens, G.

    2012-03-01

    Consideration of the models that have been applied to explain the chemical variations within granitic rock suites shows that most are inadequate to account for the main variations. This stems from a variety of model deficiencies, ranging from physical or energetic inadequacies to incompatibility with the chemical data or internal inconsistency between models based on, for example, isotope or trace-element data and major-element data. We contend that any model that fails any of these tests of internal consistency cannot be considered further. Thus, although we can point to examples in which many of the traditionally accepted mechanisms have played secondary roles in producing variation, there presently remains but one viable choice for the primary mechanism by which most granitic magmas acquire compositions beyond the range defined by the compositions of crustal melts. That primary mechanism is peritectic assemblage entrainment (PAE). We infer that once a partial melt has formed in a crustal protolith it may segregate from its complementary solid residue carrying small crystals of the peritectic phase assemblage formed in the melting reaction, and that the ratios of individual peritectic minerals in the entrained assemblage remains fixed in the ratio decreed by the stoichiometry of the melting reaction. For those elements with low solubilities in granitic melts, PAE (in varying degrees), accompanied by co-entrainment of accessory minerals, is responsible for most of the primary elemental variation in granitic magmas. In contrast, the concentrations of elements with high solubilities in silicic melts reflect the protolith compositions in a simple and direct way. The source is the primary control on granite magma chemistry; it dictates what is available to dissolve in the melt and what will be formed as the entrainable peritectic assemblage. The apparent complexity in granitic rock suites is largely a consequence of these processes in the source. All other mechanisms contribute only as a secondary overlay.

  7. Copy number variation in schizophrenia in Sweden.

    PubMed

    Szatkiewicz, J P; O'Dushlaine, C; Chen, G; Chambert, K; Moran, J L; Neale, B M; Fromer, M; Ruderfer, D; Akterin, S; Bergen, S E; Kähler, A; Magnusson, P K E; Kim, Y; Crowley, J J; Rees, E; Kirov, G; O'Donovan, M C; Owen, M J; Walters, J; Scolnick, E; Sklar, P; Purcell, S; Hultman, C M; McCarroll, S A; Sullivan, P F

    2014-07-01

    Schizophrenia (SCZ) is a highly heritable neuropsychiatric disorder of complex genetic etiology. Previous genome-wide surveys have revealed a greater burden of large, rare copy number variations (CNVs) in SCZ cases and identified multiple rare recurrent CNVs that increase risk of SCZ although with incomplete penetrance and pleiotropic effects. Identification of additional recurrent CNVs and biological pathways enriched for SCZ CNVs requires greater sample sizes. We conducted a genome-wide survey for CNVs associated with SCZ using a Swedish national sample (4719 cases and 5917 controls). High-confidence CNV calls were generated using genotyping array intensity data, and their effect on risk of SCZ was measured. Our data confirm increased burden of large, rare CNVs in SCZ 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 SCZ. Intriguingly, gene set association analyses implicate biological pathways previously associated with SCZ 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 (>500?kb) in genes present in the postsynaptic density, in genomic regions implicated via SCZ 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

  8. The Mycobacterium tuberculosis complex transcriptome of attenuation

    Microsoft Academic Search

    Serge Mostowy; Cynthia Cleto; David R. Sherman; Marcel A. Behr

    2004-01-01

    Although the deletion of RD1 is likely correlated to attenuation from virulence for members of the Mycobacterium tuberculosis (MTB) complex, the reasons for this phenotype remain to be fully explained. As genomic variation is responsible for at least a component of variability in gene expression, we looked to the in vitro global expression profile of the RD1 artificial knockout from

  9. M-Theory on Complex Spacetime

    E-print Network

    Abdul Rouf Samurah

    2012-09-26

    In this paper we will analyse ABJM theory in N=1 superspace formalism on complex spacetime. We will then analyse the BRST and anti-BRST symmetries for this theory. We will show that the sum of gauge fixing and ghost terms for this theory can be expressed as a combination of the total BRST or the total anti-BRST variations.

  10. Complex patterns and tip effect evolution

    E-print Network

    Francisco Vera

    2005-05-10

    We studied the formation of complex patterns using a variational principle and a standard energy functional. These patterns evolve by letting the system to search for the optimal configuration of a high conductivity channel, that in one dimension is equivalent to tip effect evolution (evolution towards regions of high electric field).

  11. Algorithms, complexity, and the sciences.

    PubMed

    Papadimitriou, Christos

    2014-11-11

    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. Anatomic variations of the paranasal sinuses: CT examination for endoscopic sinus surgery

    Microsoft Academic Search

    Halil Arslan; At?f Ayd?nl?o?lu; Mehmet Bozkurt; Erol Egeli

    1999-01-01

    Chronic rhinosinusitis endoscopic surgery requires an accurate evaluation of diseases and paranasal sinus anatomic variations. This study aims to show the main anatomical variations in the ostiomeatal complex and paranasal sinuses which are usually depicted by computed tomography (CT). CT scans obtained 2 mm thickness in axial and coronal plane from a series of 200 patients with chronic sinusitis were

  13. Approximating Nature's Variation: Selecting and Using Reference Information in Restoration Ecology

    Microsoft Academic Search

    Peter S. White; Joan L. Walker

    1997-01-01

    Restoration ecologists use reference information to define restoration goals, determine the restoration po- tential of sites, and evaluate the success of restoration efforts. Basic to the selection and use of reference in- formation is the need to understand temporal and spatial variation in nature. This is a challenging task: variation is likely to be scale dependent; ecosystems vary in complex

  14. 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.

  15. Transmissivity variations in mudstones.

    PubMed

    MacDonald, Alan M; Kemp, Simon J; Davies, Jeff

    2005-01-01

    Many people in sub-Saharan Africa have to rely on meager water resources within mudstones for their only water supply. Although mudstones have been extensively researched for their low permeability behavior, little research has been undertaken to examine their ability to provide sustainable water supplies. To investigate the factors controlling the occurrence of usable ground water in mudstone environments, an area of Cretaceous mudstones in southeastern Nigeria was studied over a 3 yr period. Transmissivity (T) variations in a range of mudstone environments were studied. The investigations demonstrate that within the top 40 m of mudstones, transmissivity can be sufficient to develop village water supplies (T > 1 m2/d). Transmissivity is controlled by two factors: low-grade metamorphism and the presence of other, subordinate, lithologies within the mudstones. Largely unaltered mudstones (early diagenetic zone), comprising mainly smectite clays, are mostly unfractured and have a low T of < 0.1 m2/d. Mudstones that have undergone limited metamorphism (late diagenetic zone) comprise mixed layered illite/smectite clays, and ground water is found in widely spaced fracture zones (T > 1 m2/d in large fracture zones; T < 0.1 m2/d away from fracture zones). Mudstones that have been further altered and approach the anchizone comprise illite clays, are pervasively fractured, and have the highest transmissivity values (T > 4 m2/d). Dolerite intrusions in unaltered, smectitic mudstones are highly fractured with transmissivity in the range of 1 < T < 60 m2/d. Thin limestone and sandstone layers can also enhance transmissivity sufficiently to provide community water supplies. PMID:15819947

  16. Interpreting phenotypic variation in plants

    NSDL National Science Digital Library

    This article by Coleman, McConnaughay, and Ackerly discusses how phenotypic variation (variation in observable traits) in plants is influenced by environment, genetics, and developmental stage. The authors stress that understanding the interplay of these factors is important for investigations that involve plant comparisons.

  17. SEMIANNUAL VARIATION OF GEOMAGNETIC ACTIVITY

    Microsoft Academic Search

    C.T. Russell; R. L. McPherron

    1973-01-01

    The semiannual variation in geomagnetic activity is well established in geomagnetic data Its explanation has remained elusive, however. We propose, simply, that it is caused by a semiannual variation in the effective southward component of the interplanetary field. The southward field arises because the interplanetary field is ordered in the solar equatorial coordinate system, whereas the interaction with the magnetosphere

  18. Discrete mechanics and variational integrators

    Microsoft Academic Search

    J. E. Marsden

    2001-01-01

    This paper gives a review of integration algorithms for finite dimensional mechanical systems that are based on discrete variational principles. The variational technique gives a unified treatment of many symplectic schemes, including those of higher order, as well as a natural treatment of the discrete Noether theorem. The approach also allows us to include forces, dissipation and constraints in a

  19. Classifying Measures of Biological Variation

    PubMed Central

    Gregorius, Hans-Rolf; Gillet, Elizabeth M.

    2015-01-01

    Biological variation is commonly measured at two basic levels: variation within individual communities, and the distribution of variation over communities or within a metacommunity. We develop a classification for the measurement of biological variation on both levels: Within communities into the categories of dispersion and diversity, and within metacommunities into the categories of compositional differentiation and partitioning of variation. There are essentially two approaches to characterizing the distribution of trait variation over communities in that individuals with the same trait state or type tend to occur in the same community (describes differentiation tendencies), and individuals with different types tend to occur in different communities (describes apportionment tendencies). Both approaches can be viewed from the dual perspectives of trait variation distributed over communities (CT perspective) and community membership distributed over trait states (TC perspective). This classification covers most of the relevant descriptors (qualified measures) of biological variation, as is demonstrated with the help of major families of descriptors. Moreover, the classification is shown to open ways to develop new descriptors that meet current needs. Yet the classification also reveals the misclassification of some prominent and widely applied descriptors: Dispersion is often misclassified as diversity, particularly in cases where dispersion descriptor allow for the computation of effective numbers; the descriptor GST of population genetics is commonly misclassified as compositional differentiation and confused with partitioning-oriented differentiation, whereas it actually measures partitioning-oriented apportionment; descriptors of ?-diversity are ambiguous about the differentiation effects they are supposed to represent and therefore require conceptual reconsideration. PMID:25807558

  20. 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 estimates of global sea level acceleration for time spans of less than about 50 years. This means that tide gauges alone cannot serve as a reliable leading indicator of climate change in less than many decades. This time required can be significantly reduced if the interdecadal fluctuations of sea level can be understood in terms of their forcing mechanisms, and then removed from the tide gauge records.

  1. Complex dynamics of text analysis

    NASA Astrophysics Data System (ADS)

    Ke, Xiaohua; Zeng, Yongqiang; Ma, Qinghua; Zhu, Lin

    2014-12-01

    This paper presents a novel method for the analysis of nonlinear text quality in Chinese language. Texts produced by university students in China were represented as scale-free networks (word adjacency model), from which typical network features such as the in/outdegree, clustering coefficient and network dynamics were obtained. The method integrates the classical concepts of network feature representation and text quality series variation. The analytical and numerical scheme leads to a parameter space representation that constitutes a valid alternative to represent the network features. The results reveal that complex network features of different text qualities can be clearly revealed and applied to potential applications in other instances of text analysis.

  2. Political Economy of Compensatory Conservation: A Case Study of proposed Omkareshwar National Park Complex, India

    E-print Network

    Goel, Abhineety

    2013-08-08

    National Park Complex ...... 101 3.3 Seasonal variation of economic activities ....................................................... 113 3.4 Independent t-test for income variation between villages .............................. 124 3.5 Comparison... of NTFPs share per household among the six sampled villages ............................................................................................................ 126 3.6 Independent t-test for income variation between adivasi and non...

  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. SOME VARIATIONS ON TOTAL VARIATION-BASED IMAGE SMOOTHING

    Microsoft Academic Search

    Antonin Chambolle; Stacey E. Levine; Bradley J. Lucier

    In this paper we study finite-difference approximations to the variational problem using the BV smoothness penalty that was intro- duced in an image smoothing context by Rudin, Osher, and Fatemi. We give a dual formulation for an \\

  5. 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.

  6. Complex systems and the technology of variability analysis

    Microsoft Academic Search

    Andrew JE Seely; Peter T Macklem

    2004-01-01

    Characteristic patterns of variation over time, namely rhythms, represent a defining feature of complex systems, one that is synonymous with life. Despite the intrinsic dynamic, interdependent and nonlinear relationships of their parts, complex biological systems exhibit robust systemic stability. Applied to critical care, it is the systemic properties of the host response to a physiological insult that manifest as health

  7. Modeling Wildfire Incident Complexity Dynamics

    PubMed Central

    Thompson, Matthew P.

    2013-01-01

    Wildfire management in the United States and elsewhere is challenged by substantial uncertainty regarding the location and timing of fire events, the socioeconomic and ecological consequences of these events, and the costs of suppression. Escalating U.S. Forest Service suppression expenditures is of particular concern at a time of fiscal austerity as swelling fire management budgets lead to decreases for non-fire programs, and as the likelihood of disruptive within-season borrowing potentially increases. Thus there is a strong interest in better understanding factors influencing suppression decisions and in turn their influence on suppression costs. As a step in that direction, this paper presents a probabilistic analysis of geographic and temporal variation in incident management team response to wildfires. The specific focus is incident complexity dynamics through time for fires managed by the U.S. Forest Service. The modeling framework is based on the recognition that large wildfire management entails recurrent decisions across time in response to changing conditions, which can be represented as a stochastic dynamic system. Daily incident complexity dynamics are modeled according to a first-order Markov chain, with containment represented as an absorbing state. A statistically significant difference in complexity dynamics between Forest Service Regions is demonstrated. Incident complexity probability transition matrices and expected times until containment are presented at national and regional levels. Results of this analysis can help improve understanding of geographic variation in incident management and associated cost structures, and can be incorporated into future analyses examining the economic efficiency of wildfire management. PMID:23691014

  8. Towards the blackbox computation of magnetic exchange coupling parameters in polynuclear transition-metal complexes: theory, implementation, and application.

    PubMed

    Phillips, Jordan J; Peralta, Juan E

    2013-05-01

    We present a method for calculating magnetic coupling parameters from a single spin-configuration via analytic derivatives of the electronic energy with respect to the local spin direction. This method does not introduce new approximations beyond those found in the Heisenberg-Dirac Hamiltonian and a standard Kohn-Sham Density Functional Theory calculation, and in the limit of an ideal Heisenberg system it reproduces the coupling as determined from spin-projected energy-differences. Our method employs a generalized perturbative approach to constrained density functional theory, where exact expressions for the energy to second order in the constraints are obtained by analytic derivatives from coupled-perturbed theory. When the relative angle between magnetization vectors of metal atoms enters as a constraint, this allows us to calculate all the magnetic exchange couplings of a system from derivatives with respect to local spin directions from the high-spin configuration. Because of the favorable computational scaling of our method with respect to the number of spin-centers, as compared to the broken-symmetry energy-differences approach, this opens the possibility for the blackbox exploration of magnetic properties in large polynuclear transition-metal complexes. In this work we outline the motivation, theory, and implementation of this method, and present results for several model systems and transition-metal complexes with a variety of density functional approximations and Hartree-Fock. PMID:23656122

  9. Variational Harmonic Maps for Space Deformation Mirela Ben-Chen Ofir Weber Craig Gotsman

    E-print Network

    Gotsman, Craig

    - gent, and easy to implement. CR Categories: I.3.5 [Computer Graphics]: Computational Geometry the ambient space, the computational complexity of the deformation is decoupled from the complexity. ________________________ Figure 1: The Beast model enclosed in its cage (left) and its de- formation using a variational harmonic

  10. Outburst Cycle Length Variations in Dwarf Novae

    NASA Astrophysics Data System (ADS)

    Andronov, I. L.; Chinarova, L. L.; Mikhailik, V. A.

    We have analysed variations of the cycle length for a group of Dwarf Novae. Results for certain stars are compared with that obtained for computer-simulated processs (random intervals between maxima, 2-order Markow chain). For EM Cyg, the observations of which are most numerous in our sample, the "seasonal" values of the cycle length were also obtained from a sine-like fit. All investigated stars showed significant changes of the cycle length from season to season. Existence of two groups of Cataclysmic Variables with "smooth" changes from "abruptly changing" observations by smoothing, e.g. by a "Runing Mean". THis phenomenon needs intensive investigation based on complex observations, as well as on theoretical modeling. The detailed study of the temporal behaviour of the individual time intervals showed apparent cyclicity with characteristic time of some years and similar to the solar-like activity (Bianchini, 1990) or may be "alternating" between two distinctly dufferent values (Andronov, Shakun, 1990)

  11. Variational integrators for electric circuits

    SciTech Connect

    Ober-Blöbaum, Sina, E-mail: sinaob@math.upb.de [Computational Dynamics and Optimal Control, University of Paderborn (Germany)] [Computational Dynamics and Optimal Control, University of Paderborn (Germany); Tao, Molei [Courant Institute of Mathematical Sciences, New York University (United States)] [Courant Institute of Mathematical Sciences, New York University (United States); Cheng, Mulin [Applied and Computational Mathematics, California Institute of Technology (United States)] [Applied and Computational Mathematics, California Institute of Technology (United States); Owhadi, Houman; Marsden, Jerrold E. [Control and Dynamical Systems, California Institute of Technology (United States) [Control and Dynamical Systems, California Institute of Technology (United States); Applied and Computational Mathematics, California Institute of Technology (United States)

    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.

  12. RFLP variation in diploid and tetraploid alfalfa.

    PubMed

    Brummer, E C; Kochert, G; Bouton, J H

    1991-11-01

    Alfalfa (Medicago sativa L.) is a major forage crop throughout the world. Although alfalfa has many desirable traits, continued breeding is required to incorporate pest resistances and other traits. We conducted this study to determine the amount of restriction fragment length polymorphism (RFLP) variability present within and between diploid and tetraploid alfalfa populations, and whether or not this variability is sufficient for construction of an RFLP map. Diploid plants from M. sativa ssp. falcata, ssp. coerulea, and ssp. sativa and tetraploid spp. sativa cultivars 'Apollo,' 'Florida 77,' and 'Spredor 2' were included. A total of 19 cDNA clones was probed onto genomic Southern blots containing DNA digested by EcoRI, HindIII, or BamHI. Phylogenetic trees were produced, based on parsimony analysis of shared restriction fragments. Evidence for extensive gene duplication was found; most probes detected complex patterns of restriction fragments. Large amounts of variation are present within all diploid subspecies. M. sativa ssp. falcata plants formed clusters distinct from ssp. sativa or ssp. coerulea plants, which were not distinctly clustered. Some M. sativa ssp. falcata plants were more similar to the other groups than to other plants within ssp. falcata. Variation among tetraploid cultivars showed that Florida 77 and Apollo had more similarities than either showed with Spredor 2. All three cultivars showed large within-population variation, with Apollo being the most diverse and Spredor 2 the least. Based on these results, development of an RFLP map at the diploid level appears possible. Also, differentiation of cultivars, particularly ones of divergent origin, seems possible based on RFLP patterns. PMID:24202261

  13. 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

  14. Precision variational approximations in statistical data assimilation

    NASA Astrophysics Data System (ADS)

    Ye, J.; Kadakia, N.; Rozdeba, P. J.; Abarbanel, H. D. I.; Quinn, J. C.

    2014-10-01

    Data assimilation transfers information from observations of a complex system to physically-based system models with state variables x(t). Typically, the observations are noisy, the model has errors, and the initial state of the model is uncertain, so the data assimilation is statistical. One can thus ask questions about expected values of functions ?G(X)? on the path X = {x(t0), ..., x(tm)} of the model as it moves through an observation window where measurements are made at times {t0, ..., tm}. The probability distribution on the path P(X) = exp[-A0(X)] determines these expected values. Variational methods seeking extrema of the "action" A0(X), widely known as 4DVar (Talagrand and Courtier, 1987; Evensen, 2009),, are widespread for estimating ?G(X) ? in many fields of science. In a path integral formulation of statistical data assimilation, we consider variational approximations in a standard realization of the action where measurement and model errors are Gaussian. We (a) discuss an annealing method for locating the path X0 giving a consistent global minimum of the action A0(X0), (b) consider the explicit role of the number of measurements at each measurement time in determining A0(X0), and (c) identify a parameter regime for the scale of model errors which allows X0 to give a precise estimate of ?G(X0)? with computable, small higher order corrections.

  15. 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,…

  16. Tax Law ComplexityThe Impact of Style

    Microsoft Academic Search

    Bobbie Cook Martindale; Bruce S. Koch; Stewart S. Karlinsky

    1992-01-01

    This study examines the impact of two facets of income tax law complexity-text and content complexity-to determine the effect of variation in style on professional tasks. The research results deal with the effectiveness of standard readability tests for profes sional readers, as well as how our tax laws should be drafted.The study shows that text presentation style magnifies the complexity

  17. Structure and bonding in a cyclobutyl tris(pyrazolyl)boratoniobium complex and the variation in agostic behaviour with ring size in the series Tp(Me2)NbCl(c-C(n)H(2n-1))(MeC[triple bond]CMe), n = 3-6.

    PubMed

    Besora, Maria; Maseras, Feliu; McGrady, John E; Oulié, Pascal; Dinh, Duy Hai; Duhayon, Carine; Etienne, Michel

    2006-05-21

    The synthesis and characterisation of the cyclobutyl complex Tp(Me2)NbCl(c-C4H7)(MeC[triple bond]CMe) completes the family of cycloalkyl complexes Tp(Me2)NbCl(c-C(n)H(2n-1)), n = 3-6. The properties of the cyclobutyl complex are qualitatively similar to those of its cyclopentyl and cyclohexyl analogues, and dramatically different from those of the cyclopropyl derivative. Most conspicuously, the cyclobutyl system has an alpha-C-H agostic interaction in the dominant isomer, with no evidence for the alpha-C-C agostic character found for the smaller ring. C-C agostic character therefore seems to be unique to the cyclopropyl complex, where the acute C-C-C angles destabilise the C-C bonding orbitals. PMID:16688324

  18. Variational Approach to Enhanced Sampling and Free Energy Calculations

    NASA Astrophysics Data System (ADS)

    Valsson, Omar; Parrinello, Michele

    2014-08-01

    The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo simulations, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to alleviate this problem. Many are based on the introduction of a bias potential which is a function of a small number of collective variables. However constructing such a bias is not simple. Here we introduce a functional of the bias potential and an associated variational principle. The bias that minimizes the functional relates in a simple way to the free energy surface. This variational principle can be turned into a practical, efficient, and flexible sampling method. A number of numerical examples are presented which include the determination of a three-dimensional free energy surface. We argue that, beside being numerically advantageous, our variational approach provides a convenient and novel standpoint for looking at the sampling problem.

  19. Variation in Gene Expression Patterns in Human Gastric Cancers

    PubMed Central

    Chen, Xin; Leung, Suet Y.; Yuen, Siu T.; Chu, Kent-Man; Ji, Jiafu; Li, Rui; Chan, Annie S.Y.; Law, Simon; Troyanskaya, Olga G.; Wong, John; So, Samuel; Botstein, David; Brown, Patrick O.

    2003-01-01

    Gastric cancer is the world's second most common cause of cancer death. We analyzed gene expression patterns in 90 primary gastric cancers, 14 metastatic gastric cancers, and 22 nonneoplastic gastric tissues, using cDNA microarrays representing ?30,300 genes. Gastric cancers were distinguished from nonneoplastic gastric tissues by characteristic differences in their gene expression patterns. We found a diversity of gene expression patterns in gastric cancer, reflecting variation in intrinsic properties of tumor and normal cells and variation in the cellular composition of these complex tissues. We identified several genes whose expression levels were significantly correlated with patient survival. The variations in gene expression patterns among cancers in different patients suggest differences in pathogenetic pathways and potential therapeutic strategies. PMID:12925757

  20. Anatomical variations of the carpal tunnel structures

    PubMed Central

    Mitchell, Ryan; Chesney, Amy; Seal, Shane; McKnight, Leslie; Thoma, Achilleas

    2009-01-01

    There are many anatomical variations in and around the carpal tunnel that affect the nerves, tendons and arteries in this area. Awareness of these variations is important both during the clinical examination and during carpal tunnel release. The purpose of the present review is to highlight recognized anatomical variations within the carpal tunnel including variation in nerve anatomy, tendon anatomical variants, vascular anatomical variations and muscle anatomical variations. PMID:20808747

  1. Physical and Chemical Variations Along the Central American Volcanic Arc

    NSDL National Science Digital Library

    Kent Ratajeski

    The Central American volcanic arc displays large arc-parallel variations in chemical composition that yield important clues concerning the complex origin of magmas in subduction zones. In this exercise, students use data compiled for the NSF MARGINS program to compare heights, volumes, and whole-rock compositions of 39 Quaternary volcanic centers along the Central American arc, together with crustal thicknesses, to assess the possible sources of the magmas and the petrologic processes that have modified them prior to eruption.

  2. 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 transmitted into the inclusions during magma flow. We suggest that this represents a modification of the magma dynamics from Newtonian-like to Bingham-like behaviour. Furthermore, the spatial restriction of inclusions within the sheet intrusions suggest that subtle variations in magma rheology may partition apparently continuous intrusions, perhaps affecting lateral mixing and the longevity of discrete sheet segments. Detailed fabric analysis of other inclusion-free intrusions in the Ardnamurchan Central Complex supports this interpretation. Our results highlight that the crystalline cargo of a magma can result in temporal and spatial variations in magma rheology. This can partition coalesced magma bodies into ';zones' characterised by different magma properties, potentially affecting the location of magma flow pathways or even eruption sites.

  3. Implementing variation risk management during product development

    E-print Network

    Padgalskas, Nicholas (Nicholas Keith)

    2007-01-01

    All manufactured systems exhibit some degree of variation. Manufacturing organizations should be aware of those parameters whose variation will impact product performance and customer satisfaction. Such parameters are ...

  4. Molecular complexes of iodine with metal acetylacetonates

    NASA Astrophysics Data System (ADS)

    Kulevsky, Norman; Butamina, Kabuika Ngoy

    The ability of metal acetylacetonates to act as electron donors and form molecular complexes with I 2 was studied by examining the electronic, vibrational, and NMR spectra of the complexes. The specific compounds used in the study were Al(acac) 3 Sc(acac) 3 Zr(acac) 4, and Th(acac) 4. The electronic spectra of mixtures of the metal acetylacetonates with I 2 in CHCl 3 had, in addition to the absorption peaks characteristic of the free components, two peaks that were due to the charge transfer complexes. For each complex, the highest wavelength peak (near 360 nm) was assigned to the blue shifted I 2 band, while the lower peak (between 270 nm and 305 nm) was attributed to the intermolecular charge transfer. In the i.r. spectra of each complex, the major effect of complexation was to cause the I 2 stretching frequency to appear between 145 cm -1 and 160 cm -1. The positions of the absorption peaks in both the electronic and vibrational spectra led to the conclusion that in these complexes, I 2 had received a large amount of charge from the donors. Complex formation had little effect on the NMR spectra of the donors. Association constants of 1:1 complexes were determined from the concentration dependence of the absorbance of the blue shifted I 2 bands. Values of ? Hdg and ? S° 298 for the complex formation were obtained from the temperature variation of the association constants. The data indicate that the complexes are extremely stable species. Both the stability of the complexes and the high degree of charge transfer were rationalized by considering a model for the intermolecular interactions that involved two M(acac) rings simultaneously transferring charge from one donor to an I 2 molecule.

  5. Sources of floral scent variation

    PubMed Central

    Raguso, Robert A; Ashman, Tia-Lynn

    2009-01-01

    Studies of floral scent generally assume that genetic adaptation due to pollinator-mediated natural selection explains a significant amount of phenotypic variance, ignoring the potential for phenotypic plasticity in this trait. In this paper, we assess this latter possibility, looking first at previous studies of floral scent variation in relation to abiotic environmental factors. We then present data from our own research that suggests among-population floral scent variation is determined, in part, by environmental conditions and thus displays phenotypic plasticity. Such an outcome has strong ramifications for the study of floral scent variation; we conclude by presenting some fundamental questions that should lead to greater insight into our understanding of the evolution of this trait, which is important to plant-animal interactions. PMID:19649189

  6. Rapid loss of MHC class II variation in a bottlenecked population is explained by drift and loss of copy number variation.

    PubMed

    Eimes, J A; Bollmer, J L; Whittingham, L A; Johnson, J A; VAN Oosterhout, C; Dunn, P O

    2011-09-01

    Population bottlenecks may reduce genetic variation and potentially increase the risk of extinction. Here, we present the first study to use historic samples to analyse loss of variation at the major histocompatibility complex (MHC), which plays a central role in vertebrate disease resistance. Balancing selection acts on the MHC and could moderate the loss of variation expected from drift; however, in a Wisconsin population of greater prairie-chickens (Tympanuchus cupido), the number of MHC class II B alleles per individual declined by 44% following a population bottleneck, compared to a loss of only 8% at microsatellites. Simulations indicate that drift likely reduced MHC variation at the population level, as well as within individuals by reducing the number of gene copies per individual or by fixing the same alleles across multiple loci. These multiple effects of genetic drift on MHC variation could have important implications for immunity and fitness. PMID:21605219

  7. Variations in Human Skin Color

    NSDL National Science Digital Library

    American Association for the Advancement of Science (; )

    2006-09-09

    In this lesson, the students examine their skin types, similarities, differences, etc. and discuss the social implications of each group. They also examine the factors that influence variations in skin color in greater depth. The class is separated into groups and work on presentations, designed to foster peer-teaching with guidance from the instructor. The presentations to be worked on by the students are: Modern Human Variation: Overview, Skin Color Adaptation, and A new Light on Skin Color. All of the resources needed for the students presentations are included. Following each presentation, tips for review and discussion of the learning objectives are given.

  8. Strategies to reduce variation in the use of surgery.

    PubMed

    McCulloch, Peter; Nagendran, Myura; Campbell, W Bruce; Price, Andrew; Jani, Anant; Birkmeyer, John D; Gray, Muir

    2013-09-28

    Provision rates for surgery vary widely in relation to identifiable need, suggesting that reduction of this variation might be appropriate. The definition of unwarranted variation is difficult because the boundaries of acceptable practice are wide, and information about patient preference is lacking. Very little direct research evidence exists on the modification of variations in surgery rates, so inferences must be drawn from research on the alteration of overall rates. The available evidence has large gaps, which suggests that some proposed strategies produce only marginal change. Micro-level interventions target decision making that affects individuals, whereas macro-level interventions target health-care systems with the use of financial, regulatory, or incentivisation strategies. Financial and regulatory changes can have major effects on provision rates, but these effects are often complex and can include unintended adverse effects. The net effects of micro-level strategies (such as improvement of evidence and dissemination of evidence, and support for shared decision making) can be smaller, but better directed. Further research is needed to identify what level of variation in surgery rates is appropriate in a specific context, and how variation can be reduced where desirable. PMID:24075053

  9. A model for monitoring of Hsp90-buffered genetic variations

    NASA Astrophysics Data System (ADS)

    Kozeko, Liudmyla

    Genetic material of terrestrial organisms can be considerably injured by cosmic rays and UV-radiation in the space environment. Organisms onboard are also exposed to the entire complex of negative physical factors which can generate genetic variations and affect morphogenesis. However, species phenotypes must be robust to genetic variation, requiring "buffering" systems to ensure normal development. The molecular chaperone Hsp90 can serve as such "a buffer". It is important in the maturation and conformational regulation of a diverse set of signal transducers. The requirement of many principal regulatory proteins for Hsp90 renders entire metabolic pathways sensitive to impairment of its function. So inhibition of Hsp90 function can open cryptic genetic variations and produce morphological changes. In this paper, we present a model for monitoring of cryptic Hsp90-buffered genetic variations arising during exposure to space and spaceflight factors. This model has been developed with Arabidopsis thaliana seeds gathered in natural habitats with high anthropogenic pressure and wild type (Col-0) seeds subjected to negative influences (UV, heavy metals) experimentally. The phenotypic traits of early seedlings grown under reduction of Hsp90 activity were characterized to estimate Hsp90-buffered genetic variations. Geldanamycin was used as an inhibitor of Hsp90 function.

  10. Aufbau derived from a unified treatment of occupation numbers in Hartree-Fock, Kohn-Sham, and natural orbital theories with the Karush-Kuhn-Tucker conditions for the inequality constraints n(i)or=0.

    PubMed

    Giesbertz, K J H; Baerends, E J

    2010-05-21

    In the major independent particle models of electronic structure theory-Hartree-Fock, Kohn-Sham (KS), and natural orbital (NO) theories-occupations are constrained to 0 and 1 or to the interval [0,1]. We carry out a constrained optimization of the orbitals and occupation numbers with application of the usual equality constraints summation (i) (infinity) n(i)=N and phi(i)/phi(j)=delta(ij). The occupation number optimization is carried out, allowing for fractional occupations, with the inequality constraints n(i)>or=0 and n(i)

  11. Discrete Morse Complexes

    Microsoft Academic Search

    Manoj K. Chari; Michael Joswig

    2000-01-01

    We investigate properties of the set of discrete Morse functions on a simplicial complex as defined by Forman. It is not difficult to see that the pairings of discrete Morse functions of a finite simplicial complex again form a simplicial complex, the discrete Morse complex. It turns out that several known results from combinatorial topology and enumerative combinatorics, which previously

  12. Spatiotemporal imaging of complexity.

    PubMed

    Robinson, Stephen E; Mandell, Arnold J; Coppola, Richard

    2012-01-01

    What are the functional neuroimaging measurements required for more fully characterizing the events and locations of neocortical activity? A prime assumption has been that modulation of cortical activity will inevitably be reflected in changes in energy utilization (for the most part) changes of glucose and oxygen consumption. Are such a measures complete and sufficient? More direct measures of cortical electrophysiological activity show event or task-related modulation of amplitude or band-limited oscillatory power. Using magnetoencephalography (MEG), these measures have been shown to correlate well with energy utilization sensitive BOLD fMRI. In this paper, we explore the existence of state changes in electrophysiological cortical activity that can occur independently of changes in averaged amplitude, source power or indices of metabolic rates. In addition, we demonstrate that such state changes can be described by applying a new measure of complexity, rank vector entropy (RVE), to source waveform estimates from beamformer-processed MEG. RVE is a non-parametric symbolic dynamic informational entropy measure that accommodates the wide dynamic range of measured brain signals while resolving its temporal variations. By representing the measurements by their rank values, RVE overcomes the problem of defining embedding space partitions without resorting to signal compression. This renders RVE-independent of absolute signal amplitude. In addition, this approach is robust, being relatively free of tunable parameters. We present examples of task-free and task-dependent MEG demonstrating that RVE provides new information by uncovering hidden dynamical structure in the apparent turbulent (or chaotic) dynamics of spontaneous cortical activity. PMID:23355820

  13. Spatiotemporal imaging of complexity

    PubMed Central

    Robinson, Stephen E.; Mandell, Arnold J.; Coppola, Richard

    2013-01-01

    What are the functional neuroimaging measurements required for more fully characterizing the events and locations of neocortical activity? A prime assumption has been that modulation of cortical activity will inevitably be reflected in changes in energy utilization (for the most part) changes of glucose and oxygen consumption. Are such a measures complete and sufficient? More direct measures of cortical electrophysiological activity show event or task-related modulation of amplitude or band-limited oscillatory power. Using magnetoencephalography (MEG), these measures have been shown to correlate well with energy utilization sensitive BOLD fMRI. In this paper, we explore the existence of state changes in electrophysiological cortical activity that can occur independently of changes in averaged amplitude, source power or indices of metabolic rates. In addition, we demonstrate that such state changes can be described by applying a new measure of complexity, rank vector entropy (RVE), to source waveform estimates from beamformer-processed MEG. RVE is a non-parametric symbolic dynamic informational entropy measure that accommodates the wide dynamic range of measured brain signals while resolving its temporal variations. By representing the measurements by their rank values, RVE overcomes the problem of defining embedding space partitions without resorting to signal compression. This renders RVE-independent of absolute signal amplitude. In addition, this approach is robust, being relatively free of tunable parameters. We present examples of task-free and task-dependent MEG demonstrating that RVE provides new information by uncovering hidden dynamical structure in the apparent turbulent (or chaotic) dynamics of spontaneous cortical activity. PMID:23355820

  14. Complexes of clusters and complexes of stars

    E-print Network

    Yu. N. Efremov

    2005-12-12

    Most star complexes are in fact complexes of stars, clusters and gas clouds; term "star complexes" was introduced as general one disregarding the preferential content of a complex. Generally the high rate of star formation in a complex is accompanied by the high number of bound clusters, including massive ones, what was explained by the high gas pressure in such regions. However, there are also complexes, where clusters seems to be more numerous in relation to stars than in a common complex. The high rate of clusters - but not isolated stars - formation seems to be typical for many isolated bursts of star formation, but deficit of stars might be still explained by the observational selection. The latter cannot, however, explain the complexes or the dwarf galaxies, where the high formation rate of only stars is observed. The possibility of the very fast dissolution of parental clusters just in such regions should itself be explained. Some difference in the physical conditions (turbulence parameters ?) within the initial gas supercloud might be a reason for the high or low stars/clusters number ratio in a complex.

  15. Naturally occurring genetic variation in Arabidopsis thaliana

    Microsoft Academic Search

    Maarten Koornneef; Carlos Alonso-Blanco; Dick Vreugdenhil

    2004-01-01

    Currently, genetic variation is probably the most important basic resource for plant biology. In addition to the variation artificially generated by mutants in model plants, naturally occurring genetic variation is extensively found for most species, including Arabidopsis. In many cases, natural variation present among accessions is multigenic, which has historically hampered its analysis. However, the exploitation of this resource down

  16. Mitochondrial DNA Sequence Variation in Saugers

    Microsoft Academic Search

    Matthew M. White

    2012-01-01

    Despite extensive work documenting genetic variation in walleyes Sander vitreus, relatively little is known about the distribution of variation in saugers S. canadensis. Mitochondrial DNA sequence variation was surveyed among samples of saugers to assess the magnitude and distribution of variation among sauger populations. Sequencing of 847 bases of the mitochondrial DNA control region in 60 individuals yielded 19 haplotypes

  17. Variations in Radiocarbon Concentration and Sunspot Activity

    Microsoft Academic Search

    M. Stuiver

    1961-01-01

    Variations in cosmic-ray intensities will produce variations in C 4 production in the atmosphere. A comparison is made between variations in sunspot activity and fluctuations in C 4 concentration during the past 13 centuries. Although a definite conclusion is not reached, the evidence given suggests some correspondence between sunspot activities and Ca concentration in the atmosphere. Variations in radiocarbon production.

  18. Studies of complexity in fluid systems

    SciTech Connect

    Kadanoff, L.P.; Constantin, P.; Dupont, T.F.; Nagel, S.

    1993-02-01

    Objective is to bring together researchers from several disciplines (mathematics, numerical computation, theoretical and experimental physics) who share an interest in the development of complexity in fluid systems. Work is in progress on development of singular interfluid interfaces on several fronts. Striking variations in droplet formation can be observed in physical experiments and simulations based on simple models. High-speed photographs are being taken of small liquid drop breaking into droplets. Experimental studies of granular materials are being continued.

  19. Hyper Space Complex Number

    E-print Network

    Shanguang Tan

    2007-04-23

    A new kind of numbers called Hyper Space Complex Numbers and its algebras are defined and proved. It is with good properties as the classic Complex Numbers, such as expressed in coordinates, triangular and exponent forms and following the associative and commutative laws of addition and multiplication. So the classic Complex Number is developed from in complex plane with two dimensions to in complex space with N dimensions and the number system is enlarged also.

  20. The anisotropic total variation flow

    Microsoft Academic Search

    J. S. Moll

    2005-01-01

    We prove existence and uniqueness of solutions of the Anisotropic Total Variation Flow when the initial data is an L2 function and we give a characterization of such solutions that allows us to find explicit evolutions of sets in the presence of an anisotropy.

  1. VARIATION IN CENTRAL AMERICAN FLICKERS

    Microsoft Academic Search

    LESTER L. SHORT

    HILE investigating hybridization and its effects on flicker populations, I undertook a general study of variation in the two North and Middle American species, Colaptes auratus and C. (Nesoceleus) fernandinae. For reasons presented elsewhere (Short, 1965a) the five major groups of C. auratus, namely the auratus, cafer, chrysoides, chrysocaulosus, and mexi- canoides groups, are considered conspecific. (A vernacular name for

  2. Variational problems on vector bundles

    Microsoft Academic Search

    Jürg Fröhlich; Michael Struwe

    1990-01-01

    A variety of problems in quantum physics and classical statistical mechanics, in particular the quantization of topological solitons and the statistical mechanics of defects in ordered media, are described. These problems can be studied within a semi-classical approximation, or with the help of low-temperature expansions, respectively. The calculation of the leading term in such expansions gives rise to variational problems

  3. 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…

  4. Variational Principles for Water Waves

    E-print Network

    Boris Kolev; David H. Sattinger

    2007-12-01

    We describe the Hamiltonian structures, including the Poisson brackets and Hamiltonians, for free boundary problems for incompressible fluid flows with vorticity. The Hamiltonian structure is used to obtain variational principles for stationary gravity waves both for irrotational flows as well as flows with vorticity.

  5. Cardioidal Variations Francesco De Comite

    E-print Network

    Boyer, Edmond

    -dimensional variations, and finally some artistic applications. One Curve, Two Methods Pedoe [3] describes a method: Mathematics, Music, Art, Architecture, Culture 349 #12;Figure 1 : Pedoe method for cardioid Figure 2 : String the Pedoe method: instead of simply drawing the circles in the same plane as the generative circle, apply

  6. Physiological Integration and Phenotypic Variation

    E-print Network

    Arnold, Jonathan

    Physiological Integration and Phenotypic Variation in Vertebrates Seminar and Roundtable Guest Event Schedule 4:00 - 5:00 p.m. EID Seminar, Q & A Session Ecology Building Auditorium 2:00 - 3:00 p.m. EID Roundtable Discussion: Evolutionary Ecology Meets Immunology Paul D. Coverdell Center Auditorium

  7. Influence of Coronal Abundance Variations

    NASA Technical Reports Server (NTRS)

    DeLuca, E. E.; Gurman, Joseph (Technical Monitor)

    2002-01-01

    The Multispecies loop modeling project addresses the modeling of TRACE and SOHO observations as a plasma rather than a single fluid. In the single-fluid approximation the effects of heavy species are considered in an averaged sense. Further, loop abundances are usually taken to be uniform throughout the loop, in spite of observational evidence for considerable variation in coroner abundances.

  8. Dialect Variation Along the Mura

    E-print Network

    Greenberg, Marc L.

    2006-01-01

    this 7 In the varieties of me?imurski and prekmurski I have encountered, -aj is the normal shape of the LOC PL desinence. j~êÅ=iK=dêÉÉåÄÉêÖ, Dialect variation along… `êç~íK=pä~îK=f~ÇÉêíK=N=EOMMRFI=NMTJNOP NNV= distinction consists of is uncertain...

  9. Protein Complexes in Bacteria

    PubMed Central

    Caufield, J. Harry; Abreu, Marco; Wimble, Christopher; Uetz, Peter

    2015-01-01

    Large-scale analyses of protein complexes have recently become available for Escherichia coli and Mycoplasma pneumoniae, yielding 443 and 116 heteromultimeric soluble protein complexes, respectively. We have coupled the results of these mass spectrometry-characterized protein complexes with the 285 “gold standard” protein complexes identified by EcoCyc. A comparison with databases of gene orthology, conservation, and essentiality identified proteins conserved or lost in complexes of other species. For instance, of 285 “gold standard” protein complexes in E. coli, less than 10% are fully conserved among a set of 7 distantly-related bacterial “model” species. Complex conservation follows one of three models: well-conserved complexes, complexes with a conserved core, and complexes with partial conservation but no conserved core. Expanding the comparison to 894 distinct bacterial genomes illustrates fractional conservation and the limits of co-conservation among components of protein complexes: just 14 out of 285 model protein complexes are perfectly conserved across 95% of the genomes used, yet we predict more than 180 may be partially conserved across at least half of the genomes. No clear relationship between gene essentiality and protein complex conservation is observed, as even poorly conserved complexes contain a significant number of essential proteins. Finally, we identify 183 complexes containing well-conserved components and uncharacterized proteins which will be interesting targets for future experimental studies. PMID:25723151

  10. 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.

  11. Ozonolysis reactions of monoterpenes: a variational transition state investigation.

    PubMed

    Oliveira, R C de M; Bauerfeldt, G F

    2015-03-26

    The O3-initiated oxidation reactions of ?-pinene ([1S,5S]-2,6,6-trimethylbicyclo[3.1.1]hept-2-ene), ?-pinene ([1R,5R]-6,6-dimethyl-2-methylenebicyclo[3.1.1]heptane), camphene ([1R,4S]-2,2-dimethyl-3-methylenebicyclo[2.2.1]heptane) and sabinene ([1R,5R]-4-methylene-1-(1-methylethyl)bicycle[3.1.0]hexane), four monoterpenes typically emitted into the atmosphere, were studied at the B3LYP/6-31+G(2d,2p) level of theory. The rate coefficients were calculated on the basis of the variational transition state theory for two kinetic models, in order to investigate the reaction mechanism: first assuming a direct bimolecular reaction and the second, assuming the formation of a prebarrier-complex, which further reacts forming the corresponding molozonide. The barrier heights leading to the formation of exo-conformers of the molozonides of ?-pinene and camphene are lower than the barrier heights for the formation of the endo-conformers of these molozonides, whereas the inverse trend is observed for ?-pinene and sabinene. The canonical variational rate coefficients are found in reasonable agreement with the experimental data, especially when the prebarrier complexes are considered. Microcanonical variational rate coefficients are also calculated, as a final validation test, being found in an expected agreement with the canonical rate coefficients. The best predictions for the rate coefficients at 298 K, based on the microcanonical variational method, for ?-pinene, ?-pinene, camphene, and sabine are (in units cm(3) molecule(-1) s(-1)): 6.92 × 10(-17), 1.06 × 10(-17), 4.61 × 10(-19), and 4.81 × 10(-17), respectively. Our results suggest that the prebarrier complex is an important specie in the ozone addition mechanism and should be taken into account for the proper description of the overall kinetics. PMID:25734376

  12. High fidelity? How should we consider variations in the delivery of school-based health promotion interventions?

    Microsoft Academic Search

    Jo Holliday; Suzanne Audrey; Laurence Moore; Nina Parry-Langdon; Rona Campbell

    2009-01-01

    Objective The complexity and scale of health promotion interventions present challenges for the standardization of delivery. Furthermore, health promotion practice favours adapting interventions according to perceived client need. This paper examines the fidelity of intervention delivery within A Stop Smoking in Schools Trial (ASSIST), identifying if and why variations occurred, the consequences of these variations for the integrity of the

  13. Microevolution in a philopatric rodent: MHC variation, bottleneck recovery, and fine-scale genetic structure in Dipodomys spectabilis

    Microsoft Academic Search

    Joseph D Busch

    2008-01-01

    In my dissertation, I investigated microevolution in free-living populations of a philopatric rodent, the banner-tailed kangaroo rat (Dipodomys spectabilis). Because individuals reside in permanent mounds and can be trapped repeatedly, D. spectabilis is an excellent model species for inquiries of dispersal and genetic variation. In Chapter 1, I characterized molecular variation among class II loci of the major histocompatibility complex

  14. Beyond Adomian method: The variational iteration method for solving heat-like and wave-like equations with variable coefficients

    Microsoft Academic Search

    Da-Hua Shou; Ji-Huan He

    2008-01-01

    Recently Adomian method was used to solve various kinds of heat-like and wave-like equations. In this Letter, an alternative approach called the variational iteration method is presented to overcome the demerit of complex calculation of Adomian polynomial. Some examples are given to show the reliability and the efficiency of the variational iteration method.

  15. Dispersion in microchannels with temporal temperature variations

    NASA Astrophysics Data System (ADS)

    Tripathi, Anubhav; Bozkurt, Ozgur; Chauhan, Anuj

    2005-10-01

    While amplifying DNA strands in a microfluidic device, the sample is subjected to cyclic changes in temperature. We investigate the dispersion of molecules in a microchannel, as these undergo a contraction-expansion flow that is driven by temporally changing temperatures. In this paper, the method of multiple time scales with regular expansions is used to obtain the effective dispersivity and the analytical results are compared with computational fluid dynamics simulations. Due to the thermal expansion of the carrier fluid, the cyclic temperature variations lead to both axial and lateral velocities. These periodic velocity profiles lead to an increase in axial dispersion. The dispersion coefficient increases as the square of the channel position from the center of the microchannel. Due to the quadratic variation of the dispersion coefficient in the axial direction, the concentration profile is non-Gaussian and a complex function of frequency and magnitude of the temporal oscillations and the dimensions of the microchannel. Analytical expressions for dispersion coefficient are derived for cyclic profiles of any shape; and results are computed and discussed for particular cases of cosine and step-function temperature cycles. The value for effective dispersion is also evaluated for a sample temperature profile that occurs in the microfluidic DNA amplification processes. The dispersion coefficient for step changes in temperature is found to be substantially larger than that for the case of sinusoidal temperature changes at low frequencies. We believe that the results of this study will enhance our understanding of transport in microscale systems that are subjected to temporally changing temperatures, and likely lead to technological advances in diverse areas relevant to microreactor design and DNA amplification.

  16. Mapping complex disease traits with global gene expression

    Microsoft Academic Search

    William Cookson; Liming Liang; Gonçalo Abecasis; Miriam Moffatt; Mark Lathrop

    2009-01-01

    Variation in gene expression is an important mechanism underlying susceptibility to complex disease. The simultaneous genome-wide assay of gene expression and genetic variation allows the mapping of the genetic factors that underpin individual differences in quantitative levels of expression (expression QTLs; eQTLs). The availability of systematically generated eQTL information could provide immediate insight into a biological basis for disease associations

  17. Variation of Parameters in Differential Equations (A Variation in Making Sense of Variation of Parameters)

    ERIC Educational Resources Information Center

    Quinn, Terry; Rai, Sanjay

    2012-01-01

    The method of variation of parameters can be found in most undergraduate textbooks on differential equations. The method leads to solutions of the non-homogeneous equation of the form y = u[subscript 1]y[subscript 1] + u[subscript 2]y[subscript 2], a sum of function products using solutions to the homogeneous equation y[subscript 1] and…

  18. DNA clustering and genome complexity.

    PubMed

    Dios, Francisco; Barturen, Guillermo; Lebrón, Ricardo; Rueda, Antonio; Hackenberg, Michael; Oliver, José L

    2014-12-01

    Early global measures of genome complexity (power spectra, the analysis of fluctuations in DNA walks or compositional segmentation) uncovered a high degree of complexity in eukaryotic genome sequences. The main evolutionary mechanisms leading to increases in genome complexity (i.e. gene duplication and transposon proliferation) can all potentially produce increases in DNA clustering. To quantify such clustering and provide a genome-wide description of the formed clusters, we developed GenomeCluster, an algorithm able to detect clusters of whatever genome element identified by chromosome coordinates. We obtained a detailed description of clusters for ten categories of human genome elements, including functional (genes, exons, introns), regulatory (CpG islands, TFBSs, enhancers), variant (SNPs) and repeat (Alus, LINE1) elements, as well as DNase hypersensitivity sites. For each category, we located their clusters in the human genome, then quantifying cluster length and composition, and estimated the clustering level as the proportion of clustered genome elements. In average, we found a 27% of elements in clusters, although a considerable variation occurs among different categories. Genes form the lowest number of clusters, but these are the longest ones, both in bp and the average number of components, while the shortest clusters are formed by SNPs. Functional and regulatory elements (genes, CpG islands, TFBSs, enhancers) show the highest clustering level, as compared to DNase sites, repeats (Alus, LINE1) or SNPs. Many of the genome elements we analyzed are known to be composed of clusters of low-level entities. In addition, we found here that the clusters generated by GenomeCluster can be in turn clustered into high-level super-clusters. The observation of 'clusters-within-clusters' parallels the 'domains within domains' phenomenon previously detected through global statistical methods in eukaryotic sequences, and reveals a complex human genome landscape dominated by hierarchical clustering. PMID:25182383

  19. Evolution of biological complexity

    PubMed Central

    Adami, Christoph; Ofria, Charles; Collier, Travis C.

    2000-01-01

    To make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition identifies genomic complexity with the amount of information a sequence stores about its environment. We investigate the evolution of genomic complexity in populations of digital organisms and monitor in detail the evolutionary transitions that increase complexity. We show that, because natural selection forces genomes to behave as a natural “Maxwell Demon,” within a fixed environment, genomic complexity is forced to increase. PMID:10781045

  20. Soliton dynamics in complex potentials

    NASA Astrophysics Data System (ADS)

    Kominis, Yannis

    2015-01-01

    Soliton propagation dynamics under the presence of a complex potential are investigated. Cases of both symmetric and non-symmetric potentials are studied in terms of their effect on soliton dynamics. The existence of an invariant of soliton propagation under specific symmetry conditions for the real and the imaginary part of the potential is shown. The rich set of dynamical features of soliton propagation include dynamical trapping, periodic and nonperiodic soliton mass variation and non-reciprocal dynamics. These features are systematically investigated with the utilization of an effective particle phase space approach which is shown in remarkable agreement with direct numerical simulations. The generality of the results enables the consideration of potential applications where the inhomogeneity of the gain and loss is appropriately engineered in order to provide desirable soliton dynamics.

  1. Performance of the Effective Core Potentials of Ca, Hg and Pb in Complexes with Ligands Containing N and O Donor Atoms.

    SciTech Connect

    Ramirez, Jose Z.; Vargas, Rubicelia; Garza, Jorge; Hay, Benjamin P.

    2006-11-01

    This paper presents a systematic study of the performance of the relativistic effective core potentials (RECPs) proposed by Stoll-Preuss, Christiansen-Ermler and Hay-Wadt for Ca2+, Hg2+ and Pb2+. The RECPs performance is studied when these cations are combined with ethylene glycol, 2-aminoethanol and ethylenediamine to form bidentate complexes. First, the description of the bidentate ligands is analyzed with the Kohn-Sham method by using SVWN, BLYP and B3LYP exchange-correlation functionals and they are compared with the Moeller-Plesset perturbation theory (MP2), for all these methods the TZVP basis set was used. We found that the BLYP exchange-correlation functional gives similar results that those obtained by the B3LYP and MP2 methods. Thus, the bidentate metal complexes were studied with the BLYP method combined with the RECPs. In order to compare RECPs performance, all the systems considered in this work were studied with the relativistic all-electron Douglas-Kroll (DK3) method. We observed that the Christiansen-Ermler RECPs give the best energetic and geometrical description for Ca and Hg complexes when compared with the all-electron method. For Pb complexes the spin-orbit interaction and Basis Set Superposition error must be taken into account in the RECP. In general, the trend showed in the complexation energies with the all-electron method is followed by the complexation energies computed with all the pseudopotential tested in this work. Battelle operates PNNL for the USDOE.

  2. Synthesis, Physicochemical Properties, and Antimicrobial Studies of Iron (III) Complexes of Ciprofloxacin, Cloxacillin, and Amoxicillin

    PubMed Central

    Ajali, Uzoechi; Ukoha, Pius O.

    2014-01-01

    Iron (III) complexes of ciprofloxacin, amoxicillin, and cloxacillin were synthesized and their aqueous solubility profiles, relative stabilities, and antimicrobial properties were evaluated. The complexes showed improved aqueous solubility when compared to the corresponding ligands. Relative thermal and acid stabilities were determined spectrophotometrically and the results showed that the complexes have enhanced thermal and acid stabilities when compared to the pure ligands. Antimicrobial studies showed that the complexes have decreased activities against most of the tested microorganisms. Ciprofloxacin complex, however, showed almost the same activity as the corresponding ligand. Job's method of continuous variation suggested 1?:?2 metals to ligand stoichiometry for ciprofloxacin complex but 1?:?1 for cloxacillin complex. PMID:25505991

  3. Using DeltaE metrics for measuring color variation in hard-copy pictorial images

    Microsoft Academic Search

    Susan P. Farnand

    2003-01-01

    Current color difference metrics such as DeltaE*ab, DeltaE*94, and DeltaE00 were developed using uniformly colored patches. The quantification of color variation in pictorial images is far more complex and generally requires the use of sophisticated color appearance models such as CIECAM97s and CIECAM02. In a recent study of printer color variation, the question was raised as to whether, in certain

  4. Temporal variation of heat and moisture flux divergence in the FIFE atmospheric boundary layer during spring

    NASA Technical Reports Server (NTRS)

    Grossman, Robert L.

    1990-01-01

    A one-day investigation of the atmospheric boundary layer (ABL) is reported in which an aircraft monitors the temporal and spatial variations of heat and moisture turbulent-flux divergences. Incoming solar radiation is similar over natural prairie land and agriculturally developed land although the heat and moisture values show significant differences over the surfaces. Other temporal variations are noted which demonstrate that ABL transport of sensible and latent heat is affected by complex variables even under simple synoptic conditions.

  5. Geographic Variation in the Status Signals of Polistes dominulus Paper Wasps

    PubMed Central

    Tibbetts, Elizabeth A.; Skaldina, Oksana; Zhao, Vera; Toth, Amy L.; Skaldin, Maksim; Beani, Laura; Dale, James

    2011-01-01

    Understanding intraspecific geographic variation in animal signals poses a challenging evolutionary problem. Studies addressing geographic variation typically focus on signals used in mate-choice, however, geographic variation in intrasexual signals involved in competition is also known to occur. In Polistes dominulus paper wasps, females have black facial spots that signal dominance: individuals wasps with more complex ‘broken’ facial patterns are better fighters and are avoided by rivals. Recent work suggests there is dramatic geographic variation in these visual signals of quality, though this variation has not been explicitly described or quantified. Here, we analyze variation in P. dominulus signals across six populations and explore how environmental conditions may account for this variation. Overall, we found substantial variation in facial pattern brokenness across populations and castes. Workers have less broken facial patterns than gynes and queens, which have similar facial patterns. Strepsipteran parasitism, body size and temperature are all correlated with the facial pattern variation, suggesting that developmental plasticity likely plays a key role in this variation. First, the extent of parasitism varies across populations and parasitized individuals have lower facial pattern brokenness than unparasitized individuals. Second, there is substantial variation in body size across populations and a weak but significant relationship between facial pattern brokenness and body size. Wasps from populations with smaller body size (e.g. Italy) tend to have less broken facial patterns than wasps from populations with larger body size (e.g. New York, USA). Third, there is an apparent association between facial patterns and climate, with wasp from cooler locations tending to have higher facial pattern brokenness than wasps from warmer locations. Additional experimental work testing the causes and consequences of facial pattern variation will be important, as geographic variation in signals has important consequences for the evolution of communication systems and social behavior. PMID:22174776

  6. Coastal eutrophication and temperature variation

    SciTech Connect

    Ganoulis, J.; Rafailidis, S. [Aristotle Univ. of Thessaloniki (Greece). Civil Engineering Dept.; Bogardi, I. [Univ. of Nebraska, Lincoln, NE (United States). Civil Engineering Dept.; Duckstein, L. [Univ. of Arizona, Tucson, AZ (United States). Systems and Industrial Engineering Dept.; Matyasovszky, I. [Eotvos-Lorand Univ., Budapest (Hungary). Dept. of Meteorology

    1994-12-31

    A 3-D hydroecological model has been developed to simulate the impact of climate-change-induced daily temperature variation on coastal water quality and eutrophication. Historical daily temperature time series over a thirty-year period have been used to link local meteorological variables to large-scale atmospheric circulation patterns (CPs). Then, CPs generated under a 2{times}CO{sub 2} scenario have been used to simulate climate-change-induced local daily temperature variations. Both historical and climate-change-induced temperature time series have been introduced as inputs into the hydroecological model to simulate coastal water quality and eutrophication. Subject to model validation with available data, a case study in the bay of Thessaloniki (N. Greece) indicates a risk of increasing eutrophication and oxygen depletion in coastal areas due to possible climate change.

  7. Variational method with staggered fermions

    NASA Astrophysics Data System (ADS)

    DeTar, Carleton; Lee, Song-Haeng

    2015-02-01

    The variational method is used widely for determining the hadronic spectrum for Wilson and improved Wilson fermions. The method has not been applied to staggered fermions because the hadronic correlation functions in that formalism include terms that oscillate with Euclidean time, and they often include states of both parities. We show that with a simple modification, the variational method can also be applied to staggered fermions. In some cases the method also provides a mechanism for separating the commonly paired parity-partner states. We discuss the extension to staggered fermions and illustrate it by applying it to the calculation of the spectrum of charmed-antistrange mesons consisting of a clover charm quark and a staggered strange antiquark.

  8. A variational principle in optics.

    PubMed

    Rubinstein, Jacob; Wolansky, Gershon

    2004-11-01

    We derive a new variational principle in optics. We first formulate the principle for paraxial waves and then generalize it to arbitrary waves. The new principle, unlike the Fermat principle, concerns both the phase and the intensity of the wave. In particular, the principle provides a method for finding the ray mapping between two surfaces in space from information on the wave's intensity there. We show how to apply the new principle to the problem of phase reconstruction from intensity measurements. PMID:15535374

  9. Sociophonetic variation and the lemma

    Microsoft Academic Search

    Katie K. Drager

    2011-01-01

    This paper reports on lemma-based phonetic variation observed during a year-long sociophonetic ethnography of an all girls' high school in New Zealand. In-depth acoustic analysis was conducted on tokens of the word like from the girls' speech. This is a word with a number of different grammatical functions, such as quotative like (I was LIKE “yeah okay”), discourse particle like

  10. Variational Integrators in Plasma Physics

    E-print Network

    Michael Kraus

    2014-12-05

    Variational integrators are a special kind of geometric discretisation methods applicable to any system of differential equations that obeys a Lagrangian formulation. In this thesis, variational integrators are developed for several important models of plasma physics: guiding centre dynamics (particle dynamics), the Vlasov-Poisson system (kinetic theory), and ideal magnetohydrodynamics (plasma fluid theory). Special attention is given to physical conservation laws like conservation of energy and momentum. Most systems in plasma physics do not possess a Lagrangian formulation to which the variational integrator methodology is directly applicable. Therefore the theory is extended towards nonvariational differential equations by linking it to Ibragimov's theory of integrating factors and adjoint equations. It allows us to find a Lagrangian for all ordinary and partial differential equations and systems thereof. Consequently, the applicability of variational integrators is extended to a much larger family of systems than envisaged in the original theory. This approach allows for the application of Noether's theorem to analyse the conservation properties of the system, both at the continuous and the discrete level. In numerical examples, the conservation properties of the derived schemes are analysed. In case of guiding centre dynamics, momentum in the toroidal direction of a tokamak is preserved exactly. The particle energy exhibits an error, but the absolute value of this error stays constant during the entire simulation. Therefore numerical dissipation is absent. In case of the kinetic theory, the total number of particles, total linear momentum and total energy are preserved exactly, i.e., up to machine accuracy. In case of magnetohydrodynamics, the total energy, cross helicity and the divergence of the magnetic field are preserved up to machine precision.

  11. Mitochondrial DNA sequence variation in single cells from leukemia patients

    PubMed Central

    Yao, Yong-Gang; Ogasawara, Yoji; Kajigaya, Sachiko; Molldrem, Jeffrey J.; Falcão, Roberto P.; Pintão, Maria-Carolina; McCoy, J. Philip; Rizzatti, Edgar Gil; Young, Neal S.

    2007-01-01

    A high frequency of mtDNA somatic mutation has been observed in many tumors as well as in aging tissues. In this study, we analyzed the mtDNA control region sequence variation in 3534 single normal cells and individual blasts from 18 patients with leukemia and 10 healthy donors, to address the mutation process in leukemic cells. We found significant differences in mtDNA sequence, as represented by the number of haplotypes and the mean number of cells with each nonaggregate haplotype in a population of cells, in patients compared to controls. Patients with similar clinical leukemia types, particularly acute myeloid leukemia (AML), did not show a uniform pattern of sequence variation in single blasts. Some patients at relapse presented a complex shift of major haplotypes in single cells. Four patients showed high frequencies of cells containing mutations 189, 260, 16150, and 16488, respectively, as a result of clonal expansion and could be considered as potential markers for their respective disease progression. To our knowledge, this is the first large-scale study of mtDNA variation in single malignant cells. Our results suggest that the somatic mutation process in leukemia is complex, leading to diverse levels of genetic alterations due to either intrinsic aspects of leukemia pathophysiology or chemotherapy effects. PMID:16946307

  12. The plume variation at Enceladus

    NASA Astrophysics Data System (ADS)

    Jia, Ying-Dong; Russell, Christopher; Khurana, Krishan

    2014-05-01

    It has been nine years since the discovery of the Enceladus plume, while its variation within this time is still under debate. A recent study has proposed that the vent intensity depends on the moon-Saturn distance. In our study we use a different data set to investigate this variation, and also check its co-relationship with other orbital characters. Between 2005 and 2012, Cassini has made 20 close flybys around Enceladus. Its plasma instrument has recorded the ambient magnetospheric plasma density, while its magnetometers have recorded the change in magnetic field by particle pickup. Unlike particle detectors that measure the in situ density along the path, or imagers that measure the vent temperature, the magnetometer measures the magnetic field, which provides the total momentum exchange in the whole interaction region. We use the magnetometer data and ambient plasma data along these 20 flybys, assisted with our MHD model, to determine the time variation of the total plume ejecta during these 8 years.

  13. Longitudinal Variations in Jupiter's Winds

    NASA Technical Reports Server (NTRS)

    Simon-Miller, Amy A.; Gierasch, P. J.; Tierney, G.

    2010-01-01

    Long-term studies of Jupiter's zonal wind field revealed temporal variations on the order of 20 to 40 m/s at many latitudes, greater than the typical data uncertainties of 1 to 10 m/s. No definitive periodicities were evident, however, though some latitudinally-confined signals did appear at periods relevant to the Quasi- Quadrennial Oscillation (Simon-Miller & Gierasch, Icarus, in press). As the QQO appears, from vertical temperature profiles, to propagate downward, it is unclear why a signal is not more obvious, unless other processes dominate over possibly weaker forcing from the QQO. An additional complication is that zonal wind profiles represent an average over some particular set of longitudes for an image pair and most data sets do not offer global wind coverage. Lien avoiding known features, such as the large anticyclonic vortices especially prevalent in the south, there can be distinct variations in longitude. We present results on the full wind field from Voyager and Cassini data, showing apparent longitudinal variations of up to 60 m/s or more. These are particularly obvious near disruptions such as the South Equatorial Disturbance, even when the feature itself is not clearly visible. These two dates represent very different states of the planet for comparison: Voyagers 1 & 2 flew by Jupiter shortly after a global upheaval, while many regions were in a disturbed state, while the Cassini view is typical of a more quiescent period present during much of the 1990s and early 2000s.

  14. Copy number variations among silkworms

    PubMed Central

    2014-01-01

    Background Copy number variations (CNVs), which are important source for genetic and phenotypic variation, have been shown to be associated with disease as well as important QTLs, especially in domesticated animals. However, little is known about the CNVs in silkworm. Results In this study, we have constructed the first CNVs map based on genome-wide analysis of CNVs in domesticated silkworm. Using next-generation sequencing as well as quantitative PCR (qPCR), we identified ~319 CNVs in total and almost half of them (~ 49%) were distributed on uncharacterized chromosome. The CNVs covered 10.8 Mb, which is about 2.3% of the entire silkworm genome. Furthermore, approximately 61% of CNVs directly overlapped with SDs in silkworm. The genes in CNVs are mainly related to reproduction, immunity, detoxification and signal recognition, which is consistent with the observations in mammals. Conclusions An initial CNVs map for silkworm has been described in this study. And this map provides new information for genetic variations in silkworm. Furthermore, the silkworm CNVs may play important roles in reproduction, immunity, detoxification and signal recognition. This study provided insight into the evolution of the silkworm genome and an invaluable resource for insect genomics research. PMID:24684762

  15. Intraspecific variation in Cryptocaryon irritans.

    PubMed

    Diggles, B K; Adlard, R D

    1997-01-01

    Intraspecific variation in the ciliate Cryptocaryon irritans was examined using sequences of the first internal transcribed spacer region (ITS-1) of ribosomal DNA (rDNA) combined with developmental and morphological characters. Amplified rDNA sequences consisting of 151 bases of the flanking 18 S and 5.8 S regions, and the entire ITS-1 region (169 or 170 bases), were determined and compared for 16 isolates of C. irritans from Australia, Israel and the USA. There was one variable base between isolates in the 18 S region and 11 variable bases in the ITS-1 region. Despite their similar morphology, significant sequence variation (4.1% divergence) and developmental differences indicate that Australian C. irritans isolates from estuarine (Moreton Bay) and coral reef (Heron Island) environments are distinct. The Heron Island isolate was genetically closer to morphologically dissimilar isolates from Israel (1.8% divergence) and the USA (2.3% divergence) than it was to the Moreton Bay isolates. Three isolates maintained in our laboratory since February 1994 differed in sequence from earlier laboratory isolates (2.9% to 3.5% divergence), even though all were similar morphologically and originated from the same source. During this time the sequence of the isolates from wild fish in Moreton Bay remained unchanged. These genetic differences indicate the existence of a founder effect in laboratory populations of C. irritans. The genetic variation found here, combined with known morphological and developmental differences, is used to characterise four strains of C. irritans. PMID:9172830

  16. Variational principles for circle patterns

    NASA Astrophysics Data System (ADS)

    Springborn, Boris A.

    2003-12-01

    A Delaunay cell decomposition of a surface with constant curvature gives rise to a circle pattern, consisting of the circles which are circumscribed to the facets. We treat the problem whether there exists a Delaunay cell decomposition for a given (topological) cell decomposition and given intersection angles of the circles, whether it is unique and how it may be constructed. Somewhat more generally, we allow cone-like singularities in the centers and intersection points of the circles. We prove existence and uniqueness theorems for the solution of the circle pattern problem using a variational principle. The functionals (one for the euclidean, one for the hyperbolic case) are convex functions of the radii of the circles. The analogous functional for the spherical case is not convex, hence this case is treated by stereographic projection to the plane. From the existence and uniqueness of circle patterns in the sphere, we derive a strengthened version of Steinitz' theorem on the geometric realizability of abstract polyhedra. We derive the variational principles of Colin de Verdière, Brägger, and Rivin for circle packings and circle patterns from our variational principles. In the case of Brägger's and Rivin's functionals. Leibon's functional for hyperbolic circle patterns cannot be derived directly from our functionals. But we construct yet another functional from which both Leibon's and our functionals can be derived. We present Java software to compute and visualize circle patterns.

  17. Genetics of complex traits in psychiatry.

    PubMed

    Gelernter, Joel

    2015-01-01

    Virtually all psychiatric traits are genetically complex. This article discusses the genetics of complex traits in psychiatry. The complexity is accounted for by numerous factors, including multiple risk alleles, epistasis, and epigenetic effects such as methylation. Risk alleles can individually be common or rare, and can include, for example, single nucleotide polymorphisms and copy number variants that are transmitted or are new mutations, and other kinds of variation. Many different kinds of variation can be important for trait risk, either together in various proportions or as different factors in different subjects. Until more recently, approaches to complex traits were limited, and consequently only a few variants, usually of individually minor effect, were identified. At the present time, a much richer armamentarium exists that includes the routine application of genome-wide association studies and next-generation high-throughput sequencing and the combination of this information with other biologically relevant information, such as expression data. We have also seen the emergence of large meta-analysis and mega-analysis consortia. These developments are extremely important for psychiatric genetics, have advanced the field substantially, and promise formidable gains in the years to come as they are applied more widely. PMID:25444161

  18. A transcriptional network associated with natural variation in Drosophila aggressive behavior

    PubMed Central

    Edwards, Alexis C; Ayroles, Julien F; Stone, Eric A; Carbone, Mary Anna; Lyman, Richard F; Mackay, Trudy FC

    2009-01-01

    Background Aggressive behavior is an important component of fitness in most animals. Aggressive behavior is genetically complex, with natural variation attributable to multiple segregating loci with allelic effects that are sensitive to the physical and social environment. However, we know little about the genes and genetic networks affecting natural variation in aggressive behavior. Populations of Drosophila melanogaster harbor quantitative genetic variation in aggressive behavior, providing an excellent model system for dissecting the genetic basis of naturally occurring variation in aggression. Results Correlating variation in transcript abundance with variation in complex trait phenotypes is a rapid method for identifying candidate genes. We quantified aggressive behavior in 40 wild-derived inbred lines of D. melanogaster and performed a genome-wide association screen for quantitative trait transcripts and single feature polymorphisms affecting aggression. We identified 266 novel candidate genes associated with aggressive behavior, many of which have pleiotropic effects on metabolism, development, and/or other behavioral traits. We performed behavioral tests of mutations in 12 of these candidate genes, and show that nine indeed affected aggressive behavior. We used the genetic correlations among the quantitative trait transcripts to derive a transcriptional genetic network associated with natural variation in aggressive behavior. The network consists of nine modules of correlated transcripts that are enriched for genes affecting common functions, tissue-specific expression patterns, and/or DNA sequence motifs. Conclusions Correlations among genetically variable transcripts that are associated with genetic variation in organismal behavior establish a foundation for understanding natural variation for complex behaviors in terms of networks of interacting genes. PMID:19607677

  19. Extended Scaling Factors for Estimating Solar UV Variations

    NASA Astrophysics Data System (ADS)

    DeLand, M. T.; Tiruchirapalli, R. A.

    2011-12-01

    Accurate characterization of solar ultraviolet (UV) irradiance variations is important for understanding solar behavior and for proper forcing of terrestrial atmospheric models. Determining long-term irradiance variations from satellite measurements is challenging because of the complex effects of instrument response changes and the limited lifetime of any single instrument. An alternative method of tracking long-term solar UV variations is to observe a proxy index of UV activity, and parameterize its variations to represent spectral irradiance changes. Examples of this approach using the Mg II core-to-wing ratio solar activity proxy and solar rotational irradiance variations have been developed for mid-UV wavelengths (170-300 nm) using Nimbus-7 SBUV, NOAA-9 SBUV/2, and NOAA-11 SBUV/2 irradiance data, and for far-UV wavelengths (120-180 nm) using UARS SOLSTICE irradiance data. Each of these results gives predicted long-term irradiance changes in good agreement with independent observations. However, current scaling factors are only based on data from a portion of a single solar cycle. If the scaling between proxy index variations and solar UV irradiance changes with solar cycle phase or overall activity, then the usefulness of these approaches is reduced. Numerous additional data sets (UARS SUSIM; NOAA-16, NOAA-17, NOAA-18 SBUV/2; SORCE SOLSTICE, SORCE SIM) are now available to supplement the original scaling factor studies. These measurements cover all activity phases for multiple solar cycles, and the overlapping data sets provide many opportunities for validation. We will present comparisons of these new scale factor values with previous results.

  20. Variation in reptilian brains and cognition.

    PubMed

    Northcutt, R Glenn

    2013-01-01

    The class Reptilia is monophyletic, if all synapsid tetrapods are excluded and birds are included. The phylogenetic position of turtles within the reptilian clade is still problematic, but recent microRNA data suggest that turtles are the sister group to lepidosaurians. Brain-body data for approximately 60 reptilian taxa indicate that the relative brain size for a given body weight varies some six-fold among reptiles, with some turtles and lizards having relatively large brains and other turtles and lizards having relatively small brains. Snakes appear to be characterized by relatively small brains, and crocodilians appear to possess the largest brains among living reptiles, with the exception of birds. Data on the relative size of major brain divisions among tetrapods are limited, but the telencephalic and cerebellar hemispheres account for much of the variation. Telencephalic hemispheres in reptiles are approximately twice as large as those in amphibians, and the relative size of the telencephalic hemispheres in monitor lizards and crocodilians approaches that in basal birds and mammals. New data on the relative volumes of telencephalic pallial divisions in tetrapods reveal that the dorsal ventricular ridge, a ventral pallial derivative, accounts for much of the increase in pallial size that characterizes reptiles. Studies of spatial and visual cognition in nonavian reptiles reveal that they learn mazes and make visual discriminations as rapidly as most birds and mammals. Studies of social cognition and novel behavior, including play, reveal levels of complexity not previously believed to exist among nonavian reptiles. Given this level of neural and cognitive complexity, it is possible that consciousness has evolved numerous times, independently, among reptiles. PMID:23979455