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Sample records for complex kohn variational

  1. Complex-Kohn Approach to Molecular Ionization by High-Energy Electrons: Application to H2, H2O and CH4

    NASA Astrophysics Data System (ADS)

    Lin, Chih-Yuan; McCurdy, C. W.; Rescigno, T. N.

    2014-05-01

    The complex Kohn variational method, which has been extensively applied to low-energy molecule scattering, is extended to treat molecular ionization by fast electrons under the assumption that the incident and scattered electrons can be described by plane-waves. In contrast to other perturbative approches, the interaction between the slow ejected electron and the residual molecular ion is treated by a close-coupling method and for that we employ the complex Kohn variational method. The formulation reduces to the computation of the continuum generalized oscillation strength, which amounts to a generalization of the molecular photoionization problem to which the Kohn method has been successfully applied. The essential point is that the use of a correct electron-ion scattering wave function as the final state for the ejected electron enables us to treat high-energy electron impact ionization of molecules at the same level of sophistication achieved for atomic targets. We will present fully differential cross sections for ionization of water and methane, as well as for excitation/ionization of H2, along with comparisons to available experimental data. Work performed under the auspices of the US DOE by the LBNL and supported by the U.S. DOE Office of Basic Energy Sciences, Division of Chemical Sciences.

  2. 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,

  3. 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…

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

    PubMed

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

    2012-10-28

    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)]. The performance of SAPT(UKS) and SAPT(UHF) is tested for the following open-shell van der Waals complexes: HeNH, H(2)OHO(2), HeOH, ArOH, ArNO. 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 (HeOH, ArOH, ArNO). In the interactions of transition metal dimers ((3)?(u)(+))Au(2) and ((13)?(g)(+))Cr(2) 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. PMID:23126692

  5. 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.

  6. Pores of Kohn

    PubMed Central

    Cordingley, J. L.

    1972-01-01

    The history of the investigations into interalveolar communications (pores of Kohn) shows that the question whether they exist and, if so, their nature has for approximately a century been contentious. The present electron microscopic study of the lungs of mice demonstrates that alveolar pores are normal structures, with edges composed of intact alveolar wall. A number of planes are demonstrated from which a fully compatible reconstruction is made. It is concluded that pores are round or oval structures frequently having at least one type II alveolar cell forming part of their boundary. It is further postulated that pores may be divided by a capillary column stretching across the space, resulting in two openings. A type II alveolar cell forming part of the pore wall may straddle the capillary column. Alveolar macrophages may be found lying free in the pore or lying astride a capillary column. When lying in a corner position type II cells may occupy the full wall thickness and face into three alveoli. Images PMID:5075613

  7. Meet Alfie Kohn. Part Two.

    ERIC Educational Resources Information Center

    Swan, Deborah

    1997-01-01

    An interview with educator-author Alfie Kohn discusses student motivation and the need to move away from giving rewards, praise as a form of control, the importance of genuine encouragement that fosters intrinsic motivation and lifelong learning, and the role of mentors in supporting teachers who seek to change or improve traditional teaching…

  8. Defeating the pores of Kohn.

    PubMed

    Ng, Calvin S H; Lau, Rainbow W H; Lau, Kelvin K W; Underwood, Malcolm J; Yim, Anthony P C

    2014-01-01

    In the treatment of emphysema with an endobronchial valve, entire lobar treatment is important in achieving adequate atelectasis. This case illustrates that without treatment of the entire lobe, it can fail to collapse even after several years, leading to treatment failure. Intralobar collateral ventilation through the pores of Kohn is demonstrated in this case, as endobronchial valve blockage of the remaining patent anterior segment resulted in the desired atelectasis and significant improvements in pulmonary function. PMID:24585656

  9. Talks with Teachers: Clyde F. Kohn.

    ERIC Educational Resources Information Center

    Souza, Anthony R. de

    1984-01-01

    Kohn--a geographer who has taught at all educational levels and is a former president of the National Council for Geographic Education and the American Association of Geographers--talks about his family and schooling, cooperation between professional organizations, his role in the High School Geography Project, and his interest in enology. (RM)

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

    NASA Astrophysics Data System (ADS)

    Motamarri, Phani; Gavini, Vikram; Blesgen, Thomas

    2016-03-01

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

  11. Coherent cyclotron motion beyond Kohn's theorem

    NASA Astrophysics Data System (ADS)

    Maag, T.; Bayer, A.; Baierl, S.; Hohenleutner, M.; Korn, T.; Schüller, C.; Schuh, D.; Bougeard, D.; Lange, C.; Huber, R.; Mootz, M.; Sipe, J. E.; Koch, S. W.; Kira, M.

    2016-02-01

    In solids, the high density of charged particles makes many-body interactions a pervasive principle governing optics and electronics. However, Walter Kohn found in 1961 that the cyclotron resonance of Landau-quantized electrons is independent of the seemingly inescapable Coulomb interaction between electrons. Although this surprising theorem has been exploited in sophisticated quantum phenomena, such as ultrastrong light-matter coupling, superradiance and coherent control, the complete absence of nonlinearities excludes many intriguing possibilities, such as quantum-logic protocols. Here, we use intense terahertz pulses to drive the cyclotron response of a two-dimensional electron gas beyond the protective limits of Kohn's theorem. Anharmonic Landau ladder climbing and distinct terahertz four- and six-wave mixing signatures occur, which our theory links to dynamic Coulomb effects between electrons and the positively charged ion background. This new context for Kohn's theorem unveils previously inaccessible internal degrees of freedom of Landau electrons, opening up new realms of ultrafast quantum control for electrons.

  12. Variational, Self-Consistent Implementation of the Perdew-Zunger Self-Interaction Correction with Complex Optimal Orbitals.

    PubMed

    Lehtola, Susi; Jónsson, Hannes

    2014-12-01

    A variational, self-consistent implementation of the Perdew-Zunger self-interaction correction (PZ-SIC), based on a unified Hamiltonian and complex optimal orbitals, is presented for finite systems and atom-centered basis sets. A simplifying approximation allowing the use of real canonical orbitals is proposed. The algorithm is based on two-step self-consistent field iterations, where the updates of the canonical orbitals and the optimal orbitals are done separately. Calculations of the energy of atoms ranging from H to Ar are presented, using various generalized gradient functionals (PBE, APBE, PBEsol) and a meta-generalized gradient functional (TPSS). While the energy of atoms is poorly described by PBEsol, which is a functional optimized to reproduce properties of solids, the PZ-SIC brings the calculations into good agreement with the best ab initio estimates. The importance of using complex optimal orbitals becomes particularly clear in calculations using the TPSS functional, where the original functional gives good results while the application of PZ-SIC with real orbitals gives highly inaccurate results. With complex optimal orbitals, PZ-SIC slightly improves the accuracy of the TPSS functional. The charge localization problem that plagues Kohn-Sham DFT functionals, including hybrid functionals, is illustrated by calculations on the CH3 + F(-) complex, where even PBEsol with PZ-SIC is found to give estimates of both energy and charge with accuracy comparable to that of coupled cluster calculations. PMID:26583216

  13. Galling aphids: specialization, biological complexity, and variation.

    PubMed

    Wool, David

    2004-01-01

    Gall-inducing aphids are host specific in the gall stage. Most species alternate between trees (the primary host), where the gall is induced, and shrubs and grasses (secondary hosts). Parthenogenesis during most of their life cycle is interrupted by a single stage of sexual reproduction on the primary host. Apart from these general characteristics, galling aphids present some of the most complex and diverse life histories in the insect world. In this article I review the specialized characteristics of galling aphids, as well as their complex and diverse life histories, as reported in the past 20 years. PMID:14651461

  14. On the Kohn-Luttinger conundrum

    NASA Astrophysics Data System (ADS)

    Hirata, So; He, Xiao

    2013-05-01

    Kohn and Luttinger [Phys. Rev. 118, 41 (1960)], 10.1103/PhysRev.118.41 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.

  15. On the Kohn-Luttinger conundrum

    SciTech Connect

    Hirata, So; He Xiao

    2013-05-28

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

  16. Explaining additional genetic variation in complex traits.

    PubMed

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

    2014-04-01

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

  17. Explaining additional genetic variation in complex traits

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    Pan, Xiao-Yin; Sahni, Viraht

    2015-11-01

    The Hohenberg-Kohn (HK) theorems of bijectivity between the external scalar potential and the gauge invariant nondegenerate ground state density, and the consequent Euler variational principle for the density, are proved for arbitrary electrostatic field and the constraint of fixed electron number. The HK theorems are generalized for spinless electrons to the added presence of an external uniform magnetostatic field by introducing the new constraint of fixed canonical orbital angular momentum. Thereby, a bijective relationship between the external scalar and vector potentials, and the gauge invariant nondegenerate ground state density and physical current density, is proved. A corresponding Euler variational principle in terms of these densities is also developed. These theorems are further generalized to electrons with spin by imposing the added constraint of fixed canonical orbital and spin angular momenta. The proofs differ from the original HK proof and explicitly account for the many-to-one relationship between the potentials and the nondegenerate ground state wave function. A Percus-Levy-Lieb constrained-search proof expanding the domain of validity to N-representable functions, and to degenerate states, again for fixed electron number and angular momentum, is also provided. PMID:26547156

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

    SciTech Connect

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

    2011-10-15

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

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

    SciTech Connect

    Hinckley, C.M.; Barkan, P.

    1994-03-01

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

  1. 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

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

    SciTech Connect

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

    2011-05-15

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

  3. A complex Noether approach for variational partial differential equations

    NASA Astrophysics Data System (ADS)

    Naz, R.; Mahomed, F. M.

    2015-10-01

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

  4. Kohn-Sham potentials for fullerenes and spherical molecules

    SciTech Connect

    Pavlyukh, Y.; Berakdar, J.

    2010-04-15

    We present a procedure for the construction of accurate Kohn-Sham potentials of quasispherical molecules starting from the first-principles valence densities. The method is demonstrated for the case of icosahedral C{sub 20}{sup 2+} and C{sub 60} molecules. Provided the density is N representable the Hohenberg-Kohn theorem guarantees the uniqueness of the obtained potentials. The potential is iteratively built following the suggestion of R. van Leeuwen and E. J. Baerends [Phys. Rev. A 49, 2421 (1994)]. The high symmetry of the molecules allows a parametrization of the angular dependence of the densities and the potentials using a small number of symmetry-adapted spherical harmonics. The radial behavior of these quantities is represented on a grid and the density is reconstructed from the approximate potential by numerically solving the coupled-channel Kohn-Sham equations. Subsequently, the potential is updated and the procedure is continued until convergence is achieved.

  5. Decay of the Kohn mode in hydrodynamic regime

    NASA Astrophysics Data System (ADS)

    Iqbal, A.; Levchenko, A.; Khodas, M.

    2015-07-01

    We develop a hydrodynamic description of the collective modes of interacting liquids in a quasi-one-dimensional confining potential. By solving Navier-Stokes equation we determine analytically the excitation spectrum of sloshing oscillations. For parabolic confinement, the lowest frequency eigenmode is not renormalized by interactions and is protected from decay by the Kohn theorem, which states that center of mass motion decouples from internal dynamics. We find that the combined effect of potential anharmonicity and interactions results in a frequency shift and final lifetime of the Kohn mode. All other excited modes of sloshing oscillations thermalize with the parametrically faster rate. Our results are significant for the interpretation of recent experiments with trapped Fermi gases that observed a weak violation of the Kohn theorem.

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

    SciTech Connect

    Yang Zenghui; Burke, Kieron; Faassen, Meta van

    2009-09-21

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

  7. Individual variation in the late positive complex to semantic anomalies.

    PubMed

    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

  8. Morphological Variation in Leaf Dissection of Rheum palmatum Complex (Polygonaceae)

    PubMed Central

    Wang, Xu-Mei; Hou, Xiao-Qi; Zhang, Yu-Qu; Li, Yan

    2014-01-01

    Aims Rheum palmatum complex comprises all taxa within section Palmata in the genus Rheum, including R. officinale, R. palmatum, R. tanguticum, R. tanguticum var. liupanshanense and R. laciniatum. The identification of the taxa in section Palmata is based primarily on the degree of leaf blade dissection and the shape of the lobes; however, difficulties in species identification may arise from their significant variation. The aim of this study is to analyze the patterns of variation in leaf blade characteristics within and among populations through population-based sampling covering the entire distribution range of R. palmatum complex. Methods Samples were taken from 2340 leaves from 780 individuals and 44 populations representing the four species, and the degree of leaf blade dissection and the shape of the lobe were measured to yield a set of quantitative data. Furthermore, those data were statistically analyzed. Important Findings The statistical analysis showed that the degree of leaf blade dissection is continuous from lobed to parted, and the shape of the lobe is also continuous from broadly triangular to lanceolate both within and between populations. We suggested that taxa in section Palmata should be considered as one species. Based on the research on the R. palmatum complex, we considered that the quantitative characteristics were greatly influenced by the environment. Therefore, it is not reliable to delimitate the species according to the continuously quantitative vegetative characteristics. PMID:25349989

  9. Kohn-Sham Density Functional Theory and Strong Electron Correlation

    NASA Astrophysics Data System (ADS)

    Wagner, Lucas O.

    In this thesis I study the exact functional within Kohn--Sham density functional theory, and discuss its role in developing approximations and understanding their failures. In the first part, I give an overview of both the ground-state formulation of density functional theory as well as the time-dependent version. I discuss various approximations and their deficiencies in light of departures from properties of the exact functional. In the second part of the thesis, I use the density matrix renormalization group, with its ability to obtain essentially exact wavefunctions, to study strong correlation in Kohn--Sham density functional theory. Using this powerful wavefunction solver, I set up a one-dimensional model chemistry and solid-state lab. There I discover that simple one-dimensional analogs reproduce (even quantitatively) the strong correlation behavior of three-dimensional systems, like stretched H2 . This allows me to verify properties such as the exact Kohn--Sham band gap for certain extended systems. I enable calculations with the exact functional in Kohn--Sham density functional theory, and demonstrate for stretched H2 that there is no "symmetry dilemma" for the exact functional, as there are for standard approximate ones. Finally, I consider the general case of three-dimensional systems and mathematically prove that convergence is guaranteed for the exact functional, regardless of the strength of electron correlation.

  10. The Compassion Our Children Deserve: An Interview with Alfie Kohn.

    ERIC Educational Resources Information Center

    Miller, Ron; Kohn, Alfie

    2000-01-01

    Alfie Kohn, former teacher and current educational theorist and writer, discusses his views on teaching, learning, and parenting. He addresses the problems of reward-based education, the negative effects of competition on learning, and capitalizing on the naturalness of altruistic behavior in humans. He stresses the importance of treating children…

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

    PubMed

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

    2016-02-11

    Schizophrenia is a heritable brain illness with unknown pathogenic mechanisms. Schizophrenia's strongest genetic association at a population level involves variation in the major histocompatibility complex (MHC) locus, but the genes and molecular mechanisms accounting for this have been challenging to identify. Here we show that this association arises in part from many structurally diverse alleles of the complement component 4 (C4) genes. We found that these alleles generated widely varying levels of C4A and C4B expression in the brain, with each common C4 allele associating with schizophrenia in proportion to its tendency to generate greater expression of C4A. Human C4 protein localized to neuronal synapses, dendrites, axons, and cell bodies. In mice, C4 mediated synapse elimination during postnatal development. These results implicate excessive complement activity in the development of schizophrenia and may help explain the reduced numbers of synapses in the brains of individuals with schizophrenia. PMID:26814963

  12. 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.

  13. Structural genomic variation in childhood epilepsies with complex phenotypes

    PubMed Central

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

    2014-01-01

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

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

    SciTech Connect

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

    1991-12-31

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

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

    PubMed

    Varsano, Daniele; Barborini, Matteo; Guidoni, Leonardo

    2014-02-01

    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 (H2, Be2, H2O, and C2H4). 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. PMID:24511917

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

    NASA Astrophysics Data System (ADS)

    Varsano, Daniele; Barborini, Matteo; Guidoni, Leonardo

    2014-02-01

    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 (H2, Be2, H2O, and C2H4). 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.

  17. Spectral element solution of the Kohn-Sham atom

    NASA Astrophysics Data System (ADS)

    Andersen, Kristopher; Bernstein, Noam; Pask, John

    2011-03-01

    Electronic structure calculations of atoms are important in nuclear physics, and are necessary input for most methods to construct first-principles effective potentials (i.e., pseudopotentials and projector augmented wave potentials). The standard method to solve the atomic problem within Kohn-Sham density functional theory is the shooting method. In this work, the more robust spectral element method is applied to the 1D atomic radial equation. The spectral element method provides a strict, upper-bound on the absolute error in the Kohn-Sham eigenvalues and wavefunctions enabling the solution to be converged to a well controlled accuracy. The results of this method are compared to the extensive ``NIST Atomic Reference Data for Electronic Structure Calculations'' database for elements H to U, providing a more rigourous assessment of this dataset than previously available.

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

    SciTech Connect

    Helbig, N.; Rubio, A.

    2009-12-14

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

  19. Developing the random phase approximation into a practical post-Kohn-Sham correlation model.

    PubMed

    Furche, Filipp

    2008-09-21

    The random phase approximation (RPA) to the density functional correlation energy systematically improves upon many limitations of present semilocal functionals, but was considered too computationally expensive for widespread use in the past. Here a physically appealing reformulation of the RPA correlation model is developed that substantially reduces its computational complexity. The density functional RPA correlation energy is shown to equal one-half times the difference of all RPA electronic excitation energies computed at full and first order coupling. Thus, the RPA correlation energy may be considered as a difference of electronic zero point vibrational energies, where each eigenmode corresponds to an electronic excitation. This surprisingly simple result is intimately related to plasma theories of electron correlation. Differences to electron pair correlation models underlying popular correlated wave function methods are discussed. The RPA correlation energy is further transformed into an explicit functional of the Kohn-Sham orbitals. The only nontrivial ingredient to this functional is the sign function of the response operator. A stable iterative algorithm to evaluate this sign function based on the Newton-Schulz iteration is presented. Integral direct implementations scale as the fifth power of the system size, similar to second order Moller-Plesset calculations. With these improvements, RPA may become the long-sought robust and efficient zero order post-Kohn-Sham correlation model. PMID:19044948

  20. Asymptotic form of the Kohn-Sham correlation potential

    SciTech Connect

    Joubert, D. P.

    2007-07-15

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

  1. Asymptotic form of the Kohn-Sham correlation potential

    NASA Astrophysics Data System (ADS)

    Joubert, D. P.

    2007-07-01

    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 Görling [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)].

  2. Element orbitals for Kohn-Sham density functional theory

    SciTech Connect

    Lin, Lin; Ying, Lexing

    2012-05-08

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

  3. 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

  4. Visualizing the Kohn-Sham kinetic energy density in molecules

    NASA Astrophysics Data System (ADS)

    Cancio, Antonio C.; Kuna, Aeryk

    2014-03-01

    In recent years, driven by applications at high temperature and large system size, interest has turned to the construction of orbital-free density functionals, modeling the kinetic energy solely as a functional of the electron density and its derivatives. We visualize the Kohn-Sham kinetic energy density (KED) for the AE6 test set of molecules commonly used to test density functional performance for atomization energies. Calculations are performed using the ABINIT plane-wave code with over-converged cutoffs and simulation cell sizes to produce as accurate results as possible within a pseudopotential approximation. The orbital-dependent KED is compared to simple orbital-free models such as the Thomas-Fermi and von-Weiszacker KED's and to a sophisticated metaGGA-level functional proposed by Perdew and Constantin (PC). All models fail to reproduce the Kohn-Sham KED reasonably in high density regions - covalent and polar bonds and valence lone-pairs. In particular, the PC model actually disimproves on the simpler gradient expansion model in these regions. A simple fix is proposed for the PC functional, substantially modifying its behavior for regions of high values of the Laplacian of the density and low density gradient. Based upon work supported by the National Science Foundation under Grant No. 0812195.

  5. What's It All About, Alfie? A Parent/Educator's Response to Alfie Kohn.

    ERIC Educational Resources Information Center

    Rochester, J. Martin

    1998-01-01

    Rebuts Alfie Kohn's article "Only for My Kid: How Privileged Parents are Undermining School Reform" in the April 1998 "Kappan." Kohn expects the author to pay a fortune for a home in an affluent community so his kids can get violence-prevention training and sing "Kumbaya" in a mainstreamed classroom. Earning the right to take an honors class…

  6. The role of regulatory variation in complex traits and disease.

    PubMed

    Albert, Frank W; Kruglyak, Leonid

    2015-04-01

    We are in a phase of unprecedented progress in identifying genetic loci that cause variation in traits ranging from growth and fitness in simple organisms to disease in humans. However, a mechanistic understanding of how these loci influence traits is lacking for the majority of loci. Studies of the genetics of gene expression have emerged as a key tool for linking DNA sequence variation to phenotypes. Here, we review recent insights into the molecular nature of regulatory variants and describe their influence on the transcriptome and the proteome. We discuss conceptual advances from studies in model organisms and present examples of complete chains of causality that link individual polymorphisms to changes in gene expression, which in turn result in physiological changes and, ultimately, disease risk. PMID:25707927

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

    PubMed

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

    2016-01-01

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

  8. 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

  9. 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

  10. Variation in Child Health Care Utilization by Medical Complexity

    PubMed Central

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

    2014-01-01

    Objectives 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. Methods 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. Results 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<.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 versus 8.9 out of 10, p<.001). Conclusion Health care models for CMC should account for mental health conditions that may be driving high numbers of outpatient encounters. PMID:24740726

  11. A More Complex Analysis Is Needed.

    ERIC Educational Resources Information Center

    Lickona, Thomas

    1998-01-01

    Alfie Kohn's critique of character education in the February 1997 "Kappan" is constructive but not complex enough to provide guidance for the field. Except for briefly describing the Child Development Project, Kohn omits books and articles advocating a comprehensive approach to character education and does not fairly represent some…

  12. Flow-field dependent variation method for complex relativistic fluids

    NASA Astrophysics Data System (ADS)

    Richardson, G. A.; Chung, T. J.; Karr, G. R.; Pendleton, G. N.

    2000-09-01

    Many current high-energy astrophysics problems, particularly those containing shock waves and high-speed flow, do not take advantage of new computational fluid dynamics (CFD) techniques available in such fields as aerospace engineering. We will present the flow-field dependent variation (FDV) method to accurately solve very high-speed flow problems, as well as capture relativistic shocks, all while allowing the user to apply their familiar finite difference method (FDM) or finite element method (FEM). This method is also versatile enough to apply the non-relativistic Naiver-Stokes equations to solve low speed flows. In the FDV method, numerical schemes are automatically adjusted from the current flow field information reflecting shock discontinuities and/or effects of viscosity in boundary layers. To demonstrate the validity of this theory, the shock tube using the relativistic hydrodynamic equations has been applied. .

  13. Interpreting noncoding genetic variation in complex traits and human disease.

    PubMed

    Ward, Lucas D; Kellis, Manolis

    2012-11-01

    Association studies provide genome-wide information about the genetic basis of complex disease, but medical research has focused primarily on protein-coding variants, owing to the difficulty of interpreting noncoding mutations. This picture has changed with advances in the systematic annotation of functional noncoding elements. Evolutionary conservation, functional genomics, chromatin state, sequence motifs and molecular quantitative trait loci all provide complementary information about the function of noncoding sequences. These functional maps can help with prioritizing variants on risk haplotypes, filtering mutations encountered in the clinic and performing systems-level analyses to reveal processes underlying disease associations. Advances in predictive modeling can enable data-set 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

  14. 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

  15. 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

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

    PubMed Central

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

    2016-01-01

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

  17. Projection potentials and angular momentum convergence of total energies in the full-potential Korringa-Kohn-Rostoker method.

    PubMed

    Zeller, Rudolf

    2013-03-13

    Although the full-potential Korringa-Kohn-Rostoker Green function method yields accurate results for many physical properties, the convergence of calculated total energies with respect to the angular momentum cutoff is usually considered to be less satisfactory. This is surprising because accurate single-particle energies are expected if they are calculated by Lloyd's formula and because accurate densities and hence accurate double-counting energies should result from the total energy variational principle. It is shown how the concept of projection potentials can be used as a tool to analyse the convergence behaviour. The key factor blocking fast convergence is identified and it is illustrated how total energies can be improved with only a modest increase of computing time. PMID:23396831

  18. Paired-Duplication Signatures Mark Cryptic Inversions and Other Complex Structural Variation

    PubMed Central

    Brand, Harrison; Collins, Ryan L.; Hanscom, Carrie; Rosenfeld, Jill A.; Pillalamarri, Vamsee; Stone, Matthew R.; Kelley, Fontina; Mason, Tamara; Margolin, Lauren; Eggert, Stacey; Mitchell, Elyse; Hodge, Jennelle C.; Gusella, James F.; Sanders, Stephan J.; Talkowski, Michael E.

    2015-01-01

    Copy-number variants (CNVs) have been the predominant focus of genetic studies of structural variation, and chromosomal microarray (CMA) for genome-wide CNV detection is the recommended first-tier genetic diagnostic screen in neurodevelopmental disorders. We compared CNVs observed by CMA to the structural variation detected by whole-genome large-insert sequencing in 259 individuals diagnosed with autism spectrum disorder (ASD) from the Simons Simplex Collection. These analyses revealed a diverse landscape of complex duplications in the human genome. One remarkably common class of complex rearrangement, which we term dupINVdup, involves two closely located duplications (“paired duplications”) that flank the breakpoints of an inversion. This complex variant class is cryptic to CMA, but we observed it in 8.1% of all subjects. We also detected other paired-duplication signatures and duplication-mediated complex rearrangements in 15.8% of all ASD subjects. Breakpoint analysis showed that the predominant mechanism of formation of these complex duplication-associated variants was microhomology-mediated repair. On the basis of the striking prevalence of dupINVdups in this cohort, we explored the landscape of all inversion variation among the 235 highest-quality libraries and found abundant complexity among these variants: only 39.3% of inversions were canonical, or simple, inversions without additional rearrangement. Collectively, these findings indicate that dupINVdups, as well as other complex duplication-associated rearrangements, represent relatively common sources of genomic variation that is cryptic to population-based microarray and low-depth whole-genome sequencing. They also suggest that paired-duplication signatures detected by CMA warrant further scrutiny in genetic diagnostic testing given that they might mark complex rearrangements of potential clinical relevance. PMID:26094575

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

    PubMed

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

    2010-12-01

    Horses, like many domesticated species, have been selected for broad variation in skeletal size. This variation is not only an interesting model of rapid evolutionary change during domestication, but is also directly applicable to the horse industry. Breeders select for complex traits like body size and skeletal conformation to improve marketability, function, soundness and performance in the show ring. Using a well-defined set of 35 measurements, we have identified and quantified skeletal variation in the horse species. We collected measurements from 1215 horses representing 65 breeds of diverse conformation such as the American Miniature, Shetland Pony, Arabian Horse, Thoroughbred, Shire and Clydesdale. Principal components analysis has identified two key dimensions of skeletal variation in the horse. Principal component 1 is positively correlated with every measurement and quantifies overall body size. Principal component 2 captures a pattern of bone widths vs. lengths and thus quantifies variation in overall bone thickness. By defining these complex skeletal traits, we have created a framework for whole genome association studies to identify quantitative trait loci that contribute to this variation. PMID:21070291

  20. Dominance Genetic Variation Contributes Little to the Missing Heritability for Human Complex Traits

    PubMed Central

    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

    2015-01-01

    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 (hSNP2 and δSNP2) in unrelated individuals based on an orthogonal model where the estimate of hSNP2 is independent of that of δSNP2. With this method, we analyzed 79 quantitative traits in 6,715 unrelated European Americans. The estimate of δSNP2 averaged across all the 79 quantitative traits was 0.03, approximately a fifth of that for additive variation (average hSNP2 = 0.15). There were a few traits that showed substantial estimates of δSNP2, 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

  1. 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

  2. Stochastic variational method as quantization scheme: Field quantization of the complex Klein-Gordon equation

    NASA Astrophysics Data System (ADS)

    Koide, T.; Kodama, T.

    2015-09-01

    The stochastic variational method (SVM) is the generalization of the variational approach to systems described by stochastic variables. In this paper, we investigate the applicability of SVM as an alternative field-quantization scheme, by considering the complex Klein-Gordon equation. There, the Euler-Lagrangian equation for the stochastic field variables leads to the functional Schrödinger equation, which can be interpreted as the Euler (ideal fluid) equation in the functional space. The present formulation is a quantization scheme based on commutable variables, so that there appears no ambiguity associated with the ordering of operators, e.g., in the definition of Noether charges.

  3. Alternative to the Kohn-Sham equations: The Pauli potential differential equation

    NASA Astrophysics Data System (ADS)

    Levämäki, H.; Nagy, Á.; Kokko, K.; Vitos, L.

    2015-12-01

    A recently developed theoretical framework of performing self-consistent orbital-free (OF) density functional theory (DFT) calculations at Kohn-Sham DFT level accuracy is tested in practice. The framework is valid for spherically symmetric systems. Numerical results for the Beryllium atom are presented and compared to accurate Kohn-Sham data. These calculations make use of a differential equation that we have developed for the so called Pauli potential, a key quantity in OF-DFT. The Pauli potential differential equation and the OF Euler equation form a system of two coupled differential equations, which have to be solved simultaneously within the DFT self-consistent loop.

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

    SciTech Connect

    Heller, William T; Mo, Yiming

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Mo, Yiming; Heller, William T.

    2010-11-01

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

  6. 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

  7. How selection shapes variation of the human major histocompatibility complex: a review.

    PubMed

    Meyer, D; Thomson, G

    2001-01-01

    The nature of polymorphism and molecular sequence variation in the genes of the human major histocompatibility complex (MHC) provides strong support for the idea that these genes are under selection. With the understanding that selection shapes MHC variation new questions have become the focus of study. What is the mode of selection that accounts for MHC polymorphism? Is variation maintained by pathogen pressure or by reproductive mechanisms? Discerning between these requires drawing on information from studies on association between HLA genes and infectious diseases, reproductive success and mating preferences relative to HLA genotypes, and theoretical studies that compare the outcomes of different selection regimes. The pattern that has emerged suggests that several types of selection are plausible for the maintenance of HLA polymorphism. PMID:11415519

  8. 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

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

    PubMed

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

    2010-06-01

    Chemical communication by many insect species involves complex signals of both insect and plant origin. Much attention has been focused on the behavioral activities of these components but less on their sources of variation, despite implications for evolutionary theory and pest management. We studied variation in chemical signaling at host, tree-within-host, and beetle-on-tree scales using tunneling male pine engravers [Ips pini (Say)] on jack, Pinus banksiana Lamb, red, P. resinosa Aiton, and white, P. strobus L. pines. Pine engravers are distributed transcontinentally, and stereoisomeric ratios of their principal pheromone component ipsdienol varies regionally. Linear mixed-effects models were used to examine variation in monoterpene and pheromone volatile profiles, determined by gas chromatography. Phloem from white pine had the greatest concentration of monoterpenes, although insects tunneling in white pine produced the smallest ratios of monoterpenes to pheromones (1:2) in their volatile plumes relative to jack and red pine (1:1). Beetle-to-beetle variation in plume composition was approximately 2-9 times greater than the inter-tree variation within a tree species. The stereoisomeric ratio of ipsdienol was highly consistent within the pheromone component of the plume. The little variation present existed almost entirely at the level of the insects. Within the pheromone component of the plume in a given host species, there was up to 13 times more beetle-to-beetle than tree-to-tree variation. This magnitude was almost double the magnitudes of the ratios among components within the entire plumes. Implications to the behavioral ecology of bark beetle communication, such as potential strategies of cheating and predator avoidance, are discussed. PMID:20550801

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

    ERIC Educational Resources Information Center

    Weininger, Elliot B.; Lareau, Annette

    2009-01-01

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

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

    ERIC Educational Resources Information Center

    Appleman, Deborah; Thompson, Micheal J.

    2002-01-01

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

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

    ERIC Educational Resources Information Center

    O'Neil, John; Tell, Carol

    1999-01-01

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

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

    ERIC Educational Resources Information Center

    Weininger, Elliot B.; Lareau, Annette

    2009-01-01

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

  14. The Effects of Occupational Conditions upon the Division of Household Labor: An Application of Kohn's Theory.

    ERIC Educational Resources Information Center

    Seccombe, Karen

    1986-01-01

    Tested Kohn's theory that people who work in highly supervised, routinized occupations are likely to value obedience and conformity in marital and parental relationships. Findings from 244 couples revealed that working conditions were not strong predictors of division of household labor. Concludes that nontraditional gender role values,…

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

    SciTech Connect

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

    2004-04-23

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

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

    SciTech Connect

    Yuhki, Naoya; 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. 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.

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

    PubMed Central

    Yuhki, N; O'Brien, S J

    1990-01-01

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

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

    PubMed

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

    2010-03-01

    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 reached through analysis of structural variation alone, in this review we examine the role of genetic variation in modulating gene expression. We describe the intricate architecture of the MHC class II regulatory system, indicating how its unique characteristics may relate to observed associations with disease. There is evidence that haplotype-specific variation involving proximal promoter sequences can alter the level of gene expression, potentially modifying the emergence and expression of key phenotypic traits. Although much emphasis has been placed on cis-regulatory elements, we also examine the role of more distant enhancer elements together with the evidence of dynamic inter- and intra-chromosomal interactions and epigenetic processes. The role of genetic variation in such mechanisms may hold profound implications for susceptibility to common disease. PMID:19890353

  19. Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation.

    PubMed

    Jin, Minliang; Liu, Haijun; He, Cheng; Fu, Junjie; Xiao, Yingjie; Wang, Yuebin; Xie, Weibo; Wang, Guoying; Yan, Jianbing

    2016-01-01

    Gene expression variation largely contributes to phenotypic diversity and constructing pan-transcriptome is considered necessary for species with complex genomes. However, the regulation mechanisms and functional consequences of pan-transcriptome is unexplored systematically. By analyzing RNA-seq data from 368 maize diverse inbred lines, we identified almost one-third nuclear genes under expression presence and absence variation, which tend to play regulatory roles and are likely regulated by distant eQTLs. The ePAV was directly used as "genotype" to perform GWAS for 15 agronomic phenotypes and 526 metabolic traits to efficiently explore the associations between transcriptomic and phenomic variations. Through a modified assembly strategy, 2,355 high-confidence novel sequences with total 1.9 Mb lengths were found absent within reference genome. Ten randomly selected novel sequences were fully validated with genomic PCR, including another two NBS_LRR candidates potentially affect flavonoids and disease-resistance. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes, and through developing two test-cross populations and surveying several most important yield traits, the dispensable genes were shown to contribute to heterosis. Novel perspectives and resources to discover maize quantitative trait variations were provided to better understand the kernel regulation networks and to enhance maize breeding. PMID:26729541

  20. Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation

    PubMed Central

    Jin, Minliang; Liu, Haijun; He, Cheng; Fu, Junjie; Xiao, Yingjie; Wang, Yuebin; Xie, Weibo; Wang, Guoying; Yan, Jianbing

    2016-01-01

    Gene expression variation largely contributes to phenotypic diversity and constructing pan-transcriptome is considered necessary for species with complex genomes. However, the regulation mechanisms and functional consequences of pan-transcriptome is unexplored systematically. By analyzing RNA-seq data from 368 maize diverse inbred lines, we identified almost one-third nuclear genes under expression presence and absence variation, which tend to play regulatory roles and are likely regulated by distant eQTLs. The ePAV was directly used as “genotype” to perform GWAS for 15 agronomic phenotypes and 526 metabolic traits to efficiently explore the associations between transcriptomic and phenomic variations. Through a modified assembly strategy, 2,355 high-confidence novel sequences with total 1.9 Mb lengths were found absent within reference genome. Ten randomly selected novel sequences were fully validated with genomic PCR, including another two NBS_LRR candidates potentially affect flavonoids and disease-resistance. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes, and through developing two test-cross populations and surveying several most important yield traits, the dispensable genes were shown to contribute to heterosis. Novel perspectives and resources to discover maize quantitative trait variations were provided to better understand the kernel regulation networks and to enhance maize breeding. PMID:26729541

  1. Population fragmentation and major histocompatibility complex variation in the spotted suslik, Spermophilus suslicus.

    PubMed

    Biedrzycka, Aleksandra; Radwan, Jacek

    2008-11-01

    The fragmentation of populations typically enhances depletion of genetic variation, but highly polymorphic major histocompatibility complex (MHC) genes are thought to be under balancing selection and therefore retain polymorphism despite population bottlenecks. In this study, we investigate MHC DRB (class II) exon 2 variation in 14 spotted suslik populations from two regions differing in their degree of habitat fragmentation and gene flow. We found 16 alleles that segregated in a sample of 248 individuals. The alleles were highly divergent and revealed the hallmark signs of positive selection acting on them in the past, showing a significant excess of nonsynonymous substitutions. This excess was concentrated in putative antigen-binding sites, which suggests that past selection was driven by pathogens. MHC diversity was significantly lower in fragmented western populations than in the eastern populations, characterized by significant gene flow. In contrast to neutral variation, amova did not reveal genetic differentiation between the two regions. This may indicate similar selective pressures shaping MHC variation in both regions until the recent past. However, MHC allelic richness within a population was correlated with that for microsatellites. F(ST )outlier analyses have shown that population differentiation at DRB was neither higher nor lower than expected under neutrality. The results suggest that selection on MHC is not strong enough to counteract drift that results from recent fragmentation of spotted suslik populations. PMID:19140973

  2. Variational methods for fitting complex Bayesian mixed effects models to health data.

    PubMed

    Lee, Cathy Yuen Yi; Wand, Matt P

    2016-01-30

    We consider approximate inference methods for Bayesian inference to longitudinal and multilevel data within the context of health science studies. The complexity of these grouped data often necessitates the use of sophisticated statistical models. However, the large size of these data can pose significant challenges for model fitting in terms of computational speed and memory storage. Our methodology is motivated by a study that examines trends in cesarean section rates in the largest state of Australia, New South Wales, between 1994 and 2010. We propose a group-specific curve model that encapsulates the complex nonlinear features of the overall and hospital-specific trends in cesarean section rates while taking into account hospital variability over time. We use penalized spline-based smooth functions that represent trends and implement a fully mean field variational Bayes approach to model fitting. Our mean field variational Bayes algorithms allow a fast (up to the order of thousands) and streamlined analytical approximate inference for complex mixed effects models, with minor degradation in accuracy compared with the standard Markov chain Monte Carlo methods. Copyright 2015 John Wiley & Sons, Ltd. PMID:26415742

  3. Exact Solutions of Five Complex Nonlinear Schrödinger Equations by Semi-Inverse Variational Principle

    NASA Astrophysics Data System (ADS)

    Mohammad, Najafi; Somayeh, Arbabi

    2014-09-01

    In this paper, we establish exact solutions for five complex nonlinear Schrödinger equations. The semi-inverse variational principle (SVP) is used to construct exact soliton solutions of five complex nonlinear Schrödinger equations. Many new families of exact soliton solutions of five complex nonlinear Schrödinger equations are successfully obtained.

  4. Genetic Variation in Human Vitamin C Transporter Genes in Common Complex Diseases.

    PubMed

    Shaghaghi, Mandana Amir; Kloss, Olena; Eck, Peter

    2016-03-01

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

  5. Low major histocompatibility complex class I (MHC I) variation in the European bison (Bison bonasus).

    PubMed

    Babik, Wieslaw; Kawalko, Agata; Wójcik, Jan M; Radwan, Jacek

    2012-01-01

    Variation in the major histocompatibility complex (MHC) class I of the European bison was characterized in a sample of 99 individuals using both classical cloning/Sanger sequencing and 454 pyrosequencing. Three common (frequencies: 0.348, 0.328, and 0.283) haplotypes contain 1-3 classical class I loci. A variable and difficult to estimate precisely number of nonclassical transcribed loci, pseudogenes, and/or gene fragments were also found. The presence of additional 2 rare haplotypes (frequency of 0.020 each), observed only in heterozygotes, was inferred. The overall organization of MHC I appears similar to the cattle system, but genetic variation is much lower with only 7 classical class I alleles, approximately one-tenth of the number known in cattle and a quarter known in the American bison. An extensive transspecific polymorphism was found. MHC I is in a strong linkage disequilibrium with previously studied MHC II DRB3 gene. The most likely explanation for the low variation is a drastic bottleneck at the beginning of the 20th century. Genotype frequencies conformed to Hardy-Weinberg expectations, and no signatures of selection in contemporary populations but strong signatures of historical positive selection in sequences of classical alleles were found. A quick and reliable method of MHC I genotyping was developed. PMID:22496313

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

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    The SD-SPIDER method for the characterization of ultrashort laser pulses requires the solution of a nonlinear integral equation of autoconvolution type with a device-based kernel function. Taking into account the analytical background of a variational regularization approach for solving the corresponding ill-posed operator equation formulated in complex-valued L 2-spaces over finite real intervals, we suggest and evaluate numerical procedures using NURBS and the TIGRA method for calculating the regularized solutions in a stable manner. In this context, besides the complex deautoconvolution problem with noisy but full data, a phase retrieval problem is introduced which adapts to the experimental state of the art in laser optics. For the treatment of this problem facet, which is formulated as a tensor product operator equation, we derive the well-posedness of variational regularization methods. Case studies with synthetic and real optical data show the capability of the implemented approach as well as its limitations due to measurement deficits.

  8. Genetic relationships and variation in the Stylosanthes guianensis species complex assessed by random amplified polymorphic DNA.

    PubMed

    Kazan, K; Manners, J M; Cameron, D F

    1993-02-01

    Genetic variation in the five taxonomic groups of the Stylosanthes guianensis (Aubl.) Sw. complex was investigated using random amplified polymorphic DNA markers (RAPDs). DNA samples from four plants of each of 45 accessions within the S. guianensis species complex were analyzed using 20 oligonucleotides of random sequence. Little variation was found within each of the 18 accessions (1-7% of total RAPD bands in pairwise comparisons) and none within each of the other 27 accessions. However, higher levels of polymorphisms were observed both within (index of genetic distance = 1 - F = 0.16-0.248) and between (1 - F = 0.254-0.408) the five taxa. This level of differentiation at the DNA level supported an earlier classification of the taxa as distinct species. A phenogram based on band sharing was constructed to show genetic relationships among the taxa studied. This phenogram corroborated the description of relationships based on morphological-agronomic characteristics, seed protein patterns, rhizobial affinities, crossability, and pollen stainability of the hybrids. In this phenogram, the most similar species were S. grandiflora and S. hippocampoides (1 - F = 0.264), with S. acuminata also showing closest similarity to these two species (1 - F = 0.277 and 0.283, respectively). Stylosanthes gracilis accessions showed the closest similarity (1 - F = 0.296) to S. guianensis ssp. guianensis accessions. Lowest similarity values (1 - F = 0.335-0.411) were found between these two species and S. grandiflora, S. acuminata, and S. hippocampoides. PMID:8458571

  9. Haplotype variation of cpDNA in the agamic grass complex Pennisetum section Brevivalvula (Poaceae).

    PubMed

    Renno, J F; Mariac, C; Poteaux, C; Bezançon, G; Lumaret, R

    2001-05-01

    The Brevivalvula section of the grass polyploid complex Pennisetum shows various reproductive systems, apomixis being the most widespread. Haplotype variation of chloroplast DNA was studied in the six morphological taxa (species) of this section by using RFLP analysis in 54 plants corresponding to 14 elementary taxa, each characterized on the basis of morphology and ploidy level. Two additional species, Pennisetum glaucum and P. purpureum, which belong to another section of the same genus, were analysed for comparison. In Brevivalvula, chloroplast DNA size was estimated to range between 130 and 133 kb. Thirteen of 15 distinct haplotypes identified in the study were specific to the Brevivalvula section. They were unequally distributed among the morphotypes, the ploidy levels and sampling sites. Within the Brevivalvula section, plants of P. setosum, which are perennial and reproduce vegetatively or by agamospermy, possessed a single specific haplotype. This species differed clearly from the five other morphological species, which are known to be annual, to show either sexual or agamospermic reproduction and which shared most of the 12 other haplotypes observed in the section, suggesting the occurrence of multiple hybridization events between the taxa. Chloroplast DNA variation was highly geographically structured, suggesting low seed dispersal between sites, whereas the substantial haplotype diversity observed in the sites may indicate that agamic reproduction is responsible for the maintenance of distinct genetically isolated clones. Haplotype classification using Wagner's parsimony suggested the occurrence of bidirectional gene flow between the diploids and the polyploids, as reported already in other related apomictic complexes. PMID:11554970

  10. Model organisms retain an "ecological memory" of complex ecologically relevant environmental variation.

    PubMed

    Beer, Karlyn D; Wurtmann, Elisabeth J; Pinel, Nicolás; Baliga, Nitin S

    2014-03-01

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

  11. 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

  12. Phase diagram of the Kohn-Luttinger superconducting state for bilayer graphene

    NASA Astrophysics Data System (ADS)

    Kagan, Maxim Yu.; Mitskan, Vitaly A.; Korovushkin, Maxim M.

    2015-06-01

    The effect of Coulomb interaction between Dirac fermions on the formation of the Kohn-Luttinger superconducting state in bilayer doped graphene is studied disregarding of the effect of the van der Waals potential of the substrate and impurities. The phase diagram determining the boundaries of superconductive domains with different types of symmetry of the order parameter is built using the extended Hubbard model in the Born weak-coupling approximation with allowance for the intratomic, interatomic, and interlayer Coulomb interactions between electrons. It is shown that the Kohn-Luttinger polarization contributions up to the second order of perturbation theory in the Coulomb interaction inclusively and an account for the long-range intraplane Coulomb interactions significantly affect the competition between the superconducting phases with the f-, p + ip-, and d + id-wave symmetries of the order parameter. It is demonstrated that the account for the interlayer Coulomb interaction enhances the critical temperature of the transition to the superconducting phase.

  13. Collective mode formulation of the response algorithm for solving Kohn-Sham equations

    NASA Astrophysics Data System (ADS)

    Auer, J.; Krotscheck, E.

    2003-04-01

    We have developed a "collective mode" version of the response-iteration algorithm for solving the nonlinear Kohn-Sham equations. The algorithm utilizes approximation methods for the density-density response function that are known from microscopic many-body theories of strongly interacting Fermi systems. The major advantage over our previously proposed algorithm (J. Auer and E. Krotscheck, Comput. Phys. Comm. 118 (1999) 139-144) is that the new method needs the computation of occupied states only. Using spherical jellium clusters with up to 2000 electrons as an example, we show that the approximations implicit to our new algorithms do not deteriorate the convergence rate. An even simpler version approximates the density-density response function by that of a charged bose gas with the same density. This algorithm converges somewhat more slowly, but still provides a viable method for solving Kohn-Sham equations for small clusters.

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

    PubMed

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

    2012-01-01

    Contact zones between subspecies or closely related species offer valuable insights into speciation processes. A typical feature of such zones is the presence of clinal variation in multiple traits. The nature of these traits and the concordance among clines are expected to influence whether and how quickly speciation will proceed. Learned signals, such as vocalizations in species having vocal learning (e.g. humans, many birds, bats and cetaceans), can exhibit rapid change and may accelerate reproductive isolation between populations. Therefore, particularly strong concordance among clines in learned signals and population genetic structure may be expected, even among continuous populations in the early stages of speciation. However, empirical evidence for this pattern is often limited because differences in vocalisations between populations are driven by habitat differences or have evolved in allopatry. We tested for this pattern in a unique system where we may be able to separate effects of habitat and evolutionary history. We studied geographic variation in the vocalizations of the crimson rosella (Platycercus elegans) parrot species complex. Parrots are well known for their life-long vocal learning and cognitive abilities. We analysed contact calls across a ca 1300 km transect encompassing populations that differed in neutral genetic markers and plumage colour. We found steep clinal changes in two acoustic variables (fundamental frequency and peak frequency position). The positions of the two clines in vocal traits were concordant with a steep cline in microsatellite-based genetic variation, but were discordant with the steep clines in mtDNA, plumage and habitat. Our study provides new evidence that vocal variation, in a species with vocal learning, can coincide with areas of restricted gene flow across geographically continuous populations. Our results suggest that traits that evolve culturally can be strongly associated with reduced gene flow between populations, and therefore may promote speciation, even in the absence of other barriers. PMID:23227179

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

    PubMed

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

    2015-12-01

    Pigmentation traits in adult Drosophila melanogaster were used in this study to investigate how phenotypic variations in continuous ecological traits can be maintained in a natural population. First, pigmentation variation in the adult female was measured at seven different body positions in 20 strains from the Drosophila melanogaster Genetic Reference Panel (DGRP) originating from a natural population in North Carolina. Next, to assess the contributions of cis-regulatory polymorphisms of the genes involved in the melanin biosynthesis pathway, allele-specific expression levels of four genes were quantified by amplicon sequencing using a 454 GS Junior. Among those genes, ebony was significantly associated with pigmentation intensity of the thoracic segment. Detailed sequence analysis of the gene regulatory regions of this gene indicated that many different functional cis-regulatory alleles are segregating in the population and that variations outside the core enhancer element could potentially play important roles in the regulation of gene expression. In addition, a slight enrichment of distantly associated SNP pairs was observed in the ~10 kb cis-regulatory region of ebony, which suggested the presence of interacting elements scattered across the region. In contrast, sequence analysis in the core cis-regulatory region of tan indicated that SNPs within the region are significantly associated with allele-specific expression level of this gene. Collectively, the data suggest that the underlying genetic differences in the cis-regulatory regions that control intraspecific pigmentation variation can be more complex than those of interspecific pigmentation trait differences, where causal genetic changes are typically confined to modular enhancer elements. PMID:26503353

  16. Melanoma susceptibility as a complex trait: genetic variation controls all stages of tumor progression.

    PubMed

    Ferguson, B; Ram, R; Handoko, H Y; Mukhopadhyay, P; Muller, H K; Soyer, H P; Morahan, G; Walker, G J

    2015-05-28

    Susceptibility to most common cancers is likely to involve interaction between multiple low risk genetic variants. Although there has been great progress in identifying such variants, their effect on phenotype and the mechanisms by which they contribute to disease remain largely unknown. We have developed a mouse melanoma model harboring two mutant oncogenes implicated in human melanoma, CDK4(R24C) and NRAS(Q61K). In these mice, tumors arise from benign precursor lesions that are a recognized strong risk factor for this neoplasm in humans. To define molecular events involved in the pathway to melanoma, we have for the first time applied the Collaborative Cross (CC) to cancer research. The CC is a powerful resource designed to expedite discovery of genes for complex traits. We characterized melanoma genesis in more than 50 CC strains and observed tremendous variation in all traits, including nevus and melanoma age of onset and multiplicity, anatomical site predilection, time for conversion of nevi to melanoma and metastases. Intriguingly, neonatal ultraviolet radiation exposure exacerbated nevus and melanoma formation in most, but not all CC strain backgrounds, suggesting that genetic variation within the CC will help explain individual sensitivity to sun exposure, the major environmental skin carcinogen. As genetic variation brings about dramatic phenotypic diversity in a single mouse model, melanoma-related endophenotype comparisons provide us with information about mechanisms of carcinogenesis, such as whether melanoma incidence is dependent upon the density of pre-existing nevus cells. Mouse models have been used to examine the functional role of gene mutations in tumorigenesis. This work represents their next phase of development to study how biological variation greatly influences lesion onset and aggressiveness even in the setting of known somatic driver mutations. PMID:25088201

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    SciTech Connect

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

    2014-12-15

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

  19. Development of Core Complex Domes Due to Along-Axis Variation in Diking

    NASA Astrophysics Data System (ADS)

    Buck, W. R.; Choi, E.; Tian, X.

    2014-12-01

    Continental and oceanic core complexes are characterized by fairly smooth, unfaulted, but corrugated surfaces of high grade rocks often domed both along and orthogonal to the transport direction. The corrugations, or mega-mullions, are remarkably continuous in the transport direction and may be tens of kilometers long. Spencer [1999] suggests that corrugations with across-transport wavelengths of millimeter to ~25 km scales are formed when the lower plate of a large-offset normal fault is "continuously cast," as warm, ductile mantle and gabbro is pulled up against the cooler upper plate. Continuous casting is widely accepted as a mechanism to form the shorter wavelength corrugations as a result of irregularities of the brittle upper plate surface. However, doming is generally ascribed to upflow of buoyant diapirs or transtensional deformation of the lithosphere. We suggest that doming of core complexes can be a product of continuous casting when a large-offset fault evolves to be curved in plan-view. For oceanic core complexes along-axis variation in magmatism can lead to lateral offset of a detachment fault relative to the spreading axis. We assume that near-ridge normal faults form relatively straight and consider that horizontal offsets in the along-axis position of a large-offset fault (or detachment) result from variations in the rate of magmatic diking. Assuming a sinusoidal variation in the rate of dike opening with distance along the axis the evolution of fault offset and the plan-view shape of the active fault is easy to describe. Because the fault length increases as it is offset, the work to slip on the fault increases with time. Eventually, it should be easier to slip in a new straight fault and the conditions for this can be described with an approximate analytic model. We are developing 3D numerical models to test the predictions of this analytic model and show how the topographic amplitude of the domes depends the fault dip, the amplitude of the horizontal offset of the fault and the thickness of the brittle layer. Consistent with observations, the model predicts that flexurally supported domes occur where the magma supply is the lowest.

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

    PubMed

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

    2015-03-10

    We report the first implementation of real-time time-dependent density functional theory (RT-TDDFT) at the relativistic four-component level of theory. In contrast to the perturbative linear-response TDDFT approach (LR-TDDFT), the RT-TDDFT approach performs an explicit time propagation of the Dirac-Kohn-Sham density matrix, offering the possibility to simulate molecular spectroscopies involving strong electromagnetic fields while, at the same time, treating relativistic scalar and spin-orbit corrections variationally. The implementation is based on the matrix representation of the Dirac-Coulomb Hamiltonian in the basis of restricted kinetically balanced Gaussian-type functions, exploiting the noncollinear Kramers unrestricted formalism implemented in the program ReSpect. We also present an analytic form for the delta-type impulse commonly used in RT-TDDFT calculations, as well as a dipole-weighted transition matrix analysis, facilitating the interpretation of spectral transitions in terms of ground-state molecular orbitals. The possibilities offered by the methodology are illustrated by investigating vertical excitation energies and oscillator strengths for ground-state to excited-state transitions in the Group 12 atoms and in heavy-element hydrides. The accuracy of the method is assessed by comparing the excitation energies obtained with earlier relativistic linear response TDDFT results and available experimental data. PMID:26579752

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

    PubMed

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

    2016-02-23

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

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

    PubMed

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

    2003-10-01

    The endangered Mexican wolf (Canis lupus baileyi) was recently reintroduced into Arizona and New Mexico (USA). In 1999 and 2000, pups from three litters that were part of the reintroduction program died of either canine parvovirus or canine distemper. Overall, half (seven of 14) of the pups died of either canine parvovirus or canine distemper. The parents and their litters were analyzed for variation at the class II major histocompatibility complex (MHC) gene DRB1. Similar MHC genes are related to disease resistance in other species. All six of the surviving pups genotyped for the MHC gene were heterozygous while five of the pups that died were heterozygous and one was homozygous. Resistance to pathogens is an important aspect of the management and long-term survival of endangered taxa, such as the Mexican wolf. PMID:14733289

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

    PubMed

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

    2015-10-01

    The major histocompatibility complex (MHC) plays an important role in the immune system of vertebrates. We used the second exon of four MHC class II genes (DRA, DQA1, DQA2 and DRB3) to assess the overall MHC variation in forest musk deer (Moschus berezovskii). We also compared the MHC variation in captive and wild populations. We observed 22 alleles at four loci (four at DRA, four at DQA1, four at DQA2 and 10 at DRB3), 15 of which were newly identified alleles. Results suggest that forest musk deer maintain relatively high MHC variation, which may result from balancing selection. Moreover, considerable diversity was observed at the DRA locus. We found a high frequency of Mobe-DRA*02, Mobe-DQA1*01 and Mobe-DQA2*05 alleles, which may be important for pathogen resistance. A Ewens-Watterson test showed that the DRB3 locus in the wild population had experienced recent balancing selection. We detected a small divergence at the DRA locus, suggesting the effect of weak positive selection on the DRA gene. Alternatively, this locus may be young and not yet adapted a wide spectrum of alleles for pathogen resistance. The significant heterozygosity deficit observed at the DQA1 and DRB3 loci in the captive population and at all four loci in the wild population may be the result of a population bottleneck. Additionally, MHC genetic diversity was higher in the wild population than in the captive, suggesting that the wild population may have the ability to respond to a wider range of pathogens. PMID:26370614

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

    PubMed

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

    2015-12-01

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

  5. Sequence variation at the major histocompatibility complex locus DQ beta in beluga whales (Delphinapterus leucas)

    PubMed

    Murray, B W; Malik, S; White, B N

    1995-07-01

    Genetic variation at the Major Histocompatibility Complex locus DQ beta was analyzed in 233 beluga whales (Delphinapterus leucas) from seven populations: St. Lawrence Estuary, eastern Beaufort Sea, eastern Chukchi Sea, western Hudson Bay, eastern Hudson Bay, southeastern Baffin Island, and High Arctic and in 12 narwhals (Monodon monoceros) sympatric with the High Arctic beluga population. Variation was assessed by amplification of the exon coding for the peptide binding region via the polymerase chain reaction, followed by either cloning and DNA sequencing or single-stranded conformation polymorphism analysis. Five alleles were found across the beluga populations and one in the narwhal. Pairwise comparisons of these alleles showed a 5:1 ratio of nonsynonymous to synonymous substitutions per site leading to eight amino acid differences, five of which were nonconservative substitutions, centered around positions previously shown to be important for peptide binding. Although the amount of allelic variation is low when compared with terrestrial mammals, the nature of the substitutions in the peptide binding sites indicates an important role for the DQ beta locus in the cellular immune response of beluga whales. Comparisons of allele frequencies among populations show the High Arctic population to be different (P < or = .005) from the other beluga populations surveyed. In these other populations an allele, Dele-DQ beta*0101-2, was found in 98% of the animals, while in the High Arctic it was found in only 52% of the animals. Two other alleles were found at high frequencies in the High Arctic population, one being very similar to the single allele found in narwhal. PMID:7659014

  6. 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

  7. Global patterns of large copy number variations in the human genome reveal complexity in chromosome organization.

    PubMed

    Veerappa, Avinash M; Suresh, Raviraj V; Vishweswaraiah, Sangeetha; Lingaiah, Kusuma; Murthy, Megha; Manjegowda, Dinesh S; Padakannaya, Prakash; Ramachandra, Nallur B

    2015-01-01

    Global patterns of copy number variations (CNVs) in chromosomes are required to understand the dynamics of genome organization and complexity. For this study, analysis was performed using the Affymetrix Genome-Wide Human SNP Array 6.0 chip and CytoScan High-Density arrays. We identified a total of 44 109 CNVs from 1715 genomes with a mean of 25 CNVs in an individual, which established the first drafts of population-specific CNV maps providing a rationale for prioritizing chromosomal regions. About 19 905 ancient CNVs were identified across all chromosomes and populations at varying frequencies. CNV count, and sometimes CNV size, contributed to the bulk CNV size of the chromosome. Population specific lengthening and shortening of chromosomal length was observed. Sex bias for CNV presence was largely dependent on ethnicity. Lower CNV inheritance rate was observed for India, compared to YRI and CEU. A total of 33 candidate CNV hotspots from 5382 copy number (CN) variable region (CNVR) clusters were identified. Population specific CNV distribution patterns in p and q arms disturbed the assumption that CNV counts in the p arm are less common compared to long arms, and the CNV occurrence and distribution in chromosomes is length independent. This study unraveled the force of independent evolutionary dynamics on genome organization and complexity across chromosomes and populations. PMID:26390810

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  9. Uncinate Process Variations and Their Relationship with Ostiomeatal Complex: A Pictorial Essay of Multidedector Computed Tomography (MDCT) Findings

    PubMed Central

    Güngör, Gülay; Okur, Nazan; Okur, Erdoğan

    2016-01-01

    Summary The ostiomeatal complex (OMC) is a key area for the drainage and ventilation of the paranasal sinuses. Stenosis created by inflammation and anatomic variations in this region causes an ideal ground for parasanal sinus infections, by preventing the drainage and ventilation of the sinuses. In today’s diagnostics of paranasal sinus infections, the role of evaluation of OMC anatomical variations and soft tissue pathology has increased.. Knowing the anatomical details is important in terms of directing both medical and surgical treatment. The uncinate process (UP) constitutes the most important structure of the ostiomeatal complex, playing a role in mucociliary activity. UP variations can cause mucociliary drainage and ventilation problems, causing complications during surgery. Therefore, knowing and identifying their appearances in multidetector computed tomography (MDCT), the most frequently used radiological imaging method for these variations, becomes a very important consideration. PMID:27158282

  10. The trust-region self-consistent field method in Kohn-Sham density-functional theory

    NASA Astrophysics Data System (ADS)

    Thøgersen, Lea; Olsen, Jeppe; Köhn, Andreas; Jørgensen, Poul; Sałek, Paweł; Helgaker, Trygve

    2005-08-01

    The trust-region self-consistent field (TRSCF) method is extended to the optimization of the Kohn-Sham energy. In the TRSCF method, both the Roothaan-Hall step and the density-subspace minimization step are replaced by trust-region optimizations of local approximations to the Kohn-Sham energy, leading to a controlled, monotonic convergence towards the optimized energy. Previously the TRSCF method has been developed for optimization of the Hartree-Fock energy, which is a simple quadratic function in the density matrix. However, since the Kohn-Sham energy is a nonquadratic function of the density matrix, the local energy functions must be generalized for use with the Kohn-Sham model. Such a generalization, which contains the Hartree-Fock model as a special case, is presented here. For comparison, a rederivation of the popular direct inversion in the iterative subspace (DIIS) algorithm is performed, demonstrating that the DIIS method may be viewed as a quasi-Newton method, explaining its fast local convergence. In the global region the convergence behavior of DIIS is less predictable. The related energy DIIS technique is also discussed and shown to be inappropriate for the optimization of the Kohn-Sham energy.

  11. A Century of Chemical Dynamics Traced through the Nobel Prizes. 1998: Walter Kohn and John Pople

    NASA Astrophysics Data System (ADS)

    van Houten, Josh

    2002-11-01

    The 1998 Nobel Prize was awarded to Walter Kohn "for his development of the density-functional theory" and to John Pople "for his development of computational methods in quantum chemistry." They enabled improved energy calculations on molecules and other multi-atom systems. Chemists have taken advantage of those developments to perform calculations on systems during reactive encounters, thereby obtaining a better understanding of chemical dynamics and allowing for predictions regarding the course of chemical reactions based on the energies of various possible transition states.

  12. Variation of slow-wave frequency and locking during the migrating myoelectric complex in dogs.

    PubMed

    Caenepeel, P; Janssens, W; Accarino, A; Janssens, J; Vantrappen, G; Eyssen, H

    1991-12-01

    Slow waves determine rhythm and polarity of spike bursts. We measured the variation of slow-wave frequency (swf) and locking (swl) in the canine jejunum during the various phases of the migrating myoelectric complex (MMC) and during induced phase III (erythromycin 125 micrograms/kg iv bolus or somatostatin 2.5 micrograms.kg-1.h-1 iv infusion), blocked phase III (atropine 20 micrograms/kg iv bolus), and so-called stationary phase III activity (cisapride 150 micrograms/kg iv bolus). The EMG of 4 dogs, implanted with 10 bipolar electrodes, was recorded on a polygraph. Our results indicate that swf and swl change during the MMC from a stepwise swf gradient with slow waves locked in plateaus during phase I to a continuous swf gradient without or with significantly reduced phase locking during phase III. The length of the first swf plateau decreases significantly from 42 +/- 12 cm post Treitz during phase I to 11 +/- 4 cm during spontaneous phase III. Atropine block of phase III activity prevents phase unlocking and development of a continuous swf gradient. Our hypothesis is that phase unlocking may be one of the induction mechanisms of spike-burst activity. PMID:1685071

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Lin, Lin; Shao, Sihong; E, Weinan

    2013-07-01

    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 Pt2, Au2, TlF, and Bi2Se3 indicate that the LOBPCG-F method is a robust and efficient method for investigating the relativistic effect in systems containing heavy elements.

  15. Molecular Binding in Post-Kohn-Sham Orbital-Free DFT.

    PubMed

    Borgoo, Alex; Green, James A; Tozer, David J

    2014-12-01

    Molecular binding in post-Kohn-Sham orbital-free DFT is investigated, using noninteracting kinetic energy functionals that satisfy the uniform electron gas condition and which are inhomogeneous under density scaling. A parameter is introduced that quantifies binding, and a series of functionals are determined from fits to near-exact effective homogeneities and/or Kohn-Sham noninteracting kinetic energies. These are then used to investigate the relationship between binding and the accuracy of the effective homogeneity and noninteracting kinetic energy at the equilibrium geometry. For a series of 11 molecules, the binding broadly improves as the effective homogeneity improves, although the extent to which it improves is dependent on the accuracy of the noninteracting kinetic energy; optimal binding appears to require both to be accurate simultaneously. The use of a Thomas-Fermi-von Weizsäcker form, augmented with a second gradient correction, goes some way toward achieving this, exhibiting molecular binding on average. The findings are discussed in terms of the noninteracting kinetic potential and the Hellmann-Feynman theorem. The extent to which the functionals can reproduce the system-dependence of the near-exact effective homogeneity is quantified, and potential energy curves are presented for selected molecules. The study provides impetus for including density scaling homogeneity considerations in the design of noninteracting kinetic energy functionals. PMID:26583217

  16. Self-consistency test for the exchange-only Kohn-Sham potential

    NASA Astrophysics Data System (ADS)

    Li, Yan; Krieger, J. B.; Chevary, J. A.; Vosko, S. H.

    1991-05-01

    The relationship, recently derived by Krieger, Li, and Iafrate [Phys. Lett. A 148, 470 (1990)], that ɛmσ, the exchange-only Kohn-Sham (KS) single-particle energy eigenvalue corresponding to the highest occupied orbital, exactly equals ɛ¯HFmσ, the expectation value of the Hartree-Fock (HF) single-particle Hamiltonian averaged over this Kohn-Sham orbital, is employed to test the accuracy of the local-spin-density (LSD) exchange-only potential as well as the recent results of Wang et al. [Phys. Rev. A 41, 78 (1990)]. For the eleven atoms with closed subshells from He to Xe we find that in the LSD approximation ɛmσ is only approximately equal to 60% of ɛ¯ HFmσ, whereas the potential of Wang et al. yields ɛmσ~=ɛ¯ HFmσ to within 0.5%, providing further evidence that it closely approximates the exact KS exchange-only potential.

  17. 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

  18. Pure-state noninteracting v-representability of electron densities from Kohn-Sham calculations with finite basis sets

    NASA Astrophysics Data System (ADS)

    de Silva, Piotr; Wesolowski, Tomasz A.

    2012-03-01

    Within the linear combination of atomic orbitals (LCAO) approximation, one can distinguish two different Kohn-Sham potentials. One is the potential available numerically in calculations, and the other is the exact potential corresponding to the LCAO density. The latter is usually not available, but can be obtained from the total density by a numerical inversion procedure or, as is done here, analytically using only one LCAO Kohn-Sham orbital. In the complete basis-set limit, the lowest-lying Kohn-Sham orbital suffices to perform the analytical inversion, and the two potentials differ by no more than a constant. The relation between these two potentials is investigated here for diatomic molecules and several atomic basis sets of increasing size and quality. The differences between the two potentials are usually qualitative (wrong behavior at nuclear cusps and far from the molecule even if Slater-type orbitals are used) and δ-like features at nodal planes of the lowest-lying LCAO Kohn-Sham orbital. Such nodes occur frequently in LCAO calculations and are not physical. Whereas the behavior of the potential can be systematically improved locally by the increase of the basis sets, the occurrence of nodes is not correlated with the size of the basis set. The presence of nodes in the lowest-lying LCAO orbital can be used to monitor whether the effective potential in LCAO Kohn-Sham equations can be interpreted as the potential needed for pure-state noninteracting v-representability of the LCAO density. Squares of such node-containing lowest-lying LCAO Kohn-Sham orbitals are nontrivial examples of two-electron densities which are not pure-state noninteracting v-representable.

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

    NASA Astrophysics Data System (ADS)

    Wu, Guiping; Liu, Yuanbo

    2015-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    PubMed

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

    2013-12-01

    Paragonimiasis is an important food-borne parasitic zoonosis caused by infection with lung flukes of the genus Paragonimus. Of the 7 members of the genus known in Thailand until recently, only P. heterotremus has been confirmed as causing human disease. An 8th species, P. pseudoheterotremus, has recently been proposed from Thailand, and has been found in humans. Molecular data place this species as a sister species to P. heterotremus, and it is likely that P. pseudoheterotremus is not specifically distinct from P. heterotremus. In this study, we collected metacercariae of both nominal species (identification based on metacercarial morphology) from freshwater crabs from Phetchabun Province in northern Thailand, Saraburi Province in central Thailand, and Surat Thani Province in southern Thailand. In addition, we purchased freshwater crabs imported from Myanmar at Myawaddy Province, western Thailand, close to the Myanmar-Thailand border. The DNAs extracted from excysted metacercariae were PCR-amplified and sequenced for ITS2 and cox1 genes. The ITS2 sequences were nearly identical among all samples (99-100%). Phylogenies inferred from all available partial cox1 sequences contained several clusters. Sequences from Indian P. heterotremus formed a sister group to sequences from P. pseudoheterotremus-type metacercariae. Sequences of P. heterotremus from Thailand, Vietnam, and China formed a separate distinct clade. One metacercaria from Phitsanulok Province was distinct from all others. There is clearly considerable genetic variation in the P. heterotremus complex in Thailand and the form referred to as P. pseudoheterotremus is widely distributed in Thailand and the Thai-Myanmar border region. PMID:24516273

  2. Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex

    PubMed Central

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

    2014-01-01

    The major histocompatibility complex (MHC) is a crucial component of the vertebrate immune system and shows extremely high levels of genetic polymorphism. The extraordinary genetic variation is thought to be ancient polymorphisms maintained by balancing selection. However, introgression from related species was recently proposed as an additional mechanism. Here we provide evidence for introgression at the MHC in Alpine ibex (Capra ibex ibex). At a usually very polymorphic MHC exon involved in pathogen recognition (DRB exon 2), Alpine ibex carried only two alleles. We found that one of these DRB alleles is identical to a DRB allele of domestic goats (Capra aegagrus hircus). We sequenced 2489 bp of the coding and non-coding regions of the DRB gene and found that Alpine ibex homozygous for the goat-type DRB exon 2 allele showed nearly identical sequences (99.8%) to a breed of domestic goats. Using Sanger and RAD sequencing, microsatellite and SNP chip data, we show that the chromosomal region containing the goat-type DRB allele has a signature of recent introgression in Alpine ibex. A region of approximately 750 kb including the DRB locus showed high rates of heterozygosity in individuals carrying one copy of the goat-type DRB allele. These individuals shared SNP alleles both with domestic goats and other Alpine ibex. In a survey of four Alpine ibex populations, we found that the region surrounding the DRB allele shows strong linkage disequilibria, strong sequence clustering and low diversity among haplotypes carrying the goat-type allele. Introgression at the MHC is likely adaptive and introgression critically increased MHC DRB diversity in the genetically impoverished Alpine ibex. Our finding contradicts the long-standing view that genetic variability at the MHC is solely a consequence of ancient trans-species polymorphism. Introgression is likely an underappreciated source of genetic diversity at the MHC and other loci under balancing selection. PMID:24945814

  3. 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

  4. 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

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

    ERIC Educational Resources Information Center

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

    2016-01-01

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

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

    ERIC Educational Resources Information Center

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

    2016-01-01

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

  7. Excitation energies and Stokes shifts from a restricted open-shell Kohn-Sham approach

    NASA Astrophysics Data System (ADS)

    Kowalczyk, Tim; Tsuchimochi, Takashi; Chen, Po-Ta; Top, Laken; Van Voorhis, Troy

    2013-04-01

    Restricted open-shell Kohn-Sham (ROKS) theory provides a powerful computational tool for calculating singlet excited state energies and dynamics. However, the possibility of multiple solutions to the ROKS equations — with the associated difficulty of automatically selecting the physically meaningful solution — limits its usefulness for intensive applications such as long-time Born-Oppenheimer molecular dynamics. We present an implementation of ROKS for excited states which prescribes the physically correct solution from an overlap criterion and guarantees that this solution is stationary, allowing for straightforward evaluation of nuclear gradients. The method is used to benchmark ROKS for vertical excitation energies of small and large organic dyes and for the calculation of Stokes shifts. With common density functional approximations, ROKS vertical excitation energies, and Stokes shifts show similar accuracy to those from time-dependent density functional theory and Δ-self-consistent-field approaches. Advantages of the ROKS approach for excited state structure and molecular dynamics are discussed.

  8. Elliptic preconditioner for accelerating the self consistent field iteration in Kohn-Sham density functional theory

    SciTech Connect

    Lin, Lin; Yang, Chao

    2012-06-11

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

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

    PubMed

    Culchac, F J; Capaz, Rodrigo B

    2016-02-12

    The effects of edge magnetism on the Kohn anomaly (KA) of the G-band phonons of zigzag graphene nanoribbons (ZGNRs) are studied using a combination of the tight-binding and mean-field Hubbard models. We show that the opening of an energy gap, induced by magnetic ordering, significantly changes the KA effects, particularly for narrow ribbons in which the gap is larger than the phonon energy. Therefore, the G-band phonon frequency and lifetime are altered for a magnetically-ordered edge state with respect to an unpolarized edge state. The effects of temperature, ZGNR width, doping and transverse electric fields are systematically investigated. We propose using this effect to probe the magnetic order of edge states in graphene nanoribbons using Raman spectroscopy. PMID:26762781

  10. Implementation of Kohn's theorem for the ellipsoidal quantum dot in the presence of external magnetic field

    NASA Astrophysics Data System (ADS)

    Hayrapetyan, D. B.; Kazaryan, E. M.; Sarkisyan, H. A.

    2016-01-01

    An electron gas in a strongly oblated ellipsoidal quantum dot with impenetrable walls in the presence of external magnetic field is considered. Influence of the walls of the quantum dot is assumed to be so strong in the direction of the minor axis (the OZ axis) that the Coulomb interaction between electrons in this direction can be neglected and considered as two-dimensional. On the basis of geometric adiabaticity we show that in the case of a few-particle gas a powerful repulsive potential of the quantum dot walls has a parabolic form and localizes the gas in the geometric center of the structure. Due to this fact, conditions occur to implement the generalized Kohn theorem for this system. The parabolic confinement potential depends on the geometry of the ellipsoid, which allows, together with the magnetic field to control resonance frequencies of transitions by changing the geometric dimensions of the QD.

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

    NASA Astrophysics Data System (ADS)

    Culchac, F. J.; Capaz, Rodrigo B.

    2016-02-01

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

  12. Lcao-Gáspár-Kohn-Sham energy bands of trans-polyacetylene-chain

    NASA Astrophysics Data System (ADS)

    von Boehm, J.; Kuivalainen, P.; Calais, J.-L.

    1983-12-01

    The band structure of the dimerised trans-polyacetylene-chain ( d CC = 1.35 Å, d CC = 1.46 Å, ∡ CCC = 120° , d CH = 1.09 Å) is calculated with the (parameter-free, non-self-consistent) linear-combination-of-atomic-orbitals method using the Gáspár-Kohn-Sham (GKS) potential for the exchange and correlation. The calculated dimerisation gap of 1.6 eV agrees closely with experiment and also with other GKS calculations when the degree of dimerisation is taken into account. The calculated density of states agrees closely with the X-ray photoemission spectrum of Brundle.

  13. Excitation energies and Stokes shifts from a restricted open-shell Kohn-Sham approach.

    PubMed

    Kowalczyk, Tim; Tsuchimochi, Takashi; Chen, Po-Ta; Top, Laken; Van Voorhis, Troy

    2013-04-28

    Restricted open-shell Kohn-Sham (ROKS) theory provides a powerful computational tool for calculating singlet excited state energies and dynamics. However, the possibility of multiple solutions to the ROKS equations - with the associated difficulty of automatically selecting the physically meaningful solution - limits its usefulness for intensive applications such as long-time Born-Oppenheimer molecular dynamics. We present an implementation of ROKS for excited states which prescribes the physically correct solution from an overlap criterion and guarantees that this solution is stationary, allowing for straightforward evaluation of nuclear gradients. The method is used to benchmark ROKS for vertical excitation energies of small and large organic dyes and for the calculation of Stokes shifts. With common density functional approximations, ROKS vertical excitation energies, and Stokes shifts show similar accuracy to those from time-dependent density functional theory and ?-self-consistent-field approaches. Advantages of the ROKS approach for excited state structure and molecular dynamics are discussed. PMID:23635105

  14. High order forces and nonlocal operators in a Kohn-Sham Hamiltonian.

    PubMed

    Bobbitt, N Scott; Schofield, Grady; Lena, Charles; Chelikowsky, James R

    2015-12-21

    Real space pseudopotentials have a number of advantages in solving for the electronic structure of materials. These advantages include ease of implementation, implementation on highly parallel systems, and great flexibility for describing partially periodic systems. One limitation of this approach, shared by other electronic structure methods, is the slow convergence of interatomic forces when compared to total energies. For real space methods, this requires a fine grid to converge a solution of the Kohn-Sham problem, which is accompanied by concurrent increase in memory and additional matrix-vector multiplications. Here we introduce a method to expedite the computation of interatomic forces by employing a high order integration technique. We demonstrate the usefulness of this technique by calculating accurate bond lengths and vibrational frequencies for molecules and nanocrystals without using fine real space grids. PMID:26106967

  15. Kohn-Sham theory of a rotating dipolar Fermi gas in two dimensions

    NASA Astrophysics Data System (ADS)

    Ancilotto, Francesco

    2015-12-01

    A two-dimensional dipolar Fermi gas in a harmonic trap under rotation is studied by solving ab initio Kohn-Sham equations. The physical parameters used match those of an ultracold gas of fermionic 40K23Na, a prototypical system of strongly interacting dipolar quantum matter, which was created very recently. We find that, as the critical rotational frequency is approached and the system collapses into the lowest Landau level, an array of tightly packed quantum vortices develops, in spite of the nonsuperfluid character of the system. In this state the system loses axial symmetry and the fermionic cloud boundaries assume an almost perfect square shape. At higher values of the filling factor the vortex lattice disappears, while the system still exhibits square-shaped boundaries. At lower values of the filling factor the fermions become instead localized in a Wigner cluster structure.

  16. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  18. Complex spatial and temporal variation of subtropical benthic macrofauna under sewage impact.

    PubMed

    Souza, F M; Brauko, K M; Gilbert, E R; Martins, C C; Lana, P C; Camargo, M G

    2016-05-01

    To better understand variation in sewage-impacted benthic macrofauna from subtropical tidal flats over time and space, we applied a five-factor linear model at a hierarchy of spatial (Condition - Contaminated or Non-Contaminated, Tidal Flat and Plot) and temporal scales (Season and Fortnight). The Contaminated site showed high levels of coprostanol and the presence of Paranais cf frici as markers or indicators of organic enrichment. Differences between Seasons were more pronounced for the faunal variation patterns than for the other parameters, with lower species richness and abundance in summer. There were significant interactions between Fortnight and Tidal Flat for most variables, reflecting marked heterogeneity within Tidal Flats. Benthic community has significantly changed over short periods of time. These rapid changes may lead to erroneous interpretations and mask the true sources of variation. Our results clearly demonstrate the need to better understand benthic temporal variability even at small scales. PMID:26994465

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

    PubMed

    Gu, Ming Dong

    2006-01-01

    The Oedipus complex is central to Western tradition, but not to Chinese culture. Occurrence of oedipal themes in Chinese literature is almost negligible. This phenomenon seems to support a contra-Freud claim: that a theory of European origin, the Oedipus complex, is not universal to human experience in non-Western cultures. However, this article suggests that powerful moral repression may cause the Oedipus complex to undergo structural transformations in some cultures. Through studying a sample of Chinese literary and film representations, the author argues that the Oedipus complex in Chinese culture has been transformed into a filial piety complex. Some conceptual issues are considered from a cross-cultural perspective. PMID:16482964

  20. The transient variation in 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.

    2015-09-01

    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 five GPS receiver stations in Nigeria, which lies within the equatorial ionization anomaly region. The non-linear aspects of the TEC time series were obtained by detrending the data. The detrended TEC time series were subjected to various analyses to obtain the phase space reconstruction and to compute the chaotic quantifiers, which are Lyapunov exponents LE, correlation dimension, and Tsallis entropy, for the study of dynamical complexity. 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 exponents for the entire year show a wavelike semiannual variation pattern with lower values around March, April, September and October. 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 a similar variation pattern to that of the Lyapunov exponent, with both quantifiers correlating within the range of 0.79 to 0.82. These results show that both quantifiers can be further 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 in 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 the Lyapunov exponent and Tsallis entropy during storms. The dynamical behaviour of the ionosphere throughout the year, as described by these quantifiers, was discussed in this work.

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

    ERIC Educational Resources Information Center

    Ferraris, Stefania

    2012-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  3. Structural composition of alternative complex III: variations on the same theme.

    PubMed

    Refojo, Patrícia N; Ribeiro, Miguel A; Calisto, Filipa; Teixeira, Miguel; Pereira, Manuela M

    2013-01-01

    Alternative complex III forms a recently identified family of enzymes with quinol:electron acceptor oxidoreductase activity. First biochemical and genomic analyses showed that ACIII is composed of six to eight subunits, most of which homologous to different proteins or domains already observed in other known enzymatic complexes. The increasing number of completely sequenced genomes led us to perform a new search for the genes coding for the different ACIII subunits. We have identified a larger number of gene clusters coding for ACIII, still confined to the bacterial domain, but extended to classes in which it was not observed before. We also found an unanticipated diversity in gene clusters, both in terms of its constitution and organization. The several unexpected gene arrangements brought new perspectives to the role of the different subunits of ACIII, namely in quinone binding and in proton translocation. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes. PMID:23313414

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

    USGS Publications Warehouse

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

    2008-01-01

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

  5. Sequence variation at the major histocompatibility complex DRB loci in beluga (Delphinapterus leucas) and narwhal (Monodon monoceros).

    PubMed

    Murray, B W; White, B N

    1998-09-01

    The variation at loci with similarity to DRB class II major histocompatibility complex loci was assessed in 313 beluga collected from 13 sampling locations across North America, and 11 narwhal collected in the Canadian high Arctic. Variation was assessed by amplification of exon 2, which codes for the peptide binding region, via the polymerase chain reaction, followed by either cloning and DNA sequencing or single-stranded conformation polymorphism analysis. Two DRB loci were identified in beluga: DRB1, a polymorphic locus, and, DRB2, a monomorphic locus. Eight alleles representing five distinct lineages (based on sequence similarity) were found at the beluga DRB1 locus. Although the relative number of alleles is low when compared with terrestrial mammals, the amino acid variation found among the lineages is moderate. At the DRB1 locus, the average number of nonsynonymous substitutions per site is greater than the average number of synonymous substitutions per site (0.0806 : 0.0207, respectively; P<0.01). Most of the 31 amino acid substitutions do not conserve the physiochemical properties of the residue, and 21 of these are located at positions implicated as forming pockets responsible for the selective binding of foreign peptide side chains. Only DRB1 variation was examined in 11 narwhal, revealing a low amount of variation. These data are consistent with an important role for the DRB1 locus in the cellular immune response of beluga. In addition, the ratio of nonsynonymous to synonymous substitutions is similar to that among primate alleles, arguing against a reduction in the balancing selection pressure in the marine environment. Two hypotheses may explain the modest amount of Mhc variation when compared with terrestrial mammals: small population sizes at speciation or a reduced neutral substitution rate in cetaceans. PMID:9716643

  6. Pooled ChIP-Seq Links Variation in Transcription Factor Binding to Complex Disease Risk.

    PubMed

    Tehranchi, Ashley K; Myrthil, Marsha; Martin, Trevor; Hie, Brian L; Golan, David; Fraser, Hunter B

    2016-04-21

    Cis-regulatory elements such as transcription factor (TF) binding sites can be identified genome-wide, but it remains far more challenging to pinpoint genetic variants affecting TF binding. Here, we introduce a pooling-based approach to mapping quantitative trait loci (QTLs) for molecular-level traits. Applying this to five TFs and a histone modification, we mapped thousands of cis-acting QTLs, with over 25-fold lower cost compared to standard QTL mapping. We found that single genetic variants frequently affect binding of multiple TFs, and CTCF can recruit all five TFs to its binding sites. These QTLs often affect local chromatin and transcription but can also influence long-range chromosomal contacts, demonstrating a role for natural genetic variation in chromosomal architecture. Thousands of these QTLs have been implicated in genome-wide association studies, providing candidate molecular mechanisms for many disease risk loci and suggesting that TF binding variation may underlie a large fraction of human phenotypic variation. PMID:27087447

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

    PubMed Central

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

    2015-01-01

    Although an increasing amount of human genetic variation is being identified and recorded, determining variants within repeated sequences of the human genome remains a challenge. Most population and genome-wide association studies have therefore been unable to consider variation in these regions. Core to the problem is the lack of a sequencing technology that produces reads with sufficient length and accuracy to enable unique mapping. Here, we present a novel methodology of using read clouds, obtained by accurate short-read sequencing of DNA derived from long fragment libraries, to confidently align short reads within repeat regions and enable accurate variant discovery. Our novel algorithm, Random Field Aligner (RFA), captures the relationships among the short reads governed by the long read process via a Markov Random Field. We utilized a modified version of the Illumina TruSeq synthetic long-read protocol, which yielded shallow-sequenced read clouds. We test RFA through extensive simulations and apply it to discover variants on the NA12878 human sample, for which shallow TruSeq read cloud sequencing data are available, and on an invasive breast carcinoma genome that we sequenced using the same method. We demonstrate that RFA facilitates accurate recovery of variation in 155 Mb of the human genome, including 94% of 67 Mb of segmental duplication sequence and 96% of 11 Mb of transcribed sequence, that are currently hidden from short-read technologies. PMID:26286554

  8. 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

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

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

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

  10. Genome-wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola.

    PubMed

    Raman, H; Raman, R; Coombes, N; Song, J; Prangnell, R; Bandaranayake, C; Tahira, R; Sundaramoorthi, V; Killian, A; Meng, J; Dennis, E S; Balasubramanian, S

    2016-06-01

    Optimum flowering time is the key to maximize canola production in order to meet global demand of vegetable oil, biodiesel and canola-meal. We reveal extensive variation in flowering time across diverse genotypes of canola under field, glasshouse and controlled environmental conditions. We conduct a genome-wide association study and identify 69 single nucleotide polymorphism (SNP) markers associated with flowering time, which are repeatedly detected across experiments. Several associated SNPs occur in clusters across the canola genome; seven of them were detected within 20 Kb regions of a priori candidate genes; FLOWERING LOCUS T, FRUITFUL, FLOWERING LOCUS C, CONSTANS, FRIGIDA, PHYTOCHROME B and an additional five SNPs were localized within 14 Kb of a previously identified quantitative trait loci for flowering time. Expression analyses showed that among FLC paralogs, BnFLC.A2 accounts for ~23% of natural variation in diverse accessions. Genome-wide association analysis for FLC expression levels mapped not only BnFLC.C2 but also other loci that contribute to variation in FLC expression. In addition to revealing the complex genetic architecture of flowering time variation, we demonstrate that the identified SNPs can be modelled to predict flowering time in diverse canola germplasm accurately and hence are suitable for genomic selection of adaptative traits in canola improvement programmes. PMID:26428711

  11. Variation in positively selected major histocompatibility complex class I loci in rufous-collared sparrows (Zonotrichia capensis).

    PubMed

    Jones, Matthew R; Cheviron, Zachary A; Carling, Matthew D

    2014-12-01

    The major histocompatibility complex (MHC) is a highly variable family of genes involved in parasite recognition and the initiation of adaptive immune system responses. Variation in MHC loci is maintained primarily through parasite-mediated selection or disassortative mate choice. To characterize MHC diversity of rufous-collared sparrows (Zonotrichia capensis), an abundant South American passerine, we examined allelic and nucleotide variation in MHC class I exon 3 using pyrosequencing. Exon 3 comprises a substantial portion of the peptide-binding region (PBR) of class I MHC and thus plays an important role in intracellular pathogen defense. We identified 98 putatively functional alleles that produce 56 unique protein sequences across at least 6 paralogous loci. Allelic diversity per individual and exon-wide nucleotide diversity were relatively low; however, we found specific amino acid positions with high nucleotide diversity and signatures of positive selection (elevated d N /d S ) that may correspond to the PBR. Based on the variation in physicochemical properties of amino acids at these "positively selected sites," we identified ten functional MHC supertypes. Spatial variation in nucleotide diversity and the number of MHC alleles, proteins, and supertypes per individual suggests that environmental heterogeneity may affect patterns of MHC diversity. Furthermore, populations with high MHC diversity have higher prevalence of avian malaria, consistent with parasite-mediated selection on MHC. Together, these results provide a framework for subsequent investigations of selective agents acting on MHC in Z. capensis. PMID:25186067

  12. Variations of trends of indicators describing complex systems: change of scaling precursory to extreme events.

    PubMed

    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. PMID:20887044

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

    SciTech Connect

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

    1992-01-01

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

  14. Comparative Effectiveness of Variations in the Demonstration Method of Teaching a Complex Manipulative Sequence.

    ERIC Educational Resources Information Center

    Blankenbaker, E. Keith

    There are so many methods and approaches to teaching that it is sometimes difficult to choose the approach best suited to the needs of the students. This study sought to ascertain the relative effectiveness and efficiency of selected approaches to the demonstration of complex manipulative sequences, and to test the theory that students of high…

  15. 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

  16. Variations in task constraints shape emergent performance outcomes and complexity levels in balancing.

    PubMed

    Caballero Sánchez, Carla; Barbado Murillo, David; Davids, Keith; Moreno Hernández, Francisco J

    2016-06-01

    This study investigated the extent to which specific interacting constraints of performance might increase or decrease the emergent complexity in a movement system, and whether this could affect the relationship between observed movement variability and the central nervous system's capacity to adapt to perturbations during balancing. Fifty-two healthy volunteers performed eight trials where different performance constraints were manipulated: task difficulty (three levels) and visual biofeedback conditions (with and without the center of pressure (COP) displacement and a target displayed). Balance performance was assessed using COP-based measures: mean velocity magnitude (MVM) and bivariate variable error (BVE). To assess the complexity of COP, fuzzy entropy (FE) and detrended fluctuation analysis (DFA) were computed. ANOVAs showed that MVM and BVE increased when task difficulty increased. During biofeedback conditions, individuals showed higher MVM but lower BVE at the easiest level of task difficulty. Overall, higher FE and lower DFA values were observed when biofeedback was available. On the other hand, FE reduced and DFA increased as difficulty level increased, in the presence of biofeedback. However, when biofeedback was not available, the opposite trend in FE and DFA values was observed. Regardless of changes to task constraints and the variable investigated, balance performance was positively related to complexity in every condition. Data revealed how specificity of task constraints can result in an increase or decrease in complexity emerging in a neurobiological system during balance performance. PMID:26838357

  17. Species Identification and Variation in the North American Cranberry Fruit Rot Complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Complex mixtures of pathogenic fungi cause cranberry fruit rot, with the contribution by any given fungus to the disease varying from bed to bed, cultivar to cultivar, season to season, and across regions. Furthermore, population variability within the individual fungal species across growing region...

  18. Species Identification and Variation in the North American Cranberry Fruit Rot complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Complex mixtures of pathogenic fungi cause cranberry fruit rot, with the contribution by any given fungus to the disease varying from bed to bed, cultivar to cultivar, season to season, and across regions. Furthermore, population variability within the individual fungal species across growing region...

  19. Phenotypic variation of TTC19-deficient mitochondrial complex III deficiency: a case report and literature review.

    PubMed

    Mordaunt, Dylan A; Jolley, Alexandra; Balasubramaniam, Shanti; Thorburn, David R; Mountford, Hayley S; Compton, Alison G; Nicholl, Jillian; Manton, Nicholas; Clark, Damian; Bratkovic, Drago; Friend, Kathryn; Yu, Sui

    2015-06-01

    Isolated mitochondrial respiratory chain complex III deficiency has been described in a heterogeneous group of clinical presentations in children and adults. It has been associated with mutations in MT-CYB, the only mitochondrial DNA encoded subunit, as well as in nine nuclear genes described thus far: BCS1L, TTC19, UQCRB, UQCRQ, UQCRC2, CYC1, UQCC2, LYRM7, and UQCC3. BCS1L, TTC19, UQCC2, LYRM7, and UQCC3 are complex III assembly factors. We report on an 8-year-old girl born to consanguineous Iraqi parents presenting with slowly progressive encephalomyopathy, severe failure to thrive, significant delays in verbal and communicative skills and bilateral retinal cherry red spots on fundoscopy. SNP array identified multiple regions of homozygosity involving 7.5% of the genome. Mutations in the TTC19 gene are known to cause complex III deficiency and TTC19 was located within the regions of homozygosity. Sequencing of TTC19 revealed a homozygous nonsense mutation at exon 6 (c.937C > T; p.Q313X). We reviewed the phenotypes and genotypes of all 11 patients with TTC19 mutations leading to complex III deficiency (including our case). The consistent features noted are progressive neurodegeneration with Leigh-like brain MRI abnormalities. Significant variability was observed however with the age of symptom onset and rate of disease progression. The bilateral retinal cherry red spots and failure to thrive observed in our patient are unique features, which have not been described, in previously reported patients with TTC19 mutations. Interestingly, all reported TTC19 mutations are nonsense mutations. The severity of clinical manifestations however does not specifically correlate with the residual complex III enzyme activities. PMID:25899669

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

    SciTech Connect

    Sjostrom, Travis; Crockett, Scott

    2015-09-02

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

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

    DOE PAGESBeta

    Sjostrom, Travis; Crockett, Scott

    2015-09-02

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

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

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

  3. 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.

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

    PubMed

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

    2016-03-21

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

  5. Accurate Energies and Orbital Description in Semi-Local Kohn-Sham DFT

    NASA Astrophysics Data System (ADS)

    Lindmaa, Alexander; Kuemmel, Stephan; Armiento, Rickard

    2015-03-01

    We present our progress on a scheme in semi-local Kohn-Sham density-functional theory (KS-DFT) for improving the orbital description while still retaining the level of accuracy of the usual semi-local exchange-correlation (xc) functionals. DFT is a widely used tool for first-principles calculations of properties of materials. A given task normally requires a balance of accuracy and computational cost, which is well achieved with semi-local DFT. However, commonly used semi-local xc functionals have important shortcomings which often can be attributed to features of the corresponding xc potential. One shortcoming is an overly delocalized representation of localized orbitals. Recently a semi-local GGA-type xc functional was constructed to address these issues, however, it has the trade-off of lower accuracy of the total energy. We discuss the source of this error in terms of a surplus energy contribution in the functional that needs to be accounted for, and offer a remedy for this issue which formally stays within KS-DFT, and, which does not harshly increase the computational effort. The end result is a scheme that combines accurate total energies (e.g., relaxed geometries) with an improved orbital description (e.g., improved band structure).

  6. Formal expressions and corresponding expansions for the exact Kohn-Sham exchange potential

    NASA Astrophysics Data System (ADS)

    Bulat, Felipe A.; Levy, Mel

    2009-11-01

    Formal expressions and their corresponding expansions in terms of Kohn-Sham (KS) orbitals are deduced for the exchange potential vx(r) . After an alternative derivation of the basic optimized effective potential integrodifferential equations is given through a Hartree-Fock adiabatic connection perturbation theory, we present an exact infinite expansion for vx(r) that is particularly simple in structure. It contains the very same occupied-virtual quantities that appear in the well-known optimized effective potential integral equation, but in this new expression vx(r) is isolated on one side of the equation. An orbital-energy modified Slater potential is its leading term which gives encouraging numerical results. Along different lines, while the earlier Krieger-Li-Iafrate approximation truncates completely the necessary first-order perturbation orbitals, we observe that the improved localized Hartree-Fock (LHF) potential, or common energy denominator potential (CEDA), or effective local potential (ELP), incorporates the part of each first-order orbital that consists of the occupied KS orbitals. With this in mind, the exact correction to the LHF, CEDA, or ELP potential (they are all equivalent) is deduced and displayed in terms of the virtual portions of the first-order orbitals. We close by observing that the newly derived exact formal expressions and corresponding expansions apply as well for obtaining the correlation potential from an orbital-dependent correlation energy functional.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    PubMed

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

    2015-08-01

    Recently, an approximate theoretical framework was introduced, called local reduced density matrix functional theory (local-RDMFT), where functionals of the one-body reduced density matrix (1-RDM) are minimized under the additional condition that the optimal orbitals satisfy a single electron Schrödinger equation with a local potential. In the present work, we focus on the character of these optimal orbitals. In particular, we compare orbitals obtained by local-RDMFT with those obtained with the full minimization (without the extra condition) by contrasting them against the exact NOs and orbitals from a density functional calculation using the local density approximation (LDA). We find that the orbitals from local-RMDFT are very close to LDA orbitals, contrary to those of the full minimization that resemble the exact NOs. Since local RDMFT preserves the good quality of the description of strong static correlation, this finding opens the way to a mixed density/density matrix scheme, where Kohn-Sham orbitals obtain fractional occupations from a minimization of the occupation numbers using 1-RDM functionals. This will allow for a description of strong correlation at a cost only minimally higher than a density functional calculation. PMID:26254641

  9. Comment on ``Asymptotic form of the Kohn-Sham correlation potential''

    NASA Astrophysics Data System (ADS)

    Holas, A.

    2008-02-01

    For finite systems that have the energetically highest-occupied molecular orbital (HOMO) with an asymptotic nodal surface, Joubert demonstrated recently [Phys. Rev. A 76, 012501 (2007)] strongly anisotropic behavior (in the asymptotic large- r region) of the exact correlation potential of density-functional theory. As is shown by us, this result is a direct and simple consequence of the strong anisotropy of the exact exchange potential obtained by Della Sala and Görling [Phys. Rev. Lett. 89, 033003 (2002); Della Sala and GörlingJ. Chem. Phys. 116, 5374 (2002)] and the assumption about the asymptotic isotropy of the Kohn-Sham (KS) potential (based on the investigation of Almbladh and von Barth [Phys. Rev. B 31, 3231 (1985)] for atoms). Joubert’s result remains a hypothesis only, because the last assumption is in contradiction with the asymptotic strong anisotropy of the KS potential for systems with asymptotic nodal surface of the HOMO, demonstrated by Wu, Ayers, and Yang [J. Chem. Phys. 119, 2978 (2003)]. The correlation potential in the asymptotic region, stemming from their results, is given.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  12. Excited State Dynamics of Carbon Nanotubes with Defects: A Time-Dependent Kohn-Sham Approach

    NASA Astrophysics Data System (ADS)

    Miyamoto, Yoshiyuki; Berber, Savas; Yoon, Mina; Tomanek, David; Rubio, Angel

    2002-03-01

    Unusual stability is required for nanotubes to be useful in molecular electronics devices. To analyze their stability, we performed tight-binding (TB) and first-principles molecular dynamics (MD) simulations of the narrow (3,3) nanotube, which is 0.4 nm in diameter and contains isolated monatomic vacancies. Unexpectedly, this system remains intact up to temperatures close to 4000 K according to our TB MD simulation. We also examined the stability of this nanotube under illumination, using a first-principles MD simulation along the adiabatic potential energy surface (PES) corresponding to an electronic excitation between occupied and unoccupied defect-induced states. In this simulation, the evolution in time of the valence electron distribution was treated simultaneously with the atomic motion, by solving time-dependent Kohn-Sham equations(O. Sugino and Y. Miyamoto, Phys. Rev. B 59), 2579 (1999). to follow the correct PES even in presence of level alternation. We find that optical excitations may induce significant athermal ionic motion that tends to heal rather than expand the defects sites. Our MD results thus suggest an extraordinary tolerance of nanotubes with vacancies to extreme thermal and electronic excitations.

  13. Kohn's theory of the insulating state: a quantum-chemistry viewpoint.

    PubMed

    Resta, Raffaele

    2006-03-14

    The qualitative difference between insulators and conductors not only manifests itself in the excitation spectra but also--according to Kohn's theory [Phys. Rev. 133, A171 (1964)]--in a different organization of the electrons in their ground state: the wave function is localized in insulators and delocalized in conductors. Such localization, however, is hidden in a rather subtle way in the many-body wave function. The theory has been substantially revisited and extended in modern times, invariably within a periodic-boundary-condition framework, i.e., ideally addressing an infinite condensed system. Here we show how the localization/delocalization of the many-body wave function shows up when considering either three-dimensional clusters of increasing size or quasi-one-dimensional systems (linear polymers, nanotubes, and nanowires) of increasing length, within the ordinary "open" boundary conditions adopted for finite systems. We also show that the theory, when specialized to uncorrelated wave functions, has a very close relationship with Boy's theory of localization [Rev. Mod. Phys. 32, 296 (1960)]: the Boys orbitals in the bulk of the sample behave in a qualitatively different way in insulating versus conducting cases. PMID:16542065

  14. Effect of ensemble generalization on the highest-occupied Kohn-Sham eigenvalue

    NASA Astrophysics Data System (ADS)

    Kraisler, Eli; Schmidt, Tobias; Kümmel, Stephan; Kronik, Leeor

    2015-09-01

    There are several approximations to the exchange-correlation functional in density-functional theory, which accurately predict total energy-related properties of many-electron systems, such as binding energies, bond lengths, and crystal structures. Other approximations are designed to describe potential-related processes, such as charge transfer and photoemission. However, the development of a functional which can serve the two purposes simultaneously is a long-standing challenge. Trying to address it, we employ in the current work the ensemble generalization procedure proposed by Kraisler and Kronik [Phys. Rev. Lett. 110, 126403 (2013)]. Focusing on the prediction of the ionization potential via the highest occupied Kohn-Sham eigenvalue, we examine a variety of exchange-correlation approximations: the local spin-density approximation, semi-local generalized gradient approximations, and global and local hybrid functionals. Results for a test set of 26 diatomic molecules and single atoms are presented. We find that the aforementioned ensemble generalization systematically improves the prediction of the ionization potential, for various systems and exchange-correlation functionals, without compromising the accuracy of total energy-related properties. We specifically examine hybrid functionals. These depend on a parameter controlling the ratio of semi-local to non-local functional components. The ionization potential obtained with ensemble-generalized functionals is found to depend only weakly on the parameter value, contrary to common experience with non-generalized hybrids, thus eliminating one aspect of the so-called "parameter dilemma" of hybrid functionals.

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

    PubMed

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

    2014-09-01

    A full distributed-memory implementation of the Dirac-Kohn-Sham (DKS) module of the program BERTHA (Belpassi et al., Phys. Chem. Chem. Phys. 2011, 13, 12368-12394) is presented, where the self-consistent field (SCF) procedure is replicated on all the parallel processes, each process working on subsets of the global matrices. The key feature of the implementation is an efficient procedure for switching between two matrix distribution schemes, one (integral-driven) optimal for the parallel computation of the matrix elements and another (block-cyclic) optimal for the parallel linear algebra operations. This approach, making both CPU-time and memory scalable with the number of processors used, virtually overcomes at once both time and memory barriers associated with DKS calculations. Performance, portability, and numerical stability of the code are illustrated on the basis of test calculations on three gold clusters of increasing size, an organometallic compound, and a perovskite model. The calculations are performed on a Beowulf and a BlueGene/Q system. PMID:26588521

  16. 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

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

    PubMed

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

    2010-06-12

    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

  18. Morphological and molecular variation in tiger beetles of the Cicindela hybrida complex: is an 'integrative taxonomy' possible?

    PubMed

    Cardoso, A; Serrano, A; Vogler, A P

    2009-02-01

    Current taxon assignments at the species level are frequently discordant with DNA-based analyses. Recent studies on tiger beetles in the Cicindela hybrida complex identified discordance between mtDNA patterns and the entities currently defined by the taxonomic literature. To test the accuracy of morphologically delimited groups, five named taxa (species) from 24 representative sampling sites across Europe were scored for 41 external morphological characters. Three of the named taxa were 'diagnosable', that is, defined by between one and three characters unique to each group. Newly sequenced ITS1 and existing mitochondrial cox1 markers established 20 and 22 different haplotypes, respectively, but only cox1 produced (four) diagnosable units. Phylogenetic analysis and statistical parsimony networks showed poor congruence of character variation with the taxonomic entities (and each other). Variation in morphological characters was therefore tested directly for association with DNA-based nesting groups at various hierarchical levels using permutational contingency analysis. Significant statistical associations of 11 (of 13 variable) morphological characters were observed with nesting groups from ITS1 and mitochondrial DNA markers, predominantly at the 4-step level. The analysis demonstrates the need for formal tests of congruence with morphological variation at the level of individual characters, a step that is omitted from recent studies of 'integrative taxonomy'. In addition, statistical correlation of particular morphological characters with DNA-based nesting groups can identify the lowest hierarchical level at which various character sets show congruence, as a means to define evolutionarily separated entities supported by diverse data sources. PMID:19175505

  19. Genetic variation in a tropical tree species influences the associated epiphytic plant and invertebrate communities in a complex forest ecosystem.

    PubMed

    Zytynska, Sharon E; Fay, Michael F; Penney, David; Preziosi, Richard F

    2011-05-12

    Genetic differences among tree species, their hybrids and within tree species are known to influence associated ecological communities and ecosystem processes in areas of limited species diversity. The extent to which this same phenomenon occurs based on genetic variation within a single tree species, in a diverse complex ecosystem such as a tropical forest, is unknown. The level of biodiversity and complexity of the ecosystem may reduce the impact of a single tree species on associated communities. We assessed the influence of within-species genetic variation in the tree Brosimum alicastrum (Moraceae) on associated epiphytic and invertebrate communities in a neotropical rainforest. We found a significant positive association between genetic distance of trees and community difference of the epiphytic plants growing on the tree, the invertebrates living among the leaf litter around the base of the tree, and the invertebrates found on the tree trunk. This means that the more genetically similar trees are host to more similar epiphyte and invertebrate communities. Our work has implications for whole ecosystem conservation management, since maintaining sufficient genetic diversity at the primary producer level will enhance species diversity of other plants and animals. PMID:21444307

  20. Genetic variation in a tropical tree species influences the associated epiphytic plant and invertebrate communities in a complex forest ecosystem

    PubMed Central

    Zytynska, Sharon E.; Fay, Michael F.; Penney, David; Preziosi, Richard F.

    2011-01-01

    Genetic differences among tree species, their hybrids and within tree species are known to influence associated ecological communities and ecosystem processes in areas of limited species diversity. The extent to which this same phenomenon occurs based on genetic variation within a single tree species, in a diverse complex ecosystem such as a tropical forest, is unknown. The level of biodiversity and complexity of the ecosystem may reduce the impact of a single tree species on associated communities. We assessed the influence of within-species genetic variation in the tree Brosimum alicastrum (Moraceae) on associated epiphytic and invertebrate communities in a neotropical rainforest. We found a significant positive association between genetic distance of trees and community difference of the epiphytic plants growing on the tree, the invertebrates living among the leaf litter around the base of the tree, and the invertebrates found on the tree trunk. This means that the more genetically similar trees are host to more similar epiphyte and invertebrate communities. Our work has implications for whole ecosystem conservation management, since maintaining sufficient genetic diversity at the primary producer level will enhance species diversity of other plants and animals. PMID:21444307

  1. Effects of parametric variations of complex targets on damage from projectile impact

    SciTech Connect

    Meier, R.W.

    1989-01-01

    The effects of a hypervelocity projectile striking complex targets have been investigated. The targets consisted of metallic and low-density shock attenuating layers and void regions. The major features of the targets were systematically varied to correlate changes in the targets with the projectile's effectiveness in damaging the targets. Two-dimensional numerical simulations were done with the Eulerian computational fluid dynamics program PINON. Projectile effectiveness against the various targets was measured by determining the maximum pressure, pressure integral, P{sup 2}{tau} value, and hole size at several locations in the targets. 9 refs., 13 figs., 6 tabs.

  2. Complex flow resulted from along-strike variations in slab length in the southern Chilean subduction zone

    NASA Astrophysics Data System (ADS)

    Lin, S.; Chung, S.

    2013-12-01

    Complicated patterns and trench-parallel components of seismic anisotropy in the central portion of the subduction zones have not been link to three-dimensional flow in general, as toroidal circulations may mostly occur in the vicinity of a plate edge. Nevertheless, recent dynamical models demonstrate that complex flow forms when lateral heterogeneities in the subduction zone are considered. Seismic studies often show gradual variations in slab length along strike. The southern Chilean subduction zone is a notable example. The Peru-Chile Trench roughly extending 5900 km is the longest trench worldwide. Most of the regions are distant from the subduction zone edges. In this study the effects of slab-length variations are examined with numerical experiments. The results are used to characterize the regional mantle circulations and the potential heat sources for the recent Patagonian plateau basalts in the southern South America. The model results show that rollback subduction induces both significant poloidal components and trench-parallel flow, extending over 1500 kilometers along the strike of the subduction zone. The trajectories of a set of passive tracers show intricate patterns such as helical streamlines, revealing complex mantle circulations in systems with the along-arc slab-length variations. The upwelling may lead to decompression melting of the heterogeneous asthenosphere to cause extensive lavas in the back arc. Mantle upwelling of the sub-slab mantle moving towards supra-slab regions is observed in the southernmost portion of the subduction system, but only for models with slab segments roughly deeper than 100 km depth. The results indicate that certain segments of the Antarctic slab may reach at least 100 km depth.

  3. Change of the reaction pattern by methodological variations in a multicomponent assembly promoted by Ni complexes.

    PubMed

    Garca-Gmez, G; Moret, J M

    2001-04-01

    The pi-allylnickel complex formed by the addition of trimethylsilyl chloride (TMSCl) to a mixture of [Ni-(cod)2] (cod = 1,5-cyclooctadiene) and a vinyl ketone (Mackenzie complex) carbometalates an acetylene in a completely regioselective manner resulting in the formation of the corresponding vinyl nickel species. This intermediate is capable of controlled quenching in a variety of ways to give different types of compounds: under a CO atmosphere, an acylnickel species is formed that ensues from the carbometalation of the enol ether double bond to form cyclo-pentenone derivatives. Alternatively, if acetylene is present in excess and CO is absent, another acetylene moiety will replace the CO and cyclohexadienes will result instead. Finally, if only an excess of the vinyl ketone is used, the product from a slow double addition of the vinyl ketone across the triple bond is formed. The regioselectivities obtained by the present method are different from those obtained by the involvement of nickel acyclopentadienes as intermediates when the order of addition is reversed. PMID:11330905

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

    PubMed

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

    2016-02-10

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

  5. Major histocompatibility complex variation and age-specific endoparasite load in subadult European rabbits.

    PubMed

    Oppelt, Claus; Starkloff, Anett; Rausch, Philipp; Von Holst, Dietrich; Rdel, Heiko G

    2010-10-01

    Genes of the major histocompatibility complex (MHC) play a fundamental role in the vertebrate immune response and are amongst the most polymorphic genes in vertebrate genomes. It is generally agreed that the highly polymorphic nature of the MHC is maintained through host-parasite co-evolution. Two nonexclusive mechanisms of selection are supposed to act on MHC genes: superiority of MHC heterozygous individuals (overdominance) and an advantage for rare MHC alleles. However, the precise mechanisms and their relative importance are still unknown. Here, we examined MHC dependent parasite load in European rabbits (Oryctolagus cuniculus) from a distinct population with low MHC diversity (three alleles, six genotypes). Using a multivariate approach, we tested for associations of individual MHC class II DRB constitution and the rabbits' intestinal burden with nematodes and coccidia. Rabbits having a particular allele showed lower infestations with hepatic coccidia (E.stiedai). However, a comparison of all six genotypes in the population revealed that carriers of this allele only benefit when they are heterozygous, and furthermore, MHC heterozygosity in general did not affect individual parasite load. In conclusion, this study suggests an immunogenetic basis of European rabbit resistance to hepatic coccidiosis, which can strongly limit survival to maturity in this species. Our study gives a complex picture of MHC-parasite correlations, unveiling the limits of the classical hypotheses of how MHC polymorphism is maintained in natural systems. PMID:20723049

  6. Complex Period Variations of the Neglected W UMa-type Binary System NY Lyrae

    NASA Astrophysics Data System (ADS)

    Qian, S.-B.; Liu, L.; Zhu, L.-Y.

    2009-04-01

    Orbital-period variations of the neglected W UMa-type binary star, NY Lyr, were analyzed based on two newly determined eclipse times together with the others compiled from the literature. A cyclic oscillation with a period of 82.1 yr and an amplitude of 0.0247 d was discovered to be superimposed on a continuous period increase (dP/dt = +1.33 × 10-7 d yr-1). After the long-term period increase and the large-amplitude cyclic oscillation were removed from the O-C diagram, the residuals suggest that there is another small-amplitude period oscillation (A4 = 0.0053 d, P4 = 19.4 years) in the orbital period changes. As in the cases of AH Cnc and AD Cnc, both the continuous period increase and the two cyclic period oscillations make NY Lyr an interesting system to study in the future. In order to understand the evolutionary state of the binary system, new photometric and spectroscopic observations and a careful investigation on those data are needed.

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

    PubMed Central

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

    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

  8. Variation in predicted internal concentrations in relation to PBPK model complexity for rainbow trout.

    PubMed

    Salmina, E S; Wondrousch, D; Kühne, R; Potemkin, V A; Schüürmann, G

    2016-04-15

    The present study is motivated by the increasing demand to consider internal partitioning into tissues instead of exposure concentrations for the environmental toxicity assessment. To this end, physiologically based pharmacokinetic (PBPK) models can be applied. We evaluated the variation in accuracy of PBPK model outcomes depending on tissue constituents modeled as sorptive phases and chemical distribution tendencies addressed by molecular descriptors. The model performance was examined using data from 150 experiments for 28 chemicals collected from US EPA databases. The simplest PBPK model is based on the "Kow-lipid content" approach as being traditional for environmental toxicology. The most elaborated one considers five biological sorptive phases (polar and non-polar lipids, water, albumin and the remaining proteins) and makes use of LSER (linear solvation energy relationship) parameters to describe the compound partitioning behavior. The "Kow-lipid content"-based PBPK model shows more than one order of magnitude difference in predicted and measured values for 37% of the studied exposure experiments while for the most elaborated model this happens only for 7%. It is shown that further improvements could be achieved by introducing corrections for metabolic biotransformation and compound transmission hindrance through a cellular membrane. The analysis of the interface distribution tendencies shows that polar tissue constituents, namely water, polar lipids and proteins, play an important role in the accumulation behavior of polar compounds with H-bond donating functional groups. For compounds without H-bond donating fragments preferable accumulation phases are storage lipids and water depending on compound polarity. PMID:26849323

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

    PubMed Central

    Bramer, Wichor Matthijs

    2016-01-01

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

  10. Variation of complex permittivity of soils with moisture content using VNA

    NASA Astrophysics Data System (ADS)

    Gadani, D. H.; Rana, V. A.; Bhatnagar, S. P.; Prajapati, A. N.; Vyas, A. D.

    2013-06-01

    The complex dielectric permittivity (?', ??) of sand (Kukas region field, Jaipur District, Rajasthan) and sandy loam soil (Sayla, Surendranagar District field, Gujarat) was measured in the frequency range from 100 MHz to 1.5 GHz, for various moisture contents in the soils, using a Vector Network Analyzer (VNA). It has been observed that, the dielectric constant and dielectric loss of the dry soils remain almost constant over this frequency range. The dielectric constant and dielectric loss increase with increase in moisture content in the soil, at any fixed frequency in this frequency region. At given moisture content in the soil, the dielectric constant of the soils decreases slowly with increase in frequency up to 1.5 GHz, whereas the dielectric loss of the soils decreases rapidly with increase in frequency up to 0.5 GHz, after which it decreases slowly with increase in frequency up to 1.5 GHz.

  11. 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

  12. 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

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

    PubMed

    Soley, John T

    2016-06-01

    This paper presents an overview of the structure, function and anomalies of the sperm centriolar complex (CC) on a comparative basis between mammals and birds. The information is based on selected references from the literature supplemented by original observations on spermiogenesis and sperm structure in disparate mammalian (cheetah and cane rat) and avian (ostrich, rhea and emu) species. Whereas the basic structure of the CC (a diplosome surrounded by pericentriolar material) is similar in Aves and Mammalia, certain differences are apparent. Centriole reduction does not generally occur in birds, but when present as in oscines, involves the loss of the proximal centriole. In ratites, the distal centriole forms the core of the entire midpiece and incorporates the outer dense fibres in addition to initiating axoneme formation. The elements of the connecting piece are not segmented in birds and less complex in basic design than in mammals. The functions of the various components of the CC appear to be similar in birds and mammals. Despite obvious differences in sperm head shape, the centrosomal anomalies afflicting both vertebrate groups demonstrate structural uniformity across species and display a similar range of defects. Most abnormalities result from defective migration and alignment of the CC relative to the nucleus. The most severe manifestation is that of acephalic sperm, while angled tail attachment, abaxial and multiflagellate sperm reflect additional defective forms. The stump-tail defect is not observed in birds. A comparison of defective sperm formation and centrosomal dysfunction at the molecular level is currently difficult owing to the paucity of relevant information on avian sperm. PMID:26907939

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

    USGS Publications Warehouse

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

    2014-01-01

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

  15. 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

  16. Inter- versus Intramolecular Structural Manipulation of a Dichromium(II) Pacman Complex through Pressure Variation.

    PubMed

    Stevens, Charlotte J; Prescimone, Alessandro; Tuna, Floriana; McInnes, Eric J L; Parsons, Simon; Morrison, Carole A; Arnold, Polly L; Love, Jason B

    2016-01-01

    The effect of pressure on the intranuclear M···M separation and intermolecular secondary interactions in the dinuclear chromium Pacman complex [Cr2(L)](C6H6) was evaluated because this compound contains both a short Cr···Cr separation and an exogenously bound molecule of benzene in the solid state. The electronic structure of [Cr2(L)] was determined by electron paramagnetic resonance spectroscopy, SQUID magnetometry, and density functional theory calculations and shows a diamagnetic ground state through antiferromagnetic exchange, with no evidence for a Cr-Cr bond. Analysis of the solid-state structures of [Cr2(L)](C6H6) at pressures varying from ambient to 3.0 GPa shows little deformation in the Cr···Cr separation, i.e., no Cr-Cr bond formation, but instead a significantly increased interaction between the exogenous arene and the chromium iminopyrrolide environment. It is therefore apparent from this analysis that [Cr2(L)] would be best exploited as a rigid chemical synthon, with pressure regulation being used to mediate the approach and secondary interactions of possible substrates. PMID:26683991

  17. 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

  18. 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

  19. 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.

  20. 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

  1. 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

  2. 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

  3. Genetic Variation in the Extended Major Histocompatibility Complex and Susceptibility to Childhood Acute Lymphoblastic Leukemia: A Review of the Evidence

    PubMed Central

    Urayama, Kevin Y.; Thompson, Pamela D.; Taylor, Malcolm; Trachtenberg, Elizabeth A.; Chokkalingam, Anand P.

    2013-01-01

    The enduring suspicion that infections and immunologic response may play a role in the etiology of childhood leukemia, particularly acute lymphoblastic leukemia (ALL), is now supported, albeit still indirectly, by numerous epidemiological studies. The cumulative evidence includes, for example, descriptive observations of a peculiar peak incidence at age 2–5 years for ALL in economically developed countries, clustering of cases in situations of population mixing associated with unusual patterns of personal contacts, associations with various proxy measures for immune modulatory exposures early in life, and genetic susceptibility conferred by variation in genes involved in the immune system. In this review, our focus is the extended major histocompatibility complex (MHC), an approximately 7.6 Mb region that is well-known for its high-density of expressed genes, extensive polymorphisms exhibiting complex linkage disequilibrium patterns, and its disproportionately large number of immune-related genes, including human leukocyte antigen (HLA). First discovered through the role they play in transplant rejection, the classical HLA class I (HLA-A, -B, and -C) and class II (HLA-DR, HLA-DQ, and HLA-DP) molecules reside at the epicenter of the immune response pathways and are now the targets of many disease susceptibility studies, including those for childhood leukemia. The genes encoding the HLA molecules are only a minority of the over 250 expressed genes in the xMHC, and a growing number of studies are beginning to evaluate other loci through targeted investigations or utilizing a mapping approach with a comprehensive screen of the entire region. Here, we review the current epidemiologic evidence available to date regarding genetic variation contained within this highly unique region of the genome and its relationship with childhood ALL risk. PMID:24377085

  4. Sulfur and halogen gases at Masaya Caldera Complex, Nicaragua: Total flux and variations with time

    NASA Astrophysics Data System (ADS)

    Stoiber, Richard E.; Williams, Stanley N.; Huebert, Barry J.

    1986-11-01

    Santiago Crater, of Masaya Caldera Complex near Managua, Nicaragua, entered a phase of intense magmatic degassing in late 1979. The flux of SO2 increased rapidly from a previous average of 380 t d-1 to approximately 1200 t d-1 in February 1980. We report on results of a study of the gas flux and geochemistry conducted as part of a broader interdisciplinary study of the volcano and its impact on the adjacent environment. Masaya is an unusual volcano because of its low shield like form, consistent tholeiitic basaltic composition, frequent activity, and especially because of the approximately 25 year cycle of major non-eruptive degassing crises. We have used a combination of techniques involving remote sensing (using a correlation spectrometer (COSPEC)) of the flux of SO2 and direct filter sampling of the ratios of the sulfur and halogen gases and aerosols to quantify the flux of all of these species. The three-stage filters successively trap aerosols, halogen acid gases, and sulfur dioxide and are analyzed by ion chromatography. We have used the ratios of various species, with the COSPEC measurements of the flux of SO2, to calculate that the average flux of SO2 is 1275 t d-1, HCl is 830 t d-1, HF is about 16 t d-1, and HBr is at most 1 t d-1. H2S and SO4 = are only minor sulfur species. The flux of SO2 and HCl represents the largest reported noneruptive sustained volcanic release of these species in the world. Masaya contributed 7% of the total SO2 estimated to have been released by volcanoes worldwide in 1981. The flux of SO2 has declined by about 9% each year since 1979 and can be modeled as a first-order kinetic rate law with a decay constant of approximately 0.04 yr-1. Approximately 2.2 × 106 tons of SO2 has been released between September 1979 and September 1985. The ratio S/Cl has declined more rapidly than the flux of SO2, reflecting the greater solubility of HCl than SO2 in the magma. The SO2 flux at Santiago varies more widely within a single day than observed at other degassing volcanoes and may be controlled at least in part by effects of the solid earth tide. An area larger than 500 km2 has been severely impacted downwind of the volcano. Downwind ground-level concentrations of SO2 of 0.25 ppm are frequently encountered. Acid rain, unusually chloride rich, has a pH as low as 2.63. S/Cl ratios in the gas plume increase downwind, probably as a result of the high solubility and dry-deposition velocity of HCl. Preliminary analyses of primary concentrations of sulfur and chlorine in the magma of the present lava lake are used to calculate that at least 1.2 km3 has been completely degassed, with respect to sulfur, to provide the observed flux. This implies that 10 km3 have been degassed by previous crises in the past century and further suggests a magma supply rate of approximately 0.1 km3/yr (comparable with Kilauea or Etna volcanoes). During historic time, only two lava flows have been extruded, implying an unusually low ratio of extrusion/intrusion of only 0.0007

  5. 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.

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

    DOE PAGESBeta

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

    2015-04-22

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

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

    PubMed Central

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

    2016-01-01

    Forest carbon (C) density varies tremendously across space due to the inherent heterogeneity of forest ecosystems. Variation of forest C density is especially pronounced in mountainous terrain, where environmental gradients are compressed and vary at multiple spatial scales. Additionally, the influence of environmental gradients may vary with forest age and developmental stage, an important consideration as forest landscapes often have a diversity of stand ages from past management and other disturbance agents. Quantifying forest C density and its underlying environmental determinants in mountain terrain has remained challenging because many available data sources lack the spatial grain and ecological resolution needed at both stand and landscape scales. The objective of this study was to determine if environmental factors influencing aboveground live carbon (ALC) density differed between young versus old forests. We integrated aerial light detection and ranging (lidar) data with 702 field plots to map forest ALC density at a grain of 25 m across the H.J. Andrews Experimental Forest, a 6369 ha watershed in the Cascade Mountains of Oregon, USA. We used linear regressions, random forest ensemble learning (RF) and sequential autoregressive modeling (SAR) to reveal how mapped forest ALC density was related to climate, topography, soils, and past disturbance history (timber harvesting and wildfires). ALC increased with stand age in young managed forests, with much greater variation of ALC in relation to years since wildfire in old unmanaged forests. Timber harvesting was the most important driver of ALC across the entire watershed, despite occurring on only 23% of the landscape. More variation in forest ALC density was explained in models of young managed forests than in models of old unmanaged forests. Besides stand age, ALC density in young managed forests was driven by factors influencing site productivity, whereas variation in ALC density in old unmanaged forests was also affected by finer scale topographic conditions associated with sheltered sites. Past wildfires only had a small influence on current ALC density, which may be a result of long times since fire and/or prevalence of non-stand replacing fire. Our results indicate that forest ALC density depends on a suite of multi-scale environmental drivers mediated by complex mountain topography, and that these relationships are dependent on stand age. The high and context-dependent spatial variability of forest ALC density has implications for quantifying forest carbon stores, establishing upper bounds of potential carbon sequestration, and scaling field data to landscape and regional scales. PMID:27041818

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

    SciTech Connect

    Rampino, Sergio Belpassi, Leonardo

    2015-07-14

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

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

    NASA Astrophysics Data System (ADS)

    Rampino, Sergio; Storchi, Loriano; Belpassi, Leonardo

    2015-07-01

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

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

    PubMed

    Rampino, Sergio; Storchi, Loriano; Belpassi, Leonardo

    2015-07-14

    The chemistry of superheavy elements (Z ≥ 104) is actively investigated in atom-at-a-time experiments of volatility through adsorption on gold surfaces. In this context, common guidelines for interpretation based on group trends in the periodic table should be used cautiously, because relativistic effects play a central role and may cause predictions to fall short. In this paper, we present an all-electron four-component Dirac-Kohn-Sham comparative study of the interaction of gold with Cn (Z = 112), Fl (Z = 114), and Uuo (Z = 118) versus their lighter homologues of the 6th period, Hg, Pb, and Rn plus the noble gas Xe. Calculations were carried out for Au-E (E = Hg, Cn, Pb, Fl, Xe, Rn, Uuo), Au7- and Au20-E (E = Hg, Cn, Pb, Fl, Rn) complexes, where Au7 (planar) and Au20 (pyramidal) are experimentally determined clusters having structures of increasing complexity. Results are analysed both in terms of the energetics of the complexes and of the electron charge rearrangement accompanying their formation. In line with the available experimental data, Cn and more markedly Fl are found to be less reactive than their lighter homologues. On the contrary, Uuo is found to be more reactive than Rn and Xe. Cn forms the weakest bond with the gold atom, compared to Fl and Uuo. The reactivity of Fl decreases with increasing gold-fragment size more rapidly than that of Cn and, as a consequence, the order of the reactivity of these two elements is inverted upon reaching the Au20-cluster adduct. Density difference maps between adducts and fragments reveal similarities in the behaviour of Cn and Xe, and in that of Uuo and the more reactive species Hg and Pb. These findings are given a quantitative ground via charge-displacement analysis. PMID:26178105

  11. Application of spin-restricted open-shell Kohn-Sham method to atomic and molecular multiplet states

    NASA Astrophysics Data System (ADS)

    Filatov, Michael; Shaik, Sason

    1999-01-01

    A recently proposed spin-restricted open-shell Kohn-Sham (ROKS) method is applied to investigate various atomic and molecular multiplet states. A wide range of multiplets is considered: multiplet terms for which the spin-restricted open-shell theory of Roothaan applies, as well as state situations which cannot be described by Roothaan's theory (e.g., states of square cyclobutadiene, etc.). Problems associated with the use of approximate density functionals and possible perspectives of the ROKS method are discussed.

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

    SciTech Connect

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

    2012-01-01

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

  13. 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

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

    PubMed Central

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

    2012-01-01

    GABA type-A receptors are essential for fast inhibitory neurotransmission and are critical in brain function. Surprisingly, expression of receptor subunits is highly variable among individuals, but the cause and impact of this fluctuation remains unknown. We have studied sources of variation for all 19 receptor subunits using massive expression data sets collected across multiple brain regions and platforms in mice and humans. Expression of Gabra1, Gabra2, Gabrb2, Gabrb3, and Gabrg2 is highly variable and heritable among the large cohort of BXD strains derived from crosses of fully sequenced parents—C57BL/6J and DBA/2J. Genetic control of these subunits is complex and highly dependent on tissue and mRNA region. Remarkably, this high variation is generally not linked to phenotypic differences. The single exception is Gabrb3, a locus that is linked to anxiety. We identified upstream genetic loci that influence subunit expression, including three unlinked regions of chromosome 5 that modulate the expression of nine subunits in hippocampus, and that are also associated with multiple phenotypes. Candidate genes within these loci include, Naaa, Nos1, and Zkscan1. We confirmed a high level of coexpression for subunits comprising the major channel—Gabra1, Gabrb2, and Gabrg2—and identified conserved members of this expression network in mice and humans. Gucy1a3, Gucy1b3, and Lis1 are novel and conserved associates of multiple subunits that are involved in inhibitory signaling. Finally, proximal and distal regions of the 3′ UTRs of single subunits have remarkably independent expression patterns in both species. However, corresponding regions of different subunits often show congruent genetic control and coexpression (proximal-to-proximal or distal-to-distal), even in the absence of sequence homology. Our findings identify novel sources of variation that modulate subunit expression and highlight the extraordinary capacity of biological networks to buffer 4–100 fold differences in mRNA levels. PMID:22506031

  15. Secular Variations of Soil CO2 Efflux at Santa Ana-Izalco-Coatepeque Volcanic Complex, El Salvador, Central America

    NASA Astrophysics Data System (ADS)

    Olmos, R.; Barahona, F.; Cartagena, R.; Soriano, T.; Salazar, J.; Hernandez, P.; Perez, N.; Lopez, D.

    2002-12-01

    The Santa Ana-Izalco-Coatepeque volcanic complex (2,365 m elevation), located 40 Km west of San Salvador, consists of the Coatepeque collapse caldera (a 6.5 x 10.5 Km elliptical depression), the Santa Ana and Izalco stratovolcanoes, as well as numerous cinder cones and explosion craters. The summit of the Santa Ana volcano contains an acid lake where hot springs, gas bubbling and intense fumarolic emissions occur. A volcanic plume, usually driven by the NE trades, may be seen rising up to 500 m from the summit crater of the Santa Ana volcano. The goal of this study is to provide a multidisciplinary approach for the volcanic surveillance by means of performing geochemical continuous monitoring of diffuse CO2 emission rate in addition to seismic monitoring. Temporal variations of soil CO2 efflux measured at Cerro Pacho dome, Coatepeque caldera, by means of the accumulation chamber method and using a CO2 efflux continuous monitoring station developed by WEST Systems (Italy). From May 2001 till May 2002, CO2 efflux ranged from 4.3 to 327 gm-2d-1, with a median value of 98 and a quartile range of 26 gm-2d-1. Two distinct diffuse CO2 degassing periods have been observed: (1) an increasing trend from May to July 2001, and (2) a stationary period from November 2001 to May 2002. The increasing-trend period may be due to the anomalous plume degassing at the Santa Ana volcano during 2001 and soon after the January and February 2001 earthquakes. Temporal variations of CO2 efllux during the second period seem to be coupled with those of barometric pressure and wind speed at different time scales, though most of the variance is contained at diurnal and semi-diurnal frequencies. These observations can help to explain the existence of a persistent behavior (Hurst exponent, H=0.934 +/- 0.0039) within the diffuse CO2 degassing phenomena. However, further observations are in progress to understand the long-term memory of diffuse CO2 degassing at the Santa Ana volcanic complex.

  16. 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(N3). 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(N2) 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. U.S. Department of Energy DE-AC02-05CH11231

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

    SciTech Connect

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

    2013-10-15

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

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

    PubMed

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

    2015-12-15

    The density-functional approach to quantum electrodynamics extends traditional density-functional theory and opens the possibility to describe electron-photon interactions in terms of effective Kohn-Sham potentials. In this work, we numerically construct the exact electron-photon Kohn-Sham potentials for a prototype system that consists of a trapped electron coupled to a quantized electromagnetic mode in an optical high-Q cavity. Although the effective current that acts on the photons is known explicitly, the exact effective potential that describes the forces exerted by the photons on the electrons is obtained from a fixed-point inversion scheme. This procedure allows us to uncover important beyond-mean-field features of the effective potential that mark the breakdown of classical light-matter interactions. We observe peak and step structures in the effective potentials, which can be attributed solely to the quantum nature of light; i.e., they are real-space signatures of the photons. Our findings show how the ubiquitous dipole interaction with a classical electromagnetic field has to be modified in real space to take the quantum nature of the electromagnetic field fully into account. PMID:26627715

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

    PubMed

    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

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

    SciTech Connect

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

    2015-04-22

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

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

    SciTech Connect

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

    2015-04-22

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

  2. Quantifying lithic microwear with load variation on experimental basalt flakes using LSCM and area-scale fractal complexity (Asfc)

    NASA Astrophysics Data System (ADS)

    Stemp, W. James; Morozov, Mikhail; Key, Alastair J. M.

    2015-09-01

    Working load is one factor that affects wear on stone tools. Despite the recognition of the importance of the relationship between working load and the development of microwear on stone tools, there have been few attempts to quantify differences in wear due to changes in load. In a controlled experiment, we used 30 basalt flakes knapped from raw material collected in Olduvai Gorge, Tanzania, Africa, to cut oak branches for the same number of strokes. For each flake, a different loading level was applied starting at 150 g and increasing by increments of 150 g to a maximum load of 4.5 kg. A laser scanning confocal microscope was used to mathematically document the surface texture of the flakes. The worn surface data were compared using area-scale fractal complexity (Asfc), calculated from relative areas, to determine the degree to which variation in loading significantly affected the amount of wear on the flake surfaces. Our results indicate that working load does play a role in the development of lithic microwear on these flakes and that discrimination of two worn flake surfaces, using mean square ratios of Asfc, based on variable load is consistently possible with load differences between ∼100 g and 4.5 kg. However, discrimination of microwear on flake surfaces was not consistent for all load level differences and discrimination became less consistent when working load differences were below ∼100 g.

  3. 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

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

    NASA Astrophysics Data System (ADS)

    Gómez de Castro, Ana I.; López-Santiago, Javier; López-Martínez, Fátima; Sánchez, Néstor; de Castro, Elisa; Cornide, Manuel

    2015-06-01

    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 paper, we show how the combination of near ultraviolet (NUV) and infrared (IR) photometry can be used to derive the strength of the 2175 Å bump and thus any enhancement in the abundance of small dust grains and polycyclic aromatic hydrocarbons in the dust grains size distribution. This technique is applied to the envelope of the TMC, mapped by the GALEXAll Sky Survey (AIS). Ultraviolet 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 Å bump is weaker than in the diffuse interstellar medium namely, the low column density extensions of L1495, L1498 and L1524 in Taurus, L1545, L1548, L1519, L1513 in Auriga and L1482-83 in the California region. This finding agrees with previous results on dust evolution derived from Spitzer data and suggests that dust grains begin to decouple from the environmental Galactic magnetic field already in the envelope.

  5. 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

  6. 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.

  7. 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

  8. MN15-L: A New Local Exchange-Correlation Functional for Kohn-Sham Density Functional Theory with Broad Accuracy for Atoms, Molecules, and Solids.

    PubMed

    Yu, Haoyu S; He, Xiao; Truhlar, Donald G

    2016-03-01

    Kohn-Sham density functional theory is widely used for applications of electronic structure theory in chemistry, materials science, and condensed-matter physics, but the accuracy depends on the quality of the exchange-correlation functional. Here, we present a new local exchange-correlation functional called MN15-L that predicts accurate results for a broad range of molecular and solid-state properties including main-group bond energies, transition metal bond energies, reaction barrier heights, noncovalent interactions, atomic excitation energies, ionization potentials, electron affinities, total atomic energies, hydrocarbon thermochemistry, and lattice constants of solids. The MN15-L functional has the same mathematical form as a previous meta-nonseparable gradient approximation exchange-correlation functional, MN12-L, but it is improved because we optimized it against a larger database, designated 2015A, and included smoothness restraints; the optimization has a much better representation of transition metals. The mean unsigned error on 422 chemical energies is 2.32 kcal/mol, which is the best among all tested functionals, with or without nonlocal exchange. The MN15-L functional also provides good results for test sets that are outside the training set. A key issue is that the functional is local (no nonlocal exchange or nonlocal correlation), which makes it relatively economical for treating large and complex systems and solids. Another key advantage is that medium-range correlation energy is built in so that one does not need to add damped dispersion by molecular mechanics in order to predict accurate noncovalent binding energies. We believe that the MN15-L functional should be useful for a wide variety of applications in chemistry, physics, materials science, and molecular biology. PMID:26722866

  9. 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.

  10. Climate and carbon cycle variations in the 20th and 21st centuries in a model of intermediate complexity

    NASA Astrophysics Data System (ADS)

    Eliseev, A. V.; Mokhov, I. I.; Karpenko, A. A.

    2007-02-01

    The climate model of intermediate complexity developed at the Oboukhov Institute of Atmospheric Physics, Russian Academy of Sciences (IAP RAS CM), has been supplemented by a zero-dimensional carbon cycle model. With the carbon dioxide emissions prescribed for the second half of the 19th century and for the 20th century, the model satisfactorily reproduces characteristics of the carbon cycle over this period. However, with continued anthropogenic CO2 emissions (SRES scenarios A1B, A2, B1, and B2), the climate-carbon cycle feedback in the model leads to an additional atmospheric CO2 increase (in comparison with the case where the influence of climate changes on the carbon exchange between the atmosphere and the underlying surface is disregarded). This additional increase is varied in the range 67 90 ppmv depending on the scenario and is mainly due to the dynamics of soil carbon storage. The climate-carbon cycle feedback parameter varies nonmonotonically with time. Positions of its extremes separate characteristic periods of the change in the intensity of anthropogenic emissions and of climate variations. By the end of the 21st century, depending on the emission scenario, the carbon dioxide concentration is expected to increase to 615 875 ppmv and the global temperature will rise by 2.4 3.4 K relative to the preindustrial value. In the 20th 21st centuries, a general growth of the buildup of carbon dioxide in the atmosphere and ocean and its reduction in terrestrial ecosystems can be expected. In general, by the end of the 21st century, the more aggressive emission scenarios are characterized by a smaller climate-carbon cycle feedback parameter, a lower sensitivity of climate to a single increase in the atmospheric concentration of carbon dioxide, a larger fraction of anthropogenic emissions stored in the atmosphere and the ocean, and a smaller fraction of emissions in terrestrial ecosystems.

  11. A perturbation-method-based post-processing for the planewave discretization of Kohn-Sham models

    NASA Astrophysics Data System (ADS)

    Cancès, Eric; Dusson, Geneviève; Maday, Yvon; Stamm, Benjamin; Vohralík, Martin

    2016-02-01

    In this article, we propose a post-processing of the planewave solution of the Kohn-Sham LDA model with pseudopotentials. This post-processing is based upon the fact that the exact solution can be interpreted as a perturbation of the approximate solution, allowing us to compute corrections for both the eigenfunctions and the eigenvalues of the problem in order to increase the accuracy. Indeed, this post-processing only requires the computation of the residual of the solution on a finer grid so that the additional computational cost is negligible compared to the initial cost of the planewave-based method needed to compute the approximate solution. Theoretical estimates certify an increased convergence rate in the asymptotic convergence range. Numerical results confirm the low computational cost of the post-processing and show that this procedure improves the energy accuracy of the solution even in the pre-asymptotic regime which comprises the target accuracy of practitioners.

  12. Excited state tautomerism of the DNA base guanine: A restricted open-shell Kohn-Sham study

    NASA Astrophysics Data System (ADS)

    Langer, Holger; Doltsinis, Nikos L.

    2003-03-01

    The relative stabilities of the six lowest energy tautomers of the DNA base guanine have been investigated in the first excited singlet state, S1, employing the restricted open-shell Kohn-Sham (ROKS) method. Comparison of the S1 optimized geometries to the respective ground-state structures reveals large distortions for the keto tautomers, whereas the enol tautomers remain essentially planar. Harmonic vibrational spectra in the S1 state have been calculated using the ROKS potential energy surfaces. Adiabatic excitation energies together with characteristic vibrational features of the individual guanine tautomers enable us to unambiguously assign recent experimental IR-UV spectra. Velocity autocorrelation functions obtained from adiabatic excited state Car-Parrinello molecular dynamics simulations demonstrate that anharmonic effects only play a minor role.

  13. Hydromermis contorta (Kohn) and Hydromermis pseudocontorta n. sp. from chironomids of Lake Itasca and Long Lake, Minnesota.

    PubMed

    Johnson, A A; Kleve, M G

    1999-02-01

    Hydromermis contorta (Kohn) and Hydromermis pseudocontorta n. sp. are described from chironomids in Lake Itasca and Long Lake, Minnesota, respectively. The former was recovered from adult females of Glyptotendipes paripes (Edwards) and the latter from fourth-instar larvae of Chironomus sp. Hydromermis pseudocontorta n. sp. resembles H. contorta in cephalic structures, overall size, and the presence of a restricted trophosome in the female. The terminal mouth, long uterine and vulvar limbs of the vagina, and the strongly chitinized brownish spicule of H. contorta contrast with the subventral mouth, short vaginal limbs, and the light yellow spicule of H. pseudocontorta n. sp. Both nematode species emerge from the host as sexually mature adults and both species give evidence of mating while in the host. The H. contorta described by Welch is designated as a new species, Hydromermis albionis n. sp. PMID:10207373

  14. Linear interpolation method in ensemble Kohn-Sham and range-separated density-functional approximations for excited states

    NASA Astrophysics Data System (ADS)

    Senjean, Bruno; Knecht, Stefan; Jensen, Hans Jørgen Aa.; Fromager, Emmanuel

    2015-07-01

    Gross-Oliveira-Kohn density-functional theory (GOK-DFT) for ensembles is, in principle, very attractive but has been hard to use in practice. A practical model based on GOK-DFT for the calculation of electronic excitation energies is discussed. The model relies on two modifications of GOK-DFT: use of range separation and use of the slope of the linearly interpolated ensemble energy, rather than orbital energies. The range-separated approach is appealing, as it enables the rigorous formulation of a multideterminant state-averaged DFT method. In the exact theory, the short-range density functional, which complements the long-range wave-function-based ensemble energy contribution, should vary with the ensemble weights even when the density is held fixed. This weight dependence ensures that the range-separated ensemble energy varies linearly with the ensemble weights. When the (weight-independent) ground-state short-range exchange-correlation functional is used in this context, curvature appears, thus leading to an approximate weight-dependent excitation energy. In order to obtain unambiguous approximate excitation energies, we propose to interpolate linearly the ensemble energy between equiensembles. It is shown that such a linear interpolation method (LIM) can be rationalized and that it effectively introduces weight dependence effects. As proof of principle, the LIM has been applied to He, Be, and H2 in both equilibrium and stretched geometries as well as the stretched HeH+ molecule. Very promising results have been obtained for both single (including charge transfer) and double excitations with spin-independent short-range local and semilocal functionals. Even at the Kohn-Sham ensemble DFT level, which is recovered when the range-separation parameter is set to 0, LIM performs better than standard time-dependent DFT.

  15. 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

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

    PubMed

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

    2015-08-01

    Dynamics and properties of nonlinear matter waves in a trapped BEC subject to a PT-symmetric linear potential, with the trap in the form of a super-Gaussian potential, are investigated via a variational approach accounting for the complex nature of the soliton. In the process, we address how the shape of the imaginary part of the potential, that is, a gain-loss mechanism, affects the self-localization and the stability of the condensate. Variational results are found to be in good agreement with full numerical simulations for predicting the shape, width, and chemical potential of the condensate until the PT breaking point. Variational computation also predicts the existence of solitary solution only above a threshold in the particle number as the gain-loss is increased, in agreement with numerical simulations. PMID:26382483

  17. 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

  18. 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...

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

    SciTech Connect

    Kollmar, Christian Neese, Frank

    2014-10-07

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

  20. Effect of the Long-Range Coulomb Interaction on the Phase Diagram of the Kohn-Luttinger Superconducting State in Idealized Graphene

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    The effect of the long-range Coulomb interaction on the formation of the Kohn-Luttinger superconductivity in monolayer doped graphene is studied disregarding the Van der Waals potential of the substrate and both magnetic and non-magnetic impurities. It is shown that the allowance for the Kohn-Luttinger renormalizations up to the second order in perturbation theory in the on-site Hubbard interaction inclusively, as well as in the intersite Coulomb interaction, significantly affects the interplay between the superconducting phases with the f-wave, p+ip -wave, and d + id -wave symmetries of the order parameter. It is demonstrated that taking Coulomb repulsion of electrons located at the next-nearest neighboring atoms in such a system into account changes qualitatively the phase diagram and enhances the critical temperature of the transition to the superconducting phase.

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

    SciTech Connect

    Bleiziffer, Patrick Schmidtel, Daniel; Görling, Andreas

    2014-11-28

    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 (N{sub 2}, O{sub 2}, and the polyyne C{sub 10}H{sub 2}) 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.

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

    NASA Astrophysics Data System (ADS)

    Huhn, William; Blum, Volker

    2015-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Kushwaha, Manvir S.

    2016-03-01

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

  4. Visualization and analysis of the Kohn-Sham kinetic energy density and its orbital-free description in molecules.

    PubMed

    Cancio, Antonio C; Stewart, Dane; Kuna, Aeryk

    2016-02-28

    We visualize the Kohn-Sham kinetic energy density (KED) and the ingredients - the electron density, its gradient, and Laplacian - used to construct orbital-free models of it, for the AE6 test set of molecules. These are compared to related quantities used in metaGGA's, to characterize two important limits - the gradient expansion and the localized-electron limit typified by the covalent bond. We find the second-order gradient expansion of the KED to be a surprisingly successful predictor of the exact KED, particularly at low densities where this approximation fails for exchange. This contradicts the conjointness conjecture that the optimal enhancement factors for orbital-free kinetic and exchange energy functionals are closely similar in form. In addition we find significant problems with a recent metaGGA-level orbital-free KED, especially for regions of strong electron localization. We define an orbital-free description of electron localization and a revised metaGGA that improves upon atomization energies significantly. PMID:26931681

  5. Efficient Parallel All-Electron Four-Component Dirac-Kohn-Sham Program Using a Distributed Matrix Approach II.

    PubMed

    Storchi, Loriano; Rampino, Sergio; Belpassi, Leonardo; Tarantelli, Francesco; Quiney, Harry M

    2013-12-10

    We propose a new complete memory-distributed algorithm, which significantly improves the parallel implementation of the all-electron four-component Dirac-Kohn-Sham (DKS) module of BERTHA (J. Chem. Theory Comput. 2010, 6, 384). We devised an original procedure for mapping the DKS matrix between an efficient integral-driven distribution, guided by the structure of specific G-spinor basis sets and by density fitting algorithms, and the two-dimensional block-cyclic distribution scheme required by the ScaLAPACK library employed for the linear algebra operations. This implementation, because of the efficiency in the memory distribution, represents a leap forward in the applicability of the DKS procedure to arbitrarily large molecular systems and its porting on last-generation massively parallel systems. The performance of the code is illustrated by some test calculations on several gold clusters of increasing size. The DKS self-consistent procedure has been explicitly converged for two representative clusters, namely Au20 and Au34, for which the density of electronic states is reported and discussed. The largest gold cluster uses more than 39k basis functions and DKS matrices of the order of 23 GB. PMID:26592273

  6. 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.

  7. Exact and approximate exchange potentials investigated in terms of their matrix elements with the Kohn-Sham orbitals

    SciTech Connect

    Holas, A.; Cinal, M.

    2005-09-15

    Three approximate exchange potentials of high accuracy v{sub x}{sup Y}(r), Y=A,B,C, for the density-functional theory applications are obtained by replacing the matrix elements of the exact potential between the Kohn-Sham (KS) orbitals with such elements of the Fock exchange operator (within the virtual-occupied subset only) in three representations found for any local potential. A common identity is the base of these representations. The potential v{sub x}{sup C} happens to be the same as that derived by Harbola and Sahni, and v{sub x}{sup A} as that derived by Gritsenko and Baerends, and Della Sala and Goerling. The potentials obtained can be expressed in terms of occupied KS orbitals only. At large r, their asymptotic form -1/r is the same as that of the exact potential. The high quality of these three approximations is demonstrated by direct comparison with the exact potential and using various consistency tests. A common root established for the three approximations could be helpful in finding new and better approximations via modification of identities employed in the present investigation.

  8. Visualization and analysis of the Kohn-Sham kinetic energy density and its orbital-free description in molecules

    NASA Astrophysics Data System (ADS)

    Cancio, Antonio C.; Stewart, Dane; Kuna, Aeryk

    2016-02-01

    We visualize the Kohn-Sham kinetic energy density (KED) and the ingredients — the electron density, its gradient, and Laplacian — used to construct orbital-free models of it, for the AE6 test set of molecules. These are compared to related quantities used in metaGGA's, to characterize two important limits — the gradient expansion and the localized-electron limit typified by the covalent bond. We find the second-order gradient expansion of the KED to be a surprisingly successful predictor of the exact KED, particularly at low densities where this approximation fails for exchange. This contradicts the conjointness conjecture that the optimal enhancement factors for orbital-free kinetic and exchange energy functionals are closely similar in form. In addition we find significant problems with a recent metaGGA-level orbital-free KED, especially for regions of strong electron localization. We define an orbital-free description of electron localization and a revised metaGGA that improves upon atomization energies significantly.

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

    PubMed

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

    2015-12-21

    We developed a program code of configuration interaction singles (CIS) based on a numerical grid method. We used Kohn-Sham (KS) as well as Hartree-Fock (HF) orbitals as a reference configuration and Lagrange-sinc functions as a basis set. Our calculations show that KS-CIS is more cost-effective and more accurate than HF-CIS. The former is due to the fact that the non-local HF exchange potential greatly reduces the sparsity of the Hamiltonian matrix in grid-based methods. The latter is because the energy gaps between KS occupied and virtual orbitals are already closer to vertical excitation energies and thus KS-CIS needs small corrections, whereas HF results in much larger energy gaps and more diffuse virtual orbitals. KS-CIS using the Lagrange-sinc basis set also shows a better or a similar accuracy to smaller orbital space compared to the standard HF-CIS using Gaussian basis sets. In particular, KS orbitals from an exact exchange potential by the Krieger-Li-Iafrate approximation lead to more accurate excitation energies than those from conventional (semi-) local exchange-correlation potentials. PMID:25869540

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

    SciTech Connect

    Makmal, Adi; Kronik, Leeor; Kuemmel, Stephan

    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.

  11. 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

  12. 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; Kraisler, Eli; Makmal, Adi; Kronik, Leeor

    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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  14. Complex interactions between components of individual prey specialization affect mechanisms of niche variation in a grasshopper-hunting wasp.

    PubMed

    Santoro, Davide; Polidori, Carlo; Asís, Josep D; Tormos, José

    2011-11-01

    1. Individual foraging behaviour defines the use of resources by a given population and its variation in different ways such as, for example, unpredictable interactions between taxon-biased and size-biased selection. Here we investigated how the environmental availability of prey and individual specialization, for both prey taxa and prey size, shape niche variation across generations in the grasshopper-hunting digger wasp Stizus continuus. 2. The population of S. continuus expressed selective predation, females mainly hunting species encountered on large bushes; diet changed across generations, due more to size increase in potential prey than to changes in the orthopteran community. 3. Individual females of both generations weakly overlapped the size and taxa of prey, and the niche width of the second generation increased for both prey size and taxa. 4. The greater variance in prey size in the environment accounted for the enlarged prey size niche of the second generation, but the load-lifting constraints of the wasps maintained individual prey size specialization constant. In contrast, the enlarged prey taxon niche paralleled a smaller overlap of diets between wasps in the second generation. 5. Increased niche width in the S. continuus population was thus achieved in two ways. Regarding prey size, all individuals shifted towards the use of the full set of available resources (parallel release). For prey taxa, according to the classical niche variation hypothesis, individuals diverged to minimize resource use overlap and perhaps intraspecific competition. These two mechanisms were observed for the first time simultaneously in a single predator population. PMID:21644980

  15. 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.

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

    PubMed

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

    2016-01-28

    The structure and thermodynamics of inclusion complexes of seven different γ-cyclodextrins (γCDs) and three biologically relevant bile salts (BS) were investigated in the present study. Natural γCD and six modified γCDs [two methyl-γCDs, one sulfobutyl ether-γCD (SBEγCD), and three 2-hydroxypropyl-γCDs (HPγCD)] and their complexes with BS were investigated by isothermal titration calorimetry, NMR, and molecular dynamics simulations. With the exception of the fully methylated γCD, which did not bind the BSs investigated, all of the γCDs formed 1:1 complexes with the BS, and the structures were similar to those with natural γCD; i.e., the modifications of the γCD had limited structural impact on the formation of complexes. Isothermal titration calorimetry was carried out over in the temperature interval 5-55 °C to enable the calculation of the stability constant (K) and the thermodynamic parameters enthalpy (ΔH°), entropy (ΔS°), and heat capacity (ΔCp°). The stability constants decreased with an increased degree of substitution (DS), with methyl substituents having a lower effect on the stability constant than the sulfobutyl ether and hydroxypropyl substituents on the stability constants. Enthalpy-entropy compensation was observed, since both enthalpy and entropy increased with the degree of substitution, which may reflect dehydration of the hydrophobic surface on both CD and BS. Calculations based on ΔCp° data suggested that each of the substituents dehydrated 10-20 (hydroxypropyl), 22-33 (sulfobutyl ether), and 10-15 Å(2) (methyl) of the BS surface area, in reasonable agreement with estimates from the molecular dynamics simulations. Combined with earlier investigations on modified βCDs, these results indicate general trends of the substituents on the thermodynamics of complex formation. PMID:26731242

  17. The electronic structure of alkali aurides. A four-component Dirac-Kohn-Sham study.

    PubMed

    Belpassi, Leonardo; Tarantelli, Francesco; Sgamellotti, Antonio; Quiney, Harry M

    2006-04-01

    Spectroscopic constants, including dissociation energies, harmonic and anharmonic vibrational frequencies, and dipole moments, are calculated for the complete alkali auride series (LiAu, NaAu, KAu, RbAu, CsAu). The four-component formulation of relativistic density functional theory has been employed in this study, using the G-spinor basis sets implemented recently in the program BERTHA. The performance of four standard nonrelativistic density functionals employed is investigated by comparing the results with the best available theoretical and experimental data. The present work provides the first theoretical predictions on the molecular properties of RbAu. The intermetallic bond that occurs in the alkali auride series is highly polar and is characterized by a large charge transfer from the alkali metals to gold. The extent of this electron transfer has been investigated using several different charge analysis methods, enabling us to reach some general conclusions on their relative performance. We further report a detailed analysis of the topological properties of relativistic electron density in the bonding region, discussing the features of this approach which characterize the nature of the chemical bond. We have also computed the fully relativistic density for the alkali halides MBr and MI (M = Li, Na, K, Rb, and Cs). The comparative study shows that, on the basis of several topological properties and the variation in bond lengths, the gold atom behaves similarly to a halogen intermediate between Br and I. PMID:16571062

  18. 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

  19. Use of natural tracers to identify spatial and temporal variation in runoff sources in a complex, mountainous mesoscale catchment

    NASA Astrophysics Data System (ADS)

    Soulsby, C.; Rodgers, P.; Petry, J.; Dunn, S.

    2003-04-01

    Natural tracers (18O, Si and alkalinity) were used to assess the spatial and temporal variation in runoff sources within the 230 km^2 Feshie catchment in the Cairngorm Mountains of Scotland as part of the UK Catchment Hydrology And Sustainable Management (CHASM) initiative. The elevation of the mesoscale catchment ranges between 230--1110 m and snowfall comprises, on average, ca. 30% of annual precipitation. Tracer behavior was monitored by routine sampling in gauged, nested subcatchments ranging from 3--90 km^2 over a hydrological year. In addition, extensive surveys sampled the spatial variation in tracer concentrations throughout the catchment river network at low, moderate and high flows at sampling intensities of 1 per 1 km^2. Use of tracer data and GIS-based assessment indicated that catchment characteristics, rather than scale, accounted for the major differences in contributions from contrasting hydrological sources in nested subcatchments. Most notably, geology and the distribution of soil types exerted a strong control on the partitioning of runoff sources and groundwater contributions to flow (which mixing analysis showed range between 25 and 52% of annual flow in different subcatchments). Coverage of organic peat soils and thin montane podzols strongly influenced the storm runoff response of different subcatchments (with average runoff coefficients ranging from 0.75 to 0.4 for different sub-catchments) and dominated stream hydrochemistry at high flows. Despite the dominant influence of catchment characteristics at the sub-catchment scale, as spatial scale increased beyond 100 km^2 within the mesoscale catchment, the influence of significant alluvial aquifers on hydrological response became apparent. Neverthless, at scales >3 km^2, preliminary analysis of weekly 18O data indicated that mean residence times are similar, though it is reasonable to expect that residence time distributions would vary if high resolution tracer samples (ie daily or sub-daily) were available. Tracer studies such as this provide valuable insight into catchment flow path partitioning that can inform rainfall-runoff modelling in larger mesoscale catchments. However, spatial variation in sub-catchment runoff responses indicates that knowledge of the spatial variability in precipitation and snowmelt are likely to be the main constraints on modelling in such mountainous environments as the Feshie catchment.

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

    SciTech Connect

    Thuéry, Pierre

    2015-07-15

    Terbium nitrate was reacted with 1,3-adamantanedicarboxylic acid (LH{sub 2}) under solvo-hydrothermal conditions with either N,N-dimethylformamide (DMF) or N,N-dimethylacetamide (DMA) as organic solvents. Hydrolysation of the latter co-solvents resulted in the formation of formate or acetate ions, which are present as co-ligands in the 1D coordination polymer [Tb(L)(HCOO)(H{sub 2}O){sub 2}] (1) and the 2D assembly [Tb(L)(CH{sub 3}COO)(H{sub 2}O)] (2). The increase in dimensionality in the latter arises from the higher connectivity provided by acetate versus formate, the L{sup 2−} ligand being bis-chelating in both cases. The complex [Tb{sub 2}(L){sub 3}(H{sub 2}O){sub 5}][Tb{sub 2}(L){sub 3}(H{sub 2}O){sub 4}]·3H{sub 2}O (3), another 1D species, crystallizes alongside crystals of 2. Further addition of cucurbit[6]uril (CB6), with DMF as co-solvent, gave the two complexes [Tb{sub 2}(L){sub 2}(CB6)(H{sub 2}O){sub 6}](NO{sub 3}){sub 2}·6H{sub 2}O (4) and [H{sub 2}NMe{sub 2}]{sub 2}[Tb(L)(HCOO){sub 2}]{sub 2}·CB6·3H{sub 2}O (5). Complex 4 crystallizes as a 3D framework in which Tb(L){sup +} chains are connected by tetradentate CB6 molecules, while 5 unites a carboxylate-bridged anionic 2D planar assembly and layers of CB6 molecules with counter-cations held at both portals. - Graphical abstract: One- to three-dimensional assemblies are formed in terbium(III) complexes with 1,3-adamantanedicarboxylate obtained under solvo-hydrothermal conditions, these species including formate or acetate co-ligands formed in situ, or additional cucurbit[6]uril molecules. - Highlights: • We report structures of terbium(III) complexes with 1,3-adamantanedicarboxylate. • Solvents able to generate co-ligands or counter-ions in situ have been used. • A 3D species including additional cucurbituril molecules is decribed. • One species displays an alternation of metal–organic and organic sheets.

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

    PubMed Central

    Duchoslav, Martin; Šafářová, Lenka; Jandová, Michaela

    2013-01-01

    Background and Aims Although the large variation in genome size among different species is widely acknowledged, the occurrence and extent of variation below the species level are still controversial and have not yet been satisfactorily analysed. The aim of this study was to assess genome size variation in six ploidy levels (2n = 3x–8x) of the polyploid Allium oleraceum over a large geographical gradient and to search for potential interpretations of the size variation. Methods The genome sizes of 407 individuals of A. oleraceum collected from 114 populations across Europe were determined by flow cytometry using propidium iodide staining. The genome size variation was correlated with spatial, climatic and habitat variables. Key Results The mean holoploid genome size (2C DNA) was 42·49, 52·14, 63·34, 71·94, 85·51 and 92·12 pg at the tri-, tetra-, penta-, hexa-, hepta- and octoploid levels, respectively. Genome size varied from a minimum of 2·3 % in the octoploids to a maximum of 18·3 % in the tetraploids. Spatial structuring of genome size was observed within the tetra- and pentaploids, where 2C DNA significantly increased with both latitude and longitude, and correlated with several climatic variables, suggesting a gradient of continentality. Genome size in hexaploids showed low variation, weak correlation with climatic variables and no spatial structuring. Downsizing in monoploid genome size was observed between all cytotypes except for heptaploids. Splitting populations into western and eastern European groups resulted in strong differences in monoploid genome size between groups in tetra- and pentaploids but not in hexaploids. The monoploid genome sizes of the cytotypes were similar in the western group but diverged in the eastern group. Conclusions Complex patterns of holoploid and monoploid genome size variation found both within and between A. oleraceum cytotypes are most likely the result of several interacting factors, including different evolutionary origins of cytotypes via hybridization of parental combinations with different genome sizes in the south-western and south-eastern part of Europe, introgression between cytotypes, and antropic dispersal. The role of broad-scale and fine-scale environmental variables in shaping genome size is probably of minor importance in A. oleraceum. PMID:23348752

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

    NASA Astrophysics Data System (ADS)

    Thuéry, Pierre

    2015-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  4. Evolution and phylogenetic utility of the PHOT gene duplicates in the Verbena complex (Verbenaceae): dramatic intron size variation and footprint of ancestral recombination.

    PubMed

    Yuan, Yao-Wu; Olmstead, Richard G

    2008-09-01

    A well-resolved species level phylogeny is critically important in studying organismal evolution (e.g., hybridization, polyploidization, adaptive speciation). Lack of appropriate molecular markers that give sufficient resolution to gene trees is one of the major impediments to inferring species level phylogenies. In addition, sampling multiple independent loci is essential to overcome the lineage sorting problem. The availability of nuclear loci has often been a limiting factor in plant species-level phylogenetic studies. Here the two PHOT loci were developed as new sources of nuclear gene trees. The PHOT1 and PHOT2 gene trees of the Verbena complex (Verbenaceae) are well resolved and have good clade support. These gene trees are consistent with each other and previously generated chloroplast and nuclear waxy gene trees in most of the phylogenetic backbone as well as some terminal relationships, but are incongruent in some other relationships. Locus-specific primers were optimized for amplifying and sequencing these two loci in all Lamiales. Comparing intron size in the context of the gene trees shows dramatic variation within the Verbena complex, particularly at the PHOT1 locus. These variations are largely caused by invasions of short transposable elements and frequent long deletions and insertions of unknown causes. In addition, inspection of DNA sequences and phylogenetic analyses unmask a clear footprint of ancestral recombination in one species. PMID:21632434

  5. 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

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

    PubMed Central

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

    2014-01-01

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

  7. Application of liver three-dimensional printing in hepatectomy for complex massive hepatocarcinoma with rare variations of portal vein: preliminary experience

    PubMed Central

    Xiang, Nan; Fang, Chihua; Fan, Yingfang; Yang, Jian; Zeng, Ning; Liu, Jun; Zhu, Wen

    2015-01-01

    Background: To discuss the role of Liver 3D printing in the treatment of complex massive hepatocarcinoma with rare variations of portal vein. Methods: Data of enhanced computed tomography (CT) were imported into the medical image three-dimensional visualization system (MI-3DVS) to create Standard Template Library (STL) files, which were read by 3D printer to construct life-size 3D physical liver model. The preoperative surgical planning was performed on the 3D model according to individualized segmentation, volume calculation, and virtual operation. Results: The 3D printing liver model was consistent with the model in MI-3DVS. The segment 4 portal vein (S4PV) was absent and variant S4PV originated from right anterior portal vein (RAPV). The preoperative surgical planning was designed according to the relationship between tumor and portal vein variation. Theoretically, the residual liver volume was 40.76%, if the right hemihepatctomy was carried out after the trunk of right portal vein (RPV) ligated. However, the actual residual volume was only 21.37% due to the variant S4PV originates from RAPV, thus, right trisegmentectomy would have to be performed. Interestingly, after optimization, the residual liver volume increased to 57.25% as narrow-margin right hemihepatectomy with the variant S4PV reserved were performed. The final resection was determined to be narrow-margin right hemihepatectomy. The actual surgical procedure was consistent with the preoperative surgical planning. Conclusion: Liver 3D printing may be a safe and effective technique to improve the success rate of surgery and reduce the operation risk for patients with complex massive hepatocarcinoma with variations of portal vein. PMID:26770510

  8. Re-Os isotope and Pd/Ru variations in chromitites from the Critical Zone, Bushveld Complex, South Africa

    NASA Astrophysics Data System (ADS)

    McCandless, Tom E.; Ruiz, Joaquin; Adair, B. Ivan; Freydier, Claire

    1999-07-01

    Rhenium-osmium isotope measurements of selected chromitites from the Critical Zone of the Bushveld igneous complex reveal that a significant component of radiogenic Os was present in the magma when it formed 2.06 Ga ago. Measured 187Os/ 188Os ratios increase with stratigraphic height, and individual layers have similar values across the complex. Initial 187Os/ 188Os ratios for chromitites from the western Bushveld decrease from 0.140 at the LG to 0.129 at the MG2 chromitite, increasing to 0.153 at the UG2 chromitite. The inflection at MG2/MG3 is the boundary between the lower and upper Critical Zone, consistent with previous mineralogical and geochemical studies indicating a shift in magma composition at this point. Chromite separates have γOs values of ˜12-35 at 2.06 Ga and are too radiogenic for a purely mantle derivation. Assimilation of 5% mafic granulitic lower crust in a tholeiitic parent magma can explain the radiogenic values. Pd/Ru ratios for the intergranular and chromite separate components of each layer differ by orders of magnitude, but relative shifts from layer to layer are similar. Combined with the Re-Os data, the results suggest that PGE were concentrated into chromitites by magmatic or early deuteric processes that were specific to each layer. Post-layering, upward mobilization of PGE by hydrothermal processes probably did not play a significant role in PGE enrichment.

  9. 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

  10. 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.

  11. 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.

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

    PubMed Central

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

    2015-01-01

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

  13. Genetic variation coincides with geographic structure in the common bush-tanager (Chlorospingus ophthalmicus) complex from Mexico.

    PubMed

    García-Moreno, Jaime; Navarro-Sigüenza, Adolfo G; Peterson, A Townsend; Sánchez-González, Luis A

    2004-10-01

    Cloud forests are distributed in the Neotropics, from northern Mexico to Argentina, under very specific ecological conditions, namely slopes with high humidity input from clouds and mist. Its distribution in Mesoamerica is highly fragmented, similar to an archipelago, and taxa are thus frequently represented as sets of isolated populations, each restricted to particular mountain ranges and often showing a high degree of divergence, both morphologically and genetically. The common bush-tanager (Chlorospingus ophthalmicus, Aves: Thraupidae) inhabits cloud forests from eastern and southern Mexico south to northwestern Argentina. Here we use 676bp of mtDNA (around the ATPase 8 gene) to explore the genetic variation and phylogeographic structure of the Mexican populations of C. ophthalmicus. Phylogenetic analyses of mtDNA sequences indicate deep genetic structure. Five major clades, which segregate according to geographic breaks, are identified (starting from the deepest one in the phylogeny): (1) Southern Chiapas and Northern Central America, (2) Tuxtlas massif, (3) Sierra Madre del Sur, (4) Eastern Oaxaca and Northern Chiapas, and (5) Sierra Madre Oriental. The long history of isolation undergone by each clade, as suggested by the phylogeny, implies that the species status of each of them should be revised. PMID:15324847

  14. Variation in Complexity of Infection and Transmission Stability between Neighbouring Populations of Plasmodium vivax in Southern Ethiopia

    PubMed Central

    Getachew, Sisay; To, Sheren; Trimarsanto, Hidayat; Thriemer, Kamala; Clark, Taane G.; Petros, Beyene; Aseffa, Abraham; Price, Ric N.; Auburn, Sarah

    2015-01-01

    Background P. vivax is an important public health burden in Ethiopia, accounting for almost half of all malaria cases. Owing to heterogeneous transmission across the country, a stronger evidence base on local transmission dynamics is needed to optimise allocation of resources and improve malaria interventions. Methodology and Principal Findings In a pilot evaluation of local level P. vivax molecular surveillance in southern Ethiopia, the diversity and population structure of isolates collected between May and November 2013 were investigated. Blood samples were collected from microscopy positive P. vivax patients recruited to clinical and cross-sectional surveys from four sites: Arbaminch, Halaba, Badawacho and Hawassa. Parasite genotyping was undertaken at nine tandem repeat markers. Eight loci were successfully genotyped in 197 samples (between 36 and 59 per site). Heterogeneity was observed in parasite diversity and structure amongst the sites. Badawacho displayed evidence of unstable transmission, with clusters of identical clonal infections. Linkage disequilibrium in Badawacho was higher (IAS = 0.32, P = 0.010) than in the other populations (IAS range = 0.01–0.02) and declined markedly after adjusting for identical infections (IAS = 0.06, P = 0.010). Other than Badawacho (HE = 0.70), population diversity was equivalently high across the sites (HE = 0.83). Polyclonal infections were more frequent in Hawassa (67%) than the other populations (range: 8–44%). Despite the variable diversity, differentiation between the sites was low (FST range: 5 x 10−3–0.03). Conclusions Marked variation in parasite population structure likely reflects differing local transmission dynamics. Parasite genotyping in these heterogeneous settings has potential to provide important complementary information with which to optimise malaria control interventions. PMID:26468643

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

    PubMed

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

    2014-04-01

    This study investigated the tempospatial variation of atmospheric mercury and its gas-particulate partition in the vicinity of a semiconductor manufacturing complex, where a plenty of flat-monitor manufacturing plants using elemental mercury as a light-initiating medium to produce backlight fluorescence tubes and may fugitively emit mercury-containing air pollutants to the atmosphere. Atmospheric mercury speciation, concentration, and the partition of total gaseous mercury (TGM) and particulate mercury (Hgp) were measured at four sites surrounding the semiconductor manufacturing intensive district/complex. One-year field measurement showed that the seasonal averaged concentrations of TGM and Hgp were in the range of 3.30-6.89 and 0.06-0.14ng/m(3), respectively, whereas the highest 24-h TGM and Hgp concentrations were 10.33 and 0.26ng/m(3), respectively. Atmospheric mercury apportioned as 92.59-99.01% TGM and 0.99-7.41% Hgp. As a whole, the highest and lowest concentrations of TGM were observed in the winter and summer sampling periods, respectively, whereas the concentration of Hgp did not vary much seasonally. The highest TGM concentrations were always observed at the downwind sites, indicating that the semiconductor manufacturing complex was a hot spot of mercury emission source, which caused severe atmospheric mercury contamination over the investigation region. PMID:24407780

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

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

    PubMed Central

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

    2014-01-01

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

  19. 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

  20. 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

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

    PubMed

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

    2015-09-21

    The solution of the Liouville-von Neumann equation in the relativistic Dirac-Kohn-Sham density matrix formalism is presented and used to calculate X-ray absorption cross sections. Both dynamical relaxation effects and spin-orbit corrections are included, as demonstrated by calculations of the X-ray absorption of SF6 near the sulfur L2,3-edges. We also propose an analysis facilitating the interpretation of spectral transitions from real-time simulations, and a selective perturbation that eliminates nonphysical excitations that are artifacts of the finite basis representation. PMID:26268195

  2. Magma Mixing in Uralian-Alaskan Type Complexes in the Ural Mountains, Russia: Implications from the Trace Element Variation in Clinopyroxene

    NASA Astrophysics Data System (ADS)

    Krause, J.; Bruegmann, G. E.; Pushkarev, E.

    2006-12-01

    The distinctive geologic and petrographic feature of classical Uralian-Alaskan-type zoned mafic-ultramafic complexes is a zonal distribution of mafic and ultramafic rocks, with a central dunite body that grades outward into clinopyroxenite and gabbroic lithologies. This rock association is considered to represent cumulates of a single parental melt feeding a magma chamber system. In this study we discuss in-situ trace element variations (LA-ICPMS analyses) in clinopyroxene from gabbros of the Nizhnii Tagil and Kytlym complexes in the Ural Mountains in Russia. The gabbros have porphyric textures with clinopyroxene phenocrysts in a matrix of olivine, clinopyroxene and spinel. Two gabbro types can be distinguished based on additional matrix minerals. One type of gabbro is silica saturated, contains plagioclase (An57-88) and in places orthopyroxene as matrix phases. This type occurs in all complexes. The second gabbro type is silica undersaturated and contains in the matrix plagioclase (An29-56) and pseudoleucite, a fine grained intergrowth of nepheline and K- feldspar (Or30-81). It is only observed in Nizhnii Tagil and the western part of the Kytlym Complex, however, it is interbedded on a scale of decimeter to tens of meters with the silica-saturated gabbro. Clinopyroxene of gabbros from Nizhnii Tagil and the western part of the Kytlym Complex is enriched in LREEN (4.4-33.6; normalized to the primitive mantle values of Hofmann (1988)) relative to HREEN (1.4-8.4) and have high Sr concentrations (130-470 ppm). Phenocryst cores from pseudoleucite-bearing gabbros tend to have higher La/Lu (30-35) than those of silicate-saturated gabbros (La/Lu: 17-30). Towards the phenocryst rims the La/Lu increases up to 45 in the pseudolucite bearing gabbros monitoring the trend of fractional crystallization. However, the continuous increase of La/Lu from silica-saturated to silica-undersaturated gabbro traces the mixing of two different parental magmas. Clinopyroxene from gabbros of the Tilay Mountain area in the eastern part of the Kytlym Complex are consistently less enriched in LREEN (0.9-13.1) relative to the HREEN (0.7-9.1) and have lower Sr concentrations (27-76ppm) than those from the other localities. On the scale of a thin section cores of phenocrysts with different LREE/HREE can be observed. Cores, rich in inclusions of olivine, plagioclase, spinel and phlogopite have La/Lu of 13-16, whereas other clinopyroxene cores are poor in inclusions and have lower La/Lu of 5-8 at similar Lu concentrations (0.15-0.2 ppm). Just outside of the core both phenocryst types have similar La/Lu of 9-11 and Lu 0.2-0.3 ppm. The rims of the phenocrysts and the interstitial clinopyroxene have similar trace element compositions with lower La/Lu (9-7) and higher Lu concentrations (0.3-0.5ppm). This reflects the crystallization of a common interstitial pore liquid. However, the core compositions indicate the presence of two different parental magmas. After mixing of these magmas the clinopyroxene cores were overgrown by clinopyroxene crystallizing from the hybrid magma. The observed variations in the trace element content of clinopyroxene monitor the evolution of the parental melts of Uralian-Alaskan-type Complexes and emphasize the importance of magma mixing processes. The contemporaneous occurrence of silica-saturated and -undersaturated melts appears to be a common feature of the Uralian complexes.

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

    PubMed Central

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

    2015-01-01

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

  4. 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

  5. Variation in the composition of apatite in the Munni Munni Complex and associated intrusions of the West Pilbara Block, Western Australia

    NASA Astrophysics Data System (ADS)

    Boudreau, Alan E.; Love, Coleen; Hoatson, Dean M.

    1993-09-01

    Apatite is a ubiquitous intercumulus mineral in the Archean Munni Munni, Radio Hill, and Mount Sholl layered igneous complexes of the west Pilbara Block in Western Australia. Apatite compositions from the three intrusions are relatively rich in the fluorapatite endmember and become more so in cumulates derived from compositionally evolved magmas. The most extensive stratigraphic coverage is from the Munni Munni complex, where the mole fraction of fluorapatite increases from approximately 60-70% in cumulates of the ultramafic zone to over 90% near the top of the gabbroic zone. The chlorapatite component decreases from a high of 20-30 mol% in the ultramafic zone to less than 10% in the uppermost part of the gabbroic zone. The REE content of apatite parallels stratigraphic changes in whole rock incompatible element (Zr, Rb) concentrations and is consistent with equilibration with the bulk assemblage. The stratigraphic decrease in the Cl/F and OH/F ratio of apatite can be modeled by assuming that fluid saturation of intercumulus liquids is a function of pressure and occurs prior to apatite saturation. Imposed on the stratigraphic trend are the effects of the combined processes of continuing fluid loss and fractional crystallization of apatite (and locally biotite) during solidification of the intercumulus liquid. These processes produced relative compositional variations in endmember components on the order of 50 mol% or more in individual thin sections. Because apatite crystallizes late in the solidification of intercumulus liquids, it is estimated that the Cl/F ratio of the original trapped parent liquid prior to degassing could have been more than 2 orders of magnitude higher than is now recorded by intercumulus apatite compositions. A comparison of literature apatite compositions from other intrusions shows that, with the exception of the unusually Cl-rich assemblages of the Stillwater and Bushveld complexes, processes affecting halogen geochemistry of layered intrusions do not appear to have changed significantly over the past 3 Ga.

  6. Variation of uranium and radon concentration in ground water along the track from non-HHP to HHP region of Tusham ring complex

    NASA Astrophysics Data System (ADS)

    Bikram Jit Singh, Bajwa; Harman, Singh; Vishal, Arora; Surinder, Singh

    2010-05-01

    The levels of uranium and radon concentration in groundwater samples collected from some regions along the track from Amritsar city (Punjab) to Tusham ring complex (Haryana) has been analysed using SSTNDs from the health aspects point of view and also to observe its variation with the geological formations of the respective regions. In the high heat producing (HHP) granitic region of Tusham ring complex, Bhiwani District, Haryana, known to be composed of acid volcanics & associated HHP granites, uranium concentration in the groundwater water samples varies from 7.6±0.03 - 59.6±0.20 μgl-1 with the average of 27.9 μg l-1, which is comparatively higher than the average value of 17.4 μg l-1 observed in non-HHP/non-granitic region of Amritsar, Punjab. Uranium concentration values in these samples show a wide range of variation depending upon different factors like source, location, depth and local geology etc. Except at certain specific locations in the HHP Tusham region, the levels of uranium concentration in the samples of ground water are lower than the international recommended safe limits. The radon concentration in the ground water samples along this track has also been studied using the Alpha-Scintillometer (GmBH 2002). Although the radon concentration varied from 3.4±0.6 to 15.7±0.5 Bq l-1 for the non-HHP Punjab region , but it has been to have a wide variation from 4.7±0.7 to 49.7±1.7 Bq l-1 on approaching the HHP Tusham region. Although both uranium and radon distribution in groundwater was found to be related with the acid volcanics and HHP zones in the respective regions, but no general trend was observed for any relation with the source depth and surface radionuclide content. On the other hand, a slightly positive correlation (R2 = 0.5) between radon content and uranium concentration in water samples of the studied region explicitly depicts that 222Rn concentration strongly depends on its progenitor content in water. The slightly higher values were observed from the ground water samples particularly of the areas falling in this belt of pre-Malani igneous rocks famous for lithological units, including felsite, granite and schist exposed in the area near Haryana-Rajasthan border. The values observed at certain locations are found to be higher than the international recommendations. The high uranium concentration observed particularly in some locations around Tusham Ring Complex can be attributed due to interaction of ground water with the soils as well as rock formations of this region and the local subsurface geology of the region.

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  9. 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

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

    PubMed

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

    2016-03-01

    It has been widely reported that the major histocompatibility complex (MHC) is under balancing selection due to its immune function across terrestrial and aquatic mammals. The comprehensive studies at MHC and other neutral loci could give us a synthetic evaluation about the major force determining genetic diversity of species. Previously, a low level of genetic diversity has been reported among the Indo-Pacific humpback dolphin (Sousa chinensis) in the Pearl River Estuary (PRE) using both mitochondrial marker and microsatellite loci. Here, the expression and sequence polymorphism of 2 MHC class II genes (DQB and DRB) in 32 S. chinensis from PRE collected between 2003 and 2011 were investigated. High ratios of non-synonymous to synonymous substitution rates, codon-based selection analysis, and trans-species polymorphism (TSP) support the hypothesis that balancing selection acted on S. chinensis MHC sequences. However, only 2 haplotypes were detected at either DQB or DRB loci. Moreover, the lack of deviation from the Hardy-Weinberg expectation at DRB locus combined with the relatively low heterozygosity at both DQB locus and microsatellite loci suggested that balancing selection might not be sufficient, which further suggested that genetic drift associated with historical bottlenecks was not mitigated by balancing selection in terms of the loss of MHC and neutral variation in S. chinensis. The combined results highlighted the importance of maintaining the genetic diversity of the endangered S. chinensis. PMID:26787544

  11. A large perturbation on electronic and photophysical properties of Ir(III) carbene complexes caused by the variation of N-substitution in N,N‧-heteroaromatic ligands

    NASA Astrophysics Data System (ADS)

    Liu, Yuqi; Si, Yanling; Wang, Ying; Wu, Zhijian

    2014-08-01

    DFT/TDDFT investigation was performed on the electronic and photophysical properties of blue-emitting Ir(III) carbene complexes (fpmi)3-xIr(N^N‧)x (x = 1, 2) [fpmi = 1-(4-fluorophenyl)-3-methylimidazolin-2-ylidene-C,C2‧, N^N‧ = 2-(1H-pyrazol-5-yl)pyridinato (1a(x = 1)/1a‧(x = 2)); 2-(1H-imidazol-5-yl)pyridinato (1b/1b‧); 2-(1H-imidazol-2-yl)pyridinato (1c/1c‧); 2-(1H-1,2,4-triazol-5-yl)pyridinato (2a/2a‧); 2-(1H-1,2,3-triazol-5-yl)pyridinato (2b/2b‧); 2-(4H-1,2,4-triazol-3-yl)pyridinato (2c/2c‧)]. The absorption intensities and band positions are obviously affected by the variation of N substitution in N^N‧ ligand. The emission properties show an apparent dependence on the solvent effects, and the N^N‧ ligand plays an important role in governing the emissive state. The pyrazolyl-pyridyl-based N^N‧ ligand is considered to be more beneficial for blue OLEDs emitters.

  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. 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 √{α }, where α 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.

  15. Determination of outer molecular orbitals by collisional ionization experiments and comparison with Hartree-Fock, Kohn-Sham, and Dyson orbitals

    SciTech Connect

    Yamazaki, Masakazu; Horio, Takuya; Kishimoto, Naoki; Ohno, Koichi

    2007-03-15

    Although the outer shapes of molecular orbitals (MO's) are of great importance in many phenomena, they have been difficult to be probed by experiments. Here we show that metastable helium (He{sup *}) atoms can sensitively probe the outer properties of molecules and that an electron spectroscopic technique using velocity-selected He{sup *} atoms in combination with classical trajectory simulations leads to a consistent determination of MO functions and the molecular surface. MO functions composed of linear combinations of atomic orbital functions were fitted to the observed collision energy dependences of partial ionization cross sections (CEDPICS). The obtained CEDPICS MO functions were compared with conventionally available Hartree-Fock, Kohn-Sham, and Dyson orbitals.

  16. Genetic Variation of the Major Histocompatibility Complex (MHC Class II B Gene) in the Threatened Hume’s Pheasant, Syrmaticus humiae

    PubMed Central

    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

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

    The Barzilai-Borwein (BB) 2-point step size gradient method is receiving attention for accelerating Total Variation (TV) based CBCT reconstructions. In order to become truly viable for clinical applications, however, its convergence property needs to be properly addressed. We propose a novel fast converging gradient projection BB method that requires ‘at most one function evaluation’ in each iterative step. This Selective Function Evaluation method, referred to as GPBB-SFE in this paper, exhibits the desired convergence property when it is combined with a ‘smoothed TV’ or any other differentiable prior. This way, the proposed GPBB-SFE algorithm offers fast and guaranteed convergence to the desired 3DCBCT image with minimal computational complexity. We first applied this algorithm to a Shepp-Logan numerical phantom. We then applied to a CatPhan 600 physical phantom (The Phantom Laboratory, Salem, NY) and a clinically-treated head-and-neck patient, both acquired from the TrueBeam™ system (Varian Medical Systems, Palo Alto, CA). Furthermore, we accelerated the reconstruction by implementing the algorithm on NVIDIA GTX 480 GPU card. We first compared GPBB-SFE with three recently proposed BB-based CBCT reconstruction methods available in the literature using Shepp-Logan numerical phantom with 40 projections. It is found that GPBB-SFE shows either faster convergence speed/time or superior convergence property compared to existing BB-based algorithms. With the CatPhan 600 physical phantom, the GPBB-SFE algorithm requires only 3 function evaluations in 30 iterations and reconstructs the standard, 364-projection FDK reconstruction quality image using only 60 projections. We then applied the algorithm to a clinically-treated head-and-neck patient. It was observed that the GPBB-SFE algorithm requires only 18 function evaluations in 30 iterations. Compared with the FDK algorithm with 364 projections, the GPBB-SFE algorithm produces visibly equivalent quality CBCT image for the head-and-neck patient with only 180 projections, in 131.7 s, further supporting its clinical applicability.

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

    PubMed

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

    2010-11-01

    The objective of this study is to assess the variation of pollution in the Thai-Laos Mekong associated with seasonal dynamics concomitant with the natural geological features and human activities that impact on the adverse quality of the river. The complex ecology of the 1500 km stretch of the Thai-Laos Mekong River has been studied in this paper to understand the relationship with the geomorphology, with the sub-tropical monsoonal climate and the impact of human activity. Sub-surface geology controls the nature and extent of the drainage basin and of the river channel. The volume flow of the river varies naturally and dynamically in phase with the rainfall; traditional models based on steady state hydraulics are inappropriate. Continuous erosion of the river banks and bed generates a sediment load of impure silt, mica, quartz and clay minerals that inhibits light penetration and limits the primary productivity of the river. The river separates two countries at different stages of development; it flows through or close to eight non-industrial conurbations (Populations 350,000-2,000,000) but is otherwise sparsely populated. The river is used for subsistence agriculture, village transport, fishing including aquaculture and as a source of domestic water. Hydroelectricity is generated from the Laos tributaries. The river is a depository for partially treated urban waste and untreated village waste, hence populations of E.coli bacteria sometimes render the water unsuitable for drinking unless treated with the highest value of 240/100 ml found at station 7 during the summer season of 2003. Furthermore the river is polluted by trace metals, notably cadmium and mercury, and by Polycyclic Aromatic Hydrocarbons (PAHs), which are particularly concentrated in the sediments. Previous work has shown that cadmium and mercury exceed the Probable Effect Level (PEL) values of Canadian Environmental Quality Guidelines and that the PAH concentrations were also greater than the Interim Sediment Quality Guidelines (ISQG). Consequently the fish stock, a vital source of protein for the local human population maybe seriously affected. As conflict between the demands of human activities will be exacerbated by the continuing development of the basin; monitoring must be continued and a better model of the river's ecology is needed to predict the impact of development. PMID:20859820

  19. Calculations of Al dopant in α-quartz using a variational implementation of the Perdew-Zunger self-interaction correction

    NASA Astrophysics Data System (ADS)

    Gudmundsdóttir, Hildur; Jónsson, Elvar Ö.; Jónsson, Hannes

    2015-08-01

    The energetics and atomic structure associated with the localized hole formed near an Al-atom dopant in α-quartz are calculated using a variational, self-consistent implementation of the Perdew-Zunger self-interaction correction with complex optimal orbitals. This system has become an important test problem for theoretical methodology since generalized gradient approximation energy functionals, as well as commonly used hybrid functionals, fail to produce a sufficiently localized hole due to the self-interaction error inherent in practical implementations of Kohn-Sham density functional theory. The self-interaction corrected calculations are found to give accurate results for the energy of the defect state with respect to both valence and conduction band edges as well as the experimentally determined atomic structure where only a single Al-O bond is lengthened by 11%. The HSE hybrid functional, as well as the PW91 generalized gradient approximation functional, however, gives too small an energy gap between the defect state and the valence band edge, overly delocalized spin density and lengthening of more than one Al-O bond.

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

    NASA Astrophysics Data System (ADS)

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

    1996-11-01

    We have investigated the accuracy of the local-spin-density approximation with orbital-density-dependent self-interaction correction (LSDSIC) as proposed by Perdew and Zunger within a Kohn-Sham approach in which electrons with a given spin projection all move in a single optimized effective potential (OEP). We have also studied the accuracy of the Krieger-Li-Iafrate (KLI) approximation to the OEP for the same energy functional in order to assess its applicability to systems in which the integral equation for the OEP cannot be reduced to a one-dimensional problem, e.g., molecules. Self-consistent Kohn-Sham LSDSIC calculations have been performed for atoms with atomic number Z=1-20 in the exchange-only case for the total energy, the highest-occupied orbital energy ɛm, and the expectation value of r2. In addition, the structure of the resulting exchange potential is examined and compared with the exact exchange-only density-functional theory (OEP method with Hartree-Fock exchange-energy functional) results. Furthermore, we display ɛm, the ionization potential I, and the electron affinity A when both exchange and correlation energy effects are included. Finally, we also consider the results of evaluating the LSDSIC energy functional by employing the exact (in the central-field approximation) single particle orbitals as proposed by Harrison. We find that the LSDSIC energy functional generally leads to calculated values that are superior to those provided by the LSD approximation and that the KLI approximation yields results in excellent agreement with the corresponding exact OEP results for this energy functional. In particular, quantities strongly related to the behavior of the valence electrons are nearly identical in both the OEP and KLI calculations, i.e., the difference between the and ɛm is less than 0.2% on average, while the difference between the calculated I is less than 0.2 millihartree on average with the corresponding difference of only 0.1 millihartree for A.

  1. 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.

  2. 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.

    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.

  3. Computation of the Kohn-Sham orbital kinetic energy density in the full-potential linearized augmented plane-wave method

    NASA Astrophysics Data System (ADS)

    Ye, Lin-Hui

    2015-02-01

    The Kohn-Sham orbital kinetic energy density τσ(r ) =∑iwi σ|∇ψi σ(r ) | 2 is one fundamental quantity for constructing metageneralized gradient approximations (meta-GGAs) for use by density functional theory. We present a computational scheme of τσ(r ) for the full-potential linearized augmented plane-wave (FLAPW) method. Our scheme is highly accurate and efficient and easy to implement with existing computer codes. To illustrate its performance, we construct the Becke-Johnson meta-GGA exchange potentials for Be, Ne, Mg, Ar, Ca, Zn, Kr, and Cd atoms, which are in very good agreement with the original results. For bulk solids, we construct the Tran-Blaha modified Becke-Johnson potential (mBJ) and confirm its capability to calculate band gaps with the reported bad convergence of the mBJ potential being substantially improved. The present computational scheme of τσ(r ) should also be valuable for developing other meta-GGAs in the FLAPW as well as in similar methods utilizing atom centered basis functions.

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

    PubMed

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

    2016-04-28

    The substituent effect of the amino and nitro groups on the electronic system of benzene has been investigated quantum chemically using quantitative Kohn-Sham molecular orbital theory and a corresponding energy decomposition analysis (EDA). The directionality of electrophilic substitution in aniline can accurately be explained with the amount of contribution of the 2pz orbitals on the unsubstituted carbon atoms to the highest occupied π orbital. For nitrobenzene, the molecular π orbitals cannot explain the regioselectivity of electrophilic substitution as there are two almost degenerate π orbitals with nearly the same 2pz contributions on the unsubstituted carbon atoms. The Voronoi deformation density analysis has been applied to aniline and nitrobenzene to obtain an insight into the charge rearrangements due to the substituent. This analysis method identified the orbitals involved in the C-N bond formation of the π system as the cause for the π charge accumulation at the ortho and para positions in the case of the NH2 group and the largest charge depletion at these same positions for the NO2 substituent. Furthermore, we showed that it is the repulsive interaction between the πHOMO of the phenyl radical and the πHOMO of the NH2 radical that is responsible for pushing up the πHOMO of aniline and therefore activating this π orbital of the phenyl ring towards electrophilic substitution. PMID:26800159

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

    SciTech Connect

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

    1991-11-15

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

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

    PubMed

    Lao, Ka Un; Herbert, John M

    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 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 He2, Ne2, and the S22 and S66 data sets reveal that this condition is important for accurate prediction of the non-dispersion components of the energy, although errors in SAPT(KS) dispersion energies remain unacceptably large. In conjunction with an empirical dispersion potential, however, the SAPT(KS) method affords good results for S22 and S66, and also accurately predicts the whole potential energy curve for the sandwich isomer of the benzene dimer. Tuned LRC functionals represent an attractive alternative to other asymptotic corrections that have been employed in density-functional-based SAPT calculations, and we recommend the use of tuned LRC functionals in both coupled-perturbed SAPT(DFT) calculations and dispersion-corrected SAPT(KS) calculations. PMID:25669506

  7. Prediction of core level binding energies in density functional theory: Rigorous definition of initial and final state contributions and implications on the physical meaning of Kohn-Sham energies

    NASA Astrophysics Data System (ADS)

    Pueyo Bellafont, Noèlia; Bagus, Paul S.; Illas, Francesc

    2015-06-01

    A systematic study of the N(1s) core level binding energies (BE's) in a broad series of molecules is presented employing Hartree-Fock (HF) and the B3LYP, PBE0, and LC-BPBE density functional theory (DFT) based methods with a near HF basis set. The results show that all these methods give reasonably accurate BE's with B3LYP being slightly better than HF but with both PBE0 and LCBPBE being poorer than HF. A rigorous and general decomposition of core level binding energy values into initial and final state contributions to the BE's is proposed that can be used within either HF or DFT methods. The results show that Koopmans' theorem does not hold for the Kohn-Sham eigenvalues. Consequently, Kohn-Sham orbital energies of core orbitals do not provide estimates of the initial state contribution to core level BE's; hence, they cannot be used to decompose initial and final state contributions to BE's. However, when the initial state contribution to DFT BE's is properly defined, the decompositions of initial and final state contributions given by DFT, with several different functionals, are very similar to those obtained with HF. Furthermore, it is shown that the differences of Kohn-Sham orbital energies taken with respect to a common reference do follow the trend of the properly calculated initial state contributions. These conclusions are especially important for condensed phase systems where our results validate the use of band structure calculations to determine initial state contributions to BE shifts.

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2007-11-01

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

  10. Syntheses, structural variations and fluorescence studies of two dinuclear zinc(II) complexes of a Schiff base ligand with an extended carboxylate side arm

    NASA Astrophysics Data System (ADS)

    Shit, Shyamapada; Sasmal, Ashok; Dhal, Piu; Rizzoli, Corrado; Mitra, Samiran

    2016-03-01

    A potentially tetradentate Schiff base ligand containing carboxylic acid group, HL, (E)-2-((pyridin-2-yl)methyleneamino)-5-chlorobenzoic acid is synthesized and characterized. Reaction of HL with hydrated zinc(II) trichloroacetate and zinc(II) trifluoroacetate under similar reaction condition yields two discrete dinuclear complexes, [Zn(L)(Cl)]2 (1) and [Zn(L)(CF3COO)]2 (2) and characterized by different physicochemical methods. Single crystal X-ray structural characterization reveals different ligating properties of the coordinated anionic ligand (L-) in its zinc(II) complexes. The side arm carboxylate of L- shows μ1,3-carboxylato-bridging mode in 1 and connects zinc(II) atoms in syn-anti fashion while it exhibits a μ1,1-carboxylato-bridging mode in 2. The metal ions display distorted square pyramidal geometries in both the structures and associated with different degrees of distortions. The fluorescence spectra of HL and its zinc(II) complexes recorded in methanol at room temperature which reveal the enhancement of emission intensity for the complexes compared to that of the free ligand. Thermogravimetric analyses (TGA) reveal high thermal stabilities of the complexes.

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

    PubMed Central

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

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

  13. Effect of variations of the complexity of the target variable on the assessment of Wiener-Granger causality in cardiovascular control studies.

    PubMed

    Porta, Alberto; Bari, Vlasta; Marchi, Andrea; De Maria, Beatrice; Takahashi, Anielle C M; Guzzetti, Stefano; Colombo, Riccardo; Catai, Aparecida M; Raimondi, Ferdinando

    2016-02-01

    We hypothesized that Wiener-Granger causality (WGC) indexes might have different abilities in coping with modifications of the complexity of the target variable in the context of the assessment of the cardiovascular control from spontaneous fluctuations of heart period (HP), systolic arterial pressure (SAP) and respiratory activity (R). After having defined the universe of knowledge as the set Ω  =  {HP, SAP, R} and the unpredictability decrement (UPD) as the difference between the prediction error variances of the target signal computed in Ω after excluding the presumed cause (i.e. the restricted Ω) and in Ω, we computed the following frequently utilized WGC indexes: (i) the plain UPD; (ii) the fractional UPD (FUPD) by dividing UPD by the prediction error variance in the restricted Ω; (iii) the normalized UPD (NUPD) by dividing UPD by the prediction error variance in Ω; (iv) the log-unpredictability decrement (LUPD) by applying the logarithm transformation to the prediction error variances before computing the UPD. The hypothesis was tested over two experimental protocols known to produce modifications of the complexity of HP variability: graded head-up tilt (HUT) inducing a gradual decrease of the HP complexity with tilt table inclination and head-down tilt (HDT) inducing the opposite trend. We demonstrated that: (1) when the strength of the causal relations from SAP to HP during HUT and from R to HP during HDT is assessed in Ω, WGC indexes reach different conclusions; (2) UPD is biased by modifications of the complexity of HP dynamics; (3) FUPD, NUPD and LUPD are less sensitive to changes of the complexity of the target dynamic, even though they have slightly different statistical power, being the NUPD the weakest one and FUPD and LUPD the strongest ones. We conclude that UPD should be avoided when assessing WGC and FUPD and LUPD should be privileged over NUPD. PMID:26814445

  14. The rectal complex and Malpighian tubules of the cabbage looper (Trichoplusia ni): regional variations in Na+ and K+ transport and cation reabsorption by secondary cells.

    PubMed

    O'Donnell, Michael J; Ruiz-Sanchez, Esau

    2015-10-01

    In larvae of most Lepidoptera the distal ends of the Malpighian tubules are closely applied to the rectal epithelia and are ensheathed within the perinephric membrane, thus forming the rectal complex. The cryptonephric Malpighian tubules within the rectal complex are bathed in fluid within a functional compartment, the perinephric space, which is separate from the haemolymph. In this study, the scanning ion-selective electrode technique (SIET) was used to measure transport of Na(+) and K(+) across the rectal complex and across multiple regions of the Malpighian tubules of larvae of the cabbage looper Trichoplusia ni. Measurements were made in an intact preparation in which connections of the tubules upstream to the rectal complex and downstream to the urinary bladder and gut remained intact. SIET measurements revealed reabsorption of Na(+) and K(+) across the intact rectal complex and into the bath (haemolymph), with K(+) fluxes approximately twice as large as those of Na(+). Analyses of fluxes in larvae with empty guts, found in recently moulted larvae, versus those with full guts highlighted differences in the rates of K(+) or Na(+) transport within tubule regions that appeared morphologically homogeneous, such as the rectal lead. The distal rectal lead of larvae with empty guts reabsorbed K(+), whereas the same region secreted K(+) in tubules of larvae with full guts. SIET measurements of the ileac plexus also indicated a novel role for secondary (type II) cells in cation reabsorption. Secondary cells reabsorb K(+), whereas the adjacent principal (type I) cells secrete K(+). Na(+) is reabsorbed by both principal and secondary cells, but the rate of reabsorption by the secondary cells is approximately twice the rate in the adjacent principal cells. PMID:26491192

  15. 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 αCO in the SFR-M sstarf plane and we show that the higher sSFR of distant galaxies is directly related to their larger gas fractions.

  16. Regularity underlying complexity: a redshift-independent description of the continuous variation of galaxy-scale molecular gas properties in the mass-star formation rate plane

    SciTech Connect

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

    2014-09-20

    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 {sub *} 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 α{sub CO} in the SFR-M {sub *} plane and we show that the higher sSFR of distant galaxies is directly related to their larger gas fractions.

  17. 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

  18. Evaluation of the behavior of clouds in a region of severe acid rain pollution in southern China: species, complexes, and variations.

    PubMed

    Sun, Lei; Wang, Yan; Yue, Taixing; Yang, Xueqiao; Xue, Likun; Wang, Wenxing

    2015-09-01

    Cloud samples were collected during the summer of 2011 and the spring of 2012 at a high-elevation site in southern China in an effort to examine the chemical characteristics of acid clouds. In total, 141 cloud samples were collected during 44 cloud events over the observation period. The dominant ionic species were SO4(2-), NH4(+), and NO3(-), contributing approximately 75% of the total inorganic ion concentration. The primary acidifying factors were sulfate and nitrate, and the primary neutralizing factors were ammonium and calcium. The volume-weighted mean (VWM) pH of the cloud water was 3.79, indicating an acidic nature. In these cloud samples, Zn and Al exhibited the highest trace metal concentrations, contributing approximately 60% of the total trace element concentration. Toxic metals, such as Pb, Ba, As, and Cr, were detected at high concentrations, indicating potential hazards for human health, vegetation, and waters in this region. Visual MINTEQ 3.0 results revealed that the majority of Zn(II) and Pb(II) existed in the form of free ions. The behavior of Al, however, differed from the behaviors of zinc and lead. The temporal variation in cloud chemistry indicated that temperature, sandstorms, and long-range transport could affect the concentrations of species. During the lifetime of a cloud event, the concentrations of the chemical species were controlled by the transfer of gases or particles to liquid droplets. PMID:25976330

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

    NASA Astrophysics Data System (ADS)

    Bleiziffer, Patrick; Krug, Marcel; Görling, Andreas

    2015-06-01

    A self-consistent Kohn-Sham method based on the adiabatic-connection fluctuation-dissipation (ACFD) theorem, employing the frequency-dependent exact exchange kernel fx is presented. The resulting SC-exact-exchange-only (EXX)-ACFD method leads to even more accurate correlation potentials than those obtained within the direct random phase approximation (dRPA). In contrast to dRPA methods, not only the Coulomb kernel but also the exact exchange kernel fx is taken into account in the EXX-ACFD correlation which results in a method that, unlike dRPA methods, is free of self-correlations, i.e., a method that treats exactly all one-electron systems, like, e.g., the hydrogen atom. The self-consistent evaluation of EXX-ACFD total energies improves the accuracy compared to EXX-ACFD total energies evaluated non-self-consistently with EXX or dRPA orbitals and eigenvalues. Reaction energies of a set of small molecules, for which highly accurate experimental reference data are available, are calculated and compared to quantum chemistry methods like Møller-Plesset perturbation theory of second order (MP2) or coupled cluster methods [CCSD, coupled cluster singles, doubles, and perturbative triples (CCSD(T))]. Moreover, we compare our methods to other ACFD variants like dRPA combined with perturbative corrections such as the second order screened exchange corrections or a renormalized singles correction. Similarly, the performance of our EXX-ACFD methods is investigated for the non-covalently bonded dimers of the S22 reference set and for potential energy curves of noble gas, water, and benzene dimers. The computational effort of the SC-EXX-ACFD method exhibits the same scaling of N5 with respect to the system size N as the non-self-consistent evaluation of only the EXX-ACFD correlation energy; however, the prefactor increases significantly. Reaction energies from the SC-EXX-ACFD method deviate quite little from EXX-ACFD energies obtained non-self-consistently with dRPA orbitals and eigenvalues, and the deviation reduces even further if the Coulomb kernel is scaled by a factor of 0.75 in the dRPA to reduce self-correlations in the dRPA correlation potential. For larger systems, such a non-self-consistent EXX-ACFD method is a competitive alternative to high-level wave-function-based methods, yielding higher accuracy than MP2 and CCSD methods while exhibiting a better scaling of the computational effort than CCSD or CCSD(T) methods. Moreover, EXX-ACFD methods were shown to be applicable in situation characterized by static correlation.

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

    NASA Astrophysics Data System (ADS)

    Kress, Joel

    2013-06-01

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

  1. 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

  2. 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

    2015-02-28

    Three new mixed valence trinuclear Co(II/III) compounds cis-[Co3L2(MeOH)2(N3)2(μ1,1-N3)2] (1), trans-[Co3L2(H2O)2(N3)2(μ1,1-N3)2]·(H2O)2 (2) and [Co3L(R)2(N3)3(μ1,3-N3)] (3) have been synthesized by reacting a di-Schiff base ligand (H2L) or its reduced form [H2LR] (where H2L= N,N'-bis(salicylidene)-1,3-propanediamine and H2LR= 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 2 is an angular trinuclear species in which two terminal octahedral Co(III)N2O4 centers coordinate to the central octahedral cobalt(II) ion through μ2-phenoxido oxygen and μ1,1-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 μ2-phenoxido and μ1,1-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 3, 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 μ1,3-azido bridge that participates in pnicogen bonding interactions (intermolecular N-N interaction) as an acceptor. Both the cis and trans isomeric forms of 1 and 2 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 2 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 μ1,3-azido ligand. Complexes 1-3 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: 1 (kcat = 142 h(-1)) > 3 (kcat = 99 h(-1)) > 2 (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

  3. Variation in parental magmas of Mt Rouse, a complex polymagmatic monogenetic volcano in the basaltic intraplate Newer Volcanics Province, southeast Australia

    NASA Astrophysics Data System (ADS)

    Boyce, Julie A.; Nicholls, Ian A.; Keays, Reid R.; Hayman, Patrick C.

    2015-02-01

    Monogenetic volcanoes have long been regarded as simple in nature, involving single magma batches and uncomplicated evolutions; however, recent detailed research into individual centres is challenging that assumption. Mt Rouse (Kolor) is the volumetrically largest volcano in the monogenetic Newer Volcanics Province of southeast Australia. This study presents new major, trace and Sr-Nd-Pb isotope data for samples selected on the basis of a detailed stratigraphic framework analysis of the volcanic products from Mt Rouse. The volcano is the product of three magma batches geochemically similar to Ocean-Island basalts, featuring increasing LREE enrichment with each magma batch (batches A, B and C) but no evidence of crustal contamination; the Sr-Nd-Pb isotopes define two groupings. Modelling suggests that the magmas were sourced from a zone of partial melting crossing the lithosphere-asthenosphere boundary, with batch A forming a large-volume partial melt in the deep lithosphere (1.7 GPa/55.5 km); and batches B and C from similar areas within the shallow asthenosphere (1.88 GPa/61 km and 1.94 GPa/63 km, respectively). The formation and extraction of these magmas may have been due to high deformation rates in the mantle caused by edge-driven convection and asthenospheric upwelling. The lithosphere-asthenosphere boundary is important with respect to NVP volcanism. An eruption chronology involves sequential eruption of magma batches A, C and B, followed by simultaneous eruption of batches A and B. Mt Rouse is a complex polymagmatic monogenetic volcano that illustrates the complexity of monogenetic volcanism and demonstrates the importance of combining detailed stratigraphic analysis alongside systematic geochemical sampling.

  4. Kohn's theorem and Galilean symmetry

    NASA Astrophysics Data System (ADS)

    Zhang, P.-M.; Horvathy, P. A.

    2011-08-01

    The relation between the separability of a system of charged particles in a uniform magnetic field and Galilean symmetry is revisited using Duval's “Bargmann framework”. If the charge-to-mass ratios of the particles are identical, ea/ma=ɛ for all particles, then the Bargmann space of the magnetic system is isometric to that of an anisotropic harmonic oscillator. Assuming that the particles interact through a potential which only depends on their relative distances, the system splits into one representing the center of mass plus a decoupled internal part, and can be mapped further into an isolated system using Niederer's transformation. Conversely, the manifest Galilean boost symmetry of the isolated system can be “imported” to the oscillator and to the magnetic systems, respectively, to yield the symmetry used by Gibbons and Pope to prove the separability. For vanishing interaction potential the isolated system is free and our procedure endows all our systems with a hidden Schrödinger symmetry, augmented with independent internal rotations. All these properties follow from the cohomological structure of the Galilei group, as explained by Souriau's “décomposition barycentrique”.

  5. Variational principles for breakup amplitudes: Three charged clusters

    SciTech Connect

    Rosenberg, Leonard

    2007-03-15

    Variational principles for three-body reaction amplitudes are derived which allow for colliding systems that are charged and composite and are applicable for energies lying below the threshold for breakup into four subsystems. The starting point of the analysis is a formulation of the collision dynamics based on coupled integral equations of the Faddeev type that are applicable in the presence of long-range Coulomb interactions. A variational identity (which becomes a variational approximation with the introduction of trial functions) for the amplitude for the breakup of a bound pair by a third particle is derived within the integral equation formulation. The expression is then converted to a differential form of the Kohn type involving wave functions in configuration space. Knowledge of the asymptotic form of the wave function representing the time-reversed final state, in which three unbound particles are incident, is not required in performing this derivation. The variational principle is enhanced by the existence of a subsidiary minimum principle satisfied by that component of the wave function describing virtual excitations of one or more of the three clusters that make up the scattering system.

  6. Categorical complexities of Plasmodium falciparum malaria in individuals is associated with genetic variations in ADORA2A and GRK5 genes.

    PubMed

    Gupta, Himanshu; Jain, Aditya; Saadi, Abdul Vahab; Vasudevan, Thanvanthri G; Hande, Manjunath H; D'Souza, Sydney C; Ghosh, Susanta K; Umakanth, Shashikiran; Satyamoorthy, Kapaettu

    2015-08-01

    In the erythrocytes, malaria parasite entry and infection is mediated through complex membrane sorting and signaling processes. We investigated the effects of single-locus and multilocus interactions to test the hypothesis that the members of the GPCR family genes, adenosine A2a receptor (ADORA2A) and G-protein coupled receptor kinase5 (GRK5), may contribute to the pathogenesis of malaria caused by Plasmodium falciparum (Pf) independently or through complex interactions. In a case-control study of adults, individuals affected by Pf malaria (complicated n=168; uncomplicated n=282) and healthy controls (n=450) were tested for their association to four known SNPs in GRK5 (rs2230345, rs2275036, rs4752307 and rs11198918) and two in ADORA2A (rs9624472 and rs5751876) genes with malaria susceptibility, using techniques of polymerase chain reaction-restriction fragment length polymorphisms and direct DNA sequencing. Single-locus analysis showed significant association of 2 SNPs; rs5751876 (OR=3.2(2.0-5.2); p=0.0006) of ADORA2A and rs2230345 (OR=0.3(0.2-0.5); p=0.0006) of GRK5 with malaria. The mean of the serum creatinine levels were significantly higher in patients with variant GG (p=0.006) of rs9624472 in ADORA2A gene compared to AA and AG genotypes in complicated Pf malaria cases, with the G allele also showing increased risk for malaria (OR=1.3(1.1-1.6); p=0.017). Analyses of predicted haplotypes of the two ADORA2A and the four GRK5 SNPs have identified the haplotypes that conferred risk as well as resistance to malaria with statistical significance. Molecular docking analysis of evolutionary rs2230345 SNP indicated a stable activity of GRK5 for the mutant allele compared to the wild type. Further, generalized multifactor dimensionality reduction to test the contribution of individual effects of the six polymorphisms and higher-order interactions to risk of symptoms/clinical complications of malaria suggested a best six-locus model showing statistical significance. The study provides evidence for the role of ADORA2A and GRK5 that might influence the etiology of malaria infection. PMID:26066465

  7. Changes in the Plasma Proteome of Manduca sexta Larvae in Relation to the Transcriptome Variations after an Immune Challenge: Evidence for High Molecular Weight Immune Complex Formation.

    PubMed

    He, Yan; Cao, Xiaolong; Zhang, Shuguang; Rogers, Janet; Hartson, Steve; Jiang, Haobo

    2016-04-01

    Manduca sextais a lepidopteran model widely used to study insect physiological processes, including innate immunity. In this study, we explored the proteomes of cell-free hemolymph from larvae injected with a sterile buffer (C for control) or a mixture of bacteria (I for induced). Of the 654 proteins identified, 70 showed 1.67 to >200-fold abundance increases after the immune challenge; 51 decreased to 0-60% of the control levels. While there was no strong parallel between plasma protein levels and their transcript levels in hemocytes or fat body, the mRNA level changes (i.e.I/C ratios of normalized read numbers) in the tissues concurred with their protein level changes (i.e.I/C ratios of normalized spectral counts) with correlation coefficients of 0.44 and 0.57, respectively. Better correlations support that fat body contributes a more significant portion of the plasma proteins involved in various aspects of innate immunity. Consistently, ratios of mRNA and protein levels were better correlated for immunity-related proteins than unrelated ones. There is a set of proteins whose apparent molecular masses differ considerably from the calculatedMr's, suggestive of posttranslational modifications. In addition, some lowMrproteins were detected in the range of 80 to >300 kDa on a reducing SDS-polyacrylamide gel, indicating the existence of highMrcovalent complexes. We identified 30 serine proteases and their homologs, 11 of which are known members of an extracellular immune signaling network. Along with our quantitative transcriptome data, the protein identification, inducibility, and association provide leads toward a focused exploration of humoral immunity inM. sexta. PMID:26811355

  8. 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 δ (r)=1/(ν 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 δ(r) changes its scaling behavior. This reproduces a result on the minimum scale rmin in turbulence: r_min^2 Vert nabla {u}Vert _infty ∝ ν , 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* ∝ νa with a=4/3(3-q)-1. Parametric representations are then obtained as Vert nabla {u}Vert _infty ∝ ν ^{-(1+3a)/2} and rmin ∝ ν3(a+1)/4. By the assumptions of the regularity and finite energy dissipation rate in the inviscid limit, we derive lim _{p rArr infty }ζ _p/p=1 - ζ _2 for any phenomenological models on intermittency, where ζp is the exponent of pth order (longitudinal) velocity structure function. It follows that ζp ⩽ (1 - ζ2)(p - 3) + 1 for any p ⩾ 3 without invoking fractal energy cascade. Second, we determine the scaling behavior of δ(r) in direct numerical simulations of the Navier-Stokes equations. In isotropic turbulence around Rλ ≈ 100 starting from random initial conditions, we have found that δ(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 β-model is perfectly correct, the intermittency parameter a must be related to the dissipation correlation exponent μ as μ =4a/1+a ≈ 0.8, which is larger than the observed μ ≈ 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.

  9. pre-miRNA profiles obtained through application of locked nucleic acids and deep sequencing reveals complex 5′/3′ arm variation including concomitant cleavage and polyuridylation patterns

    PubMed Central

    Burroughs, A. Maxwell; Kawano, Mitsuoki; Ando, Yoshinari; Daub, Carsten O.; Hayashizaki, Yoshihide

    2012-01-01

    Recent research hints at an underappreciated complexity in pre-miRNA processing and regulation. Global profiling of pre-miRNA and its potential to increase understanding of the pre-miRNA landscape is impeded by overlap with highly expressed classes of other non coding (nc) RNA. Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3′- and 5′-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Additionally, examination of nuclear-enriched flanking sequences of pre-miRNA, particularly those derived from polycistronic miRNA transcripts, provides insight into miRNA and miRNA-offset (moRNA) production, specifically identifying novel classes of RNA potentially functioning as moRNA precursors. Our findings point to particularly intricate regulation of the let-7 family in many ways reminiscent of DICER1-independent, pre-mir-451-like processing, introduce novel and unify known forms of pre-miRNA regulation and processing, and shed new light on overlooked products of miRNA processing pathways. PMID:22058130

  10. FROG - Fingerprinting Genomic Variation Ontology

    PubMed Central

    Bhardwaj, Anshu

    2015-01-01

    Genetic variations play a crucial role in differential phenotypic outcomes. Given the complexity in establishing this correlation and the enormous data available today, it is imperative to design machine-readable, efficient methods to store, label, search and analyze this data. A semantic approach, FROG: “FingeRprinting Ontology of Genomic variations” is implemented to label variation data, based on its location, function and interactions. FROG has six levels to describe the variation annotation, namely, chromosome, DNA, RNA, protein, variations and interactions. Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant. For example, in chromosome level, one of the attributes is location of variation and which has two properties, allosomes or autosomes. Another attribute is variation kind which has four properties, namely, indel, deletion, insertion, substitution. Likewise, there are 48 attributes and 278 properties to capture the variation annotation across six levels. Each property is then assigned a bit score which in turn leads to generation of a binary fingerprint based on the combination of these properties (mostly taken from existing variation ontologies). FROG is a novel and unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis. A web-based platform is designed as a test case for users to navigate sample datasets and generate fingerprints. The platform is available at http://ab-openlab.csir.res.in/frog. PMID:26244889

  11. Natural Variation in Small Molecule–Induced TIR-NB-LRR Signaling Induces Root Growth Arrest via EDS1- and PAD4-Complexed R Protein VICTR in Arabidopsis[C][W

    PubMed Central

    Kim, Tae-Houn; Kunz, Hans-Henning; Bhattacharjee, Saikat; Hauser, Felix; Park, Jiyoung; Engineer, Cawas; Liu, Amy; Ha, Tracy; Parker, Jane E.; Gassmann, Walter; Schroeder, Julian I.

    2012-01-01

    In a chemical genetics screen we identified the small-molecule [5-(3,4-dichlorophenyl)furan-2-yl]-piperidine-1-ylmethanethione (DFPM) that triggers rapid inhibition of early abscisic acid signal transduction via PHYTOALEXIN DEFICIENT4 (PAD4)- and ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1)-dependent immune signaling mechanisms. However, mechanisms upstream of EDS1 and PAD4 in DFPM-mediated signaling remain unknown. Here, we report that DFPM generates an Arabidopsis thaliana accession-specific root growth arrest in Columbia-0 (Col-0) plants. The genetic locus responsible for this natural variant, VICTR (VARIATION IN COMPOUND TRIGGERED ROOT growth response), encodes a TIR-NB-LRR (for Toll-Interleukin1 Receptor–nucleotide binding–Leucine-rich repeat) protein. Analyses of T-DNA insertion victr alleles showed that VICTR is necessary for DFPM-induced root growth arrest and inhibition of abscisic acid–induced stomatal closing. Transgenic expression of the Col-0 VICTR allele in DFPM-insensitive Arabidopsis accessions recapitulated the DFPM-induced root growth arrest. EDS1 and PAD4, both central regulators of basal resistance and effector-triggered immunity, as well as HSP90 chaperones and their cochaperones RAR1 and SGT1B, are required for the DFPM-induced root growth arrest. Salicylic acid and jasmonic acid signaling pathway components are dispensable. We further demonstrate that VICTR associates with EDS1 and PAD4 in a nuclear protein complex. These findings show a previously unexplored association between a TIR-NB-LRR protein and PAD4 and identify functions of plant immune signaling components in the regulation of root meristematic zone-targeted growth arrest. PMID:23275581

  12. Anatomic Variations in Head and Neck Reconstruction

    PubMed Central

    Tan, Bien-Keem; Wong, Chin-Ho; Chen, Hung-Chi

    2010-01-01

    Head and neck reconstruction is a technically challenging procedure. Variations encountered in the recipient vessels and commonly used flaps add to the complexity of surgery. This article reviews the commonly encountered variations in the recipient vessels in the neck with emphasis on alternatives and techniques to circumvent these variations. Flaps commonly used in head and neck reconstruction are also reviewed in detail. Furthermore, safety, potential pitfalls, and technical pearls are highlighted. PMID:22550436

  13. Velocity resolved [C ii], [C i], and CO observations of the N159 star-forming region in the Large Magellanic Cloud: a complex velocity structure and variation of the column densities

    NASA Astrophysics Data System (ADS)

    Okada, Yoko; Requena-Torres, Miguel Angel; Güsten, Rolf; Stutzki, Jürgen; Wiesemeyer, Helmut; Pütz, Patrick; Ricken, Oliver

    2015-08-01

    Context. The [C ii] 158 μm fine structure line is one of the dominant cooling lines in star-forming active regions. Together with models of photon-dominated regions, the data is used to constrain the physical properties of the emitting regions, such as the density and the radiation field strength. According to the modeling, the [C ii] 158 μm line integrated intensity compared to the CO emission is expected to be stronger in lower metallicity environments owing to lower dust shielding of the UV radiation, a trend that is also shown by spectral-unresolved observations. In the commonly assumed clumpy UV-penetrated cloud scenario, the models predict a [C ii] line profile similar to that of CO. However, recent spectral-resolved observations by Herschel/HIFI and SOFIA/GREAT (as well as the observations presented here) show that the velocity resolved line profile of the [C ii] emission is often very different from that of CO lines, indicating a more complex origin of the line emission including the dynamics of the source region. Aims: The Large Magellanic Cloud (LMC) provides an excellent opportunity to study in great detail the physics of the interstellar medium (ISM) in a low-metallicity environment by spatially resolving individual star-forming regions. The aim of our study is to investigate the physical properties of the star-forming ISM in the LMC by separating the origin of the emission lines spatially and spectrally. In this paper, we focus on the spectral characteristics and the origin of the emission lines, and the phases of carbon-bearing species in the N159 star-forming region in the LMC. Methods: We mapped a 4' × (3'-4') region in N159 in [C ii] 158 μm and [N ii] 205 μm with the GREAT instrument on board SOFIA. We also observed CO(3-2), (4-3), (6-5), 13CO(3-2), and [C i] 3P1-3P0 and 3P2-3P1 with APEX. All spectra are velocity resolved. Results: The emission of all transitions observed shows a large variation in the line profiles across the map and in particular between the different species. At most positions the [C ii] emission line profile is substantially wider than that of CO and [C i]. We estimated the fraction of the [C ii] integrated line emission that cannot be fitted by the CO line profile to be 20% around the CO cores, and up to 50% at the area between the cores, indicating a gas component that has a much larger velocity dispersion than the ones probed by the CO and [C i] emission. We derived the relative contribution from C+, C, and CO to the column density in each velocity bin. The result clearly shows that the contribution from C+ dominates the velocity range far from the velocities traced by the dense molecular gas. Spatially, the region located between the CO cores of N159 W and E has a higher fraction of C+ over the whole velocity range. We estimate the contribution of the ionized gas to the [C ii] emission using the ratio to the [N ii] emission, and find that the ionized gas contributes ≤19% to the [C ii] emission at its peak position, and ≤15% over the whole observed region. Using the integrated line intensities, we present the spatial distribution of I[CII]/IFIR. Conclusions: This study demonstrates that the [C ii] emission in the LMC N159 region shows significantly different velocity profiles from that of CO and [C i] emissions, emphasizing the importance of velocity resolved observations in order to distinguish different cloud components.

  14. Calculation of the 4,5-dihydro-1,3,2-dithiazolyl radical g tensor components by the coupled-perturbed Kohn-Sham hybrid density functional and configuration interaction methods: a comparative study.

    PubMed

    Mattar, Saba M; Durelle, Jeremy

    2010-12-01

    The g tensor components of the 4,5-dihydro-1,3,2-dithiazolyl (H2DTA•) radical, which is a basic building block for molecular magnets and spintronic devices, is calculated by the coupled-perturbed Kohn-Sham (CPKS) hybrid density functional (HDF) and multireference configuration interaction-sum over states (MRCI-SOS) techniques. In both methods, the diagonalized g tensor principal axes are found to be aligned with the radical's inertial axes. The tensor components are in very good agreement with those determined experimentally by electron paramagnetic resonance (EPR) spectroscopy. The MRCI technique produced g tensor components that are more accurate than those obtained by the CPKS-HDF method. Nonetheless, to get reasonable MRCI results, one must include the in-plane and out-of-plane interactions in an unbiased way. The minimum reference space that satisfies these conditions is generated from a complete active space of nine electrons in six orbitals [CAS(9,6)] and contains a(1), a(2), b(1) and b(2) type orbitals. In addition, the number of roots in the MRCI-SOS g tensor expansion should include all excited states that range from 0 to 56,000 cm(-1). The most accurate results are obtained using an MRCI-SOS/CAS(13,9) calculation. These g tensor components are within the experimental accuracy range of 1000 ppm. The one- and two-electron contributions to the g tensor components are separated and individually analyzed. The very good agreement with experiment opens the door for further accurate calculations of spin Hamiltonian tensors of larger DTA• radicals. PMID:20625978

  15. Variational principles for locally variational forms

    SciTech Connect

    Brajercik, J.; Krupka, D.

    2005-05-01

    We present the theory of higher order local variational principles in fibered manifolds, in which the fundamental global concept is a locally variational dynamical form. Any two Lepage forms, defining a local variational principle for this form, differ on intersection of their domains, by a variationally trivial form. In this sense, but in a different geometric setting, the local variational principles satisfy analogous properties as the variational functionals of the Chern-Simons type. The resulting theory of extremals and symmetries extends the first order theories of the Lagrange-Souriau form, presented by Grigore and Popp, and closed equivalents of the first order Euler-Lagrange forms of Hakova and Krupkova. Conceptually, our approach differs from Prieto, who uses the Poincare-Cartan forms, which do not have higher order global analogues.

  16. Tooth Size Variation in Pinniped Dentitions

    PubMed Central

    Wolsan, Mieczyslaw; Suzuki, Satoshi; Asahara, Masakazu; Motokawa, Masaharu

    2015-01-01

    It is contentious whether size variation among mammalian teeth is heterogeneous or homogeneous, whether the coefficient of variation is reliable, and whether the standard deviation of log-transformed data and the residual of standard deviation on mean variable size are useful replacements for the coefficient of variation. Most studies of tooth size variation have been on mammals with complex-crowned teeth, with relatively little attention paid to taxa with simple-crowned teeth, such as Pinnipedia. To fill this gap in knowledge and to resolve the existing controversies, we explored the variation of linear size variables (length and width) for all teeth from complete permanent dentitions of four pinniped species, two phocids (Histriophoca fasciata, Phoca largha) and two otariids (Callorhinus ursinus, Eumetopias jubatus). Size variation among these teeth was mostly heterogeneous both along the toothrow and among species. The incisors, canines, and mesial and distal postcanines were often relatively highly variable. The levels of overall dental size variation ranged from relatively low as in land carnivorans (Phoca largha and both otariids) to high (Histriophoca fasciata). Sexual size dimorphism varied among teeth and among species, with teeth being, on average, larger in males than in females. This dimorphism was more pronounced, and the canines were larger and more dimorphic relative to other teeth in the otariids than in the phocids. The coefficient of variation quantified variation reliably in most cases. The standard deviation of log-transformed data was redundant with the coefficient of variation. The residual of standard deviation on mean variable size was inaccurate when size variation was considerably heterogeneous among the compared variables, and was incomparable between species and between sexes. The existing hypotheses invoking developmental fields, occlusal complexity, and the relative timing of tooth formation and sexually dimorphic hormonal activity do not adequately explain the differential size variation along the pinniped toothrow. PMID:26317362

  17. Calculation of longitudinal polarizability and second hyperpolarizability of polyacetylene with the coupled perturbed Hartree-Fock/Kohn-Sham scheme: Where it is shown how finite oligomer chains tend to the infinite periodic polymer

    NASA Astrophysics Data System (ADS)

    Lacivita, Valentina; Rèrat, Michel; Orlando, Roberto; Ferrero, Mauro; Dovesi, Roberto

    2012-03-01

    The longitudinal polarizability, αxx, and second hyperpolarizability, γxxxx, of polyacetylene are evaluated by using the coupled perturbed Hartree-Fock/Kohn-Sham (HF/KS) scheme as implemented in the periodic CRYSTAL code and a split valence type basis set. Four different density functionals, namely local density approximation (LDA) (pure local), Perdew-Becke-Ernzerhof (PBE) (gradient corrected), PBE0, and B3LYP (hybrid), and the Hartree-Fock Hamiltonian are compared. It is shown that very tight computational conditions must be used to obtain well converged results, especially for γxxxx, that is, very sensitive to the number of k points in reciprocal space when the band gap is small (as for LDA and PBE), and to the extension of summations of the exact exchange series (HF and hybrids). The band gap in LDA is only 0.01 eV: at least 300 k points are required to obtain well converged total energy and equilibrium geometry, and 1200 for well converged optical properties. Also, the exchange series convergence is related to the band gap. The PBE0 band gap is as small as 1.4 eV and the exchange summation must extend to about 130 Å from the origin cell. Total energy, band gap, equilibrium geometry, polarizability, and second hyperpolarizability of oligomers -(C2H2)m-, with m up to 50 (202 atoms), and of the polymer have been compared. It turns out that oligomers of that length provide an extremely poor representation of the infinite chain polarizability and hyperpolarizability when the gap is smaller than 0.2 eV (that is, for LDA and PBE). Huge differences are observed on αxx and γxxxx of the polymer when different functionals are used, that is in connection to the well-known density functional theory (DFT) overshoot, reported in the literature about short oligomers: for the infinite model the ratio between LDA (or PBE) and HF becomes even more dramatic (about 500 for αxx and 1010 for γxxxx). On the basis of previous systematic comparisons of results obtained with various approaches including DFT, HF, Moller-Plesset (MP2) and coupled cluster for finite chains, we can argue that, for the infinite chain, the present HF results are the most reliable.

  18. Strong correlation in Kohn-Sham DFT

    NASA Astrophysics Data System (ADS)

    Malet Giralt, Francesc; Mirtschink, André; Cremon, Jonas; Mendl, Christian; Giesbertz, Klaas; Reimann, Stephanie; Gori-Giorgi, Paola; Mathematical Physics, Lund University Collaboration; Mathematics Department, Technische Universität München Collaboration

    2014-03-01

    The knowledge on the strong-interacting limit of density functional theory can be used to construct exchange- correlation functionals able to address strongly-correlated systems without introducing any symmetry breaking. We report calculations on semiconductor nanostructures and one-dimensional models for chemical systems, showing that this approach yields quantitatively good results in both the weakly- and the strongly-correlated regimes, with a numerical cost much lower than the traditional wavefunction methods. This work has been supported by a VIDI grant of the NWO and a Marie Curie grant within the FP7 programme.

  19. Adaptive major histocompatibility complex (MHC) and neutral genetic variation in two native Baltic Sea fishes (perch Perca fluviatilis and zander Sander lucioperca) with comparisons to an introduced and disease susceptible population in Australia (P. fluviatilis): assessing the risk of disease epidemics.

    PubMed

    Faulks, L K; Östman, Ö

    2016-04-01

    This study assessed the major histocompatibility complex (MHC) and neutral genetic variation and structure in two percid species, perch Perca fluviatilis and zander Sander lucioperca, in a unique brackish ecosystem, the Baltic Sea. In addition, to assess the importance of MHC diversity to disease susceptibility in these populations, comparisons were made to an introduced, disease susceptible, P. fluviatilis population in Australia. Eighty-three MHC class II B exon 2 variants were amplified: 71 variants from 92 P. fluviatilis samples, and 12 variants from 82 S. lucioperca samples. Microsatellite and MHC data revealed strong spatial genetic structure in S. lucioperca, but not P. fluviatilis, across the Baltic Sea. Both microsatellite and MHC data showed higher levels of genetic diversity in P. fluviatilis from the Baltic Sea compared to Australia, which may have facilitated the spread of an endemic virus, EHNV in the Australian population. The relatively high levels of genetic variation in the Baltic Sea populations, together with spatial genetic structure, however, suggest that there currently seems to be little risk of disease epidemics in this system. To ensure this remains the case in the face of ongoing environmental changes, fisheries and habitat disturbance, the conservation of local-scale genetic variation is recommended. PMID:26940068

  20. Effects of soluble organic complexants and their degradation products on the removal of selected radionuclides from high-level waste. Part 3, Distributions of Sr, Cs, Tc, Pu, and Am onto 33 absorbers from four variations of a 3:1 dilution of Hanford complexant concentrate (CC) simulant: Part 4, The effects of varying dilution ratios on the distributions of Sr, Cs, Tc, Pu, and Am onto 12 absorbers

    SciTech Connect

    Marsh, S.F.; Svitra, Z.V.; Bowen, S.M.

    1995-09-01

    Many of the radioactive waste storage tanks at USDOE facilities contain organic compounds that have been degraded by radiolysis and chemical reactions during decades of storage. Objective of this study was to measure effects of soluble organic complexants and their degradation products on sorption of Sr, Cs, Tc, Pu and Am onto 33 absorbers that in the absence of these organic compounds offer high sorption of these elements. The elements were in a generic simulant for Hanford complexant concentrate supernate that initially contained six organic complexants: EDTA, HEDTA, NTA, citrate, gluconate, and iminodiacetate. This simulant was tested as prepared and after gamma-irradiation to approximately 34 Mrads. Two other variations consisted of the unirradiated and irradiated simulants after treatment at 450C and 15,000 psi in a hydrothermal organic-destruction process. These experiments were conducted with a 3:1 water-to-simulant dilution of each of the four simulant variations. To determine effects of varying dilution ratios on the sorption of these five elements from the unirradiated and gamma-irradiated simulants that were not treated with the hydrothermal process, we measured their distribution from a 1:1 dilution, using 1 M NaOH as the diluent, onto the 12 best-performing absorbers. We then measured the sorption of these five elements from solutions having diluent-simulant ratios of 0, 0.5, 2.0, and 3.0 onto the three absorbers that performed best for sorbing Sr, Pu and Am from the 1:1 dilution. For each of 900 element/absorber/solution combinations, we measured distribution coefficients (Kd values) twice for each period for dynamic contact periods of 30 min, 2 h, and 6 h to obtain information about absorber stability and sorption kinetics. The 5400 measured Kd values indicate that the sorption of Sr, Pu, and Am is significantly decreased by the organic complexants in these simulant solutions, whereas the sorption of Cs and Tc is much less affected.

  1. Complexity Survey.

    ERIC Educational Resources Information Center

    Gordon, Sandra L.; Anderson, Beth C.

    To determine whether consensus existed among teachers about the complexity of common classroom materials, a survey was administered to 66 pre-service and in-service kindergarten and prekindergarten teachers. Participants were asked to rate 14 common classroom materials as simple, complex, or super-complex. Simple materials have one obvious part,…

  2. Nd, Sr, and O isotopic variations in metaluminous ash-flow tuffs and related volcanic rocks at the Timber Mountain/Oasis Valley Caldera, Complex, SW Nevada: implications for the origin and evolution of large-volume silicic magma bodies

    USGS Publications Warehouse

    Farmer, G.L.; Broxton, D.E.; Warren, R.G.; Pickthorn, W.

    1991-01-01

    Nd, Sr and O isotopic data were obtained from silicic ash-flow tuffs and lavas at the Tertiary age (16-9 Ma) Timber (Mountain/Oasis Valley volcanic center (TMOV) in southern Nevada, to assess models for the origin and evolution of the large-volume silicic magma bodies generated in this region. The large-volume (>900 km3), chemically-zoned, Topopah Spring (TS) and Tiva Canyon (TC) members of the Paintbrush Tuff, and the Rainier Mesa (RM) and Ammonia Tanks (AT) members of the younger Timber Mountain Tuff all have internal Nd and Sr isotopic zonations. In each tuff, high-silica rhyolites have lower initial e{open}Nd values (???1 e{open}Nd unit), higher87Sr/86Sr, and lower Nd and Sr contents, than cocrupted trachytes. The TS, TC, and RM members have similar e{open}Nd values for high-silica rhyolites (-11.7 to -11.2) and trachytes (-10.5 to -10.7), but the younger AT member has a higher e{open}Nd for both compositional types (-10.3 and -9.4). Oxygen isotope data confirm that the TC and AT members were derived from low e{open}Nd magmas. The internal Sr and Nd isotopic variations in each tuff are interpreted to be the result of the incorporation of 20-40% (by mass) wall-rock into magmas that were injected into the upper crust. The low e{open}Nd magmas most likely formed via the incorporation of low ??18O, hydrothermally-altered, wall-rock. Small-volume rhyolite lavas and ash-flow tuffs have similar isotopic characteristics to the large-volume ash-flow tuffs, but lavas erupted from extracaldera vents may have interacted with higher ??18O crustal rocks peripheral to the main magma chamber(s). Andesitic lavas from the 13-14 Ma Wahmonie/Salyer volcanic center southeast of the TMOV have low e{open}Nd (-13.2 to -13.8) and are considered on the basis of textural evidence to be mixtures of basaltic composition magmas and large proportions (70-80%) of anatectic crustal melts. A similar process may have occurred early in the magmatic history of the TMOV. The large-volume rhyolites may represent a mature stage of magmatism after repeated injection of basaltic magmas, crustal melting, and volcanism cleared sufficient space in the upper crust for large magma bodies to accumulate and differentiate. The TMOV rhyolites and 0-10 Ma old basalts that erupted in southern Nevada all have similar Nd and Sr isotopic compositions, which suggests that silicic and mafic magmatism at the TMOV were genetically related. The distinctive isotopic compositions of the AT member may reflect temporal changes in the isotopic compositions of basaltic magmas entering the upper crust, possibly as a result of increasing "basification" of a lower crustal magma source by repeated injection of mantle-derived mafic magmas. ?? 1991 Springer-Verlag.

  3. Memory Development: Sources of the Age Variation.

    ERIC Educational Resources Information Center

    von Eye, Alexander; Hussy, Walter

    Research has not clearly determined whether memory development in childhood and adulthood can be accounted for by the age variation of cognitive processes other than memory. To examine this issue, a study was conducted based on a model of structures and processes in complex information processing. Subjects (N=162) were presented with two lists of…

  4. Communication complexity and information complexity

    NASA Astrophysics Data System (ADS)

    Pankratov, Denis

    Information complexity enables the use of information-theoretic tools in communication complexity theory. Prior to the results presented in this thesis, information complexity was mainly used for proving lower bounds and direct-sum theorems in the setting of communication complexity. We present three results that demonstrate new connections between information complexity and communication complexity. In the first contribution we thoroughly study the information complexity of the smallest nontrivial two-party function: the AND function. While computing the communication complexity of AND is trivial, computing its exact information complexity presents a major technical challenge. In overcoming this challenge, we reveal that information complexity gives rise to rich geometrical structures. Our analysis of information complexity relies on new analytic techniques and new characterizations of communication protocols. We also uncover a connection of information complexity to the theory of elliptic partial differential equations. Once we compute the exact information complexity of AND, we can compute exact communication complexity of several related functions on n-bit inputs with some additional technical work. Previous combinatorial and algebraic techniques could only prove bounds of the form theta( n). Interestingly, this level of precision is typical in the area of information theory, so our result demonstrates that this meta-property of precise bounds carries over to information complexity and in certain cases even to communication complexity. Our result does not only strengthen the lower bound on communication complexity of disjointness by making it more exact, but it also shows that information complexity provides the exact upper bound on communication complexity. In fact, this result is more general and applies to a whole class of communication problems. In the second contribution, we use self-reduction methods to prove strong lower bounds on the information complexity of two of the most studied functions in the communication complexity literature: Gap Hamming Distance (GHD) and Inner Product mod 2 (IP). In our first result we affirm the conjecture that the information complexity of GHD is linear even under the uniform distribution. This strengthens the O(n) bound shown by Kerenidis et al. (2012) and answers an open problem by Chakrabarti et al. (2012). We also prove that the information complexity of IP is arbitrarily close to the trivial upper bound n as the permitted error tends to zero, again strengthening the O(n) lower bound proved by Braverman and Weinstein (2011). More importantly, our proofs demonstrate that self-reducibility makes the connection between information complexity and communication complexity lower bounds a two-way connection. Whereas numerous results in the past used information complexity techniques to derive new communication complexity lower bounds, we explore a generic way, in which communication complexity lower bounds imply information complexity lower bounds in a black-box manner. In the third contribution we consider the roles that private and public randomness play in the definition of information complexity. In communication complexity, private randomness can be trivially simulated by public randomness. Moreover, the communication cost of simulating public randomness with private randomness is well understood due to Newman's theorem (1991). In information complexity, the roles of public and private randomness are reversed: public randomness can be trivially simulated by private randomness. However, the information cost of simulating private randomness with public randomness is not understood. We show that protocols that use only public randomness admit a rather strong compression. In particular, efficient simulation of private randomness by public randomness would imply a version of a direct sum theorem in the setting of communication complexity. This establishes a yet another connection between the two areas. (Abstract shortened by UMI.).

  5. 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.

  6. Genetic Variation and its Role in Malignancy

    PubMed Central

    Talseth-Palmer, Bente A.; Scott, Rodney J.

    2011-01-01

    Genetic variation has long been thought associated with common complex disease and has therefore been widely studied. Genetic variation in the human genome is present in many forms and have been summarised in this review. The potential role of DNA damage, DNA repair and environmental influence on genetic variation in the development of cancer will be discussed, before significant genome projects are reviewed. All the various forms of genetic variation have been associated with malignancies and have been extensively studied and this is a review of the state of the field. We also discuss the road ahead in fulfilling the ultimate goal in all cancer genetic studies, which is decreasing deaths caused by cancer. PMID:23675233

  7. Optical spectrum variations of IL Cep A

    NASA Astrophysics Data System (ADS)

    Ismailov, N. Z.; Khalilov, O. V.; Bakhaddinova, G. R.

    2016-02-01

    The results of many-year uniform spectroscopic observations of the Herbig Ae/Be star IL Cep A are presented. Its Hα line has either a single or a barely resolved two-component emission profile. The H β emission line is clearly divided into two components with a deep central absorption. Smooth variations of the observed parameters of individual spectral lines over nine years are observed. The He I λ5876 Å line has a complex absorption profile, probably with superposed emission components. The NaI D1, D2 doublet exhibits weak changes due to variations in the circumstellar envelope. The variations observed in the stellar spectrum can be explained by either binarity or variations of the magnetic field in the stellar disk. Difficulties associated with both these possibilities are discussed.

  8. Variations in abundance: genome-wide responses to genetic variation and vice versa.

    PubMed

    Hamilton, Bruce A

    2002-09-19

    How do naturally occurring polymorphisms in DNA sequence relate to variation in gene expression? Recent work to map genetic sources of expression variation has shown a surprising balance between cis and trans effects. Other work suggests some chromosomal clustering of genes by expression pattern. A synthesis of approaches may provide new insight in to adaptive mechanisms in evolution and the population basis of complex traits. PMID:12372150

  9. 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.

  10. Generalized quasi variational inequalities

    SciTech Connect

    Noor, M.A.

    1996-12-31

    In this paper, we establish the equivalence between the generalized quasi variational inequalities and the generalized implicit Wiener-Hopf equations using essentially the projection technique. This equivalence is used to suggest and analyze a number of new iterative algorithms for solving generalized quasi variational inequalities and the related complementarity problems. The convergence criteria is also considered. The results proved in this paper represent a significant improvement and refinement of the previously known results.

  11. Crystallization of macromolecular complexes: combinatorial complex crystallization

    NASA Astrophysics Data System (ADS)

    Stura, Enrico A.; Graille, Marc; Charbonnier, Jean-Baptiste

    2001-11-01

    The usefulness of antibody complexation, as a way of increasing the chances of crystallization needs to be re-evaluated after many antibody complexes have been crystallized and their structure determined. It is somewhat striking that among these, only a small number is a complex with a large protein antigen. The problem is that the effort of raising, cleaving and purifying an Fab is rewarded only by an extra chance of getting crystals; depending on the relative likelihood of crystallization of the complexed and uncomplexed protein. The example of the complex between HIV gp120, CD4 and an Fab fragment from a neutralizing antibody suggests that further complexation of an antigen-antibody complex with a third protein could, by increasing the number of possible combinations, improve the likelihood of crystallization. We propose the use of Ig-binding proteins as a way of extending the method from HIV gp120 to all proteins for which there are monoclonal antibodies. We discuss this technique, combinatorial complex crystallization (CCC), as part of a multi-component system for the enhancement of crystallization of macromolecular complexes. The method makes use of single Ig-binding domains from Staphylococcus aureus protein A (SpA), Peptostreptococcus magnus protein L (PpL) and the streptococcal protein G (SpG). The generality of the method depends on the ability of these domains to interact with a large repertoire of antibodies without affecting antigen binding. There is strong evidence to suggest that these Ig-binding domains bind outside the antigen-combining site of the antibody without perturbing antigen binding. It is clear from the crystal structure of the single SpG domain complexed with an Fab that the interaction involves mainly the immunoglobulin CH1 domain, a region not involved in antigen recognition. We have recently determined the structure of the complex between a human Fab and the domain D from SpA and found that steric hindrance is unlikely even for large antigens. We find that such binding involves only the well conserved framework region of the variable domain of the antibody heavy chain (VH) and does not affect the conformation of the hypervariable loops that define the antigen recognition site. Thus this domain could be used to complex to Fab or Fv fragments derived from a wide variety of antibodies. While protein A complexes with the VH domain, protein L recognizes the VL region of immunoglobulins. Our recent study of the interaction between an Fab and a domain of protein L shows that the situation is very similar. Indeed this domain binds to the VL framework region outside the antigen binding site. Since individual domains from each of these three multi-domain proteins bind to well separated and independent locations on immunoglobulins, they can be combined to search for a suitable crystalline lattice. This allows us to propose a combinatorial method as a rational way to exploit antibody complexation for the crystallographic structure determination of proteins that are otherwise difficult to crystallize. The overall method has strong parallels with other combinatorial methods used elsewhere in biology and chemistry, and we propose that together with stoichiometry variation screening (SVS), it may further enhance the probability of crystallization.

  12. Complex derivatives

    NASA Astrophysics Data System (ADS)

    Battiston, Stefano; Caldarelli, Guido; Georg, Co-Pierre; May, Robert; Stiglitz, Joseph

    2013-03-01

    The intrinsic complexity of the financial derivatives market has emerged as both an incentive to engage in it, and a key source of its inherent instability. Regulators now faced with the challenge of taming this beast may find inspiration in the budding science of complex systems.

  13. 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…

  14. Deming's Quality: Our Last but Best Hope.

    ERIC Educational Resources Information Center

    Schenkat, Randy

    1993-01-01

    If educators endorse Alfie Kohn's surface message about Total Quality Management, they may miss opportunity to professionalize education. Deming's system of profound knowledge (interaction of theories of systems, knowledge, psychology, and variation) is a model for educated people grappling with life's complexities. Moreover, gaining community…

  15. 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…

  16. Complexity and synchronization in stochastic chaotic systems

    NASA Astrophysics Data System (ADS)

    Dang, Thai Son; Palit, Sanjay Kumar; Mukherjee, Sayan; Hoang, Thang Manh; Banerjee, Santo

    2016-02-01

    We investigate the complexity of a hyperchaotic dynamical system perturbed by noise and various nonlinear speech and music signals. The complexity is measured by the weighted recurrence entropy of the hyperchaotic and stochastic systems. The synchronization phenomenon between two stochastic systems with complex coupling is also investigated. These criteria are tested on chaotic and perturbed systems by mean conditional recurrence and normalized synchronization error. Numerical results including surface plots, normalized synchronization errors, complexity variations etc show the effectiveness of the proposed analysis.

  17. Mediterranean sea level variations.

    NASA Astrophysics Data System (ADS)

    Vigo, I.; Sánchez Reales, J. M.; García, D.; Chao, B. F.

    2009-04-01

    In this work we report an updated study of the sea level variations for the Mediterranean sea for the period from October 1992 to January 2008. The study addresses two mayor issues: (i)The analysis of the spatial and temporal variability of sea surface height (SSH) from radar altimetry measurements (from TOPEX/Poseidon (T/P) + Jason-1, etc.). We use EOF analysis to explain most of its interannual variation, and how the different basins interact. (ii) The analysis of dynamics and balance of water mass transport for the whole period. We estimate the steric SSH by combining the steric SSH estimated from temperature and salt profiles simulated by the ECCO model with time-variable gravity (TVG) data (from GRACE) for the Mediterranean Sea. The estimated steric SSH together with the SSH obtained from altimetry allow for a more realistic estimation of the water mass variations in the Mediterranean for the whole period.

  18. Essential Variational Poisson Cohomology

    NASA Astrophysics Data System (ADS)

    De Sole, Alberto; Kac, Victor G.

    2012-08-01

    In our recent paper "The variational Poisson cohomology" (2011) we computed the dimension of the variational Poisson cohomology {{{H}^bullet_K({V})}} for any quasiconstant coefficient ℓ × ℓ matrix differential operator K of order N with invertible leading coefficient, provided that {{{V}}} is a normal algebra of differential functions over a linearly closed differential field. In the present paper we show that, for K skewadjoint, the {{{Z}}} -graded Lie superalgebra {{{H}^bullet_K({V})}} is isomorphic to the finite dimensional Lie superalgebra {{widetilde{H}(Nell,S)}} . We also prove that the subalgebra of "essential" variational Poisson cohomology, consisting of classes vanishing on the Casimirs of K, is zero. This vanishing result has applications to the theory of bi-Hamiltonian structures and their deformations. At the end of the paper we consider also the translation invariant case.

  19. Softball Complex

    ERIC Educational Resources Information Center

    Ellis, Jim

    1977-01-01

    The Parks and Recreation Department of Montgomery, Alabama, has developed a five-field softball complex as part of a growing community park with facilities for camping, golf, aquatics, tennis, and picnicking. (MJB)

  20. Non-differentiable variational principles

    NASA Astrophysics Data System (ADS)

    Cresson, Jacky

    2005-07-01

    We develop a calculus of variations for functionals which are defined on a set of non-differentiable curves. We first extend the classical differential calculus in a quantum calculus, which allows us to define a complex operator, called the scale derivative, which is the non-differentiable analogue of the classical derivative. We then define the notion of extremals for our functionals and obtain a characterization in term of a generalized Euler-Lagrange equation. We finally prove that solutions of the Schrödinger equation can be obtained as extremals of a non-differentiable variational principle, leading to an extended Hamilton's principle of least action for quantum mechanics. We compare this approach with the scale relativity theory of Nottale, which assumes a fractal structure of space-time.Résumé (Principes variationnels non différentiable). Nous développons un calcul des variations pour des fonctionnelles définies sur un ensemble de courbes non différentiables. Pour cela, nous étendons le calcul différentiel classique, en calcul appelé calcul quantique, qui nous permet de définir un opérateur à valeur complexes, appelé dérivée d'échelle, qui est l'analogue non différentiable de la dérivée usuelle. On définit alors la notion d'extremale pour ces fonctionnelles pour lesquelles nous obtenons une caractérisation via une équation d'Euler-Lagrange généralisée. On prouve enfin que les solutions de l'équation de Schrödinger peuvent s'obtenir comme solution d'un problème variationnel non différentiable, étendant ainsi le principe de moindre action de Hamilton au cadre de la mécanique quantique. On discute enfin la connexion entre ce travail et la théorie de la relativité d'échelle développée par Nottale, et qui suppose une structure fractale de l'espace-temps.

  1. 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 adverse impact of within-die variations on multi-core platforms. For multi-threaded programs executing on variation-impacted multi-cores platforms, we make the key observation that thread performance is not only a function of the frequency of the core on which it is executing on, but also depends upon the amount of shared system resources allocated to it. We utilize this insight to design a variation-aware runtime scheme which allocates the ways of a last-level shared L2 cache amongst the different cores/threads of a multi-core platform taking into account both application characteristics as well as chip specific variation profiles. Our experiments on 100 quad-core chips, each with a distinct variation profile, shows on an average 15% performance improvements for a suite of multi-threaded benchmarks. Our final contribution investigates the variation-tolerant design of domain-specific accelerators and demonstrates how the unique architectural properties of these accelerators can be leveraged to create highly effective variation tolerance mechanisms. We explore this concept through the variation-tolerant design of a vector processor that efficiently executes applications from the domains of recognition, mining and synthesis (RMS). We develop a novel design approach for variation tolerance, which leverages the unique nature of the vector reduction operations performed by this processor to effectively predict and preempt the occurrence of timing errors under variations and subsequently restore the correct output at the end of each vector reduction operation. We implement the above predict, preempt and restore operations by suitably enhancing the processor hardware and the application software and demonstrate considerable energy benefits (on an average 32%) across six applications from the domains of RMS. In conclusion, our work provides system designers with powerful tools and mechanisms in their efforts to combat variations, resulting in improved designer productivity and variation-tolerant systems.

  2. 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…

  3. Structural genomic variation in intellectual disability.

    PubMed

    Pfundt, Rolph; Veltman, Joris A

    2012-01-01

    The genetic causes of mental retardation are highly heterogeneous and for a large proportion unknown. Mutations as well as large chromosomal abnormalities are known to contribute to mental retardation, and recently more subtle structural genomic variations have been shown to contribute significantly to this common and complex disorder. Genomic microarrays with increasing resolution levels have revealed the presence of rare de novo CNVs in approximately 15% of all mentally retarded patients. Microarray-based CNV screening is rapidly replacing conventional karyotyping in the diagnostic workflow, resulting in an increased diagnostic yield as well as biological insight into this disorder. In this chapter, an overview is given of the detection and interpretation of copy number variations in mental retardation, with a focus on diagnostic applications. In addition, a detailed protocol is provided for the diagnostic interpretation of copy-number variations in mental retardation. PMID:22228007

  4. Variations in the rotation of the earth

    NASA Astrophysics Data System (ADS)

    Carter, W. E.; Robertson, D. S.; Pettey, J. E.; Tapley, B. D.; Schutz, B. E.; Eanes, R. J.; Miao, L.

    Variations in the earth's rotation (UTI) and length of day have been tracked at the submillisecond level by astronomical radio interferometry and laser ranging to the LAGEOS satellite. Three years of regular measurements reveal complex patterns of variations including UTI fluctuations as large as 5 milliseconds in a few weeks. Comparison of the observed changes in length of day with variations in the global atmospheric angular momentum indicates that the dominant cause of changes in the earth's spin rate, on time scales from a week to several years, is the exchange of angular momentum between the atmosphere and the mantle. The unusually intense El Nino of 1982-1983 was marked by a strong peak in the length of day.

  5. Sociolinguistic Variation and Change.

    ERIC Educational Resources Information Center

    Trudgill, Peter

    This book examines linguistic variation and change. Section 1, "Sociohistorical Linguistics," includes: (1) "British Vernacular Dialects in the Formation of American English: The Case of East Anglian 'Do'"; (2) "'Short o' in East Anglia and New England"; and (3) "Sociohistorical Linguistics and Dialect Survival: A Note on Another Nova Scotian…

  6. Variational transition state theory

    SciTech Connect

    Truhlar, D.G.

    1993-12-01

    This research program involves the development of variational transition state theory (VTST) and semiclassical tunneling methods for the calculation of gas-phase reaction rates and selected applications. The applications are selected for their fundamental interest and/or their relevance to combustion.

  7. Variation and Linguistic Theory.

    ERIC Educational Resources Information Center

    Bailey, Charles-James N.

    This volume presents principles and models for describing language variation, and introduces a time-based, dynamic framework for linguistic description. The book first summarizes some of the problems of grammatical description encountered from Saussure through the present and then outlines possibilities for new descriptions of language which take…

  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. 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…

  10. Reducing GWAS Complexity.

    PubMed

    Hazelett, Dennis J; Conti, David V; Han, Ying; Al Olama, Ali Amin; Easton, Doug; Eeles, Rosalind A; Kote-Jarai, Zsofia; Haiman, Christopher A; Coetzee, Gerhard A

    2016-01-01

    Genome-wide association studies (GWAS) have revealed numerous genomic 'hits' associated with complex phenotypes. In most cases these hits, along with surrogate genetic variation as measure by numerous single nucleotide polymorphisms (SNPs) that are in linkage disequilibrium, are not in coding genes making assignment of functionality or causality intractable. Here we propose that fine-mapping along with the matching of risk SNPs at chromatin biofeatures lessen this complexity by reducing the number of candidate functional/causal SNPs. For example, we show here that only on average 2 SNPs per prostate cancer risk locus are likely candidates for functionality/causality; we further propose that this manageable number should be taken forward in mechanistic studies. The candidate SNPs can be looked up for each prostate cancer risk region in 2 recent publications in 2015 (1,2) from our groups. PMID:26771711

  11. Diurnal variations of Titan

    NASA Astrophysics Data System (ADS)

    Cui, J.; Galand, M.; Yelle, R. V.; Vuitton, V.; Wahlund, J.-E.; Lavvas, P. P.; Mueller-Wodarg, I. C. F.; Kasprzak, W. T.; Waite, J. H.

    2009-04-01

    We present our analysis of the diurnal variations of Titan's ionosphere (between 1,000 and 1,400 km) based on a sample of Ion Neutral Mass Spectrometer (INMS) measurements in the Open Source Ion (OSI) mode obtained from 8 close encounters of the Cassini spacecraft with Titan. Though there is an overall ion depletion well beyond the terminator, the ion content on Titan's nightside is still appreciable, with a density plateau of ~700 cm-3 below ~1,300 km. Such a plateau is associated with the combination of distinct diurnal variations of light and heavy ions. Light ions (e.g. CH5+, HCNH+, C2H5+) show strong diurnal variation, with clear bite-outs in their nightside distributions. In contrast, heavy ions (e.g. c-C3H3+, C2H3CNH+, C6H7+) present modest diurnal variation, with significant densities observed on the nightside. We propose that the distinctions between light and heavy ions are associated with their different chemical loss pathways, with the former primarily through "fast" ion-neutral chemistry and the latter through "slow" electron dissociative recombination. The INMS data suggest day-to-night transport as an important source of ions on Titan's nightside, to be distinguished from the conventional scenario of auroral ionization by magnetospheric particles as the only ionizing source on the nightside. This is supported by the strong correlation between the observed night-to-day ion density ratios and the associated ion lifetimes. We construct a time-dependent ion chemistry model to investigate the effects of day-to-night transport on the ionospheric structures of Titan. The predicted diurnal variation has similar general characteristics to those observed, with some apparent discrepancies which could be reconciled by imposing fast horizontal thermal winds in Titan's upper atmosphere.

  12. Controlling complexity

    NASA Astrophysics Data System (ADS)

    Zelinka, Ivan; Skanderova, Lenka; Davendra, Donald D.; Senkerik, Roman; Oplatkova, Zuzana

    2012-09-01

    Complex systems and dynamics are present in many parts of daily life and branches of science. This participation is continuation of our previous research, that introduced a novelty method of visualization and possible control of complex networks, that are used to visualize dynamics of evolutionary algorithms. Selected evolutionary algorithms are used as an example in order to show how its behavior can be understood as complex network and controlled via conversion into CML system - a model based on mutually joined nonlinear n equations. The main aim of this investigation was to show that dynamics of evolutionary algorithms can be converted to CML system and then controlled. Selected results of evolutionary controlled CML system are discussed here.

  13. Holographic complexity

    NASA Astrophysics Data System (ADS)

    Alishahiha, Mohsen

    2015-12-01

    For a field theory with a gravitational dual, following Susskind's proposal we define holographic complexity for a subsystem. The holographic complexity is proportional to the volume of a codimension one time slice in the bulk geometry enclosed by the extremal codimension two hypersurface appearing in the computation of the holographic entanglement entropy. The proportionally constant, up to a numerical order of 1 factor is G R where G is the Newton constant and R is the curvature of the space-time. We study this quantity in certain holographic models. We also explore a possible relation between the defined quantity and fidelity appearing in quantum information literature.

  14. 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.

  15. Genetic Variation and Atherosclerosis

    PubMed Central

    Biros, Erik; Karan, Mirko; Golledge, Jonathan

    2008-01-01

    A family history of atherosclerosis is independently associated with an increased incidence of cardiovascular events. The genetic factors underlying the importance of inheritance in atherosclerosis are starting to be understood. Genetic variation, such as mutations or common polymorphisms has been shown to be involved in modulation of a range of risk factors, such as plasma lipoprotein levels, inflammation and vascular calcification. This review presents examples of present studies of the role of genetic polymorphism in atherosclerosis. PMID:19424482

  16. Pacific geomagnetic secular variation.

    PubMed

    Doell, R R; Cox, A

    1971-01-22

    We have considered several different types of records of long-period geomagnetic secular variation: direct measurements made in geomagnetic observatories; paleomagnetic measurements on Hawaiian lava flows with accurately known ages in the interval 0 to 200 years; paleomagentic measurements on Hawaiian lava flows with loosely determined ages within the interval 200 to 10,000 years ago; and worldwide paleomagnetic measurements of the average geomagnetic angular dispersion recorded in lava flows that formed during the past 0.7 million years. All these magnetic records indicate that, during this time, the nondipole component of the earth's field was lower in the central Pacific than elsewhere, as it is today. This, in turn, indicates that there is some type of inhomogeneity in the lower mantle which is coupled to the earth's core in such a way as to suppress the generation of the nondipole field beneath the central Pacific. With the present incomplete state of knowledge about the processes that give rise to the earth's field, it is uncertain whether undulations in the core-mantle interface or lateral variations in the composition and physical state of the lower mantle are ultimately responsible for the pattern of secular variation seen at the earth's surface. PMID:17736217

  17. Variation, Repetition, And Choice

    PubMed Central

    Abreu-Rodrigues, Josele; Lattal, Kennon A; dos Santos, Cristiano V; Matos, Ricardo A

    2005-01-01

    Experiment 1 investigated the controlling properties of variability contingencies on choice between repeated and variable responding. Pigeons were exposed to concurrent-chains schedules with two alternatives. In the REPEAT alternative, reinforcers in the terminal link depended on a single sequence of four responses. In the VARY alternative, a response sequence in the terminal link was reinforced only if it differed from the n previous sequences (lag criterion). The REPEAT contingency generated low, constant levels of sequence variation whereas the VARY contingency produced levels of sequence variation that increased with the lag criterion. Preference for the REPEAT alternative tended to increase directly with the degree of variation required for reinforcement. Experiment 2 examined the potential confounding effects in Experiment 1 of immediacy of reinforcement by yoking the interreinforcer intervals in the REPEAT alternative to those in the VARY alternative. Again, preference for REPEAT was a function of the lag criterion. Choice between varying and repeating behavior is discussed with respect to obtained behavioral variability, probability of reinforcement, delay of reinforcement, and switching within a sequence. PMID:15828592

  18. Researching Complexity.

    ERIC Educational Resources Information Center

    Sumara, Dennis J.

    2000-01-01

    Discusses what Complexity Theory (presented as a rubric that collects theoretical understandings from a number of domains such as ecology, biology, neurology, and education) suggests about mind, selfhood, intelligence, and practices of reading, and the import of these reconceptualizations to reader-response researchers. Concludes that developing…

  19. Complex interactions

    NASA Astrophysics Data System (ADS)

    de Régules, Sergio

    2016-04-01

    Complexity science – which describes phenomena such as collective and emergent behaviour – is the focus of a new centre where researchers are examining everything from the spread of influenza to what a healthy heartbeat looks like. Sergio de Régules reports.

  20. Amorphic complexity

    NASA Astrophysics Data System (ADS)

    Fuhrmann, G.; Gröger, M.; Jäger, T.

    2016-02-01

    We introduce amorphic complexity as a new topological invariant that measures the complexity of dynamical systems in the regime of zero entropy. Its main purpose is to detect the very onset of disorder in the asymptotic behaviour. For instance, it gives positive value to Denjoy examples on the circle and Sturmian subshifts, while being zero for all isometries and Morse-Smale systems. After discussing basic properties and examples, we show that amorphic complexity and the underlying asymptotic separation numbers can be used to distinguish almost automorphic minimal systems from equicontinuous ones. For symbolic systems, amorphic complexity equals the box dimension of the associated Besicovitch space. In this context, we concentrate on regular Toeplitz flows and give a detailed description of the relation to the scaling behaviour of the densities of the p-skeletons. Finally, we take a look at strange non-chaotic attractors appearing in so-called pinched skew product systems. Continuous-time systems, more general group actions and the application to cut and project quasicrystals will be treated in subsequent work.

  1. Population Structure of the North American Cranberry Fruit Rot Complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cranberry fruit rot is caused by a complex of pathogenic fungi. Variation in the populations within this complex from region to region could delay identification of the causal agents(s) and complicate management strategies. Our objective was to assess genetic variation within the four major fruit ro...

  2. 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.

  3. Time complexity and gate complexity

    SciTech Connect

    Koike, Tatsuhiko; Okudaira, Yosuke

    2010-10-15

    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. 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

  5. Variations in brain DNA

    PubMed Central

    Avila, Jesús; Gómez-Ramos, Alberto; Soriano, Eduardo

    2014-01-01

    It is assumed that DNA sequences are conserved in the diverse cell types present in a multicellular organism like the human being. Thus, in order to compare the sequences in the genome of DNA from different individuals, nucleic acid is commonly isolated from a single tissue. In this regard, blood cells are widely used for this purpose because of their availability. Thus blood DNA has been used to study genetic familiar diseases that affect other tissues and organs, such as the liver, heart, and brain. While this approach is valid for the identification of familial diseases in which mutations are present in parental germinal cells and, therefore, in all the cells of a given organism, it is not suitable to identify sporadic diseases in which mutations might occur in specific somatic cells. This review addresses somatic DNA variations in different tissues or cells (mainly in the brain) of single individuals and discusses whether the dogma of DNA invariance between cell types is indeed correct. We will also discuss how single nucleotide somatic variations arise, focusing on the presence of specific DNA mutations in the brain. PMID:25505410

  6. Anisotropic Total Variation Filtering

    SciTech Connect

    Grasmair, Markus; Lenzen, Frank

    2010-12-15

    Total variation regularization and anisotropic filtering have been established as standard methods for image denoising because of their ability to detect and keep prominent edges in the data. Both methods, however, introduce artifacts: In the case of anisotropic filtering, the preservation of edges comes at the cost of the creation of additional structures out of noise; total variation regularization, on the other hand, suffers from the stair-casing effect, which leads to gradual contrast changes in homogeneous objects, especially near curved edges and corners. In order to circumvent these drawbacks, we propose to combine the two regularization techniques. To that end we replace the isotropic TV semi-norm by an anisotropic term that mirrors the directional structure of either the noisy original data or the smoothed image. We provide a detailed existence theory for our regularization method by using the concept of relaxation. The numerical examples concluding the paper show that the proposed introduction of an anisotropy to TV regularization indeed leads to improved denoising: the stair-casing effect is reduced while at the same time the creation of artifacts is suppressed.

  7. 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.

  8. Seasonal Variation in Human Gut Microbiome Composition

    PubMed Central

    Davenport, Emily R.; Mizrahi-Man, Orna; Michelini, Katelyn; Barreiro, Luis B.; Ober, Carole; Gilad, Yoav

    2014-01-01

    The composition of the human gut microbiome is influenced by many environmental factors. Diet is thought to be one of the most important determinants, though we have limited understanding of the extent to which dietary fluctuations alter variation in the gut microbiome between individuals. In this study, we examined variation in gut microbiome composition between winter and summer over the course of one year in 60 members of a founder population, the Hutterites. Because of their communal lifestyle, Hutterite diets are similar across individuals and remarkably stable throughout the year, with the exception that fresh produce is primarily served during the summer and autumn months. Our data indicate that despite overall gut microbiome stability within individuals over time, there are consistent and significant population-wide shifts in microbiome composition across seasons. We found seasonal differences in both (i) the abundance of particular taxa (false discovery rate <0.05), including highly abundant phyla Bacteroidetes and Firmicutes, and (ii) overall gut microbiome diversity (by Shannon diversity; P = 0.001). It is likely that the dietary fluctuations between seasons with respect to produce availability explain, at least in part, these differences in microbiome composition. For example, high levels of produce containing complex carbohydrates consumed during the summer months might explain increased abundance of Bacteroidetes, which contain complex carbohydrate digesters, and decreased levels of Actinobacteria, which have been negatively correlated to fiber content in food questionnaires. Our observations demonstrate the plastic nature of the human gut microbiome in response to variation in diet. PMID:24618913

  9. 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)

  10. Gene copy number variation in schizophrenia.

    PubMed

    Sutrala, Smitha R; Goossens, Dirk; Williams, Nigel M; Heyrman, Lien; Adolfsson, Rolf; Norton, Nadine; Buckland, Paul R; Del-Favero, Jurgen

    2007-11-01

    The possibility that gene copy number variations play a role in the development of complex disorders is a topic of considerable interest. Recent reports have highlighted the large number of such variations that exist and that their occurrence varies considerably between populations. A recent report has suggested that copy number variations in four genes (GRIK3, EFNA5, AKAP5 and CACNG2) may be associated with schizophrenia. One problem with this area of study is the validation of high throughput methods such as comparative genomic hybridisation, as the latter inevitably generates false positives. We have used two contrasting methodologies to determine the validity of the findings reported above which if true would have major implications for the pathogenesis of schizophrenia. Samples from a UK population were tested using a method of allele quantification by DNA pooling and samples from Belgium and northern Sweden were tested using Multiplex Amplicon Quantification (MAQ). Both methods were used to test DNA samples used in the original investigation. No copy number variations were found for any of the genes in any samples. Our data suggests that more reliable methods need to be used to validate the existence of CNVs before full scale association studies are carried out. PMID:17826036

  11. The ribosomes of Drosophila. II. Studies on intraspecific variation.

    PubMed

    Berger, E M; Weber, L

    1974-12-01

    Electrophoretic comparisons of 40S and 55S ribosomal subunit proteins from 18 strains of Drosophila melanogaster revealed the virtual absence of allelic variation. More detailed two-dimensional studies on the large subunit proteins in 6 of the strains demonstrated additional complexity but still no interstrain variation. The significance of these results is discussed with respect to present estimates of genic heterozygosity in natural populations. PMID:4218180

  12. Algorithm of detecting structural variations in DNA sequences

    NASA Astrophysics Data System (ADS)

    Na?ecz-Charkiewicz, Katarzyna; Nowak, Robert

    2014-11-01

    Whole genome sequencing enables to use the longest common subsequence algorithm to detect genetic structure variations. We propose to search position of short unique fragments, genetic markers, to achieve acceptable time and space complexity. The markers are generated by algorithms searching the genetic sequence or its Fourier transformation. The presented methods are checked on structural variations generated in silico on bacterial genomes giving the comparable or better results than other solutions.

  13. Sequential variational data assimilation

    NASA Astrophysics Data System (ADS)

    Penenko, A. V.

    2006-02-01

    The algorithm of variational data assimilation in real time [1] is considered. It is a modification of the general algorithm of inverse modeling [2,3] under condition that the time interval of data assimilation is equal to one step of discretization of the model of processes and target functional. The purpose of work is to carry out investigation of the quality of numerical schemes and algorithms of this technique taking one and two-dimensional non-stationary models of advective - diffusive transport of pollutants in the atmosphere as examples. The comparison of data assimilation schemes based on the time-local adjoint problems with Kalman type algorithms show the advantage of the former in efficiency and labor cost. Some numerical results are presented.

  14. Variations of hybrid damping

    NASA Astrophysics Data System (ADS)

    Lam, Margaretha J.; Inman, Daniel J.; Saunders, William R.

    1998-06-01

    Damping is important to structures and can be achieved through the addition of viscoelastic materials (VEM). The damping of the VEM is enhanced if a constraining layer is attached to the VEM. If this constraining layer is active, the treatment is called active constrained layer damping (ACLD). In the last few years, ACLD has proven to be superior in vibration control to active or passive damping. The active element makes ACLD more effective than passive constrained layer damping. It also provides a fail-safe in case of breakdown of the active element that is not present for purely active control. It is shown that the control effort needed to damp vibration using ACLD can be significantly higher than purely active control. In order to combine the inherent damping of passive control with the effectiveness of the active element, this paper will explore different variations of active, passive and hybrid damping. Some of the variations include: passive constrained layer damping (PCLD) separate from active element but on the same side of beam, PCLD separate from active on the opposite side of the beam, and active element underneath PCLD. The discretized system equations will be obtained using assumed modes method and Lagrange's equation. The damping will be modeled using the Golla-Hughes-McTavish (GHM) method. The optimal placement and size of the active, passive, ACLD and hybrid treatments will be found using different schemes. The issue of overshoot and settling time of the output and control force using LQR will be addressed, as well as the control effort, passive and active vibration suppression, and LQR cost function. It will be shown that the hybrid treatments are capable of greater vibration control for lower control effort for different optimization schemes. 31

  15. 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 -- but we don't know for sure. And life went on to cause new Instabilities, constantly evolving, with living things in an extraordinary range of environments, changing the global environment, with boom-and-bust cycles. with predators for every kInd of prey, with criminals for every possible crime, with governments to prevent them, and instabilities of the governments themselves. One of the instabilities Is that humans demand new weapons and new products of all sort, leading to serious investments in science and technology. So the natural/human world of competition and combat is structured to lead to advanced weaponry and cell phones. So here we are In 2012, with people writing essays and wondering whether their descendents will be artificial life forms travelling back into space. And, pondering what are the origins of those forces of nature that give rise to everything. Verllnde has argued that gravitation, the one force that has so far resisted our efforts at a Quantum description, is not even a fundamental force, but is itself it a statistical force, like osmosis. What an amazing turn of events! But after all I've just said, I should not be surprised a bit.

  16. Stochastic variation: from single cells to superorganisms

    PubMed Central

    Kilfoil, Maria L.; Lasko, Paul; Abouheif, Ehab

    2009-01-01

    Observed phenotype often fails to correspond with genotype. Although it is well established that uncontrolled genetic modifier effects and environmental variability can affect phenotype, stochastic variation in gene expression can also contribute to phenotypic differences. Here we examine recent work that has provided insights into how fundamental physical properties of living cells, and the probabilistic nature of the chemical reactions that underlie gene expression, introduce noise. We focus on instances in which a stochastic decision initiates an event in the development of a multicellular organism and how that decision can be subsequently fixed. We present an example indicating that a similar interplay between an initial stochastic decision and subsequent fixation may underlie the regulation of reproduction in social insects. We argue, therefore, that stochasticity affects biological processes from the single-gene scale through to the complex organization of an ant colony, and represents a largely neglected component of phenotypic variation and evolution. PMID:20514130

  17. Comprehensive variation discovery in single human genomes

    PubMed Central

    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.

    2014-01-01

    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 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 several-fold, with the greatest impact in challenging regions of the human genome. PMID:25326702

  18. The Power of Natural Variation for Model Organism Biology.

    PubMed

    Gasch, Audrey P; Payseur, Bret A; Pool, John E

    2016-03-01

    Genetic background effects have long been recognized and, in some cases studied, but they are often viewed as a nuisance by molecular biologists. We suggest that genetic variation currently represents a critical frontier for molecular studies. Human genetics has seen a surge of interest in genetic variation and its contributions to disease, but insights into disease mechanisms are difficult since information about gene function is lacking. By contrast, model organism genetics has excelled at revealing molecular mechanisms of cellular processes, but often de-emphasizes genetic variation and its functional consequences. We argue that model organism biology would benefit from incorporating natural variation, both to capture how well laboratory lines exemplify the species they represent and to inform on molecular processes and their variability. Such a synthesis would also greatly expand the relevance of model systems for studies of complex trait variation, including disease. PMID:26777596

  19. An index of floodplain surface complexity

    NASA Astrophysics Data System (ADS)

    Scown, M. W.; Thoms, M. C.; De Jager, N. R.

    2015-04-01

    Floodplain surface topography is an important component of floodplain ecosystems. It is the primary physical template upon which ecosystem processes are acted out. There has been a limited appreciation of floodplain surface complexity because of the traditional focus on temporal variability in floodplains as well as limitations to quantifying spatial complexity. An index of floodplain surface complexity (FSC) is developed in this paper and applied to eight floodplains from different geographic settings. The index is based on the two key indicators of complexity; variability in surface geometry (VSG) and the spatial organization of surface conditions (SOC) and was determined at three sampling scales. Relationships between these measures of spatial complexity and environmental drivers, namely; flow variability (mean daily discharge [Q], the coefficient of variation of daily discharge [QCV], the coefficient of variation of mean annual discharge [QCVAnn], the coefficient of variation of maximum annual discharge [QCVMax]), sediment yield (SY), valley slope (Vs), and floodplain width (Fpw) were examined. FSC, VSG, and SOC varied between the eight floodplains and this was dependent upon sampling scale. All complexity values declined with increasing Fpw in either a power, logarithmic, or exponential function. There was little change in surface complexity with floodplain widths greater than 10 km. VSG was significantly related to SY and no significant relationships were determined between any of the hydrological variables and floodplain surface complexity.

  20. Symmetry and complexity

    NASA Astrophysics Data System (ADS)

    Mainzer, Klaus

    Symmetry and complexity in early culture and philosophy -- Symmetry and complexity in mathematics -- Symmetry and complexity in physical sciences -- Symmetry and complexity in chemical sciences -- Symmetry and complexity in life sciences -- Symmetry and complexity in economic and social sciences -- Symmetry and complexity in computer science -- Symmetry and complexity in philosophy and arts.

  1. Gene Transposition Causing Natural Variation for Growth in Arabidopsis thaliana

    PubMed Central

    Vlad, Daniela; Rappaport, Fabrice; Simon, Matthieu; Loudet, Olivier

    2010-01-01

    A major challenge in biology is to identify molecular polymorphisms responsible for variation in complex traits of evolutionary and agricultural interest. Using the advantages of Arabidopsis thaliana as a model species, we sought to identify new genes and genetic mechanisms underlying natural variation for shoot growth using quantitative genetic strategies. More quantitative trait loci (QTL) still need be resolved to draw a general picture as to how and where in the pathways adaptation is shaping natural variation and the type of molecular variation involved. Phenotypic variation for shoot growth in the Bur-0 × Col-0 recombinant inbred line set was decomposed into several QTLs. Nearly-isogenic lines generated from the residual heterozygosity segregating among lines revealed an even more complex picture, with major variation controlled by opposite linked loci and masked by the segregation bias due to the defective phenotype of SG3 (Shoot Growth-3), as well as epistasis with SG3i (SG3-interactor). Using principally a fine-mapping strategy, we have identified the underlying gene causing phenotypic variation at SG3: At4g30720 codes for a new chloroplast-located protein essential to ensure a correct electron flow through the photosynthetic chain and, hence, photosynthesis efficiency and normal growth. The SG3/SG3i interaction is the result of a structural polymorphism originating from the duplication of the gene followed by divergent paralogue's loss between parental accessions. Species-wide, our results illustrate the very dynamic rate of duplication/transposition, even over short periods of time, resulting in several divergent—but still functional—combinations of alleles fixed in different backgrounds. In predominantly selfing species like Arabidopsis, this variation remains hidden in wild populations but is potentially revealed when divergent individuals outcross. This work highlights the need for improved tools and algorithms to resolve structural variation polymorphisms using high-throughput sequencing, because it remains challenging to distinguish allelic from paralogous variation at this scale. PMID:20485571

  2. 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

  3. 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

  4. 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.

  5. [Carney complex].

    PubMed

    Losada Grande, Eladio José; Al Kassam Martínez, Daniel; González Boillos, Margarita

    2011-01-01

    Carney complex (CNC) is an autosomal dominantly inherited syndrome characterized by spotty skin pigmentation, cardiac and cutaneous myxoma, and endocrine overactivity. Skin pigmentation includes lentigines and blue nevi. Myxomas may occur in breast, skin and heart. Cardiac myxomas may be multiple and occur in any cardiac chamber, and are more prone to recurrence. The most common endocrine gland manifestation is an ACTH-independent Cushing's syndrome due to primary pigmented nodular adrenocortical disease (PPNAD). PPNAD may occur isolated, with no other signs of CNC. Pituitary and thyroid glands and gonads are also involved. The PRKAR1A gene, located in 17 q22-24, encodes type 1A regulatory subunit of protein kinase A. Inactivating germline mutations of this gene are found in 70% of patients with CNC. PRKAR1A is a key component of the c-AMP signaling pathway that has been implicated in endocrine tumorigenesis. Many different mutations have been reported in the PRKAR1A gene. In almost all cases the sequence change was predicted to lead to a premature stop codon and the resultant mutant mRNA was subject to nonsense-mediated mRNA decay. There is no clear genotype-phenotype correlation in patients with CNC. Genetic analysis should be performed in all CNC index cases. All affected patients should be monitored for clinical signs of CNC at least once a year. Genetic diagnosis allows for more effective preparation of more appropriate and effective therapeutic strategies and genetic counseling for patients and gene carriers, and to avoid unnecessary tests to relatives not carrying the gene. PMID:21536508

  6. Explorations in Regional Variation: A Variational Pragmatic Perspective

    ERIC Educational Resources Information Center

    Barron, Anne

    2015-01-01

    The present article introduces the Special Issue entitled "A Variational Pragmatic Approach to Regional Variation in Language," a collection of papers which celebrates the work of Klaus P. Schneider (Rheinische Friedrich-Wilhelms-Universität Bonn, Germany) on the occasion of his 60th birthday.

  7. Developmental and Genetic Origins of Murine Long Bone Length Variation

    PubMed Central

    Sanger, Thomas J.; Norgard, Elizabeth A.; Pletscher, L. Susan; Bevilacqua, Michael; Brooks, Victoria R.; Sandell, Linda M.; Cheverud, James M.

    2011-01-01

    If we wish to understand whether development influences the rate or direction of morphological evolution, we must first understand the developmental bases of morphological variation within species. However, quantitative variation in adult morphology is the product of molecular and cellular processes unfolding from embryonic development through juvenile growth to maturity. The Atchley-Hall model provides a useful framework for dissecting complex morphologies into their component parts as a way of determining which developmental processes contribute to variation in adult form. We have examined differences in postnatal allometry and the patterns of genetic correlation between age-specific traits for 10 recombinant inbred strains of mice generated from an intercross of LG/J and SM/J. Long bone length is closely tied to body size, but variation in adult morphology is more closely tied to differences in growth rate between 3 and 5 weeks of age. These analyses show that variation generated during early development is overridden by variation generated later in life. To more precisely determine the cellular processes generating this variation we then examined the cellular dynamics of long bone growth plates at the time of maximum elongation rate differences in the parent strains. Our analyses revealed that variation in long bone length is the result of faster elongation rates of the LG/J stain. The developmental bases for these differences in growth rate involve the rate of cell division and chondrocyte hypertrophy in the growth plate. PMID:21328530

  8. The complexity of anatomical systems

    PubMed Central

    Grizzi, Fabio; Chiriva-Internati, Maurizio

    2005-01-01

    Background The conception of anatomical entities as a hierarchy of infinitely graduated forms and the increase in the number of observed anatomical sub-entities and structural variables has generated a growing complexity, thus highlighting new properties of organised biological matter. Results (1) Complexity is so pervasive in the anatomical world that it has come to be considered as a primary characteristic of anatomical systems. (2) Anatomical entities, when viewed at microscopic as well as macroscopic level of observation, show a different degree of complexity. (3) Complexity can reside in the structure of the anatomical system (having many diverse parts with varying interactions or an intricate architecture) or in its behaviour. Often complexity in structure and behaviour go together. (4) Complex systems admit many descriptions (ways of looking at the system) each of which is only partially true. Each way of looking at a complex system requires its own description, its own mode of analysis and its own breaking down of the system in different parts; (5) Almost all the anatomical entities display hierarchical forms: their component structures at different spatial scales or their process at different time scales are related to each other. Conclusion The need to find a new way of observing and measuring anatomical entities, and objectively quantifying their different structural changes, prompted us to investigate the non-Euclidean geometries and the theories of complexity, and to apply their concepts to human anatomy. This attempt has led us to reflect upon the complex significance of the shape of an observed anatomical entity. Its changes have been defined in relation to variations in its status: from a normal (i.e. natural) to a pathological or altered state introducing the concepts of kinematics and dynamics of anatomical forms, speed of their changes, and that of scale of their observation. PMID:16029490

  9. Systematic theoretical study of the zero-field splitting in coordination complexes of Mn(III). Density functional theory versus multireference wave function approaches.

    PubMed

    Duboc, Carole; Ganyushin, Dmitry; Sivalingam, Kantharuban; Collomb, Marie-Nolle; Neese, Frank

    2010-10-01

    This paper presents a detailed evaluation of the performance of density functional theory (DFT) as well as complete active space self-consistent field (CASSCF)-based methods (CASSCF and second-order N-electron valence state perturbation theory, NEVPT2) to predict the zero-field splitting (zfs) parameters for a series of coordination complexes containing the Mn(III) ion. The physical origin of the experimentally determined zfs's was investigated by studying the different contributions to these parameters. To this end, a series of mononuclear Mn(III) complexes was chosen for which the structures have been resolved by X-ray diffraction and the zfs parameters have been accurately determined by high-field EPR spectroscopy. In a second step, small models have been constructed to allow for a systematic assessment of the factors that dominate the variations in the observed zfs parameters and to establish magnetostructural correlations. Among the tested functionals, the best predictions have been obtained with B3LYP, followed by the nonhybrid BP86 functional, which in turn is more successful than the meta-hybrid GGA functional TPSSh. For the estimation of the spin-orbit coupling (SOC) part of the zfs, it was found that the coupled perturbed SOC approach CP is more successful than the Pederson-Khanna method. Concerning the spin-spin interaction (SS), the restricted open-shell Kohn-Sham (ROKS) approach led to a slightly better agreement with the experiment than the unrestricted KS (UKS) approach. The ab initio state-averaged CASSCF (SA-CASSCF) method with a minimal active space and the most recent implementation that treats the SOC and SS contributions on an equal footing provides the best predictions for the zfs. The analysis demonstrates that the major contribution to the axial zfs parameter (D) originates from the SOC interaction but that the SS part is far from being negligible (between 10 and 20% of D). Importantly, the various excited triplet ligand field states account for roughly half of the value of D, contrary to popular ligand field models. Despite covering dynamic correlation contributions to the transition energies, NEVPT2 does not lead to large improvements in the results as the excitation energies of the Mn(III) d-d transitions are already fairly accurate at the SA-CASSCF level. For a given type of coordination sphere (e.g., elongated or compressed octahedron), the magnetic anisotropy of the Mn(III) ion, D, does not appear to be highly sensitive to the nature of the ligands, while the E/D ratio is notably affected by all octahedral distortions. Furthermore, the introduction of different halides into the coordination sphere of Mn(III) only leads to small effects on D. Nevertheless, it appears that oxygen-based ligands afford larger D values than nitrogen-based ligands. PMID:20828179

  10. The goldstini variations

    NASA Astrophysics Data System (ADS)

    Craig, Nathaniel; March-Russell, John; McCullough, Matthew

    2010-10-01

    We study the goldstini scenario of Cheung, Nomura, and Thaler, in which multiple independent supersymmetry (SUSY) breaking sectors lead to multiple would-be goldstinos, changing collider and cosmological phenomenology. In supergravity, potentially large corrections to the previous prediction of twice the gravitino mass for goldstini masses can arise when their scalar partners are stabilized far from the origin. Considerations arising from the complexity of realistic string compactifications indicate that many of the independent SUSY-breaking sectors should be conformally sequestered or situated in warped Randall-Sundrum-like throats, further changing the predicted goldstini masses. If the sequestered hidden sector is a metastable SUSY-breaking sector of the Intriligator-Seiberg-Shih (ISS) type then multiple goldstini can originate from within a single sector, along with many supplementary modulini, all with masses of order twice the gravitino mass. These fields can couple to the Supersymmetric Standard Model (SSM) via the Goldstino Portal. Collider signatures involving SSM sparticle decays can provide strong evidence for warped-or-conformally-sequestered sectors, and of the ISS mechanism of SUSY breaking. Along with axions and photini, the Goldstino Portal gives another potential window to the hidden sectors of string theory.

  11. Discovery of rare variants for complex phenotypes.

    PubMed

    Kosmicki, Jack A; Churchhouse, Claire L; Rivas, Manuel A; Neale, Benjamin M

    2016-06-01

    With the rise of sequencing technologies, it is now feasible to assess the role rare variants play in the genetic contribution to complex trait variation. While some of the earlier targeted sequencing studies successfully identified rare variants of large effect, unbiased gene discovery using exome sequencing has experienced limited success for complex traits. Nevertheless, rare variant association studies have demonstrated that rare variants do contribute to phenotypic variability, but sample sizes will likely have to be even larger than those of common variant association studies to be powered for the detection of genes and loci. Large-scale sequencing efforts of tens of thousands of individuals, such as the UK10K Project and aggregation efforts such as the Exome Aggregation Consortium, have made great strides in advancing our knowledge of the landscape of rare variation, but there remain many considerations when studying rare variation in the context of complex traits. We discuss these considerations in this review, presenting a broad range of topics at a high level as an introduction to rare variant analysis in complex traits including the issues of power, study design, sample ascertainment, de novo variation, and statistical testing approaches. Ultimately, as sequencing costs continue to decline, larger sequencing studies will yield clearer insights into the biological consequence of rare mutations and may reveal which genes play a role in the etiology of complex traits. PMID:27221085

  12. Variational Infinite Hidden Conditional Random Fields.

    PubMed

    Bousmalis, Konstantinos; Zafeiriou, Stefanos; Morency, Louis-Philippe; Pantic, Maja; Ghahramani, Zoubin

    2015-09-01

    Hidden conditional random fields (HCRFs) are discriminative latent variable models which have been shown to successfully learn the hidden structure of a given classification problem. An Infinite hidden conditional random field is a hidden conditional random field with a countably infinite number of hidden states, which rids us not only of the necessity to specify a priori a fixed number of hidden states available but also of the problem of overfitting. Markov chain Monte Carlo (MCMC) sampling algorithms are often employed for inference in such models. However, convergence of such algorithms is rather difficult to verify, and as the complexity of the task at hand increases the computational cost of such algorithms often becomes prohibitive. These limitations can be overcome by variational techniques. In this paper, we present a generalized framework for infinite HCRF models, and a novel variational inference approach on a model based on coupled Dirichlet Process Mixtures, the HCRF-DPM. We show that the variational HCRF-DPM is able to converge to a correct number of represented hidden states, and performs as well as the best parametric HCRFs-chosen via cross-validation-for the difficult tasks of recognizing instances of agreement, disagreement, and pain in audiovisual sequences. PMID:26353136

  13. 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.

  14. Exterior complex scaling method in TDDFT: HHG of Ar atoms in intense laser fields

    NASA Astrophysics Data System (ADS)

    Sosnova, K. E.; Telnov, D. A.; Rozenbaum, E. B.; Chu, S. I.

    2014-04-01

    The exterior complex scaling (ECS) method is applied in the framework of time-dependent density-functional theory (TDDFT) to study high-order harmonic generation (HHG) of multielectron atoms in intense laser fields. With the help of ECS, correct outgoing-wave boundary conditions can be imposed on the wave functions at large distances. In our implementation, ECS is combined with the time-dependent generalized pseudospectral method for accurate and efficient solution of the time-dependent Kohn-Sham equations. We make use of LB94 exchange-correlation potential which appears quite accurate in calculations of unperturbed electronic structure of Ar. Calculations of HHG are performed for the laser fields with the wavelength of 800 nm and several peak intensities. The HHG spectrum exhibits an intensity-independent minimum corresponding to the photon energy of about 51 eV which is closely related to the Cooper minimum in the photoionization cross section of Ar. We found that HHG spectra calculated with the frozen-core potential (not including dynamic response of the electron density) differ significantly from those obtained by TDDFT.

  15. 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

  16. 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

  17. The calculation of the static first and second susceptibilities of crystalline urea: A comparison of Hartree-Fock and density functional theory results obtained with the periodic coupled perturbed Hartree-Fock/Kohn-Sham scheme.

    PubMed

    Ferrero, Mauro; Civalleri, Bartolomeo; Rérat, Michel; Orlando, Roberto; Dovesi, Roberto

    2009-12-01

    The static polarizability alpha and first hyperpolarizability beta tensors of crystalline urea and the corresponding first-(chi((1))) and second-(chi((2))) susceptibilities are calculated and compared to the same quantities obtained for the molecule by using the same code (a development version of CRYSTAL), basis set, and level of theory. In order to separate geometrical and solid state effects, two geometries are considered for the molecule in its planar conformation: (i) as cut out from the bulk structure and (ii) fully optimized. First, the effect of basis sets on computed properties is explored at the B3LYP level by employing basis sets of increasing complexity, from 6-31G(d,p) to 6-311G(2df,2pd) (Pople's family) and from DZP to QZVPPP (Thakkar/Ahlrichs/Dunning's family) on alpha and beta for both the molecule and the bulk. Then, five different levels of theory, namely, SVWN (local density approximation), PBE (generalized gradient approximation), PBE0 and B3LYP (hybrid), and Hartree-Fock are compared in combination with a TZPP basis set. Present results show that hybrid methods, in particular, B3LYP, are remarkably successful in predicting correctly both the first and second susceptibilities of urea bulk when combined at least with a triple-zeta quality basis set containing a double set of polarization functions. It is also shown that diffuse functions that are needed for molecular calculations are less crucial for the crystalline structure, as expected. Indeed, B3LYP/TZPP computed chi((1)) and chi((2)) tensor components (chi(aa) ((1))=1.107, chi(cc) ((1))=1.459, and chi((2))=-0.93 a.u.) are in very good agreement with experimental values. At variance with respect to previous periodic ab initio calculations, but in agreement with recent supermolecular results, the negative sign of chi((2)) is confirmed. Overall, static linear and nonlinear optical properties such as dielectric constants, refractive, and birefringence indices and second-harmonic generation coefficient of crystalline urea are very well reproduced by present calculations. PMID:19968357

  18. 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…

  19. The overdue promise of short tandem repeat variation for heritability

    PubMed Central

    Press, Maximilian O.; Carlson, Keisha D.; Queitsch, Christine

    2014-01-01

    Short tandem repeat (STR) variation has been proposed as a major explanatory factor in the heritability of complex traits in humans and model organisms. However, we still struggle to incorporate STR variation into genotype-phenotype maps. Here, we review the promise of STRs in contributing to complex trait heritability, and highlight the challenges that STRs pose due to their repetitive nature. We argue that STR variants are more likely than single nucleotide variants to have epistatic interactions, reiterate the need for targeted assays to accurately genotype STRs, and call for more appropriate statistical methods in detecting STR-phenotype associations. Lastly, we suggest that somatic STR variation within individuals may serve as a read-out of disease susceptibility, and is thus potentially a valuable covariate for future association studies. PMID:25182195

  20. Semiannual variation of geomagnetic activity.

    NASA Technical Reports Server (NTRS)

    Russell, C. T.; Mcpherron, R. L.

    1973-01-01

    It is proposed that the semiannual variation in geomagnetic activity 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 is controlled by a magnetospheric system. Several simple models utilizing this effective modulation of the southward component of the interplanetary field are examined. One of these closely predicts the observed phase and amplitude of the semiannual variation. This model assumes that northward interplanetary fields are noninteracting and that the interaction with southward fields is ordered in solar magnetospheric coordinates. The prediction of the diurnal variation of the strength of the interaction at the magnetopause by this model, does not, however, match the diurnal variation of geomagnetic activity as derived from ground-based data.

  1. 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.

  2. Genetics of the dentofacial variation in human malocclusion

    PubMed Central

    Moreno Uribe, L. M.; Miller, S. F.

    2015-01-01

    Malocclusions affect individuals worldwide, resulting in compromised function and esthetics. Understanding the etiological factors contributing to the variation in dentofacial morphology associated with malocclusions is the key to develop novel treatment approaches. Advances in dentofacial phenotyping, which is the comprehensive characterization of hard and soft tissue variation in the craniofacial complex, together with the acquisition of large-scale genomic data have started to unravel genetic mechanisms underlying facial variation. Knowledge on the genetics of human malocclusion is limited even though results attained thus far are encouraging, with promising opportunities for future research. This review summarizes the most common dentofacial variations associated with malocclusions and reviews the current knowledge of the roles of genes in the development of malocclusions. Lastly, this review will describe ways to advance malocclusion research, following examples from the expanding fields of phenomics and genomic medicine, which aim to better patient outcomes. PMID:25865537

  3. 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

  4. Tailoring the physical properties of Ni-based single-phase equiatomic alloys by modifying the chemical complexity

    SciTech Connect

    Jin, Ke; Sales, Brian C; Stocks, George Malcolm; Samolyuk, German D.; Daene, Markus; Weber, William J.; Zhang, Yanwen; Bei, Hongbin

    2016-01-01

    We discovered that equiatomic alloys (e.g. high entropy alloys) have recently attracted considerable interest due to their exceptional properties, which might be closely related to their extreme disorder induced by the chemical complexity. To understand the effects of chemical complexity on their fundamental physical properties, a family of (eight) Ni-based, face-center-cubic (FCC), equiatomic alloys, extending from elemental Ni to quinary high entropy alloys, has been synthesized, and their electrical, thermal, and magnetic properties are systematically investigated in the range of 4–300 K by combining experiments with ab initio Korring-Kohn-Rostoker coherent-potential-approximation (KKR-CPA) calculations. The scattering of electrons is significantly increased due to the chemical (especially magnetic) disorder. It has weak correlation with the number of elements but strongly depends on the type of elements. Thermal conductivities of the alloys are largely lower than pure metals, primarily because the high electrical resistivity suppresses the electronic thermal conductivity. Moreover, the temperature dependence of the electrical and thermal transport properties is further discussed, and the magnetization of five alloys containing three or more elements is measured in magnetic fields up to 4 T.

  5. Tailoring the physical properties of Ni-based single-phase equiatomic alloys by modifying the chemical complexity.

    PubMed

    Jin, K; Sales, B C; Stocks, G M; Samolyuk, G D; Daene, M; Weber, W J; Zhang, Y; Bei, H

    2016-01-01

    Equiatomic alloys (e.g. high entropy alloys) have recently attracted considerable interest due to their exceptional properties, which might be closely related to their extreme disorder induced by the chemical complexity. In order to understand the effects of chemical complexity on their fundamental physical properties, a family of (eight) Ni-based, face-center-cubic (FCC), equiatomic alloys, extending from elemental Ni to quinary high entropy alloys, has been synthesized, and their electrical, thermal, and magnetic properties are systematically investigated in the range of 4-300 K by combining experiments with ab initio Korring-Kohn-Rostoker coherent-potential-approximation (KKR-CPA) calculations. The scattering of electrons is significantly increased due to the chemical (especially magnetic) disorder. It has weak correlation with the number of elements but strongly depends on the type of elements. Thermal conductivities of the alloys are largely lower than pure metals, primarily because the high electrical resistivity suppresses the electronic thermal conductivity. The temperature dependence of the electrical and thermal transport properties is further discussed, and the magnetization of five alloys containing three or more elements is measured in magnetic fields up to 4 T. PMID:26832223

  6. Tailoring the physical properties of Ni-based single-phase equiatomic alloys by modifying the chemical complexity

    NASA Astrophysics Data System (ADS)

    Jin, K.; Sales, B. C.; Stocks, G. M.; Samolyuk, G. D.; Daene, M.; Weber, W. J.; Zhang, Y.; Bei, H.

    2016-02-01

    Equiatomic alloys (e.g. high entropy alloys) have recently attracted considerable interest due to their exceptional properties, which might be closely related to their extreme disorder induced by the chemical complexity. In order to understand the effects of chemical complexity on their fundamental physical properties, a family of (eight) Ni-based, face-center-cubic (FCC), equiatomic alloys, extending from elemental Ni to quinary high entropy alloys, has been synthesized, and their electrical, thermal, and magnetic properties are systematically investigated in the range of 4-300 K by combining experiments with ab initio Korring-Kohn-Rostoker coherent-potential-approximation (KKR-CPA) calculations. The scattering of electrons is significantly increased due to the chemical (especially magnetic) disorder. It has weak correlation with the number of elements but strongly depends on the type of elements. Thermal conductivities of the alloys are largely lower than pure metals, primarily because the high electrical resistivity suppresses the electronic thermal conductivity. The temperature dependence of the electrical and thermal transport properties is further discussed, and the magnetization of five alloys containing three or more elements is measured in magnetic fields up to 4 T.

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

    NASA Astrophysics Data System (ADS)

    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.

  8. Tailoring the physical properties of Ni-based single-phase equiatomic alloys by modifying the chemical complexity

    DOE PAGESBeta

    Jin, Ke; Sales, Brian C.; Stocks, George Malcolm; Samolyuk, German D.; Daene, Markus; Weber, William J.; Zhang, Yanwen; Bei, Hongbin

    2016-02-01

    We discovered that equiatomic alloys (e.g. high entropy alloys) have recently attracted considerable interest due to their exceptional properties, which might be closely related to their extreme disorder induced by the chemical complexity. To understand the effects of chemical complexity on their fundamental physical properties, a family of (eight) Ni-based, face-center-cubic (FCC), equiatomic alloys, extending from elemental Ni to quinary high entropy alloys, has been synthesized, and their electrical, thermal, and magnetic properties are systematically investigated in the range of 4–300 K by combining experiments with ab initio Korring-Kohn-Rostoker coherent-potential-approximation (KKR-CPA) calculations. The scattering of electrons is significantly increased duemore » to the chemical (especially magnetic) disorder. It has weak correlation with the number of elements but strongly depends on the type of elements. Thermal conductivities of the alloys are largely lower than pure metals, primarily because the high electrical resistivity suppresses the electronic thermal conductivity. Moreover, the temperature dependence of the electrical and thermal transport properties is further discussed, and the magnetization of five alloys containing three or more elements is measured in magnetic fields up to 4 T.« less

  9. Tailoring the physical properties of Ni-based single-phase equiatomic alloys by modifying the chemical complexity

    PubMed Central

    Jin, K.; Sales, B. C.; Stocks, G. M.; Samolyuk, G. D.; Daene, M.; Weber, W. J.; Zhang, Y.; Bei, H.

    2016-01-01

    Equiatomic alloys (e.g. high entropy alloys) have recently attracted considerable interest due to their exceptional properties, which might be closely related to their extreme disorder induced by the chemical complexity. In order to understand the effects of chemical complexity on their fundamental physical properties, a family of (eight) Ni-based, face-center-cubic (FCC), equiatomic alloys, extending from elemental Ni to quinary high entropy alloys, has been synthesized, and their electrical, thermal, and magnetic properties are systematically investigated in the range of 4–300 K by combining experiments with ab initio Korring-Kohn-Rostoker coherent-potential-approximation (KKR-CPA) calculations. The scattering of electrons is significantly increased due to the chemical (especially magnetic) disorder. It has weak correlation with the number of elements but strongly depends on the type of elements. Thermal conductivities of the alloys are largely lower than pure metals, primarily because the high electrical resistivity suppresses the electronic thermal conductivity. The temperature dependence of the electrical and thermal transport properties is further discussed, and the magnetization of five alloys containing three or more elements is measured in magnetic fields up to 4 T. PMID:26832223

  10. 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.

  11. Statistics, Uncertainty, and Transmitted Variation

    SciTech Connect

    Wendelberger, Joanne Roth

    2014-11-05

    The field of Statistics provides methods for modeling and understanding data and making decisions in the presence of uncertainty. When examining response functions, variation present in the input variables will be transmitted via the response function to the output variables. This phenomenon can potentially have significant impacts on the uncertainty associated with results from subsequent analysis. This presentation will examine the concept of transmitted variation, its impact on designed experiments, and a method for identifying and estimating sources of transmitted variation in certain settings.

  12. Derivation of the RPA (Random Phase Approximation) Equation of ATDDFT (Adiabatic Time Dependent Density Functional Ground State Response Theory) from an Excited State Variational Approach Based on the Ground State Functional.

    PubMed

    Ziegler, Tom; Krykunov, Mykhaylo; Autschbach, Jochen

    2014-09-01

    The random phase approximation (RPA) equation of adiabatic time dependent density functional ground state response theory (ATDDFT) has been used extensively in studies of excited states. It extracts information about excited states from frequency dependent ground state response properties and avoids, thus, in an elegant way, direct Kohn-Sham calculations on excited states in accordance with the status of DFT as a ground state theory. Thus, excitation energies can be found as resonance poles of frequency dependent ground state polarizability from the eigenvalues of the RPA equation. ATDDFT is approximate in that it makes use of a frequency independent energy kernel derived from the ground state functional. It is shown in this study that one can derive the RPA equation of ATDDFT from a purely variational approach in which stationary states above the ground state are located using our constricted variational DFT (CV-DFT) method and the ground state functional. Thus, locating stationary states above the ground state due to one-electron excitations with a ground state functional is completely equivalent to solving the RPA equation of TDDFT employing the same functional. The present study is an extension of a previous work in which we demonstrated the equivalence between ATDDFT and CV-DFT within the Tamm-Dancoff approximation. PMID:26588541

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

    NASA Astrophysics Data System (ADS)

    Borchert, Manuela; Wilke, Max; Schmidt, Christian; Kvashnina, Kristina

    2010-05-01

    At crustal conditions, the fluid-melt partitioning of Sr is mainly controlled by the salinity of the fluid and the composition of the melt (Borchert et al., 2010). The data show a sharp increase in the Sr partition coefficient with the alumina saturation index (ASI) to a maximum of 0.3 at an ASI of 1.05. Because fluid-melt partitioning of a given element depends on its complexation in the fluid and its incorporation in the melt, these data imply a change in the Sr speciation at least one of the two phases. For silicate melts, Kohn et al. (1990) found only small changes in the first coordination shell of Sr in a suite of melts with various degrees of polymerization, and argued that incorporation of Sr in the melt should not play a major role in controlling Sr partitioning. For the aqueous fluid, Bai and Koster van Groos (1999) and Webster et al. (1989) suggested a control of the Sr partition coefficient by SrCl2 complexes based on the correlation between partition coefficient and Cl concentration in the fluid after quenching. Both hypotheses cannot explain our partitioning data. Thus, new information on Sr complexation is required. Here, we studied the complexation of Sr in peraluminous or peralkaline melt dissolved in aqueous fluids in-situ at elevated PT conditions using hydrothermal diamond-anvil cells (HDAC) and X-ray absorption near edge structure (XANES) spectroscopy. The starting materials were peraluminous or peralkaline glass and H2O or a chloridic solution. The glass was doped with high concentrations of 5000 or 10000 ppm Sr. We used bulk compositions with 10 to 15 wt.% glass to ensure that the melt was completely dissolved in the fluid at high PT conditions. For qualitative evaluation, we analyzed the starting glasses and various crystalline compounds and standard solutions. The experiments were performed at beamline ID26 at ESRF (Grenoble, France) using a high resolution emission spectrometer and Si(311) monochromator crystals for high resolution and Si(111) for low resolution measurements. An overall resolution of 1.98 eV (Si(311)) and 3 eV (Si(111)) was achieved using a beamsize of 120x400 μm, Si(777) analyzer crystals and a Rowland circle diameter of 1 m. Strontium XANES spectra of peraluminous and peralkaline starting glasses show distinct differences in pre-edge, main edge and position of the first EXAFS maximum which is directly correlated to the distance of Sr and its nearest neighbor. Therefore, the spectra indicate an effect of the ASI on the local structure around Sr. Spectra of standard solution at various PT conditions indicate detectable temperature-dependent changes in the intensity and peak width of the white line. The XANES spectra of chloridic solutions with peraluminous or peralkaline melt dissolved differ 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 spectroscopic evidence on Sr complexation at elevated PT condition indicates significant speciation changes in both fluid and melt, and suggest ASI-dependent formation of Sr-Si complexes in the fluids. Literature Bai and Koster van Groos (1999), GCA 63, 1117-1131. Borchert et al. (2010), GCA 74, 1057-1076. Kohn et al. (1990), CMP 105, 359-368. Webster et al. (1989), Econ. Geol. 84, 116-134.

  14. Statistical Analysis of Variation in the Human Plasma Proteome

    DOE PAGESBeta

    Corzett, Todd H.; Fodor, Imola K.; Choi, Megan W.; Walsworth, Vicki L.; Turteltaub, Kenneth W.; McCutchen-Maloney, Sandra L.; Chromy, Brett A.

    2010-01-01

    Quantifying the variation in the human plasma proteome is an essential prerequisite for disease-specific biomarker detection. We report here on the longitudinal and individual variation in human plasma characterized by two-dimensional difference gel electrophoresis (2-D DIGE) using plasma samples from eleven healthy subjects collected three times over a two week period. Fixed-effects modeling was used to remove dye and gel variability. Mixed-effects modeling was then used to quantitate the sources of proteomic variation. The subject-to-subject variation represented the largest variance component, while the time-within-subject variation was comparable to the experimental variation found in a previous technical variability study where onemore » human plasma sample was processed eight times in parallel and each was then analyzed by 2-D DIGE in triplicate. Here, 21 protein spots had larger than 50% CV, suggesting that these proteins may not be appropriate as biomarkers and should be carefully scrutinized in future studies. Seventy-eight protein spots showing differential protein levels between different individuals or individual collections were identified by mass spectrometry and further characterized using hierarchical clustering. The results present a first step toward understanding the complexity of longitudinal and individual variation in the human plasma proteome, and provide a baseline for improved biomarker discovery.« less

  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. 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…

  17. 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...

  18. Martian Craters at the Simple-Complex Transition Diameter

    NASA Astrophysics Data System (ADS)

    Herrick, R. R.

    2012-03-01

    The simple-complex crater transition on Mars occurs over a large diameter range, so there are craters with similar diameter that have widely varying morphologies. I show that the variations are determined primarily by specific target properties.

  19. Experimental and Theoretical Determination of Dissociation Energies of Dispersion-Dominated Aromatic Molecular Complexes.

    PubMed

    Frey, Jann A; Holzer, Christof; Klopper, Wim; Leutwyler, Samuel

    2016-05-11

    The dissociation energy (D0) of an isolated and cold molecular complex in the gas-phase is a fundamental measure of the strength of the intermolecular interactions between its constituent moieties. Accurate D0 values are important for the understanding of intermolecular bonding, for benchmarking high-level theoretical calculations, and for the parametrization of force-field models used in fields ranging from crystallography to biochemistry. We review experimental and theoretical methods for determining gas-phase D0 values of M·S complexes, where M is a (hetero)aromatic molecule and S is a closed-shell "solvent" atom or molecule. The experimental methods discussed involve M-centered (S0 → S1) electronic excitation, which is often followed by ionization to the M(+)·S ion. The D0 is measured by depositing a defined amount of vibrational energy in the neutral ground state, giving M(‡)·S, the neutral S1 excited state, giving M*·S, or the M(+)·S ion ground state. The experimental methods and their relative advantages and disadvantages are discussed. Based on the electronic structure of M and S, we classify the M·S complexes as Type I, II, or III, and discuss characteristic properties of their respective potential energy surfaces that affect or hinder the determination of D0. Current theoretical approaches are reviewed, which comprise methods based on a Kohn-Sham reference determinant as well as wave function-based methods based on coupled-cluster theory. PMID:27055105

  20. Variation of fundamental constants: theory

    NASA Astrophysics Data System (ADS)

    Flambaum, Victor

    2008-05-01

    Theories unifying gravity with other interactions suggest temporal and spatial variation of the fundamental ``constants'' in expanding Universe. There are some hints for the variation of different fundamental constants in quasar absorption spectra and Big Bang nucleosynthesis data. A large number of publications (including atomic clocks) report limits on the variations. We want to study the variation of the main dimensionless parameters of the Standard Model: 1. Fine structure constant alpha (combination of speed of light, electron charge and Plank constant). 2. Ratio of the strong interaction scale (LambdaQCD) to a fundamental mass like electron mass or quark mass which are proportional to Higgs vacuum expectation value. The proton mass is propotional to LambdaQCD, therefore, the proton-to-electron mass ratio comes into this second category. We performed necessary atomic, nuclear and QCD calculations needed to study variation of the fundamental constants using the Big Bang Nucleosynthsis, quasar spectra, Oklo natural nuclear reactor and atomic clock data. The relative effects of the variation may be enhanced in transitions between narrow close levels in atoms, molecules and nuclei. If one will study an enhanced effect, the relative value of systematic effects (which are not enhanced) may be much smaller. Note also that the absolute magnitude of the variation effects in nuclei (e.g. in very narrow 7 eV transition in 229Th) may be 5 orders of magnitude larger than in atoms. A different possibility of enhancement comes from the inversion transitions in molecules where splitting between the levels is due to the quantum tunneling amplitude which has strong, exponential dependence on the electron to proton mass ratio. Our study of NH3 quasar spectra has already given the best limit on the variation of electron to proton mass ratio.

  1. Holding the Words in Our Mouths: Responses to Dialect Variations in Oral Reading

    ERIC Educational Resources Information Center

    Van Duinen, Deborah Vriend; Wilson, Marilyn J.

    2008-01-01

    Deborah Vriend Van Duinen and Marilyn J. Wilson confront normalized notions of "correct" English. They offer suggestions for teaching about marginalized voices and introducing students to the complexities of English dialect variations. (Contains 1 figure.)

  2. 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 ...

  3. Interannual Length-of-Day Variations and the ENSO Phenomenon: Insights via Singular Spectral Analysis

    NASA Technical Reports Server (NTRS)

    Dickey, J. O.; Keppenne, C. L.

    1997-01-01

    Singular spectrum analysis (SSA), used in both single channel and complex SSA (CSSA) modes, is applied to time series of Length-of-Day (LOD) variations and the Modified Southern Oscillation Index (MSOI), focusing on interannual periods.

  4. Variational integrators for electric circuits

    SciTech Connect

    Ober-Blöbaum, Sina; Tao, Molei; Cheng, Mulin; Owhadi, Houman; Marsden, Jerrold E.; Applied and Computational Mathematics, California Institute of Technology

    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.

  5. 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

  6. On State Complexes and Special Cube Complexes

    ERIC Educational Resources Information Center

    Peterson, Valerie J.

    2009-01-01

    This thesis presents the first steps toward a classification of non-positively curved cube complexes called state complexes. A "state complex" is a configuration space for a "reconfigurable system," i.e., an abstract system in which local movements occur in some discrete manner. Reconfigurable systems can be used to describe, for example,…

  7. 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,

  8. Structural and functional impacts of copy number variations on the cattle genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although there have been significant advances in resolving the pattern and nature of single nucleotide polymorphisms (SNPs), similar realizations for larger, more complex forms of genetic variation have just emerged. Several recent publications reveal that copy number variations (CNVs) are common an...

  9. 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.

  10. Modeling wildfire incident complexity dynamics.

    PubMed

    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

  11. Is there much variation in variation? Revisiting statistics of small area variation in health services research

    PubMed Central

    Ibáñez, Berta; Librero, Julián; Bernal-Delgado, Enrique; Peiró, Salvador; López-Valcarcel, Beatriz González; Martínez, Natalia; Aizpuru, Felipe

    2009-01-01

    Background The importance of Small Area Variation Analysis for policy-making contrasts with the scarcity of work on the validity of the statistics used in these studies. Our study aims at 1) determining whether variation in utilization rates between health areas is higher than would be expected by chance, 2) estimating the statistical power of the variation statistics; and 3) evaluating the ability of different statistics to compare the variability among different procedures regardless of their rates. Methods Parametric bootstrap techniques were used to derive the empirical distribution for each statistic under the hypothesis of homogeneity across areas. Non-parametric procedures were used to analyze the empirical distribution for the observed statistics and compare the results in six situations (low/medium/high utilization rates and low/high variability). A small scale simulation study was conducted to assess the capacity of each statistic to discriminate between different scenarios with different degrees of variation. Results Bootstrap techniques proved to be good at quantifying the difference between the null hypothesis and the variation observed in each situation, and to construct reliable tests and confidence intervals for each of the variation statistics analyzed. Although the good performance of Systematic Component of Variation (SCV), Empirical Bayes (EB) statistic shows better behaviour under the null hypothesis, it is able to detect variability if present, it is not influenced by the procedure rate and it is best able to discriminate between different degrees of heterogeneity. Conclusion The EB statistics seems to be a good alternative to more conventional statistics used in small-area variation analysis in health service research because of its robustness. PMID:19341469

  12. Color image segmentation considering human sensitivity for color pattern variations

    NASA Astrophysics Data System (ADS)

    Yoon, Kuk-Jin; Kweon, In-So

    2001-10-01

    Color image segmentation plays an important role in the computer vision and image processing area. In this paper, we propose a novel color image segmentation algorithm in consideration of human visual sensitivity for color pattern variations by generalizing K-means clustering. Human visual system has different color perception sensitivity according to the spatial color pattern variation. To reflect this effect, we define the CCM (Color Complexity Measure) by calculating the absolute deviation with Gaussian weighting within the local mask and assign weight value to each color vector using the CCM values.

  13. Fc? receptors: genetic variation, function, and disease.

    PubMed

    Hargreaves, Chantal E; Rose-Zerilli, Matthew J J; Machado, Lee R; Iriyama, Chisako; Hollox, Edward J; Cragg, Mark S; Strefford, Jonathan C

    2015-11-01

    Fc? receptors (Fc?Rs) are key immune receptors responsible for the effective control of both humoral and innate immunity and are central to maintaining the balance between generating appropriate responses to infection and preventing autoimmunity. When this balance is lost, pathology results in increased susceptibility to cancer, autoimmunity, and infection. In contrast, optimal Fc?R engagement facilitates effective disease resolution and response to monoclonal antibody immunotherapy. The underlying genetics of the Fc?R gene family are a central component of this careful balance. Complex in humans and generated through ancestral duplication events, here we review the evolution of the gene family in mammals, the potential importance of copy number, and functionally relevant single nucleotide polymorphisms, as well as discussing current approaches and limitations when exploring genetic variation in this region. PMID:26497510

  14. Kohn's localization in disordered fermionic systems with and without interactions

    NASA Astrophysics Data System (ADS)

    Kerala Varma, Vipin; Pilati, Sebastiano

    2015-10-01

    Understanding the metal-insulator transition in disordered many-fermion systems, both with and without interactions, is one of the most challenging and consequential problems in condensed matter physics. In this paper, we address this issue from the perspective of the modern theory of the insulating state (MTIS), which has already proven to be effective for band and Mott insulators in clean systems. First, we consider noninteracting systems with different types of aperiodic external potentials: uncorrelated disorder (one-dimensional Anderson model), deterministic disorder (Aubry-André Hamiltonian and its modification including next-nearest-neighbor hopping), and disorder with long-range correlations (self-affine potential). We show how the many-body localization tensor defined within the MTIS may be used as a powerful probe to discriminate the insulating and the metallic phases, and to locate the transition point. Then, we investigate the effect of weak repulsive interactions in the Aubry-André Hamiltonian, a model which describes a recent cold-atoms experiment. By treating the weak interactions within a mean-field approximation we obtain a linear shift of the transition point towards stronger disorder, providing evidence for delocalization induced by interactions.

  15. 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.

  16. Iron Under Pressure: ``Kohn Tweezers'' and Remnant Magnetism

    NASA Astrophysics Data System (ADS)

    Monza, A.; Meffre, A.; Baudelet, F.; Rueff, J.-P.; D'Astuto, M.; Munsch, P.; Huotari, S.; Lachaize, S.; Chaudret, B.; Shukla, Abhay

    2011-06-01

    In this work we investigate the magnetic and structural properties of bulk Fe and Fe nanoparticles under pressure with x-ray absorption and emission spectroscopies providing answers to two fundamental questions: (a) the chicken-or-egg problem for the magnetic and structural transitions and (b) magnetism in the high pressure hcp phase. The two transitions, inextricably linked in the bulk, are clearly decoupled in the nanoparticles, with the magnetic collapse preceding the structural transition. Ultrafast x-ray emission spectroscopy detects remnant magnetism, probably antiferromagnetic fluctuations, up to pressures of about 40 GPa in the hcp phase. This could be of direct relevance to the superconductivity in ɛ-Fe [K. Shimizu , Nature (London)NATUAS0028-0836 412, 316 (2001)10.1038/35085536] through the existence of a quantum critical point and associated magnetic fluctuations.

  17. Iron under pressure: "Kohn tweezers" and remnant magnetism.

    PubMed

    Monza, A; Meffre, A; Baudelet, F; Rueff, J-P; d'Astuto, M; Munsch, P; Huotari, S; Lachaize, S; Chaudret, B; Shukla, Abhay

    2011-06-17

    In this work we investigate the magnetic and structural properties of bulk Fe and Fe nanoparticles under pressure with x-ray absorption and emission spectroscopies providing answers to two fundamental questions: (a) the chicken-or-egg problem for the magnetic and structural transitions and (b) magnetism in the high pressure hcp phase. The two transitions, inextricably linked in the bulk, are clearly decoupled in the nanoparticles, with the magnetic collapse preceding the structural transition. Ultrafast x-ray emission spectroscopy detects remnant magnetism, probably antiferromagnetic fluctuations, up to pressures of about 40 GPa in the hcp phase. This could be of direct relevance to the superconductivity in ϵ-Fe [K. Shimizu et al., Nature (London) 412, 316 (2001)] through the existence of a quantum critical point and associated magnetic fluctuations. PMID:21770592

  18. High Noon for High Stakes: Alfie Kohn at Middlebury College.

    ERIC Educational Resources Information Center

    Barna, Ed

    2002-01-01

    The tougher standards movement has five fatal flaws. An emphasis on scores limits student willingness to experiment and be challenged. The "basic skills" approach to teaching--pouring knowledge down student throats--has never worked well. Standardized testing necessarily creates winners and losers. Accountability is coercive and unnecessarily…

  19. 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

  20. Diffusion and thermodynamic equilibrium under pressure variations

    NASA Astrophysics Data System (ADS)

    Moulas, Evangelos; Tajčmanová, Lucie; Vrijmoed, Johannes; Podladchikov, Yuri

    2015-04-01

    Pressure is one of the most fundamental variables in mineral thermodynamics. In that respect, pressure-sensitive mineral reactions provide an important constraint on pressure under which the rock was developed. One implicit assumption when interpreting such pressure estimates is that the state-of-stress is close to hydrostatic, homogeneous and that the differential stress is negligible. Recent spectroscopic data from the mineral scale documenting pressure variations do not support this assumption. In addition to observations, mechanical models (numerical and analytical) suggest that rocks can develop and maintain heterogeneous pressure distributions at geological time scales. The recently developed unconventional barometry explains chemical zoning in minerals as a result of a pressure variation. We focus to apply the unconventional barometry in cases where chemical zoning in minerals cannot be explained by sluggish kinetics. In that respect, the unconventional barometry offers an alternative view of the chemical zoning which is consistent with thermodynamic equilibrium. However, to distinguish between a pressure-controlled chemical zoning and a zoning reflecting an incomplete chemical reaction is still challenging, especially for multicomponent systems. In this contribution, different types of chemical zoning are discussed. We investigate plagioclase rims around kyanite from an amphibolitized eclogite from Rhodope Metamorphic Complex (Greece-Bulgaria) as a case study and compare them with similar published textures from the Bohemian Massif. Mineral microstructures and phase equilibrium suggest that both rocks experienced near-isothermal decompression at high (>700C) temperatures. However, several distinct microstructural features suggest the development and/or the decay of mechanically maintained heterogeneous pressure distributions. We discuss our results and interpretations based on phase-equilibrium modeling, unconventional barometry and diffusion modeling under pressure variations.

  1. Genomic characteristics of cattle copy number variations

    PubMed Central

    2011-01-01

    Background Copy number variation (CNV) represents another important source of genetic variation complementary to single nucleotide polymorphism (SNP). High-density SNP array data have been routinely used to detect human CNVs, many of which have significant functional effects on gene expression and human diseases. In the dairy industry, a large quantity of SNP genotyping results are becoming available and can be used for CNV discovery to understand and accelerate genetic improvement for complex traits. Results We performed a systematic analysis of CNV using the Bovine HapMap SNP genotyping data, including 539 animals of 21 modern cattle breeds and 6 outgroups. After correcting genomic waves and considering the pedigree information, we identified 682 candidate CNV regions, which represent 139.8 megabases (~4.60%) of the genome. Selected CNVs were further experimentally validated and we found that copy number "gain" CNVs were predominantly clustered in tandem rather than existing as interspersed duplications. Many CNV regions (~56%) overlap with cattle genes (1,263), which are significantly enriched for immunity, lactation, reproduction and rumination. The overlap of this new dataset and other published CNV studies was less than 40%; however, our discovery of large, high frequency (> 5% of animals surveyed) CNV regions showed 90% agreement with other studies. These results highlight the differences and commonalities between technical platforms. Conclusions We present a comprehensive genomic analysis of cattle CNVs derived from SNP data which will be a valuable genomic variation resource. Combined with SNP detection assays, gene-containing CNV regions may help identify genes undergoing artificial selection in domesticated animals. PMID:21345189

  2. Understanding and using quantitative genetic variation

    PubMed Central

    Hill, William G.

    2010-01-01

    Quantitative genetics, or the genetics of complex traits, is the study of those characters which are not affected by the action of just a few major genes. Its basis is in statistical models and methodology, albeit based on many strong assumptions. While these are formally unrealistic, methods work. Analyses using dense molecular markers are greatly increasing information about the architecture of these traits, but while some genes of large effect are found, even many dozens of genes do not explain all the variation. Hence, new methods of prediction of merit in breeding programmes are again based on essentially numerical methods, but incorporating genomic information. Long-term selection responses are revealed in laboratory selection experiments, and prospects for continued genetic improvement are high. There is extensive genetic variation in natural populations, but better estimates of covariances among multiple traits and their relation to fitness are needed. Methods based on summary statistics and predictions rather than at the individual gene level seem likely to prevail for some time yet. PMID:20008387

  3. Variational elliptic solver for atmospheric applications

    SciTech Connect

    Smolarkiewicz, P.K.; Margolin, L.G.

    1994-03-01

    We discuss a conjugate gradient type method -- the conjugate residual -- suitable for solving linear elliptic equations that result from discretization of complex atmospheric dynamical problems. Rotation and irregular boundaries typically lead to nonself-adjoint elliptic operators whose matrix representation on the grid is definite but not symmetric. On the other hand, most established methods for solving large sparse matrix equations depend on the symmetry and definiteness of the matrix. Furthermore, the explicit construction of the matrix can be both difficult and computationally expensive. An attractive feature of conjugate gradient methods in general is that they do not require any knowledge of the matrix; and in particular, convergence of conjugate residual algorithms do not rely on symmetry for definite operators. We begin by reviewing some basic concepts of variational algorithms from the perspective of a physical analogy to the damped wave equation, which is a simple alternative to the traditional abstract framework of the Krylov subspace methods. We derive two conjugate residual schemes from variational principles, and prove that either definiteness or symmetry ensures their convergence. We discuss issues related to computational efficiency and illustrate our theoretical considerations with a test problem of the potential flow of a Boussinesq fluid flow past a steep, three-dimensional obstacle.

  4. Body composition variations in ageing.

    PubMed

    Buffa, Roberto; Floris, Giovanni U; Putzu, Paolo F; Marini, Elisabetta

    2011-03-01

    Age-related physiological variations of body composition concern both the fat-free mass (FFM) and the fat mass (FM). These variations expose the elderly person to the risk of malnutrition and could lead to conditions of disability. This paper aims to review the current state of knowledge on body composition in the aged population. The pattern of qualitative variations in body composition in old age is fairly well defined. In adulthood, the physiological variation of body mass involves a first increasing phase followed by a decreasing trend. The reduction is due mainly to the loss of fat-free mass, especially muscle mass. Total body water and bone mass also decrease. Fat mass tends to decrease and the reduction seems to be due mainly to the loss of subcutaneous fat. The quantitative aspects of the age of onset, rate and intensity of the physiological variations are still not completely clear. This poor quantitative definition is due to the variable and multifactorial phenomenology of ageing, the heterogeneity of assessment techniques and sampling models, and the limited number of empirical observations in oldest-old individuals. PMID:21667542

  5. Complex disease, gender and epigenetics.

    PubMed

    Kaminsky, Zachary; Wang, Sun-Chong; Petronis, Arturas

    2006-01-01

    Gender differences in susceptibility to complex disease such as asthma, diabetes, lupus, autism and major depression, among numerous other disorders, represent one of the hallmarks of non-Mendelian biology. It has been generally accepted that endocrinological differences are involved in the sexual dimorphism of complex disease; however, specific molecular mechanisms of such hormonal effects have not been elucidated yet. This paper will review evidence that sex hormone action may be mediated via gene-specific epigenetic modifications of DNA and histones. The epigenetic modifications can explain sex effects at DNA sequence polymorphisms and haplotypes identified in gender-stratified genetic linkage and association studies. Hormone-induced DNA methylation and histone modification changes at specific gene regulatory regions may increase or reduce the risk of a disease. The epigenetic interpretation of sexual dimorphism fits well into the epigenetic theory of complex disease, which argues for the primary pathogenic role of inherited and/or acquired epigenetic misregulation rather than DNA sequence variation. The new experimental strategies, especially the high throughput microarray-based epigenetic profiling, can be used for testing the epigenetic hypothesis of gender effects in complex diseases. PMID:17438668

  6. Complex Regional Pain Syndrome

    MedlinePlus

    ... Diversity Find People About NINDS NINDS Complex Regional Pain Syndrome Information Page Synonym(s): Reflex Sympathetic Dystrophy Syndrome, ... Additional resources from MedlinePlus What is Complex Regional Pain Syndrome? Complex regional pain syndrome (CRPS) is a ...

  7. Variational Lie derivative and cohomology classes

    NASA Astrophysics Data System (ADS)

    Palese, Marcella; Winterroth, Ekkehart

    2011-07-01

    We relate cohomology defined by a system of local Lagrangian with the cohomology class of the system of local variational Lie derivative, which is in turn a local variational problem; we show that the latter cohomology class is zero, since the variational Lie derivative `trivializes' cohomology classes defined by variational forms. As a consequence, conservation laws associated with symmetries of the second variational derivative of a local variational problem are globally defined.

  8. 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

  9. Variational Bayesian method for Retinex.

    PubMed

    Wang, Liqian; Xiao, Liang; Liu, Hongyi; Wei, Zhihui

    2014-08-01

    In this paper, we propose a variational Bayesian method for Retinex to simulate and interpret how the human visual system perceives color. To construct a hierarchical Bayesian model, we use the Gibbs distributions as prior distributions for the reflectance and the illumination, and the gamma distributions for the model parameters. By assuming that the reflection function is piecewise continuous and illumination function is spatially smooth, we define the energy functions in the Gibbs distributions as a total variation function and a smooth function for the reflectance and the illumination, respectively. We then apply the variational Bayes approximation to obtain the approximation of the posterior distribution of unknowns so that the unknown images and hyperparameters are estimated simultaneously. Experimental results demonstrate the efficiency of the proposed method for providing competitive performance without additional information about the unknown parameters, and when prior information is added the proposed method outperforms the non-Bayesian-based Retinex methods we compared. PMID:24846606

  10. Antigenic Variation in Bacterial Pathogens.

    PubMed

    Palmer, Guy H; Bankhead, Troy; Seifert, H Steven

    2016-02-01

    Antigenic variation is a strategy used by a broad diversity of microbial pathogens to persist within the mammalian host. Whereas viruses make use of a minimal proofreading capacity combined with large amounts of progeny to use random mutation for variant generation, antigenically variant bacteria have evolved mechanisms which use a stable genome, which aids in protecting the fitness of the progeny. Here, three well-characterized and highly antigenically variant bacterial pathogens are discussed: Anaplasma, Borrelia, and Neisseria. These three pathogens display a variety of mechanisms used to create the structural and antigenic variation needed for immune escape and long-term persistence. Intrahost antigenic variation is the focus; however, the role of these immune escape mechanisms at the population level is also presented. PMID:26999387

  11. Algorithms, complexity, and the sciences

    PubMed Central

    Papadimitriou, Christos

    2014-01-01

    Algorithms, perhaps together with Moore’s law, compose the engine of the information technology revolution, whereas complexity—the antithesis of algorithms—is one of the deepest realms of mathematical investigation. After introducing the basic concepts of algorithms and complexity, and the fundamental complexity classes P (polynomial time) and NP (nondeterministic polynomial time, or search problems), we discuss briefly the P vs. NP problem. We then focus on certain classes between P and NP which capture important phenomena in the social and life sciences, namely the Nash equlibrium and other equilibria in economics and game theory, and certain processes in population genetics and evolution. Finally, an algorithm known as multiplicative weights update (MWU) provides an algorithmic interpretation of the evolution of allele frequencies in a population under sex and weak selection. All three of these equivalences are rife with domain-specific implications: The concept of Nash equilibrium may be less universal—and therefore less compelling—than has been presumed; selection on gene interactions may entail the maintenance of genetic variation for longer periods than selection on single alleles predicts; whereas MWU can be shown to maximize, for each gene, a convex combination of the gene’s cumulative fitness in the population and the entropy of the allele distribution, an insight that may be pertinent to the maintenance of variation in evolution. PMID:25349382

  12. 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.

  13. Small Scale Abundance Variations in TMC-1

    NASA Astrophysics Data System (ADS)

    Dickens, J. E.; Langer, W. D.; Velusamy, T.

    2000-12-01

    The preprotostellar core TMC-1 is carbon-rich and exhibits large chemical abundance gradients. Various scenarios have been invoked to explain the gradients, such as differences in density, C/O ratio, or chemical evolutionary state. We present results of our study of complex hydrocarbons and prebiotic molecules in TMC-1, including new abundances and evidence for small scale abundance variations, using NASA's Deep Space Network (DSN) 70-meter antenna. We use TMC-1's low temperature environment (≈ 10 K) to observe species via their lowest energy rotational transitions, which occur at centimeter wavelengths for heavy molecules. But without a mechanism for replenishment, gas phase species would be quickly frozen onto grains. Recently, Markwick et al. (2000) constructed a dynamical-chemical model, involving grain mantle removal induced by Alfven wave propagation, which reproduces the large scale abundance gradients along the TMC-1 ridge. Mechanisms for grain mantle removal and production of rich organic species make TMC-1 an ideal target for complex molecule searches. We report abundances for carbon chains, such as C7H (upper limit) versus C8H, and upper limits for the linear chain H2C5, its related cyclic species c-C5H2, and the important prebiotic molecules pyrrole (c-C4H5N) and glycine (NH2CH2COOH). We also present evidence for small scale variations within TMC-1 from the spatial and velocity structure of dense gas tracers. We determined that emission from multiple CCS clumps (Peng et al. 1998) are present within our 50 arcsec beam. The CCS and HC7N spectra show evidence for at least 3 velocity components. Assuming the velocity components represent emission from distinct clumps, we calculate large abundance variations ([HC7N]/[CCS]=0.5--6.3) at 3 velocities within our beam. This research was conducted at the Jet Propulsion Laboratory, California Institute of Technology, under support from the National Aeronautics and Space Administration. The work was performed while J.E.D. held a National Research Council-JPL Research Associateship.

  14. Elastic electron scattering from formic acid

    SciTech Connect

    Trevisan, Cynthia S.; Orel, Ann E.; Rescigno, Thomas N.

    2006-07-31

    Following our earlier study on the dynamics of low energy electron attachment to formic acid, we report the results of elastic low-energy electron collisions with formic acid. Momentum transfer and angular differential cross sections were obtained by performing fixed-nuclei calculations employing the complex Kohn variational method. We make a brief description of the technique used to account for the polar nature of this polyatomic target and compare our results with available experimental data.

  15. Effective permittivity of saline ice under thermal variation

    NASA Technical Reports Server (NTRS)

    Nghiem, S. V.; Kwok, R.; Kong, J. A.; Shin, R. T.; Gow, A. J.; Arcone, S. A.

    1992-01-01

    A model for calculating the effective permittivity of saline ice under thermal variation is presented. The model includes multiphase inhomogeneities with multiple species characterized by orientation, size and shape distributions. The model is used to derive the effective permittivity as a function of temperature under the strong fluctuation theory which is extended to account for the complexity. The results calculated from the model are compared with experimental data at 4.8 GHz for saline ice grown at the US Army Cold Regions Research and Engineering Laboratory (CRREL). The comparison between measured and calculated complex permittivities is good for the imaginary part, and the difference is within 10 percent for the real part.

  16. Environmental stress and the expression of genetic variation.

    PubMed

    Jenkins, N L; Sgrò, C M; Hoffmann, A A

    1997-01-01

    We have started to test the effects of environmental extremes on the expression of genetic variation for traits likely to be under selection in natural populations. We have shown that field heritability may be high for stress response traits in contrast to morphological traits, which tend to show lower levels of heritable variation in nature compared with the laboratory. Selection for increased stress resistance can lead to a number of other evolutionary changes, and these may underlie trade-offs between favourable and stressful environments. Temperature extremes can have a marked influence on the heritability of life history traits. Heritabilities for fecundity can be high when parental flies are reared at low temperatures and under field conditions. The expression of genetic variation for development time is somewhat more complex when temperature extremes are considered. Populations at species margins may be ideal for studying the effects of environmental stress on evolution. PMID:9342844

  17. Hotspots for copy number variation in chimpanzees and humans

    PubMed Central

    Perry, George H.; Tchinda, Joelle; McGrath, Sean D.; Zhang, Junjun; Picker, Simon R.; Cáceres, Angela M.; Iafrate, A. John; Tyler-Smith, Chris; Scherer, Stephen W.; Eichler, Evan E.; Stone, Anne C.; Lee, Charles

    2006-01-01

    Copy number variation is surprisingly common among humans and can be involved in phenotypic diversity and variable susceptibility to complex diseases, but little is known of the extent of copy number variation in nonhuman primates. We have used two array-based comparative genomic hybridization platforms to identify a total of 355 copy number variants (CNVs) in the genomes of 20 wild-born chimpanzees (Pan troglodytes) and have compared the identified chimpanzee CNVs to known human CNVs from previous studies. Many CNVs were observed in the corresponding regions in both chimpanzees and humans; especially those CNVs of higher frequency. Strikingly, these loci are enriched 20-fold for ancestral segmental duplications, which may facilitate CNV formation through nonallelic homologous recombination mechanisms. Therefore, some of these regions may be unstable “hotspots” for the genesis of copy number variation, with recurrent duplications and deletions occurring across and within species. PMID:16702545

  18. 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. Molecular Darwinism: the contingency of spontaneous genetic variation.

    PubMed

    Arber, Werner

    2011-01-01

    The availability of spontaneously occurring genetic variants is an important driving force of biological evolution. Largely thanks to experimental investigations by microbial geneticists, we know today that several different molecular mechanisms contribute to the overall genetic variations. These mechanisms can be assigned to three natural strategies to generate genetic variants: 1) local sequence changes, 2) intragenomic reshuffling of DNA segments, and 3) acquisition of a segment of foreign DNA. In these processes, specific gene products are involved in cooperation with different nongenetic elements. Some genetic variations occur fully at random along the DNA filaments, others rather with a statistical reproducibility, although at many possible sites. We have to be aware that evolution in natural ecosystems is of higher complexity than under most laboratory conditions, not at least in view of symbiotic associations and the occurrence of horizontal gene transfer. The encountered contingency of genetic variation can possibly best ensure a long-term persistence of life under steadily changing living conditions. PMID:21979160

  20. Variation in Swedish Address Practices

    ERIC Educational Resources Information Center

    Norrby, Catrin

    2006-01-01

    This article explores variation in address in contemporary Swedish in Sweden-Swedish and Finland-Swedish. The research is part of a large-scale Australian project on changes in the address systems of French, German and Swedish. The present article focuses on results from 72 social network interviews conducted in Sweden (Gothenburg) and Finland…

  1. 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

  2. Strain variation in corrugated graphene

    NASA Astrophysics Data System (ADS)

    Wang, Xuanye; Tantiwanichapan, Khwanchai; Christopher, Jason; Paiella, Roberto; Swan, Anna

    2015-03-01

    Raman spectroscopy is a powerful non-destructive technique for analyzing strain in graphene. Recently there has been interest in making corrugated graphene devices with varying spatial wavelengths Λ for plasmonic and THz applications. Transferring graphene onto corrugated substrates introduces strain, which if there was perfect clamping (high fraction) would cause a periodic strain variation. However, the strain variation for pattern size smaller than the diffraction limit λ makes it hard to precisely model the strain distribution. Here we present a detailed study on how strain varies in corrugated graphene with sub-diffraction limit periodicity Λ < λ. Mechanically exfoliated graphene was deposited onto sinusoidal shape silicon dioxide gratings with Λ=400 nm period using the pick and place transfer technique. We observed that the graphene is not rigidly clamped, but partially slides to relieve the strain. We model the linewidth variation to extract the local strain variation as well as the sliding in the presence of charge puddling in graphene. The method gives us a better understanding on graphene slippage and strain distribution in graphene on a corrugated substrate with sub-diffraction limit spatial period.

  3. The Dimensionality of Grammatical Variation

    ERIC Educational Resources Information Center

    Sankoff, David; Cedergren, Henrietta J.

    1976-01-01

    Computer-based multidimensional scaling techniques are used to determine the dimensionality of grammatical variation in three large sets of data: Ross' (1973) Noun Phrase and fake Noun Phrase data; Sankoff's (1974) complementizer "que"-deletion (Montreal French) data; and Cedergren's (1973) syllable-final S-reduction (Panamanian Spanish) data. (DB)

  4. 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…

  5. The complex business of survival by aposematism.

    PubMed

    Mappes, Johanna; Marples, Nicola; Endler, John A

    2005-11-01

    The theory of warning signals dates back to Wallace but is still confusing, controversial and complex. Because predator avoidance of warningly coloured prey (aposematism) is based upon learning and reinforcement, it is difficult to understand how initially rare conspicuous forms subsequently become common. Here, we discuss several possible resolutions to this apparent paradox. Many of these ideas have been largely ignored as a result of implicit assumptions about predator behaviour and assumed lack of variation in the predators, prey and the predation process. Considering the spatial and temporal variation in and mechanisms of behaviour of both predators and prey will make it easier to understand the process and evolution of aposematism. PMID:16701442

  6. 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

  7. Mitochondrial Dysfunction may explain symptom variation in Phelan-McDermid Syndrome

    PubMed Central

    Frye, Richard E.; Cox, Devin; Slattery, John; Tippett, Marie; Kahler, Stephen; Granpeesheh, Doreen; Damle, Shirish; Legido, Agustin; Goldenthal, Michael J.

    2016-01-01

    Phelan-McDermid Syndrome (PMS), which is defined by a deletion within 22q13, demonstrates significant phenotypic variation. Given that six mitochondrial genes are located within 22q13, including complex I and IV genes, we hypothesize that mitochondrial complex activity abnormalities may explain phenotypic variation in PMS symptoms. Complex I, II, II + III and IV activity was measured in 51 PMS participants. Caretakers completed questionnaires and provided genetic information through the PMS foundation registry. Complex activity was abnormal in 59% of PMS participants. Abnormalities were found in complex I and IV but not complex II + III and II activity, consistent with disruption of genes within the 22q13 region. However, complex activity abnormalities were not related to specific gene deletions suggesting a “neighboring effect” of regional deletions on adjacent gene expression. A specific combination of symptoms (autism spectrum disorder, developmental regression, failure-to-thrive, exercise intolerance/fatigue) was associated with complex activity abnormalities. 64% of 106 individuals in the PMS foundation registry who did not have complex activity measured also endorsed this pattern of symptoms. These data suggest that mitochondrial abnormalities, specifically abnormalities in complex I and IV activity, may explain some phenotypic variation in PMS individuals. These results point to novel pathophysiology mechanisms and treatment targets for PMS patients. PMID:26822410

  8. CONSERTING: integrating copy number analysis with structural variation detection

    PubMed Central

    Chen, Xiang; Gupta, Pankaj; Wang, Jianmin; Nakitandwe, Joy; Roberts, Kathryn; Dalton, James D.; Parker, Matthew; Patel, Samir; Holmfeldt, Linda; Payne, Debbie; Easton, John; Ma, Jing; Rusch, Michael; Wu, Gang; Patel, Aman; J. Baker, Suzanne; Dyer, Michael A.; Shurtleff, Sheila; Espy, Stephen; Pounds, Stanley; Downing, James R.; Ellison, David W.; Mullighan, Charles G.; Zhang, Jinghui

    2015-01-01

    We developed Copy Number Segmentation by Regression Tree in Next Generation Sequencing (CONSERTING), a novel algorithm for detecting somatic copy number alteration (CNA) using whole-genome sequencing (WGS) data. CONSERTING performs iterative analysis of segmentation by read depth change and localized structural variation detection, achieving high accuracy and sensitivity. Analysis of 43 pediatric and adult cancer genomes revealed novel oncogenic CNAs, complex re-arrangements and subclonal CNAs missed by alternative approaches. PMID:25938371

  9. Effects of angular variation on split D differential eddy current probe response

    NASA Astrophysics Data System (ADS)

    Mooers, Ryan D.; Aldrin, John C.

    2016-02-01

    The complexity of the models used in validation studies over the last few years has increased. Complexity has been included in the probe operation, the core/coil shape, the inclusion of ferrite cores, and the inclusion of dimension and orientation variation. An issue with these validation studies is there is no quantitative understanding of how a small change in a parameter affects the probe response. This study will look at the variation of probe response over a range of variations in multiple orientations. In addition, a sensitivity study will be performed to determine which orientations produce the greatest variations in response and if there are parameter levels where the response is more affected by the variation.

  10. Variation in Medicaid Coverage for Hematopoietic Cell Transplantation

    PubMed Central

    Preussler, Jaime M.; Farnia, Stephanie H.; Denzen, Ellen M.; Majhail, Navneet S.

    2014-01-01

    Purpose: Variation in Medicaid policies among states may lead to differences in coverage for complex treatments. This article uses hematopoietic cell transplantation (HCT), an established treatment for patients with hematologic cancers, as a case study to highlight state variation in Medicaid coverage of complex oncology treatments. Methods: Information on HCT coverage benefits for 2012 was collected from state Medicaid Web sites and was compared with recommended HCT benefits developed by multiple stakeholders. Coverage was reviewed for five categories: one, transplantation procedure; two, donor search; three, prescriptions; four, clinical trials; and five, patient food, lodging, and transportation. Coverage was coded on a three-point scale for each category for each state. States were ranked by the number of variables for which they met recommended benefits criteria (maximum rank score, 5). Results: Detailed information on Medicaid coverage was available for 47 states. No state provided the recommended coverage benefits in all five categories. Prescription coverage most often met the recommended criteria, whereas only a small number of states provided clinical trial coverage for HCT. There was substantial variation in Medicaid coverage for HCT by state. Conclusion: Findings highlight substantial variation in Medicaid coverage for HCT by state, which may increase disparities in access for already medically underserved populations. PMID:24715266

  11. Geometric constrained variational calculus. III: The second variation (Part II)

    NASA Astrophysics Data System (ADS)

    Massa, Enrico; Luria, Gianvittorio; Pagani, Enrico

    2016-03-01

    The problem of minimality for constrained variational calculus is analyzed within the class of piecewise differentiable extremaloids. A fully covariant representation of the second variation of the action functional based on a family of local gauge transformations of the original Lagrangian is proposed. The necessity of pursuing a local adaptation process, rather than the global one described in [1] is seen to depend on the value of certain scalar attributes of the extremaloid, here called the corners’ strengths. On this basis, both the necessary and the sufficient conditions for minimality are worked out. In the discussion, a crucial role is played by an analysis of the prolongability of the Jacobi fields across the corners. Eventually, in the appendix, an alternative approach to the concept of strength of a corner, more closely related to Pontryagin’s maximum principle, is presented.

  12. Statistical mechanics of macromolecular complexation

    NASA Astrophysics Data System (ADS)

    Nakamura, Issei

    The self-assembly of macromolecules through molecular association has attracted long-standing attention in soft-condensed matter physics. The hierarchical formation from small-scale building blocks into larger-scale complex structures often leads to very rich phase behavior controlled by various ambient conditions. The understanding and control of the phase behavior of self-assembling systems require detailed knowledge about the entropy and enthalpy contributions to the free energy of the system. However, this knowledge is limited at the present time because a comprehensive theoretical description of molecular association is still lacking. In this thesis, four tales of achievements in developing theories of macromolecular complexation are presented. (1) We begin with an analytically solvable model of the self-assembly of rigid macromolecules with surface adsorption. A generic understanding of the driving force and the role of entropy is obtained from the exact solutions. (2) We move on to further development of the theory in order to study the complexation between polymers and ionic molecules. The extension of the first model to chain-like molecules is performed using a well-established method in polymer physics, the self-consistent field theory (SCFT) of polymers. We also discuss gelation in this system within the scope of mean-filed approximations. (3) Then, a ladder-like polymer-polymer complexation is studied. Unconventional phase diagrams are predicted from the modified SCFT, indicating a large effect of variations in entropy due to the complexation on bulk properties. (4) Finally, the kinetic aspect of macromolecular binding reactions is discussed.

  13. 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.

  14. Mapping the epistatic network underlying murine reproductive fatpad variation.