Note: This page contains sample records for the topic complex kohn variational from Science.gov.
While these samples are representative of the content of Science.gov,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of Science.gov
to obtain the most current and comprehensive results.
Last update: November 12, 2013.
1

Equivalence of the generalized and complex Kohn variational methods  

NASA Astrophysics Data System (ADS)

For Kohn variational calculations on low energy (e+ - H2) elastic scattering, we prove that the phase shift approximation, obtained using the complex Kohn method, is precisely equal to a value which can be obtained immediately via the real-generalized Kohn method. Our treatment is sufficiently general to be applied directly to arbitrary potential scattering or single open channel scattering problems, with exchange if required. In the course of our analysis, we develop a framework formally to describe the anomalous behaviour of our generalized Kohn calculations in the regions of the well-known Schwartz singularities. This framework also explains the mathematical origin of the anomaly-free singularities we reported in a previous article. Moreover, we demonstrate a novelty: that explicit solutions of the Kohn equations are not required in order to calculate optimal phase shift approximations. We relate our rigorous framework to earlier descriptions of the Kohn-type methods.

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

2010-04-01

2

Complex Kohn variational principle for two-nucleon bound-state and scattering  

SciTech Connect

The Complex Kohn variational principle (CKVP) is applied to the numerical solution of the fully off-shell Lippmann-Schwinger equation for nucleon-nucleon scattering, using the Reid soft core potential, for various partial waves including the coupled {sup 3}{ital S}{sub 1}{minus}{sup 3}{ital D}{sub 1} channel. The method converges faster than other solution schemes not only for the phase shift but also for the off-shell {ital t} matrix elements. We also extend the method for bound-state, calculating the deuteron binding, wave function, and the {ital D} state asymptotic parameters. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

Tomio, L.; de Araujo, C.F. Jr.; Adhikari, S.K. [Instituto de Fisica Teorica, Universidade Estadual Paulista 01405-000 Sao Paulo, Sao Paulo (Brazil)

1995-05-10

3

Complex Kohn variational principle for the solution of Lippmann-Schwinger equations  

SciTech Connect

A recently proposed version of the Kohn variational principle for the t matrix incorporating the correct boundary condition is applied for the first time to the study of nucleon-nucleon scattering. Analytic expressions can be obtained for all the integrals in the method for a wide class of potentials and for a suitable choice of trial functions. Closed-form analytic expressions for these integrals are given for Yakawa and exponential potentials. Calculations with two commonly used S-wave nucleon-nucleon potentials show that the method may converge faster than other solution schemes not only for the phase-shifts but also for the off-shell t matrix elements if the freedom in the choice of the trial function is exploited. 19 refs., 3 tabs.

Adhikari, S.K. (Universidade Estadual Paulista, Sao Paulo (Brazil))

1992-12-01

4

Electronic excitation of formaldehyde by low-energy electrons - A theoretical study using the complex Kohn variational method  

NASA Astrophysics Data System (ADS)

Results of a fully ab initio treatment of electronic excitation in a polyatomic molecule by electron impact are reported; total and differential cross sections are calculated for exciting the two lowest excited states of H2CO for collision energies between 5 and 20 eV. The calculations were carried out in a three-state close-coupling approximation using the complex Kohn variational method. The absence of any backward peaking in the cross sections calculcated for the 3A2 state is reminiscent of a rigorous selection rule for Sigma(+)-Sigma(-) transitions in linear molecules. However, with no experimental studies available for comparison, the present results must be regarded as predictive.

Rescigno, T. N.; Lengsfield, Byron H., III; McCurdy, C. William

1990-03-01

5

The Convergence of the Kohn Variational Method.  

National Technical Information Service (NTIS)

A theorem about the convergence of the Kohn variational method in the case of s-wave single-particle scattering in a well-behaved potential is proved. Provided enough expansion functions are used, the estimated value of the phase shift can be made as near...

J. Nuttall

1968-01-01

6

Computation of Low-Energy Positronium-Hydrogen Collisions using the Kohn Variational Method  

NASA Astrophysics Data System (ADS)

The Kohn variational method is an established method that can provide benchmark calculations for quantum few-body systems. We consider the four-body Coulomb process of positronium-hydrogen (Ps-H) scattering. We improve upon the numerics of prior accurate S- and P-wave Kohn variational calculations of Ps-H elastic scattering [1,2]. For instance, we use a procedure that removes Hylleraas-type terms that lead to linear dependence [3]. In addition to using the Kohn and inverse Kohn variational methods as previously used, we use the generalized and complex Kohn variational methods [4]. We are extending the calculations of Ps-H to include the D-wave.[4pt] [1] P. Van Reeth and J. W. Humberston, J. Phys. B 36, 1923 (2003).[0pt] [2] P. Van Reeth and J. W. Humberston, Nucl. Instrum. Methods B 221, 140 (2004).[0pt] [3] A. Todd, Ph.D. thesis, The University of Nottingham, (2007), unpublished.[0pt] [4] J.N. Cooper, M. Plummer, and E.A.G. Armour, J. Phys. A 43, 175302 (2010).

Woods, Denton; Ward, S. J.; van Reeth, P.

2013-03-01

7

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

NASA Astrophysics Data System (ADS)

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: 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.

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

2012-10-01

8

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

PubMed

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: He···NH, H(2)O···HO(2), 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)(+))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

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

2012-10-28

9

Axiomatic formulations of the Hohenberg-Kohn functional  

SciTech Connect

Properties of the Hohenberg-Kohn functional are considered. In particular, the Hohenberg-Kohn functional should (a) give correct results in the variational principle and should be (b) continuous, (c) convex, and (d) size consistent. All of these properties are satisfied by the Legendre-transform functional (equivalently, the density matrix constrained search functional) and, moreover, this is the only functional that possesses all these properties. Not only that, but the Legendre-transform functional is determined uniquely by requiring (a) (b), and either (c) or (d). This shows how an 'axiomatic' approach to constructing the Hohenberg-Kohn functional leads naturally to the Legendre-transform functional. Among all functionals consistent with the variational principle, the Legendre-transform functional is the smallest. One corollary to this approach is a simple proof of the equivalence of the Legendre-transform and density-matrix constrained search functionals. For completeness, the Appendix shows that ensemble-v-representable densities lie dense in the set of N-representable densities.

Ayers, Paul W. [Department of Chemistry, McMaster University, Hamilton, Ontario, Canada L8S 4M1 (Canada)

2006-01-15

10

Kohn singularity and Kohn anomaly in conventional superconductors—role of pairing mechanism  

NASA Astrophysics Data System (ADS)

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

Chaudhury, Ranjan; Das, Mukunda P.

2013-03-01

11

Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits  

Microsoft Academic Search

Loss or gain of DNA methylation can affect gene expression and is sometimes transmitted across generations. Such epigenetic alterations are thus a possible source of heritable phenotypic variation in the absence of DNA sequence change. However, attempts to assess the prevalence of stable epigenetic variation in natural and experimental populations and to quantify its impact on complex traits have been

Frank Johannes; Emmanuelle Porcher; Felipe K. Teixeira; Vera Saliba-Colombani; Matthieu Simon; Nicolas Agier; Agnès Bulski; Juliette Albuisson; Fabiana Heredia; Pascal Audigier; David Bouchez; Christine Dillmann; Philippe Guerche; Vincent Colot

2009-01-01

12

Human genetic variation and its contribution to complex traits  

Microsoft Academic Search

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

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

2009-01-01

13

Epistasis and balanced polymorphism influencing complex trait variation  

Microsoft Academic Search

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

Juergen Kroymann; Thomas Mitchell-Olds

2005-01-01

14

Characterizing complex structural variation in germline and somatic genomes  

PubMed Central

Genome structural variation (SV) is a major source of genetic diversity in mammals and a hallmark of cancer. While SV is typically defined by its canonical forms – duplication, deletion, insertion, inversion and translocation – recent breakpoint mapping studies have revealed a surprising number of “complex” variants that evade simple classification. Complex SVs are defined by clustered breakpoints that arose through a single mutation but cannot be explained by one simple end-joining or recombination event. Some complex variants exhibit profoundly complicated rearrangements between distinct loci from multiple chromosomes, while others involve more subtle alterations at a single locus. These diverse and unpredictable features present a challenge for SV mapping experiments. Here, we review current knowledge of complex SV in mammals, and outline techniques for identifying and characterizing complex variants using next-generation DNA sequencing.

Quinlan, Aaron R.; Hall, Ira M.

2011-01-01

15

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

SciTech Connect

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.

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

2011-05-15

16

Complex refractive index variation in proton-damaged diamond.  

PubMed

An accurate control of the optical properties of single crystal diamond during microfabrication processes such as ion implantation plays a crucial role in the engineering of integrated photonic devices. In this work we present a systematic study of the variation of both real and imaginary parts of the refractive index of single crystal diamond, when damaged with 2 and 3 MeV protons at low-medium fluences (range: 10(15) - 10(17) cm(-2)). After implanting in 125 × 125 ?m(2) areas with a scanning ion microbeam, the variation of optical pathlength of the implanted regions was measured with laser interferometric microscopy, while their optical transmission was studied using a spectrometric set-up with micrometric spatial resolution. On the basis of a model taking into account the strongly non-uniform damage profile in the bulk sample, the variation of the complex refractive index as a function of damage density was evaluated. PMID:23038581

Lagomarsino, S; Olivero, P; Calusi, S; Monticone, D Gatto; Giuntini, L; Massi, M; Sciortino, S; Sytchkova, A; Sordini, A; Vannoni, M

2012-08-13

17

Linear aspects of the Korringa Kohn Rostoker formalism  

NASA Astrophysics Data System (ADS)

We present the one-dimensional Korringa-Kohn-Rostoker (KKR) method with the aim of elucidating its linear features, particularly important in optimizing the numerical algorithms in energy band computations. The conventional KKR equations based on multiple scattering theory as well as novel forms of the secular matrix with nearly linear energy dependency of the eigenvalues are presented. The quasi-linear behaviour of these eigenvalue functions appears after (i) re-normalizing the wavefunctions in such a way that 'irregular' solutions vanish on the boundary of the 'muffin-tin' segments, and (ii) integrating the full Green function over the whole Wigner-Seitz cell. In addition, using the aforementioned approach we derive a one-dimensional analogue of the generalized Lloyd formula. The novel KKR approach illustrated in one dimension can be almost directly applied to higher dimensional cases. This should open prospects for the accurate KKR band structure computations of very complex materials.

Stopa, T.; Kaprzyk, S.; Tobola, J.

2004-07-01

18

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

PubMed Central

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

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

1999-01-01

19

On the Kohn-Luttinger conundrum  

NASA Astrophysics Data System (ADS)

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.

Hirata, So; He, Xiao

2013-05-01

20

Variational Methods for Multichannel Scattering.  

National Technical Information Service (NTIS)

Several methods have recently been proposed for avoiding computational anomalies in the multichannel variational formalism of Kohn. The proposed methods themselves have characteristic difficulties, discussed in detail here, leading to ambiguous or discond...

R. K. Nesbet R. S. Oberoi

1972-01-01

21

Open-system Kohn-Sham density functional theory.  

PubMed

A simple model for electron transport through molecules is provided by the source-sink potential (SSP) method [F. Goyer, M. Ernzerhof, and M. Zhuang, J. Chem. Phys. 126, 144104 (2007)]. In SSP, the boundary conditions of having an incoming and outgoing electron current are enforced through complex potentials that are added to the Hamiltonian. Depending on the sign of the imaginary part of the potentials, current density is generated or absorbed. In this way, a finite system can be used to model infinite molecular electronic devices. The SSP has originally been developed for the Hu?ckel method and subsequently it has been extended [F. Goyer and M. Ernzerhof, J. Chem. Phys. 134, 174101 (2011)] to the Hubbard model. Here we present a step towards its generalization for first-principles electronic structure theory methods. In particular, drawing on our earlier work, we discuss a new generalized density functional theory for complex non-Hermitian Hamiltonians. This theory enables us to combine SSP and Kohn-Sham theory to obtain a method for the description of open systems that exchange current density with their environment. Similarly, the Hartree-Fock method is extended to the realm of non-Hermitian, SSP containing Hamiltonians. As a proof of principle, we present the first applications of complex-density functional theory (CODFT) as well as non-Hermitian Hartree-Fock theory to electron transport through molecules. PMID:22401427

Zhou, Yongxi; Ernzerhof, Matthias

2012-03-01

22

Breakdown of the Kohn theorem near a Feshbach resonance in a magnetic trap  

NASA Astrophysics Data System (ADS)

We study the collective excitation frequencies of a harmonically trapped 85Rb Bose-Einstein condensate (BEC) in the vicinity of a Feshbach resonance. To this end, we solve the underlying Gross-Pitaevskii (GP) equation by using a Gaussian variational approach and obtain the coupled set of ordinary differential equations for the widths and the center of mass of the condensate. A linearization shows that the dipole-mode frequency decreases when the bias magnetic field approaches the Feshbach resonance, so the Kohn theorem is violated.

Al-Jibbouri, Hamid; Pelster, Axel

2013-09-01

23

Role of variation, error, and complexity in manufacturing defects.  

National Technical Information Service (NTIS)

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 ar...

C. M. Hinckley P. Barkan

1994-01-01

24

Must Kohn-Sham oscillator strengths be accurate at threshold?  

SciTech Connect

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.

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

2009-09-21

25

Kohn-Sham Self-Interaction Correction in Real Time  

NASA Astrophysics Data System (ADS)

We present a solution scheme for the time-dependent Kohn-Sham self-interaction correction. Based on the generalized optimized effective potential approach, the multiplicative Kohn-Sham potential is constructed in real time and real space for the self-interaction corrected local density approximation. Excitations of different character, including charge-transfer excitations that had been regarded as prime examples for the failure of standard time-dependent density functionals, are described correctly by this approach. We analyze the time-dependent exchange-correlation potential and density, revealing features that are decisive for the correct description of the response.

Hofmann, D.; Körzdörfer, T.; Kümmel, S.

2012-04-01

26

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

NASA Astrophysics Data System (ADS)

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.

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

2012-02-01

27

A proof of hypoellipticity for Kohn's operator via FBI  

Microsoft Academic Search

A new proof of both analytic and $C^{\\\\infty} $ hypoellipticity of Kohn's\\u000aoperator is given using FBI techniques introduced by J. Sjöstrand.\\u000aThe same proof allows us to obtain both kind of hypoellipticity at the same time.

Gregorio Chinni

2011-01-01

28

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

SciTech Connect

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.

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

1991-12-31

29

Variations in recollection: The effects of complexity on source recognition  

PubMed Central

Whether recollection is a threshold or signal detection process is highly controversial. U-shaped zROCs observed in tests thought to rely heavily on recollection, such as source memory tests, have provided evidence in favor of the threshold assumption, but zROCs are not always as U-shaped as threshold theory predicts. Source zROCs have been shown to become more linear when the contribution of familiarity to source discriminations is increased, and this may account for the existing results. However, another way in which source zROCs may become more linear is if recollection can become more graded under certain conditions. We tested the ‘graded recollection’ account in the current study. We found that increasing stimulus complexity (i.e., changing from single words to sentences), or increasing source complexity (i.e., changing the sources from audio to videos of speakers), resulted in flatter source zROCs. In addition, conditions expected to reduce recollection (i.e., divided attention and amnesia) had comparable effects on source memory in simple and complex conditions, suggesting that differences between simple and complex conditions were due to differences in the nature of recollection, rather than differences in the utility of familiarity. The results suggest that under conditions of high complexity recollection can appear more graded and it can produce curved ROCs. The results have implications for measurement models and for current theories of recognition memory.

Parks, Colleen M.; Murray, Linda J.; Elfman, Kane; Yonelinas, Andrew P.

2011-01-01

30

Major Histocompatibility Complex Variation in the Endangered Przewalski's Horse  

Microsoft Academic Search

The major histocompatibility complex (MHC) is a fundamental part of the vertebrate immune system, and the high variability in many MHC genes is thought to play an essential role in recognition of parasites. The Przewalski's horse is extinct in the wild and all the living individuals descend from 13 founders, most of whom were captured around the turn of the

Philip W. Hedrick; Karen M. Parker; Ellen L. Miller; Philip S. Miller

31

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

ERIC Educational Resources Information Center

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

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

2010-01-01

32

Major Histocompatibility Complex Variation in the Endangered Crested Ibis Nipponia nippon and Implications for Reintroduction  

Microsoft Academic Search

   The major histocompatibility complex (MHC), with its extraordinary levels of genetic variation, is thought to be an essential aspect of the ability of an organism to recognize different parasites and pathogens. It has also been proposed to regulate reproductive processes in many aspects. Here we examine the genetic variation of the second exon of the MHC class II B genes

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

2006-01-01

33

Ecological variation within Sellaphora species complexes (Bacillariophyceae): specialists or generalists?  

Microsoft Academic Search

The genus Sellaphora has become a model system for studies of the species concept, speciation and automated identification in diatoms. Three species,\\u000a S. pupula, S. bacillum and S. laevissima, have proved to be complexes containing several or many species, which are difficult to distinguish morphologically but which\\u000a are genetically differentiated and (where tested) reproductively isolated. Until now, however, there has been little information

Aloisie Poulí?ková; Jana Špa?ková; Martyn G. Kelly; Martin Duchoslav; David G. Mann

2008-01-01

34

REVALUATION OF THE CONTINUOUS VARIATION METHOD AS APPLIED TO THE URANYL AZIDE COMPLEXES  

Microsoft Academic Search

The method of continuous variation is discussed critically, particularly ; when applied to solutions containing more than one complex. The deformations in ; the curves obtained can be interpreted by following the contours of these curves ; at different wavelengths and concentrations. The presence of mono-, di-, and tri-; azido uranyl complex ions is revealed. (auth);

F. G. Sherif; A. M. Awad

1962-01-01

35

A Model for Transgenerational Imprinting Variation in Complex Traits  

PubMed Central

Despite the fact that genetic imprinting, i.e., differential expression of the same allele due to its different parental origins, plays a pivotal role in controlling complex traits or diseases, the origin, action and transmission mode of imprinted genes have still remained largely unexplored. We present a new strategy for studying these properties of genetic imprinting with a two-stage reciprocal F mating design, initiated with two contrasting inbred lines. This strategy maps quantitative trait loci that are imprinted (i.e., iQTLs) based on their segregation and transmission across different generations. By incorporating the allelic configuration of an iQTL genotype into a mixture model framework, this strategy provides a path to trace the parental origin of alleles from previous generations. The imprinting effects of iQTLs and their interactions with other traditionally defined genetic effects, expressed in different generations, are estimated and tested by implementing the EM algorithm. The strategy was used to map iQTLs responsible for survival time with four reciprocal F populations and test whether and how the detected iQTLs inherit their imprinting effects into the next generation. The new strategy will provide a tool for quantifying the role of imprinting effects in the creation and maintenance of phenotypic diversity and elucidating a comprehensive picture of the genetic architecture of complex traits and diseases.

Wang, Chenguang; Wang, Zhong; Luo, Jiangtao; Li, Qin; Li, Yao; Ahn, Kwangmi; Prows, Daniel R.; Wu, Rongling

2010-01-01

36

Exact Kohn-Sham potential of strongly correlated finite systems  

NASA Astrophysics Data System (ADS)

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.

Helbig, N.; Tokatly, I. V.; Rubio, A.

2009-12-01

37

Spectral element solution of the Kohn-Sham atom  

NASA Astrophysics Data System (ADS)

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.

Andersen, Kristopher; Bernstein, Noam; Pask, John

2011-03-01

38

Guaranteed convergence of the kohn-sham equations.  

PubMed

A sufficiently damped iteration of the Kohn-Sham (KS) equations with the exact functional is proven to always converge to the true ground-state density, regardless of the initial density or the strength of electron correlation, for finite Coulomb systems. We numerically implement the exact functional for one-dimensional continuum systems and demonstrate convergence of the damped KS algorithm. More strongly correlated systems converge more slowly. PMID:24033030

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

2013-08-28

39

Guaranteed Convergence of the Kohn-Sham Equations  

NASA Astrophysics Data System (ADS)

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

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

2013-08-01

40

Concentration-Dependent Kohn Effect in Cubic Tungsten Bronzes  

Microsoft Academic Search

Inelastic neutron scattering measurements on single crystals of cubic NaxWO3 reveal a large concentration-dependent Kohn anomaly in the [100] longitudinal acoustic-phonon dispersion curve. The results demonstrate the two-dimensional character of the Fermi surface, support the rigid-band model for 0.56

W. A. Kamitakahara; B. N. Harmon; J. G. Taylor; L. Kopp; H. R. Shanks; J. Rath

1976-01-01

41

Interpreting non-coding variation in complex disease genetics  

PubMed Central

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.

Ward, Lucas D.; Kellis, Manolis

2012-01-01

42

Improving the charge density normalization in Korringa Kohn Rostoker Green-function calculations  

NASA Astrophysics Data System (ADS)

The truncation of angular momentum expansions in the Korringa-Kohn-Rostoker Green-function method introduces a charge normalization error and disallows calculation of the Fermi level and the charge density in a consistent manner. It is shown how this error can be compensated by Lloyd's formula, in particular if this formula is applied to normalize the Green function everywhere along the complex energy contour used for the integration of the charge density. The advantages of the improved normalization over the conventional one are illustrated by density-functional calculations for CrAs, the dilute magnetic semiconductor Ga1-xMnxN and a Si12Fe8 multilayer. It is shown that only the improved normalization leads to correct integer values of the magnetic moments in the half-metallic state of CrAs and Ga1-xMnxN and to a correct band alignment of Fe and Si states in the multilayer.

Zeller, Rudolf

2008-01-01

43

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

ERIC Educational Resources Information Center

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

Snyder, William

2001-01-01

44

Low Complexity Variational Bayes Iterative Receiver for MIMO-OFDM Systems  

Microsoft Academic Search

A low complexity iterative receiver is proposed in this paper for MIMO-OFDM systems in time-varying multi-path channel based on the variational Bayes (VB) method. According to the VB method, the estimation algorithms of the signal distribution and the channel distribution are derived for the receiver. With the aid of the soft-output QRD-M algorithm, whose complexity is fixed and relatively low,

Chun-lin Xiong; Hua Wang; Xiao-ying Zhang; Ji-bo Wei; Chao-jing Tang

2009-01-01

45

MR Arthrography of the Labral Capsular Ligamentous Complex in the Shoulder: Imaging Variations and Pitfalls  

Microsoft Academic Search

OBJECTIVE. Using MR arthrography, we examined normal anatomy, anatomic variations, and pitfalls of imaging the labral capsular ligamentous complex in the asymptomatic shoulder. SUBJECTS AND METHODS. We obtained 108 MR arthrograms of the glenohumeral joint in 95 asymptomatic volunteers with axial (108 shoulders) and oblique coronal (56 shoulders) im- ages. We examined labral shape, patterns of capsular insertion, presence or

Yang Hee Park; Ji Yeon Lee; Sung Hee Moon; Jong Hyun Mo; Bo Kyu Yang; Sung Ho Hahn; Donald Resnick

46

Propagators for the time-dependent Kohn-Sham equations  

NASA Astrophysics Data System (ADS)

In this paper we address the problem of the numerical integration of the time-dependent Schrödinger equation i?tJ=?J. In particular, we are concerned with the important case where ? is the self-consistent Kohn-Sham Hamiltonian that stems from time-dependent functional theory. As the Kohn-Sham potential depends parametrically on the time-dependent density, ? is in general time dependent, even in the absence of an external time-dependent field. The present analysis also holds for the description of the excited state dynamics of a many-electron system under the influence of arbitrary external time-dependent electromagnetic fields. Our discussion is separated in two parts: (i) First, we look at several algorithms to approximate exp(Â), where  is a time-independent operator [e.g., Â=-i?t?(?) for some given time ?]. In particular, polynomial expansions, projection in Krylov subspaces, and split-operator methods are investigated. (ii) We then discuss different approximations for the time-evolution operator, such as the midpoint and implicit rules, and Magnus expansions. Split-operator techniques can also be modified to approximate the full time-dependent propagator. As the Hamiltonian is time dependent, problem (ii) is not equivalent to (i). All these techniques have been implemented and tested in our computer code OCTOPUS, but can be of general use in other frameworks and implementations.

Castro, Alberto; Marques, Miguel A. L.; Rubio, Angel

2004-08-01

47

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

PubMed Central

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

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

2011-01-01

48

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

SciTech Connect

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.

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

2010-01-01

49

CHIC-an automated approach for the detection of dynamic variations in complex microbial communities.  

PubMed

Altering environmental conditions change structures of microbial communities. These effects have an impact on the single-cell level and can be sensitively detected using community flow cytometry. However, although highly accurate, microbial monitoring campaigns are still rarely performed applying this technique. One reason is the limited access to pattern analysis approaches for the evaluation of microbial cytometric data. In this article, a new analyzing tool, Cytometric Histogram Image Comparison (CHIC), is presented, which realizes trend interpretation of variations in microbial community structures (i) without any previous definition of gates, by working (ii) person independent, and (iii) with low computational demand. Various factors influencing a sensitive determination of changes in community structures were tested. The sensitivity of this technique was found to discriminate down to 0.5% internal variation. The final protocol was exemplarily applied to a complex microbial community dataset, and correlations to experimental variation were successfully shown. PMID:23568809

Koch, Christin; Fetzer, Ingo; Harms, Hauke; Müller, Susann

2013-04-08

50

Natural Genetic Variation in Complex Mating Behaviors of Male Drosophila melanogaster  

Microsoft Academic Search

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

Elizabeth A. Ruedi; Kimberly A. Hughes

2008-01-01

51

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

PubMed Central

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.

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

2010-01-01

52

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

ERIC Educational Resources Information Center

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

Kuiken, Folkert; Vedder, Ineke

2012-01-01

53

Reply to "Comment on `Electron removal energies in Kohn-Sham density-functional theory' "  

NASA Astrophysics Data System (ADS)

A local Kohn-Sham potential can be constructed explicitly either in the "exchange-only" density-functional theory of Talman, which does not constrain the density to its Hartree-Fock value, or in the "Hartree-Fock" density-functional theory of von Barth, which does. The Kohn-Sham orbital energies are essentially the same by either choice, as shown here for the beryllium atom. Our conclusion still stands that the exact Kohn-Sham orbital energies for tightly bound electrons are not physical removal energies.

Perdew, John P.; Norman, Michael R.

1984-09-01

54

Self-optimizing Kohn-Sham hybrid functional  

NASA Astrophysics Data System (ADS)

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

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

2011-03-01

55

Physical Origin of Discontinuity of Kohn - Sham Theory Effective Potential  

NASA Astrophysics Data System (ADS)

We explain the physical origin of the discontinuity of the electron-interaction potential of Kohn-Sham theory from the perspective of its rigorous quantum-mechanical interpretation (V. Sahni, Phys. Rev. A55, 1846 (1997).). The description is in terms of a conservative field representative of Pauli-Coulomb correlations and correlation-kinetic effects that contribute to the potential. Provided an ensemble definition of the source is employed, the asymptotic structure in the classically forbidden region of the fields for the neutral and fractionally charged systems, for small fractional charge, is different. Elsewhere the fields are equivalent. The corresponding potentials, obtained as the work done to move an electron in these fields, thus differ by a constant. An expression for the constant in terms of the fields is thereby obtained. Furthermore, all the different electron correlations thus contribute to the discontinuity.

Qian, Z.; Sahni, V.

1998-03-01

56

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

SciTech Connect

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.

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

2004-04-23

57

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

PubMed Central

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

Yuhki, N; O'Brien, S J

1990-01-01

58

Expression variation of the porcine ADRB2 has a complex genetic background.  

PubMed

Porcine adrenergic receptor beta 2 (ADRB2) gene exhibits differential allelic expression in skeletal muscle, and its genetic variation has been associated with muscle pH. Exploring the molecular-genetic background of expression variation for porcine ADRB2 will provide insight into the mechanisms driving its regulatory divergence and may also contribute to unraveling the genetic basis of muscle-related traits in pigs. In the present study, we therefore examined haplotype effects on the expression of porcine ADRB2 in four tissues: longissimus dorsi muscle, liver, subcutaneous fat, and spleen. The diversity and structure of haplotypes of the proximal gene region segregating in German commercial breeds were characterized. Seven haplotypes falling into three clades were identified. Two clades including five haplotypes most likely originated from introgression of Asian genetics during formation of modern breeds. Expression analyses revealed that the Asian-derived haplotypes increase expression of the porcine ADRB2 compared to the major, wild-type haplotype independently of tissue type. In addition, several tissue-specific differences in the expression of the Asian-derived haplotypes were found. Inspection of haplotype sequences showed that differentially expressed haplotypes exhibit polymorphisms in a polyguanine tract located in the core promoter region. These findings demonstrate that expression variation of the porcine ADRB2 has a complex genetic basis and suggest that the promoter polyguanine tract is causally involved. This study highlights the challenges of finding causal genetic variants underlying complex traits. PMID:23996144

Murani, Eduard; Ponsuksili, Siriluck; Reyer, Henry; Wittenburg, Dörte; Wimmers, Klaus

2013-08-31

59

On tensor approximation of Green iterations for Kohn-Sham equations  

Microsoft Academic Search

In the present paper we discuss efficient rank-structured tensor approximation methods for 3D integral transforms representing\\u000a the Green iterations for the Kohn-Sham equation. We analyse the local convergence of the Newton iteration to solve the Green’s\\u000a function integral formulation of the Kohn-Sham model in electronic structure calculations. We prove the low-separation rank\\u000a approximations for the arising discrete convolving kernels given

Boris N. Khoromskij

2008-01-01

60

Measuring method for contour of object in complex high temperature variation environment  

NASA Astrophysics Data System (ADS)

The real-time measurement for contour of object would be influenced by many environmental factors when it is taken in complex temperature variation environment. The influence must be eliminated to get effective and accurate measuring results. A new measuring method based on binocular stereo vision is presented. The spectral property of high temperature object is analyzed and adaptive optical band pass filter is designed according to the spectrum. Then the gray value of image is adjusted to get clear images for satisfying the measuring requirement under special conditions.

Liang, Yajun; Miao, Yinxiao; Chen, Xiaohui; Sun, Zengyu

2013-01-01

61

Chemical Data and Variation Diagrams of Igneous Rocks from the Timber Mountain-Oasis Valley, Caldera Complex, Southern Nevada.  

National Technical Information Service (NTIS)

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 caldera. Most of t...

W. D. Quinlivan F. M. Byers

1977-01-01

62

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

NASA Astrophysics Data System (ADS)

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.

Zeller, Rudolf

2013-03-01

63

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

PubMed

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

Zeller, Rudolf

2013-02-08

64

The molecular and morphological variations of Culex pipiens complex (Diptera: Culicidae) in Iran.  

PubMed

Background & objectives: Taxonomic status of Culex pipiens is well-known as many years with such a wide variety of morphological and biological characteristics. These changes have been the subject of extensive investigation by many researchers. There are a little information about the morphology and molecular data of Cx. pipiens complex in Iran. The taxonomic status of the complex is very important because of medical and veterinary importance and wide distribution in the country. Methods: This study was carried out in 11 areas in Iran using dipping technique from April 2009 to October 2010. Molecular study was carried out using primers F1457 as forward and B1256 as reverse, which amplified Ace.2 gene and performed PCR-RFLP using ScaI restriction enzyme. Results: Culex quinquefasciatus found in south to central areas of Iran and reported as sympatric with Cx. pipiens in the central regions. Culex pipiens distributed in many areas of the country. Sequencing alignment of Ace.2 gene of Cx. quinquefasciatus and Cx. pipiens showed 6.5% variation in 46bp, especially in intron locus of gene. Culex pipiens complex from Iran are located in two separate clades with sister branches using phylogenetic sequencing tree. Interpretation & conclusion: The male genitalia found as the most reliable diagnostic characters for identification of Cx. pipiens complex in Iran that confirmed by amplify the Ace.2 gene in the samples but we recommended the use of sequencing PCR products of microsatellite loci and COI gene in future study. PMID:23995312

Dehghan, H; Sadraei, J; Moosa-Kazemi, S H; Baniani, N Akbari; Nowruzi, F

65

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

PubMed

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

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

1993-02-01

66

Density-on-wave-function mapping beyond the Hohenberg-Kohn theorem  

NASA Astrophysics Data System (ADS)

Density-functional theory is based on the Hohenberg-Kohn theorem, establishing a one-on-one mapping between ground-state densities and wave functions. That theorem does not, however, make a direct statement on whether two wave functions that are in some sense close are mapped on two densities that are also close, and vice versa. In this work, a metric is defined that allows to quantify the meaning of ``close'' in the preceding sentence. This metric stratifies Hilbert space into concentric spheres on which maximum and minimum distances between states can be defined and geometrically interpreted. Numerical calculations for the Helium atom, Hooke's atom and a lattice Hamiltonian show that the mapping between densities and ground states, which is highly complex and nonlocal in the coordinate description, in metric space becomes a monotonic and nearly linear mapping of vicinities onto vicinities. In this sense, the density-on-wave-function mapping is not only simpler than expected; it is as simple as it could be. [4pt] I. D'Amico, J. P. Coe, V. V. Franca, and K. Capelle, Phys. Rev. Lett. 106, 050401 (2011) and Phys. Rev. Lett. 107, 188902 (2011). See also E. Artacho, Phys. Rev. Lett. 107, 188901 (2011).

Capelle, Klaus

2012-02-01

67

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

PubMed

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

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

2003-10-01

68

Ensemble/Variational Estimation (EnVE) and its application to turbulent flows in complex geometries  

NASA Astrophysics Data System (ADS)

A new algorithm, Ensemble/Variational Estimation (EnVE), has been developed as a consistent hybrid data assimilation method that combines the nonlinear statistical propagation properties of the Ensemble Kalman Filter (EnKF) and the retrospective analysis capabilities of 4DVar/Moving Horizon Estimation (MHE). A sophisticated C++ object-oriented framework has been developed that implements the EnVE algorithm to facilitate its application to any complex (multiscale/multiphysics) flow code of interest in a highly parallel fashion with minimal changes to the existing flow solver. In the present work, this framework has been applied to the flagship unstructured LES code (CDP) developed at the Center for Integrated Turbulence Simulations (CITS) at Stanford University.

Cessna, Joseph; Colburn, Christopher; Bewley, Thomas; Ham, Frank; Wang, Qiqi; Iaccarino, Gianluca

2008-11-01

69

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

PubMed

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

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

1995-07-01

70

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

PubMed Central

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

2011-01-01

71

Efficient construction of exchange and correlation potentials by inverting the Kohn-Sham equations.  

PubMed

Given a set of canonical Kohn-Sham orbitals, orbital energies, and an external potential for a many-electron system, one can invert the Kohn-Sham equations in a single step to obtain the corresponding exchange-correlation potential, vXC(r). For orbitals and orbital energies that are solutions of the Kohn-Sham equations with a multiplicative vXC(r) this procedure recovers vXC(r) (in the basis set limit), but for eigenfunctions of a non-multiplicative one-electron operator it produces an orbital-averaged potential. In particular, substitution of Hartree-Fock orbitals and eigenvalues into the Kohn-Sham inversion formula is a fast way to compute the Slater potential. In the same way, we efficiently construct orbital-averaged exchange and correlation potentials for hybrid and kinetic-energy-density-dependent functionals. We also show how the Kohn-Sham inversion approach can be used to compute functional derivatives of explicit density functionals and to approximate functional derivatives of orbital-dependent functionals. PMID:23968077

Kananenka, Alexei A; Kohut, Sviataslau V; Gaiduk, Alex P; Ryabinkin, Ilya G; Staroverov, Viktor N

2013-08-21

72

Efficient construction of exchange and correlation potentials by inverting the Kohn-Sham equations  

NASA Astrophysics Data System (ADS)

Given a set of canonical Kohn-Sham orbitals, orbital energies, and an external potential for a many-electron system, one can invert the Kohn-Sham equations in a single step to obtain the corresponding exchange-correlation potential, vXC(r). For orbitals and orbital energies that are solutions of the Kohn-Sham equations with a multiplicative vXC(r) this procedure recovers vXC(r) (in the basis set limit), but for eigenfunctions of a non-multiplicative one-electron operator it produces an orbital-averaged potential. In particular, substitution of Hartree-Fock orbitals and eigenvalues into the Kohn-Sham inversion formula is a fast way to compute the Slater potential. In the same way, we efficiently construct orbital-averaged exchange and correlation potentials for hybrid and kinetic-energy-density-dependent functionals. We also show how the Kohn-Sham inversion approach can be used to compute functional derivatives of explicit density functionals and to approximate functional derivatives of orbital-dependent functionals.

Kananenka, Alexei A.; Kohut, Sviataslau V.; Gaiduk, Alex P.; Ryabinkin, Ilya G.; Staroverov, Viktor N.

2013-08-01

73

The Fine-Scale and Complex Architecture of Human Copy-Number Variation  

PubMed Central

Despite considerable excitement over the potential functional significance of copy-number variants (CNVs), we still lack knowledge of the fine-scale architecture of the large majority of CNV regions in the human genome. In this study, we used a high-resolution array-based comparative genomic hybridization (aCGH) platform that targeted known CNV regions of the human genome at approximately 1 kb resolution to interrogate the genomic DNAs of 30 individuals from four HapMap populations. Our results revealed that 1020 of 1153 CNV loci (88%) were actually smaller in size than what is recorded in the Database of Genomic Variants based on previously published studies. A reduction in size of more than 50% was observed for 876 CNV regions (76%). We conclude that the total genomic content of currently known common human CNVs is likely smaller than previously thought. In addition, approximately 8% of the CNV regions observed in multiple individuals exhibited genomic architectural complexity in the form of smaller CNVs within larger ones and CNVs with interindividual variation in breakpoints. Future association studies that aim to capture the potential influences of CNVs on disease phenotypes will need to consider how to best ascertain this previously uncharacterized complexity.

Perry, George H.; Ben-Dor, Amir; Tsalenko, Anya; Sampas, Nick; Rodriguez-Revenga, Laia; Tran, Charles W.; Scheffer, Alicia; Steinfeld, Israel; Tsang, Peter; Yamada, N. Alice; Park, Han Soo; Kim, Jong-Il; Seo, Jeong-Sun; Yakhini, Zohar; Laderman, Stephen; Bruhn, Laurakay; Lee, Charles

2008-01-01

74

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

Microsoft Academic Search

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

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

2008-01-01

75

A massively multicore parallelization of the Kohn-Sham energy gradients.  

PubMed

In a previous article [Brown et al., J Chem Theory Comput 2009, 4, 1620], we described a quadrature-based formulation of the Kohn-Sham Coulomb problem that allows for efficient parallelization over thousands of small processor cores. Here, we present the analytic gradients of this modified Kohn-Sham scheme, and describe the parallel implementation of the gradients on a numerical accelerator architecture. We demonstrate an order-of-magnitude acceleration for the combined energy and gradient calculation over a conventional single-core implementation. PMID:20127716

Brown, Philip; Woods, Christopher J; McIntosh-Smith, Simon; Manby, Frederick R

2010-07-30

76

Localising Loci underlying Complex Trait Variation Using Regional Genomic Relationship Mapping  

PubMed Central

The limited proportion of complex trait variance identified in genome-wide association studies may reflect the limited power of single SNP analyses to detect either rare causative alleles or those of small effect. Motivated by studies that demonstrate that loci contributing to trait variation may contain a number of different alleles, we have developed an analytical approach termed Regional Genomic Relationship Mapping that, like linkage-based family methods, integrates variance contributed by founder gametes within a pedigree. This approach takes advantage of very distant (and unrecorded) relationships, and this greatly increases the power of the method, compared with traditional pedigree-based linkage analyses. By integrating variance contributed by founder gametes in the population, our approach provides an estimate of the Regional Heritability attributable to a small genomic region (e.g. 100 SNP window covering ca. 1 Mb of DNA in a 300000 SNP GWAS) and has the power to detect regions containing multiple alleles that individually contribute too little variance to be detectable by GWAS as well as regions with single common GWAS-detectable SNPs. We use genome-wide SNP array data to obtain both a genome-wide relationship matrix and regional relationship (“identity by state" or IBS) matrices for sequential regions across the genome. We then estimate a heritability for each region sequentially in our genome-wide scan. We demonstrate by simulation and with real data that, when compared to traditional (“individual SNP") GWAS, our method uncovers new loci that explain additional trait variation. We analysed data from three Southern European populations and from Orkney for exemplar traits – serum uric acid concentration and height. We show that regional heritability estimates are correlated with results from genome-wide association analysis but can capture more of the genetic variance segregating in the population and identify additional trait loci.

Nagamine, Yoshitaka; Pong-Wong, Ricardo; Navarro, Pau; Vitart, Veronique; Hayward, Caroline; Rudan, Igor; Campbell, Harry; Wilson, James; Wild, Sarah; Hicks, Andrew A.; Pramstaller, Peter P.; Hastie, Nicholas; Wright, Alan F.; Haley, Chris S.

2012-01-01

77

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

PubMed Central

The genetic architecture of plant defense against microbial pathogens may be influenced by pathogen lifestyle. While plant interactions with biotrophic pathogens are frequently controlled by the action of large-effect resistance genes that follow classic Mendelian inheritance, our study suggests that plant defense against the necrotrophic pathogen Botrytis cinerea is primarily quantitative and genetically complex. Few studies of quantitative resistance to necrotrophic pathogens have used large plant mapping populations to dissect the genetic structure of resistance. Using a large structured mapping population of Arabidopsis thaliana, we identified quantitative trait loci influencing plant response to B. cinerea, measured as expansion of necrotic lesions on leaves and accumulation of the antimicrobial compound camalexin. Testing multiple B. cinerea isolates, we identified 23 separate QTL in this population, ranging in isolate-specificity from being identified with a single isolate to controlling resistance against all isolates tested. We identified a set of QTL controlling accumulation of camalexin in response to pathogen infection that largely colocalized with lesion QTL. The identified resistance QTL appear to function in epistatic networks involving three or more loci. Detection of multilocus connections suggests that natural variation in specific signaling or response networks may control A. thaliana–B. cinerea interaction in this population.

Rowe, Heather C.; Kliebenstein, Daniel J.

2008-01-01

78

Characterization of metal-deferoxamine complexes by continuous variation method: A new approach using capillary zone electrophoresis  

Microsoft Academic Search

Siderophores are low molecular weight non-ribosomal peptides with extremely high affinity by iron. However, other metals present affinity for siderophores but to a smaller degree. Deferoxamine is an example of a bacterial hydroxamic siderophore, which was investigated herein. Capillary zone electrophoresis (CZE) was used as a new approach in the continuous variation method for the characterization of metal-deferoxamine complexes. A

Ana Valéria Colnaghi Simionato; Marcelo Delmar Cantú; Emanuel Carrilho

2006-01-01

79

Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework  

NASA Astrophysics Data System (ADS)

Uniform discretization of the Kohn-Sham Hamiltonian generally results in a large number of basis functions per atom in order to resolve the rapid oscillations of the Kohn-Sham orbitals around the nuclei even in the pseudopotential framework. Atomic orbitals and similar objects significantly reduces the number of basis functions, but these basis sets generally require fine tuning of the parameters in order to reach high accuracy. We present a novel discretization scheme that adaptively and systematically builds the rapid oscillations of the Kohn-Sham orbitals around the nuclei as well as environmental effects into the basis functions. The resulting basis functions are localized in the real space, and are discontinuous in the global domain. The continuous Kohn-Sham orbitals and the electron density are evaluated from the discontinuous basis functions using the discontinuous Galerkin (DG) framework. Our method is implemented in parallel and the current implementation is able to handle systems with at least thousands of atoms. Numerical examples indicate that our method can reach very high accuracy (less than 1meV) with a very small number (4˜40) of basis functions per atom.

Lin, Lin; Lu, Jianfeng; Ying, Lexing; E, Weinan

2012-02-01

80

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

Microsoft Academic Search

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

Amihai Radzyner

2010-01-01

81

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

Microsoft Academic Search

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

Amihai Radzyner

2010-01-01

82

Some new and short proofs for a class of Caffarelli-Kohn-Nirenberg type inequalities  

NASA Astrophysics Data System (ADS)

In this note we provide simple and short proofs for a class of inequalities of Caffarelli-Kohn-Nirenberg type with sharp constants. Our approach suggests some definitions of weighted Sobolev spaces and their embedding into weighted L2 spaces. These may be useful in studying solvability of problems involving new singular PDEs.

Costa, David G.

2008-01-01

83

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

ERIC Educational Resources Information Center

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…

Weininger, Elliot B.; Lareau, Annette

2009-01-01

84

Combining Genome-Wide Methods to Investigate the Genetic Complexity of Courtship Song Variation in Drosophila melanogaster.  

PubMed

Little is currently known about the genetic complexity of quantitative behavioral variation, the types of genes involved, or their effects on intermediate phenotypes. Here, we conduct a genome-wide association study of Drosophila melanogaster courtship song variation using 168 sequenced inbred lines, and fail to find highly significant associations. However, by combining these data with results from a well-powered Evolve and Resequence (E&R) study on the same trait, we provide statistical evidence that some power to associate genotype and phenotype is available. Genes that are significant in both analyses are enriched for expression in the nervous system, and affect neural development and synaptic growth when perturbed. Quantitative complementation at one of these loci, Syntrophin-like 1, supports a hypothesis that variation at this locus affects variation in the inter-pulse interval of courtship song. These results suggest that experimental evolution may provide an approach for genome-scale replication in Drosophila. PMID:23777628

Turner, Thomas L; Miller, Paige M; Cochrane, Veronica A

2013-06-18

85

DFT study of metal-complex structural variation on tensile force profiles  

NASA Astrophysics Data System (ADS)

We present calculations on metal-ligand complexes for the evaluation of mechanical properties as they pertain to the inclusion in polymer-linked supramolecular complexes. To this end, we investigate the energy profiles of stretching various complexes according to external forces exerted on each complex via the attached polymer strands. Zn2+ and Fe2+ complexated by 2,6-bisbenzimidazolyl-pyridine (BP) were considered in the presence of tetrafluoro borate. We find that the yield characteristics are subject to a complex interplay of steric and electronic effects of the ligands and metal center.

Rinderspacher, B. Christopher; Andzelm, Jan W.; Lambeth, Robert H.

2012-12-01

86

Variational scattering theory with functionals of fractional form  

SciTech Connect

The recently proposed functional of Takatsuka and McKoy, derived from the Schwinger-type Newton functional, is shown to follow from the usual Hulthen-Kohn variational principle. A generalization of their method becomes obvious in this approach and its better convergence is demonstrated on a simple example.

Darewych, J.W.; Horbatsch, M.

1983-04-01

87

Complex patterns of copy number variation at sites of segmental duplications: an important category of structural variation in the human genome.  

PubMed

The structural diversity of the human genome is much higher than previously assumed although its full extent remains unknown. To investigate the association between segmental duplications that display constitutive copy number differences (CNDs) between humans and the great apes and those which exhibit polymorphic copy number variations (CNVs) between humans, we analysed a BAC array enriched with segmental duplications displaying such CNDs. This study documents for the first time that in addition to human-specific gains common to all humans, these duplication clusters (DCs) also exhibit polymorphic CNVs > 40 kb. Segmental duplication is known to have been a frequent event during human genome evolution. Importantly, among the CNV-associated genes identified here, those involved in transcriptional regulation were found to be significantly overrepresented. Complex patterns of variation were evident at sites of DCs, manifesting as inter-individual differentially sized copy number alterations at the same genomic loci. Thus, CNVs associated with segmental duplications do not simply represent insertion/deletion polymorphisms, but rather constitute a wide variety of rearrangements involving differential amplification and partial gains and losses with high inter-individual variability. Although the number of CNVs was not found to differ between Africans and Caucasians/Asians, the average number of variant patterns per locus was significantly lower in Africans. Thus, complex variation patterns characterizing segmental duplications result from relatively recent genomic rearrangements. The high number of these rearrangements, some of which are potentially recurrent, together with differences in population size and expansion dynamics, may account for the greater diversity of CNV in Caucasians/Asians as compared with Africans. PMID:16838144

Goidts, Violaine; Cooper, David N; Armengol, Lluis; Schempp, Werner; Conroy, Jeffrey; Estivill, Xavier; Nowak, Norma; Hameister, Horst; Kehrer-Sawatzki, Hildegard

2006-07-13

88

Finite-volume variational method for the Dirac equation  

Microsoft Academic Search

A finite-volume variational principle based on the Dirac Hamiltonian is formulated in a way similar to the Kohn variational principle for the logarithmic derivative used in nonrelativistic electron-atom scattering. As in R-matrix methods, the essential idea is to solve the Dirac equation variationally within a finite reaction volume for a given total energy of the system. In contrast to previous

Peter Hamacher; Jürgen Hinze

1991-01-01

89

Novel chloroplast markers for the study of intraspecific variation and hybridisation in the Lepidosperma costale species complex (Cyperaceae)  

Microsoft Academic Search

To investigate intraspecific variation and hybridisation in the Lepidosperma costale species complex, forty-one primers to amplify regions containing chloroplast microsatellites and insertions\\/deletions were\\u000a designed using de novo sequencing. Twenty-six loci were polymorphic within three diploid populations, with 2 to 9 alleles\\u000a per locus. A further 15 loci exhibited fixed size differences between the diploid individuals and a population of putative

Mark J. WallaceMatthew; Matthew D. Barrett; Russell L. Barrett

2011-01-01

90

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

Microsoft Academic Search

Spin-unrestricted Kohn-Sham (KS) solutions are constructed from accurate ab initio spin densities for the prototype doublet molecules NO2, ClO2, and NF2 with the iterative local updating procedure of van Leeuwen and Baerends (LB). A qualitative justification of the LB procedure is given with a ``strong'' form of the Hohenberg-Kohn theorem. The calculated energies ?isigma of the occupied KS spin orbitals

O. V. Gritsenko; E. J. Baerends

2004-01-01

91

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

SciTech Connect

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.

Hinckley, C.M.

1994-01-01

92

Nonequilibrium Green's functions and Korringa-Kohn-Rostoker method: Open planar junctions  

NASA Astrophysics Data System (ADS)

We describe an implementation of an ab initio method for calculating the electronic structure for systems under finite bias voltage. Our method is based on density functional theory as implemented in the (screened) Korringa-Kohn-Rostoker Green's function method for open systems with two-dimensional translation invariance using the atomic sphere and the full-charge-density approximation. We test our method for metallic lithium separated by vacuum.

Achilles, Steven; Czerner, Michael; Henk, Jürgen; Mertig, Ingrid; Heiliger, Christian

2013-09-01

93

Correlation Kohn-Sham potential for quasi-two-dimensional electron gases  

Microsoft Academic Search

The optimized effective potential (OEP) method of density functional theory (DFT) has been developed for the study of the Kohn-Sham (KS) correlation potential of quasi-two-dimensional electron gases, for zero temperature and in an open configuration. The correlation energy functional has been generated by second-order perturbation theory, using the KS Hamiltonian as the unperturbed Hamiltonian. Its more important feature is that

S. Rigamonti; C. R. Proetto

2006-01-01

94

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

NASA Astrophysics Data System (ADS)

Although deformation and physical/chemical properties variation in aseismic-seismic transition zone were essential to examine critical changes in environmental parameters that result in earthquake, they are poorly understood because the appropriate samples buried 2-4 km have not been collected yet (scientific drilling has never reached there and most of ancient examples experienced the deeper burial depth and suffered thermal and physical overprinting). The lower to middle Miocene Hota accretionary complex is a unique example of on land accretionary complex, representing deformation and its physical/chemical properties of sediments just prior to entering the seismogenic realm. The maximum paleotemperature was estimated approximately 55-70°C (based on vitrinite reflectance) indicative of a maximum burial depth about 2-3 km assuming a paleo-geothermal gradient as 25-35°C/km. Accretionary complex in this temperature/depth range corresponds with an intermediate range between the core samples collected from the modern accretionary prism (e.g. Nankai, Barbados, and so on) and rocks in the ancient accretionary complexes on land. This presentation will treat the detailed structural and chemical analyses of the Hota accretionary complex to construct deformation properties of décollement zone and accretionary complex in its 2-3 km depth range and to discuss the interrelation between the early diagenesis (hydrocarbon/cations generation and sediment dewatering, etc.) and transition of the deformation properties. The deformation in this accretionary complex is characterized by two deformation styles: one is a few centimeter-scale phacoidal deformation representing clay minerals preferred orientation in the outer rim, whereas random fabric in the core, quite similar texture to the rocks in the present-Nankai décollement. The other is S-C style deformation (similar deformation to the mélanges in ancient accretionary complex on land) exhibiting block-in-matrix texture and quite intense clay minerals preferred orientation in the matrix, cutting the phacoidal deformation. The host and faulted (S-C structure) rocks composed of hemipelagic siltstone containing 70-80% of clay minerals. Considerable-smectite reduction and positive anomaly of illite/smectite ratio were clearly identified inside the latter S-C structure, which would cause remarkable increase in friction coefficient. Such strain hardening associated with dynamic clay-mineral variation would be the primary mechanism in décollement -zone and/or mélange-zone thickening and fundamental mechanical transition just prior to entering the seismogenic zone. Positive anomaly of the vitrinite reflectance data (Ro) inside infers frictional heating during the deformation plausibly caused the clay mineral variation.

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

2009-12-01

95

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

PubMed

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

Gu, Ming Dong

2006-01-01

96

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

ERIC Educational Resources Information Center

|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…

Ferraris, Stefania

2012-01-01

97

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

SciTech Connect

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

NONE

1995-06-01

98

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

PubMed

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

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

2013-01-09

99

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

SciTech Connect

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.

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

1992-01-01

100

Complex cratonic seismic structure from thermal models of the lithosphere: effects of variations in deep radiogenic heating  

NASA Astrophysics Data System (ADS)

Cratons are the long-term tectonically stable cores of the continents. Despite their thermal stability they display substantial seismic complexity with lateral and vertical lithospheric anomalies of up to several percent in both VS and VP. Although some of these anomalies have been correlated with compositional variations, others are too large to be explained with any common mantle lithosphere compositions ranging from fertile peridotites to highly melt-depleted dunites, under the assumption that thermal perturbations are negligible. To test whether temperature anomalies could contribute to seismic complexity, we performed a set of 2-D thermal calculations for a range of cratonic tectonic models and converted them into seismic structure, accounting for variations in phase and elastic and anelastic response to pressure and temperature. With the long thermal equilibration time in cratonic settings, even relatively mild variations in concentrations of radioactive elements can leave long-lasting lithospheric thermal anomalies of 100-300°C. Concentrations of radioactive elements decrease with increasing melt depletion (or decreasing metasomatic refertilization), resulting in lower temperatures and increased seismic velocities. This thermal seismic effect enhances the intrinsic velocity-increasing compositional seismic signature of melt depletion. The joint thermochemical effects can leave cratonic seismic anomalies of up to 3-4.5 per cent in VS and up to 2.5-4 per cent in VP, with gradients sometimes as sharp as a few kilometre in width. Thus the variations in major and minor element mantle lithosphere composition commonly seen in mantle samples can account for much of the variability in imaged seismic structure of cratonic lithosphere.

Hieronymus, C. F.; Goes, S.

2010-03-01

101

Deconstructing a complex molecular phenotype: population-level variation in individual venom proteins in Eastern Massasauga Rattlesnakes (Sistrurus c. catenatus).  

PubMed

Identifying the molecular basis for complex adaptations such as the toxic proteins used by venomous snakes to subdue and digest prey is an important step in understanding the evolutionary and functional basis for such traits. Recent proteomics-based analyses have made possible the identification of all constituent proteins in whole venom samples. Here we exploit this advance to study patterns of population-level variation in venom proteins from 254 adult eastern massasauga rattlesnakes (Sistrurus c. catenatus) collected from 10 populations. Analysis of presence-absence variation in specific proteins from 1D PAGE gels shows that: (1) The frequency spectra for individual protein bands is U-shaped with a large number of specific proteins either being consistently "common" or "rare" across populations possibly reflecting functional differences. (2) Multivariate axes which summarize whole venom variation consist of bands from all major types of proteins implying the integration of functionally distinct components within the overall venom phenotype. (3) There is significant differentiation in venom proteins across populations and the specific classes of proteins contributing to this differentiation have been identified. (4) Levels of population differentiation in venom proteins are not correlated with levels of neutral genetic differentiation, or genetically effective population sizes which argues that patterns of venom variation are not simply a consequence of population structure but leaves open the role of selection in generating population differences in venom. Our results identify particular classes of venom proteins and their associated genes as being fruitful targets for future studies of the molecular and functional basis for this complex adaptive phenotype. PMID:21394489

Lisle Gibbs, H; Chiucchi, James E

2011-03-11

102

Genome partitioning of genetic variation for complex traits using common SNPs  

Microsoft Academic Search

We estimate and partition genetic variation for height, body mass index (BMI), von Willebrand factor and QT interval (QTi) using 586,898 SNPs genotyped on 11,586 unrelated individuals. We estimate that ?45%, ?17%, ?25% and ?21% of the variance in height, BMI, von Willebrand factor and QTi, respectively, can be explained by all autosomal SNPs and a further ?0.5–1% can be

Jian Yang; Teri A Manolio; Louis R Pasquale; Eric Boerwinkle; Neil Caporaso; Julie M Cunningham; Mariza de Andrade; Bjarke Feenstra; Eleanor Feingold; M Geoffrey Hayes; William G Hill; Maria Teresa Landi; Alvaro Alonso; Guillaume Lettre; Peng Lin; Hua Ling; William Lowe; Rasika A Mathias; Mads Melbye; Elizabeth Pugh; Marilyn C Cornelis; Bruce S Weir; Michael E Goddard; Peter M Visscher

2011-01-01

103

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

Microsoft Academic Search

Background  Evidence for historical, demographic and selective factors affecting enzyme evolution can be obtained by examining nucleotide\\u000a sequence variation in candidate genes such as Lactate dehydrogenase (Ldh). Two closely related Daphnia species can be distinguished by their electrophoretic Ldh genotype and habitat. Daphnia pulex populations are fixed for the S allele and inhabit temporary ponds, while D. pulicaria populations are fixed

Teresa J Crease; Robin Floyd; Melania E Cristescu; David Innes

2011-01-01

104

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

PubMed Central

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.

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

2008-01-01

105

Compositional variation of Fe?Ti oxides from the Sokli complex, northeastern Finland  

Microsoft Academic Search

The phoscorite-carbonatite complex at Sokli, northeastern Finland, is composed of five stages of intrusions of phoscorites\\u000a and carbonatites (P1-C1, P2-C2, P3-C3 phoscorites and calcite carbonatites, D4 and D5 dolomite carbonatites) which are cut\\u000a by numerous lamprophyric dikes. Magnetite is ubiquitous in all constituent rock units of the complex and frequently associates\\u000a with ilmenite. Most ilmenite intergrowths from the Sokli phoscorite-carbonatite

Mi Jung Lee; Jong Ik Lee; Jaques Moutte

2005-01-01

106

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

SciTech Connect

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

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

1993-12-31

107

ANALYSIS OF COMPLEX VARIATION: DICHOTOMOUS SORTING OF PREDATOR-ELICITED CALLS OF THE FLORIDA SCRUB JAY  

Microsoft Academic Search

The acoustically complex predator-elicited calls of the Florida scrub jay Aphelocoma c. coerulescens were classified operationally by a new procedure, dichotomous sorting. Vocalizations were tape-recorded in the field during natural and experimental encounters between scrub jays and several types of live and mounted predators. Six continuous, independent variables of frequency and duration were measured in 539 randomly selected calls. Principal

A. MARGARET ELOWSON; JACK P. HAILMAN

1991-01-01

108

Main sequence: An index for detecting mental workload variation in complex tasks  

Microsoft Academic Search

The primary aim of this study was to validate the saccadic main sequence, in particular the peak velocity [PV], as an alternative psychophysiological measure of Mental Workload [MW]. Taking the Wickens’ multiple resource model as the theoretical framework of reference, an experiment was conducted using the Firechief® microworld. MW was manipulated by changing the task complexity (between groups) and the

Leandro Luigi Di Stasi; Adoración Antolí; José Juan Cañas

2011-01-01

109

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...

110

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

NASA Astrophysics Data System (ADS)

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.

Thøgersen, Lea; Olsen, Jeppe; Köhn, Andreas; Jørgensen, Poul; Sa?ek, Pawe?; Helgaker, Trygve

2005-08-01

111

Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework I: Total energy calculation  

NASA Astrophysics Data System (ADS)

Kohn-Sham density functional theory is one of the most widely used electronic structure theories. In the pseudopotential framework, uniform discretization of the Kohn-Sham Hamiltonian generally results in a large number of basis functions per atom in order to resolve the rapid oscillations of the Kohn-Sham orbitals around the nuclei. Previous attempts to reduce the number of basis functions per atom include the usage of atomic orbitals and similar objects, but the atomic orbitals generally require fine tuning in order to reach high accuracy. We present a novel discretization scheme that adaptively and systematically builds the rapid oscillations of the Kohn-Sham orbitals around the nuclei as well as environmental effects into the basis functions. The resulting basis functions are localized in the real space, and are discontinuous in the global domain. The continuous Kohn-Sham orbitals and the electron density are evaluated from the discontinuous basis functions using the discontinuous Galerkin (DG) framework. Our method is implemented in parallel and the current implementation is able to handle systems with at least thousands of atoms. Numerical examples indicate that our method can reach very high accuracy (less than 1 meV) with a very small number (4-40) of basis functions per atom.

Lin, Lin; Lu, Jianfeng; Ying, Lexing; E, Weinan

2012-02-01

112

Predation, habitat complexity, and variation in density-dependent mortality of temperate reef fishes.  

PubMed

Density dependence in demographic rates can strongly affect the dynamics of populations. However, the mechanisms generating density dependence (e.g., predation) are also dynamic processes and may be influenced by local conditions. Understanding the manner in which local habitat features affect the occurrence and/or strength of density dependence will increase our understanding of population dynamics in heterogeneous environments. In this study I conducted two separate field experiments to investigate how local predator density and habitat complexity affect the occurrence and form of density-dependent mortality of juvenile rockfishes (Sebastes spp.). I also used yearly censuses of rockfish populations on nearshore reefs throughout central California to evaluate mortality of juvenile rockfish at large spatial scales. Manipulations of predators (juvenile bocaccio, S. paucispinus) and prey (kelp, gopher, and black-and-yellow [KGB] rockfish, Sebastes spp.) demonstrated that increasing the density of predators altered their functional response and thus altered patterns of density dependence in mortality of their prey. At low densities of predators, the number of prey consumed per predator was a decelerating function, and mortality of prey was inversely density dependent. However, at high densities of predators, the number of prey killed per predator became an accelerating response, and prey mortality was directly density dependent. Results of field experiments and large-scale surveys both indicated that the strength of density-dependent mortality may also be affected by the structural complexity of the habitat. In small-scale field experiments, increased habitat complexity increased the strength of density-dependent mortality. However, at large scales, increasing complexity resulted in a decrease in the strength of density dependence. I suggest that these differences resulted from scale-dependent changes in the predatory response that generated mortality. Whether increased habitat complexity leads to an increase or a decrease in the strength of density-dependent mortality may depend on how specific predatory responses (e.g., functional or aggregative) are altered by habitat complexity. Overall, the findings of this study suggest that rates of demographic density dependence and the resulting dynamics of local populations may largely depend upon attributes of the local habitat. PMID:16761597

Johnson, Darren W

2006-05-01

113

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

PubMed

Species with extensive ranges experience highly variable environments with respect to temperature, light and soil moisture. Synchronizing the transition from vegetative to floral growth is important to employ favorable conditions for reproduction. Optimal timing of this transition might be different for semelparous annual plants and iteroparous perennial plants. We studied variation in the critical photoperiod necessary for floral induction and the requirement for a period of cold-chilling (vernalization) in 46 populations of annuals and perennials in the Mimulus guttatus species complex. We then examined critical photoperiod and vernalization QTLs in growth chambers using F(2) progeny from annual and perennial parents that differed in their requirements for flowering. We identify extensive variation in critical photoperiod, with most annual populations requiring substantially shorter day lengths to initiate flowering than perennial populations. We discover a novel type of vernalization requirement in perennial populations that is contingent on plants experiencing short days first. QTL analyses identify two large-effect QTLs which influence critical photoperiod. In two separate vernalization experiments we discover each set of crosses contain different large-effect QTLs for vernalization. Mimulus guttatus harbors extensive variation in critical photoperiod and vernalization that may be a consequence of local adaptation. PMID:23600522

Friedman, Jannice; Willis, John H

2013-04-22

114

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

PubMed

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

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

2011-05-12

115

4d Architectural Variation in the Gobi-Tienshan Intrusive Complex, Southern Mongolia  

Microsoft Academic Search

The Gobi-Tienshan Intrusive Complex is a recently characterized tilted section through the upper 15 km of a Carboniferous aged continental margin arc in the Gobi desert, southern Mongolia. Preliminary geochronology indicates that the GTIC, a 2,500 km2 batholith, intruded over a 21 m.y. timespan. This high- flux magmatic event is reflected in field relationships identified through detailed mapping of a

R. C. Economos; S. R. Paterson

2008-01-01

116

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

PubMed

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

Green, Tim; Rosen, Stuart

2013-10-01

117

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

PubMed

Insular populations have attracted the attention of evolutionary biologists because of their morphological and ecological peculiarities with respect to their mainland counterparts. Founder effects and genetic drift are known to distribute neutral genetic variability in these demes. However, elucidating whether these evolutionary forces have also shaped adaptive variation is crucial to evaluate the real impact of reduced genetic variation in small populations. Genes of the major histocompatibility complex (MHC) are classical examples of evolutionarily relevant loci because of their well-known role in pathogen confrontation and clearance. In this study, we aim to disentangle the partial roles of genetic drift and natural selection in the spatial distribution of MHC variation in insular populations. To this end, we integrate the study of neutral (22 microsatellites and one mtDNA locus) and MHC class II variation in one mainland (Iberia) and two insular populations (Fuerteventura and Menorca) of the endangered Egyptian vulture (Neophron percnopterus). Overall, the distribution of the frequencies of individual MHC alleles (n=17 alleles from two class II B loci) does not significantly depart from neutral expectations, which indicates a prominent role for genetic drift over selection. However, our results point towards an interesting co-evolution of gene duplicates that maintains different pairs of divergent alleles in strong linkage disequilibrium on islands. We hypothesize that the co-evolution of genes may counteract the loss of genetic diversity in insular demes, maximize antigen recognition capabilities when gene diversity is reduced, and promote the co-segregation of the most efficient allele combinations to cope with local pathogen communities. PMID:21535276

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

2011-05-03

118

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

NASA Astrophysics Data System (ADS)

We present an efficient computational approach to perform real-space electronic structure calculations using an adaptive higher-order finite-element discretization of Kohn-Sham density-functional theory (DFT). To this end, we develop an a priori mesh-adaption technique to construct a close to optimal finite-element discretization of the problem. We further propose an efficient solution strategy for solving the discrete eigenvalue problem by using spectral finite-elements in conjunction with Gauss-Lobatto quadrature, and a Chebyshev acceleration technique for computing the occupied eigenspace. The proposed approach has been observed to provide a staggering 100-200-fold computational advantage over the solution of a generalized eigenvalue problem. Using the proposed solution procedure, we investigate the computational efficiency afforded by higher-order finite-element discretizations of the Kohn-Sham DFT problem. Our studies suggest that staggering computational savings—of the order of 1000-fold—relative to linear finite-elements can be realized, for both all-electron and local pseudopotential calculations, by using higher-order finite-element discretizations. On all the benchmark systems studied, we observe diminishing returns in computational savings beyond the sixth-order for accuracies commensurate with chemical accuracy, suggesting that the hexic spectral-element may be an optimal choice for the finite-element discretization of the Kohn-Sham DFT problem. A comparative study of the computational efficiency of the proposed higher-order finite-element discretizations suggests that the performance of finite-element basis is competing with the plane-wave discretization for non-periodic local pseudopotential calculations, and compares to the Gaussian basis for all-electron calculations to within an order of magnitude. Further, we demonstrate the capability of the proposed approach to compute the electronic structure of a metallic system containing 1688 atoms using modest computational resources, and good scalability of the present implementation up to 192 processors.

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

2013-11-01

119

Dynamical correction to linear Kohn-Sham conductances from static density functional theory.  

PubMed

For molecules weakly coupled to leads the exact linear Kohn-Sham (KS) conductance can be orders of magnitude larger than the true linear conductance due to the lack of dynamical exchange-correlation (xc) corrections. In this work we show how to incorporate dynamical effects in KS transport calculations. The only quantity needed is the static xc potential in the molecular junction. Our scheme provides a comprehensive description of Coulomb blockade without breaking the spin symmetry. This is explicitly demonstrated in single-wall nanotubes where the corrected conductance is in good agreement with experimental data whereas the KS conductance fails dramatically. PMID:23909303

Kurth, S; Stefanucci, G

2013-07-19

120

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

NASA Astrophysics Data System (ADS)

The incorrect fractional-charge dissociation of stretched diatomic molecules, predicted by semi-local exchange-correlation functionals, is revisited. This difficulty can be overcome with asymptotically correct non-local potential operators, but should also be absent in exact Kohn-Sham theory, where the potential is local. Here, we show, for the illustrative case of the LiF dimer, that the exact-exchange local Kohn-Sham potential, constructed within the Krieger, Li, and Iafrate (KLI) approximation, can lead to binding energy and charge dissociation curves that are qualitatively correct. This correct behavior is traced back to a characteristic "step" structure in the local exchange potential and its relation to the Kohn-Sham eigenvalues is analyzed.

Makmal, Adi; Kuemmel, Stephan; Kronik, Leeor

2011-03-01

121

Linear-scaling subspace-iteration algorithm with optimally localized nonorthogonal wave functions for Kohn-Sham density functional theory  

NASA Astrophysics Data System (ADS)

We present a linear-scaling method for electronic structure computations in the context of Kohn-Sham density functional theory (DFT). The method is based on a subspace iteration, and takes advantage of the nonorthogonal formulation of the Kohn-Sham functional, and the improved localization properties of nonorthogonal wave functions. A one-dimensional linear problem is presented as a benchmark for the analysis of linear-scaling algorithms for Kohn-Sham DFT. Using this one-dimensional model, we study the convergence properties of the localized subspace-iteration algorithm presented. We demonstrate the efficiency of the algorithm for practical applications by performing fully three-dimensional computations of the electronic density of alkane chains.

García-Cervera, C. J.; Lu, Jianfeng; Xuan, Yulin; E, Weinan

2009-03-01

122

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

NASA Astrophysics Data System (ADS)

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.

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

2009-04-01

123

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

PubMed

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

Chou, Charissa J

2006-06-07

124

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

SciTech Connect

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

Chou, Charissa J.

2006-08-01

125

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

PubMed

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

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

2013-04-18

126

A quadratic form of the Coulomb operator and an optimization scheme for the extended Kohn-Sham models.  

PubMed

To construct an optimization scheme for an extension of the Kohn-Sham approach, I introduce an operator form of the Coulomb interaction. This form is the sum of quadratic form pairs, which can be redefined in a self-consistent calculation of a multi-reference density functional theory. A detailed derivation of the form is given. A fluctuation term introduced in the extended Kohn-Sham scheme is expressed in this form for regularization. The present procedure also provides an exact derivation of effective negative interactions in charge fluctuation channels. Relevance to high-temperature superconductors is discussed. PMID:21715914

Kusakabe, Koichi

2009-01-20

127

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

NASA Astrophysics Data System (ADS)

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.

Eisenberg, Bob; Hyon, Yunkyong; Liu, Chun

2010-09-01

128

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

PubMed

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

Eisenberg, Bob; Hyon, Yunkyong; Liu, Chun

2010-09-14

129

Time Average Field and Secular Variations of Pleistocene to Recent Lava Flows From the Ruiz-Tolima Volcanic Complex (Colombia)  

NASA Astrophysics Data System (ADS)

Thirty three Pleistocene to recent lava flows from the Ruiz-Tolima Volcanic Complex (Colombian Andes) have been sampled for time average field (TAF) and paleosecular variation studies. A total of 10 cores were drilled per flow (site) and stepwise AF demagnetization has been carried out. After principal component analysis and mean-site direction calculations, 29 sites (25 and 4 with normal and reverse polarity, respectively), with ?95 < 5.5° were selected for further calculations. The overall mean direction among the sites (D = 1.8°, I = 6.3°, ?95 = 5.6°) closely fits (at the 95% confidence level) the expected paleomagnetic direction (at the area of study) of a geomagnetic field composed primarily by a geocentric axial dipole with 5% axial quadrupole component (I = 5.72°), but also coincides with a simple GAD model. VGP scatter (13°) is similar to that expected from Model G (12.8°).

Mejia, V.; Sánchez-Duque, A.; Opdyke, N. D.; Huang, K.; Rosales, A.

2009-05-01

130

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

PubMed Central

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.

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

131

Application of Quantum Mechanical Interpretation of Kohn-Sham Theory to the Hooke's Atom.  

NASA Astrophysics Data System (ADS)

The quantum-mechanical interpretation of Kohn-Sham theory is in terms of two fields. The first E_ee(r), representative of Pauli and Coulomb correlations, is determined by Coulomb's law from the pair-correlation density. The second Z_t_c(r) is representative of the correlation contribution to the kinetic energy, and is proportional to the difference in fields obtained as the derivative of the noninteracting and interacting system kinetic-energy-density tensors. The potential (functional derivative) v_ee^KS(r)=?E_ee^KS[?]/?? (r) where E_ee^KS[ ?] is the Kohn-Sham electron-interaction energy functional, is the work done to move an electron in the sum of the fields. The quantum-mechanical electron-interaction E_ee[?] and correlation-kinetic T_c[?] energy components of E_ee^KS[?] can also be expressed in virial form in terms of the fields E_ee(r) and Z_t_c(r) , respectively. In this paper we consider the ground state of the Hooke's atom from this physical perspective, and present an entirely analytical solution of the kinetic-energy-density tensors, the Hartree, Pauli, Coulomb, and correlation-kinetic components of the fields, potentials, their asymptotic structure, and energies.

Qian, Z.; Sahni, V.

1997-03-01

132

Kohn's localization in the insulating state: One-dimensional lattices, crystalline versus disordered  

NASA Astrophysics Data System (ADS)

The qualitative difference between insulators and metals stems from the nature of the low-lying excitations, but also-according to Kohn's theory [W. Kohn, Phys. Rev. 133, A171 (1964)]-from a different organization of the electrons in their ground state: electrons are localized in insulators and delocalized in metals. We adopt a quantitative measure of such localization, by means of a ``localization length'' ?, finite in insulators and divergent in metals. We perform simulations over a one-dimensional binary alloy model, in a tight-binding scheme. In the ordered case the model is either a band insulator or a band metal, whereas in the disordered case it is an Anderson insulator. The results show indeed a localized/delocalized ground state in the insulating/metallic cases, as expected. More interestingly, we find a significant difference between the two insulating cases: band versus Anderson. The insulating behavior is due to two very different scattering mechanisms; we show that the corresponding values of ? differ by a large factor for the same alloy composition. We also investigate the organization of the electrons in the many body ground state from the viewpoint of the density matrices and of Boys' theory of localization.

Bendazzoli, Gian Luigi; Evangelisti, Stefano; Monari, Antonio; Resta, Raffaele

2010-08-01

133

Dielectric screening of the Kohn anomaly of graphene on hexagonal boron nitride  

NASA Astrophysics Data System (ADS)

Kohn anomalies in three-dimensional metallic crystals are dips in the phonon dispersion that are caused by abrupt changes in the screening of the ion cores by the surrounding electron gas. These anomalies are also present at the high-symmetry points ? and K in the phonon dispersion of two-dimensional graphene, where the phonon wave vector connects two points on the Fermi surface. The linear slope around the kinks in the highest optical branch is proportional to the electron-phonon coupling. Here, we present a combined theoretical and experimental study of the influence of the dielectric substrate on the vibrational properties of graphene. We show that screening by the dielectric substrate reduces the electron-phonon coupling at the high-symmetry point K and leads to an upshift of the Raman 2D line. This results in the observation of a Kohn anomaly that can be tuned by screening. The exact position of the 2D line can thus be taken also as a signature for changes in the (electron-phonon limited) conductivity of graphene.

Forster, F.; Molina-Sanchez, A.; Engels, S.; Epping, A.; Watanabe, K.; Taniguchi, T.; Wirtz, L.; Stampfer, C.

2013-08-01

134

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

NASA Astrophysics Data System (ADS)

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

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

135

Major histocompatibility complex variation at class II DQA locus in the brown hare (Lepus europaeus).  

PubMed

The major histocompatability complex (MHC) is a multigene family of receptors that bind and present antigenic peptides to T-cells. Genes of the MHC are characterized by an outstanding genetic polymorphism, which is considered to be maintained by positive selection. Sites involved in peptide binding form binding pockets (P) that are collectively termed the peptide-binding region (PBR). In this study, we examined the level of MHC genetic diversity within and among natural populations of brown hare (Lepus europaeus) from Europe and Anatolia choosing for analysis of the second exon of the DQA locus, one of the most polymorphic class II loci. We aimed at an integrated population genetic analysis of L. europeaus by (i) correlating MHC polymorphism to genetic variability and phylogenetic status estimated previously from maternally (mtDNA) and biparentally (allozymes, microsatellites) inherited loci; and (ii) comparing full-length exon amino acid polymorphism with functional polymorphism in the PBR and the binding pockets P1, P6 and P9. A substantial level of DQA exon 2 polymorphism was detected with two completely different set of alleles between the Anatolian and European populations. However, the phylogeny of full-length exon 2 Leeu-DQA alleles did not show a strong phylogeographic signal. The presence of balancing selection was supported by a statistically significant excess of nonsynonymous substitutions over synonymous in the PBR and a trans-species pattern of evolution detected after phylogenetic reconstruction. The differentiating patterns detected between genetic and functional polymorphism, i.e. the number and the distribution of pocket variants within and among populations, indicated a hierarchical action of selection pressures. PMID:19845856

Koutsogiannouli, E A; Moutou, K A; Sarafidou, T; Stamatis, C; Spyrou, V; Mamuris, Z

2009-10-21

136

Complexity, self-organisation and variation in behaviour in meandering rivers  

NASA Astrophysics Data System (ADS)

River meanders are natural features on the surface of Earth that present some degree of regularity of form. They range from being highly dynamic to being stable under present conditions. Conventional theory is that meanders develop to an equilibrium form which is related to discharge and sediment load. Other research has demonstrated that many highly active meanders exhibit a continuous evolution over time and a non-linearity in rate of development. Ideas of autogenesis and of self-organised criticality as being an explanation of some meander changes have been proposed. In this paper data from rivers around the world are examined for further evidence of autogenic, self-organised or non-linear behaviour through analysis of change in sinuosity over time for reaches and change in individual bend form, particularly bend curvature and bend elongation. Some examples do exhibit trends of increasing sinuosity over time and a few show limits from which large decreases occur. Several case studies show non-linearity of behaviour and increasing complexity of form. Other case studies, however, do not exhibit such trends. Phase space plots are used to help uncover emergent behaviour but show a variety of patterns. The example of a reach in which multiple cut-offs occurred is analysed for mechanisms of self-organisation of the planform and in the pool-riffle pattern. Riffles are more closely spaced and also more transient in the more rapidly changing and higher sinuosity parts of the channel. Hypothetical trajectories of different meander behaviour, including for bedrock meanders, are plotted but the challenge remains to uncover the conditions for occurrence and for divergence of tendencies to stability and instability. Identification of attractors and phase space of behaviour of different meandering systems offer the potential for application to sustainable channel management.

Hooke, J. M.

2007-11-01

137

Variation in the Complex Carbohydrate Biosynthesis Loci of Acinetobacter baumannii Genomes  

PubMed Central

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.

Kenyon, Johanna J.; Hall, Ruth M.

2013-01-01

138

Fault geometric complexity and how it may cause temporal slip-rate variation within an interacting fault system  

NASA Astrophysics Data System (ADS)

Slip-rates along individual faults may differ as a function of measurement time scale. Short-term slip-rates may be higher than the long term rate and vice versa. For example, vertical slip-rates along the Wasatch Fault, Utah are 1.7+/-0.5 mm/yr since 6ka, <0.6 mm/yr since 130ka, and 0.5-0.7 mm/yr since 10Ma (Friedrich et al., 2003). Following conventional earthquake recurrence models like the characteristic earthquake model, this observation implies that the driving strain accumulation rates may have changed over the respective time scales as well. While potential explanations for such slip-rate variations may be found for example in the reorganization of plate tectonic motion or mantle flow dynamics, causing changes in the crustal velocity field over long spatial wavelengths, no single geophysical explanation exists. Temporal changes in earthquake rate (i.e., event clustering) due to elastic interactions within a complex fault system may present an alternative explanation that requires neither variations in strain accumulation rate or nor changes in fault constitutive behavior for frictional sliding. In the presented study, we explore this scenario and investigate how fault geometric complexity, fault segmentation and fault (segment) interaction affect the seismic behavior and slip-rate along individual faults while keeping tectonic stressing-rate and frictional behavior constant in time. For that, we used FIMozFric--a physics-based numerical earthquake simulator, based on Okada's (1992) formulations for internal displacements and strains due to shear and tensile faults in a half-space. Faults are divided into a large number of equal-sized fault patches which communicate via elastic interaction, allowing implementation of geometrically complex, non-planar faults. Each patch has assigned a static and dynamic friction coefficient. The difference between those values is a function of depth--corresponding to the temperature-dependence of velocity-weakening that is observed in laboratory friction experiments and expressed in an [a-b] term in Rate-State-Friction (RSF) theory. Patches in the seismic zone are incrementally loaded during the interseismic phase. An earthquake initiates if shear stress along at least one (seismic) patch exceeds its static frictional strength and may grow in size due to elastic interaction with other fault patches (static stress transfer). Aside from investigating slip-rate variations due to the elastic interactions within a fault system with this tool, we want to show how such modeling results can be very useful in exploring the physics underlying the patterns that the paleoseismology sees and that those methods (simulation and observations) can be merged, with both making important contributions. Using FIMozFric, we generated synthetic seismic records for a large number of fault geometries and structural scenarios to investigate along-fault slip accumulation patterns and the variability of slip at a point. Our simulations show that fault geometric complexity and the accompanied fault interactions and multi-fault ruptures may cause temporal deviations from the average fault slip-rate, in other words phases of earthquake clustering or relative quiescence. Slip-rates along faults within an interacting fault system may change even when the loading function (stressing rate) remains constant and the magnitude of slip rate change is suggested to be proportional to the magnitude of fault interaction. Thus, spatially isolated and structurally mature faults are expected to experience less slip-rate changes than strongly interacting and less mature faults. The magnitude of slip-rate change may serve as a proxy for the magnitude of fault interaction and vice versa.

Zielke, Olaf; Arrowsmith, Ramon

2010-05-01

139

Effects of carbonate host rock assimilation on trace element and isotopic variation in minerals from a layered alkaline intrusive complex  

NASA Astrophysics Data System (ADS)

The 466Ma Hortavær complex is a layered intrusion in north-central Norway; it evolved by assimilation of carbonate and silicate rocks. Carbonate assimilation involved expulsion of Ca-rich melt from calc-silicates into host magmas and reactive assimilation to produce clinopyroxene, titanite, Ca-amphibole, grossular- andradite garnet, and calcite. The complex was constructed by batch-wise intrusion and subsequent assimilation, leading to compositional and isotopic heterogeneity. Original evidence for carbonate assimilation came from delta 13C in interstital calcite (1). Isotopic variation of mafic compositions are epsilon Nd +4 to -7 over a range of 87Sr/86Sr(466Ma) from 0.707 to 0.708, which overlap those of calcite marble host rocks. Evolved rocks have higher 87Sr/86Sr (> 0.7080) and lower epsilon Nd (< -7); values similar to metapelitic host rocks. Some garnet, amphibole and cpx grains are zoned in 87Sr/86Sr, epsilon Nd, or both. Trends and ranges of variation within minerals are similar to the whole rocks; an indication carbonate and silicate rocks were assimilated, generally within individual magma batches. From gabbro to syenite, cpx ranges from diopside to hedenbergite and amphibole from pargasite to hastingsite. Cpx and amphibole from syenite have high calculated Fe3+ and anomalously high HREE. We infer that oxidation of the magma was in the presence of a mixed CO2 + H2O fluid that formed during carbonate assimilation (2). Increased Fe3+ in cpx allowed for enrichment of the HREE by exchange on the M1 site. The calcite from host-rock screens has REE abundances <5x, and generally <2x chondrites. In contrast, calcite grains in dioritic rocks have REE abundances up to 100x chondritic values. Calcite from two syenitic samples is variable, with abundances of heavy and middle REE from 1 to 10x chondrites. A clue to this variability comes from calcite in melasyenitic endoskarn, where calcite inclusions in garnet show higher REE contents (20-50x chondritic La and 10x chondritic Lu), but interstitial calcite has positive slopes and a wide range of LREE contents. Calcite with high LREE contents is interpreted as of igneous origin; interstitial calcite with positive slopes and low LREE contents is taken to be hydrothermal. Grossular-andradite garnet in endoskarn has Lu from 100 to 1000x chondritic values, and this variation may be observed within a single sample. All garnets have steep positive slopes from La to Sm but variable M- and HREE patterns: negative, flat, or cup-shaped. Si and Ti contents indicate a mixed igneous and hydrothermal origin. The Horta complex was constructed by a complex process involving assimilation of calcareous and silicate rocks in many magma batches. Evolution of a mixed CO2 + H2O fluid increased the oxidation state of the system, permitting growth of Fe3+ rich cpx and grossular-andradite garnet. 1. Barnes et al., 2005, Lithos, 80, 179-199. 2. Iacono Marziano et al., 2007, J volc and geothermal res., 66, 91-105.

Li, Y.; Barnes, C. G.; Frost, C. D.; Prestvik, T.; Allen, C. M.

2008-12-01

140

Cationic rhodium(I) complexes containing 4,4?-disubstituted 2,2?-bipyridines: A systematic variation on electron density over the metal centre  

Microsoft Academic Search

A series of [Rh(COD)(X2-bipy)]BF4 complexes (COD=1,5-cyclooctadiene; X2-bipy=4,4?-disubstituted 2,2?-bipyridines; X=OCH3, CH3, H, Cl or NO2) has been prepared from [Rh(COD)Cl]2. The complexes for X=OCH3, Cl and NO2 have not been described previously in the literature. All complexes have been characterised by elemental analysis, IR, 1H NMR and UV–Vis spectrometry. This series of complexes presents a wide variation on electron density over

Paulo E. A. Ribeiro; Claudio L. Donnici; Eduardo N. dos Santos

2006-01-01

141

Accurate Kohn-Sham potential for the 1s2s S-3 state of the helium atom: Tests of the locality and the ionization-potential theorems  

NASA Astrophysics Data System (ADS)

The local Kohn-Sham potential is constructed for the 1s2s S-3 state of the helium atom, using the procedure proposed by van Leeuwen and Baerends (Phys. Rev. A, 49, 2138 (1994)) and the many-body electron density, obtained from the pair-correlation program of Salomonson and Oster (Phys. Rev. A, 40, 5559 (1989)). The Kohn-Sham orbitals reproduce the many-body density very accurately, demonstrating the validity of the Kohn-Sham model and the locality theorem in this case. The ionization-potential theorem, stating that the Kohn-Sham energy eigenvalue of the outermost electron orbital agrees with the negative of the corresponding many-body ionization energy (including electronic relaxation), is verified in this case to nine digits. A Kohn-Sham potential is also constructed to reproduce the Hartree-Fock density of the same state, and the Kohn-Sham 2s eigenvalue is then found to agree with the same accuracy with the corresponding Hartree-Fock eigenvalue. This is consistent with the fact that in this model the energy eigenvalue equals the negative of the ionization energy without relaxation due to Koopmans' theorem. Related calculations have been performed previously, particularly for atomic and molecular ground states, but none of matching accuracy. In the computations presented here there is no conflict between the locality of the Kohn-Sham potential and the exclusion principle, as claimed by Nesbet (Phys. Rev. A, 58, R12 (1998)).

Salomonson, S.; Moller, F.; Lindgren, I.

2005-01-01

142

Optimized local basis set for Kohn-Sham density functional theory  

NASA Astrophysics Data System (ADS)

We develop a technique for generating a set of optimized local basis functions to solve models in the Kohn-Sham density functional theory for both insulating and metallic systems. The optimized local basis functions are obtained by solving a minimization problem in an admissible set determined by a large number of primitive basis functions. Using the optimized local basis set, the electron energy and the atomic force can be calculated accurately with a small number of basis functions. The Pulay force is systematically controlled and is not required to be calculated, which makes the optimized local basis set an ideal tool for ab initio molecular dynamics and structure optimization. We also propose a preconditioned Newton-GMRES method to obtain the optimized local basis functions in practice. The optimized local basis set is able to achieve high accuracy with a small number of basis functions per atom when applied to a one dimensional model problem.

Lin, Lin; Lu, Jianfeng; Ying, Lexing; E, Weinan

2012-05-01

143

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

NASA Astrophysics Data System (ADS)

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.

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

2013-04-01

144

Analyzing effects of strong electron correlation within Kohn-Sham density-functional theory  

NASA Astrophysics Data System (ADS)

A density-functional-theory method for analyzing effects of strong electron correlation is presented, based on a single Kohn-Sham determinant. It yields the population of effectively unpaired (odd) electrons and depicts the strength of nondynamic correlation, both locally and globally. It provides also a quantitative estimate of localized magnetic moments without invoking symmetry-breaking procedures. Preliminary tests on some exemplary systems of strong correlation such as C2, Cr2, the NO dimer, and dissociating H2 and N2 are discussed in comparison with available post-Hartree-Fock wave-function studies. We show that the bond in C2 is unlikely to have diradical character in its ground state, but may have it in some excited state. The singlet ground state of the NO dimer, however, does have a diradical character of the bonding. Quite interestingly, the bond in Cr2 has a quad-radical nature.

Proynov, Emil; Liu, Fenglai; Kong, Jing

2013-09-01

145

The Use of Trust Regions in Kohn-Sham Total EnergyMinimization  

SciTech Connect

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

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

2006-05-30

146

The problem of interlab variation in methods for mitochondrial disease diagnosis: enzymatic measurement of respiratory chain complexes.  

PubMed

Due to the large importance of mitochondrial function for numerous diseases the detection of respiratory chain defects for diagnostic purposes is an important task of mitochondrial medicine. For comparing the methods, standard mitochondrial homogenate prepared from bovine skeletal muscle was sent on dry ice to 14 labs of 8 countries. Activities of complexes I, I + III, II, II + III, IV (cytochrome c oxidase) and V (F0F1ATPase) as well as of citrate synthase were measured. For all enzymes the results differed at more than one order of magnitude. From eight labs we were able to compare the results with their control values for human skeletal muscle. Four labs found normal activity of cytochrome-c-oxidase whereas three labs found higher and one lab found lower activities compared to the own controls. Since all labs used different temperatures (25, 30 and 37 degrees C) in one lab the temperature dependencies were measured experimentally. The temperature correction did not much reduce the divergence of the results. It is concluded that differences in the lab protocols are the reason for the large variation of results. Since the experimental results strongly depend on the used method a strict standardization is necessary. PMID:16120404

Gellerich, Frank Norbert; Mayr, Johannes A; Reuter, Sebastian; Sperl, Wolfgang; Zierz, Stephan

2004-10-18

147

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

PubMed Central

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.

2011-01-01

148

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

Microsoft Academic Search

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

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

2010-01-01

149

Complex L[sup 2] calculation of the variation of resonance widths of HOCl with total angular momentum  

SciTech Connect

Complex L[sup 2] calculations of the variation of the resonance width of HOCl(6[nu][sub OH])[r arrow]Cl+OH with total angular momentum, [ital J], are reported, using a recently developed, accurate [ital ab initio] potential energy surface [S. Skokov, J. M. Bowman, and K. A. Peterson, J. Chem. Phys. [bold 109], 2662 (1998)]. The calculations are carried out using the adiabatic rotation approximation for the overall rotation and a truncation/recoupling method for the vibrational states. An [ital ab initio] calculation of the [ital J] and [ital K] dependence of the intensity of the absorption spectrum of the [ital Q] branch in the neighborhood of the 2[nu][sub OH][r arrow]6[nu][sub OH] transition is presented, and compared to results of recent experiments of Rizzo and co-workers. The variation of the resonance width of the 6,0,0 and the 3,8,0 states with [ital J] and [ital K] is presented, and comparisons with recent double-resonance experiments of the Rizzo and Sinha groups for the 6,0,0 state show encouraging qualitative agreement. The fluctuations of the dissociation rate with [ital J] is shown to be due to rotation-induced coupling of the 6[nu][sub OH] state to a dense set of highly excited OCl stretch states. A simple model describing the coupling of 6[nu][sub OH] with background states, using a coupling constant of 0.05 cm[sup [minus]1] is shown to give a qualitatively correct picture of the fluctuation of the resonance width with [ital J]. Finally, the energies of many nonoverlapping resonances, some of which are assigned, for J=18 and K=0 are presented and compared to Rice[endash]Ramsperger[endash]Kassel[endash]Marcus (RRKM) theory. It is found that due to slow, rate limiting, intramolecular vibrational relaxation the RRKM overestimates the average dissociation rate by an order of magnitude. [copyright] [ital 1999 American Institute of Physics.

Skokov, S.; Bowman, J.M. (Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322 (United States))

1999-09-01

150

Multichannel variational expressions of scattering theory  

SciTech Connect

We have compared variational functionals for multichannel scattering. The functionals considered were Schwinger-type functionals based on the close-coupling equations, the Schwinger-type variational functionals of Takatsuka and McKoy (Phys. Rev. A 24, 2473 (1981)), and a Kohn-type variational functional. The results for a simple Huck-model potential containing both open and closed channels indicate that the Schwinger-type variational functionals yielded very similar results and that all the methods considered converged at a similar rate with respect to the closed-channel expansion. To obtain good convergence with any of these methods it was essential to include separate trial functions outside the range of the Huck square-well potential in the channels where a correct asymptotic form of the wave function was required, those being only the closed channels for the Schwinger-type functionals and both open and closed channels for the Kohn-type functionals. These asymptotic functions were needed to reproduce the discontinuity in the second derivative of the wave function due to the discontinuities in the model potential. Convergence characteristics of these methods with respect to target-state expansions were also considered.

Lucchese, R.R.

1986-03-01

151

Genetic Variation among Panton-Valentine Leukocidin-Encoding Bacteriophages in Staphylococcus aureus Clonal Complex 30 Strains  

PubMed Central

Clonal complex 30 (CC30), one of the major Staphylococcus aureus lineages, has caused extensive hospital-acquired and community-acquired infections worldwide. Recent comparative genomics studies have demonstrated that three CC30 clones—phage type 80/81, Southwest Pacific (SWP), and contemporary EMRSA-16 associated (Con) strains—shared a recent common ancestor more than 100 years ago. Panton-Valentine leukocidin (PVL), a bacteriophage encoded toxin that has been epidemiologically linked with community-associated methicillin-resistant S. aureus (CA-MRSA), has frequently been identified in CC30 clones, although the pvl gene variation and distribution of PVL-encoding phages are poorly understood. We determined here the distribution of PVL phages, PVL gene sequences, and chromosomal phage insertion sites in 52 S. aureus CC30 PVL-harboring isolates, collected from four continents over a 75-year period. Our results indicate that PVL phages with icosahedral heads, including ?108PVL and ?PVL, were mainly associated with phage 80/81 strains, whereas phages with elongated heads were predominantly found in SWP (?Sa2958 and ?TCH60) and Con (?Sa2USA) strains. Nine single-nucleotide polymorphisms were identified in the lukSF-PV gene, with six isolates harboring the R variant that has been previously associated with CA-MRSA strains. Interestingly, all six R variant strains belonged to the same Con CC30 clone and carried a ?Sa2USA-like phage. Similar chromosomal phage insertion sites were also identified in all 52 PVL-harboring CC30 strains. These analyses provide important insights into the microepidemiology of PVL-harboring CC30 strains, while the discovery of ?Sa2USA-associated R variant strains sheds further light on the evolution of PVL-positive CA-MRSA.

Chen, Liang; Chavda, Kalyan D.; Solanki, Mihir; Mediavilla, Jose R.; Mathema, Barun; Schlievert, Patrick M.

2013-01-01

152

Genetic variation among Panton-Valentine leukocidin-encoding bacteriophages in Staphylococcus aureus clonal complex 30 strains.  

PubMed

Clonal complex 30 (CC30), one of the major Staphylococcus aureus lineages, has caused extensive hospital-acquired and community-acquired infections worldwide. Recent comparative genomics studies have demonstrated that three CC30 clones-phage type 80/81, Southwest Pacific (SWP), and contemporary EMRSA-16 associated (Con) strains-shared a recent common ancestor more than 100 years ago. Panton-Valentine leukocidin (PVL), a bacteriophage encoded toxin that has been epidemiologically linked with community-associated methicillin-resistant S. aureus (CA-MRSA), has frequently been identified in CC30 clones, although the pvl gene variation and distribution of PVL-encoding phages are poorly understood. We determined here the distribution of PVL phages, PVL gene sequences, and chromosomal phage insertion sites in 52 S. aureus CC30 PVL-harboring isolates, collected from four continents over a 75-year period. Our results indicate that PVL phages with icosahedral heads, including ?108PVL and ?PVL, were mainly associated with phage 80/81 strains, whereas phages with elongated heads were predominantly found in SWP (?Sa2958 and ?TCH60) and Con (?Sa2USA) strains. Nine single-nucleotide polymorphisms were identified in the lukSF-PV gene, with six isolates harboring the R variant that has been previously associated with CA-MRSA strains. Interestingly, all six R variant strains belonged to the same Con CC30 clone and carried a ?Sa2USA-like phage. Similar chromosomal phage insertion sites were also identified in all 52 PVL-harboring CC30 strains. These analyses provide important insights into the microepidemiology of PVL-harboring CC30 strains, while the discovery of ?Sa2USA-associated R variant strains sheds further light on the evolution of PVL-positive CA-MRSA. PMID:23284024

Chen, Liang; Chavda, Kalyan D; Solanki, Mihir; Mediavilla, José R; Mathema, Barun; Schlievert, Patrick M; Kreiswirth, Barry N

2013-01-02

153

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

PubMed Central

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

Yokoyama, I; Waxman, F

1993-01-01

154

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

Microsoft Academic Search

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

Donelle M. Robinson; Molly R. Morris

2010-01-01

155

More than the sum of its parts: a complex epistatic network underlies natural variation in thermal preference behavior in Caenorhabditis elegans.  

PubMed

Behavior is a complex trait that results from interactions among multiple genes and the environment. Both additive and nonadditive effects are expected to contribute to broad-sense heritability of complex phenotypes, although the relative contribution of each of these mechanisms is unknown. Here, we mapped genetic variation in the correlated phenotypes of thermal preference and isothermal dispersion in the nematode Caenorhabditis elegans. Genetic variation underlying these traits is characterized by a set of linked quantitative trait loci (QTL) that interact in a complex epistatic network. In particular, two loci located on the X chromosome interact with one another to generate extreme thermophilic behavior and are responsible for ?50% of the total variation observed in a cross between two parental lines, even though these loci individually explain very little of the among-line variation. Our results demonstrate that simultaneously considering the influence of a quantitative trait locus (QTL) on multiple scales of behavior can inform the physiological mechanism of the QTL and show that epistasis can explain significant proportions of otherwise unattributed variance within populations. PMID:23086219

Gaertner, Bryn E; Parmenter, Michelle D; Rockman, Matthew V; Kruglyak, Leonid; Phillips, Patrick C

2012-10-19

156

Localized exchange-correlation potential from second-order self-energy for accurate Kohn-Sham energy gap  

NASA Astrophysics Data System (ADS)

A local Kohn-Sham (KS) exchange-correlation potential is derived by localizing the second-order self-energy operator, using approximations to the linear response Sham-Schlüter equation. Thanks to the use of the resolution-of-identity technique for the calculation of the self-energy matrix elements, the method is very efficient and can be applied to large systems. The authors investigate the KS energy gaps and lowest excitation energies of atoms and small- and medium-size molecules. Reference KS energy gaps (from accurate densities) of atoms and small molecules can be reproduced with great accuracy. For larger systems they found that the KS energy gap is smaller than the one obtained from the local-density approximation, showing the importance of an ab initio correlation in the Kohn-Sham potential.

Fabiano, E.; Della Sala, F.

2007-06-01

157

From electron densities to Kohn-Sham kinetic energies, orbital energies, exchange-correlation potentials, and exchange-correlation energies  

Microsoft Academic Search

By developing our previous method [Phys. Rev. A 46, 2337 (1992); J. Chem. Phys. 98, 543 (1993)], we show how to calculate Kohn-Sham kinetic energies, orbitals, orbital energies, and exchange-correlation potentials, starting from accurate ground-state electron densities. In addition, given correct total energies, we also show how to obtain exchange-correlation energies. The scheme used is based on the Levy constrained-search

Qingsheng Zhao; Robert C. Morrison; Robert G. Parr

1994-01-01

158

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

NASA Astrophysics Data System (ADS)

N "exotic" [alias non-commutative] particles with masses m, charges e and non-commutative parameters ?, moving in a uniform magnetic field B, separate into center-of-mass and internal motions if Kohn's condition e/m=const is supplemented with e?=const. Then the center-of-mass behaves as a single exotic particle carrying the total mass and charge of the system, M and e, and a suitably defined non-commutative parameter ?. For vanishing electric field off the critical case e?B?1, the particles perform the usual cyclotronic motion with modified but equal frequency. The system is symmetric under suitable time-dependent translations which span a (4+2)-parameter centrally-extended subgroup of the "exotic" [i.e., two-parameter centrally-extended] Newton-Hooke group. In the critical case B=B=( the system is frozen into a static "crystal" configuration. Adding a constant electric field, all particles perform, collectively, a cyclotronic motion combined with a drift perpendicular to the electric field when e?B?1. For B=B the cyclotronic motion is eliminated and all particles move, collectively, following the Hall law. Our time-dependent symmetries are reduced to the (2+1)-parameter Heisenberg group of centrally-extended translations.

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

2012-01-01

159

Difficulties in applying pure Kohn-Sham density functional theory electronic structure methods to protein molecules  

NASA Astrophysics Data System (ADS)

Self-consistency-based Kohn-Sham density functional theory (KS-DFT) electronic structure calculations with Gaussian basis sets are reported for a set of 17 protein-like molecules with geometries obtained from the Protein Data Bank. It is found that in many cases such calculations do not converge due to vanishing HOMO-LUMO gaps. A sequence of polyproline I helix molecules is also studied and it is found that self-consistency calculations using pure functionals fail to converge for helices longer than six proline units. Since the computed gap is strongly correlated to the fraction of Hartree-Fock exchange, test calculations using both pure and hybrid density functionals are reported. The tested methods include the pure functionals BLYP, PBE and LDA, as well as Hartree-Fock and the hybrid functionals BHandHLYP, B3LYP and PBE0. The effect of including solvent molecules in the calculations is studied, and it is found that the inclusion of explicit solvent molecules around the protein fragment in many cases gives a larger gap, but that convergence problems due to vanishing gaps still occur in calculations with pure functionals. In order to achieve converged results, some modeling of the charge distribution of solvent water molecules outside the electronic structure calculation is needed. Representing solvent water molecules by a simple point charge distribution is found to give non-vanishing HOMO-LUMO gaps for the tested protein-like systems also for pure functionals.

Rudberg, Elias

2012-02-01

160

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

NASA Astrophysics Data System (ADS)

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.

Holas, A.

2008-02-01

161

Applications of electrostatic interpretation of components of effective Kohn-Sham potential in atoms  

NASA Astrophysics Data System (ADS)

The fundamental significance of the components of the electronic Kohn-Sham potential evaluated at the nucleus is highlighted via the numerical studies on atoms He-Lu which suggest their formally similar power-law relationship in expressing the associated components of total electronic energy. Similar studies on the isoelectronic series of closed shell atoms lead to the linear correlations. The proposed static exchange-correlation charge density concept [S. Liu, P. A. Ayers, and R. G. Parr, J. Chem. Phys. 111, 6197 (1999)] is used to interpret these relationships. The maxima in the static integrated radial exchange-correlation charge density function, Qxc)(r, in atoms are shown to reflect the shell boundaries. The quantum Monte Carlo density derived exchange-correlation potentials for Be and Ne are used to obtain Qxc)(r that can be used as standards to directly assess the quality of approximate exchange-correlation potentials. For the negative ions, Qxc)(r displays a characterstic outer minimum as a consequence of the Sen-Politzer theorem [K. D. Sen and P. Politzer, J. Chem. Phys. 90, 4370 (1989)]. This minimum is found to be related with the stability of negative ions.

Sen, K. D.; De Proft, Frank; Geerlings, Paul

2002-09-01

162

Efficient treatment of the Hartree interaction in the relativistic Kohn-Sham problem  

NASA Astrophysics Data System (ADS)

We elaborate the two-component Douglas-Kroll reduction of the Dirac-Kohn-Sham problem of relativistic density-functional theory as introduced by Matveev and Rösch [J. Chem. Phys. 118, 3997 (2003)]. That method retains corrections to the Coulomb self-interaction (or Hartree) term of the energy functional that are due to the picture change. Using analytic expressions for the matrix elements, one is able to abandon the resolution of the identity approach for a crucial step of the relativistic transformation. Thus, a major source of uncertainties of the method is eliminated because basis sets no longer have to be extended by functions of higher angular momentum, previously required to ensure kinetic balance. This approach also relies on the electron charge-density fitting scheme via an auxiliary basis set. An efficient approximate implementation results if one restricts the relativistic transformation to the spherically symmetric atom-centered auxiliary functions. It provides accurate results while simplifying greatly the expressions for the matrix elements of the relativistically transformed operators and significantly reducing the computational effort. We demonstrate the performance of the method for the fine structure of one-electron levels of the Hg atom, the g-tensor shifts of NO2, and the properties of the diatomic molecules Bi2, Pb2, PbO, and TlH.

Matveev, Alexei V.; Majumder, Sonjoy; Rösch, Notker

2005-10-01

163

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

NASA Astrophysics Data System (ADS)

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

Schauer, Volker; Linder, Christian

2013-10-01

164

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

PubMed

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

Wallace, Douglas C

2013-06-10

165

Population genetic variation, structure, and evolution in Engelmann spruce, white spruce, and their natural hybrid complex in Alberta  

Microsoft Academic Search

Genetic variation, structure, and evolution of 12 populations of putative Engelmann spruce ( Picea engelmanii Parry), white spruce (Picea glauca (Moench) Voss), and Engelmann - white spruce natural hybrids from the sympatric areas and two populations of white spruce from the allopatric areas in Alberta were examined using 23 allozyme loci coding for 13 enzymes in needles. Although most of

Om P. Rajora; Bruce P. Dancik

2000-01-01

166

Variational scattering theory using a functional of fractional form. I. General theory  

SciTech Connect

We propose a variational method for scattering in which the functional is of a fractional form as for the Schwinger variational principle. However, our functional does not involve the Green's function, but the Hamiltonian and the potential function. This method shows features of both the Schwinger-type variational principles and the Kohn-type standard variational principles. As a result, our method can derive distinct advantages from both of these approaches. The resultant K matrix is symmetric and anomaly-free. Some other properties, including a minimum principle, which is useful in the selection of an optimum basis for the expansion of the scattering functions are also discussed.

Takatsuka, K.; McKoy, V.

1981-05-01

167

Effects of carbonate host rock assimilation on trace element and isotopic variation in minerals from a layered alkaline intrusive complex  

Microsoft Academic Search

The 466Ma Hortavær complex is a layered intrusion in north-central Norway; it evolved by assimilation of carbonate and silicate rocks. Carbonate assimilation involved expulsion of Ca-rich melt from calc-silicates into host magmas and reactive assimilation to produce clinopyroxene, titanite, Ca-amphibole, grossular- andradite garnet, and calcite. The complex was constructed by batch-wise intrusion and subsequent assimilation, leading to compositional and isotopic

Y. Li; C. G. Barnes; C. D. Frost; T. Prestvik; C. M. Allen

2008-01-01

168

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

NASA Astrophysics Data System (ADS)

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

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

2006-02-01

169

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

SciTech Connect

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.

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

2012-01-01

170

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

PubMed

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

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

2010-08-19

171

Effect of long-range interactions on the Kohn-Luttinger mechanism of the cooper instability in the Shubin-Vonsowsky model  

NASA Astrophysics Data System (ADS)

The problem of Cooper instability is studied by implementing the Kohn-Luttinger mechanism in the framework of the Shubin-Vonsowsky model taking into account the intersite Coulomb interactions within the first and second coordination spheres. It is shown that the Kohn-Luttinger renormalization for the effective interaction in the second-order terms of perturbation theory, as well as the inclusion of intersite hoppings in the second and third coordination spheres, significantly affects the interplay between the superconducting phases with d xy -, p-, s-, and d_{x^2 - y^2 }-wave symmetries of the order parameter.

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

2013-04-01

172

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

PubMed

Corticosterone influences emotion and cognition via actions in a diversity of corticolimbic structures, including the amygdala. Since extracellular levels of corticosterone in brain have rarely been studied, we characterized a specific and sensitive enzymatic immunoassay for microdialysis quantification of corticosterone in the basolateral amygdaloid complex of freely-moving rats. Corticosterone levels showed marked diurnal variation with an evening (dark phase) peak and stable, low levels during the day (light phase). The "anxiogenic agents", FG7142 (20 mg/kg) and yohimbine (10 mg/kg), and an environmental stressor, 15-min forced-swim, induced marked and sustained (1-3 h) increases in dialysis levels of corticosterone in basolateral amygdaloid complex. They likewise increased dialysis levels of dopamine and noradrenaline, but not serotonin and GABA. As compared to basal corticosterone levels of ~200-300 pg/ml, the elevation provoked by forced-swim was ca. 20-fold and this increase was abolished by adrenalectomy. Interestingly, stress-induced rises of corticosterone levels in basolateral amygdaloid complex were abrogated by combined but not separate administration of the corticotrophin releasing factor(1) (CRF(1)) receptor antagonist, CP154,526, and the vasopressin(1b) (V(1b)) receptor antagonist, SSR149,415. Underpinning their specificity, they did not block forced-swim-induced elevations in dopamine and noradrenaline. In conclusion, extracellular levels of corticosterone in the basolateral amygdaloid complex display marked diurnal variation. Further, they are markedly elevated by acute stressors, the effects of which are mediated (in contrast to concomitant elevations in levels of monoamines) by co-joint recruitment of CRF(1) and V(1b) receptors. PMID:22464880

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

2012-01-16

173

Application of autospectral and regression analysis to the study of temporal-spacial variation of winds in complex terrain  

Microsoft Academic Search

How many meteorological stations, where they should be placed and how often the data should be taken to characterize wind flow in complex terrain continues to be a problem for pollution transport studies as well as wind energy prospecting. A two month (June and July 1978) field study was conducted using laser anemometers (Lawrence, et al., 1976) across a windy

Porch

1979-01-01

174

Intersex variation in synaptonemal complex lengths largely determine the different recombination rates in male and female germ cells  

Microsoft Academic Search

Meiotic chromosomes in human oocytes are packaged differently than in spermatocytes at the pachytene stage of meiosis I, when crossing-over takes place. Thus the meiosis-specific pairing structure, the synaptonemal complex (SC), is considerably longer in oocytes in comparison to spermatocytes. The aim of the present study was to examine the influence of this length factor on meiotic recombination in male

C. Tease; M. A. Hultén

2004-01-01

175

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

SciTech Connect

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

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

2009-04-15

176

Synthesis of Binucleating Macrocycles and their Nickel(II) Hydroxo- and Cyano-Bridged Complexes with Divalent Ions: Anatomical Variation of Ligand Features  

PubMed Central

The planar NNN-pincer complexes [MII(pyN Me2)(OH)]1? (MII = Ni, Cu) fix CO2 in ?1-OCO2H complexes; results for the copper system are described. MnII, FeII, CoII, and ZnII behave differently, forming [MII(pyN2Me)2]2? with N4O2 coordination. Incorporation of the NiII pincer into binucleating macrocycle 2 containing a triamino MII locus connected by two 1,3-biphenylene groups affords proximal NiII and MII sites for investigation of the synthesis, structure, and reactivity of Ni-X-M bridge units. This ligand structure is taken as a reference for variations in MII atoms and binding sites and bridges X = OH? and CN? to produce additional members of the macrocyclic family with improved properties. Macrocycle 2 with a 22-membered ring is shown to bind MII = Mn, Fe, and Cu with hydroxo bridges. Introduction of the 4-BuiO group (macrocycle 3) improves the solubility of neutral complexes such as those with NiII-OH-CuII and NiII-CN-FeII bridges. The syntheses of macrocycle 5 with a 7-Me-[12]aneSN3 and macrocycle 6 with a 1,8-Me2-[14]aneN4 MII binding site are described to together with hydoxo-bridged Ni-Cu and cyano-bridged Ni-Fe complexes. This work was motivated by the presence of a Ni?(HO)-Fe bridge grouping in a reactive state of carbon monoxide dehydrogenase. Attempted decrease in Ni-(OH)-M distances (3.70-3.87 Å) to smaller values observed in the enzyme by use of macrocycle 4 having 1,2-biphenylene connectors led to a mononuclear octahedral NiII complex. Bridge structural units are summarized and the structures of fourteen macrocyclic complexes including eight with bridges are described.

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

2012-01-01

177

Do biodiversity patterns in Dutch wetland complexes relate to variation in urbanisation, intensity of agricultural land use or fragmentation?  

Microsoft Academic Search

Red list species densities of birds (maximally 22 km?2), and angiosperms (maximally 39 km?2) were used as biodiversity indicators in 21 larger complexes of wetlands across the Netherlands. Their covariability with\\u000a a range of indicators of human land use was assessed, including population, road and visitor density, area covered by agriculture,\\u000a open water, forest and residential housing. Data were collected on the

Jan E. Vermaat; Hasse Goosen; Nancy Omtzigt

2007-01-01

178

Do biodiversity patterns in Dutch wetland complexes relate to variation in urbanisation, intensity of agricultural land use or fragmentation?  

Microsoft Academic Search

Red list species densities of birds (maximally 22 km?2), and angiosperms (maximally 39 km?2) were used as biodiversity indicators in 21 larger complexes of wetlands across the Netherlands. Their covariability with\\u000a a range of indicators of human land use was assessed, including population, road and visitor density, area covered by agriculture,\\u000a open water, forest and residential housing. Data were collected on the

Jan E. Vermaat; Hasse Goosen; Nancy Omtzigt

179

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

PubMed Central

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

2013-01-01

180

Tuning Spin-Spin Coupling in Quinonoid-Bridged Dicopper(II) Complexes through Rational Bridge Variation.  

PubMed

Bridged metal complexes [{Cu(tmpa)}2(?-L(1)-2H)](ClO4)2 (1), [{Cu(tmpa)}2(?-L(2)-2H)](ClO4)2 (2), [{Cu(tmpa)}2(?-L(3)-2H)](BPh4)2 (3), and [{Cu(tmpa)}2(?-L(4)-2H)](ClO4)2 (4) (tmpa = tris(2-pyridylmethyl)amine, L(1) = chloranilic acid, L(2) = 2,5-dihydroxy-1,4-benzoquinone, L(3) = (2,5-di-[2-(methoxy)-anilino]-1,4-benzoquinone, L(4) = azophenine) were synthesized from copper(II) salts, tmpa, and the bridging quinonoid ligands in the presence of a base. X-ray structural characterization of the complexes showed a distorted octahedral environment around the copper(II) centers for the complexes 1-3, the donors being the nitrogen atoms of tmpa, and the nitrogen or oxygen donors of the bridging quinones. In contrast, the copper(II) centers in 4 display a distorted square-pyramidal coordination, where one of the pyridine arms of each tmpa remains uncoordinated. Bond-length analyses within the bridging ligand exhibit localization of the double bonds inside the bridge for 1-3. In contrast, complete delocalization of double bonds within the bridging ligand is observed for 4. Temperature-dependent magnetic susceptibility measurements on the complexes reveal an antiferromagnetic coupling between the copper(II) ions. The strength of antiferromagnetic coupling was observed to depend on the energy of the HOMO of the bridging quinone ligands, with exchange coupling constants J in the range between -23.2 and -0.6 cm(-1) and the strength of antiferromagnetic coupling of 4 > 3 > 2 > 1. Broken-symmetry density functional theory calculations (DFT) revealed that the orientation of magnetic orbitals in 1 and 2 is different than that in 3 and 4, and this results in two different exchange pathways. These results demonstrate how bridge-mediated spin-spin coupling in quinone-bridged metal complexes can be strongly tuned by a rational design of the bridging ligand employing the [O] for [NR] isoelectronic analogy. PMID:24010410

Schweinfurth, David; Khusniyarov, Marat M; Bubrin, Denis; Hohloch, Stephan; Su, Cheng-Yong; Sarkar, Biprajit

2013-09-06

181

Dissection of a QTL reveals an adaptive, interacting gene complex associated with transgressive variation for flowering time in rice.  

PubMed

A days to heading QTL (dth1.1) located on the short arm of rice chromosome 1 was sub-divided into eight sub-introgression lines (SILs) to analyze the genetic basis of transgressive variation for flowering time. Each SIL contained one or more introgression(s) from O. rufipogon in the genetic background of the elite Oryza sativa cultivar, Jefferson. Each introgression was defined at high resolution using molecular markers and those in the dth1.1 region were associated with the presence of one or more flowering time genes (GI, SOC1, FT-L8, EMF1, and PNZIP). SILs and controls were evaluated for flowering time under both short- and long-day growing conditions. Under short-day lengths, lines with introgressions carrying combinations of linked flowering time genes (GI/SOC1, SOC1/FT-L8, GI/SOC1/FT-L8 and EMF1/PNZIP) from the late parent, O. rufipogon, flowered earlier than the recurrent parent, Jefferson, while recombinant lines carrying smaller introgressions marked by the presence of GI, SOC1, EMF1 or PNZIP alone no longer flowered early. Under long-day length, lines carrying SOC1/FT-L8, SOC1 or PNZIP flowered early, while those carrying GI or EMF1 delayed flowering. Across all experiments and in the field, only SIL_SOC1/FT-L8 was consistently early. A preliminary yield evaluation indicated that the transgressive early flowering observed in several of the SILs was also associated with a measurable and positive effect on yield. These SILs represent a new source of variation that can be used in breeding programs to manipulate flowering time in rice cultivars without the reduction in yield that is often associated with early maturing phenotypes. PMID:19949767

Maas, Luis F; McClung, Anna; McCouch, Susan

2009-12-01

182

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

NASA Astrophysics Data System (ADS)

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 log10 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.

Sommers, Christopher H.; Boyd, Glenn

2006-07-01

183

Construction of accurate Kohn-Sham potentials for the lowest states of the helium atom: Accurate test of the ionization-potential theorem  

NASA Astrophysics Data System (ADS)

Accurate local Kohn-Sham potentials have been constructed for the ground 1s21S state and, in particular, for the lowest triplet 1s2s3S state of the helium atom, using electron densities from many-body calculations and the procedure of van Leeuwen and Baerends. The resulting Kohn-Sham orbitals reproduce the many-body densities very accurately; furthermore, we have demonstrated that the negative of the energy eigenvalue of the outermost electron orbital agrees with the corresponding ionization energy with extreme accuracy. The procedure is also applied to the Hartree-Fock density of the 1s2s3S state, and the Kohn-Sham eigenvalue of the 2s orbital is found to agree very well with the corresponding Hartree-Fock eigenvalue, which is the negative of the ionization energy in this model due to Koopmans' theorem. The results clearly demonstrate that there is no conflict between the locality of the Kohn-Sham potential and the exclusion principle, as claimed by Nesbet. Content:text/plain; charset="UTF-8"

Lindgren, I.; Salomonson, S.; Möller, F.

184

Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes  

PubMed Central

Summary Although the major food-borne pathogen Campylobacter jejuni has been isolated from diverse animal, human and environmental sources, our knowledge of genomic diversity in C. jejuni is based exclusively on human or human food-chain-associated isolates. Studies employing multilocus sequence typing have indicated that some clonal complexes are more commonly associated with particular sources. Using comparative genomic hybridization on a collection of 80 isolates representing diverse sources and clonal complexes, we identified a separate clade comprising a group of water/wildlife isolates of C. jejuni with multilocus sequence types uncharacteristic of human food-chain-associated isolates. By genome sequencing one representative of this diverse group (C. jejuni 1336), and a representative of the bank-vole niche specialist ST-3704 (C. jejuni 414), we identified deletions of genomic regions normally carried by human food-chain-associated C. jejuni. Several of the deleted regions included genes implicated in chicken colonization or in virulence. Novel genomic insertions contributing to the accessory genomes of strains 1336 and 414 were identified. Comparative analysis using PCR assays indicated that novel regions were common but not ubiquitous among the water/wildlife group of isolates, indicating further genomic diversity among this group, whereas all ST-3704 isolates carried the same novel accessory regions. While strain 1336 was able to colonize chicks, strain 414 was not, suggesting that regions specifically absent from the genome of strain 414 may play an important role in this common route of Campylobacter infection of humans. We suggest that the genomic divergence observed constitutes evidence of adaptation leading to niche specialization.

Hepworth, Philip J; Ashelford, Kevin E; Hinds, Jason; Gould, Katherine A; Witney, Adam A; Williams, Nicola J; Leatherbarrow, Howard; French, Nigel P; Birtles, Richard J; Mendonca, Chriselle; Dorrell, Nick; Wren, Brendan W; Wigley, Paul; Hall, Neil; Winstanley, Craig

2011-01-01

185

Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes.  

PubMed

Although the major food-borne pathogen Campylobacter jejuni has been isolated from diverse animal, human and environmental sources, our knowledge of genomic diversity in C. jejuni is based exclusively on human or human food-chain-associated isolates. Studies employing multilocus sequence typing have indicated that some clonal complexes are more commonly associated with particular sources. Using comparative genomic hybridization on a collection of 80 isolates representing diverse sources and clonal complexes, we identified a separate clade comprising a group of water/wildlife isolates of C. jejuni with multilocus sequence types uncharacteristic of human food-chain-associated isolates. By genome sequencing one representative of this diverse group (C. jejuni 1336), and a representative of the bank-vole niche specialist ST-3704 (C. jejuni 414), we identified deletions of genomic regions normally carried by human food-chain-associated C. jejuni. Several of the deleted regions included genes implicated in chicken colonization or in virulence. Novel genomic insertions contributing to the accessory genomes of strains 1336 and 414 were identified. Comparative analysis using PCR assays indicated that novel regions were common but not ubiquitous among the water/wildlife group of isolates, indicating further genomic diversity among this group, whereas all ST-3704 isolates carried the same novel accessory regions. While strain 1336 was able to colonize chicks, strain 414 was not, suggesting that regions specifically absent from the genome of strain 414 may play an important role in this common route of Campylobacter infection of humans. We suggest that the genomic divergence observed constitutes evidence of adaptation leading to niche specialization. PMID:21418497

Hepworth, Philip J; Ashelford, Kevin E; Hinds, Jason; Gould, Katherine A; Witney, Adam A; Williams, Nicola J; Leatherbarrow, Howard; French, Nigel P; Birtles, Richard J; Mendonca, Chriselle; Dorrell, Nick; Wren, Brendan W; Wigley, Paul; Hall, Neil; Winstanley, Craig

2011-03-21

186

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

NASA Astrophysics Data System (ADS)

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

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

187

Novel mutations in 21 patients with tuberous sclerosis complex and variation of tandem splice-acceptor sites in TSC1 exon 14.  

PubMed

Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterized by epilepsy, mental retardation, skin lesions, and tumors in various organs. However, TSC is sometimes difficult to diagnose because of its broad phenotypic spectrum. In such cases, it is essential to find a mutation in the disease-causing genes, TSC1 and TSC2. In this study, we analyzed 21 TSC patients from 16 families using a combination method of DHPLC and nucleotide sequencing. We identified 16 novel mutations in the 16 families: nine mutations in TSC1 (1 insertion, 7 deletion and 1 nonsense mutations) and seven mutations in TSC2 (2 insertion, 2 deletion, 1 missense mutations and 2 splicing abnormalities). We also tested the possibility of very short alternative splicing due to a variation of the tandem splice-acceptor sites of TSC1 exon 14 in a patient. RT-PCR and sequencing analysis indicated that no alternative splicing occurred in the patient. In conclusion, we confirmed the diagnosis of all patients using mutation analysis and clarified that variation of the tandem splice-acceptor sites in TSC1 exon 14 does not cause a splicing abnormality. PMID:18772611

Sasongko, Teguh Haryo; Wataya-Kaneda, Mari; Koterazawa, Keiko; Gunadi; Yusoff, Surini; Harahap, Indra Sari Kusuma; Lee, Myeong Jin; Matsuo, Masafumi; Nishio, Hisahide

2008-05-23

188

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

PubMed

A fully analytical method for calculating Born charges and, hence, infrared intensities of periodic systems, is formulated and implemented in the CRYSTAL program, which uses a local gaussian type basis set. Our efficient formalism combines integral gradients with first-order coupled perturbed Hartree-Fock/Kohn Sham electronic response to an electric field. It avoids numerical differentiation with respect to wave vectors, as in some Berry phase approaches, and with respect to atomic coordinates. No perturbation equations for the atomic displacements need to be solved. Several tests are carried out to verify numerical stability, consistency in one, two, and three dimensions, and applicability to large unit cells. Future extensions to piezoelectricity and Raman intensities are noted. PMID:23205987

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

2012-11-28

189

Restoration of the Derivative Discontinuity in Kohn-Sham Density Functional Theory: An Efficient Scheme for Energy Gap Correction  

NASA Astrophysics Data System (ADS)

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

Chai, Jeng-Da; Chen, Po-Ta

2013-01-01

190

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

PubMed

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

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

2012-10-03

191

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

PubMed Central

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.

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

2011-01-01

192

Pressure dissociation of integration host factor-DNA complexes reveals flexibility-dependent structural variation at the protein-DNA interface  

PubMed Central

E. coli Integration host factor (IHF) condenses the bacterial nucleoid by wrapping DNA. Previously, we showed that DNA flexibility compensates for structural characteristics of the four consensus recognition elements associated with specific binding (Aeling et al., J. Biol. Chem. 281, 39236–39248, 2006). If elements are missing, high-affinity binding occurs only if DNA deformation energy is low. In contrast, if all elements are present, net binding energy is unaffected by deformation energy. We tested two hypotheses for this observation: in complexes containing all elements, (1) stiff DNA sequences are less bent upon binding IHF than flexible ones; or (2) DNA sequences with differing flexibility have interactions with IHF that compensate for unfavorable deformation energy. Time-resolved Förster resonance energy transfer (FRET) shows that global topologies are indistinguishable for three complexes with oligonucleotides of different flexibility. However, pressure perturbation shows that the volume change upon binding is smaller with increasing flexibility. We interpret these results in the context of Record and coworker's model for IHF binding (J. Mol. Biol. 310, 379–401, 2001). We propose that the volume changes reflect differences in hydration that arise from structural variation at IHF–DNA interfaces while the resulting energetic compensation maintains the same net binding energy.

Senear, Donald F.; Tretyachenko-Ladokhina, Vira; Opel, Michael L.; Aeling, Kimberly A.; Wesley Hatfield, G.; Franklin, Laurie M.; Darlington, Reuben C.

2007-01-01

193

Variations in transitional magnetic field geometries during the Matayuma-Brunhes reversal: Data from the Tatara-San Pedro volcanic complex, Chilean Andes  

NASA Astrophysics Data System (ADS)

Two facets of paleomagnetism are discussed as part of this study; the use of paleomagnetic records to improve our understanding of magnetic field reversals, and the use of paleosecular variation in volcanology studies. A detailed volcanic record of the Matuyama-Brunhes (MBR) reversal (780 ka) suggests that the reversing magnetic field remains dipolar throughout the transition. This record, taken from the Tatara-San Pedro Volcanic Complex located in the Andean region (36sp°S, 71sp°W) of central Chile, is recorded in 29 andesite flows. The record is exceptionally well constrained temporally and geochemically as well as paleomagnetically. The lavas record a quick change from reversed polarity to a period of transitional stability, with virtual geomagnetic poles (VGP) forming a cluster centered in Australia, followed by a quick swing to normal polarity. The Chilean data demonstrate that the dipole assumes an intermediate subequatorial position before completing the transition. VGP data from the four other available MBR lava records are largely coincident with the Chilean grouping and further strengthen the suggestion of a dipolar Matuyama-Brunhes reversal field geometry. The integration of paleomagnetism with geochemistry offers volcanologists an efficient and independent correlation tool for studying geochemical trends and growth morphology in volcanic centers. The Tatara-San Pedro Volcanic Complex, a Quaternary arc volcanic center in the Chilean Andes (Singer et al., in press), serves as an excellent model of complex stratocone evolution and lends itself well to a demonstration of this technique. Three fundamental relationships between paleomagnetic and geochemical data are demonstrated within the TSPVC: an absolute correlation, a paleomagnetic dependent correlation, and a geochemical dependent correlation. These correlations provide a degree of temporal insight into the rates of magma productivity that would be difficult to gain through conventional radiometric dating techniques.

Pickens, James Cecil

194

Variations at the semiconserved glycine in the IQ domain consensus sequence have a major impact on Ca2+-dependent switching in calmodulin-IQ domain complexes.  

PubMed

We have replaced the semiconserved Gly in the IQ domain consensus sequence with Ala, Arg, or Met in a reference sequence and determined how this affects its complexes with calmodulin. The K(d) for the Ca(2+)-free reference complex is 2.4 +/- 0.3 microM. The Ala and Arg replacements increase this to 5.4 +/- 0.4 and 6.2 +/- 0.5 microM, while the Met increases it to 26.4 +/- 2.5 microM. When Ca(2+) is bound to both calmodulin lobes, the K(d) for the reference complex is not significantly affected, but the K(d) for the Ala variant decreases to 0.9 +/- 0.04 microM, and the values for the Arg and Met variants decrease to 0.4 +/- 0.03 microM. Using mutant calmodulins, we defined the effect of Ca(2+) binding to each lobe, with the C-terminal preceding the N-terminal (C-->N) or vice versa (N-->C). In the C-->N order the first step increases the reference K(d) approximately 5-fold, while it decreases the values for the variants approximately 2- to approximately 10-fold. The second step decreases the K(d) values for the all of the complexes approximately 5-fold, suggesting that the N-terminal lobe does not interact with the semiconserved position after the first step. In the N-->C order the first step increases the K(d) values for the reference complex and Met and Ala variants approximately 15- to approximately 200-fold but does not affect the value for the Arg variant. The second step decreases the K(d) values for the reference and Arg variant approximately 10- and approximately 15-fold and the Ala and Met variants approximately 2000-fold. Thus, both steps in the N-->C order are sensitive to variations at the semiconserved position, while only the first is in the C-->N order. Due to energy coupling, this order is followed under equilibrium conditions. PMID:19954189

Black, D J; Persechini, Anthony

2010-01-12

195

Variational definitions of orbital energies  

NASA Astrophysics Data System (ADS)

A formulation of Koopmans' theorem is derived for high-spin half-filled open shells in the restricted openshell Hartree-Fock (ROHF) method based on a variational treatment of both the initial (non-ionized) open-shell system X with spin S and the corresponding ions having a hole or an extra electron in the closed, open and virtual shells respectively. The six processes for forming ions with spin S+/-1/2 require two different definitions for canonical orbitals within each shell. These processes may be treated equivalently within a restricted CI using arbitrary non-canonical linear transforms of the ROHF orbitals optimal for the initial system. Canonical UHF orbitals also obey a variational principle for the ion energies, but they provide less appropriate estimates for actual states of the ion. Canonical spin-unrestricted Kohn-Sham orbitals with common exchange-correlation functionals suffer from all of the UHF problems and from selfinteraction error. They generally are not useful estimates for ion energies.

Davidson, Ernest R.

2012-12-01

196

Hybrid ab initio Kohn-Sham density functional theory\\/frozen-density orbital-free density functional theory simulation method suitable for biological systems  

Microsoft Academic Search

A hybrid computational method intended for simulations of biomolecules in solution is described. The ab initio Kohn-Sham (KS) density functional theory (DFT) method is used to describe the chemically active part of the system and its first solvation shells, while a frozen-density orbital-free (FDOF) DFT method is used to treat the rest of the solvent. The molecules in the FDOF

Miroslav Hodak; Wenchang Lu; J. Bernholc

2008-01-01

197

Kohn-Sham density-functional study of the adsorption of acetylene and vinylidene on iron clusters, Fen\\/Fen+ (n=1-4)  

Microsoft Academic Search

This is the first paper in a series dealing with the formation of benzene from acetylene on iron clusters, Fen\\/Fen+ (n=1-4). In the present study, we have performed all-electron Kohn-Sham density-functional theory calculations on the adsorption of acetylene and vinylidene on small iron clusters. Many starting structures were fully optimized without geometric and symmetric constraints for at least three different

Steeve Chrétien; Dennis R. Salahub

2003-01-01

198

Kohn–Sham density-functional study of the adsorption of acetylene and vinylidene on iron clusters, Fen\\/Fen+(n=1–4)  

Microsoft Academic Search

This is the first paper in a series dealing with the formation of benzene from acetylene on iron clusters, Fen\\/Fen+(n=1–4). In the present study, we have performed all-electron Kohn–Sham density-functional theory calculations on the adsorption of acetylene and vinylidene on small iron clusters. Many starting structures were fully optimized without geometric and symmetric constraints for at least three different spin

Steeve Chre´tien; Dennis R. Salahub

2003-01-01

199

Variable path length and counter-flow continuous variation methods for the study of the formation of high-affinity complexes by absorbance spectroscopy. An application to the studies of substrate binding in cytochrome P450  

Microsoft Academic Search

Studies of the equilibrium of protein–ligand interactions and determination of the stoichiometry of protein complexes constitute an important element of routine biochemical practice. In this paper we describe two innovative modifications of Job's method of continuous variation, which allow us to analyze tight interactions and determine stoichiometry in multi-site binding systems, including cases where the absorbance of the ligand overlaps

Dmitri R. Davydov; Harshica Fernando; James R. Halpert

2006-01-01

200

Estimation of formamide harmonic and anharmonic modes in the Kohn-Sham limit using the polarization consistent basis sets.  

PubMed

Formamide harmonic and anharmonic frequencies of fundamental vibrations in the gas phase and in several solvents were successfully estimated in the B3LYP Kohn-Sham complete basis set limit (KS CBS). CBS results were obtained by extrapolating a power function (two-parameter formula) to the results calculated with polarization-consistent basis sets. Anharmonic corrections using the second order perturbation treatment (PT2) and hybrid B3LYP functional combined with polarization consistent pc-n (n=0, 1, 2, 3, 4) and several Pople's basis sets were analyzed for all fundamental formamide vibrational modes in the gas phase and solution. Solvent effects were modeled within a PCM method. The anharmonic frequency of diagnostic amide vibration C=O in the gas phase and the CCl(4) solution calculated with the VPT2 method was significantly closer to experimental data than the corresponding harmonic frequency. Both harmonic and anharmonic frequencies of C=O stretching mode decreased linearly with solvent polarity, expressed by relative environment permittivity (?) ratio (?-1)/(2?+1). However, an unphysical behavior of solvent dependence of some low frequency anharmonic amide modes of formamide (e.g., CN stretch, NH(2) scissoring, and NH(2) in plane bend) was observed, probably due to the presence of severe anharmonicity and Fermi resonance. PMID:21267754

Buczek, Aneta; Kupka, Teobald; Broda, Ma?gorzata A

2011-01-26

201

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

SciTech Connect

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.

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

2011-06-15

202

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

NASA Astrophysics Data System (ADS)

Three approximate exchange potentials of high accuracy vxY(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 vxC happens to be the same as that derived by Harbola and Sahni, and vxA as that derived by Gritsenko and Baerends, and Della Sala and Görling. 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.

Holas, A.; Cinal, M.

2005-09-01

203

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

PubMed

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

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

204

Genetic variation and evolutionary history of holly oak: a circum-Mediterranean species-complex [ Quercus coccifera L.\\/ Q . calliprinos (Webb) Holmboe, Fagaceae  

Microsoft Academic Search

Holly oak is the only evergreen oak possessing a circum-Mediterranean range; it has two predominant morphological forms, calliprinos\\u000a and coccifera, described in the eastern and western Mediterranean Basin respectively. The concordance of allozyme and morphotype\\u000a variation was analysed in the whole holly oak range, and the most plausible historical events responsible for the current\\u000a geographic pattern of genetic variation were

Lamjed Toumi; Roselyne Lumaret

2010-01-01

205

Complex genetics controls natural variation among seed quality phenotypes in a recombinant inbred population of an interspecific cross between Solanum lycopersicum × Solanum pimpinellifolium  

Microsoft Academic Search

Seed quality in tomato is associated with many complex physiological and genetic traits. While plant processes are frequently controlled by the action of small- to large-effect genes that follow classic Mendelian inheritance, our study suggests that seed quality is primarily quantitative and genetically complex. Using a recombinant inbred line population of Solanum lycopersicum × Solanum pimpinellifolium, we identified quantitative trait

R. H. Kazmi; N. Khan; L. A. J. Willems; Heusden van A. W; J. W. Ligterink; H. W. M. Hilhorst

2012-01-01

206

Direct Variation  

NSDL National Science Digital Library

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

2012-01-01

207

Color variations of cotton dyed with reactive Cu-complex azo dyes by histidine, and testing methods for color fastness to perspiration  

Microsoft Academic Search

The adsorption of histidine (His) on cellophane films dyed with five reactive Cu-complex azo dyes, CI Reactive Red 23, CI Reactive Violet 5, and 1:1 and 1:2 Cu-complex azo dyes, from aqueous His was estimated as a function of immersing time. During the incomplete abstraction of copper on immersion, the dyed films adsorbed His to a larger extent than the

Yasuyo Okada; Tomoko Nagashima; Hiromi Iizuka; Masako Asano; Zenzo Morita

1997-01-01

208

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

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.

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

2010-01-01

209

Variations in Intensity and Frequency Moderate the Facilitative Effects of a Complex Rhythm Stimulus on Long-Term Memory Consolidation in the Day-Old Chick (Gallus gallus )  

Microsoft Academic Search

The authors have previously shown that exposure to 1 min of a complex, but not an isochronous, rhythm stimulus facilitates long-term memory consolidation in chicks (Gallus gallus) trained on a passive- avoidance task (S. R. Toukhsati & N. S. Rickard, 2001). The acoustic parameters of this stimulus were explored further in the current study. Retention was found to be best

S. R. Toukhsati; N. S. Rickard

2004-01-01

210

Novel Mutations in 21 Patients with Tuberous Sclerosis Complex and Variation of Tandem Splice-acceptor Sites in TSC1 exon 14  

Microsoft Academic Search

Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterized by epilepsy, mental retardation, skin lesions, and tumors in various organs. However, TSC is sometimes difficult to diagnose because of its broad phenotypic spectrum. In such cases, it is essential to find a mutation in the disease-causing genes, TSC1 and TSC2. In this study, we analyzed 21 TSC patients from

TEGUH HARYO SASONGKO; MARI WATAYA-KANEDA; KEIKO KOTERAZAWA; SURINI YUSOFF; INDRA SARI; KUSUMA HARAHAP; MYEONG JIN LEE; MASAFUMI MATSUO; HISAHIDE NISHIO

2008-01-01

211

An assessment of haplotype variation in ribosomal and mitochondrial DNA fragments suggests incomplete lineage sorting in some species of the Paramecium aurelia complex (Ciliophora, Protozoa).  

PubMed

The Paramecium aurelia complex (Ciliophora, Protozoa) Sonneborn (1975) is composed of 15 sibling species, which are morphologically indistinguishable but sexually isolated. Therefore, the P. aurelia complex seems to be an ideal model for testing hypotheses about recent speciation events. Here we present two-locus (ITS1-5.8S-ITS2-5'LSU rDNA and COI mtDNA) analyses using over 120 strains collected from around the world and representing all currently known species of the complex. According to our findings, the studied species show different levels of haplotype variability. Some of them appear on the obtained trees as polyphyletic (e.g., P. dodecaurelia), while others as monophyletic (e.g., P. quadecaurelia), clusters. The revealed discrepancies, which are manifested by different mating behavior and haplotypes not characteristic of particular species, may be explained by incomplete lineage sorting. Furthermore, the phenomena of hybridization and introgression are considered as another explanation for our results. Despite the above discrepancies, "polyphyletic taxa" should be considered true biological species based on the results of genetic crosses. Using a combination of both strain crosses (the biological species concept) and molecular methods (the phylogenetic species concept) seems to be the appropriate way of delimiting species in closely related eukaryotic microorganisms such as the P. aurelia complex. PMID:23396203

Tarcz, Sebastian; Przybo?, Ewa; Surmacz, Marta

2013-02-08

212

Analytical Asymptotic Structure of the Pauli, Coulomb, and Correlation-Kinetic Components of the Kohn- Sham Exchange - Correlation Potential in Atoms  

NASA Astrophysics Data System (ADS)

We derive the analytical asymptotic structure in atoms of the Kohn-Sham (KS) exchange-correlation potential via its quantum-mechanical interpretation (V. Sahni, Phys. Rev. A55, 1846 (1997)). In this manner, the components of this structure due to the separate correlations arising from the Pauli exclusion principle, Coulomb repulsion, and correlation-kinetic effects are explicitly determined. The calculations are performed in terms of quasi-particle amplitudes (C.-O. Almbladh and U. von Barth, Phys. Rev. B31, 3231 (1985)), which are the interacting system counterparts of the KS orbitals. The results derived are for the case in which the N-electron system may be orbitally degenerate but where the (N-1)-electron ion is spherically symmetric.

Sahni, V.; Qian, Z.

1998-03-01

213

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

Microsoft Academic Search

A phenylthiophenyl-bearing Ru(II) complex of [Ru(bpy)2(Hbptip)](PF6)2 {bpy?=?2,2?-bipyridine, Hbptip?=?2-(4-phenylthiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline} was synthesized and characterized by elemental analysis, H NMR spectroscopy, and electrospray ionization mass spectrometry. The ground- and excited-state acid–base properties of the complex were studied by UV–visible absorption and photoluminescence spectrophotometric pH titrations and the negative logarithm values of the ground-state acid ionization constants were derived to be pKa1?=?1.31?±?0.09 and pKa2?=?5.71?±?0.11

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

2012-01-01

214

Genetic and morphological variation in the Bulbophyllum exaltatum (Orchidaceae) complex occurring in the Brazilian “campos rupestres”: implications for taxonomy and biogeography  

Microsoft Academic Search

The Bulbophyllum exaltatum complex comprises 15 described taxa, and present a number of unresolved taxonomic questions, especially among populations\\u000a found in the Brazilian campo rupestre vegetation. Allozymes were examined in 33 populations to determine the degree of genetic variability between them and their\\u000a degree of differentiation to better define the taxa of this group. Additionally morphometric analyses were also performed

P. Luz Ribeiro; E. Leite Borba; E. de Camargo Smidt; S. Mota Lambert; A. Selbach Schnadelbach; C. van den Berg

2008-01-01

215

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

PubMed

A phenylthiophenyl-bearing Ru(II) complex of [Ru(bpy)?(Hbptip)](PF?)? {bpy?=?2,2'-bipyridine, Hbptip?=?2-(4-phenylthiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline} was synthesized and characterized by elemental analysis, ¹H NMR spectroscopy, and electrospray ionization mass spectrometry. The ground- and excited-state acid-base properties of the complex were studied by UV-visible absorption and photoluminescence spectrophotometric pH titrations and the negative logarithm values of the ground-state acid ionization constants were derived to be pK(a1)?=?1.31 ±?0.09 and pK(a2)?=?5.71 ± 0.11 with the pK(a2) associated deprotonation/protonation process occurring over 3 pK(a) units more acidic than thiophenyl-free parent complex of [Ru(bpy)?(Hpip)]²? {Hpip?=?2-phenyl-1H-imidazo[4,5-f][1,10]phenanthroline}. The calf thymus DNA-binding properties of [Ru(bpy)?(Hbptip)]²? in Tris-HCl buffer (pH 7.1 and 50?mM NaCl) were investigated by DNA viscosities and density functional theoretical calculations as well as UV-visible and emission spectroscopy techniques of UV-visible and luminescence titrations, steady-state emission quenching by [Fe(CN)?]??, DNA competitive binding with ethidium bromide, DNA melting experiments, and reverse salt effects. The complex was evidenced to bind to the DNA intercalatively with binding affinity being greater than those for previously reported analogs of [Ru(bpy)?(Hip)]²?, [Ru(bpy)?(Htip)]²?, and [Ru(bpy)?(Haptip)]²? {Hip?=?1H-imidazo[4,5-f][1,10]phenanthroline, Htip?=?2-thiophenimidazo[4,5-f][1,10]phenanthroline, Haptip?=?2-(5-phenylthiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline}. PMID:22831393

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

2012-07-25

216

Karyological and genetic variation in Middle Eastern lacertid lizards, Lacerta laevis and the Lacerta kulzeri complex: a case of chromosomal allopatric speciation  

Microsoft Academic Search

Karyological (standard and C, Ag-NOR and Alu-I banding methods) and mtDNA analyses (cytochrome b and 12S rRNA) were conducted on specimens from eight allopatric populations of the Lacerta kulzeri complex. Parallel analyses were performed for comparison on Lacerta laevis specimens. Karyological and molecular studies support the morphological and ethological evidence indicating the specific separation between Lacerta laevis and Lacerta kulzeri

Herman A. J. in den Bosch; Gaetano Odierna; Gennaro Aprea; Marco Barucca; Adriana Canapa; Teresa Capriglione; Ettore Olmo

2003-01-01

217

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

NASA Astrophysics Data System (ADS)

Using 1,9-salicylamide bissubstituted oxadecane ligand, 1,9-bis [2-(2?-picolylaminoformyl)-1,4,7,9-tetraoxadecane (L), two novel lanthanide complexes have been prepared and well characterized by means of elemental analysis, IR spectroscopy, UV-vis spectroscopy, TGA analysis and single-crystal X-ray diffraction. {[PrL(NO3)3(H2O)2]·CH3OH}n is a 1D zigzag polymer with three-dimensional supramolecular structure formed by hydrogen bonds, while [EuL(NO3)3(H2O)]n is a linear coordination polymer and present an interesting supramolecular double chain, which are very different from the structure of terbium complex reported before. The result reported herein demonstrated that steric crowding associated with the decreasing lanthanide ion radius causes changes of the conformation of the ligand as well as structures. Luminescence studies for the Eu(III) complexes demonstrated that the salicylamide ligand also exhibits a good antennae effect for the Eu(III) ion due to efficient intersystem crossing and ligand-to-metal energy transfer and the Eu(III) ion is well shielded from the surrounding environment.

Song, Xue-Qin; Zang, Zhi-Peng; Liu, Wei-Sheng; Zhang, Yu-Jie

2009-04-01

218

Pharmacokinetic variation  

Microsoft Academic Search

Pharmacokinetics is the study of how a drug is handled within the body. Variations in drug absorption, distribution, metabolism or excretion will alter drug concentrations at its target site. Appreciation of the causes of pharmacokinetic variation will ensure avoidance of sub-therapeutic drug regimes and unnecessary side effects through over-dosage. The processes of absorption, distribution, metabolism and excretion can be affected

Marc Chikhani; Jonathan G. Hardman

2011-01-01

219

Small-angle scattering, contrast variation and the study of complex composite materials: A study of the structure of carbon black  

SciTech Connect

Detailed studies are presented on the structure and aggregation of an experimental high surface area carbon black (HSA) using small-angle neutron scattering and the method of contrast variation. We find that the approximately 27 mn HSA particle form small, linear aggregates of average aggregation number 5 when suspended in cyclohexane. There is considerable density fluctuation in the interior of these particles, with the denser regions being toward the outer part of the spherically-averaged structure. This information would not have been obtained from studies of carbon black without solvent. The results will be applied to similar scattering studies on solvent-swollen bound rubber gels made from HSA-polyisoprene. These result show, however, that the strong internal fluctuations of the carbon black will limit the information that can be obtained on the structure and conformation of the elastomer in the gel. There are additional limitation from compositional heterogeneity of the sample.

Hjelm, R.P. Jr.; Seeger, P.A. (Los Alamos National Lab., NM (United States)); Wampler, W.A. (Sid Richardson Carbon Co., Fort Worth, TX (United States))

1993-01-01

220

Small-angle scattering, contrast variation and the study of complex composite materials: A study of the structure of carbon black  

SciTech Connect

Detailed studies are presented on the structure and aggregation of an experimental high surface area carbon black (HSA) using small-angle neutron scattering and the method of contrast variation. We find that the approximately 27 mn HSA particle form small, linear aggregates of average aggregation number 5 when suspended in cyclohexane. There is considerable density fluctuation in the interior of these particles, with the denser regions being toward the outer part of the spherically-averaged structure. This information would not have been obtained from studies of carbon black without solvent. The results will be applied to similar scattering studies on solvent-swollen bound rubber gels made from HSA-polyisoprene. These result show, however, that the strong internal fluctuations of the carbon black will limit the information that can be obtained on the structure and conformation of the elastomer in the gel. There are additional limitation from compositional heterogeneity of the sample.

Hjelm, R.P. Jr.; Seeger, P.A. [Los Alamos National Lab., NM (United States); Wampler, W.A. [Sid Richardson Carbon Co., Fort Worth, TX (United States)

1993-05-01

221

Density functional theory with an approximate kinetic energy functional applied to study structure and stability of weak van der Waals complexes  

Microsoft Academic Search

In view of further application to the study of molecular and atomic sticking on dust particles, we investigated the capability of the ``freeze-and-thaw'' cycle of the Kohn-Sham equations with constrained electron density (KSCED) to describe potential energy surfaces of weak van der Waals complexes. We report the results obtained for C6H6...X (X=O2, N2, and CO) as test cases. In the

T. A. Wesolowski; Y. Ellinger; J. Weber

1998-01-01

222

Complex genetics controls natural variation among seed quality phenotypes in a recombinant inbred population of an interspecific cross between Solanum lycopersicum × Solanum pimpinellifolium.  

PubMed

Seed quality in tomato is associated with many complex physiological and genetic traits. While plant processes are frequently controlled by the action of small- to large-effect genes that follow classic Mendelian inheritance, our study suggests that seed quality is primarily quantitative and genetically complex. Using a recombinant inbred line population of Solanum lycopersicum?×?Solanum pimpinellifolium, we identified quantitative trait loci (QTLs) influencing seed quality phenotypes under non-stress, as well as salt, osmotic, cold, high-temperature and oxidative stress conditions. In total, 42 seed quality traits were analysed and 120 QTLs were identified for germination traits under different conditions. Significant phenotypic correlations were observed between germination traits under optimal conditions, as well as under different stress conditions. In conclusion, one or more QTLs were identified for each trait with some of these QTLs co-locating. Co-location of QTLs for different traits can be an indication that a locus has pleiotropic effects on multiple traits due to a common mechanistic basis. However, several QTLs also dissected seed quality in its separate components, suggesting different physiological mechanisms and signalling pathways for different seed quality attributes. PMID:22074055

Kazmi, Rashid H; Khan, Noorullah; Willems, Leo A J; VAN Heusden, Adriaan W; Ligterink, Wilco; Hilhorst, Henk W M

2011-12-08

223

Variation of flux control coefficient of cytochrome c oxidase and of the other respiratory chain complexes at different values of protonmotive force occurs by a threshold mechanism.  

PubMed

The metabolic control analysis was applied to digitonin-permeabilized HepG2 cell line to assess the flux control exerted by cytochrome c oxidase on the mitochondrial respiration. Experimental conditions eliciting different energy/respiratory states in mitochondria were settled. The results obtained show that the mitochondrial electrochemical potential accompanies a depressing effect on the control coefficient exhibited by the cytochrome c oxidase. Both the components of the protonmotive force, i.e. the voltage (??(m)) and the proton (?pH(m)) gradient, displayed a similar effect. Quantitative estimation of the ??(m) unveiled that the voltage-dependent effect on the control coefficient of cytochrome c oxidase takes place sharply in a narrow range of membrane potential from 170-180 to 200-210mV consistent with the physiologic transition from state 3 to state 4 of respiration. Extension of the metabolic flux control analysis to the NADH dehydrogenase and bc(1) complexes of the mitochondrial respiratory chain resulted in a similar effect. A mechanistic model is put forward whereby the respiratory chain complexes are proposed to exist in a voltage-mediated threshold-controlled dynamic equilibrium between supercomplexed and isolated states. PMID:21565165

Quarato, Giovanni; Piccoli, Claudia; Scrima, Rosella; Capitanio, Nazzareno

2011-05-01

224

Regulation of genes encoding subunits of the trehalose synthase complex in Saccharomyces cerevisiae: novel variations of STRE-mediated transcription control?  

PubMed

Saccharomyces cerevisiae cells show under suboptimal growth conditions a complex response that leads to the acquisition of tolerance to different types of environmental stress. This response is characterised by enhanced expression of a number of genes which contain so-called stress-responsive elements (STREs) in their promoters. In addition, the cells accumulate under suboptimal conditions the putative stress protectant trehalose. In this work, we have examined the expression of four genes encoding subunits of the trehalose synthase complex, GGS1/TPS1, TPS2, TPS3 and TSL1. We show that expression of these genes is coregulated under stress conditions. Like for many other genes containing STREs, expression of the trehalose synthase genes is also induced by heat and osmotic stress and by nutrient starvation, and negatively regulated by the Ras-cAMP pathway. However, during fermentative growth only TSL1 shows an expression pattern like that of the STRE-controlled genes CTT1 and SSA3, while expression of the three other trehalose synthase genes is only transiently down-regulated. This difference in expression might be related to the known requirement of trehalose biosynthesis for the control of yeast glycolysis and hence for fermentative growth. We conclude that the mere presence in the promoter of (an) active STRE(s) does not necessarily imply complete coregulation of expression. Additional mechanisms appear to fine tune the activity of STREs in order to adapt the expression of the downstream genes to specific requirements. PMID:8879249

Winderickx, J; de Winde, J H; Crauwels, M; Hino, A; Hohmann, S; Van Dijck, P; Thevelein, J M

1996-09-25

225

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

NASA Astrophysics Data System (ADS)

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

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

2010-08-01

226

Preliminary Microwave Palaeointensity Results From the Tatara-San Pedro Volcanic Complex, Chile - Intensity Variation Through the Matuyama-Brunhes Transition?  

NASA Astrophysics Data System (ADS)

A sequence of lavas from the Tatara-San Pedro volcanic complex (Andes, Chile) recording transitional directions has been dated and palaeomagnetic directions obtained (Brown et al., in press. J. Geophys. Res.). Ar/Ar dates from this study suggest this sequence records an event preceding the main Matuyama-Brunhes transition (MBT), though some normal polarity directions are recorded from the upper part of the lava sequence. Microwave palaeointensity determinations at the Liverpool University Geomagnetism Laboratory have been made to ascertain whether these normal polarities are related to the pre-cursor event or represent the end of the main MBT. Preliminary results yielding high intensity values from the normal polarity flows (up to ten times that of the transitional field intensity) suggest that the post-reversal field is recorded in these flows.

Gratton, M. N.; Brown, L.; Shaw, J.

2004-12-01

227

New Isotopic Measurements of Carbonate Minerals from the Cascadia Accretionary Prism Confirm Indications of Past Warm Fluid Flow and Reveal Complex Spatial Variations in Fluid Isotopic Patterns  

NASA Astrophysics Data System (ADS)

The Cascadia subduction zone is a site of significant gas hydrate and carbonate formation. At ODP Sites 891 and 892, which penetrated the deformed sediment of the accretionary prism to depths of 472 and 176 m, respectively, carbonate cements and veins occur throughout the section. Previous isotopic studies of the carbonates indicate that at several horizons the ?18OVPDB values of carbonates are low (commonly < -5 ‰) and are substantially out of equilibrium with modern pore water isotopic compositions and temperature. At Site 892, ?18O values are consistent with precipitation temperatures of 100°C at a depth of 67 meters below seafloor (mbsf). A proposed explanation is that periodic upward migration of warm fluids occurred at short time scales. But the ambiguity of interpreting oxygen isotope variations in carbonates in relation to precipitation temperature or past variations in fluid oxygen isotope composition allows for the possibility of isotopically light fluids causing the low ?18O values. We used the technique of clumped isotope analysis, which relies on the correlation between the prevalence of 13C-18O-16O isotopologues (?47 measurements) in carbonate with temperature during carbonate formation, to determine temperature and oxygen isotopic composition of fluids. The samples are mainly from two horizons at Site 892 - a zone of faulting and coarse sediment at 66.7 mbsf, and the main thrust fault at 106.2 mbsf. A variety of evidence suggests these horizons are active fluid conduits. The resulting temperatures calculated using ?47 measurements of four samples from the 66.7 mbsf horizon range from 80.3°C to 103.6°C (± 3.1° to 4.6°C 1?). This range is very similar to previous estimates from conventional ?18O isotope-ratio mass-spectrometry (IRMS) measurements of 80°C to 101°C. For the main thrust horizon at 106.2 mbsf, calculated temperatures from ?47 measurements of three samples are 38.4 ± 4.4°C, 63.6 ± 4.4°C, and 70.5 ± 4.2°C. These are somewhat higher than temperatures calculated from previous IRMS analyses (24°C to 60°C). The new data presented here corroborate a model of periodic, nonsteady-state fluid migration in the Cascadia accretionary prism, perhaps related to large-magnitude earthquakes that appear to be rare along this margin. Further, ?47 measurements indicate a large range in fluid isotopic compositions during carbonate mineral formation, from ?18OVSMOW = -3.5‰ to +6.5‰. This suggests that during nonsteady-state flow events a variety of fluid reservoirs are tapped. All analyzed samples occurred at depths well below the depth of gas hydrates and thus the process of hydrate formation did not likely influence pore-fluid isotopic compositions. A more thorough understanding of the processes at Cascadia is important for understanding the deformation and seismicity along the margin, and the potential destabilizing impact on gas hydrates and sudden release of greenhouse gases into the atmosphere. Additional results from Sites 891 and 892 will be presented.

Sample, J. C.; Tripati, A. K.

2010-12-01

228

Reliable Modeling of Complex Organic/Metal Interfaces  

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

229

Presence of proNGF-sortilin signaling complex in nigral dopamine neurons and its variation in relation to aging, lactacystin and 6-OHDA insults.  

PubMed

Growing evidence has shown that proNGF-p75NTR-sortilin signaling might be a crucial factor in neurodegeneration, but it remains unclear if it may function in nigral neurons under aging and disease. The purpose of this study is to examine and quantify proNGF and sortilin expression in the substantia nigra and dynamic changes of aging in lactacystin and 6-hydroxydopamine (6-OHDA) rat models of Parkinson's disease using immunofluorescence, electronic microscopy, western blot and FLIVO staining methods. The expression of proNGF and sortilin was abundantly and selectively identified in tyrosine hydroxylase (TH)-containing dopamine neurons in the substantia nigra. These proNGF/TH, sortilin/TH-positive neurons were densely distributed in the ventral tier, while they were less distributed in the dorsal tier, where calbindin-D28K-containing neurons were numerously located. A correlated decrease of proNGF, sortilin and TH was also detected during animal aging process. While increase of proNGF, sortilin and cleaved (active) caspase-3 expression was found in the lactacystin model, dynamic proNGF and sortilin changes along with dopamine neuronal loss were demonstrated in the substantia nigra of both the lactacystin and 6-OHDA models. This study has thus revealed the presence of the proNGF-sortilin signaling complex in nigral dopamine neurons and its response to aging, lactacystin and 6-OHDA insults, suggesting that it might contribute to neuronal apoptosis or neurodegeneration during pathogenesis and disease progression of Parkinson's disease; the underlying mechanism and key signaling pathways involved warrant further investigation. PMID:23880857

Xia, Yi; Chen, Bei-Yu; Sun, Xiao-Long; Duan, Li; Gao, Guo-Dong; Wang, Jing-Jie; Yung, Ken Kam-Lin; Chen, Liang-Wei

2013-07-08

230

Molybdenum triamidoamine complexes that contain hexa-tert-butylterphenyl, hexamethylterphenyl, or p-bromohexaisopropylterphenyl substituents. An examination of some catalyst variations for the catalytic reduction of dinitrogen.  

PubMed

Three new tetramines, (ArNHCH(2)CH(2))(3)N, have been synthesized in which Ar = 3,5-(2,4,6-t-Bu(3)C(6)H(2))(2)C(6)H(3) (H(3)[HTBTN(3)N]), 3,5-(2,4,6-Me(3)C(6)H(2))(2)C(6)H(3) (H(3)[HMTN(3)N]), or 4-Br-3,5-(2,4,6-i-Pr(3)C(6)H(2))(2)C(6)H(2) (H(3)[pBrHIPTN(3)N]). The diarylated tetramine, [3,5-(2,4,6-t-Bu(3)C(6)H(2))(2)C(6)H(3)NHCH(2)CH(2)](2)NCH(2)CH(2)NH(2), has also been isolated, and the "hybrid" tetramine [3,5-(2,4,6-t-Bu(3)C(6)H(2))(2)C(6)H(3)NHCH(2)CH(2)](2)NCH(2)CH(2)NH(4-t-BuC(6)H(4)) has been prepared from it. Monochloride complexes, [(TerNCH(2)CH(2))(3)N]MoCl, have been prepared, as well as a selection of intermediates that would be expected in a catalytic dinitrogen reduction such as [(TerNCH(2)CH(2))(3)N]Mo[triple bond]N and [[(TerNCH(2)CH(2))(3)N]Mo(NH(3))][BAr'(4)] (Ter = HTBT, HMT, or pBrHIPT and Ar' = 3,5-(CF(3))(2)C(6)H(3))). Intermediates that contain the new terphenyl-substituted ligands are then evaluated for their efficiency for the catalytic reduction of dinitrogen under conditions where analogous [HIPTN(3)N]Mo species give four turnovers to ammonia under "standard" conditions with an efficiency of approximately 65%. Only [pBrHIPTN(3)N]Mo compounds are efficient catalysts for dinitrogen reduction. The reasons are explored and discussed. PMID:15137780

Ritleng, Vincent; Yandulov, Dmitry V; Weare, Walter W; Schrock, Richard R; Hock, Adam S; Davis, William M

2004-05-19

231

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

PubMed

We report the implementation of nuclear magnetic resonance (NMR) shielding tensors within the four-component relativistic Kohn-Sham density functional theory including non-collinear spin magnetization and employing London atomic orbitals to ensure gauge origin independent results, together with a new and efficient scheme for assuring correct balance between the large and small components of a molecular four-component spinor in the presence of an external magnetic field (simple magnetic balance). To test our formalism we have carried out calculations of NMR shielding tensors for the HX series (X = F, Cl, Br, I, At), the Xe atom, and the Xe dimer. The advantage of simple magnetic balance scheme combined with the use of London atomic orbitals is the fast convergence of results (when compared with restricted kinetic balance) and elimination of linear dependencies in the basis set (when compared to unrestricted kinetic balance). The effect of including spin magnetization in the description of NMR shielding tensor has been found important for hydrogen atoms in heavy HX molecules, causing an increase of isotropic values of 10%, but negligible for heavy atoms. PMID:22239770

Olejniczak, Ma?gorzata; Bast, Radovan; Saue, Trond; Pecul, Magdalena

2012-01-01

232

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

PubMed

The structural properties of several plutonium(IV) and (VI) complexes have been examined in the gaseous and aqueous phases using Kohn-Sham density functional theory calculations with scalar relativistic effective core potentials and the polarizable continuum solvation model. The aquo and nitrate complexes of PuO(2)(2+) and Pu(4+) were considered in addition to the aquo-chloro complexes of PuO(2)(2+). The nitrate and chloro- complexes formed with triphenylphosphine oxide (TPPO) and tributylphosphate (TBP) respectively were also studied. The structural parameters of the plutonyl complexes were compared to their uranyl and neptunyl analogues. The bond lengths and vibrational frequencies of the plutonyl complexes can generally be computed with sufficient accuracy with the pure PBE density functional with shorter bond lengths being predicted by the B3LYP functional. The structural parameters of the [PuO(2)Cl(2)L(2)] systems formed with TPPO and TBP as well as the aqueous [PuO(2)Cl(2)(H(2)O)(3)] complex are matched to previous experimental results. Overall, the inclusion of ligands in the equatorial region results in significant changes in the stretching frequency of the plutonyl group. The structural features of the plutonyl (VI) systems are rather similar to those of their 5f(0) uranyl and 5f(1) neptunyl counterparts. For the Pu(IV) aquo and nitrate complexes, the average of the calculated Pu-OH(2) and Pu-O(nitrate) bond lengths are generally within 0.04 Å of the reported experimental values. Overall Kohn-Sham DFT can be used successfully in predicting the structures of this diverse set of Pu(VI) and Pu(IV) complexes. PMID:22040181

Odoh, Samuel O; Schreckenbach, Georg

2011-11-11

233

Heritable Epigenetic Variation among Maize Inbreds  

Microsoft Academic Search

Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. There is the potential for pure epigenetic variation that occurs in the absence of any genetic change or for more complex situations that involve both genetic and epigenetic differences. Methylation of cytosine residues provides one mechanism for the inheritance of epigenetic information. A genome-wide profiling of

Steve R. Eichten; Ruth A. Swanson-Wagner; James C. Schnable; Amanda J. Waters; Peter J. Hermanson; Sanzhen Liu; Cheng-Ting Yeh; Yi Jia; Karla Gendler; Michael Freeling; Patrick S. Schnable; Matthew W. Vaughn; Nathan M. Springer

2011-01-01

234

Nonlinear realizations, the orbit method and Kohn?s theorem  

NASA Astrophysics Data System (ADS)

The orbit method is used to describe the centre-of-mass motion of the system of particles with fixed charge-to-mass ratio moving in homogeneous magnetic field and confined by harmonic potential. The nonlinear action of symmetry group on phase space is identified and compared with the one obtained with the help of the Eisenhart-Duval lift.

Andrzejewski, K.; Gonera, J.; Kosi?ski, P.

2012-05-01

235

Kohn's theorem and Galilean symmetry  

NASA Astrophysics Data System (ADS)

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, e/m=? 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".

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

2011-08-01

236

BUILDING A SCIENCE OF COMPLEXITY  

Microsoft Academic Search

It is argued that in order to solve complex problems we need a new approach, which is neither reductionistic nor holistic, but based on the entanglement of distinction and connection, of disorder and order, thus defining a science of complexity . A model of complex evolution is proposed, based on distributed variation through recombination and mutation, and selective retention of

Francis HEYLIGHEN

237

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

Microsoft Academic Search

The diploid–polyploid Squalius alburnoides complex resulted from interspecific hybridization. The chromosomal mapping of 28S and 5S ribosomal genes and of (TTAGGG)n telomeric repeats was performed on specimens from the complex and from the sympatric bisexual species S. pyrenaicus (the complex maternal ancestor) as part of an investigation of the evolutionary relationships between genomic constitutions\\u000a and the consequences of the ongoing

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

2006-01-01

238

Patterned variation in prehistoric chiefdoms  

PubMed Central

Comparative study of early complex societies (chiefdoms) conjures visions of a cultural evolutionary emphasis on similarities and societal typology. Variation within the group has not been as systematically examined but offers an even more productive avenue of approach to fundamental principles of organization and change. Three widely separated trajectories of early chiefdom development are compared here: the Valley of Oaxaca (Mexico), the Alto Magdalena (Colombia), and Northeast China. Archaeological data from all three regions are analyzed with the same tools to reveal variation in human activities, relationships, and interactions as these change in the emergence of chiefly communities. Patterning in this variation suggests the operation of underlying general principles, which are offered as hypotheses that merit further investigation and evaluation in comparative study of a much larger number of cases.

Drennan, Robert D.; Peterson, Christian E.

2006-01-01

239

Heritable epigenetic variation among maize inbreds.  

PubMed

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

Eichten, Steve R; Swanson-Wagner, Ruth A; Schnable, James C; Waters, Amanda J; Hermanson, Peter J; Liu, Sanzhen; Yeh, Cheng-Ting; Jia, Yi; Gendler, Karla; Freeling, Michael; Schnable, Patrick S; Vaughn, Matthew W; Springer, Nathan M

2011-11-17

240

Koopmans-like approximation in the Kohn-Sham method and the impact of the frozen core approximation on the computation of the reactivity parameters of the density functional theory.  

PubMed

A Koopmans-like approximation is introduced in the spin-polarized version of the Kohn-Sham (KS) density functional theory to obtain a relation between KS orbital energies and vertical ionization potential and electron affinity. Expressions for reactivity indexes (like electronegativity, hardness, electrophilicity, and excitation energies) include KS frontier orbital energies and additional contributions associated with the self-interaction correction. Those reactivity parameters were computed with different exchange-correlation functionals to test the approach for a set of small molecules. The results show that the present approximation provides a better way to estimate hardness, electronegativity, and electrophilicity than just the use of frontier orbital energy values. However KS HOMO and LUMO energy gap gives a better agreement with excitation energies. PMID:16834292

Vargas, Rubicelia; Garza, Jorge; Cedillo, Andrés

2005-10-01

241

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 ni<=1 and ni>=0  

NASA Astrophysics Data System (ADS)

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 ?i? ni=N and =?ij. The occupation number optimization is carried out, allowing for fractional occupations, with the inequality constraints ni>=0 and ni<=1 with the Karush-Kuhn-Tucker method. This leads in all cases to an orbital energy spectrum with (only for NO and KS) possibly fractionally occupied degenerate levels at energy equal to the Lagrange multiplier ? for the first equality constraint, completely occupied levels at lower energies and completely unoccupied levels at higher energies. Aufbau thus follows in all cases directly from this general derivation.

Giesbertz, K. J. H.; Baerends, E. J.

2010-05-01

242

Lesson 21: Variation  

NSDL National Science Digital Library

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

2011-01-01

243

Meisenheimer Complexes (sigma Complexes).  

National Technical Information Service (NTIS)

Meisenheimer complexes are known to form in aromatic nucleophilic substitution reactions. The purpose of the present study is to collect as much information as possible in this important field of organic chemistry. The interaction of nitro aromatics with ...

A. S. Mirza

1990-01-01

244

Detection of copy number variation from next generation sequencing data with total variation penalized least square optimization  

Microsoft Academic Search

The detection of copy number variation is important to understand complex diseases such as autism, schizophrenia, cancer, etc. In this paper we propose a method to detect copy number variation from next generation sequencing data. Compared with conventional methods to detect copy number variation like array comparative genomic hybridization (aCGH), the next generation sequencing data provide higher resolution of genomic

Junbo Duan; Ji-Gang Zhang; John Lefante; Hong-Wen Deng; Yu-Ping Wang

2011-01-01

245

Association between Common Variation at the FTO Locus and Changes in Body Mass Index from Infancy to Late Childhood: The Complex Nature of Genetic Association through Growth and Development  

Microsoft Academic Search

An age-dependent association between variation at the FTO locus and BMI in children has been suggested. We meta-analyzed associations between the FTO locus (rs9939609) and BMI in samples, aged from early infancy to 13 years, from 8 cohorts of European ancestry. We found a positive association between additional minor (A) alleles and BMI from 5.5 years onwards, but an inverse

Ulla Sovio; Dennis O. Mook-Kanamori; Nicole M. Warrington; Robert Lawrence; Laurent Briollais; Colin N. A. Palmer; Joanne Cecil; Johanna K. Sandling; Ann-Christine Syvänen; Marika Kaakinen; Lawrie J. Beilin; Iona Y. Millwood; Amanda J. Bennett; Jaana Laitinen; Anneli Pouta; John Molitor; George Davey Smith; Yoav Ben-Shlomo; Vincent W. V. Jaddoe; Lyle J. Palmer; Craig E. Pennell; Tim J. Cole; Mark I. McCarthy; Marjo-Riitta Järvelin; Nicholas J. Timpson

2011-01-01

246

Synthesis and Characterization of Luminescent Cyclometalated Platinum(II) Complexes of 1,3-Bis-Hetero-Azolylbenzenes with Tunable Color for Applications in Organic Light-Emitting Devices through Extension of ? Conjugation by Variation of the Heteroatom.  

PubMed

A series of luminescent cyclometalated platinum(II) complexes of N^C^N ligands [N^C^N=2,6-bis(benzoxazol-2'-yl)benzene (bzoxb), 2,6-bis(benzothiazol-2'-yl)benzene (bzthb), and 2,6-bis(N-alkylnaphthoimidazol-2'-yl)benzene (naphimb)] has been synthesized and characterized. Two of the platinum(II) complexes have been structurally characterized by X-ray crystallography. Their electrochemical, electronic absorption, and luminescence properties have been investigated. In dichloromethane solution at room temperature, the cyclometalated N^C^N platinum(II) complexes exhibited rich luminescence with well-resolved vibronic-structured emission bands. The emission energies of the complexes are found to be closely related to the electronic properties of the N^C^N ligands. By varying the electronic properties of the cyclometalated ligands, a fine-tuning of the emission energies can be achieved, as supported by computational studies. Multilayer organic light-emitting devices have been prepared by utilizing two of these platinum(II) complexes as phosphorescent dopants, in which a saturated yellow emission with Commission International de I'Eclairage coordinates of (0.50, 0.49) was achieved. PMID:23999951

Chan, Alan Kwun-Wa; Lam, Elizabeth Suk-Hang; Tam, Anthony Yiu-Yan; Tsang, Daniel Ping-Kuen; Lam, Wai Han; Chan, Mei-Yee; Wong, Wing-Tak; Yam, Vivian Wing-Wah

2013-09-02

247

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

Microsoft Academic Search

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

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

2006-01-01

248

The Acid-Labile Subunit of Human Ternary Insulin-Like Growth Factor Binding Protein Complex in Serum: Hepatosplanchnic Release, Diurnal Variation, Circulating Concentrations in Healthy Subjects, and Diagnostic Use in Patients with Growth Hormone Deficiency  

Microsoft Academic Search

Circulating insulin-like growth factor-I (IGF-I) is predominantly bound in the trimeric complex comprised of IGF binding protein-3 (IGFBP-3) and acid-labile subunit (ALS). Circulating concentrations of IGF-I, IGFBP-3 and ALS are believed to reflect the GH secretory status, but the clinical use of ALS determination is not known. We therefore, determined the: 1) hepatosplanchnic release of ALS by liver vein catheterization

ANDERS JUUL; SØREN MØLLER; EVA MOSFELDT-LAURSEN; MICHAEL HØJBY RASMUSSEN; THOMAS SCHEIKE; SØREN A. PEDERSEN; KNUD W. KASTRUP; HERBERT YU; JEHANGIR MISTRY; SUSANNE RASMUSSEN; JØRN MULLER; JENS HENRIKSEN; NIELS E. SKAKKEBÆK

249

Studies of a Series of [Ni(PR2NPh2)2(CH3CN)]2+ Complexes as Electrocatalysts for H2 Production: Substituent Variation at the Phosphorus Atom of the P2N2 Ligand  

SciTech Connect

A series of [Ni(PR2NPh2)2(CH3CN)](BF4)2 complexes containing the cyclic diphosphine ligands (PR2NPh2 = 1,5-diaza-3,7-diphosphacyclooctane; R = benzyl (Bn), n-butyl (n-Bu), 2-phenylethyl (PE), 2,4,4-trimethylpentyl (TP), and cyclohexyl (Cy)) have been synthesized and characterized. X-ray diffraction studies reveal that the cations of [Ni(PBn2NPh2)2(CH3CN)](BF4)2 and [Ni(Pn-Bu2NPh2)2(CH3CN)](BF4)2 have distorted trigonal bipyramidal geometries. The Ni(0) complex [Ni(PBn2NPh2)2 (CH3CN)] was also synthesized and characterized by X-ray diffraction studies and shown to have a distorted tetrahedral structure. These complexes, with the exception of [Ni(PCy2NPh2)2(CH3CN)](BF4)2, all exhibit reversible electron transfer processes for both the Ni(II/I) and Ni(I/0) couples and are electrocatalysts for the production of H2 in acidic acetonitrile solutions. The heterolytic cleavage of H2 by [Ni(PR2NPh2)2(CH3CN)](BF4)2 complexes in the presence of p-anisidine or p-bromoaniline was used to determine the hydride donor abilities of the corresponding [HNi(PR2NPh2)2](BF4) complexes. However, the failure to observe a strong correlation between the turnover frequencies for H2 production and the hydride donor abilities, along with structural features of [Ni(PBn2NPh2)2(CH3CN)], suggest that steric interactions between the alkyl substituents on phosphorus and the nitrogen atom of the pendant amines play an important role in determining the overall catalytic rate. This material is based upon work supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences.

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

2011-11-07

250

Non-uniform random variate generation  

Microsoft Academic Search

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

L. Devroye

1986-01-01

251

New Variational Bounds on Generalized Polarizabilities.  

National Technical Information Service (NTIS)

New variational bounds are derived on the generalized polarizabilities of a quantum-mechanical system, for arbitrary complex frequencies zeta=nu+i omega and two different perturbations u and v. No power of the Hamiltonian h higher than h squared is involv...

P. D. Robinson

1977-01-01

252

HEAT TRANSFER VARIATIONS OF BICYCLE HELMETS  

Microsoft Academic Search

Bicycle helmets exhibit complex structures so as to combine impact protection with ventilation. A quantitative experimental measure of the state of the art and variations therein is a first step towards establishing principles of bicycle helmet ventilation. A thermal headform mounted in a climate-regulated wind tunnel was used to study the ventilation efficiency of 24 bicycle helmets at two wind

Paul A. Brühwiler; Munkhbayar Buyan; Roman Huber; Josué Sznitman; Siegfried F. Graf; Thomas Rösgen

253

Heat transfer variations of bicycle helmets  

Microsoft Academic Search

Bicycle helmets exhibit complex structures so as to combine impact protection with ventilation. A quantitative experimental measure of the state of the art and variations therein is a first step towards establishing principles of bicycle helmet ventilation. A thermal headform mounted in a climate-regulated wind tunnel was used to study the ventilation efficiency of 24 bicycle helmets at two wind

P. A. Brühwiler; M. Buyan; R. Huber; C. P. Bogerd; J. Sznitman; S. F. Graf; T. Rösgen

2006-01-01

254

Non-differentiable variational principles  

NASA Astrophysics Data System (ADS)

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.

Cresson, Jacky

2005-07-01

255

Azimuthal variation of dilatancy  

Microsoft Academic Search

In triaxial laboratory tests, variation of circumferential strain in dilatant granite may reach 100% or more at high stresses. Pseudoelastic compliances s13 and s23 in the plane perpendicular to the maximum stress may differ by a factor of 2-10. Given the magnitude of these differences, in situ azimuthal variation of dilatancy should be the observed rule rather that the exception.

Kate Hadley

1975-01-01

256

Fire and climate variation in western North America from fire-scar ...  

Treesearch

USA.gov Government Made Easy ... Bottom-up controls include local variations in topographic, fuel and weather factors at the time of a ... Examples include variation in fuel consumption, tree mortality and soil effects, which create complex  ...

257

Multi-objective optimization shapes ecological variation.  

PubMed

Ecological systems contain a huge amount of quantitative variation between and within species and locations, which makes it difficult to obtain unambiguous verification of theoretical predictions. Ordinary experiments consider just a few explanatory factors and are prone to providing oversimplified answers because they ignore the complexity of the factors that underlie variation. We used multi-objective optimization (MO) for a mechanistic analysis of the potential ecological and evolutionary causes and consequences of variation in the life-history traits of a species of moth. Optimal life-history solutions were sought for environmental conditions where different life stages of the moth were subject to predation and other known fitness-reducing factors in a manner that was dependent on the duration of these life stages and on variable mortality rates. We found that multi-objective optimal solutions to these conditions that the moths regularly experience explained most of the life-history variation within this species. Our results demonstrate that variation can have a causal interpretation even for organisms under steady conditions. The results suggest that weather and species interactions can act as underlying causes of variation, and MO acts as a corresponding adaptive mechanism that maintains variation in the traits of organisms. PMID:21849318

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

2011-08-17

258

Complex polarization propagator calculations of magnetic circular dichroism spectra  

NASA Astrophysics Data System (ADS)

It is demonstrated that the employment of the nonlinear complex polarization propagator enables the calculation of the complete magnetic circular dichroism spectra of closed-shell molecules, including at the same time both the so-called Faraday and terms. In this approach, the differential absorption of right and left circularly polarized light in the presence of a static magnetic field is determined from the real part of the magnetic field-perturbed electric dipole polarizability. The introduction of the finite lifetimes of the electronically excited states into the theory results in response functions that are well behaved in the entire spectral region, i.e., the divergencies that are found in conventional response theory approaches at the transition energies of the system are not present. The applicability of the approach is demonstrated by calculations of the ultraviolet magnetic circular dichroism spectra of para-benzoquinone, tetrachloro-para-benzoquinone, and cyclopropane. The present results are obtained with the complex polarization propagator approach in conjunction with Kohn-Sham density functional theory and the standard adiabatic density functionals B3LYP, CAM-B3LYP, and BHLYP.

Solheim, Harald; Ruud, Kenneth; Coriani, Sonia; Norman, Patrick

2008-03-01

259

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

SciTech Connect

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.

Rescigno, T.N.

1991-08-01

260

Variational calculation of positron-atom scattering using configuration-interaction-type wave functions  

SciTech Connect

The Kohn variational method is used with a configuration-interaction (CI)-type wave function to determine the phase shifts and Z{sub eff} for positron-copper scattering. The method is first tested for positron-hydrogen scattering and it is found to give phase shifts and Z{sub eff} within 1-2% of the best previous calculations. Although the phase shift for Cu converged more slowly with L{sub max} (the maximum angular momentum of the electron and positron orbitals included in the short-range basis), it was still possible to get reliable estimates of the phase shifts by including orbitals with l{<=}18 and the use of an extrapolation technique. Calculation of Z{sub eff} was more problematic since the convergence of Z{sub eff} with respect to L{sub max} was very slow. Despite the uncertainties, it was clear that the p-wave phase shift was showing signs of forming a shape resonance at about 0.5 eV incident energy. This resulted in a p-wave contribution to Z{sub eff} that was larger than that of the s wave for k{>=}0.1a{sub 0}{sup -1}. Speculative calculations based upon a model potential suggest that a p-wave shape resonance centered at thermal energies, e.g., about 0.025 eV, could result in a thermally averaged Z{sub eff} exceeding 10,000.

Bromley, M.W.J.; Mitroy, J. [Faculty of SITE, Northern Territory University, Darwin, Northern Territory 0909 (Australia)

2003-06-01

261

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

NASA Astrophysics Data System (ADS)

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

Zope, Rajendra; Dunlap, Brett

2005-03-01

262

Syntheses, structures and luminescence behaviors of zinc(II) complexes containing a tetradentate Schiff base: Variation in nuclearity and geometry with the change of halide/pseudohalide/carboxylate and counter anion  

NASA Astrophysics Data System (ADS)

A series of pentacoordinated mono-/dinuclear compounds, [Zn(L)(Br)]PF6 (1), [Zn(L)(NCS)]ClO4 (2) and [Zn2(L)2(?-tp)](ClO4/PF6)2 (3/4) [L = N,N?-(bis(pyridin-2-yl)benzylidene)-1,3-propanediamine, tp = terephthalate dianion], have been synthesized using one-pot reactions of the building components. All the complexes are characterized using microanalytical, spectroscopic and other physicochemical results. Structures of 1–4 are solved by single crystal X-ray diffraction measurements. Structural analyses reveal that each zinc(II) center in 1 and 3 adopts a distorted trigonal bipyramidal geometry with ZnN4Br and ZnN4O chromophores, respectively, whereas zinc(II) centers in 2 and 4 have a distorted square pyramidal geometry with ZnN5 and ZnN4O chromophores, respectively. Intermolecular CH⋯Br, CH⋯F and CH⋯O hydrogen bondings along with CH⋯? and ?⋯? interactions as the case in 1–4 lead to different crystalline aggregates. The compounds show intraligand ?–?* fluorescence in solid states and in DMF solutions at room temperature.

Roy, Subhasis; Sarkar, Bhola Nath; Bhar, Kishalay; Satapathi, Smita; Mitra, Partha; Ghosh, Barindra Kumar

2013-04-01

263

Human olfaction: from genomic variation to phenotypic diversity  

Microsoft Academic Search

The sense of smell is a complex molecular device, encompassing several hundred olfactory receptor proteins (ORs). These receptors, encoded by the largest human gene superfamily, integrate odorant signals into an accurate 'odor image' in the brain. Widespread phe- notypic diversity in human olfaction is, in part, attribu- table to prevalent genetic variation in OR genes, owing to copy number variation,

Yehudit Hasin-Brumshtein; Doron Lancet; Tsviya Olender

2009-01-01

264

COMPLEX DIFFUSION ON IMAGE GRAPHS  

PubMed Central

Complex diffusion was introduced in image processing literature as a means to achieve simultaneous denoising and enhancement of scalar valued images. In this paper, we present a novel geometric framework for achieving complex diffusion on color images expressed as image graphs. In this framework, we develop a new variational formulation for achieving complex diffusion. This formulation involves a modified harmonic map functional and is quite distinct from the Polyakov action described in earlier work by Sochen et al. Our formulation provides a framework for simultaneous (feature preserving) denoising and enhancement. We present results of comparison between the complex diffusion, and Beltrami flow all in the image graph framework.

Seo, Dohyung; Vemuri, Baba C

2009-01-01

265

Ensembl variation resources  

PubMed Central

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

2010-01-01

266

Variation of the ground spin state in homo- and hetero-octanuclear copper(II) and nickel(II) double-star complexes with a meso-helicate-type metallacryptand core.  

PubMed

Homo- and heterometallic octanuclear complexes of formula Na?{[Cu?(mpba)?][Cu(Me?dien)]?}-(ClO?)?·12H?O (1), Na?{[Cu?(Mempba)?][Cu(Me?dien)]?}(ClO?)?·12H?O (2), Na?{[Ni?(mpba)?]-[Cu(Me?dien)]?}(ClO?)?·12H?O (3), Na?{[Ni?(Mempba)?][Cu(Me?dien)]?}(ClO?)?·9H?O (4), {[Ni?(mpba)?][Ni(dipn)(H?O)]?}(ClO?)?·12.5H?O (5), and {[Ni?(Mempba)?][Ni(dipn)-(H?O)]?}(ClO?)?·12H?O (6) [mpba = 1,3-phenylenebis(oxamate), Mempba = 4-methyl-1,3-phenylenebis(oxamate), Me?dien = N,N,N',N'',N''-pentamethyldiethylenetriamine, and dipn = dipropylenetriamine] have been synthesized through the "complex-as-ligand/complex-as-metal" strategy. Single-crystal X-ray diffraction analyses of 1, 3, and 5 show cationic M(II)?M'(II)? entities (M, M' = Cu and Ni) with an overall double-star architecture, which is made up of two oxamato-bridged M(II)M'(II)? star units connected through three meta-phenylenediamidate bridges between the two central metal atoms leading to a binuclear metallacryptand core of the meso-helicate-type. Dc magnetic susceptibility data for 1-6 in the temperature range 2-300 K have been analyzed through a "dimer-of-tetramers" model [H = - J(S(1A)·S(3A) + S(1A)·S(4A) + S(1A)·S(5A) + S(2B)·S(6B) + S(2B)·S(7B) + S(2B)·S(8B)) - J'S(1A)·S(2B), with S(1A) = S(2B) = S(M) and S(3A) = S(4A) = S(5A) = S(6B) = S(7B) = S(8B) = S(M')]. The moderate to strong antiferromagnetic coupling between the M(II) and M'(II) ions through the oxamate bridge in 1-6 (-J(Cu-Cu) = 52.0-57.0 cm?¹, -J(Ni-Cu) = 39.1-44.7 cm?¹, and -J(Ni-Ni) = 26.3-26.6 cm?¹) leads to a non-compensation of the ground spin state for the tetranuclear M(II)M'(II)? star units [S(A) = S(B) = 3S(M') - S(M) = 1 (1 and 2), 1/2 (3 and 4), and 2 (5 and 6)]. Within the binuclear M(II)? meso-helicate cores of 1-4, a moderate to weak antiferromagnetic coupling between the M(II) ions (-J'(Cu-Cu) = 28.0-48.0 cm?¹ and -J'(Ni-Ni) = 0.16-0.97 cm?¹) is mediated by the triple m-phenylenediamidate bridge to give a ground spin singlet (S = S(A) - S(B) = 0) state for the octanuclear M(II)?Cu(II)? molecule. Instead, a weak ferromagnetic coupling between the Ni(II) ions (J'(Ni-Ni) = 2.07-3.06 cm?¹) operates in the binuclear Ni(II)? meso-helicate core of 5 and 6 leading thus to a ground spin nonet (S = S(A) + S(B) = 4) state for the octanuclear Ni(II)? molecule. Dc magnetization data for 5 reveal a small but non-negligible axial magnetic anisotropy (D = -0.23 cm?¹) of the S = 4 Ni(II)? ground state with an estimated value of the energy barrier for magnetization reversal of 3.7 cm?¹ (U = -DS²). Ac magnetic susceptibility data for 5 show an unusual slow magnetic relaxation behaviour at low temperatures which is typical of "cluster glasses". The temperature dependence of the relaxation time for 5 has been interpreted on the basis of the Vogel-Fulcher law for weakly interacting clusters, with values of 2.5 K, 1.4 × 10?? s, and 4.0 cm?¹ for the intermolecular interaction parameter (T?), the pre-exponential factor (??), and the effective energy barrier (U(eff)), respectively. PMID:21491690

Pardo, Emilio; Dul, Marie-Claire; Lescouëzec, Rodrigue; Chamoreau, Lise-Marie; Journaux, Yves; Pasán, Jorge; Ruiz-Pérez, Catalina; Julve, Miguel; Lloret, Francesc; Ruiz-García, Rafael; Cano, Joan

2010-05-28

267

Masks: Interpretations and Variations.  

ERIC Educational Resources Information Center

Presents a high school art teacher's views of and experiences with masks. Outlines a maskmaking activity in which students were required to create variations on existing masks. Emphasizes use of experimental materials. Displays examples of student-created masks. (DB)

Basso, Robert

1990-01-01

268

Nucleotide Variation in Wild and Inbred Mice  

PubMed Central

The house mouse is a well-established model organism, particularly for studying the genetics of complex traits. However, most studies of mice use classical inbred strains, whose genomes derive from multiple species. Relatively little is known about the distribution of genetic variation among these species or how variation among strains relates to variation in the wild. We sequenced intronic regions of five X-linked loci in large samples of wild Mus domesticus and M. musculus, and we found low levels of nucleotide diversity in both species. We compared these data to published data from short portions of six X-linked and 18 autosomal loci in wild mice. We estimate that M. domesticus and M. musculus diverged <500,000 years ago. Consistent with this recent divergence, some gene genealogies were reciprocally monophyletic between these species, while others were paraphyletic or polyphyletic. In general, the X chromosome was more differentiated than the autosomes. We resequenced classical inbred strains for all 29 loci and found that inbred strains contain only a small amount of the genetic variation seen in wild mice. Notably, the X chromosome contains proportionately less variation among inbred strains than do the autosomes. Moreover, variation among inbred strains derives from differences between species as well as from differences within species, and these proportions differ in different genomic regions. Wild mice thus provide a reservoir of additional genetic variation that may be useful for mapping studies. Together these results suggest that wild mice will be a valuable complement to laboratory strains for studying the genetics of complex traits.

Salcedo, Tovah; Geraldes, Armando; Nachman, Michael W.

2007-01-01

269

Direct and Inverse Variation  

NSDL National Science Digital Library

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

Media, Annenberg

2009-12-23

270

Phenotypic Variation in Plants  

NSDL National Science Digital Library

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

Lawrence Blumer (Morehouse College;)

1997-01-01

271

Diurnal H-reflex variation in mice.  

PubMed

Mice exhibit diurnal variation in complex motor behaviors, but little is known about diurnal variation in simple spinally mediated functions. This study describes diurnal variation in the H-reflex (HR), a wholly spinal and largely monosynaptic reflex. Six mice were implanted with tibial nerve cuff electrodes and electrodes in the soleus and gastrocnemius muscles, for recording of ongoing and nerve-evoked electromyographic activity (EMG). Stimulation and recording were under computer control 24 h/day. During a 10-day recording period, HR amplitude varied throughout the day, usually being larger in the dark than in the light. This diurnal HR variation could not be attributed solely to differences in the net ongoing level of descending and segmental excitation to the spinal cord or stimulus intensity. HRs were larger in the dark than in the light even after restricting the evoked responses to subsets of trials having similar ongoing EMG and M-responses. The diurnal variation in the HR was out of phase with that reported previously for rats, but was in phase with that observed in monkeys. These data, supported by those in other species, suggest that the supraspinal control of the excitability of the HR pathway varies throughout the day in a species-specific pattern. This variation should be taken into account in experimental and clinical studies of spinal reflexes recorded at different times of day. PMID:16151781

Carp, Jonathan S; Tennissen, Ann M; Chen, Xiang Yang; Wolpaw, Jonathan R

2005-09-07

272

Emerging patterns of epigenomic variation  

PubMed Central

Fuelled by new sequencing technologies, epigenome mapping projects are revealing epigenomic variation at all levels of biological complexity, from species to cells. Comparisons of methylation profiles among species reveal evolutionary conservation of gene body methylation patterns, pointing to the fundamental role of epigenomes in gene regulation. At the human population level, epigenomic changes provide footprints of the effects of genomic variants within the vast non-protein coding fraction of the genome while comparisons of the epigenomes of parents and their offspring point to quantitative epigenomic parent-of-origin effects confounding classical Mendelian genetics. At the organismal level, comparisons of epigenomes from diverse cell types provide insights into cellular differentiation. Finally, comparisons of epigenomes from monozygotic twins help dissect genetic and environmental influences on human phenotypes and longitudinal comparisons reveal aging-associated epigenomic drift. The development of new bioinformatic frameworks for comparative epigenome analysis is putting epigenome maps within reach of researchers across a wide spectrum of biological disciplines.

Milosavljevic, Aleksandar

2011-01-01

273

Variations in the rotation of the earth  

NASA Astrophysics Data System (ADS)

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.

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

274

Medically Complex Home Care and Caregiver Strain  

ERIC Educational Resources Information Center

|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…

Moorman, Sara M.; Macdonald, Cameron

2013-01-01

275

Variations in earth rotation  

NASA Astrophysics Data System (ADS)

The present conference on variations in the earth's rotation encompasses geophysical effects on earth rotation (ER) parameters, the relationship of ER with tides and oceans, terrestrial and celestial reference systems for measuring ER, refinements of terrestial reference frames, the relationship between length of day and atmospheric angular momentum, and long-term fluctuations of ER parameters. Specific issues addressed include the variational calculation of wobble modes, the long-period elastic behavior of the earth, tidal deceleration of the earth, geophysical implications of the earth's forced nutations, and the study of fluid-solid earth-coupling processes with satellite altimeter data. Also addressed are atmospheric excitation of the ER rate, ER and climatic periodicities, ENSO-related signals in ER, station coordinates and ER parameters, short-period UT1 variations from Iris daily VLBI observations, and the definition and realization of terrestrial reference systems for monitoring ER.

McCarthy, Dennis D.; Carter, William E.

276

MHC variation in birds and reptiles  

Microsoft Academic Search

The major histocompatibility complex (MHC) has been studied in a multitude of mammals by now, but much less is known about\\u000a its organisation and variation in other vertebrate species. The mammalian MHC is organised as a single gene cluster, but recent\\u000a studies on birds suggest that this paradigm of MHC organisation has to be supplemented. The domestic chicken thus possesses

Håkan Wittzell; Thomas Madsen; Helena Westerdahl; Richard Shine; Torbjörn von Schantz

1998-01-01

277

Multiscale variety in complex systems  

Microsoft Academic Search

number of variations in control that is necessary for effective response. The Law of Requisite Variety does not consider the components of a system and how they must act together to respond effectively. Here we consider the additional requirement of scale of response and the effect of coordinated versus uncoordinated response as a key attribute of complex systems. The components

Yaneer Bar-yam

2004-01-01

278

Cellular genomics for complex traits  

Microsoft Academic Search

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

Emmanouil T. Dermitzakis

2012-01-01

279

Epistasis correlates to genomic complexity  

Microsoft Academic Search

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

Rafael Sanjuán; Santiago F. Elena

2006-01-01

280

Spin transport in bimetallic pentalene complexes  

NASA Astrophysics Data System (ADS)

Spin transport in bimetallic pentalene complexes (CpM(pentalene)M?Cp;M,M?=Fe,Co,Ni) between two gold electrodes was investigated, using a Green’s function formalism under density functional theory. Variation of the metal atom species in the complexes gives a considerable change in their spin properties, with hetero-bimetallic complexes containing an odd number of electrons exhibiting spin filter behaviour. In contrast, alternation in the contact condition, whether Cp-anchoring or adducting by sulphur-gold bonds, had almost no effect on spin filter behaviour, but did lead to variation in electrical conduction. We examined suitable bimetallic pentalene complexes in order to enhance their spin filter efficiency. We examined spin transport in bimetallic pentalene complexes between two gold electrodes. Variation of the metal atom species gives a considerable change in their spin properties. In contrast, alternation in the contact condition had almost no effect on spin filter behaviour.

Matsuura, Yukihito

2011-12-01

281

Designing Complexity  

ERIC Educational Resources Information Center

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…

Glanville, Ranulph

2007-01-01

282

Hamiltonian complexity  

NASA Astrophysics Data System (ADS)

In recent years we have seen the birth of a new field known as Hamiltonian complexity lying at the crossroads between computer science and theoretical physics. Hamiltonian complexity is directly concerned with the question: how hard is it to simulate a physical system? Here I review the foundational results, guiding problems, and future directions of this emergent field.

Osborne, Tobias J.

2012-02-01

283

Hamiltonian complexity.  

PubMed

In recent years we have seen the birth of a new field known as Hamiltonian complexity lying at the crossroads between computer science and theoretical physics. Hamiltonian complexity is directly concerned with the question: how hard is it to simulate a physical system? Here I review the foundational results, guiding problems, and future directions of this emergent field. PMID:22790342

Osborne, Tobias J

2012-01-24

284

Complex derivatives  

NASA Astrophysics Data System (ADS)

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.

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

2013-03-01

285

Bone conduction variation poststapedotomy  

Microsoft Academic Search

We evaluated the variation in bone conduction auditory thresholds in patients undergoing surgical intervention for otosclerosis as part of our report on the use of surgery in patients with a small air-bone gap. Of the 110 patients who underwent stapedotomy, 45 were treated by traditional surgery and 65 with carbon dioxide laser, with a follow-up of 3 years at 500-,

Luca Moscillo; Micaela Imperiali; Paola Carra; Ferdinando Catapano; Gaetano Motta

2006-01-01

286

MINIMIZING TOTAL VARIATION FLOW  

Microsoft Academic Search

We prove existence and uniqueness of weak solutions for the minimizing total variation ?ow with initial data in L1. We prove that the length of the level sets of the solution, i.e., the boundaries of the level sets, decreases with time, as one would expect, and the solution converges to the spatial average of the initial datum as t !1

F. Andreu; C. Ballester; V. Caselles; J. M. Mazon

1998-01-01

287

Thinking Tools and Variation  

ERIC Educational Resources Information Center

|This article discusses five papers focused on "Research on Reasoning about Variation and Variability", by Hammerman and Rubin, Ben-Zvi, Bakker, Reading, and Gould, which appeared in a special issue of the "Statistics Education Research Journal" (No. 3(2) November 2004). Three issues emerged from these papers. First, there is a link between the…

Pfannkuch, Maxine

2005-01-01

288

Total Variation in Imaging  

Microsoft Academic Search

The use of total variation as a regularization term in imaging problems was motivated by its ability to recover the image discontinuities. This is at the basis of his numerous applications to denoising, optical flow, stereo imaging and 3D surface reconstruction, segmentation, or interpolation, to mention some of them. On one hand, we review here the main theoretical arguments that

V. Caselles; A. Chambolle; M. Novaga

289

Climatic Variation of Storms.  

National Technical Information Service (NTIS)

Long-term variation of U.S. tornadoes were studied by obtaining the best possible data during the 75 years, 1916-90. The most difficult task was to estimate the number of early tornadoes in 1916-50 when the reporting efficiency was very bad, resulting in ...

T. Fujita

1993-01-01

290

Sunspot Number Variations  

NSDL National Science Digital Library

In this activity students find the patterns that emerge when sunspot numbers are plotted over a period of time. Students learn about sunspot variations and the solar cycle, and are able to predict future solar minimums and solar maximums. The required sunspot charts can be downloaded along with the student worksheets.

Meier, Beverly

291

Trifling variation in truffles  

Microsoft Academic Search

Of the ten species of European truffle (fungi of the genus Tuber, phylum Ascomycota), some have economic value because of their organoleptic properties (taste and perfume), in particular the black truffle (Tuber melanosporum Vitt.) and the summer and burgundy truffles,. The black truffle is mainly found in Spain, France and Italy (Fig. 1a), and it shows variation in several traits,

G. Bertault; M. Raymond; A. Berthomieu; G. Callot; D. Fernandez

1998-01-01

292

Algebra Lab: Inverse Variation  

NSDL National Science Digital Library

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

2012-01-01

293

A variational principle of hydromechanics  

Microsoft Academic Search

1. The purpose of this paper is to reveal the part played in variational principles of hydromechanics by a certain group of infinitesimal transformations of the fields of density and velocity. This group, called here the hydromechanical variation and originating from some elementary requirement concerning variation of matter, seems to be essential in variational principles of hydromechanic,4, iaot only in

S. Drobot; A. Rybarski

1958-01-01

294

Variations in sending Morse code  

Microsoft Academic Search

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

Charles Windle

1955-01-01

295

Diurnal variations of Titan  

NASA Astrophysics Data System (ADS)

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.

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

296

Variations in Recollection: The Effects of Complexity on Source Recognition  

ERIC Educational Resources Information Center

|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…

Parks, Colleen M.; Murray, Linda J.; Elfman, Kane; Yonelinas, Andrew P.

2011-01-01

297

Complex variation of spectral line widths observed in polar corona  

NASA Astrophysics Data System (ADS)

Spectroscopic observations of the solar corona, using high spatial and spectral resolution 25cm coronagraph, at Norikura observatory, were made on large number of days during 2004 at the mid latitude and polar coronal regions. We have analyzed several raster scans that cover mid and high latitude regions on the off-limb corona in four bright emission lines of iron, namely, [Fe X] 6374 Å, [Fe XI]~7892~Å, [Fe XIII] 10747~Å, and [Fe XIV]~5303~Å. We find that the FWHM of red line increases with height and that of green line decreases with height as observed earlier, at equatorial regions. The comparison of line widths and their gradients with the results from equatorial regions indicate that these are higher for polar regions for the observed emission lines except for the green line. FWHM values show an increase towards poles in all the lines except for the green line which shows little or no change. Higher values of FWHM at polar regions may imply higher non-thermal velocities which could be linked to the solar wind, but the behavior of green emission line with almost same values of FWHM at equatorial and polar regions is surprising. This may also give some indications on the existence of preferential heating.

Prasad Samayamanthula, Krishna; Banerjee, Dipankar; Singh, Jagdev

2012-07-01

298

Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes  

Microsoft Academic Search

Extensive studies are currently being performed to associate disease susceptibility with one form of genetic variation, namely, single-nucleotide polymorphisms (SNPs). In recent years, another type of common genetic variation has been characterized, namely, structural variation, including copy number variants (CNVs). To determine the overall contribution of CNVs to complex phenotypes, we have performed association analyses of expression levels of 14,925

Barbara E. Stranger; Matthew S. Forrest; Mark Dunning; Catherine E. Ingle; Claude Beazley; Natalie Thorne; Richard Redon; Christine P. Bird; Anna de Grassi; Charles Lee; Chris Tyler-Smith; Nigel Carter; Stephen W. Scherer; Simon Tavaré; Panagiotis Deloukas; Matthew E. Hurles; Emmanouil T. Dermitzakis

2007-01-01

299

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

NASA Astrophysics Data System (ADS)

Experimental data show that fluid-melt partitioning of Sr is controlled by the bulk chemistry of the system. For chloridic fluids, there is a sharp increase in the Sr partition coefficient with the alumina saturation index (ASI) to a maximum of 0.3 at an ASI of 1.05. Because fluid-melt partitioning of a given element depends on its complexation in the fluid and its incorporation in the melt, these data imply a change in the Sr speciation at least one of the two phases. For silicate melts, Kohn et al. (1990) found only small changes in the first coordination shell of Sr in a suite of melts with various degrees of polymerization, and argued that incorporation of Sr in the melt should not play a major role in controlling Sr partitioning. For the aqueous fluid, Bai and Koster van Groos (1999) suggested formation of SrCl2 complexes based on the correlation between partition coefficient and Cl concentration in the fluid after quenching. Here, we studied the complexation of Sr in peraluminous or peralkaline melt dissolved in aqueous fluids in-situ at elevated PT conditions using hydrothermal diamond-anvil cells (HDAC) and X-ray absorption near edge structure (XANES) spectroscopy. The starting materials were peraluminous or peralkaline glass and H2O or a chloridic solution. The glass was doped with high concentrations of 5000 or 10000 ppm Sr to facilitate in-situ analyses of the aqueous fluids. We used bulk compositions of 10 to 15 wt.% glass to ensure that the melt was completely dissolved in the fluid at high PT conditions. For qualitative evaluation, we analyzed the starting glasses and various crystalline compounds and standard solutions. The experiments were performed at beamline ID26 at ESRF (Grenoble, France) using a high resolution emission spectrometer. We applied different monochromator crystals, Si311 for high resolution and Si111 for low resolution measurements. An overall resolution of 1.98 eV (Si311) and 3 eV (Si111) was achieved using a beamsize of 120x400 ?m, Si(777) analyzer crystals and a Rowland circle diameter of 1 m. In contrast to the study by Kohn et al. (1990), XANES spectra of peraluminous and peralkaline starting glasses show distinct differences in pre-edge, main edge and position of the first EXAFS maximum. The latter is directly correlated to the distance of Sr and its nearest neighbor. The spectra of SrCl2 and Sr(OH)2 standard solutions at various PT conditions indicate very small temperature-dependent changes of the complexation. The XANES spectra of solutions after dissolution of peraluminous or peralkaline melt in chloridic fluids vary significantly from each other. The latter are similar to the one of the peralkaline starting glass, while this is not the case for solutions with peraluminous melt. The spectra of water with dissolved peralkaline melt distinctly differ from those using chloridic fluids. In conclusion, the first direct information on Sr complexation at elevated PT condition indicates significant speciation changes in both fluid and melt. Bai and Koster van Groos (1999), GCA 63, 1117-1131. Kohn et. Al. (1990), CMP 105, 359-368.

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

2009-12-01

300

Variational transcorrelated method  

NASA Astrophysics Data System (ADS)

We propose a new approach to the use of Jastrow ansatz in the calculation of electron correlations, based on a modification of the transcorrelated method of Boys and Handy [Proc. R. Soc. London, Ser. A 309, 209 (1969)]. In this new method, the original transcorrelated orbital equation is replaced with a general variational equation for the reference wave function, whereas the equation for the correlation factor remains the same. The method can be applied to a single determinant Jastrow ansatz as well as to a multideterminant one. For the single determinant ansatz, we obtain a Hartree-Fock type self-consistent equation for the optimization of orbitals, and for the multideterminant ansatz we have tested a CI type equation. We apply the new method in calculations of the C2 molecule and compare the results with those of variational quantum Monte Carlo calculations.

Luo, Hongjun

2010-10-01

301

Complex Numbers  

NSDL National Science Digital Library

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

Kuphaldt, Tony R.

2008-07-15

302

Solutions by Variational Method  

Microsoft Academic Search

\\u000a The variational method for solving stochastic partial differential equations (SPDE’s) of evolutionary type involves recasting\\u000a them as SDE’s in a Gelfand triplet of Hilbert or Banach spaces V?H?V\\u000a ?, where the embeddings are dense and continuous. We discuss only the case of separable Hilbert spaces. In order to construct\\u000a a weak solution, we assume that the embeddings are compact, and

Leszek Gawarecki; Vidyadhar Mandrekar

303

Variational methods in electrohydrodyanmics  

SciTech Connect

The authors consider the motion in an electric field of a two-component compressible fluid consisting of neutral polarizable particles and charged particles of one type in the approximation of electrohydrodynamics for large electric Reynolds numbers. They show that the developed variational formulation implies an equation for the momenta of nondissipative motion of a polarizable charge compressible fluid. The rotational motion of the fluid under investigation is studied.

Gorskii, V.B.; Annenkova, O.G.; Makarova, I.A.

1985-10-01

304

Total variation blind deconvolution  

Microsoft Academic Search

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

Tony F. Chan; Chiu-Kwong Wong

1998-01-01

305

Antigenic Variation in Giardia  

Microsoft Academic Search

\\u000a \\u000a Giardia lamblia trophozoites undergo surface antigenic variation where one member of a family of related proteins, variant specific surface\\u000a proteins (VSPs), is expressed but periodically replaced by another. It is the only intestinal dwelling organism to do this.\\u000a Switching occurs spontaneously in culture in vitro in the absence of defined environmental triggers. The two major Giardia groups infecting humans differ

Theodore E. Nash

306

Complex societies  

Microsoft Academic Search

The complexity of human societies of the past few thousand years rivals that of social insect societies. We hypothesize that\\u000a two sets of social “instincts” underpin and constrain the evolution of complex societies. One set is ancient and shared with\\u000a other social primate species, and one is derived and unique to our lineage. The latter evolved by the late Pleistocene,

Peter J. Richerson; Robert Boyd

1999-01-01

307

Variation, Repetition, And Choice  

PubMed Central

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.

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

2005-01-01

308

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

PubMed Central

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

Ziegler, Tom; Krykunov, Mykhaylo; Cullen, John

2012-01-01

309

Multistage machining processes variation propagation analysis based on machining processes weighted network performance  

Microsoft Academic Search

To quantitatively analyze variation propagation in multistage machining processes, a method of variation propagation analysis\\u000a and variation source identification based on manufacturing cost was proposed in this paper. With the method, a weighted network\\u000a of multistage machining processes based on complex network theory was introduced, and variation propagation stability of multistage\\u000a machining processes was analyzed by virus-spreading model. Furthermore, key

Yongtao Qin; Liping Zhao; Yiyong Yao; Damin Xu

2011-01-01

310

Controlling complexity  

NASA Astrophysics Data System (ADS)

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.

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

2012-09-01

311

Meiosis-Driven Genome Variation in Plants  

PubMed Central

Meiosis includes two successive divisions of the nucleus with one round of DNA replication and leads to the formation of gametes with half of the chromosomes of the mother cell during sexual reproduction. It provides a cytological basis for gametogenesis and nheritance in eukaryotes. Meiotic cell division is a complex and dynamic process that involves a number of molecular and cellular events, such as DNA and chromosome replication, chromosome pairing, synapsis and recombination, chromosome segregation, and cytokinesis. Meiosis maintains genome stability and integrity over sexual life cycles. On the other hand, meiosis generates genome variations in several ways. Variant meiotic recombination resulting from specific genome structures induces deletions, duplications, and other rearrangements within the genic and non-genic genomic regions and has been considered a major driving force for gene and genome evolution in nature. Meiotic abnormalities in chromosome segregation lead to chromosomally imbalanced gametes and aneuploidy. Meiotic restitution due to failure of the first or second meiotic division gives rise to unreduced gametes, which triggers polyploidization and genome expansion. This paper reviews research regarding meiosis-driven genome variation, including deletion and duplication of genomic regions, aneuploidy, and polyploidization, and discusses the effect of related meiotic events on genome variation and evolution in plants. Knowledge of various meiosis-driven genome variations provides insight into genome evolution and genetic variability in plants and facilitates plant genome research.

Cai, Xiwen; Xu, Steven S

2007-01-01

312

Magnetic Daily Variation at Koror  

Microsoft Academic Search

A method of exhibiting the magnetic daily variations using contours based on running means can give a more precise indication of the seasonal changes in daily variation than conventional methods. This method is applied to the variations at Koror, which are of particular interest owing to Koror's location, almost exactly on the magnetic dip equator. The contour charts give new

1962-01-01

313

Biodiversity and intraspecific genetic variation  

Microsoft Academic Search

Biodiversity is mostly discussed at the level of species, but genetic variation within species may be as important as variation between species. It enables organisms to adapt to environmental changes. The requirement for genetic variation differs however widely between species and groups of species. Animal species at the top of the food web, such as large carnivorous mammals, tend to

Claes Ramel

1998-01-01

314

SCHUR FUNCTIONS : THEME AND VARIATIONS  

Microsoft Academic Search

this article we shall survey various generalizations, analogues anddeformations of Schur functions --- some old, some new --- that havebeen proposed at various times. We shall present these as a sequence ofvariations on a theme and (unlike e.g. Bourbaki) we shall proceed fromthe particular to the general. Thus Variations 1 and 2 are included inVariation 3 ; Variations 4 and

I. G. MACDONALD

1992-01-01

315

Quantitative measurement of variational approximations  

Microsoft Academic Search

Variational problems have long been used to mathematically model physical systems. Their advantage has been the simplicity of the model as well as the ability to deduce information concerning the functional dependence of the system on various parameters embedded in the variational trial functions. However, the only method in use for estimating the error in a variational approximation has been

D. J. Kaup; T. K. Vogel

2007-01-01

316

DC electrical conductivity of polydithiooxamide–metal complexes  

Microsoft Academic Search

Five polymer–metal complexes of iron(II), cobalt(II), nickel(II), copper(II) and zinc(II) were prepared from the reaction of dithiooxamide with metal salts. Elemental analysis, UV–VIS and IR investigations were carried out for the polymer complexes. The temperature variation of the DC electrical conductivity was measured in the range 298–498 K for the five polymer complexes. The proposed mechanism for the variation is

Ali El-Shekeil; Maarib A Khalid; Hussein Al-Maydama; Ashour Al-Karbooly

2001-01-01

317

Anisotropic Total Variation Filtering  

SciTech Connect

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.

Grasmair, Markus, E-mail: Markus.Grasmair@univie.ac.a [University of Vienna, Computational Science Center (Austria); Lenzen, Frank, E-mail: Frank.Lenzen@iwr.uni-heidelberg.d [University of Heidelberg, Heidelberg Collaboratory for Image Processing (Germany)

2010-12-15

318

Harmonically excited orbital variations  

SciTech Connect

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.

Morgan, T.

1985-08-06

319

Genome variation: a review of Web resources.  

PubMed

An enormous number of high-quality Web-based resources are now available to facilitate research into genome variation. Although identification of the most appropriate and informative resources can be challenging, a number of key sites provide links to more specialized resources that may be useful to follow up. Given ongoing research, focussing on the sequencing of many different genomes, we can expect sequence databases and their associated polymorphism-based resources to greatly increase in depth and complexity in a relatively short period of time. However, databases and tools developed to date, and described here, provide a sound basis for accommodating this next generation of genomic data. As well as sequence-oriented resources this review presents databases providing genotypic and common disease phenotype data, copy number variation, genetic maps, cytogenetic data, and gives an overview of key software tools, with the emphasis on analysis of the genetic basis of common disease. PMID:21153616

Collins, Andrew; Tapper, William J

2011-01-01

320

Complexity and \\  

Microsoft Academic Search

This paper has two main purposes. First, it will provide an introductory discussion of hyperset theory, and show that it is useful for modeling complex systems. Second, it will use hyperset theory to analyze Robert Rosen's metabolism- repair systems and his claim that living things are closed to efficient cause. It will also briefly compare closure to efficient cause to

Anthony Chemero; Michael T. Turvey

2006-01-01

321

Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation.  

PubMed

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

Hedrick, Philip W

2013-08-01

322

Crouching variation revealed.  

PubMed

The term 'phenotypic capacitance' was introduced nearly 15 years ago to describe the strain-specific effects of impairing Hsp90, a molecular chaperone, in the fly Drosophila melanogaster (Rutherford & Lindquist 1998). In one genetic background, Hsp90 depletion caused deformed eyes, whereas in other genetic backgrounds, the wings or abdomens or other aspects of morphology were affected. Hsp90 was therefore viewed as acting like a capacitor, allowing genetic differences to build up and to be released at a later time. In the years since, it has been debated whether capacitance is a laboratory curiosity or a major force in evolution. In this issue of Molecular Ecology, Takahashi (2013) presents evidence, from high-resolution morphometric analysis of fly wings, that a large number of other capacitors exist in D. melanogaster, and that the variation they reveal can be quite subtle. His results advance our understanding of capacitance and contribute to a new view of its role in evolutionary adaptation. PMID:23437837

Siegal, Mark L

2013-03-01

323

Variations on tremor parameters.  

PubMed

This paper describes our analysis procedure for long-term tremor EMG recordings, as well as three examples of applications. The description of the method focuses on how characteristics of the tremor (e.g. frequency, intensity, agonist-antagonist interaction) can be defined and calculated based on surface EMG data. The resulting quantitative characteristics are called "tremor parameters." We discuss sinusoidally modulated, band-limited white noise as a model for pathological tremor-EMG, and show how the basic parameters can be extracted from this class of signals. The method is then applied to (1) estimate tremor severity in clinical studies, (2) quantify agonist-antagonist interaction, and (3) investigate the variations of the tremor parameters using simple methods from time-series analysis. (c) 1995 American Institute of Physics. PMID:12780155

Boose, A.; Jentgens, Ch.; Spieker, S.; Dichgans, J.

1995-03-01

324

Geomagnetic Secular Variation  

NASA Astrophysics Data System (ADS)

We analyse over 175000 magnetic observations from an interval spanning 1695-1980 to produce a sequence of maps of the magnetic field at the core-mantle boundary; we find that even the earlier data enable us to determine reliable maps. We produce these maps at approximately 60-year intervals through the eighteenth and nineteenth centuries, and at 10-year intervals in the twentieth century. This span of maps is long enough to render straightforward the distinction between static and drifting features in the field: we observe that some features show no sign whatsoever of drift over the entire 285-year time interval, although others drift westwards. In particular, we observe that the secular variation is very low beneath the Pacific ocean, but beneath southern Africa and the South Atlantic ocean we observe rapid secular variation. We interpret the morphology of the static field in terms of a simple model of the dynamo, and conjecture that interactions between the core and the mantle are an important element of the process. As part of the static field we identify four main concentrations of flux, two in each hemisphere, at high latitudes: these features largely account for the Earth's axial dipole moment. We find unequivocal evidence that magnetic flux has not remained frozen over the time span of our models; much of the diffusive behaviour that we identify is associated with the formation of a pair of flux spots (a `core spot') beneath southern Africa, early in this century. Nevertheless, we are able to construct maps that satisfy a set of necessary conditions for frozen-flux, and use these maps to construct maps of the core surface fluid flow, based on the steady flow hypothesis. Although we find no strong evidence against the steady flow hypothesis, we do find some grounds on which to doubt the validity of the flow maps.

Bloxham, J.; Gubbins, D.; Jackson, A.

1989-11-01

325

Lunar Global Petrologic Variations  

NASA Astrophysics Data System (ADS)

An initial attempt at producing petrologic province maps of the lunar highlands combined orbital and sample geochemical data in variation diagrams.Three different variation diagrams were produced: Mg* (= 100 Mg/Mg+Fe) vs. [(Th/Ti)c, Al vs. Mg*/(Th/Ti)c, and Fe vs. (Th/Ti)c. ([Th/Ti]c is the ratio of Th to Ti, normalized to the chrondritic ratio for these elements.] Later work applied a ternary diagram approach to look at global lunar petrologic variations. This work used the Fe-(Th/Ti)c technique as this had the most spatial coverage with the available data and also appeared to be adequate at distinguishing between different rock types. In the ternary diagram, the apexes were assigned the average Fe and (Th/Ti), values of ferroan anorthosite, mare basalt, and KREEP rocks. Each apex was assigned a primary color while the center of the triangle was represented by gray. Each point on the lunar surface, covered by the Apollo geochemical instruments, was then assigned a color depending on where in the ternary their composition placed them. The resultant petrologic classification map shows how the petrologic units vary spatially. The main results from this work were as follows: (1) The highlands contain large areas of relatively pure ferroan anorthosite; (2) KREEP/Mg suite rocks represent a small percentage of the upper lunar crust; (3) farside outcrops of KREEP/ Mg suite rocks are associated with areas of crustal thinning, particularly on the floor of South Pole Aitken Basin; (4) the average composition of the highlands is richer in Fe than ferroan anorthosite, which supports the magma ocean hypothesis of crystal formation; and (5) regions of the eastern limb and farside highlands are relatively more mafic than average highlands. These areas have a high density of dark halo craters, supporting the idea that mare volcanism occurred in this region before the end of the heavy bombardment. This earlier work utilized the Apollo gamma and X-ray orbital datasets. These data provided limited coverage of the lunar surface (mostly confined to the equatorial latitudes). The gamma ray instrument covered approximately 19% of the lunar surface while the X-ray only covered 9%. With the Clementine and Lunar Prospector datasets, we now have global maps of Fe, Ti, and Th. Apart from global coverage, another important advantage of the new datasets is higher spatial resolution. The resolution of the Apollo instruments was 15 km for the X-ray and 100 km for the gamma ray. The Fe and Ti maps are derived from the full-resolution Clementine UV-VIS data, i.e., about 250 m/pixel. The resolution of the Th data, obtained by Lunar Prospector's neutron spectrometer, is currently about 150 km, but will be available in the future with a spatial resolution of 60 km. The other improvement provided by the recent lunar missions is the error associated with the data. The errors associated with the Fe, Ti, and Th values obtained by Apollo were 10-25 wt%. The error of the Clementine-derived Fe and Ti values is about 1% while the Th data have an error of about 1 ppm. We intend to investigate the petrologic variations on the Moon at a global scale using the new Clementine and Lunar Prospector elemental maps for Fe, Ti, and Th. We shall use the technique described in Davis and Spudis. An initial study has been undertaken that looks at some regions that were covered by the Apollo geochemistry data. Two mare regions, one in Imbrium and the other in Procellarum, match well with the results using the Apollo data. The highland terrain appears problematic. The calibration of the Th data is based on the assumption of a constant background. This is a valid assumption where Th counts are well above background limits, but as count rates decrease variations in Th concentration are more sensitive to background fluctuations. Eventually we will circumvent this problem by using the lower-altitude (i.e., higher resolution) Prospector data and a calibration derived from deconvolution of the gamma ray spectra with proper attention to background variations. The Th/Ti vs. Fe technique p

Bussey, D. B. J.; Spudis, P. D.; Gillis, J. J.

1999-01-01

326

Electronic Properties and Bonding in Transition Metal Complexes: Influence of Pressure  

Microsoft Academic Search

Changes undergone by optical and magnetic properties of Oh, Td and D4h Transition metal (TM) complexes induced by variations of the metal-ligand distance, R, are explored in this work. In parallel, the corresponding variations experienced by the chemical bonding in the complex are analysed in detail. Particular attention is addressed to TM complexes associated with impurities in insulating lattices with

M. Moreno; J. A. Aramburu; M. T. Barriuso

327

Time complexity and gate complexity  

SciTech Connect

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.

Koike, Tatsuhiko [Department of Physics, Keio University, Yokohama (Japan); Okudaira, Yosuke [Department of Physics, Tokyo Institute of Technology, Tokyo (Japan)

2010-10-15

328

Managing Complexity  

SciTech Connect

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.

Chassin, David P.; Posse, Christian; Malard, Joel M.

2004-08-01

329

Variational Principle for the Pareto Power Law  

NASA Astrophysics Data System (ADS)

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

Chakraborti, Anirban; Patriarca, Marco

2009-11-01

330

Epistasis: too often neglected in complex trait studies?  

Microsoft Academic Search

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

Chris S. Haley; Örjan Carlborg

2004-01-01

331

Genomics and variation of ionotropic glutamate receptors.  

PubMed

Sequencing of the human, mouse, and rat genomes has enabled a comprehensive informatics approach to gene families. This approach is informative for identification of new members of gene families, for cross-species sequence conservation related to functional conservation, for within-species diversity related to functional variation, and for historical effects of selection. This genome informatics approach also focuses our attention on genes whose genomic locations coincide with linkages to phenotypes. We are identifying ionotropic glutamate receptor (IGR) sequence variation by resequencing technologies, including denaturing high-performance liquid chromoatography (dHPLC), for screening and direct sequencing, and by information mining of public (e.g., dbSNP and ENSEMBL) and private (i.e., Celera Discovery System) sequence databases. Each of the 16 known IGRs is represented in these databases, their positions on a canonical physical map (for example, the Celera map) are established, and comparison to mouse and rat sequences has been performed, revealing substantial conservation of these genes, which are located on different chromosomes but found within syntenic groups of genes. A collection of 38 missense variants were identified by the informatics and resequencing approaches in several of these receptor genes, including GRIN2B, GRIN3B, GRIA2, GRIA3, and GRIK1. This represents only a fraction of the sequence variation across these genes, but, in fact, these may constitute a large fraction of the common polymorphisms at these genes, and these polymorphisms are a starting point for understanding the role of these receptors in neurogenetic variation. Genetically influenced human neurobehavioral phenotypes that are likely to be linked to IGR genetic variants include addictions, anxiety/dysphoria disorders, post-brain injury behavioral disorders, schizophrenia, epilepsy, pain perception, learning, and cognition. Thus, the effects of glutamate receptor variation may be protean, and the task of relating variation to behavior difficult. However, functional variants of (1) catechol-O-methyltransferase, (2) serotonin transporter, and (3) brain-derived neurotrophic factor have recently been linked both to behavioral differences and to intermediate phenotypes, suggesting a pathway by which functional variation at IGRs can be tied to an etiologically complex phenotype. PMID:14684433

Lipsky, Robert H; Goldman, David

2003-11-01

332

Replica Cluster Variational Method  

NASA Astrophysics Data System (ADS)

We present a general formalism to make the Replica-Symmetric and Replica-Symmetry-Breaking ansatz in the context of Kikuchi's Cluster Variational Method (CVM). Using replicas and the message-passing formulation of CVM we obtain a variational expression of the replicated free energy of a system with quenched disorder, both averaged and on a single sample, and make the hierarchical ansatz using functionals of functions of fields to represent the messages. We obtain a set of integral equations for the message functionals. The main difference with the Bethe case is that the functionals appear in the equations in implicit form and are not positive definite, thus standard iterative population dynamic algorithms cannot be used to determine them. In the simplest cases the solution could be obtained iteratively using Fourier transforms. We begin to study the method considering the plaquette approximation to the averaged free energy of the Edwards-Anderson model in the paramagnetic Replica-Symmetric phase. In two dimensions we find that the spurious spin-glass phase transition of the Bethe approximation disappears and the paramagnetic phase is stable down to zero temperature on the square lattice for different random interactions. The quantitative estimates of the free energy and of various other quantities improve those of the Bethe approximation. The plaquette approximation fails to predict a second-order spin-glass phase transition on the cubic 3D lattice but yields good results in dimension four and higher. We provide the physical interpretation of the beliefs in the replica-symmetric phase as disorder distributions of the local Hamiltonian. The messages instead do not admit such an interpretation and indeed they cannot be represented as populations in the spin-glass phase at variance with the Bethe approximation. The approach can be used in principle to study the phase diagram of a wide range of disordered systems and it is also possible that it can be used to get quantitative predictions on single samples. These further developments present however great technical challenges.

Rizzo, Tommaso; Lage-Castellanos, Alejandro; Mulet, Roberto; Ricci-Tersenghi, Federico

2010-05-01

333

DFT Description of the Electronic Structure and Spectromagnetic Properties of Strongly Correlated Electronic Systems: Ni, CuI and Zn o-Dioxolene Complexes  

SciTech Connect

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

Bencini, Alessandro; Carbonera, Chiara; Totti, Federico

2004-03-15

334

The influence of variation in litter habitats on spider communities  

Microsoft Academic Search

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

George W. Uetz

1979-01-01

335

Genome-Wide Associations of Gene Expression Variation in Humans  

Microsoft Academic Search

The exploration of quantitative variation in human populations has become one of the major priorities for medical genetics. The successful identification of variants that contribute to complex traits is highly dependent on reliable assays and genetic maps. We have performed a genome-wide quantitative trait analysis of 630 genes in 60 unrelated Utah residents with ancestry from Northern and Western Europe

Barbara E. Stranger; Matthew S. Forrest; Andrew G. Clark; Mark J. Minichiello; Samuel Deutsch; Robert Lyle; Sarah Hunt; Brenda Kahl; Stylianos E. Antonarakis; Simon Tavaré; Panagiotis Deloukas; Emmanouil T. Dermitzakis

2005-01-01

336

SUBSPECIFIC VARIATION IN THE WIDESPREAD BURL-FORMING ARCTOSTAPHYLOS GLANDULOSA  

Microsoft Academic Search

The genus Arctostaphylos consists mostly of chaparral shrubs known by the common name manzanita, and one of the widest ranging of these is A. glandulosa Eastw., distributed from Baja California to Oregon. Particularly in the southern half of its range it exhibits complex patterns of morphological variation that have long presented taxonomic challenges. Phenetic analysis of morphological traits from over

Jon E. Keeley; Michael C. Vasey; V. Thomas Parker

2007-01-01

337

Copy-number variation and association studies of human disease  

Microsoft Academic Search

The central goal of human genetics is to understand the inherited basis of human variation in phenotypes, elucidating human physiology, evolution and disease. Rare mutations have been found underlying two thousand mendelian diseases; more recently, it has become possible to assess systematically the contribution of common SNPs to complex disease. The known role of copy-number alterations in sporadic genomic disorders,

Steven A McCarroll; David M Altshuler

2007-01-01

338

Nuthatches eavesdrop on variations in heterospecific chickadee mobbing alarm calls  

Microsoft Academic Search

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

C. N. Templeton; Erick Greene

2007-01-01

339

Saturn chorus intensity variations  

NASA Astrophysics Data System (ADS)

mode chorus plasma wave emissions have been observed at Saturn near the magnetic equator and the source region. During crossings of the magnetic equator along nearly constant L shells, the Cassini Radio and Plasma Wave Science Investigation often observes a local decrease in whistler mode intensity and bandwidth closest to the magnetic equator, where linear growth appears to dominate, with nonlinear structures appearing at higher latitudes and higher frequencies. We investigate linear growth rate using the Waves in a Homogeneous, Anisotropic, Multi-component Plasma dispersion solver and locally observed electron phase space density measurements from the Electron Spectrometer sensor of the Cassini Plasma Spectrometer Investigation to determine the parameters responsible for the variation in chorus intensity and bandwidth. We find that a temperature anisotropy (T?/T? ~ 1.3) can account for linear spatiotemporal growth rate of whistler mode waves, which provides a majority of the observed frequency-integrated power. At the highest frequencies, intense, nonlinear, frequency-drifting structures (drift rates ~ 200 Hz/s) are observed a few degrees away from the equator and can account for a significant fraction of the total power. Chorus emission at higher frequencies is distinct from lower frequency whistler mode emission and is sometimes correlated with simultaneously observed low-frequency electromagnetic ion cyclotron waves. These electromagnetic ion cyclotron waves appear to modulate a slow frequency drift (~15 Hz/s) which develops into nonlinear growth with much larger frequency drift associated only with the higher-frequency chorus.

Menietti, J. D.; Schippers, P.; Katoh, Y.; Leisner, J. S.; Hospodarsky, G. B.; Gurnett, D. A.; Santolik, O.

2013-09-01

340

[Carney complex].  

PubMed

Carney complex is a clinically and genetically heterogeneous disease, with at least two genetic loci including the PRKAR1A gene located on chromosome 17 and the CNC2 locus mapped to chromosome 2. Clinically this syndrome is characterized by multiple myxomas occurring in different anatomic sites, mucocutaneous pigmentary lesions, and a variety of non-endocrine and endocrine tumors, often causing endocrine abnormalities, involving various organs. Knowledge of morphological findings in CNC patients with their typical locations is necessary to raise suspicion of this syndrome by pathologists. Confirmation of the diagnosis allows regular clinical check-ups and early treatment of these patients. PMID:22145222

Kacerovská, D; Michal, M; Síma, R; Grossmann, P; Kazakov, D V

2011-10-01

341

Bimetallic complexes  

Microsoft Academic Search

The synthesis and reactions of bimetallic Zr(II)–Mo(0) complexes with bridging C5H4PPh2 ligands (henceforth abbreviated as Cp?) are described. Reaction of Cp2?ZrCl2 (1) with n-butyllithium in THF produces a metastable material tentatively formulated as Cp2?Zr·2 LiCl·4 THF (2). Diphenyldisulfide instantaneously converts 2 into the Zr(IV) dithiolate Cp2?Zr(SPh)2 (3). When 2 is treated with [Mo(CO)4(norbornadiene)], an unstable intermediate is formed which can

Wolfdieter A. Schenk; Thomas Gutmann

1998-01-01

342

Modeling Wildfire Incident Complexity Dynamics  

PubMed Central

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.

Thompson, Matthew P.

2013-01-01

343

Carney complex.  

PubMed

Carney complex is a rare, dominantly inherited multiple endocrine neoplasia syndrome, affecting endocrine glands as the adrenal cortex (causing Cushing's syndrome), the pituitary and the thyroid. It is associated with many other nonendocrine tumors, including cardiac myxomas, testicular tumors, melanotic schwannoma, breast myxomatosis, and abnormal pigmentation (lentiginosis) or myxomas of the skin. The gene located on the CNC1 locus was identified 12 years ago as the regulatory subunit 1A (R1A) of the protein kinase A (PRKAR1A) located at 17q22-24. Inactivating heterozygous germline mutations of PRKAR1A are observed in about two thirds of Carney complex patients with some genotype-phenotype correlation useful for follow-up and prognosis. More rarely, mutations of phosphodiesterase genes have been reported in patients presenting mainly with Cushing's syndrome. In vitro and in vivo studies help to understand how R1A inactivation leads to tumorigenesis. PRKAR1A appears to be a relatively weak tumorigenic signal which can cooperate with other signaling pathways and tumor suppressors. PMID:23652670

Espiard, Stéphanie; Bertherat, Jérôme

2013-03-19

344

Transmissivity variations in mudstones.  

PubMed

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

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

345

Forced obliquity variations of Mercury  

Microsoft Academic Search

The spin pole of Mercury is very nearly, but not quite, aligned with its orbit pole. Tidal dissipation has driven the free obliquity to very small values, and the high rate of spin pole precession allows the forced obliquity variations to remain small despite significant variations in orbital inclination and eccentricity. We present calculations of the obliquity for a 10

Bruce G. Bills; Robert L. Comstock

2005-01-01

346

SEMIANNUAL VARIATION OF GEOMAGNETIC ACTIVITY  

Microsoft Academic Search

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

C.T. Russell; R. L. McPherron

1973-01-01

347

Variational Bounds for Creeping Composites  

NASA Astrophysics Data System (ADS)

In the paper time dependent variational bounds are derived based on Extended Hashin-Shtrikman variational principles. Direct calculation leads to explicit formulas to be presented in the text. For various mechanical properties easy coding in Excel, say, can be used and verification of accuracy for numerical procedures is available using the derived formulas.

Procházka, Petr

2010-05-01

348

Population genetic variation in gene expression is associated withphenotypic variation in Saccharomyces cerevisiae  

SciTech Connect

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.

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

2004-02-25

349

The complexity of anatomical systems  

PubMed Central

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.

Grizzi, Fabio; Chiriva-Internati, Maurizio

2005-01-01

350

Genetic architecture of regulatory variation in Arabidopsis thaliana.  

PubMed

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

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

2011-04-05

351

Holding the Words in Our Mouths: Responses to Dialect Variations in Oral Reading  

ERIC Educational Resources Information Center

|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.)|

Van Duinen, Deborah Vriend; Wilson, Marilyn J.

2008-01-01

352

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 ...

353

Some Dimensions of Intercultural Variation and Their Implication for Interpersonal Behavior.  

National Technical Information Service (NTIS)

A review of a broad literature suggested certain dimensions of cultural variation that influence social behavior. Table 1 shows these dimensions. Table 2 shows how these dimensions are related to higher order dimensions of cultural complexity, modernity, ...

H. C. Triandis

1981-01-01

354

Martian Craters at the Simple-Complex Transition Diameter  

NASA Astrophysics Data System (ADS)

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.

Herrick, R. R.

2012-03-01

355

Variation in teachers' descriptions of teaching: Broadening the understanding of teaching in higher education  

Microsoft Academic Search

In the present study 71 university teachers from several disciplines were interviewed in order to capture the variation in descriptions of teaching. Two broad categories of description were identified: the learning-focused and the content-focused approaches to teaching. The results showed that the relationship between the two approaches was complex and variation could be captured in detail only after considering the

Liisa Postareff; Sari Lindblom-Ylänne

2008-01-01

356

The Architecture of Gene Regulatory Variation across Multiple Human Tissues: The MuTHER Study  

Microsoft Academic Search

While there have been studies exploring regulatory variation in one or more tissues, the complexity of tissue-specificity in multiple primary tissues is not yet well understood. We explore in depth the role of cis-regulatory variation in three human tissues: lymphoblastoid cell lines (LCL), skin, and fat. The samples (156 LCL, 160 skin, 166 fat) were derived simultaneously from a subset

Alexandra C. Nica; Leopold Parts; Daniel Glass; James Nisbet; Amy Barrett; Magdalena Sekowska; Mary Travers; Simon Potter; Elin Grundberg; Kerrin Small; Åsa K. Hedman; Veronique Bataille; Jordana Tzenova Bell; Gabriela Surdulescu; Antigone S. Dimas; Catherine Ingle; Frank O. Nestle; Paola di Meglio; Josine L. Min; Alicja Wilk; Christopher J. Hammond; Neelam Hassanali; Tsun-Po Yang; Stephen B. Montgomery; Steve ORahilly; Cecilia M. Lindgren; Krina T. Zondervan; Nicole Soranzo; Inês Barroso; Richard Durbin; Kourosh Ahmadi; Panos Deloukas; Mark I. McCarthy; Emmanouil T. Dermitzakis; Timothy D. Spector

2011-01-01

357

Genetic Association Studies of Copy-Number Variation: Should Assignment of Copy Number States Precede Testing?  

Microsoft Academic Search

Recently, structural variation in the genome has been implicated in many complex diseases. Using genomewide single nucleotide polymorphism (SNP) arrays, researchers are able to investigate the impact not only of SNP variation, but also of copy-number variants (CNVs) on the phenotype. The most common analytic approach involves estimating, at the level of the individual genome, the underlying number of copies

Patrick Breheny; Prabhakar Chalise; Anthony Batzler; Liewei Wang; Brooke L. Fridley

2012-01-01

358

Wintertime surface energy budget variations in the Grand Canyon region  

SciTech Connect

Few detailed technical studies of the spatial variation of long and shortwave radiation or individual components of the surface energy budget have yet been conducted in areas of complex terrain. The interested observer or resident of complex terrain areas is quite familiar, however, with the rapid variations in climate and weather that occur over short spatial scales. These variations arise on clear undistributed days as well as on days with varying cloud cover, and can be attributed to the propagation of shadows across the landscape, the varying angles of insolation of inclined slopes, the different types of land surface cover (e.g., snow, rock, forests), variations in soil moisture, and the degree of confinement of the topography (deep valley, broad basin, etc.), among other factors. The present paper is an initial attempt to quantify the effects of such factors using a digital topographic model of the complicated topography of the Grand Canyon area of Arizona. This area was chosen for simulation because of the opportunities offered by a winter field experiment conducted there in 1990 by Arizona's Salt River Project. While the field experiment was focused primarily on visibility and air pollution studies, the comprehensive data sets from the experiment are a valuable resource for basic studies of complex terrain weather and climate. 2 refs., 9 figs.

Ruffieux, D.C. (Colorado Univ., Boulder, CO (USA). Cooperative Inst. for Research in Environmental Sciences National Oceanic and Atmospheric Administration, Boulder, CO (USA). Wave Propagation Lab.); Whiteman, C.D. (Pacific Northwest Lab., Richland, WA (USA))

1991-02-01

359

Drosophila bristles and the nature of quantitative genetic variation  

PubMed Central

Numbers of Drosophila sensory bristles present an ideal model system to elucidate the genetic basis of variation for quantitative traits. Here, we review recent evidence that the genetic architecture of variation for bristle numbers is surprisingly complex. A substantial fraction of the Drosophila genome affects bristle number, indicating pervasive pleiotropy of genes that affect quantitative traits. Further, a large number of loci, often with sex- and environment-specific effects that are also conditional on background genotype, affect natural variation in bristle number. Despite this complexity, an understanding of the molecular basis of natural variation in bristle number is emerging from linkage disequilibrium mapping studies of individual candidate genes that affect the development of sensory bristles. We show that there is naturally segregating genetic variance for environmental plasticity of abdominal and sternopleural bristle number. For abdominal bristle number this variance can be attributed in part to an abnormal abdomen-like phenotype that resembles the phenotype of mutants defective in catecholamine biosynthesis. Dopa decarboxylase (Ddc) encodes the enzyme that catalyses the final step in the synthesis of dopamine, a major Drosophila catecholamine and neurotransmitter. We found that molecular polymorphisms at Ddc are indeed associated with variation in environmental plasticity of abdominal bristle number.

Mackay, Trudy F.C; Lyman, Richard F

2005-01-01

360

Complexities in diluted magnetic semiconductors-a theoretical perspective from ab-initio electronic structure calculations  

NASA Astrophysics Data System (ADS)

Diluted magnetic semiconductors (DMS), the essential materials for semiconductor spintronics, show a variety of complex properties, e.g., defect-mediated (ferro/antiferro)magnetic interactions and the disorder leading to magnetic percolation effects. Using the ab-initio Korringa-Kohn-Rostoker-Coherent-Potential-Approximation, the magnetic pair exchange parameters of a Heisenberg model have been calculated for Mn doped ZnO and half-Heusler NiTiSn hosts followed by the calculation of transition temperatures using Monte-Carlo simulations. Zinc vacancies and nitrogen substituting oxygen atoms lead to ferromagnetic interactions in Mn doped ZNO while in a defect free case, the interaction between Mn atoms is antiferromagnetic. The calculated critical temperatures are low (˜35 K) due to the short-ranged exchange interactions and low defect concentration. In the other case, Mn doped NiTiSn shows a high critical temperature (˜300 K) for 22 % Mn concentration. Below 3% Mn, there is no magnetic long range order as the magnetic percolation is not established. The results are in good agreement with experiments.

Sanyal, Biplab; Iusan, Diana; Eriksson, Olle

2007-03-01

361

[Carney complex].  

PubMed

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

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

2011-05-04

362

Genomic mining for complex disease traits with \\  

Microsoft Academic Search

Our rapidly growing knowledge regarding genetic variation in the human genome offers great potential for understanding the genetic etiology of disease. This, in turn, could revolutionize detection, treatment, and in some cases prevention of disease. While genes for most of the rare monogenic diseases have already been discovered, most common diseases are complex traits, resulting from multiple gene-gene and gene-environment

Margaret J. Eppstein; Joshua L. Payne; Bill C. White; Jason H. Moore

2007-01-01

363

Genetic and epigenetic contribution to complex traits.  

PubMed

Much of the recent advances in functional genomics owe to developments in next-generation sequencing technology, which has contributed to the exponential increase of genomic data available for different human disease and population samples. With functional sequencing assays available to query both the transcriptome and the epigenome, annotation of the non-coding, regulatory genome is steadily improving and providing means to interpret the functional consequences of genetic variants associated with human complex traits. This has highlighted the need to better understand the normal variation in various cellular phenotypes, such as epigenetic modifications, and their transgenerational inheritance. In this review, we discuss different aspects of epigenetic variation in the context of DNA sequence variation and its contribution to complex phenotypes. PMID:22976472

Kilpinen, Helena; Dermitzakis, Emmanouil T

2012-09-12

364

Investigating the Conceptual Variation of Major Physics Textbooks  

NASA Astrophysics Data System (ADS)

The conceptual problem content of the electricity and magnetism chapters of seven major physics textbooks was investigated. The textbooks presented a total of 1600 conceptual electricity and magnetism problems. The solution to each problem was decomposed into its fundamental reasoning steps. These fundamental steps are, then, used to quantify the distribution of conceptual content among the set of topics common to the texts. The variation of the distribution of conceptual coverage within each text is studied. The variation between the major groupings of the textbooks (conceptual, algebra-based, and calculus-based) is also studied. A measure of the conceptual complexity of the problems in each text is presented.

Stewart, John; Campbell, Richard; Clanton, Jessica

2008-04-01

365

1990 lectures in complex systems  

SciTech Connect

This report contains the following papers: modeling complex systems: Stochastic processes, stochastic differential equations, and fokker-planck equations; complexity in fluids; pattern formation in chemical systems: Roles of open reactors; experimental analysis of disordered systems; theory and applications of information-based complexity; some learning tasks from a control perspective; moving a human or robot arm with many degrees of freedom: Issues and ideas; control of tongue movement dynamics; models of somatotopic map organization; sex and evolution; dynamics of neutral excitability; linking structure and function: Information processing in the brain; physiological studies in silico; nonlinear dynamics of neutral delayed feedback; functional self-organization in complex systems; forecasting chaotic computational ecosystems; singularities for complex hyperbolic equations; an overview of the minimum description length principle; equations of motion from data with hidden variables; spectral entropy and self-organization; asynchronous parallel simulated annealing; dynamics of a trapped ion driven by stochastic optical processes; undecidability in the adaptive system; bifurications and chaos in a Paradigm equation for delayed mixed feedback; asymptotic periodicity in one-dimensional maps; and theme and variations: Spin glasses, neutral networks, and prebiotic evolution.

Nadel, L.; Stein, D.L. (eds.)

1991-01-01

366

Applications of the Variation Method  

Microsoft Academic Search

The variation method is applied to two examples selected for illustration of fundamental principles of the method along with ease of calculation. The first example applies the linear version of the variation method to the particle in a box model, using a basis with explicit parity symmetry, Phik(t) = N (1-t2)tk, where t = 2x\\/L -1 and N is the

Stephen K. Knudson

1997-01-01

367

Hollow glass waveguides: New variations  

Microsoft Academic Search

This study is an effort to develop new variations on the infrared silver-silver iodide hollow glass waveguide (HGW) with application specific properties. Four variations are presented: a HGW with a long, gradual taper, a HGW with a rectangular cross-section, curved HGW tips and a new all-dielectric hollow waveguide based on photonic bandgap guidance principles. A hollow glass waveguide tapered over

Daniel Joseph Gibson

2003-01-01

368

Complex fuzzy logic  

Microsoft Academic Search

A novel framework for logical reasoning, termed complex fuzzy logic, is presented in this paper. Complex fuzzy logic is a generalization of traditional fuzzy logic, based on complex fuzzy sets. In complex fuzzy logic, inference rules are constructed and \\

D. Ramot; M. Friedman; G. Langholz; A. Kandel

2003-01-01

369

Complex Partial Seizures  

MedlinePLUS

Complex Partial Seizures You are here: Home About Epilepsy Seizures Partial Seizures Complex Partial Seizures Email Print Twitter Facebook MySpace Delicous ... Complex Partial Seizures ] First Aid for Complex Partial Seizures Do not restrain the person. Remove dangerous objects ...

370

Pure variation and organic stratification.  

PubMed

The fundamental problem posed by Darwin distinguishes his theory from any transformism of the past as well as any evolutionism to come: since variation is inherent to the living, it is a question of explaining, not at all why the living varies, but instead why the living does not vary in all directions to the point of constituting a continuum of forms varying ad infinitum. What limits and stabilizes this intrinsically unlimited variation, allowing certain forms to subsist and multiply to the detriment of others, is natural selection. This double principle of intrinsic variation/extrinsic selection constitutes a vector for the unification of reality that underlies Jean-Jacques Kupiec's ontophylogenesis as well as Deleuze and Guattari's global philosophy of Nature. Therefore, everything would potentially tend to incessantly vary. The work of Kupiec and others identifies an intrinsic random variation within ontogenesis itself. For Deleuze and Guattari, it is nothing but the figure, already selected by the organic stratum, of a more fundamental or pure variation. But, in fact, nothing really varies incessantly: everything undergoes a selective pressure according to which nothing subsists as such except what manages to endure through invariance (physical stratum) or reproduction (organic stratum). Thus, organic stratification only retains from variation what ensures and augments this reproduction. In this sense, every organism stratifies, i.e. submits to its imperative of subsistence and reproduction, a body without organs that varies in itself and always tends to escape the organism, for better (intensifications of life) or worse (cancerous pathologies). PMID:22884711

Rosanvallon, Jérôme

2012-07-31

371

Epistasis, complexity, and multifactor dimensionality reduction.  

PubMed

Genome-wide association studies (GWASs) and other high-throughput initiatives have led to an information explosion in human genetics and genetic epidemiology. Conversion of this wealth of new information about genomic variation to knowledge about public health and human biology will depend critically on the complexity of the genotype to phenotype mapping relationship. We review here computational approaches to genetic analysis that embrace, rather than ignore, the complexity of human health. We focus on multifactor dimensionality reduction (MDR) as an approach for modeling one of these complexities: epistasis or gene-gene interaction. PMID:23756906

Pan, Qinxin; Hu, Ting; Moore, Jason H

2013-01-01

372

Cognitive complexity, introversion, and preference for complexity  

Microsoft Academic Search

Obtained complexity preferences among random polygons from 40 undergraduates, cross-classified on cognitive complexity-simplicity and introversion-extroversion, while GSR was monitored. Complex Ss manifest higher GSRs in attending to the stimuli. Examinations of preferences across 2 different sets of stimuli and methods of preferential rating demonstrated that (a) extraverts preferred moderate levels of complexity, regardless of classification as cognitively complex or simple;

Jeff B. Bryson; Michael J. Driver

1972-01-01

373

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

PubMed

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

Phillips, Jordan J; Peralta, Juan E

2013-05-01

374

Mutations and quantitative genetic variation: lessons from Drosophila  

PubMed Central

A central issue in evolutionary quantitative genetics is to understand how genetic variation for quantitative traits is maintained in natural populations. Estimates of genetic variation and of genetic correlations and pleiotropy among multiple traits, inbreeding depression, mutation rates for fitness and quantitative traits and of the strength and nature of selection are all required to evaluate theoretical models of the maintenance of genetic variation. Studies in Drosophila melanogaster have shown that a substantial fraction of segregating variation for fitness-related traits in Drosophila is due to rare deleterious alleles maintained by mutation–selection balance, with a smaller but significant fraction attributable to intermediate frequency alleles maintained by alleles with antagonistic pleiotropic effects, and late-age-specific effects. However, the nature of segregating variation for traits under stabilizing selection is less clear and requires more detailed knowledge of the loci, mutation rates, allelic effects and frequencies of molecular polymorphisms affecting variation in suites of pleiotropically connected traits. Recent studies in D. melanogaster have revealed unexpectedly complex genetic architectures of many quantitative traits, with large numbers of pleiotropic genes and alleles with sex-, environment- and genetic background-specific effects. Future genome wide association analyses of many quantitative traits on a common panel of fully sequenced Drosophila strains will provide much needed empirical data on the molecular genetic basis of quantitative traits.

Mackay, Trudy F. C.

2010-01-01

375

Reduced variational space analysis of methane adducts  

SciTech Connect

Methane is the major component of natural gas, and hence its catalytic conversion to functionalized products (e.g., methanol) is of great interest. A variety of transition metal complexes have been investigated experimentally for the selective activation of methane. Recent experiments and computations suggest that weakly bound methane adducts play a pivotal role in metal-mediated methane activation. Calculation of the intrinsic reaction coordinates for methane activation by d{sup 0} imidos indicates that the adduct lies along the pathway for methane activation. Isolation of a stable methane adduct, suitable for experimental characterization, would be aided by a greater understanding of their chemistry. Given the short-lived nature of these adducts and the limited direct experimental information, computational chemistry is a useful tool for understanding the bonding and structure of these catalytic intermediates. This research investigated the bonding forces in methane adducts of transition metal (TM) complexes. The calculations reported here employed effective core potential (ECP) methods within the Hartree-Fock approximation using the GAMESS quantum chemistry program. The reduced variational space self-consistent field (RVS-SCF) method developed by Stevens and Fink was employed. This technique was used to analyze the Coulomb and exchange energy (CEX), polarization energy (POL), and charge transfer energy (CT) contributions to the binding energy ({Delta}E{sub add}) of methane to a TM complex. Adducts of high-valent (d{sup 0}) transition metal complexes were studied. The role of metal, ligand, and charge on the different contributions to the binding energy were analyzed.

Cundari, T.R.; Klinckman, T.R. [Univ. of Memphis, TN (United States). Dept. of Chemistry

1998-10-05

376

A variational multiscale method for LES  

NASA Astrophysics Data System (ADS)

The variational multiscale method is based on an a priori separation of scales into two parts, a large scale (well resolved) set and a fine scale (marginally resolved) set. The large scale equations are solved without modeling though they do depend on information contained in the small scales. The small scales are modeled using more or less traditional LES models. This a priori separation of scales obviates the usual filtering process and prevents models from directly impacting the well resolved scales. The scale separation is trivial to cary out in spectral methods. To extend to complex geometries we have extended the method to a hierarchical basis finite elment code. Here, the basis functions of order k are a subset of the basis functions for k+1 which enables the a priori scale separation. Preliminary calculations on decay of isotropic turbulence and channel flow will be shown.

Jansen, Kenneth; Hughes, Thomas; Whiting, Christian

1999-11-01

377

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

NASA Astrophysics Data System (ADS)

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 ?m, 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.

Borchert, Manuela; Wilke, Max; Schmidt, Christian; Kvashnina, Kristina

2010-05-01

378

Supramolecular calsequestrin complex.  

PubMed

As recently demonstrated by overlay assays using calsequestrin-peroxidase conjugates, the major 63 kDa Ca(2+)-binding protein of the sarcoplasmic reticulum forms complexes with itself, and with junctin (26 kDa), triadin (94 kDa) and the ryanodine receptor (560 kDa) [Glover, L., Culligan, K., Cala, S., Mulvey, C. & Ohlendieck, K. (2001) Biochim. Biophys. Acta1515, 120-132]. Here, we show that variations in the relative abundance of these four central elements of excitation-contraction coupling in different fiber types, and during chronic electrostimulation-induced fiber type transitions, are reflected by distinct alterations in the calsequestrin overlay binding patterns. Comparative immunoblotting with antibodies to markers of the junctional sarcoplasmic reticulum, in combination with the calsequestrin overlay binding patterns, confirmed a lower ryanodine receptor expression in slow soleus muscle compared to fast fibers, and revealed a drastic reduction of the RyR1 isoform in chronic low-frequency stimulated tibialis anterior muscle. The fast-to-slow transition process included a distinct reduction in fast calsequestrin and triadin and a concomitant reduction in calsequestrin binding to these sarcoplasmic reticulum elements. The calsequestrin-binding protein junctin was not affected by the muscle transformation process. The increase in calsequestrin and decrease in junctin expression during postnatal development resulted in similar changes in the intensity of binding of the calsequestrin conjugate to these sarcoplasmic reticulum components. Aged skeletal muscle fibers tended towards reduced protein interactions within the calsequestrin complex. This agrees with the physiological concept that the key regulators of Ca(2+) homeostasis exist in a supramolecular membrane assembly and that protein-protein interactions are affected by isoform shifting underlying the finely tuned adaptation of muscle fibers to changed functional demands. PMID:12230573

Glover, Louise; Quinn, Sandra; Ryan, Michelle; Pette, Dirk; Ohlendieck, Kay

2002-09-01

379

Modeling wildfire incident complexity dynamics.  

PubMed

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

Thompson, Matthew P

2013-05-14

380

Environmental stress and the expression of genetic variation.  

PubMed

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

Jenkins, N L; Sgrò, C M; Hoffmann, A A

1997-01-01

381

Hotspots for copy number variation in chimpanzees and humans  

PubMed Central

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.

Perry, George H.; Tchinda, Joelle; McGrath, Sean D.; Zhang, Junjun; Picker, Simon R.; Caceres, Angela M.; Iafrate, A. John; Tyler-Smith, Chris; Scherer, Stephen W.; Eichler, Evan E.; Stone, Anne C.; Lee, Charles

2006-01-01

382

Molecular Darwinism: the contingency of spontaneous genetic variation.  

PubMed

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

Arber, Werner

2011-01-01

383

Small Scale Abundance Variations in TMC-1  

NASA Astrophysics Data System (ADS)

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.

Dickens, J. E.; Langer, W. D.; Velusamy, T.

2000-12-01

384

Complex systems and the technology of variability analysis  

Microsoft Academic Search

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

Andrew JE Seely; Peter T Macklem

2004-01-01

385

Visual Complexity and Pictorial Memory: A Fifteen Year Research Perspective.  

ERIC Educational Resources Information Center

|For 15 years an ongoing research project at the University of Pittsburgh has focused on the effects of variations in visual complexity and color on the storage and retrieval of visual information by learners. Research has shown that visual materials facilitate instruction, but has not fully delineated the interactions of visual complexity and…

Berry, Louis H.

386

The Growth of Structural and Functional Complexity during Evolution  

Microsoft Academic Search

Although the growth of complexity during evolution seems obvious to most observers, it has recently been questioned whether such increase objectively exists. The present paper tries to clarify the issue by analysing the concept of complexity as a combination of variety and dependency. It is argued that variation and selection automatically produce differentiation (variety) and integration (dependency), for living as

Francis HEYLIGHEN

1996-01-01

387

The Complex Image Approximation for Induction in a Multilayered Earth  

Microsoft Academic Search

It is shown that many geophysical problems involving the induction of earth currents by external magnetic variations can be solved by a method of images in which the earth is replaced by the image of the inducing source located at some complex depth beneath the earth's surface. An expression for this complex depth in a horizontally stratified earth is derived,

D. J. Thomson; J. T. Weaver

1975-01-01

388

Transit variations in WASP-3  

NASA Astrophysics Data System (ADS)

The variations in the period and duration of the transits of exoplanets allow us to obtain some of their orbital properties. Here we investigate the variations in the transit parameters of WASP-3 over a period of time that covers more than three years. Apart from providing complementary information on the geometrical configuration of the system, the investigation of transit duration (TDV) can also provide indirect evidence of the presence of additional planets. The WASP-3 system constitutes the first example for which the TDV have been tracked over a long period of time, allowing for the easier detection of secular variations of the orbital parameters. This work shows that the effects of nodal precession are clearly discernible in the TDV of WASP-3, as the theory predicts. We also confirm the presence of strong transit time (TTV) in a shorter time scale but in this case the periodicity of the signal is not so clear.

Cuesta, L.; Teresa Eibe, M.; Ullán, A.; Pérez-Verde, A.; Navas, J.

2013-05-01

389

Extensions of Variational Methods, I ---Super-Stationary Variational Method  

Microsoft Academic Search

Several methods to improve the degree of approximation for the stationary character in variational methods, are discussed. By selecting a set of trial functions as prescribed in the present paper, it is shown that we can construct quite generally a super-stationary expression for the quantity we wish to find. By ``super-stationary'' we mean that, the first, second and third varitions

Takashi Kikuta

1955-01-01

390

Variation in fibular robusticity reflects variation in mobility patterns  

Microsoft Academic Search

During hominin plantigrade locomotion, the weight-bearing function of the fibula has been considered negligible. Nevertheless, studies conducted on human samples have demonstrated that, even if less than that of the tibia, the load-bearing function of the fibula still represents a considerable portion of the entire load borne by the leg. The present study assesses whether variation in habitual lower limb

Damiano Marchi; Colin N. Shaw

2011-01-01

391

Population variation in sexual dimorphism in the human innominate  

Microsoft Academic Search

In the adult human innominate, pubis length and sciatic notch width are generally considered to offer the best prospect for\\u000a reliable sex identification. Population variation in the extent of sexual dimorphism in these features was examined in two\\u000a temporally distinct European skeletal collections of documented age and sex. (English and Dutch). A complex relationship was\\u000a found to exist between pubis

S. M. MacLaughlin; M. F. Bruce

1986-01-01

392

Physical and Chemical Variations Along the Central American Volcanic Arc  

NSDL National Science Digital Library

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

Ratajeski, Kent

393

Variational approximations for stationary states of Ising-like models  

NASA Astrophysics Data System (ADS)

We introduce a new variational approach to the stationary state of kinetic Ising-like models. The approach is based on the cluster expansion of the entropy term appearing in a functional which is minimized by the system history. We rederive a known mean-field theory and propose a new method, here called diamond approximation, which turns out to be more accurate and faster than other methods of comparable computational complexity.

Pelizzola, Alessandro

2013-04-01

394

Mössbauer and positron annihilation studies of pharmaceutically important iron-dextran complexes  

NASA Astrophysics Data System (ADS)

Iron-dextran complexes are pharmaceutically important models of iron-storage protein ferritin. These complexes are used for treatment of iron-deficiency anemias. In this work we present the results of the study of various iron-dextran complexes by Mössbauer spectroscopy and the positron annihilation technique. Mössbauer spectroscopy indicated the differences between the electronic and magnetic structures of iron cores in iron-dextran complexes while positron annihilation showed variations of dextran shells in those complexes. Both techniques appeared to be useful to study microstructural variations in iron-dextran complexes.

Oshtrakh, M. I.; Kopelyan, E. A.; Semionkin, V. A.; Livshits, A. B.; Krylova, V. E.; Kozlov, A. A.

1993-04-01

395

Variations in Human Skin Color  

NSDL National Science Digital Library

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

American Association for the Advancement of Science (;)

2006-09-09

396

k-parameter geodesic variations  

NASA Astrophysics Data System (ADS)

Suppose S is a semispray on a manifold M. We know that the complete lift Sc of S is a semispray on TM with the property that geodesics of Sc correspond to Jacobi fields of S. In this note we generalise this result and show how geodesic variations of k variables are related to geodesics of the kth iterated complete lift of S. Moreover, for sprays (that is, homogeneous semisprays) we show how geodesic variations of (n-1) variables are related to a natural generalisation of Jacobi tensors.

Bucataru, Ioan; Dahl, Matias F.

2012-11-01

397

Exploiting natural variation in Arabidopsis.  

PubMed

Natural variation for many traits is present within the species Arabidopsis thaliana. This chapter describes the use of natural variation to elucidate genes underlying the regulation of quantitative traits. It deals with the development and use of mapping populations, the detection and handling of genetic markers, the phenotyping of quantitative traits, and, finally, QTL analyses. The focus of the chapter is on the use and development of recombinant inbred lines, but other types of segregating populations, including genome-wide association mapping in natural populations, are also discussed. PMID:24057363

Molenaar, Johanna A; Keurentjes, Joost J B

2014-01-01

398

a Variational Derivation of P  

NASA Astrophysics Data System (ADS)

Multigroup P_{N} theory is a widely-used approximation to multigroup transport theory. However, there are aspects of multigroup P _{N} theory that are not satisfactory, particularly regarding boundary conditions at a boundary having a prescribed incident flux. Historically, P _{N} boundary conditions at such a boundary have been assumed to be in the form given by Marshak or Mark, although Federighi and Pomraning have considered other possibilities for the case of one energy group. In this work we introduce two new variational principles. The first principle, unambiguously leads from a steady-state, first order, slab geometry multigroup transport problem to a multigroup P_{N} problem. The variationally-derived P_{N } problem consists of the conventional multigroup P_{N} equations and variational boundary conditions. At a boundary with a prescribed incident flux, these conditions are new and consistitute a generalization of Pomraning's boundary conditions applied to each energy group. For a vacuum boundary, these conditions reduce the Federighi's boundary condition applied to each energy group. Therefore, we refer to these newly developed P _{N} boundary conditions as the Generalized Federighi-Pomraning (GFP) boundary conditions. The second variational principle introduced in this work leads from a steady-state, even-parity slab geometry, multigroup transport problem to a multigroup, second-order P _{N} problem. This problem consists of the multigroup second-order P_{N } equations and Marshak boundary conditions. We generalize the second-order variational procedure to the three-dimensional geometry and obtain the general geometry multigroup second-order P_{N} equations and the three-dimensional Marshak-like boundary conditions. We also show how the first-order variational principle can be used to derive rigorous boundary conditions for the even-order P_{N}~imations and that these P_{N} approximations can provide accurate numerical results. Finally, a numerical comparison of the Generalized Federighi-Pomraning, Mark, Marshak and (newly developed by Larsen and Pomraning) variational-asymptotic boundary conditions shows that outside the asymptotic limit in which the variational-asymptotic and GFP boundary conditions are always superior, different boundary conditions perform best in different physical situations.

Rulko, Robert Pawel

399

Crystallization of macromolecular complexes: combinatorial complex crystallization  

Microsoft Academic Search

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

Enrico A Stura; Marc Graille; Jean-Baptiste Charbonnier

2001-01-01

400

COMPLEX TRAUMA, COMPLEX REACTIONS: ASSESSMENT AND TREATMENT  

Microsoft Academic Search

Complex trauma occurs repeatedly and escalates over its duration. In families, it is exemplified by domestic violence and child abuse and in other situations by war, prisoner of war or refugee status, and human trafficking. Complex trauma also refers to situations such as acute\\/chronic illness that requires intensive medical intervention or a single traumatic event that is calamitous. Complex trauma

Christine A. Courtois

2004-01-01

401

Complex Trauma, Complex Reactions: Assessment and Treatment  

Microsoft Academic Search

Complex trauma occurs repeatedly and escalates over its duration. In families, it is exemplified by domestic violence and child abuse and in other situations by war, prisoner of war or refugee status, and human trafficking. Complex trauma also refers to situations such as acute\\/chronic illness that requires intensive medical intervention or a single traumatic event that is calamitous. Complex trauma

Christine A. Courtois

2008-01-01

402

On State Complexes and Special Cube Complexes  

ERIC Educational Resources Information Center

|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,…

Peterson, Valerie J.

2009-01-01

403

Mapping the Epistatic Network Underlying Murine Reproductive Fatpad Variation  

PubMed Central

Genome-wide mapping analyses are now commonplace in many species and several networks of interacting loci have been reported. However, relatively few details regarding epistatic interactions and their contribution to complex trait variation in multicellular organisms are available and the identification of positional candidate loci for epistatic QTL (epiQTL) is hampered, especially in mammals, by the limited genetic resolution inherent in most study designs. Here we further investigate the genetic architecture of reproductive fatpad weight in mice using the F10 generation of the LG,SM advanced intercross (AI) line. We apply multiple mapping techniques including a single-locus model, locus-specific composite interval mapping (CIM), and tests for multiple QTL per chromosome to the 12 chromosomes known to harbor single-locus QTL (slQTL) affecting obesity in this cross. We also perform a genome-wide scan for pairwise epistasis. Using this combination of approaches we detect 199 peaks spread over all 19 autosomes, which potentially contribute to trait variation including all eight original F2 loci (Adip1-8), novel slQTL peaks on chromosomes 7 and 9, and several novel epistatic loci. Extensive epistasis is confirmed involving both slQTL confidence intervals (C.I.) as well as regions that show no significant additive or dominance effects. These results provide important new insights into mapping complex genetic architectures and the role of epistasis in complex trait variation.

Jarvis, Joseph P.; Cheverud, James M.

2011-01-01

404

Elastic electron scattering from formic acid  

SciTech Connect

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.

Trevisan, Cynthia S.; Orel, Ann E.; Rescigno, Thomas N.

2006-07-31

405

Variational solutions to stochastic quantization  

SciTech Connect

We show that the Langevin equation, when used in stochastic quantization, can provide a simple variational principle for field theories. We test the method on exactly soluble models in zero dimensions and on the quantum-mechanical anharmonic oscillator in one dimension.

Amundsen, P.A.; Damgaard, P.H.

1984-01-15

406

Variational Approach to Melting. Ii.  

National Technical Information Service (NTIS)

A variational approach to the equilibrium thermodynamic properties of an original system based upon an inequality for the Helmholtz free energy of that system is introduced. A system with molecules obeying the cell model of Lennard-Jones and Devonshire, a...

G. A. Mansoori F. B. Canfield

1969-01-01

407

GENOME VARIATION IN ALLOPOLYPLOID TRITICALE  

Technology Transfer Automated Retrieval System (TEKTRAN)

Genome variation in allopolyploid triticale was investigated using both AFLP and RFLP analyses. The restriction enzymes used for AFLP analyses were selected to primarily amplify repetitive and low-copy sequences with two sets of primers, EcoRI/MseI and PstI/MseI, respectively. To estimate the amount...

408

Super-stationary Variational Method  

Microsoft Academic Search

The stationary character in the usual variational method is extended by using a trial function with stationary character. A successive method for the improvement of the stationary character is also indicated. We have applied this method both for bound state problems and for continuous spectra (scattering problems).

Takashi Kikuta

1954-01-01

409

Variational Methods for Field Theories  

Microsoft Academic Search

The thesis has four parts, dealing with four field theory models: Periodic Quantum Electrodynamics (PQED) in (2 + 1) dimensions, free scalar field theory in (1 + 1) dimensions, the Quantum XY model in (1 + 1) dimensions, and the (1 + 1) dimensional Ising model in a transverse magnetic field. The last three parts deal exclusively with variational methods;

Shahar Ben-Menahem

1982-01-01

410

Modeling Natural Variation through Distribution  

ERIC Educational Resources Information Center

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…

Lehrer, Richard; Schauble, Leona

2004-01-01

411

Influence of Coronal Abundance Variations  

NASA Astrophysics Data System (ADS)

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

DeLuca, E. E.

2002-05-01

412

Variation and the Interlanguage Hypothesis.  

ERIC Educational Resources Information Center

Suggests that interlanguage morphology research contradictions have occurred as a result of a descriptively inadequate variation model. This assertion provides the basis for proposing and applying a multivariate model (acquisition stage, linguistic environment, and communicative redundancy) to an analysis of native Mandarin Chinese speakers'…

Young, Richard

1988-01-01

413

VARIATION IN PEREGRINE FALCON EGGS  

Microsoft Academic Search

Eggs collected from captive and wild Peregrine Falcons (Falco peregrinus) were used to examine variation in eggshell thickness, length, breadth, and initial weight to resolve questions about eggshell data from wild falcons. For captive falcons, shell thickness of first clutches did not change over the years a falcon laid or with embryonic development. Egg- shells in third clutches, but not

WILLIAM A. BURNHAM; JAMES H. ENDERSON

1984-01-01

414

Human subtelomeric copy number variations  

Microsoft Academic Search

Copy number variation is a defining characteristic of human subtelomeres. Human subtelomeric segmental duplication regions (‘Subtelomeric Repeats’) comprise about 25% of the most distal 500 kb and 80% of the most distal 100 kb in human DNA. Huge allelic disparities seen in subtelomeric DNA sequence content and organization are postulated to have an impact on the dosage of transcripts embedded

H. Riethman

2008-01-01

415

Geometrical Variations of Gain Patterns  

Microsoft Academic Search

This paper studies the effect of the altitude and the elliptical nature of the Earth on projected antenna pattern functions (APFs). These variations can play a significant role in spatial filter algorithms, such as the Backus-Gilbert method. In this paper, a solution for projecting an APF from an arbitrary sensor and platform onto an elliptical Earth is presented. A general

Philip J. Stephens; Andrew S. Jones

2007-01-01

416

Variational nodal transport perturbation theory  

Microsoft Academic Search

A perturbation method based on the variational nodal method for solving the neutron transport equation is developed for multidimensional geometries. The method utilizes the solution of the corresponding adjoint transport equation to calculate changes in the critical eigenvalue due to cross-section changes. Both first-order and exact perturbation theory expressions are derived. The adjoint solution algorithm has been formulated and incorporated

K. F. Laurin-Kovitz; E. E. Lewis

1996-01-01

417

Somatic variation in Lolium perenne  

Microsoft Academic Search

An investigation of somatic variation in 10 plants of Lolium perenne, using a two-stage cloning process followed by two further cycles of vegetative propagation, has revealed that persistent differences in tiller number and plant height may arise at the time of the initial cloning. These effects were dependent upon the age of the clone and its past vegetative history. Transmissibility

Y Shimamoto; M D Hayward

1975-01-01

418

Variations of the solar constant  

SciTech Connect

The variations in data received from rocket-borne and balloon-borne instruments are discussed. Indirect techniques to measure and monitor the solar constant are presented. Emphasis is placed on the correlation of data from the Solar Maximum Mission and the Nimbus 7 satellites. Abstracts of individual items from the workshop were prepared separately for the data base.

Sofia, S. (ed.)

1981-12-01

419

Modeling Natural Variation through Distribution  

ERIC Educational Resources Information Center

|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…

Lehrer, Richard; Schauble, Leona

2004-01-01

420

Seasonal variation of the global electrical circuit  

Microsoft Academic Search

The effects of boundary layer aerosol particles on the electric field measurement of the DC global circuit are considered. Aitken (condensation) nuclei concentrations are found to have systematic local seasonal variations which obscure the global behavior of the DC circuit. These local variations appear to be the result of several seasonal factors, including variations in atmospheric mixed layer heights, variations

Edwin J. Adlerman; Earle R. Williams

1996-01-01

421

Structure of variational principles in nonequilibrium thermodynamics  

Microsoft Academic Search

There are a lot of different methods to construct variational principles in physics. In this paper we investigate and classify some of the known methods, focusing our treatment mainly on the variational principles in nonequilibrium thermodynamics. This area of physics is remarkably rich in different variational methods, because here we cannot obtain a classical, Hamiltonian variational principle for the transport

Péter Ván; Wolfgang Muschik

1995-01-01

422

Naturally occurring genetic variation in Arabidopsis thaliana  

Microsoft Academic Search

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

Maarten Koornneef; Carlos Alonso-Blanco; Dick Vreugdenhil

2004-01-01

423

Mapping and sequencing of structural variation from eight human genomes  

PubMed Central

Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale—particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence map of human structural variation—a standard for genotyping platforms and a prelude to future individual genome sequencing projects.

Kidd, Jeffrey M.; Cooper, Gregory M.; Donahue, William F.; Hayden, Hillary S.; Sampas, Nick; Graves, Tina; Hansen, Nancy; Teague, Brian; Alkan, Can; Antonacci, Francesca; Haugen, Eric; Zerr, Troy; Yamada, N. Alice; Tsang, Peter; Newman, Tera L.; Tuzun, Eray; Cheng, Ze; Ebling, Heather M.; Tusneem, Nadeem; David, Robert; Gillett, Will; Phelps, Karen A.; Weaver, Molly; Saranga, David; Brand, Adrianne; Tao, Wei; Gustafson, Erik; McKernan, Kevin; Chen, Lin; Malig, Maika; Smith, Joshua D.; Korn, Joshua M.; McCarroll, Steven A.; Altshuler, David A.; Peiffer, Daniel A.; Dorschner, Michael; Stamatoyannopoulos, John; Schwartz, David; Nickerson, Deborah A.; Mullikin, James C.; Wilson, Richard K.; Bruhn, Laurakay; Olson, Maynard V.; Kaul, Rajinder; Smith, Douglas R.; Eichler, Evan E.

2008-01-01

424

Strategies to reduce variation in the use of surgery.  

PubMed

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

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

2013-09-28

425

On complex Douglas spaces  

NASA Astrophysics Data System (ADS)

In this paper we survey projective curvature invariants of Douglas type and use these to give some generalizations for the notion of a complex Berwald space. Various descriptions of complex Douglas spaces are given in relation to other special classes of complex Finsler spaces. This study was performed from the viewpoint of the equations of a complex geodesic curve. Complex Randers spaces offer examples of complex Douglas spaces.

Aldea, Nicoleta; Munteanu, Gheorghe

2013-04-01

426

Vectorial total variation-based regularization for variational image registration.  

PubMed

To use interdependence between the primary components of the deformation field for smooth and non-smooth registration problems, the channel-by-channel total variation- or standard vectorial total variation (SVTV)-based regularization has been extended to a more flexible and efficient technique, allowing high quality regularization procedures. Based on this method, this paper proposes a fast nonlinear multigrid (NMG) method for solving the underlying Euler-Lagrange system of two coupled second-order nonlinear partial differential equations. Numerical experiments using both synthetic and realistic images not only confirm that the recommended VTV-based regularization yields better registration qualities for a wide range of applications than those of the SVTV-based regularization, but also that the proposed NMG method is fast, accurate, and reliable in delivering visually-pleasing registration results. PMID:23893729

Chumchob, Noppadol

2013-07-24

427

Relating Human Genetic Variation to Variation in Drug Responses  

PubMed Central

Although sequencing a single human genome was a monumental effort a decade ago, more than one thousand genomes have now been sequenced. The task ahead lies in transforming this information into personalized treatment strategies that are tailored to the unique genetics of each individual. One important aspect of personalized medicine is patient-to-patient variation in drug response. Pharmacogenomics addresses this issue by seeking to identify genetic contributors to human variation in drug efficacy and toxicity. Here, we present a summary of the current status of this field, which has evolved from studies of single candidate genes to comprehensive genome-wide analyses. Additionally, we discuss the major challenges in translating this knowledge into a systems-level understanding of drug physiology with the ultimate goal of developing more effective personalized clinical treatment strategies.

Madian, Ashraf G.; Wheeler, Heather E.; Jones, Richard Baker; Dolan, M. Eileen

2012-01-01

428

Genetic variation and its maintenance  

SciTech Connect

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.

Roberts, D.F.; De Stefano, G.F.

1986-01-01

429

Colonial Variation in Actinobacillus Mallei.  

National Technical Information Service (NTIS)

An examination of colonies of 51 strains of Actinobacillus mallei grown on a complex agar medium containing heart infusion broth, yeast extract, glucose, and glycerol indicated a high degree of heterogeneity in respect of colonial morphology both within a...

D. H. Evans

1965-01-01

430

Variation of Parameters in Differential Equations (A Variation in Making Sense of Variation of Parameters)  

ERIC Educational Resources Information Center

|The method of variation of parameters can be found in most undergraduate textbooks on differential equations. The method leads to solutions of the non-homogeneous equation of the form y = u[subscript 1]y[subscript 1] + u[subscript 2]y[subscript 2], a sum of function products using solutions to the homogeneous equation y[subscript 1] and…

Quinn, Terry; Rai, Sanjay

2012-01-01

431

Statistical mechanics of macromolecular complexation  

NASA Astrophysics Data System (ADS)

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.

Nakamura, Issei

432

Genetic Variation in Healthy Oldest-Old  

PubMed Central

Individuals who live to 85 and beyond without developing major age-related diseases may achieve this, in part, by lacking disease susceptibility factors, or by possessing resistance factors that enhance their ability to avoid disease and prolong lifespan. Healthy aging is a complex phenotype likely to be affected by both genetic and environmental factors. We sequenced 24 candidate healthy aging genes in DNA samples from 47 healthy individuals aged eighty-five years or older (the ‘oldest-old’), to characterize genetic variation that is present in this exceptional group. These healthy seniors were never diagnosed with cancer, cardiovascular disease, pulmonary disease, diabetes, or Alzheimer disease. We re-sequenced all exons, intron-exon boundaries and selected conserved non-coding sequences of candidate genes involved in aging-related processes, including dietary restriction (PPARG, PPARGC1A, SIRT1, SIRT3, UCP2, UCP3), metabolism (IGF1R, APOB, SCD), autophagy (BECN1, FRAP1), stem cell activation (NOTCH1, DLL1), tumor suppression (TP53, CDKN2A, ING1), DNA methylation (TRDMT1, DNMT3A, DNMT3B) Progeria syndromes (LMNA, ZMPSTE24, KL) and stress response (CRYAB, HSPB2). We detected 935 variants, including 848 single nucleotide polymorphisms (SNPs) and 87 insertion or deletions; 41% (385) were not recorded in dbSNP. This study is the first to present a comprehensive analysis of genetic variation in aging-related candidate genes in healthy oldest-old. These variants and especially our novel polymorphisms are valuable resources to test for genetic association in models of disease susceptibility or resistance. In addition, we propose an innovative tagSNP selection strategy that combines variants identified through gene re-sequencing- and HapMap-derived SNPs.

Halaschek-Wiener, Julius; Amirabbasi-Beik, Mahsa; Monfared, Nasim; Pieczyk, Markus; Sailer, Christian; Kollar, Anita; Thomas, Ruth; Agalaridis, Georgios; Yamada, So; Oliveira, Lisa; Collins, Jennifer A.; Meneilly, Graydon; Marra, Marco A.; Madden, Kenneth M.; Le, Nhu D.; Connors, Joseph M.; Brooks-Wilson, Angela R.

2009-01-01

433

Genetic variation of St. Louis encephalitis virus.  

PubMed

St. Louis encephalitis virus (SLEV) has been regularly isolated throughout the Americas since 1933. Previous phylogenetic studies involving 62 isolates have defined seven