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1

Integrals in the complex Kohn variational calculation for electron scattering by a screened Coulomb potential  

SciTech Connect

Programs were developed to calculate integrals involving spherical Bessel, spherical Neumann, and spherical Hankel functions needed for Kohn and complex Kohn variational scattering calculations. In particular, all types needed for a screened coulomb potential for all 1 were evaluated. Some of these integrals are expressable in closed form, whereas others must be expressed in terms of hypergeometric functions, which must be calculated numerically. In many instances, recursion procedures lead to quick and accurate evaluation of some related integrals. In most cases, the integrals were evaluated using several different procedures to allow accuracy checks on their numerical values. Agreement in the calculation of integrals using different methods was usually to at least six (6) places of accuracy.

Kinser, H.B. (Dalton College, GA (USA)); Crawford, O.H.

1990-01-01

2

Theoretical study of (e ,2e) from outer- and inner-valence orbitals of CH4: A complex Kohn treatment  

NASA Astrophysics Data System (ADS)

Triply differential cross sections for electron-impact ionization of the 1t2 and 2a1 orbitals of methane are calculated using the complex Kohn variational method. The calculations are carried out for scattered electron energies of 500 eV and coplanar asymmetric kinematics far from the Bethe ridge, where previous experiment and theory are available for comparison. The present results are in reasonably good agreement with experiment for 1t2 ionization and in excellent agreement for 2a1 ionization, in contrast with previous theory.

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

2014-05-01

3

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

NASA Technical Reports Server (NTRS)

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

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

2001-01-01

4

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

NASA Technical Reports Server (NTRS)

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

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

1990-01-01

5

Competition: Was Kohn Right?  

ERIC Educational Resources Information Center

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

Shields, David Light; Bredemeier, Brenda Light

2010-01-01

6

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

7

Hohenberg-Kohn redux  

E-print Network

The Hohenberg-Kohn theorem is a cornerstone of electronic density functional theory, yet its proof requires an {\\em assumption} that ground state wavefunctions never vanish on a set of nonzero Lebesgue measure. Since DFT is supposed to obviate knowledge of many-body wavefunctions, this is an unsatisfactory situation. Here, the question, "how many potentials will yield this as a ground-state density?" is approached from a different direction. Using ordinary Hilbert space analysis we prove: If the density $\\rho$ is continuous and everywhere nonzero, then there can be at most one potential (modulo constants) in the large class $\\mathsf{Kato}$ (expressible as a square-integrable plus a bounded function) with $\\rho$ as a ground state density. In case $\\rho$ is not nonzero everywhere, the theorem allows an independent constant on each connected component of the set where $\\rho > 0$ (and no control at all where $\\rho = 0$). Using a unique continuation result of Schechter and Simon, the ambiguity can be reduced to an overall constant on $\\{\\rho > 0\\}$ if the potential is required to be weak-$L^3$.

Paul E. Lammert

2014-12-12

8

Variations on Muchnik's Conditional Complexity Theorem  

E-print Network

Variations on Muchnik's Conditional Complexity Theorem Daniil Musatov1 , Andrei Romashchenko2 from IITP RAS, alexander.shen@lif.univ-mrs.fr Abstract. Muchnik's theorem about simple conditional of this theorem. The first one is based on the on-line matching algorithm for bipartite graphs. The sec- ond one

Paris-Sud XI, Université de

9

ENERGETIC VARIATIONAL APPROACH IN COMPLEX FLUIDS: MAXIMUM DISSIPATION PRINCIPLE  

E-print Network

ENERGETIC VARIATIONAL APPROACH IN COMPLEX FLUIDS: MAXIMUM DISSIPATION PRINCIPLE By Yunkyong Hyon Do­0436 Phone: 612/624-6066 Fax: 612/626-7370 URL: http://www.ima.umn.edu #12;ENERGETIC VARIATIONAL APPROACH the general energetic variational approaches for hydrodynamic systems of complex fluids. In these energetic

10

ENERGETIC VARIATIONAL APPROACH IN COMPLEX FLUIDS : MAXIMUM DISSIPATION PRINCIPLE  

E-print Network

ENERGETIC VARIATIONAL APPROACH IN COMPLEX FLUIDS : MAXIMUM DISSIPATION PRINCIPLE Y. HYON , D. Y. KWAK, AND C. LIU§ Abstract. We discuss the general energetic variational approaches for hydrodynamic systems of complex fluids. In these energetic variational approaches, the least action principle (LAP

Hyon, YunKyong

11

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

SciTech Connect

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

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

1994-03-01

12

Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits  

PubMed Central

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

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

2009-01-01

13

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

14

Kohn anomaly in phonon driven superconductors  

NASA Astrophysics Data System (ADS)

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

Das, M. P.; Chaudhury, R.

2014-08-01

15

Individual Variation in the Late Positive Complex to Semantic Anomalies  

PubMed Central

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

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

2012-01-01

16

On the Kohn-Luttinger conundrum  

SciTech Connect

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

2013-05-28

17

The Kohn Social Competence Scale and Kohn Symptom Checklist for the Preschool Child: A Follow-Up Report  

ERIC Educational Resources Information Center

The paper focuses on two research instruments, the Kohn Social Competence Scale and the Kohn Symptom Checklist, designed to assess the behavior of children in a preschool setting as well as on two factor-analytically derived dimensions of social-emotional functioning which the instruments measure. (SBH)

Kohn, Martin

1977-01-01

18

Climatic variation and the distribution of an amphibian polyploid complex  

USGS Publications Warehouse

1. The establishment of polyploid populations involves the persistence and growth of the polyploid in the presence of the progenitor species. Although there have been a number of animal polyploid species documented, relatively few inquiries have been made into the large-scale mechanisms of polyploid establishment in animal groups. Herein we investigate the influence of regional climatic conditions on the distributional patterns of a diploid-tetraploid species pair of gray treefrogs, Hyla chrysoscelis and H. versicolor (Anura: Hylidae) in the mid-Atlantic region of eastern North America. 2. Calling surveys at breeding sites were used to document the distribution of each species. Twelve climatic models and one elevation model were generated to predict climatic and elevation values for gray treefrog breeding sites. A canonical analysis of discriminants was used to describe relationships between climatic variables, elevation and the distribution of H. chrysoscelis and H. versicolor. 3. There was a strong correlation between several climatic variables, elevation and the distribution of the gray treefrog complex. Specifically, the tetraploid species almost exclusively occupied areas of higher elevation, where climatic conditions were relatively severe (colder, drier, greater annual variation). In contrast, the diploid species was restricted to lower elevations, where climatic conditions were warmer, wetter and exhibited less annual variation. 4. Clusters of syntopic sites were associated with areas of high variation in annual temperature and precipitation during the breeding season. 5. Our data suggest that large-scale climatic conditions have played a role in the establishment of the polyploid H. versicolor in at least some portions of its range. The occurrence of the polyploid and absence of the progenitor in colder, drier and more varied environments suggests the polyploid may posses a tolerance of severe environmental conditions that is not possessed by the diploid progenitor. 6. Our findings support the hypothesis that increased tolerance to severe environmental conditions is a plausible mechanism of polyploid establishment.

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

2007-01-01

19

Does the ring species concept predict vocal variation in the crimson rosella, Platycercus elegans, complex?  

Microsoft Academic Search

Vocal variation may be important in population divergence. We studied geographical variation in contact calls of parrots of the crimson rosella, Platycercus elegans, complex, which is characterized by striking geographical plumage coloration variation. This complex has long been considered a rare example of a ring species (where two divergent forms coexist in sympatry but are connected by a chain of

Raoul F. H. Ribot; Mathew L. Berg; Katherine L. Buchanan; Jan Komdeur; Leo Joseph; Andrew T. D. Bennett

2009-01-01

20

Time-dependent Kohn-Sham approach to quantum electrodynamics  

SciTech Connect

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

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

2011-10-15

21

Variation at the major histocompatibility complex in Savannah sparrows.  

PubMed

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

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

2002-06-01

22

Kohn-Sham equations for nanowires with direct current  

NASA Astrophysics Data System (ADS)

The paper describes the derivation of the Kohn-Sham equations for a nanowire with direct current. A value of the electron current enters the problem as an input via a subsidiary condition imposed by pointwise Lagrange multiplier. Using the constrained minimization of the Hohenberg-Kohn energy functional, we derive a set of self-consistent equations for current carrying orbitals of the molecular wire.

Kosov, D. S.

2003-07-01

23

Luminescence modulations of rhenium tricarbonyl complexes induced by structural variations.  

PubMed

Octahedral d(6) low-spin Re(I) tricarbonyl complexes are of considerable interest as noninvasive imaging probes and have been deeply studied owing to their biological stability, low toxicity, large Stokes shifts, and long luminescence lifetimes. We reported recently the bimodal IR and luminescence imaging of a Re(I) tricarbonyl complex with a Pyta ligand (4-(2-pyridyl)-1,2,3-triazole) in cells and labeled such metal-carbonyl complexes SCoMPIs for single-core multimodal probes for imaging. Re(I) tricarbonyl complexes have unique photophysical properties allowing for their unequivocal detection in cells but also present some weaknesses such as a very low luminescence quantum yield in aqueous medium. Further optimizations would thus be desirable. We therefore developed new Re(I) tricarbonyl complexes prepared from different ancillary ligands. Complexes with benzothiadiazole-triazole ligands show interesting luminescent quantum yields in acetonitrile and may constitute valuable luminescent metal complexes in organic media. A series of complexes with bidentate 1-(2-quinolinyl)-1,2,3-triazole (Taquin) and 1-(2-pyridyl)-1,2,3-triazole (Tapy) ligands bearing various 4-substituted alkyl side chains has been designed and synthesized with efficient procedures. Their photophysical properties have been characterized in acetonitrile and in a H2O/DMSO (98/2) mixture and compared with those of the parent Quinta- and Pyta-based complexes. Tapy complexes bearing long alkyl chains show impressive enhancement of their luminescent properties relative to the parent Pyta complex. Theoretical calculations have been performed to further characterize this new class of rhenium tricarbonyl complexes. Preliminary cellular imaging studies in MDA-MB231 breast cancer cells reveal a strong increase in the luminescence signal in cells incubated with the Tapy complex substituted with a C12 alkyl chain. This study points out the interesting potential of the Tapy ligand in coordination chemistry, which has been so far underexploited. PMID:24905983

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

2014-06-16

24

Kohn-Sham Theory in the Presence of Magnetic Field  

E-print Network

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

Andre Laestadius

2014-04-11

25

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

26

A Kohn-Sham system at zero temperature  

E-print Network

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

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

2008-01-17

27

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

28

Interpreting noncoding genetic variation in complex traits and human disease  

E-print Network

Association studies provide genome-wide information about the genetic basis of complex disease, but medical research has focused primarily on protein-coding variants, owing to the difficulty of interpreting noncoding ...

Kellis, Manolis

29

Copy number variation in autoimmunity--importance hidden in complexity?  

PubMed

Copy number variation, namely regions of the genome that can be either deleted or duplicated in a variable way, has emerged as an important source of genetic variance in the human genome. Genes with immunological functions are particularly prone to copy number variation, in part because this is a mechanism to expand the recognition repertoire; however, immunological genes not directly involved in immune recognition are also copy number variable but, despite the link between immunological function and copy number variation, very few copy number variants (CNVs) have been found to be associated with autoimmune diseases, even in recent large genome-wide CNV-association studies. Nonetheless, CNVs in FCGR3B, DEFB4, CCL3L1, C4A/B and NCF1 have been suggested to be associated with autoimmune diseases, although there is conflicting evidence in all cases. The reasons for the lack of definitive data on CNV-autoimmunity associations, as well as the technical challenges for the field are the focus of this review. PMID:22865047

Olsson, Lina M; Holmdahl, Rikard

2012-08-01

30

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

31

Variation in child health care utilization by medical complexity.  

PubMed

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

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

2015-01-01

32

Variational Approach in Two-Phase Flows of Complex Fluids: Transport and Induced Elastic Stress  

E-print Network

-rheological fluids, magneto-rheological fluids and blood suspensions exhibit many intricate rheologicalVariational Approach in Two-Phase Flows of Complex Fluids: Transport and Induced Elastic Stress of mixtures of complex fluids is de- scribed in this paper. In particular, the special coupling between

Feng, James J.

33

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

SciTech Connect

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

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

2014-02-07

34

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

NASA Astrophysics Data System (ADS)

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

Bao, Gang; Hu, Guanghui; Liu, Di

2015-01-01

35

Extensive Genomic Variation within Clonal Complexes of Neisseria meningitidis  

PubMed Central

Meningococcal disease is a widely distributed complex disease affecting all age categories. It can cause severe meningitis and septicemia, especially in unvaccinated infants and young children. The causative agent, Neisseria meningitidis (Nm), can be phenotypically and genetically differentiated into serogroups and sequence types (STs) and has a highly dynamic population structure. To obtain a deeper understanding of the epidemiology of Nm, we sequenced seven Nm genomes. Large-scale genomic analysis was conducted with these 7 Nm genomes, 27 additional Nm genomes from GenBank, and 4 other Neisseria genomes. We observed extensive homologous recombination in all gene functional categories among different Nm genomes. Homologous recombination is so frequent that it has resulted in numerous chimeric open reading frames, including genes in the capsule biosynthesis cluster and loci targeted by commercial vaccines. Our results reveal that, despite widespread use, evolutionary relationships inferred from the standard seven-gene multilocus sequence typing (MLST) method could not predict virulence gene content or strain phenotype. In fact, up to 28% of the virulence-associated genes could differ between strains of identical STs. Consistent with previous studies, we found that allelic recombination is also associated with alterations in antibiotic susceptibility. Overall, these findings emphasize the extensive genomic plasticity of Nm and the limitations of standard molecular methods to quantify this genotypic and phenotypic diversity. PMID:22084315

Hao, Weilong; Ma, Jennifer H.; Warren, Keisha; Tsang, Raymond S.W.; Low, Donald E.; Jamieson, Frances B.; Alexander, David C.

2011-01-01

36

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. PMID:23138309

Ward, Lucas D.; Kellis, Manolis

2012-01-01

37

Seasonal Variation of Lipid-Lowering Effects of Complex Spa Therapy  

Microsoft Academic Search

SummaryBackground and Objective: It has been shown that spa therapy has a lipid-lowering effect. Also, seasonal variations in spa therapy effects have been found for some outcome measures. The aim of the present study is to investigate whether the lipid-lowering effects of spa therapy as a complex health intervention also are subject to seasonal variation. Method: The effect of 3-week

G. Strauss-Blasche; C. Ekmekcioglu; V. Leibetseder; W. Marktl

2003-01-01

38

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

E-print Network

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 for extending 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.

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

2012-02-24

39

The Kohn-Luttinger superconductivity in idealized doped graphene  

NASA Astrophysics Data System (ADS)

Idealized graphene monolayer is considered neglecting the van der Waals potential of the substrate and the role of the nonmagnetic impurities. The effect of the long-range Coulomb repulsion in an ensemble of Dirac fermions on the formation of the superconducting pairing in a monolayer is studied in the framework of the Kohn-Luttinger mechanism. The electronic structure of graphene is described in the strong coupling Wannier representation on the hexagonal lattice. We use the Shubin-Vonsowsky model which takes into account the intra- and intersite Coulomb repulsions of electrons. The Cooper instability is established by solving the Bethe-Salpeter integral equation, in which the role of the effective interaction is played by the renormalized scattering amplitude. The renormalized amplitude contains the Kohn-Luttinger polarization contributions up to and including the second-order terms in the Coulomb repulsion. We construct the superconductive phase diagram for the idealized graphene monolayer and show that the Kohn-Luttinger renormalizations and the intersite Coulomb repulsion significantly affect the interplay between the superconducting phases with f-, d+id-, and p+ip-wave symmetries of the order parameter.

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

2014-06-01

40

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

41

Variation of large elastodynamic earthquakes on complex fault systems Bruce E. Shaw  

E-print Network

. Lett., 31, L18609, doi:10.1029/2004GL019943. 1. Introduction [2] The faults on which earthquake occur occurring during the earthquake cycle, and the time dependence of long term probabilities become negligibleVariation of large elastodynamic earthquakes on complex fault systems Bruce E. Shaw Lamont

Shaw, Bruce E.

42

Major histocompatibility complex (MHC) variation in the endangered Mexican wolf and related canids1  

Microsoft Academic Search

We have examined in Mexican wolves and related canids the amount of genetic variation for a class II gene in the major histocompatibility complex (MHC), thought to be part of the most important genetic basis for pathogen resistance in vertebrates. In Mexican wolves, descended from only seven founders over three lineages, there were five different alleles. These were in three

Philip W. Hedrick; Rhonda N. Lee; Karen M. Parker

2000-01-01

43

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

PubMed Central

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

Higham, Timothy E.; Biewener, Andrew A.

2011-01-01

44

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. PMID:21712968

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

2011-01-01

45

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

PubMed

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

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

2011-07-01

46

Asymptotic form of the Kohn-Sham correlation potential  

SciTech Connect

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

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

2007-07-15

47

Long-term survival of a urodele amphibian despite depleted major histocompatibility complex variation.  

PubMed

Depletion of polymorphism at major histocompatibility complex (MHC) genes has been hypothesized to limit the ability of populations to respond to emerging pathogens, thus putting their survival at risk. As pathogens contribute substantially to the global amphibian decline, assessing patterns of MHC variation is important in devising conservation strategies. Here, we directly compare levels of MHC class II and neutral variation between multiple populations of the great crested newt (Triturus cristatus) from refugial (REF: Romania) and postglacial expansion (PGE: Germany, Poland and UK) areas. REF populations harboured high levels of adaptive variation (24 expressed alleles), exhibiting clear signatures of historical positive selection, which points to the overall importance of MHC class II variation in this species. On the other hand, PGE populations were extremely depauperate (two alleles) but nevertheless have survived for c. 10,000 years, since the postglacial expansion. Variation in putative MHC class II pseudogenes, microsatellites and allozymes also showed a significant southern richness-northern purity pattern. The populations in the postglacial expansion area thus provide the clearest example to date of the long-term survival of populations in which MHC variation, historically under positive selection, has been depleted. PMID:19207255

Babik, W; Pabijan, M; Arntzen, J W; Cogâlniceanu, D; Durka, W; Radwan, J

2009-03-01

48

Variational principles for reactive collisions based on the generalized Lagrange multiplier method  

NASA Astrophysics Data System (ADS)

In this study is discussed a general approach to derive variational principles for physical magnitudes Q(?) which are dependent on functions ? known to be solutions of physical equations [see Gerjuoy et al., Rev. Mod. Phys. 55, 725 (1983)]. The approach is based on Lagrange multipliers which are incorporated into the expression for calculating Q by demanding that the functions ? fulfill their equations. This approach is first applied to derive a general variational principle for the T-matrix elements based on the Lippmann-Schwinger equation. As special cases we obtained the bilinear forms of the Schwinger and the Newton variational principles. Next this approach is employed to derive a new Kohn-type variational principle for the S-matrix elements for reactive collisions based on the Schrödinger equation which contains complex potentials. Finally, this approach is further utilized to derive a novel variational principle for the flux function.

Baer, Michael; Nakamura, Hiroki

1992-05-01

49

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

PubMed

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

Ruedi, Elizabeth A; Hughes, Kimberly A

2008-07-01

50

Mitochondrial DNA Sequence Variation in the Spruce Budworm Species Complex (Choristoneura: Lepidoptera)  

Microsoft Academic Search

A combination of polymerase-chain-reaction amplification and automated DNA sequencing was used to survey variation in a species complex of pest insects, the spruce budworms (Choristoneuru fumiferana species group), and an outgroup species, C. rosaceana. We sequenced an mtDNA region of 1,573 bp that extends from the middle of cytochrome oxidase subunit I (COI) through tRNA leucine (UUR) to the end

Felix A. H. Sperling; Donal A. Hickey

51

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?t?=??. 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( ), where is a time-independent operator [e.g., =-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

52

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

PubMed

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

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

2010-06-01

53

VOLUME 79, NUMBER 20 P H Y S I C A L R E V I E W L E T T E R S 17 NOVEMBER 1997 Sparsity of the Density Matrix in Kohn-Sham Density Functional Theory  

E-print Network

(1996)]. These estimates are used to study the complexity of several linear system-size scaling to scale linearly with system size. This can be achieved for both KS-DFT and Hartree-Fock effect of the Density Matrix in Kohn-Sham Density Functional Theory and an Assessment of Linear System-Size Scaling

Baer, Roi

54

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 PMID:1967831

Yuhki, N; O'Brien, S J

1990-01-01

55

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

SciTech Connect

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

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

1990-01-01

56

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

PubMed Central

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

Levy, Morris; Levin, Donald A.

1975-01-01

57

Time-dependent Internal DFT formalism and Kohn-Sham scheme  

E-print Network

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

J. Messud

2009-08-07

58

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

59

Mechanisms of copy number variation and hybrid gene formation in the KIR immune gene complex  

PubMed Central

The fine-scale structure of the majority of copy number variation (CNV) regions remains unknown. The killer immunoglobulin receptor (KIR) gene complex exhibits significant CNV. The evolutionary plasticity of the KIRs and their broad biomedical relevance makes it important to understand how these immune receptors evolve. In this paper, we describe haplotype re-arrangement creating novel loci at the KIR complex. We completely sequenced, after fosmid cloning, two rare contracted haplotypes. Evidence of frequent hybrid KIR genes in samples from many populations suggested that re-arrangements may be frequent and selectively advantageous. We propose mechanisms for formation of novel hybrid KIR genes, facilitated by protrusive non-B DNA structures at transposon recombination sites. The heightened propensity to generate novel hybrid KIR receptors may provide a proactive evolutionary measure, to militate against pathogen evasion or subversion. We propose that CNV in KIR is an evolutionary strategy, which KIR typing for disease association must take into account. PMID:19959527

Traherne, James A.; Martin, Maureen; Ward, Rosemary; Ohashi, Maki; Pellett, Fawnda; Gladman, Dafna; Middleton, Derek; Carrington, Mary; Trowsdale, John

2010-01-01

60

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

Microsoft Academic Search

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

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

1991-01-01

61

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

PubMed Central

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

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

2014-01-01

62

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

PubMed Central

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

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

2012-01-01

63

Functional dependence of the exact time-dependent Kohn-Sham potential for quantum transport  

NASA Astrophysics Data System (ADS)

We present methods for determining exact steady-state and time-dependent Kohn-Sham potentials from known charge and current densities. Applying these methods to cases of a single electron added to the conduction band of a model semiconductor, we calculate the exact Kohn-Sham potentials and discuss their meaning in the context of describing quantum transport. We show that the inclusion of a longitudinal Kohn-Sham vector potential is quite unavoidable in describing steady-state current-carrying systems, whereas the addition of an electron in a wavepacket state necessitates, inter alia, the appearance of an exchange-correlation electric field. We also present our findings on the functional dependence of the exact Kohn-Sham scalar and vector potentials on the charge and current density.

Ramsden, James; Godby, Rex

2012-02-01

64

Variations of oxygen and carbon isotopes in carbonatites: A study of Brazilian alkaline complexes  

NASA Astrophysics Data System (ADS)

We have studied the oxygen and carbon isotopic compositions of carbonatite complexes from South America (Jacupiranga, Araxá, Catalão, Tapira, and Mato Preto) and interpreted the results in terms of magmatism, contamination by country rocks, and hydrothermal processes. These complexes range in age from 130 to 65 Ma and were emplaced during the reactivation of the South American Platform during the Mesozoic Era. Except for the samples from Mato Preto ( ?13C = -6.9 to + 0.8%), which have been contaminated by limestone from the country rock, there are no large carbon isotope differences among the samples of Jacupiranga (-7.3 to -6.6%), Araxá (-7.5 to -4.8%), Catalão (-7.1 to -5.3%), and Tapira (-6.8 to -4.8%). In contrast, the carbonatites have a wide range in oxygen isotopic composition, which seems to be related to their degree of hydrothermal alteration and their emplacement level. For instance, while the samples from Jacupiranga have a narrow range of ?18O (6.6 to 7.3%) and have not been extensively affected by fertilization, the carbonatites from the complexes of Araxa (8.7 to 16.3%o), Catalão (7.3 to 19.3%), and Tapira (9.7 to 15.4%) have a wide range in ?18O and are accompanied by pervasive potash-fenitization of their host rock. The potash-fenitization is marked by the replacement of carbonatite host rock (mainly pyroxenite) by carbonate-phlogopite-magnetite-rich rocks. We conclude that fractional crystallization and liquid immiscibility may not significantly affect the oxygen and carbon isotopic composition of carbonatites. Large isotopic variations may be produced when these rocks intrude limestone country rocks (i.e., Mato Preto) and/or have been subjected to postcrystallization alteration processes. Variations of ?18O and ?13C in the carbonatites may be explained by isotopic exchange between these rocks and H 20?CO 2-fluids at different temperatures and with different H 2O/CO 2 ratios. The isotope exchange model implies that the isotopic variations in carbonatites take place under low-temperature conditions (below 300°C) and involve fluids with high H 2O/CO 2 ratios.

Santos, Roberto V.; clayton, Robert N.

1995-04-01

65

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

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

Variation in dust properties in a dense filament of the Taurus molecular complex (L1506)  

E-print Network

We observed the L1506 filament, which is located in the Taurus molecular complex, with the Herschel PACS and SPIRE instruments. Our aim is to prove the variation in grain properties along the entire length of the filament. In particular, we want to determine above which gas density this variation arises and what changes in the grain optical properties/size distribution are required. We use the 3D radiative transfer code CRT, coupled to the dust emission and extinction code DustEM, to model the emission and extinction of the dense filament. We test a range of optical properties and size distributions for the grains: dust of the diffuse interstellar medium (interstellar PAHs and amorphous carbons and silicates) and both compact and fluffy aggregates. We find that the grain opacity has to increase across the filament to fit simultaneously the near-IR extinction and Herschel emission profiles of L1506. We interpret this change to be a consequence of the coagulation of dust grains to form fluffy aggregates. Grains...

Ysard, Nathalie; Ristorcelli, Isabelle; Juvela, Mika; Pagani, Laurent; Konyves, Vera; Spencer, Locke; White, Glenn; Zavagno, Annie

2013-01-01

68

Intragenomic rDNA ITS2 variation in the neotropical Anopheles (Nyssorhynchus) albitarsis complex (Diptera: Culicidae).  

PubMed

We cloned and sequenced the rDNA internal transcribed spacer 2 (ITS2) of 4 species belonging to the neotropical Anopheles (Nyssorhynchus) albitarsis complex, that is, A. albitarsis; A. albitarsis B; Anopheles marajoara, a proven malaria vector; and Anopheles deaneorum, a suspected vector. Even though the ITS2 sequences of these species were very similar (< or =1.17% divergence), we found differences suitable for species identification and intragenomic variation of possible consequence in phylogenetic reconstruction. Variation came from 2 microsatellite regions and a number of indels and base substitutions. The existence of partially correlated subsets of clones in A. albitarsis is hypothesized either to be separate rDNA loci or to be semi-independently evolving portions of a single rDNA locus. No differences were found between males and females, suggesting that similar rDNA arrays exist on both the X and Y chromosomes. In addition, highly variant clones, possibly pseudogenes, were found in A. marajoara from Venezuela. PMID:17158469

Li, Cong; Wilkerson, Richard C

2007-01-01

69

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

PubMed Central

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

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

2014-01-01

70

The Variational Theory of Complex Rays: An answer to the resolution of mid-frequency 3D engineering problems  

NASA Astrophysics Data System (ADS)

The Variational Theory of Complex Rays (VTRC) is an approach to the simulation of mid-frequency phenomena whose wavelengths are relatively small compared to the dimensions of the domain. This is a wave-based computational technique which involves a nonclassical variational formulation. This paper focuses on the development of the approach for 3D engineering problems and shows that it is a mature technique. Illustrations are given to show the capabilities of this method.

Riou, H.; Ladevèze, P.; Kovalevsky, L.

2013-04-01

71

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

NASA Astrophysics Data System (ADS)

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

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

2012-01-01

72

Variation in dust properties in a dense filament of the Taurus molecular complex (L1506)  

NASA Astrophysics Data System (ADS)

Aims: We observed the L1506 filament, which is located in the Taurus molecular complex, with the Herschel PACS and SPIRE instruments. Our aim is to prove the variation in grain properties along the entire length of the filament. In particular, we want to determine above which gas density this variation arises and what changes in the grain optical properties/size distribution are required. Methods: We use the 3D radiative transfer code CRT, coupled to the dust emission and extinction code DustEM, to model the emission and extinction of the dense filament. We test a range of optical properties and size distributions for the grains: dust of the diffuse interstellar medium (interstellar PAHs and amorphous carbons and silicates) and both compact and fluffy aggregates. Results: We find that the grain opacity has to increase across the filament to fit simultaneously the near-IR extinction and Herschel emission profiles of L1506. We interpret this change to be a consequence of the coagulation of dust grains to form fluffy aggregates. Grains similar to those in the diffuse medium have to be present in the outer layers of the cloud, whereas aggregates must prevail above gas densities of a few 103 H/cm3. This corresponds to line-of-sights with visual extinction in the V band of the order of 2 to 3. The dust opacity at 250 ?m is raised by a factor of 1.8 to 2.2, while the grain average size is increased by a factor of 5. These exact numbers depend naturally on the dust model chosen to fit the data. Our findings agree with the constraints given by the study of the gas molecular lines. Using a simple approach, we show that the aggregates may have time to form inside the filament within the cloud lifetime. Our model also characterises the density structure of the filament, showing that the filament width is not constant along L1506 but instead varies by a factor of the order of 4. Conclusions: We confirm the need for an increase in the far-IR dust opacity to explain the emission and extinction in L1506C, which we interpret as being due to dust growth. We also show that this opacity variation is valid along the entire length of the L1506 dense filament.

Ysard, N.; Abergel, A.; Ristorcelli, I.; Juvela, M.; Pagani, L.; Könyves, V.; Spencer, L.; White, G.; Zavagno, A.

2013-11-01

73

Numerical implementation of a variational method for electrical impedance tomography  

Microsoft Academic Search

A variational method for computing electrical conductivity distributions from boundary measurements was proposed by Kohn and Vogelius (1987). The authors explore the numerical performance of that technique. A version of Newton's method is used for the minimisation, and synthetic data for the boundary measurements. The variational method is found to be generally stable and robust, reproducing the locations and shapes

R. V. Kohn; A. McKenney

1990-01-01

74

TBX6, LHX1 and copy number variations in the complex genetics of Müllerian aplasia  

PubMed Central

Background Müllerian aplasia (MA) is a congenital disorder of the female reproductive tract with absence of uterus and vagina with paramount impact on a woman’s life. Despite intense research, no major genes have been found to explain the complex genetic etiology. Methods and Results We have used several genetic methods to study 112 patients with MA. aCGH identified CNVs in 8/50 patients (16%), including 16p11.2 and 17q12 deletions previously associated with MA. Subsequently, another four patients were shown to carry the ~0.53 Mb deletion in 16p11.2. More importantly, sequencing of TBX6, residing within 16p11.2, revealed two patients carrying a splice site mutation. Two previously reported TBX6 variants in exon 4 and 6 were shown to have a significantly higher frequency in patients (8% and 5%, respectively) than in controls (2% each). We also sequenced LHX1 and found three apparently pathogenic missense variants in 5/112 patients. Altogether, we identified either CNVs or variations in TBX6 or LHX1 in 30/112 (26.8%) MA patients. CNVs were found in 12/112 (10.7%), patients, novel variants in TBX6 or LHX1 in 7/112 (6.3%), and rare variants in TBX6 in 15/112 (13.4%) patients. Furthermore, four of our patients (4/112, 3.6%) were shown to carry variants in both TBX6 and LHX1 or a CNV in combination with TBX6 variants lending support to the complex genetic etiology of MA. Conclusions We have identified TBX6 as a new gene associated with MA. Our results also support the relevance of LHX1 and CNVs in the development of this congenital malformation. PMID:23954021

2013-01-01

75

Evaluation and Application of Microsatellite and Major Histocompatibility Complex Variation for Stock Identification of Coho Salmon in British Columbia  

Microsoft Academic Search

Variation at eight microsatellite loci and two linked exons of a major histocompatibility complex (MHC) locus was surveyed in approximately 21,000 coho salmon Oncorhynchus kisutch sampled from 138 localities ranging from southeast Alaska to the Columbia River, the majority of the sites being in British Columbia. The observed regional population structure enabled evaluation of the utility of using microsatellite and

Terry D. Beacham; John R. Candy; K. Janine Supernault; Tobi Ming; Bruce Deagle; Angela Schulze; Debra Tuck; Karia H. Kaukinen; James R. Irvine; Kristina M. Miller; Ruth E. Withler

2001-01-01

76

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

PubMed Central

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

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

2013-01-01

77

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

PubMed Central

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

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

2015-01-01

78

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

E-print Network

Kohn-Sham density functional theory is one of the most widely used electronic structure theories. 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 the chemical 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...

Lin, Lin; Ying, Lexing; E, Weinan

2011-01-01

79

Molecular Variation in the Paragonimus heterotremus Complex in Thailand and Myanmar  

PubMed Central

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

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

2013-01-01

80

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

PubMed

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

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

2014-06-01

81

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

PubMed Central

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

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

2014-01-01

82

Exchange and correlation Kohn–Sham functionals for the helium atom: locality and homogeneity  

Microsoft Academic Search

The locality and homogeneous nature of the exchange and correlation functionals for the ground state of the helium atom, in the Kohn–Sham formulation, are revisited. Our analysis is focused on the integrands of both functionals, although the integrated quantities are compared with previous results. Both functionals are not local, and the correlation functional is not homogeneous. To study the non-locality,

Federico Moscardó; J. C. Sancho-Garc??a

1998-01-01

83

Density functional theory and Kohn-Sham scheme for self-bound systems  

SciTech Connect

We demonstrate how the separation of the total energy of a self-bound system into a functional of the internal one-body Fermionic density and a function of an arbitrary wave vector describing the center-of-mass kinetic energy can be used to set up an 'internal' Kohn-Sham scheme.

Messud, Jeremie; Suraud, Eric [Universite de Toulouse, UPS, Laboratoire de Physique Theorique (IRSAMC), F-31062 Toulouse (France); CNRS, LPT (IRSAMC), F-31062 Toulouse (France); Bender, Michael [Universite Bordeaux, Centre d'Etudes Nucleaires de Bordeaux Gradignan, UMR5797, F-33175 Gradignan (France); CNRS/IN2P3, Centre d'Etudes Nucleaires de Bordeaux Gradignan, UMR5797, F-33175 Gradignan (France)

2009-11-15

84

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

E-print Network

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

Van Stryland, Eric

85

Stimulus-Evoked Modulation of Sensorimotor Pyramidal Neuron ADAM KOHN,1  

E-print Network

Stimulus-Evoked Modulation of Sensorimotor Pyramidal Neuron EPSPs ADAM KOHN,1 CAROL METZ,2 MARK A EPSPs. J Neurophysiol 88: 3331­3347, 2002; 10.1152/jn.01012.2001. Sensory cortical neurons display transiently potentiated excitatory postsynaptic po- tentials (EPSPs) evoked by electrical stimulation of layer

Kohn, Adam

86

(17) Hohenberg. P.: Kohn. W. Inhomogeneous Electron Gas. Phys. Rei'. B 1964, /36.864-871.  

E-print Network

Anions (17) Hohenberg. P.: Kohn. W. Inhomogeneous Electron Gas. Phys. Rei'. B 1964, /36. Are Atoms Intrinsic to Molecular Electronic " Wavefunctions? Clzem. Phys. 1982. 7/,41-65. . (22) Roos, B. O in Electronic Spectroscopy. Adv. Clzem. fizys. 1996, 93,219-331. , (25) Hirao, K. Multireference Moller

Simons, Jack

87

On the performance of the Kohn-Sham orbital approach in the calculation of electron transfer parameters. The three state model.  

PubMed

We have tested the performance of the Kohn-Sham orbital approach to obtain the electronic coupling and the energetics for hole transfer (HT) in the guanine-indole pair, using a three-state model. The parameters are derived from the simple DFT calculations with 10 different functionals, and compared with benchmark MS-CASPT2 calculations. The guanine-indole pair is a simple model for HT in DNA-protein complexes, which has been postulated as a protection mechanism for DNA against oxidative damage. In this pair, the first excited state of the indole radical cation has low energy (less than 0.3 eV relative to the ground state of the cation), which requires the application of very accurate quantum chemical methods and the invocation of a 3-state model. The Kohn-Sham orbital approach has been tested on six ? stacked and three T-shaped conformers. It has been shown to provide quite accurate results for all ten tested functionals, compared to the reference MS-CASPT2 values. The best performance has been found for the long-range corrected CAM-B3LYP functional. Our results suggest that the Kohn-Sham orbital method can be used to estimate the excited state properties of radical cation systems studied using transient spectroscopy. Because of its accuracy and its low computational cost, the approach allows one to calculate relatively large models and to account for the effects of conformational dynamics on HT between DNA and a protein environment. PMID:25010229

Butchosa, C; Simon, S; Blancafort, L; Voityuk, A A

2014-08-28

88

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

89

On the Efficient Solution of Variational Inequalities; Complexity and Computational Efficiency  

E-print Network

In this paper we combine ideas from cutting plane and interior point methods in order to solve variational inequality problems efficiently. In particular, we introduce a general framework that incorporates nonlinear as ...

Perakis, Georgia

90

Time-dependent internal density functional theory formalism and Kohn-Sham scheme for self-bound systems  

SciTech Connect

The stationary internal density functional theory (DFT) formalism and Kohn-Sham scheme are generalized to the time-dependent case. It is proven that, in the time-dependent case, the internal properties of a self-bound system (such as an atomic nuclei or a helium droplet) are all defined by the internal one-body density and the initial state. A time-dependent internal Kohn-Sham scheme is set up as a practical way to compute the internal density. The main difference from the traditional DFT formalism and Kohn-Sham scheme is the inclusion of the center-of-mass correlations in the functional.

Messud, Jeremie [Universite de Toulouse, UPS, Laboratoire de Physique Theorique (IRSAMC), F-31062 Toulouse, France, and CNRS, LPT (IRSAMC), F-31062 Toulouse (France)

2009-11-15

91

Quantum scattering via the S?matrix version of the Kohn variational principle  

E-print Network

scattering (and also in electron–atom/molecule scattering). The particular version developed in this paper has a more general structure than an earlier one by Miller and Jansen op de Haar [J. Chem. Phys. 8 6, 6213 (1987)], and applications...

Zhang, John Z. H.; Chu, Shih-I; Miller, William H.

1988-11-17

92

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

93

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

NASA Astrophysics Data System (ADS)

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

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

2005-08-01

94

Variations of oxygen and carbon isotopes in carbonatites: A study of Brazilian alkaline complexes  

Microsoft Academic Search

We have studied the oxygen and carbon isotopic compositions of carbonatite complexes from South America (Jacupiranga, Araxá, Catalão, Tapira, and Mato Preto) and interpreted the results in terms of magmatism, contamination by country rocks, and hydrothermal processes. These complexes range in age from 130 to 65 Ma and were emplaced during the reactivation of the South American Platform during the

Roberto V. Santos; Robert N. clayton

1995-01-01

95

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

PubMed

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

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

2014-12-01

96

Mycological Society of America Isozyme Variation and Species Delimitation in the Ceratocystis coerulescens Complex  

E-print Network

Mycological Society of America Isozyme Variation and Species Delimitation in the Ceratocystis, Vol. 88, No. 1 (Jan. - Feb., 1996), pp. 104-113 Published by: Mycological Society of America Stable of scholarship. For more information about JSTOR, please contact support@jstor.org. Mycological Society

Harrington, Thomas C.

97

Genome-partitioning of genetic variation for complex traits using common SNPs  

PubMed Central

Recently, we reported a method to estimate the proportion of phenotypic variance explained by all SNPs from genome-wide association studies, and estimated that half of the heritability for human height was captured by common SNPs. Here we partition genetic variation for height, body mass index (BMI), von Willebrand factor (vWF) and QT interval (QTi) onto chromosomes and chromosome segments, using 586,898 SNPs genotyped on 11,586 unrelated individuals. We estimate that ~45%, ~17%, ~25% and ~21% of variance in height, BMI, vWF and QTi, respectively, can be explained by considering all autosomal SNPs simultaneously, and a further ~0.5–1% by X-chromosome SNPs for height, BMI and vWF. We show that variance explained by each chromosome for height and QTi is proportional to the total gene length on that chromosome. In genome-wide analyses, common SNPs in or near genes explain more variation than SNPs between genes. We propose a novel approach to estimate variation due to cryptic relatedness and population stratification. Our results provide further evidence that a substantial proportion of heritability is accounted for by causal variants in linkage disequilibrium with common SNPs; that height, BMI and QTi are highly polygenic traits; and that the additive variation explained by a part of the genome is approximately proportional to the total length of DNA contained within genes therein. PMID:21552263

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

2015-01-01

98

Self-consistent solution of Kohn-Sham equations for infinitely extended systems with inhomogeneous electron gas  

Microsoft Academic Search

The density functional approach in the Kohn-Sham approximation is widely used to study properties of many-electron systems.\\u000a Due to the nonlinearity of the Kohn-Sham equations, the general self-consistence searching method involves iterations with\\u000a alternate solving of the Poisson and Schrödinger equations. One of problems of such an approach is that the charge distribution\\u000a renewed by means of the solution of

D. V. Posvyanskii; A. Ya. Shul’man

2009-01-01

99

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

E-print Network

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

Marinescu, Smaranda C.

100

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

PubMed

Somaclonal variation during interior spruce (Picea glauca engelmannii complex) somatic embryogenesis was evaluated using culture morphology and isozyme analysis. Genotype-specific abscisic acid-dependent developmental profiles and isozyme patterns were similar for subclone and parent line embryogenic cultures and cotyledonary somatic embryos. Extensive analysis of fifteen hundred subclone embryos of one genotype revealed no isozyme pattern variation. Initiation of embryogenic cultures was dependent on the developmental stage of the explant although cultures derived from different stages were morphologically similar. The embryogenic cultures initiated from interior spruce embryos show a high degree of genetic stability in that the morphological behavior and isozyme phenotype were always consistent with that of the explant genotype. These results support the conclusion that this culture system is appropriate for clonal propagation of interior spruce. PMID:24221739

Eastman, P A; Webster, F B; Pitel, J A; Roberts, D R

1991-10-01

101

On the Solution of the Self-Interaction Problem in Kohn-Sham Density Functional Theory  

E-print Network

We report on a methodology for the treatment of the Coulomb energy and potential in Kohn-Sham density functional theory that is free from self-interaction effects. Specifically, we determine the Coulomb potential given as the functional derivative of the Coulomb energy with respect to the density, where the Coulomb energy is calculated explicitly in terms of the pair density of the Kohn-Sham orbitals. An orthonormal and complete basis that is an explicit functional of the density is used to perform the functional differentiation. This leads to a new formalism that provides an analytic, closed-form determination of the exchange potential. This method is applied to one-dimensional model systems and to the atoms Helium through Krypton based on an exchange only implementation. We compare and contrast the results of the present method with those obtained in the Hartree-Fock formalism and within the optimized effective potential method.

Däne, M; Nicholson, D M; Stocks, G M

2013-01-01

102

Calculating excited state properties using Kohn-Sham density functional theory.  

PubMed

The accuracy of excited states calculated with Kohn-Sham density functional theory using the maximum overlap method has been assessed for the calculation of adiabatic excitation energies, excited state structures, and excited state harmonic and anharmonic vibrational frequencies for open-shell singlet excited states. The computed Kohn-Sham adiabatic excitation energies are improved significantly by post self-consistent field spin-purification, but remain too low compared with experiment with a larger error than time-dependent density functional theory. Excited state structures and vibrational frequencies are also improved by spin-purification. The structures show a comparable accuracy to time-dependent density functional theory, while the harmonic vibrational frequencies are found to be more accurate for the majority of vibrational modes. The computed harmonic vibrational frequencies are also further improved by perturbative anharmonic corrections, suggesting a good description of the potential energy surface. Overall, excited state Kohn-Sham density functional theory is shown to provide an efficient method for the calculation of excited state structures and vibrational frequencies in open-shell singlet systems and provides a promising technique that can be applied to study large systems. PMID:23425455

Hanson-Heine, Magnus W D; George, Michael W; Besley, Nicholas A

2013-02-14

103

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

NASA Astrophysics Data System (ADS)

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

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

2013-02-01

104

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

PubMed Central

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

Comstock, J P; Ehleringer, J R

1992-01-01

105

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

NASA Technical Reports Server (NTRS)

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

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

2001-01-01

106

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

USGS Publications Warehouse

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

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

1977-01-01

107

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

PubMed

Socioeconomic and natural complex systems persistently generate extreme events also known as disasters, crises, or critical transitions. Here we analyze patterns of background activity preceding extreme events in four complex systems: economic recessions, surges in homicides in a megacity, magnetic storms, and strong earthquakes. We use as a starting point the indicators describing the system's behavior and identify changes in an indicator's trend. Those changes constitute our background events (BEs). We demonstrate a premonitory pattern common to all four systems considered: relatively large magnitude BEs become more frequent before extreme event. A premonitory change of scaling has been found in various models and observations. Here we demonstrate this change in scaling of uniformly defined BEs in four real complex systems, their enormous differences notwithstanding. PMID:20887044

Keilis-Borok, V I; Soloviev, A A

2010-09-01

108

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

PubMed Central

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

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

2010-01-01

109

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

110

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

PubMed Central

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.

2011-01-01

111

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

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

112

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

113

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

PubMed

Three new bivalent nickel hydrazone complexes have been synthesised from the reactions of [NiCl(2)(PPh(3))(2)] with H(2)L {L = dianion of the hydrazones derived from the condensation of o-hydroxynaphthaldehyde with furoic acid hydrazide (H(2)L(1)) (1)/thiophene-2-acid hydrazide (H(2)L(2)) (2)/isonicotinic acid hydrazide (H(2)L(3)) (3)} and formulated as [Ni(L(1))(PPh(3))] (4), [Ni(L(2))(PPh(3))] (5) and [Ni(L(3))(PPh(3))] (6). Structural characterization of these compounds 4-6 were accomplished by using various physico-chemical techniques. Single crystal X-ray diffraction data of complexes 4 and 5 proved their distorted square planar geometry. In order to ascertain the potential of the above synthesised compounds towards biomolecular interactions, additional experiments involving interaction with calf thymus DNA (CT DNA) and bovine serum albumin (BSA) were carried out. All the ligands and corresponding nickel(ii) chelates have been screened for their scavenging effect towards O(2)(-), OH and NO radicals. The efficiency of complexes 4-6 to arrest the growth of HeLa, HepG-2 and A431 tumour cell lines has been studied along with the cell viability test against the non-cancerous NIH 3T3 cells under in vitro conditions. PMID:22506273

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

2012-06-14

114

The aesthetasc concept: structural variations of putative olfactory receptor cell complexes in Crustacea.  

PubMed

The structure of the aesthetascs has been investigated in the prawn Macrobrachium rosenbergii (larvae and juveniles), the opossum shrimp Neomysis integer, the euphausid Meganyctiphanes, and in the water-fleas Daphnia magna and D. longispina. The aesthetascs, that are thought to represent olfactory receptors, exhibit a considerable structural variation, ranging from the well known aesthetascs of higher crustaceans (lobster, crab, crayfish) to the corresponding sensilla found in the water-fleas and the males of opossum shrimps. The two following morphological characteristics of the aesthetascs are thought to indicate an olfactory function: the shape of the cuticular hair that is long and essentially hose-shaped, and the thin, loosely arranged cuticle of at least the outer part of the cuticular hair. The presence of other structural elements such as sensory cells, cilia, and enveloping cells are vital for the olfactory function, but the development is variable, which makes their use in the morphological definition of aesthetascs problematic. PMID:1392063

Hallberg, E; Johansson, K U; Elofsson, R

1992-09-01

115

Variations in predicted risks in personal genome testing for common complex diseases  

PubMed Central

Purpose The promise of personalized genomics for common complex diseases depends, in part, on the ability to predict genetic risks on the basis of single nucleotide polymorphisms. We examined and compared the methods of three companies (23andMe, deCODEme, and Navigenics) that have offered direct-to-consumer personal genome testing. Methods We simulated genotype data for 100,000 individuals on the basis of published genotype frequencies and predicted disease risks using the methods of the companies. Predictive ability for six diseases was assessed by the AUC. Results AUC values differed among the diseases and among the companies. The highest values of the AUC were observed for age related macular degeneration, celiac disease, and Crohn disease. The largest difference among the companies was found for celiac disease: the AUC was 0.73 for 23andMe and 0.82 for deCODEme. Predicted risks differed substantially among the companies as a result of differences in the sets of single nucleotide polymorphisms selected and the average population risks selected by the companies, and in the formulas used for the calculation of risks. Conclusion Future efforts to design predictive models for the genomics of common complex diseases may benefit from understanding the strengths and limitations of the predictive algorithms designed by these early companies. PMID:23807614

Kalf, Rachel R.J.; Mihaescu, Raluca; Kundu, Suman; de Knijff, Peter; Green, Robert C.; Janssens, A. Cecile J.W.

2013-01-01

116

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

PubMed Central

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.

2013-01-01

117

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

2013-05-01

118

Variation of complex permittivity of soils with moisture content using VNA  

NASA Astrophysics Data System (ADS)

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

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

2013-06-01

119

Predicting Intra-Urban Variation in Air Pollution Concentrations with Complex Spatio-Temporal Dependencies  

PubMed Central

We describe a methodology for assigning individual estimates of long-term average air pollution concentrations that accounts for a complex spatio-temporal correlation structure and can accommodate spatio-temporally misaligned observations. This methodology has been developed as part of the Multi-Ethnic Study of Atherosclerosis and Air Pollution (MESA Air), a prospective cohort study funded by the U.S. EPA to investigate the relationship between chronic exposure to air pollution and cardiovascular disease. Our hierarchical model decomposes the space-time field into a “mean” that includes dependence on covariates and spatially varying seasonal and long-term trends and a “residual” that accounts for spatially correlated deviations from the mean model. The model accommodates complex spatio-temporal patterns by characterizing the temporal trend at each location as a linear combination of empirically derived temporal basis functions, and embedding the spatial fields of coefficients for the basis functions in separate linear regression models with spatially correlated residuals (universal kriging). This approach allows us to implement a scalable single-stage estimation procedure that easily accommodates a significant number of missing observations at some monitoring locations. We apply the model to predict long-term average concentrations of oxides of nitrogen (NOx) from 2005–2007 in the Los Angeles area, based on data from 18 EPA Air Quality System regulatory monitors. The cross-validated R2 is 0.67. The MESA Air study is also collecting additional concentration data as part of a supplementary monitoring campaign. We describe the sampling plan and demonstrate in a simulation study that the additional data will contribute to improved predictions of long-term average concentrations. PMID:24860253

Szpiro, Adam A.; Sampson, Paul D.; Sheppard, Lianne; Lumley, Thomas; Adar, Sara D.; Kaufman, Joel

2014-01-01

120

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

121

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

PubMed Central

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

2010-01-01

122

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

123

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

PubMed Central

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

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

2013-01-01

124

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

PubMed Central

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

2014-01-01

125

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

E-print Network

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

P-M. Zhang; P. A. Horvathy

2011-11-15

126

Existence of minimizers for Kohn–Sham within the local spin density approximation  

NASA Astrophysics Data System (ADS)

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

Gontier, David

2015-01-01

127

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

NASA Astrophysics Data System (ADS)

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

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

2015-01-01

128

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

USGS Publications Warehouse

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

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

2014-01-01

129

Nitrogen and phosphorus variation in shallow groundwater and assimilation in plants in complex riparian buffer zones.  

PubMed

The study of purification efficiency and nutrient assimilation in plants was made in two riparian buffer zones with a complex of wet meadow and grey alder (Alnus incana) stand. In the less polluted Porijõgi test site, the 31 m wide buffer zone removed 40% of total nitrogen (total-N) and 78% of total phosphorus (total-P), while a heavily polluted 51 m wide buffer zone in Viiratsi retained 85% of total-N and 84% of total-P. The input of nutrients and purification efficiency displayed a significant relationship. The total-N removal in buffer zone was negative when the input value was less than 0.3 mg l(-1) and the purification efficiency was always positive when the input value exceeded 5 mg l(-1). The purification efficiency of total-P was positive when the input value exceeded 0.15 mg l(-1). Grass vegetation plays an important role in nutrient retention in riparian buffer strips. The maximum phytomass production was measured in Porijõgi site where production of the Filipendula ulmaria community was up to 2,358 g m(-2), assimilation of N 32.1 and of P 4.9 g m(-2), respectively. This is much higher than the biomass production and N and P uptake of the grey alders (Alnus incana) at the same site--1,730, 20.5 and 1.5 g m(-2), respectively. PMID:11804159

Kuusemets, V; Mander, U; Lõhmus, K; Ivask, M

2001-01-01

130

Geographic variation of the major histocompatibility complex in Eastern Atlantic grey seals (Halichoerus grypus).  

PubMed

Pathogen-driven balancing selection maintains high genetic diversity in many vertebrates, particularly in the major histocompatibility complex (MHC) immune system gene family, which is often associated with disease susceptibility. In large natural populations where subpopulations face different pathogen pressures, the MHC should show greater genetic differentiation within a species than neutral markers. We examined genetic diversity at the MHC-DQB locus and nine putatively neutral microsatellite markers in grey seals (Halichoerus grypus) from eight United Kingdom (UK) colonies, the Faeroe Islands and Sable Island, Canada. Five DQB alleles were identified in grey seals, which varied in prevalence across the grey seal range. Among the seal colonies, significant differences in DQB allele and haplotype frequencies and in average DQB heterozygosity were observed. Additionally, the DQB gene exhibited greater differentiation among colonies compared with neutral markers, yet a weaker pattern of isolation by distance (IBD). After correcting for the underlying IBD pattern, subpopulations breeding in similar habitats were more similar to one another in DQB allele frequencies than populations breeding in different habitats, but the same did not hold true for microsatellites, suggesting that habitat-specific pathogen pressure influences MHC evolution. Overall, the data are consistent with selection at MHC-DQB loci in grey seals with both varying selective pressures and geographic population structure appearing to influence the DQB genetic composition of breeding colonies. PMID:21199032

Cammen, K; Hoffman, J I; Knapp, L A; Harwood, J; Amos, W

2011-02-01

131

Influence of Gene Interaction on Complex Trait Variation with Multilocus Models  

PubMed Central

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

Mäki-Tanila, Asko; Hill, William G.

2014-01-01

132

Regional Heritability Mapping to identify loci underlying genetic variation of complex traits  

PubMed Central

Background Genome-wide association studies can have limited power to identify QTL, partly due to the stringent correction for multiple testing and low linkage-disequilibrium between SNPs and QTL. Regional Heritability Mapping (RHM) has been advanced as an alternative approach to capture underlying genetic effects. In this study, RHM was used to identify loci underlying variation in the 16th QTLMAS workshop simulated traits. Methods The method was implemented by fitting a mixed model where a genomic region and the overall genetic background were added as random effects. Heritabilities for the genetic regional effects were estimated, and the presence of a QTL in the region was tested using a likelihood ratio test (LRT). Several region sizes were considered (100, 50 and 20 adjacent SNPs). Bonferroni correction was used to calculate the LRT thresholds for genome-wide (p < 0.05) and suggestive (i.e., one false positive per genome scan) significance. Results Genomic heritabilities (0.31, 0.32 and 0.48, respectively) and genetic correlations (0.80, -0.42 and 0.19, between trait-pairs 1&2, 1&3 and 2&3) were similar to the simulated ones. RHM identified 7 QTL (4 at genome-wide and 3 at suggestive level) for Trait1; 4 (2 genome-wide and 2 suggestive) for Trait2; and 7 (6 genome-wide and 1 suggestive) for Trait3. Only one of the identified suggestive QTL was a false-positive. The position of these QTL tended to coincide with the position where the largest QTL (or several of them) were simulated. Several signals were detected for the simulated QTL with smaller effect. A combined analysis including all significant regions showed that they explain more than half of the total genetic variance of the traits. However, this might be overestimated, due to Beavis effect. All QTL affecting traits 1&2 and 2&3 had positive correlations, following the trend of the overall correlation of both trait-pairs. All but one QTL affecting traits 1&3 were negatively correlated, in agreement with the simulated situation. Moreover, RHM identified extra loci that were not found by association and linkage analysis, highlighting the improved power of this approach. Conclusions RHM identified the largest QTL among the simulated ones, with some signals for the ones with small effect. Moreover, RHM performed better than association and linkage analysis, in terms of both power and resolution. PMID:25519517

2014-01-01

133

Trace Element Variations Across the Marcy Anorthosite Massif - New Russia Complex Contact, Elizabethtown Area, NY  

NASA Astrophysics Data System (ADS)

The purpose of this study was to determine if migmatitic gneisses of the New Russia complex (NRC)adjacent to the Marcy Anorthosite massif (MAM) near Elizabethtown, NY display geochemical signatures indicative of partial melting. Alcock and Muller (2000) proposed that intrusion of the easternmost portion of the MAM into the NRC resulted in a thermal aureole in which gabbroic, mangeritic, and charnockitic gneisses of NRC experienced local anatexis. Petrologic and microtextural data indicate dehydration melting involving the following reaction: hbl + ksp+ qz = ga + cpx + Pl(antiperthitic) + melt +/- oxide at T greater than 900 C and P greater than 700 MPa. Fine-grained mangerite close to the anorthosite contacts has significantly greater amounts of garnet and oxides than mangerites further away from the contact. Field relationships indicate melt segregated into lenses and pods near the end of and after regional foliation formation. Eight samples taken along a transect at a high angle the steeply-dipping MAM/NRC contact were collected and locations were determined using a handheld GPS unit. Samples were cleaned, powdered, and dissolved for ICP-AES analysis for the following elements: Ba, Co, Cr, Eu, La, Mn, Nb, Ni, P, Sc, Sr, V, Yb, and Zr. Of these elements, Co, Ba, V, Yb, and Zr display patterns suggestive of partial melting and melt loss in mangeritic gneiss near the MAM/NRC contact. Ba and Zr concentrations in the mangerites are up to several hundred ppm lower than values reported for other Grenville mangerites. Ba depletion is consistent with breakdown of K-bearing phases such as Hbl and perthitic feldspar and removal with the melt. Co, and V show concentrations up to several hundred ppm higher than reported values for other Grenville mangerites. While we have no Yb concentration data to compare our values to, our Yb values are several times higher than those of other Grenville jotunites and which should have higher concentrations than mangerites. Further, Yb has been shown to concentrate in garnet formed during partial melting reactions such as those that occurred in the mangerites. We have no mineral chemistry data to document which mineral phases contain Co, however, we assume it partitions in a similar fashion to Yb and occurs as a trace component of pyroxene, garnet, and oxides, all of which are products of the melting reaction given above. This would explain its enrichment in the melt depleted contact zone gneisses.

Krone, F.; Muller, P. D.; Silverman, J.; Schaumloffel, J.

2004-05-01

134

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

135

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

NASA Astrophysics Data System (ADS)

A fundamental assumption in mapping geochemical variability of the upper mantle is that the isotope composition of mid-ocean ridge basalt is representative of its mantle source region, being largely unmodified during its transport through the crust and eruption on the seafloor. We have begun to test this assumption through measurement of He isotopes in a suite of rocks from the Kane oceanic core complex (OCC) along the Mid-Atlantic Ridge (23oN). The Kane OCC provides a valuable window into crustal architecture and chemical composition of a slow-spreading ridge (Dick et. al. 2008, 2010). A suite of > 30 samples (comprised of whole rocks, mineral separates and basalt glasses) has been analyzed for 3He/4He and He concentrations. Gas extraction experiments included crushing in vacuum, step heating, and fusion in a high-vacuum furnace. We found 3He/4He in the two freshest peridotites (harzburgite and olivine websterite) to be identical to that measured in the most depleted MORB glasses collected from the ridge axis (8.4-8.7 RA). Notably, the freshest and least deformed peridotite (a porphyroclastic harzburgite) has the highest helium content of any of the OCC rocks (~200 ncc/g), and the majority of its helium (>2/3) is only released by melting. In contrast to the results of Kurz et al. (2009), which clearly show increasing helium concentration levels with increasing deformation in abyssal peridotites from other localities, at the Kane OCC we found lower helium contents in three mylonitized peridotites compared to the less deformed peridotites. Troctolites from the Kane OCC experienced very late-stage melt impregnation fed through a conduit represented by a large dunite body near the MOHO. 3He/4He ratios in the troctolites (8.6-9.0 RA) also overlap with values in the fresh peridotites and in the most depleted basalts from the area. Collectively, fresh Kane OCC peridotites and troctolites, having [He] above 10 ncc/g, show a narrow range of 3He/4He ratio (8.4-9.0 RA). This value is elevated compared to the median value for MORBs (8 RA). Our observations suggest that domains of highly depleted MORB mantle tend to have higher 3He/4He ratios, approaching 9 RA, consistent with what is observed in depleted MORB glasses globally. Kane gabbroic rocks are more variable, and typically show lower 3He/4He ratios, often accompanied by lower He concentrations. This likely reflects an increased importance of atmospheric and radiogenic components. Lower initial 3He/4He ratios (<8 RA) may also be present in some of the gabbros, perhaps from partial meting of a lithologically heterogeneous mantle source.

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

2012-12-01

136

Symmetry Properties of the Kohn Potential, and its Relation to the External Potential  

NASA Astrophysics Data System (ADS)

The density functional theory (DFT) of Kohn and coworkers is nowadays a popular tool in atomic, molecular and solid state calculations. Its advanage is that in practice one has to solve a system of single particle Schroedinger equations by means of which one can construct a noninteracting state, having the same density as the exact ground state of the many electron system under consideration. A fundamental problem of DFT is the determination of the Kohn potential, VK, (Hartree plus Exchange and correlation potential) as a functional of the density. We show that this potential must have the same symmetry properties as the external potential V. As the density does not have in general the symmetry properties of the external potential, we express VK as a function of V, demanding that the two potentials have the same transfomation properties. We show that this dependence has the form VK(r;V) = aV(r) + b ? K(|r - r'|)V(r')d3r', i.e the kernel K must be invariant under I33, the group generated by all rotations and translations in the three dimensional Eucledean space.

Theophilou, Andreas K.; Papaconstantinou, Petros

2001-04-01

137

The education of Walter Kohn and the creation of density functional theory  

E-print Network

The theoretical solid-state physicist Walter Kohn was awarded one-half of the 1998 Nobel Prize in Chemistry for his mid-1960's creation of an approach to the many-particle problem in quantum mechanics called density functional theory (DFT). In its exact form, DFT establishes that the total charge density of any system of electrons and nuclei provides all the information needed for a complete description of that system. This was a breakthrough for the study of atoms, molecules, gases, liquids, and solids. Before DFT, it was thought that only the vastly more complicated many-electron wave function was needed for a complete description of such systems. Today, fifty years after its introduction, DFT (in one of its approximate forms) is the method of choice used by most scientists to calculate the physical properties of materials of all kinds. In this paper, I present a biographical essay of Kohn's educational experiences and professional career up to and including the creation of DFT.

Zangwill, Andrew

2014-01-01

138

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

PubMed

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

Winternitz, Jamie C; Wares, John P

2013-06-01

139

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

PubMed Central

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

Winternitz, Jamie C; Wares, John P

2013-01-01

140

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

E-print Network

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

Bjørnstad, Ottar Nordal

141

AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 90:3548 (1993) Cranial Deformation and Nonmetric Trait Variation  

E-print Network

AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 90:3548 (1993) Cranial Deformation and Nonmetric Trait Variation LYLE W. KONIGSBERG, LUCI A.P.KOHN, AND JAMES M. CHEVERUD Department of Anthropology, University, it is possible that deformation Address reprint requests to Lyle W. Konigsberg, Department ofAnthropology,252

Cheverud, James M.

142

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

E-print Network

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

Kidd, William S. F.

143

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

PubMed

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

Wayland, Matthew T

2013-01-01

144

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

USGS Publications Warehouse

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

Nakano, M.; Kumagai, H.

2005-01-01

145

Exact Time-Dependent Kohn-Sham Potential for an Interacting Few-Body System  

NASA Astrophysics Data System (ADS)

Time-dependent density functional theory enables practical simulations of the dynamic many-electron systems, but one of the biggest obstacles to reliable application is the quality of the approximate potential. It is often difficult to determine whether ever-more sophisticated approximations properly include new physics, as there exist few benchmark exact potentials. Towards this ends, we have developed and tested a scheme to extract the exact (non-adiabatic) time-dependent Kohn-Sham potential for few body systems. We will present some examples on 1D model systems. The approach is general and can be used to back engineer high-level quantum mechanical simulations to gain insight into TDDFT on a broad scale. Sandia National Laboratories is a multi-program laboratory operated by Sandia Corporation, a wholly owned subsidiary of the Lockheed Martin company, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Magyar, Rudolph J.

2011-03-01

146

Kohn-Sham potentials in exact density-functional theory at noninteger electron numbers  

NASA Astrophysics Data System (ADS)

Within exact electron density-functional theory, we investigate Kohn-Sham (KS) potentials, orbital energies, and noninteracting kinetic energies of the fractional ions of Li, C, and F. We use quantum Monte Carlo densities as input, which are then fitted, interpolated at noninteger electron numbers N , and inverted to produce accurate KS potentials vsN(r ) . We study the dependence of the KS potential on N , and in particular we numerically reproduce the theoretically predicted spatially constant discontinuity of vsN(r ) as N passes through an integer. We further show that, for all the cases considered, the inner orbital energies and the noninteracting kinetic energy are nearly piecewise linear functions of N . This leads us to propose a simple approximation of the KS potential vsN(r ) at any fractional electron number N which uses only quantities of the systems with the adjacent integer electron numbers.

Gould, Tim; Toulouse, Julien

2014-11-01

147

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

E-print Network

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

Lin, Lin

2013-01-01

148

Exact and approximate Kohn-Sham potentials in ensemble density-functional theory  

NASA Astrophysics Data System (ADS)

We construct exact Kohn-Sham potentials for the ensemble density-functional theory (EDFT) from the ground and excited states of helium. The exchange-correlation (XC) potential is compared with the quasi-local-density approximation and both single-determinant and symmetry-eigenstate ghost-corrected exact exchange approximations. Symmetry-eigenstate Hartree exchange recovers distinctive features of the exact XC potential and is used to calculate the correlation potential. Unlike the exact case, excitation energies calculated from these approximations depend on ensemble weight, and it is shown that only the symmetry-eigenstate method produces an ensemble derivative discontinuity. Differences in asymptotic and near-ground-state behavior of exact and approximate XC potentials are discussed in the context of producing accurate optical gaps.

Yang, Zeng-hui; Trail, John R.; Pribram-Jones, Aurora; Burke, Kieron; Needs, Richard J.; Ullrich, Carsten A.

2014-10-01

149

Human cognitive ability is influenced by genetic variation in components of postsynaptic signalling complexes assembled by NMDA receptors and MAGUK proteins  

PubMed Central

Differences in general cognitive ability (intelligence) account for approximately half of the variation in any large battery of cognitive tests and are predictive of important life events including health. Genome-wide analyses of common single-nucleotide polymorphisms indicate that they jointly tag between a quarter and a half of the variance in intelligence. However, no single polymorphism has been reliably associated with variation in intelligence. It remains possible that these many small effects might be aggregated in networks of functionally linked genes. Here, we tested a network of 1461 genes in the postsynaptic density and associated complexes for an enriched association with intelligence. These were ascertained in 3511 individuals (the Cognitive Ageing Genetics in England and Scotland (CAGES) consortium) phenotyped for general cognitive ability, fluid cognitive ability, crystallised cognitive ability, memory and speed of processing. By analysing the results of a genome wide association study (GWAS) using Gene Set Enrichment Analysis, a significant enrichment was found for fluid cognitive ability for the proteins found in the complexes of N-methyl-D-aspartate receptor complex; P=0.002. Replication was sought in two additional cohorts (N=670 and 2062). A meta-analytic P-value of 0.003 was found when these were combined with the CAGES consortium. The results suggest that genetic variation in the macromolecular machines formed by membrane-associated guanylate kinase (MAGUK) scaffold proteins and their interaction partners contributes to variation in intelligence. PMID:24399044

Hill, W D; Davies, G; van de Lagemaat, L N; Christoforou, A; Marioni, R E; Fernandes, C P D; Liewald, D C; Croning, M D R; Payton, A; Craig, L C A; Whalley, L J; Horan, M; Ollier, W; Hansell, N K; Wright, M J; Martin, N G; Montgomery, G W; Steen, V M; Le Hellard, S; Espeseth, T; Lundervold, A J; Reinvang, I; Starr, J M; Pendleton, N; Grant, S G N; Bates, T C; Deary, I J

2014-01-01

150

Diameter dependence of TO phonon frequencies and the Kohn anomaly in armchair single-wall carbon nanotubes  

NASA Astrophysics Data System (ADS)

We present resonant Raman scattering experiments on nanotube samples enriched in metallic armchair single-wall carbon nanotubes (SWCNTs). We establish the transverse optical (ATO) phonon frequency for the (5,5) through (10,10) armchair species, ranging in diameter from 0.68 to 1.36 nm. The frequencies show a strong diameter dependence similar to that previously observed in semiconducting nanotubes. We show that the ATO frequencies in armchair SWCNTs are dramatically upshifted from those of semiconducting SWCNTs. Furthermore, using electrochemical doping, we demonstrated that the ATO frequencies in armchair SWCNTs are independent of the position of the Fermi level. These results suggest that the upshift is a result of a Kohn anomaly involving a forward-scattering mechanism of electrons close to the Fermi level. This is in contrast to the well-known Kohn anomaly that dominates the downshift of the ALO and E2 g phonons in nonarmchair metallic SWCNTs and graphene, respectively.

Telg, Hagen; Hároz, Erik H.; Duque, Juan G.; Tu, Xiaomin; Khripin, Constantine Y.; Fagan, Jeffrey A.; Zheng, Ming; Kono, Junichiro; Doorn, Stephen K.

2014-12-01

151

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

PubMed Central

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

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

1977-01-01

152

Application of light-absorption ratio variation approach as an optimum spectrophotometry to determination of Mn(II) in ng ml -1 level using a competitive replacement complexation  

NASA Astrophysics Data System (ADS)

The light-absorption ratio variation approach (LARVA) which produces an outstandingly increasing of analytical sensitivity was applied to the quantitative detection of ultramicro amounts of Mn(II) by light-absorption spectrometry using the competitive replacement complexation among 1,5-di(2-hydroxy-5-sulfophenyl)-3-cyanoformazan (DSPCF), Zn(II) and Mn(II) in the presence of o-phenanthroline (OPTL). Not only masks OPTL foreign metal ions but also seriously sensitize the competitive complexation. All the binary and ternary complexes were characterized by the break point approach. Results have shown that the limit of detection (3 ?) of Mn(II) is only 0.7 ng ml -1. This method has been applied to analysis of water quality with satisfactory results.

Gao, Hong-Wen; Zhang, Sheng-Yi; Wang, Hong-Yan; Xia, Si-Qing; Zhang, Ya-Lei

2005-01-01

153

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

2013-07-19

154

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

PubMed Central

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.

2013-01-01

155

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

E-print Network

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

G. W. Gibbons; C. N. Pope

2010-11-10

156

The Distribution of Life-History Variation in the Daphnia pulex Complex Michael Lynch; Ken Spitze; Teresa Crease  

E-print Network

population in reproductive isolation from the parental species. Although the frequency of asexuality may and asexual populations, providing a useful model system for studying the evolutionary forces underlying the maintenance of sex. One asexual and two sexual populations were surveyed for genetic variation for isozymes

Lynch, Michael

157

The Stage 3 interstadial complex (Karginskii\\/middle Wisconsinan interval) of Beringia: variations in paleoenvironments and implications for paleoclimatic interpretations  

Microsoft Academic Search

Questionable chronologies have limited detailed reconstructions of past vegetation and climate trends for the Karginskii\\/Middle Wisconsinan interstade (abbreviated here as MW). However, recent results from continuous lake records, while not resolving all the dating issues, do provide a new framework within which to examine this intriguing period. Paleobotanical data suggest significant regional variations in the interstadial vegetation of Beringia. Larix

Patricia M. Anderson; Anatoly V. Lozhkin

2001-01-01

158

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

159

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

EPA Science Inventory

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

160

Textural and Compositional Variations in a Large Mafic Enclave from the Purico-Chascon Volcanic Complex: Understanding Mafic Recharge in a Large Continental Magmatic System  

NASA Astrophysics Data System (ADS)

Mafic enclaves in silicic volcanic rocks provide vital information regarding the role of mafic replenishment in the long-term evolution and triggering of eruptions in silicic magma systems. In this study, we are investigating textural and compositional variations in a single large (~25 x 10 cm) mafic enclave from the Cerro Chascon lava dome in the Purico-Chascon Volcanic Complex of Northern Chile. The Cerro Chascon lava dome is predominantly high-K crystal-rich dacite, similar to other major volcanic units in the region, but is rare in that it contains significant basaltic-andesite mafic enclaves. The mafic enclave analyzed in this study is porphyritic containing plagioclase + amphibole + clinopyroxene + olivine + Fe-Ti oxides in a groundmass of high-silica (~69-73 wt.% SiO2) glass with plagioclase and amphibole micro-phenocrysts, and acicular plagioclase microlites. There is also strong evidence for the incorporation of crystalline material from the dacite host. In particular, the mafic enclave contains large embayed quartz crystals that are rimmed with clinopyroxene, and large plagioclase crystals with heavily sieved high anorthite (An70-85) rims and clear cores that are compositionally indistinguishable from plagioclase crystals in the host (An45-50). There do not appear to be significant variations in the distribution of the xenocrysts within the enclave, but there are significant variations in the texture, composition, and microlite content of the groundmass glass. More specifically, there is a systematic increase in the amount of vesicularity (~3-5 vol.%) and decrease in vesicle size from the enclave interior to the enclave-host contact. These textural variations are accompanied by small but significant variations in the major element chemistry, (SiO2 and K2O increase from rim-ward, and CaO, Na2O, and Cl decrease) and a rim-ward increase in the proportion of plagioclase microlites. The random distribution of xenocrysts and systematic textural, chemical, and modal (microlites) variations within the mafic enclave indicate the transfer of crystalline material into the enclave occurred prior to the formation of the textural, chemical, and microlite gradients. We believe that the xenocrysts were incorporated prior to the emplacement of the enclave into the dacite host, and that the variations in vesicularity, major element chemistry, and microlite content formed post emplacement. Furthermore, there is strong evidence that the observed major element variations resulted from the increase in microlite crystallization near the enclave-host contact. The rim-ward increase in vesicularity is consistent with this model, assuming the amount of crystallization is sufficient to cause vapor oversaturation in the residual melt.

Burns, D. H.; Tepley, F. J.; de Silva, S. L.; Carter, Z. G.

2011-12-01

161

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

PubMed

A cobalt(III) complex (1) of a salcy-type ligand tethering 4 quaternary ammonium salts, which is thought to act as a highly active catalyst for CO2/propylene oxide (PO) copolymerization, also shows high activity (TOF, 25,900 h(-1); TON, 518,000; 2.72 kg polymer per g cat) and selectivity (>98%) for CO2/ethylene oxide (EO) copolymerization that results in high-molecular-weight polymers (M(n), 200,000-300,000) that have strictly alternating repeating units. The related cobalt(III) complexes 11-14 were prepared through variations of the ligand framework of 1 by replacing the trans-1,2-diaminocyclohexane unit with 2,2-dimethyl-1,3-propanediamine, trans-1,2-diaminocyclopentane, or 1,1'-binaphthyl-2,2'-diamine or by replacing the aldimine bond with ketimine. These ligand frameworks are thought to favour the formation of the cis-? configuration in complexation, and the formation of the cis-? configuration in 11-14 was confirmed through NMR studies or X-ray crystallographic studies of model complexes not bearing the quaternary ammonium salts. Complexes 11, 13, and 14, which adopt the cis-? configuration even in DMSO did not show any activity for CO2/PO copolymerization. Complex 12, which was constructed with trans-1,2-diaminocyclopentane and fluctuated in DMSO between the coordination and de-coordination of the acetate ligand as observed for 1, showed fairly high activity (TOF, 12,400 h(-1)). This fluctuating behaviour may play a role in polymerization. However, complex 12 did not compete with 1 in terms of activity, selectivity, and the catalyst cost. PMID:23104466

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

2013-07-01

162

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

163

Self-consistent solution of Kohn-Sham equations for infinitely extended systems with inhomogeneous electron gas  

SciTech Connect

The density functional approach in the Kohn-Sham approximation is widely used to study properties of many-electron systems. Due to the nonlinearity of the Kohn-Sham equations, the general self-consistence searching method involves iterations with alternate solving of the Poisson and Schroedinger equations. One of problems of such an approach is that the charge distribution renewed by means of the solution of the Schroedinger equation does not conform to boundary conditions of the Poisson equation for the Coulomb potential. The resulting instability or even divergence of iterations manifests itself most appreciably in the case of infinitely extended systems. The known attempts to deal with this problem are reduced in fact to abandoning the original iterative method and replacing it with some approximate calculation scheme, which is usually semi-empirical and does not permit to evaluate the extent of deviation from the exact solution. In this work, we realize the iterative scheme of solving the Kohn-Sham equations for extended systems with inhomogeneous electron gas, which is based on eliminating the long-range character of Coulomb interaction as the cause of tight coupling between charge distribution and boundary conditions. The suggested algorithm is employed to calculate energy the spectrum, self-consistent potential, and electrostatic capacitance of the semi-infinite degenerate electron gas bounded by an infinitely high barrier, as well as the work function and surface energy of simple metals in the model with homogeneous distribution of positive background. The difference between self-consistent Hartree solutions and those taking into account the exchange-correlation interaction is analyzed. The comparison with the results previously published in the literature is carried out. The case study of the metal-semiconductor tunnel contact shows this method as applied to an infinitely extended system where the steady-state current can flow.

Posvyanskii, D. V., E-mail: posvyanskii@cplire.ru; Shul'man, A. Ya., E-mail: ash@cplire.r [Russian Academy of Sciences, Kotel'nikov Institute of Radio Engineering and Electronics (Russian Federation)

2009-07-15

164

Genetic Analysis of TOR Complex Gene Variation With Human Longevity: A Nested Case-Control Study of American Men of Japanese Ancestry.  

PubMed

The mechanistic target of rapamycin (mTOR) pathway is crucial for life span determination in model organisms. The aim of the present study was to test tagging single-nucleotide polymorphisms that captured most of the genetic variation across key TOR complex 1 (TORC1) and TOR complex 2 (TORC2) genes MTOR, RPTOR, and RICTOR and the important downstream effector gene RPS6KA1 for association with human longevity (defined as attainment of at least 95 years of age) as well as health span phenotypes. Subjects comprised a homogeneous population of American men of Japanese ancestry, well characterized for aging phenotypes and who have been followed for 48 years. The study used a nested case-control design involving 440 subjects aged 95 years and older and 374 controls. It found no association of 6 tagging single-nucleotide polymorphisms for MTOR, 61 for RPTOR, 7 for RICTOR, or 5 for RPS6KA1 with longevity. Of 40 aging-related phenotypes, no significant association with genotype was seen. Thus common genetic variation (minor allele frequency ?10%) in MTOR, RPTOR, RICTOR, and RPS6KA1 is not associated with extreme old age or aging phenotypes in this population. Further research is needed to assess the potential genetic contribution of other mTOR pathway genes to human longevity, gene expression, upstream and downstream targets, and clinically relevant aging phenotypes. PMID:24589862

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

2015-02-01

165

Quantifying complex patterns of bioacoustic variation: use of a neural network to compare killer whale (Orcinus orca) dialects.  

PubMed

A quantitative measure of acoustic similarity is crucial to any study comparing vocalizations of different species, social groups, or individuals. The goal of this study was to develop a method of extracting frequency contours from recordings of pulsed vocalizations and to test a nonlinear index of acoustic similarity based on the error of an artificial neural network at classifying them. Since the performance of neural networks depends on the amount of consistent variation in the training data, this technique can be used to assess such variation from samples of acoustic signals. The frequency contour extraction and the neural network index were tested on samples of one call type shared by nine social groups of killer whales. For comparison, call similarity was judged by three human subjects in pairwise classification tasks. The results showed a significant correlation between the neural network index and the similarity ratings by the subjects. Both measures of acoustic similarity were significantly correlated with the groups' association patterns, indicating that both methods of quantifying acoustic similarity are biologically meaningful. An index based on neural network analysis therefore represents an objective and repeatable means of measuring acoustic similarity, and allows comparison of results across studies, species and time. PMID:10212431

Deecke, V B; Ford, J K; Spong, P

1999-04-01

166

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

PubMed Central

Comparative genomic hybridization to bacterial artificial chromosome (BAC)-arrays (array-CGH) is a highly efficient technique, allowing the simultaneous measurement of genomic DNA copy number at hundreds or thousands of loci, and the reliable detection of local one-copy-level variations. We report a genome-wide amplification method allowing the same measurement sensitivity, using 1 ng of starting genomic DNA, instead of the classical 1 ?g usually necessary. Using a discrete series of DNA fragments, we defined the parameters adapted to the most faithful ligation-mediated PCR amplification and the limits of the technique. The optimized protocol allows a 3000-fold DNA amplification, retaining the quantitative characteristics of the initial genome. Validation of the amplification procedure, using DNA from 10 tumour cell lines hybridized to BAC-arrays of 1500 spots, showed almost perfectly superimposed ratios for the non-amplified and amplified DNAs. Correlation coefficients of 0.96 and 0.99 were observed for regions of low-copy-level variations and all regions, respectively (including in vivo amplified oncogenes). Finally, labelling DNA using two nucleotides bearing the same fluorophore led to a significant increase in reproducibility and to the correct detection of one-copy gain or loss in >90% of the analysed data, even for pseudotriploid tumour genomes. PMID:15284333

Guillaud-Bataille, Marine; Valent, Alexander; Soularue, Pascal; Perot, Christine; Inda, Maria-del-Mar; Receveur, Aline; Smaïli, Sadek; Crollius, Hugues Roest; Bénard, Jean; Bernheim, Alain; Gidrol, Xavier; Danglot, Gisèle

2004-01-01

167

Variations of the parameters of ionospheric wave structures from data of the SUNDIAL complex experiment during September-October 1989  

NASA Astrophysics Data System (ADS)

The parameters characterizing shifting ionospheric disturbances were determined in a complex SUNDIAL experiment conducted during the time period September 11-October 6, 1989, which included vertical sounding of the ionosphere and satellite radioscopy. Results are also presented on quantitive verifications of the dispersion ratios of the acoustic-gravitational waves and on the correlation between the statistical parameters of ionospheric disturbances during the September-October period with magnitudes of the magnetic disturbance for that period.

Biriukov, O. V.; Saenko, Iu. S.; Shagimuratov, I. I.

1993-02-01

168

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

2013-09-16

169

Trinuclear heterometallic Cu(II)-Mn(II) complexes of a salen type Schiff base ligand: anion dependent variation of phenoxido bridging angles and magnetic coupling.  

PubMed

Five new trinuclear heterometallic Cu(II)-Mn(II) complexes [(CuL)2Mn(O2CPh)2] (1), [(CuL)2Mn(N3)2] (2), [(CuL)2Mn(NCO)2] (3), [(CuL)2Mn(NO3)2] (4) and [(CuL)2Mn(Sal)2]·CH2Cl2 (5) have been synthesized with the di-Schiff base ligand H2L (where H2L = N,N'-bis(salicylidene)-1,3-propanediamine and Sal = salicylate). These complexes with different anionic co-ligands have been synthesized to attain a large variation in phenoxido bridging angles and to investigate its consequence on magnetic properties. Single crystal X-ray diffraction analyses reveal that complexes 1, 2, 4 and 5 are linear, whereas 3 has an angular geometry. Variable temperature magnetic susceptibility measurements suggest that all five complexes possess an overall antiferromagnetic interaction between Cu(II) and Mn(II) ions, which results in a final ferrimagnetic ground state with spin 3/2 in the Cu(II)-Mn(II)-Cu(II) trinuclear structure. The weakest antiferromagnetic interaction (J(Cu-Mn) = -7.0 cm(-1)) is observed for 2 having the lowest value of the Cu-O-Mn angle (92.0°), while the strongest antiferromagnetic interaction (J(Cu-Mn) = -26.5 cm(-1)) is observed for 3 having the largest Cu-O-Mn angle (101.4°). Complexes 1, 4 and 5 show average Cu-O-Mn angles of 98.2°, 97.6° and 97.7°, respectively, that lead to intermediate antiferromagnetic interactions (J(Cu-Mn) = -9.6, -9.7, -9.3 cm(-1) respectively). PMID:24162065

Seth, Piya; Ghosh, Soumavo; Figuerola, Albert; Ghosh, Asutosh

2014-01-21

170

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 Central

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 Kd for the Ca2+-free reference complex is 2.4 ± 0.3 ?M. The Ala and Arg replacements increase this to 5.4 ± 0.4 and 6.2 ± 0.5 ?M, while the Met increases it to 26.4 ± 2.5 ?M. When Ca2+ is bound to both calmodulin lobes, the Kd for the reference complex is not significantly affected, but the Kd for the Ala variant decreases to 0.9 ± 0.04 ?M, and the values for the Arg and Met variants decrease to 0.4 ± 0.03 ?M. Using mutant calmodulins, we defined the effect of Ca2+ 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 Kd ~5-fold, while it decreases the values for the variants ~2- to ~10-fold. The second step decreases the Kd values for the all of the complexes ~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 Kd values for the reference complex and Met and Ala variants ~15- to ~200-fold but does not affect the value for the Arg variant. The second step decreases the Kd values for the reference and Arg variant ~10- and ~15-fold and the Ala and Met variants ~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

2011-01-01

171

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

2010-03-01

172

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

PubMed Central

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

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

2009-01-01

173

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 log 10 of pathogen, by bacterium species, were 0.61, 0.54, 0.47, 0.36 and 0.15 kGy for Salmonella spp., S. aureus, L. monocytogenes, E. coli O157:H7, and Y. enterocolitica, respectively when inoculated onto the three product types. These results indicate that irradiation may be an effective means for inactivating common foodborne pathogens including Salmonella spp, S. aureus, L. monocytogenes, E. coli O157:H7 and Y. enterocolitica in complex RTE food products such as 'heat and eat" sandwich products.

Sommers, Christopher H.; Boyd, Glenn

2006-07-01

174

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

USGS Publications Warehouse

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

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

2009-01-01

175

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

NASA Astrophysics Data System (ADS)

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

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

2010-05-01

176

Hydrogen-bonded complexes upon spatial confinement: structural and energetic aspects.  

PubMed

In the present study we consider structural and energetic aspects of spatial confinement of the H-bonded systems. The model dimeric systems: HF···HF, HCN···HCN and HCN···HCCH have been chosen for a case study. Two-dimensional harmonic oscillator potential, mimicking a cylindrical confinement, was applied in order to render the impact of orbital compression on the analyzed molecular complexes. The calculations have been performed employing the MP2 method as well as the Kohn-Sham formulation of density functional theory. In the latter case, two exchange-correlation potentials have been used, namely B3LYP and M06-2X. The geometries of studied complexes have been optimized (without any constraints) in the presence of the applied model confining potential. A thorough analysis of topological parameters characterizing hydrogen bonds upon orbital compression has been performed within the Quantum Theory of Atoms in Molecules (QTAIM). Furthermore, an energetic analysis performed for the confined H-bonded complexes has shown a different trend in the interaction energy changes. Additionally, a variational-perturbational decomposition scheme was applied to study the interaction energy components in the presence of spatial confinement. PMID:24296646

Lipkowski, Pawe?; Koz?owska, Justyna; Roztoczy?ska, Agnieszka; Bartkowiak, Wojciech

2014-01-28

177

Genetic drift vs. natural selection in a long-term small isolated population: major histocompatibility complex class II variation in the Gulf of California endemic porpoise (Phocoena sinus).  

PubMed

Although many studies confirm long-term small isolated populations (e.g. island endemics) commonly sustain low neutral genetic variation as a result of genetic drift, it is less clear how selection on adaptive or detrimental genes interplay with random forces. We investigated sequence variation at two major histocompatibility complex (Mhc) class II loci on a porpoise endemic to the upper Gulf of California, México (Phocoena sinus, or vaquita). Its unique declining population is estimated around 500 individuals. Single-strand conformation polymorphism analysis revealed one putative functional allele fixed at the locus DQB (n = 25). At the DRB locus, we found two presumed functional alleles (n = 29), differing by a single nonsynonymous nucleotide substitution that could increase the stability at the dimer interface of alphabeta-heterodimers on heterozygous individuals. Identical trans-specific DQB1 and DRB1 alleles were identified between P. sinus and its closest relative, the Burmeister's porpoise (Phocoena spinipinnis). Comparison with studies on four island endemic mammals suggests fixation of one allele, due to genetic drift, commonly occurs at the DQA or DQB loci (effectively neutral). Similarly, deleterious alleles of small effect are also effectively neutral and can become fixed; a high frequency of anatomical malformations on vaquita gave empirical support to this prediction. In contrast, retention of low but functional polymorphism at the DRB locus was consistent with higher selection intensity. These observations indicated natural selection could maintain (and likely also purge) some crucial alleles even in the face of strong and prolonged genetic drift and inbreeding, suggesting long-term small populations should display low inbreeding depression. Low levels of Mhc variation warn about a high susceptibility to novel pathogens and diseases in vaquita. PMID:17727623

Munguia-Vega, Adrian; Esquer-Garrigos, Yareli; Rojas-Bracho, Lorenzo; Vazquez-Juarez, Ricardo; Castro-Prieto, Aines; Flores-Ramirez, Sergio

2007-10-01

178

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

PubMed

The role the major histocompatibility complex (MHC) plays in response to exposure to environmental toxins is relatively poorly understood, particularly in comparison to its well-described role in pathogen immunity. We investigated associations between MHC diversity and resistance to brevetoxins in common bottlenose dolphins (Tursiops truncatus). A previous genome-wide association study investigating an apparent difference in harmful algal bloom (HAB) resistance among dolphin populations in the Gulf of Mexico identified genetic variation associated with survival in close genomic proximity to multiple MHC class II loci. Here, we characterized genetic variation at DQA, DQB, DRA, and DRB loci in dolphins from central-west Florida and the Florida Panhandle, including dolphins that died during HABs and dolphins presumed to have survived HAB exposure. We found that DRB and DQB exhibited patterns of genetic differentiation among geographic regions that differed from neutral microsatellite loci. In addition, genetic differentiation at DRB across multiple pairwise comparisons of live and dead dolphins was greater than differentiation observed at neutral loci. Our findings at these MHC loci did not approach the strength of association with survival previously described for a nearby genetic variant. However, the results provide evidence that selective pressures at the MHC vary among dolphin populations that differ in the frequency of HAB exposure and that the overall composition of DRB variants differs between dolphin survivors and non-survivors of HABs. These results may suggest a potential role of MHC diversity in variable survival of bottlenose dolphins exposed to HABs. PMID:25475909

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

2015-02-01

179

Inter and intra ethnic variation of vitamin K epoxide reductase complex and cytochrome P450 4F2 genetic polymorphisms and their prevalence in South Indian population  

PubMed Central

BACKGROUND: Genetic variation in the vitamin K epoxide reductase complex (VKORC1) and cytochrome P450 4F2 (CYP4F2) genes were found to be strongly associated with the oral anticoagulant (OA) dose requirement. The distribution of genetic variation in these two genes was found to show large inter- and intra-ethnic difference. MATERIALS AND METHODS: A total of 470 unrelated, healthy volunteers of South Indians of either sex (age: 18-60 years) were enrolled for the study. A 5 ml of venous blood was collected and the genomic deoxyribonucleic acid (DNA) was extracted by using phenol-chloroform extraction method. Real-time quantitative polymerase chain reaction (RT-PCR) method was used for genotyping. RESULTS: The variant allele frequencies of VKORC1 rs2359612 (T), rs8050894 (C), rs9934438 (T) and rs9923231 (A) were found to be 11.0%, 11.8%, 11.7% and 12.0%, respectively. The variant allele VKORC1 rs7294 was (80.1%) more frequent and the variant allele CYP4F2 * 3 was found to be 41.8% in South Indians. The allele, genotype and haplotype frequencies of VKORC1 and CYP4F2 gene were distinct from other compared HapMap populations (P < 0.0001). CONCLUSION: The findings of our study provide the basic genetic information for further pharmacogenetic based investigation of OA therapy in the population. PMID:24339542

Kumar, Dhakchinamoorthi Krishna; Shewade, Deepak Gopal; Manjunath, Sajjanavar; Ushakiran, Prayaga; Reneega, Gangadharan; Adithan, Chandrasekaran

2013-01-01

180

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

PubMed

The major histocompatibility complex is one of the best studied systems in vertebrates providing evidence for the long-term action of selection. Here, we examined the intra- and inter-population genetic diversity of the MHC class II DRB locus in European brown hare (Lepus europaeus) and correlated the results with genetic variability already estimated from the MHC DQA locus and from maternally (mitochondrial DNA (mtDNA)) and biparentally (allozymes, microsatellites) inherited loci. L. europaeus showed remarkable genetic polymorphism in both DQA and DRB1 loci. The Anatolian populations exhibited the highest genetic polymorphism for both loci. Balancing selection has established increased variability in the European populations despite the founder effects after the last glaciation. Different evolutionary rates were traced for DRB1 and DQA loci, as evidenced by the higher number of common DRB1 than DQA alleles and the greater differences between DRB1 alleles with common origin in comparison with DQA alleles. The high number of rare alleles with low frequencies detected implies that frequency-dependent selection drives MHC evolution in the brown hare through the advantage of rare alleles. Both loci were under the influence of positive selection within the peptide-binding region. The functional polymorphism, recorded as amino acid substitutions within the binding pockets, fell also within distinct geographic patterns, yet it was much narrower than the genetic polymorphism. We hypothesize that certain structural and functional characteristics of the binding pockets set limitations to the actual shape of genetic polymorphism in MHC. PMID:24743946

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

2014-06-01

181

Scanning and transmission electron microscopy of the tegument of Paranaella luquei Kohn, Baptista-Farias & Cohen, 2000 (Microcotylidae, Monogenea), parasite of a Brazilian catfish, Hypostomus regani  

Microsoft Academic Search

The surface topography and ultrastructure of the tegument of Paranaella luquei Kohn, Baptista- Farias & Cohen, 2000, a microcotylid monogenean parasite from the gills of Hypostomus regani (Ihering, 1905) (Loricariidae) was studied by scanning (SEM) and transmission electron microscopy (TEM). By SEM, it was observed that the tegument presents transversal ridges, forming folds in the ventral and dorsal surfaces and

SC Cohen; A Kohn; MFD Baptista-Farias

2001-01-01

182

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

PubMed

Sandy beach ecological theory states that physical features of the beach control macrobenthic community structure on all but the most dissipative beaches. However, few studies have simultaneously evaluated the relative importance of physical, chemical and biological factors as potential explanatory variables for meso-scale spatio-temporal patterns of intertidal community structure in these systems. Here, we investigate macroinfaunal community structure of a micro-tidal sandy beach that is located on an oligotrophic subtropical coast and is influenced by seasonal estuarine input. We repeatedly sampled biological and environmental variables at a series of beach transects arranged at increasing distances from the estuary mouth. Sampling took place over a period of five months, corresponding with the transition between the dry and wet season. This allowed assessment of biological-physical relationships across chemical and nutritional gradients associated with a range of estuarine inputs. Physical, chemical, and biological response variables, as well as measures of community structure, showed significant spatio-temporal patterns. In general, bivariate relationships between biological and environmental variables were rare and weak. However, multivariate correlation approaches identified a variety of environmental variables (i.e., sampling session, the C?N ratio of particulate organic matter, dissolved inorganic nutrient concentrations, various size fractions of photopigment concentrations, salinity and, to a lesser extent, beach width and sediment kurtosis) that either alone or combined provided significant explanatory power for spatio-temporal patterns of macroinfaunal community structure. Overall, these results showed that the macrobenthic community on Mtunzini Beach was not structured primarily by physical factors, but instead by a complex and dynamic blend of nutritional, chemical and physical drivers. This emphasises the need to recognise ocean-exposed sandy beaches as functional ecosystems in their own right. PMID:21858213

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

2011-01-01

183

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

PubMed Central

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

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

2014-01-01

184

Genetic variation on the BAT1-NFKBIL1-LTA region of major histocompatibility complex class III associates with periodontitis.  

PubMed

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

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

2014-05-01

185

On the Convergence of the Self-Consistent Field Iteration in Kohn-Sham Density Functional Theory  

E-print Network

It is well known that the self-consistent field (SCF) iteration for solving the Kohn-Sham (KS) equation often fails to converge, yet there is no clear explanation. In this paper, we investigate the SCF iteration from the perspective of minimizing the corresponding KS total energy functional. By analyzing the second-order Taylor expansion of the KS total energy functional and estimating the relationship between the Hamiltonian and the part of the Hessian which is not used in the SCF iteration, we are able to identify some conditions to ensure global convergence from an arbitrary initial point to and local linear convergence from an initial point sufficiently close to the solution of the KS equation. Our analysis holds under mild assumptions that the second-order derivatives of the exchange correlation functional are uniformly bounded from above.

Liu, Xin; Wen, Zaiwen; Yuan, Yaxiang

2013-01-01

186

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

PubMed

Humans have introduced many species onto remote oceanic islands. The house mouse (Mus musculus) is a human commensal and has consequently been transported to oceanic islands around the globe as an accidental stowaway. The history of these introductions can tell us not only about the mice themselves but also about the people that transported them. Following a phylogeographic approach, we used mitochondrial D-loop sequence variation (within an 849- to 864-bp fragment) to study house mouse colonization of the Azores. A total of 239 sequences were obtained from all nine islands, and interpretation was helped by previously published Iberian sequences and 66 newly generated Spanish sequences. A Bayesian analysis revealed presence in the Azores of most of the D-loop clades previously described in the domesticus subspecies of the house mouse, suggesting a complex colonization history of the archipelago as a whole from multiple geographical origins, but much less heterogeneity (often single colonization?) within islands. The expected historical link with mainland Portugal was reflected in the pattern of D-loop variation of some of the islands but not all. A more unexpected association with a distant North European source area was also detected in three islands, possibly reflecting human contact with the Azores prior to the 15th century discovery by Portuguese mariners. Widening the scope to colonization of the Macaronesian islands as a whole, human linkages between the Azores, Madeira, the Canaries, Portugal and Spain were revealed through the sharing of mouse sequences between these areas. From these and other data, we suggest mouse studies may help resolve historical uncertainties relating to the 'Age of Discovery'. PMID:25394749

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

2014-11-14

187

Variation of radon concentration levels in the Tusham Ring Complex: influence of trace elements, exhalation rate, gamma levels and regional geology  

NASA Astrophysics Data System (ADS)

In the present study, an attempt has been made to study the influence of exhalation rate, trace element concentration, gamma levels & regional geology on the variation of indoor radon concentration levels in the dwellings around the Tusham Ring Complex, Bhiwani, Haryana, a region famous for acid volcanic & the associated high heat producing (HHP) granitic rock formations. The indoor radon measurements have been carried out in dwellings using the passive technique employing Solid State Nuclear Track Detector (LR-115 type 2). The indoor radon levels in these dwellings have been found to be varying from 109±10 to 1006±107 Bqm-3 whereas these vary from 60±17 to 235±55 Bqm-3 for the dwellings studied in Amritsar District, Punjab. The indoor radon concentration levels only at some places, which are close to the exposed HHP granite rock formations, have been found to be higher. The study of the exhalation rate measurements of the rock/soil samples have also been carried out by the passive technique using the LR-115 films and slightly higher exhalation rates have been observed from samples collected from HHP granitic rock formation regions of the Tusham ring complex, as compared to other adjoining regions. It has also been observed that especially in dwellings situated on or around the exposed HHP granitic formations, where the indoor radon concentrations are higher, the gamma activities are also high. Particularly for these places, a good correlation (R2=0.64) has been observed between indoor radon and gamma activity, indicating that along with the surface-soil, the exposed HHP granitic rocks belonging to the Malani igneous suite are actively contributing towards higher activities observed at certain places. Typical activity concentrations for radium and thorium content in the rock specimens of this region carried out by the Gamma Spectrometry varies from 115.4 - 694.8 Bqkg-1 and 109.5 - 1463.7 Bqkg-1 respectively. The results of the indoor Rn/Th variations in dwellings obtained by the active-technique using RAD-7, will also be discussed.

Bajwa, B. S.; Singh, H.; Singh, J.; Singh, S.; Kochhar, N.; Sonikawade, R.

2009-04-01

188

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

PubMed Central

Background Pattern-oriented chemical profiling is increasingly being used to characterize the phytochemical composition of herbal medicines for quality control purposes. Ideally, a fingerprint of the biological effects should complement the chemical fingerprint. For ethical and practical reasons it is not possible to test each herbal extract in laboratory animals or humans. What is needed is a test system consisting of an organism with relevant biology and complexity that can serve as a surrogate in vitro system. The purpose of this study was to test the hypothesis that the Saccharomyces cerevisiae transcriptome might be used as an indicator of phytochemical variation of closely-related yet distinctly different extracts prepared from a single species of a phytogeographically widely distributed medicinal plant. We combined phytochemical profiling using chromatographic methods (HPTLC, HPLC-PDA-MS/MS) and gene expression studies using Affymetrix Yeast 2.0 gene chip with principal component analysis and k-nearest neighbor clustering analysis to test this hypothesis using extracts prepared from the phytogeographically widely distributed medicinal plant Equisetum arvense as a test case. Results We found that the Equisetum arvense extracts exhibited qualitative and quantitative differences in their phytochemical composition grouped along their phytogeographical origin. Exposure of yeast to the extracts led to changes in gene expression that reflected both the similarities and differences in the phytochemical composition of the extracts. The Equisetum arvense extracts elicited changes in the expression of genes involved in mRNA translation, drug transport, metabolism of energy reserves, phospholipid metabolism, and the cellular stress response. Conclusions Our data show that functional genomics in S. cerevisiae may be developed as a sensitive bioassay for the scientific investigation of the interplay between phytochemical composition and transcriptional effects of complex mixtures of chemical compounds. S. cerevisiae transcriptomics may also be developed for testing of mixtures of conventional drugs (“polypills”) to discover novel antagonistic or synergistic effects of those drug combinations. PMID:23826764

2013-01-01

189

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

PubMed Central

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

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

2008-01-01

190

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

PubMed Central

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

2013-01-01

191

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

PubMed

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

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

2008-07-01

192

Variation in Number and Formation of Repeat Sequences in the rDNA ITS2 Region of Five Sibling Species in the Anopheles barbirostris Complex in Thailand  

PubMed Central

Repeat sequences of approximately 100 base pairs in length were found in the rDNA ITS2 region of Anopheles barbirostris van der Wulp (Diptera: Culicidae) species A1, A2, A3, A4, and An. campestris-like in the An. barbirostris complex. Variation in the number of repeats was observed among the five sibling species. Specifically, 10 repeats were observed in A1, eight in A2, A4, and campestris-like, and three in A3. Based on similarities in the sequences of the repeats, related repeats were classified into nine groups. Although A2, A4, and the campestris-like species had the same number of repeats, the ITS2 region of the three species contained different groups of repeats. Excluding the repeat sequences facilitated good alignment of the ITS2 region in the five sibling species. Phylogenetic analyses of the 95 isolines were compared with results obtained from mitochondrial genes (COI and COII). The results revealed marked differences among the five sibling species, particularly regarding the ITS2 region of A3, which was more distinct from the other four species than COI and COIL Repeat sequences in the ITS2 region of other Anopheles species retrieved from GenBank also were analyzed. New repeat sequences were found in An. beklemishevi Stegnii and Kabanova, An. crucians Wiedemann and An. funestus Giles, suggesting that the occurrence of repeat sequences in the ITS2 region are not rare in anopheline mosquitoes. PMID:22233453

Otsuka, Yasushi

2011-01-01

193

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

194

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

PubMed

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

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

2012-12-14

195

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

NASA Astrophysics Data System (ADS)

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

Bleiziffer, Patrick; Schmidtel, Daniel; Görling, Andreas

2014-11-01

196

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

PubMed

The occurrence of instabilities, in particular singlet-triplet and singlet-singlet instabilities, in the exact-exchange (EXX) Kohn-Sham method is investigated. Hessian matrices of the EXX electronic energy with respect to the expansion coefficients of the EXX effective Kohn-Sham potential in an auxiliary basis set are derived. The eigenvalues of these Hessian matrices determine whether or not instabilities are present. Similar as in the corresponding Hartree-Fock case instabilities in the EXX method are related to symmetry breaking of the Hamiltonian operator for the EXX orbitals. In the EXX methods symmetry breaking can easily be visualized by displaying the local multiplicative exchange potential. Examples (N2, O2, and the polyyne C10H2) for instabilities and symmetry breaking are discussed. The relation of the stability conditions for EXX methods to approaches calculating the Kohn-Sham correlation energy via the adiabatic-connection fluctuation-dissipation (ACFD) theorem is discussed. The existence or nonexistence of singlet-singlet instabilities in an EXX calculation is shown to indicate whether or not the frequency-integration in the evaluation of the correlation energy is singular in the EXX-ACFD method. This method calculates the Kohn-Sham correlation energy through the ACFD theorem theorem employing besides the Coulomb kernel also the full frequency-dependent exchange kernel and yields highly accurate electronic energies. For the case of singular frequency-integrands in the EXX-ACFD method a regularization is suggested. Finally, we present examples of molecular systems for which the self-consistent field procedure of the EXX as well as the Hartree-Fock method can converge to more than one local minimum depending on the initial conditions. PMID:25429933

Bleiziffer, Patrick; Schmidtel, Daniel; Görling, Andreas

2014-11-28

197

Regarding the validity of the time-dependent Kohn–Sham approach for electron-nuclear dynamics via trajectory surface hopping  

Microsoft Academic Search

The implementation of fewest-switches surface-hopping (FSSH) within time-dependent Kohn–Sham (TDKS) theory [Phys. Rev. Lett. 95, 163001 (2005)] has allowed us to study successfully excited state dynamics involving many electronic states in a variety of molecular and nanoscale systems, including chromophore–semiconductor interfaces, semiconductor and metallic quantum dots, carbon nanotubes and graphene nanoribbons, etc. At the same time, a concern has been

Sean A. Fischer; Bradley F. Habenicht; Angeline B. Madrid; Walter R. Duncan; Oleg V. Prezhdo

2011-01-01

198

Regarding the validity of the time-dependent Kohn-Sham approach for electron-nuclear dynamics via trajectory surface hopping  

Microsoft Academic Search

The implementation of fewest-switches surface-hopping (FSSH) within time-dependent Kohn-Sham (TDKS) theory [Phys. Rev. Lett. 95, 163001 (2005)] has allowed us to study successfully excited state dynamics involving many electronic states in a variety of molecular and nanoscale systems, including chromophore-semiconductor interfaces, semiconductor and metallic quantum dots, carbon nanotubes and graphene nanoribbons, etc. At the same time, a concern has been

Sean A. Fischer; Bradley F. Habenicht; Angeline B. Madrid; Walter R. Duncan; Oleg V. Prezhdo

2011-01-01

199

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

SciTech Connect

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

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

2014-05-14

200

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

PubMed Central

Major histocompatibility complex (MHC) genes are the most polymorphic genes in vertebrates and encode molecules that play a crucial role in pathogen resistance. As a result of their diversity, they have received much attention in the fields of evolutionary and conservation biology. Here, we described the genetic variation of MHC class II B (MHCIIB) exon 2 in a wild population of Hume’s pheasant (Syrmaticus humiae), which has suffered a dramatic decline in population over the last three decades across its ranges in the face of heavy exploitation and habitat loss. Twenty-four distinct alleles were found in 73 S. humiae specimens. We found seven shared alleles among four geographical groups as well as six rare MHCIIB alleles. Most individuals displayed between one to five alleles, suggesting that there are at least three MHCIIB loci of the Hume’s pheasant. The dN ? dS ratio at putative antigen-binding sites (ABS) was significantly greater than one, indicating balancing selection is acting on MHCIIB exon 2. Additionally, recombination and gene conversion contributed to generating MHCIIB diversity in the Hume’s pheasant. One to three recombination events and seventy-five significant gene conversion events were observed within the Hume’s pheasant MHCIIB loci. The phylogenetic tree and network analysis revealed that the Hume’s pheasant alleles do not cluster together, but are scattered through the tree or network indicating a trans-species evolutionary mode. These findings revealed the evolution of the Hume’s pheasant MHC after suffering extreme habitat fragmentation. PMID:25629763

Chen, Weicai; Bei, Yongjian; Li, Hanhua

2015-01-01

201

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

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

202

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

203

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

NASA Astrophysics Data System (ADS)

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

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

2013-07-01

204

Density Functional Resonance Theory: complex density functions, convergence, orbital energies, and functionals  

E-print Network

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

Daniel L. Whitenack; Adam Wasserman

2012-02-23

205

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

206

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

NASA Astrophysics Data System (ADS)

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

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

2014-11-01

207

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

PubMed

The Barzilai-Borwein (BB) 2-point step size gradient method is receiving attention for accelerating Total Variation (TV) based CBCT reconstructions. In order to become truly viable for clinical applications, however, its convergence property needs to be properly addressed. We propose a novel fast converging gradient projection BB method that requires 'at most one function evaluation' in each iterative step. This Selective Function Evaluation method, referred to as GPBB-SFE in this paper, exhibits the desired convergence property when it is combined with a 'smoothed TV' or any other differentiable prior. This way, the proposed GPBB-SFE algorithm offers fast and guaranteed convergence to the desired 3DCBCT image with minimal computational complexity. We first applied this algorithm to a Shepp-Logan numerical phantom. We then applied to a CatPhan 600 physical phantom (The Phantom Laboratory, Salem, NY) and a clinically-treated head-and-neck patient, both acquired from the TrueBeam™ system (Varian Medical Systems, Palo Alto, CA). Furthermore, we accelerated the reconstruction by implementing the algorithm on NVIDIA GTX 480 GPU card. We first compared GPBB-SFE with three recently proposed BB-based CBCT reconstruction methods available in the literature using Shepp-Logan numerical phantom with 40 projections. It is found that GPBB-SFE shows either faster convergence speed/time or superior convergence property compared to existing BB-based algorithms. With the CatPhan 600 physical phantom, the GPBB-SFE algorithm requires only 3 function evaluations in 30 iterations and reconstructs the standard, 364-projection FDK reconstruction quality image using only 60 projections. We then applied the algorithm to a clinically-treated head-and-neck patient. It was observed that the GPBB-SFE algorithm requires only 18 function evaluations in 30 iterations. Compared with the FDK algorithm with 364 projections, the GPBB-SFE algorithm produces visibly equivalent quality CBCT image for the head-and-neck patient with only 180 projections, in 131.7?s, further supporting its clinical applicability. PMID:25320866

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

2014-11-01

208

Computational complexity of time-dependent density functional theory  

E-print Network

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

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

2014-08-21

209

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

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

210

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

Microsoft Academic Search

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

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

2008-01-01

211

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.

2012-08-29

212

Hierarchy of model Kohn–Sham potentials for orbital-dependent functionals: A practical alternative to the optimized effective potential method  

SciTech Connect

We describe a method for constructing a hierarchy of model potentials approximating the functional derivative of a given orbital-dependent exchange-correlation functional with respect to electron density. Each model is derived by assuming a particular relationship between the self-consistent solutions of Kohn–Sham (KS) and generalized Kohn–Sham (GKS) equations for the same functional. In the KS scheme, the functional is differentiated with respect to density, in the GKS scheme—with respect to orbitals. The lowest-level approximation is the orbital-averaged effective potential (OAEP) built with the GKS orbitals. The second-level approximation, termed the orbital-consistent effective potential (OCEP), is based on the assumption that the KS and GKS orbitals are the same. It has the form of the OAEP plus a correction term. The highest-level approximation is the density-consistent effective potential (DCEP), derived under the assumption that the KS and GKS electron densities are equal. The analytic expression for a DCEP is the OCEP formula augmented with kinetic-energy-density-dependent terms. In the case of exact-exchange functional, the OAEP is the Slater potential, the OCEP is roughly equivalent to the localized Hartree–Fock approximation and related models, and the DCEP is practically indistinguishable from the true optimized effective potential for exact exchange. All three levels of the proposed hierarchy require solutions of the GKS equations as input and have the same affordable computational cost.

Kohut, Sviataslau V.; Staroverov, Viktor N., E-mail: vstarove@uwo.ca [Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7 (Canada); Ryabinkin, Ilya G. [Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4 (Canada)] [Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4 (Canada)

2014-05-14

213

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

Microsoft Academic Search

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

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

1996-01-01

214

Electron-impact ionization of atomic hydrogen: dynamical variational treatment  

NASA Astrophysics Data System (ADS)

A simple and straightforward calculating scheme is proposed for electron-impact single and multiple ionization of atoms. The method is based on the application of the Hulthén-Kohn dynamical variational principle. An effective charge seen by the scattered electron is determined for a certain type of trial wave functions mathematically in a rigorous way excluding any empirical assumptions. Validity of the elaborated approach is assessed by calculating triply differential cross section (TDCS) for electron-impact ionization of hydrogen. It is shown that, inclusion of the effective charge into the calculation reduces height of a "binary peak" in comparison with the first Born approximation result. The height of a "recoil peak" depends on the sign of the effective charge. The calculated TDCS are compared with the available experimental data and with the results of sophisticated theories and agreement is found.

Defrance, P.; Kereselidze, T.; Lecointre, J.; Machavariani, Z. S.

2011-10-01

215

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

216

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

PubMed Central

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

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

2013-01-01

217

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

Microsoft Academic Search

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

James B. Shaklee; Stevan R. Phelps

1992-01-01

218

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

PubMed

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

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

2013-01-01

219

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

PubMed Central

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

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

2013-01-01

220

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

NASA Astrophysics Data System (ADS)

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

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

2015-01-01

221

Kohn-Sham Kinetic Energy Density in the Nuclear and Asymptotic Regions: Deviations from the Von Weizs\\"acker Behavior and Applications to Density Functionals  

E-print Network

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

Della Sala, F; Constantin, L A

2014-01-01

222

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

PubMed

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

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

2015-02-10

223

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

PubMed Central

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

2012-01-01

224

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

PubMed Central

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

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

1997-01-01

225

Variation of Kondo peak observed in the assembly of heteroleptic 2,3-naphthalocyaninato phthalocyaninato Tb(III) double-decker complex on Au(111).  

PubMed

By using scanning tunneling microscopy (STM), we studied the heteroleptic double-decker complex TbNPcPc (NPc = naphthalocyaninato and Pc = phthalocyaninato), where two different planar ligands sandwich a Tb(III) ion and an unpaired ? electron causes Kondo resonance upon adsorption on the Au(111) surface. Kondo resonance is a good conductance control mechanism originating from interactions between conduction electrons and a localized spin. Two types of adsorption geometries appear depending on which side contacts the substrate surface, which we call Pc-up and NPc-up molecules. They make intriguing molecular assemblies by segregation. In addition, different adsorption geometries and molecular assemblies provide a variety of spin and electronic configurations. Pc-up and NPc-up molecules both showed the Kondo resonance when they were isolated from other molecules, but their Kondo temperatures were different. A one-dimensional chain composed of only NPc-up molecules was found, in which the dI/dV plot showed a conversion from the Kondo peak to a dip at the Fermi energy. In addition, a two-dimensional lattice with an ordering of Pc-up and NPc-up molecules in an alternative manner was observed, in which no Kondo peak was detected in the molecule. The absence of the Kondo peak was accounted for by the change of azimuthal rotational angle of the two ligands of both molecules. The results imply that a molecule design and adsorption configuration tailoring can be used for the spin-mediated control of the electronic conductance of the molecule. PMID:23363375

Komeda, Tadahiro; Isshiki, Hironari; Liu, Jie; Katoh, Keiichi; Shirakata, Minoru; Breedlove, Brian K; Yamashita, Masahiro

2013-02-26

226

Modelling excited states of weakly bound complexes with density functional theory.  

PubMed

The binding within the ethene-argon and formaldehyde-methane complexes in the ground and electronically excited states is studied with equation of motion coupled cluster theory (EOM-CCSD), second-order Møller-Plesset perturbation theory (MP2) and density functional theory with dispersion corrections (DFT-D). Electronically excited states are studied within MP2 and Kohn-Sham DFT formalisms by exploiting a procedure called the maximum overlap method that allows convergence of the relevant self-consistent field equations to higher energy (or excited state) solutions. Potential energy curves computed using MP2 are in good agreement with the EOM-CCSD calculations for both the valence and Rydberg excited states studied. For the DFT-D approach, B3LYP-D3/aug-cc-pVTZ calculations are found to be in agreement with EOM-CCSD for the ground and valence excited states. However, for the ?3s Rydberg state of ethene-argon and the n3s Rydberg state of formaldehyde-methane significant deviation is observed, and this disagreement with EOM-CCSD is present for a variety of DFT-D based approaches. Variation of the parameters within the D2 dispersion correction results in closer agreement with EOM-CCSD for the Rydberg states but demonstrates that a different parameterisation from the ground state is required for these states. This indicates that time-dependent density functional theory calculations based upon a DFT-D reference may be satisfactory for excitations to valence states, but will potentially be inaccurate for excitations to Rydberg states, or more generally states where the nature of the electron density is significantly different from the ground state. PMID:24531883

Briggs, Edward A; Besley, Nicholas A

2014-07-28

227

Seasonal Variation  

PubMed Central

Background: In the general population, rates of certain respiratory infections (and mortality from these infections) are higher in winter. We hypothesized that in patients with idiopathic pulmonary fibrosis (IPF) and/or pulmonary fibrosis (PF) from any cause, death rates would be increased during the winter season, independent of recognized infection. Our objective was to determine if mortality rates from IPF and/or PF of any cause exhibit seasonal variation. Methods: Using death records from the National Center for Health Statistics, we calculated monthly mortality rates for persons with PF and developed a multivariable model to determine if these mortality rates exhibited seasonal variation. Results: From spring of 1992 to fall of 2003, there were 27,367,580 deaths in the United States and 170,984 decedents with PF. The average mortality rate among all persons with PF was 17.1% higher in winter (p < 0.0001), 12.7% higher in spring (p < 0.0001), and 5.2% higher in fall (p = 0.0002) than in summer months. These findings persisted when records with a diagnostic code for pneumonia were excluded from the analysis as well as when only records in which PF was the underlying cause of death were included in the analysis. Conclusions: Mortality rates from PF exhibit significant seasonal variation, with the highest ratesoccurring in the winter, even when recognized infection is excluded. Further studies arenecessary to determine if this seasonal variation exists in a prospective cohort and, if so, touncover its etiology. PMID:18689582

Swigris, Jeffrey J.; Raghu, Ganesh; Brown, Kevin K.

2009-01-01

228

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

SciTech Connect

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

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

1991-11-15

229

Space Complexity Algorithms & Complexity  

E-print Network

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

Way, Andy

230

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

NASA Astrophysics Data System (ADS)

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

Motamarri, Phani; Gavini, Vikram

2014-09-01

231

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

PubMed Central

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

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

2012-01-01

232

Hartree-Fock via variational coupled cluster theory: An alternative way to diagonalization free algorithm  

NASA Astrophysics Data System (ADS)

It is shown that the non-terminating expansions of the wave function within the variational coupled cluster singles (VCCS) can be exactly treated by summing up the one-particle density matrix elements in the occupied block using simple recurrence relation. At the same time, this leads to an extremely simple 'a priori' diagonalization free algorithm for the solution of the Hartree-Fock equations. This treatment corresponds to a non-unitary transformation of orbitals, however, preserving the norm and idempotency of the density matrix. The resulting algorithm enables a Hartree-Fock solution with 'a priori' localized orbitals. Similar approach can be applied within the Kohn-Sham theory. Analysis of the VCCS expansion in terms of the generalized perturbation theory is also presented. Numerical results are presented for model systems N2, F2, H2O, NH3 but also for a larger Uracile molecule and an interaction of four Guanine molecules.

Šimunek, Ján; Noga, Jozef

2012-12-01

233

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

2011-12-01

234

Transport properties calculated from complex energy Fermi surface and Boltzmann approach: Example of TiFe1-xNixSb half-Heusler compound  

NASA Astrophysics Data System (ADS)

The Green function Korringa-Kohn-Rostoker methodology with the coherent potential approximation was used to calculate complex energy band structure. In the framework of Boltzmann approach life time and velocity of electron were determined on complex energy Fermi surface. Then electron transport properties as temperature dependent Seebeck coefficient, residual resistivity were investigated. Calculations were performed with several approximations, compared and demonstrated for the TiFe1-xNixSb half-Heusler compound that experimentally revealed tunable electron transport properties, i.e. a metal-semiconductor-metal crossover and change in sign of thermopower.

Kutorasinski, K.; Tobola, J.; Kaprzyk, S.

2012-06-01

235

Variational Molecular Dynamics  

E-print Network

We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. We show that within this framework it is possible to simulate on a small computer cluster conformational reactions as complex as protein folding, using state-of-the-art all-atom force fields in explicit solvent. The same approach also yields the potential of mean-force for reaction coordinates, the reaction rate and transition path time. For illustration and validation purposes, we test this method against the results of protein folding MD simulations which were obtained on the Anton supercomputer, using the same all-atom force field. We find that our approach yields consistent results at a computational cost which is many orders of magnitude smaller than that required by standard MD simulations.

S. a Beccara; P. Faccioli

2014-05-23

236

Architecting complex systems for robustness  

E-print Network

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

Slagle, Jason C

2007-01-01

237

Irreducible Complexity Revisited  

Microsoft Academic Search

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

William A. Dembski

2004-01-01

238

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

239

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

PubMed

A series of [Ni(P(R)(2)N(Ph)(2))(2)(CH(3)CN)](BF(4))(2) complexes containing the cyclic diphosphine ligands [P(R)(2)N(Ph)(2) = 1,5-diaza-3,7-diphosphacyclooctane; R = benzyl (Bn), n-butyl (n-Bu), 2-phenylethyl (PE), 2,4,4-trimethylpentyl (TP), and cyclohexyl (Cy)] have been synthesized and characterized. X-ray diffraction studies reveal that the cations of [Ni(P(Bn)(2)N(Ph)(2))(2)(CH(3)CN)](BF(4))(2) and [Ni(P(n-Bu)(2)N(Ph)(2))(2)(CH(3)CN)](BF(4))(2) have distorted trigonal bipyramidal geometries. The Ni(0) complex [Ni(P(Bn)(2)N(Ph)(2))(2)] was also synthesized and characterized by X-ray diffraction studies and shown to have a distorted tetrahedral structure. These complexes, with the exception of [Ni(P(Cy)(2)N(Ph)(2))(2)(CH(3)CN)](BF(4))(2), all exhibit reversible electron transfer processes for both the Ni(II/I) and Ni(I/0) couples and are electrocatalysts for the production of H(2) in acidic acetonitrile solutions. The heterolytic cleavage of H(2) by [Ni(P(R)(2)N(Ph)(2))(2)(CH(3)CN)](BF(4))(2) complexes in the presence of p-anisidine or p-bromoaniline was used to determine the hydride donor abilities of the corresponding [HNi(P(R)(2)N(Ph)(2))(2)](BF(4)) complexes. However, for the catalysts with the most bulky R groups, the turnover frequencies do not parallel the driving force for elimination of H(2), suggesting that steric interactions between the alkyl substituents on phosphorus and the nitrogen atom of the pendant amines play an important role in determining the overall catalytic rate. PMID:21999814

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

2011-11-01

240

Variation of the stability of complexes of Al(III) with a fulvic acid extracted from a humic cambisol soil in the pH range three to five  

SciTech Connect

The interaction of the aluminum ion [Al(III)] with the major constituent of soil organic matter, fulvic acids (FA), was investigated in the acid pH range. The complexation of a FA extracted from a humic cambisol soil (at a concentration of 80 mg/L) when titrated with Al(III) were monitored directly by synchronous fluorescence (SyF) spectroscopy at five pH values (3.0, 3.5, 4.0, 4.5, and 5.0), at 25 C and with 0.1 N KNO{sub 3}. Inverted second derivative SyF data were preprocessed by a self-modeling mixture analysis method to obtain fluorescence enhancement profiles as a function of the increasing Al(III) concentration. Assuming that the concentration of complexes formed between Al(III) and FA is proportional to the fluorescence intensity, these profiles were adjusted to a 1:1 complexation model and the following conditional stability constants (log K{sub c}) were calculated (standard deviation in parenthesis), pH = 3.0, 4.3 (1); pH = 3.5, 4.3 (1); pH = 4.0, 5.0 (1); pH = 4.5, 5.1 (3); and pH = 5.0, 5.3 (2). These constants show that the stability of the complexes decreases markedly at pH < 4. The environmental implication of this result is that an increase in the extent of the dissociation of the Al(III) + FA complexes is expected at pH < 4, increasing the free Al(III) concentration and probably its ecotoxicity.

Esteves da Silva, J.C.G.; Machado, A.A.S.C. [LAQUIPAI, Porto (Portugal). Faculdade de Ciencias; Ramos, M.A.; Arce, F. [Univ. de Santiago de Compostela (Spain). Dept. de Quimica Fisica; Rey, F. [Univ. de Vigo (Spain). Dept. de Quimica Fisica

1997-09-01

241

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

SciTech Connect

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

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

1995-09-01

242

Variational, V-representable, and variable-occupation-number perturbation theories  

NASA Astrophysics Data System (ADS)

Density-functional perturbation theory with variationally fitted Kohn-Sham (KS) potentials is described. Requiring the Fock matrix and density matrix to commute through each order of perturbation theory determines the off-diagonal elements of the density matrix, and thus the effect of changing occupation numbers in density-functional perturbation theory. At each order of perturbation theory, the change in occupation numbers at that order enters only the diagonal part of the density matrix. The theory contains no phases, and a limiting process relates the rest of the diagonal density matrix element, obtained from wave function perturbation theory, to the off-diagonal part, obtained by commutation. V-representable density-functional theory is most practical when the KS potential is expanded in a finite basis to create the Sambe-Felton (SF) potential of analytic density-functional theory. This reduces the dimensionality of perturbation theory from order N2 in the orbital basis to order N in the SF basis. Computing the (occupied-virtual)2, i.e., N4, sum over states once at the end of a self-consistent-field molecular orbital calculation removes the orbitals from all higher orders of perturbation theory. The rank-N2 iterative coupled-perturbed equations are replaced by rank-N matrix inversion, to fit variationally the perturbed SF potential at each order. As an example of the 2n+1 rule of perturbation theory, the variational, first-order potential is used to give precise second and third derivatives of the energy with respect to occupation number. The hardness and hyperhardness are computed for a standard set of molecules. Both are essentially independent of how the variational SF potential is constrained for four different constraint combinations. With variational fitting, the precision of derivatives and the fidelity of the fit to the SF potential are not related. Analytic derivatives are accurate to machine precision for any constraint and all fitting basis sets.

Dunlap, Brett I.

2008-12-01

243

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

244

Variational Study of Mott Transition by Means of Drude Weight and Superfluid Density  

NASA Astrophysics Data System (ADS)

To distinguish a metal from an insulator, the Drude weight (D, zero-frequency component of conductivity) is a useful measure, as Kohn pointed out long ago: D > 0(=0) for a metal (insulator). Later, Millis and Coppersmith showed that a variational wave function ?Q in which the key ingredient for a Mott transition (a doublon-holon binding effect) is introduced exhibits D > 0 (metallic) even for sufficiently large correlation strength, namely, a Mott transition is absent from. ?Q In contrast, variational Monte Carlo studies using ?Q confirmed, by studying relevant quantities such as doublon density d and a superconducting correlation function, Pd? that ?Q undoubtedly raises a Mott transition. This contradiction has been a long-standing perplexing problem. We definitely settle this problem by adding ?Q to a configuration-dependent phase factor P?, which has been hitherto overlooked. This factor appropriately picks out a negative counterpart in D for insulators, so that D vanishes. Because P? does not affect the quantities such as d and Pd?, the previous results of ?Q on the Mott transition remain intact for P??Q.

Tamura, S.; Yokoyama, H.

245

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

246

A rare variation of the vertebral artery.  

PubMed

Variations of the vertebrobasilar arterial complex are important with regard to their potential clinical impact. We present an unusual case of the vertebral artery, in which the left vertebral artery in its ascent in the neck through the transverse foramina passed posteriorly between the transverse processes of C3 and C4 and supplied the posterior muscles of the neck without continuing intracranially. Albeit speculatively, we hypothesise that the variation of the vertebral artery reported here was caused by degeneration of the proximal portion of the left postcostal longitudinal anastomosis (i.e. C1 and C2 intersegmental arteries) in the context of a persistent third cervical intersegmental artery. Our case is unique in that the left vertebral artery terminated extracranially. Knowledge of the variations of the vertebrobasilar arterial complex is important for surgeons operating at the skull base, craniocervical junction, and cervical region, and for clinicians interpreting the imaging of this region. PMID:16773609

Shoja, M M; Tubbs, R S; Khaki, A A; Shokouhi, G; Farahani, R M; Moein, A

2006-05-01

247

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

PubMed Central

An age-dependent association between variation at the FTO locus and BMI in children has been suggested. We meta-analyzed associations between the FTO locus (rs9939609) and BMI in samples, aged from early infancy to 13 years, from 8 cohorts of European ancestry. We found a positive association between additional minor (A) alleles and BMI from 5.5 years onwards, but an inverse association below age 2.5 years. Modelling median BMI curves for each genotype using the LMS method, we found that carriers of minor alleles showed lower BMI in infancy, earlier adiposity rebound (AR), and higher BMI later in childhood. Differences by allele were consistent with two independent processes: earlier AR equivalent to accelerating developmental age by 2.37% (95% CI 1.87, 2.87, p?=?10?20) per A allele and a positive age by genotype interaction such that BMI increased faster with age (p?=?10?23). We also fitted a linear mixed effects model to relate genotype to the BMI curve inflection points adiposity peak (AP) in infancy and AR. Carriage of two minor alleles at rs9939609 was associated with lower BMI at AP (?0.40% (95% CI: ?0.74, ?0.06), p?=?0.02), higher BMI at AR (0.93% (95% CI: 0.22, 1.64), p?=?0.01), and earlier AR (?4.72% (?5.81, ?3.63), p?=?10?17), supporting cross-sectional results. Overall, we confirm the expected association between variation at rs9939609 and BMI in childhood, but only after an inverse association between the same variant and BMI in infancy. Patterns are consistent with a shift on the developmental scale, which is reflected in association with the timing of AR rather than just a global increase in BMI. Results provide important information about longitudinal gene effects and about the role of FTO in adiposity. The associated shifts in developmental timing have clinical importance with respect to known relationships between AR and both later-life BMI and metabolic disease risk. PMID:21379325

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

2011-01-01

248

PDE for Finance Notes, Spring 2011 Section 8 Notes by Robert V. Kohn, Courant Institute of Mathematical Sciences. For use only in  

E-print Network

, A First Course in Partial Differential Equations with Complex Variables and Trans- form Methods (an distributed. In practice however the observed distributions are not normal ­ they have "fat tails," i by a Gaussian. The jump-diffusion model provides a plausible mechanism for explaining the fat tails

249

Genetic Variation and its Role in Malignancy  

PubMed Central

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

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

2011-01-01

250

First evidence for heritable variation in cooperative breeding behaviour  

Microsoft Academic Search

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

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

2007-01-01

251

Complex Numbers  

NSDL National Science Digital Library

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

2010-04-01

252

Carney Complex  

MedlinePLUS

... Ephelides (freckles) LAMB syndrome – Lentigines, Atrial Myxoma, and Blue nevi What causes Carney complex? Carney complex is ... melanotic schwannoma, meaning tumors that grow on nerves Blue nevi, which are blue-black moles Osteochondromyxoma (bone ...

253

A methodology for quantifying time variations of the turbidity/electrical conductivity relationship during complex floods: application to the delineation of particle and dissolved materials transfer at a karst spring  

NASA Astrophysics Data System (ADS)

In Upper Normandy, where drinking water supply comes from karst aquifers, rainfall events may involve turbid runoffs. These events induce sanitary crises and shutdowns of the water supply. The springs of Fontaine-Sous-Préaux provide 60% of Rouen's population (400,000) (France). These springs are highly vulnerable and their exploitation is confronted with the recurrence of turbid events, which can reach up to 150 NTU during highly rain events. The turbidity observed at karst springs is a complex signal composed by two parts of different origins: a first part coming from the direct transfer of particles from the surface following runoff events, and a second part involving the resuspension of materials previously deposited within karst conduits. The disctinction between those two part has always been very challenging. In this study, taking the example of a karst spring in Upper Normandy (Fontaine Sous Préaux spring), we attempted to refine a turbidigraph decomposition method based on the comparison between electrical conductivity (EC) and turbidity (T) using separated modelled hysteresis curves. In a first step, the EC and T breakthrough curves are modelled using an appropriate number of sub-peaks. Second, local EC-T hysteresis curves are builded up in order to characterize the time-varying changes of the dissolved/particulate transports relationships and to assess the respective contribution of the direct transfer and resuspended parts of turbidity throughout complex floods. Associated to cross-correlation analyses of the EC and T sub-peaks separated, the method allowed identification of the (potentially changing) lag time between EC and T. The results obtained highlighted the pre-eminence of resuspension phenomena at the spring for all floods studied. Nevertheless, four different types of hysteresis curves could be distinguished: i) wide clockwise hysteresis expressing the pre-eminence of resuspension accompanied by pressure pulse transfer phenomena; ii) wide clockwise hysteresis expressing the pre-eminence of resuspension of sediments arriving simultaneously with surface waters; iii) a thin hystérésis equivalent to an almost linear relationship between EC and T, corresponding to a simultaneous transfer of surface water and particles, iv) a thin and curved counter-clockwise hysteresis representing a direct transfer of particles and water from the surface characterizing a deficit of available sedimentary stock. Keywords : transport processes, hysteresis, resuspension, direct transfer, deposition.

Mouhri, A.; Motelay, A.; Hanin, G.; Massei, N.; Fournier, M.; Dupont, J. P.; Laignel, B.

2009-04-01

254

Evidence for variation in the optimal translation initiation complex: plant eIF4B, eIF4F, and eIF(iso)4F differentially promote translation of mRNAs.  

PubMed

Eukaryotic initiation factor (eIF) 4B is known to interact with multiple initiation factors, mRNA, rRNA, and poly(A) binding protein (PABP). To gain a better understanding of the function of eIF4B, the two isoforms from Arabidopsis (Arabidopsis thaliana) were expressed and analyzed using biophysical and biochemical methods. Plant eIF4B was found by ultracentrifugation and light scattering analysis to most likely be a monomer with an extended structure. An extended structure would facilitate the multiple interactions of eIF4B with mRNA as well as other initiation factors (eIF4A, eIF4G, PABP, and eIF3). Eight mRNAs, barley (Hordeum vulgare) alpha-amylase mRNA, rabbit beta-hemoglobin mRNA, Arabidopsis heat shock protein 21 (HSP21) mRNA, oat (Avena sativa) globulin, wheat (Triticum aestivum) germin, maize (Zea mays) alcohol dehydrogenase, satellite tobacco necrosis virus RNA, and alfalfa mosaic virus (AMV) 4, were used in wheat germ in vitro translation assays to measure their dependence on eIF4B and eIF4F isoforms. The two Arabidopsis eIF4B isoforms, as well as native and recombinant wheat eIF4B, showed similar responses in the translation assay. AMV RNA 4 and Arabidopsis HSP21 showed only a slight dependence on the presence of eIF4B isoforms, whereas rabbit beta-hemoglobin mRNA and wheat germin mRNA showed modest dependence. Barley alpha-amylase, oat globulin, and satellite tobacco necrosis virus RNA displayed the strongest dependence on eIF4B. These results suggest that eIF4B has some effects on mRNA discrimination during initiation of translation. Barley alpha-amylase, oat globulin, and rabbit beta-hemoglobin mRNA showed the highest activity with eIF4F, whereas Arabidopsis HSP21 and AMV RNA 4 used both eIF4F and eIF(iso)4F equally well. These results suggest that differential or optimal translation of mRNAs may require initiation complexes composed of specific isoforms of initiation factor gene products. Thus, individual mRNAs or classes of mRNAs may respond to the relative abundance of a particular initiation factor(s), which in turn may affect the amount of protein translated. It is likely that optimal multifactor initiation complexes exist that allow for optimal translation of mRNAs under a variety of cellular conditions. PMID:19493973

Mayberry, Laura K; Allen, M Leah; Dennis, Michael D; Browning, Karen S

2009-08-01

255

Seasonal variations in cryptorchidism.  

PubMed Central

The month of birth of boys undergoing orchidopexy in the Oxfordshire Health District during the years 1974-83 was analysed. A significant seasonal variation with a peak in April was found for those boys operated upon by paediatric surgeons at a young age (0-4). Possible causes of this variation and its relationship to the aetiology of cryptorchidism are discussed. PMID:2877045

Jackson, M B; Swerdlow, A J

1986-01-01

256

Mixed quasi variational inequalities  

Microsoft Academic Search

In this paper, we use the resolvent operator and auxiliary principle techniques to suggest and analyze several iterative algorithms for solving mixed quasi variational inequalities and related problems. We study the convergence criteria of these algorithms under mild conditions. We also study the global stability and existence of a unique solution of these quasi variational inequalities by using the dynamical

Muhammad Aslam Noor

2003-01-01

257

Complexity Survey.  

ERIC Educational Resources Information Center

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

Gordon, Sandra L.; Anderson, Beth C.

258

Sexual Dimorphism in the Sceloporus undulatus Species Complex  

E-print Network

, S. cowlesi, S. tristichus) of the S. undulatus complex. Sexual confusion, was recently described in a population of the Sceloporus undulatus complex occurring in White Sands, New Mexico and the behavior is correlated with variation in badge size...

Dittmer, Drew

2012-10-19

259

Separation of the geomagnetic variation of cosmic rays  

NASA Astrophysics Data System (ADS)

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

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

260

Analysis of biomarkers for complex human diseases   

E-print Network

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

Ansari, Morad

2009-01-01

261

Solar EUV induced variations in the thermosphere  

NASA Technical Reports Server (NTRS)

The effects of solar activity on the thermosphere are reviewed. The neutral total density, temperature, and electron density increase with solar activity, and their variations are fairly well correlated with variations in solar 10.7-cm flux. The electron temperature, by contrast, has a complex behavior with solar activity, depending on altitude and season, as increased heat input is balanced by increased cooling provided by the enhanced electron density. Also, individual neutral species do not all increase in step but are influenced by dissociation and dynamical processes. The increased ion drag at higher solar activities inhibits the neutral wind from increasing in the same proportion as the neutral temperatures and densities.

Hedin, A. E.; Mayr, H. G.

1987-01-01

262

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. PMID:20459805

2010-01-01

263

Computational complexity of time-dependent density functional theory  

NASA Astrophysics Data System (ADS)

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

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

2014-08-01

264

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

265

Regular Variation Standardization  

E-print Network

, Cornell University Ithaca NY 14853 USA http://legacy.orie.cornell.edu/sid sir1@cornell.edu October 12, 2008 Work with: J. Heffernan, B. Das (Cornell) #12;Intro Regular Variation EVT & E Standardization Asy

Resnick, Sidney

266

Variation tolerant SoC design  

NASA Astrophysics Data System (ADS)

The scaling of integrated circuits into the nanometer regime has led to variations emerging as a primary concern for designers of integrated circuits. Variations are an inevitable consequence of the semiconductor manufacturing process, and also arise due to the side-effects of operation of integrated circuits (voltage, temperature, and aging). Conventional design approaches, which are based on design corners or worst-case scenarios, leave designers with an undesirable choice between the considerable overheads associated with over-design and significantly reduced manufacturing yield. Techniques for variation-tolerant design at the logic, circuit and layout levels of the design process have been developed and are in commercial use. However, with the incessant increase in variations due to technology scaling and design trends such as near-threshold computing, these techniques are no longer sufficient to contain the effects of variations, and there is a need to address variations at all stages of design. This thesis addresses the problem of variation-tolerant design at the earliest stages of the design process, where the system-level design decisions that are made can have a very significant impact. There are two key aspects to making system-level design variation-aware. First, analysis techniques must be developed to project the impact of variations on system-level metrics such as application performance and energy. Second, variation-tolerant design techniques need to be developed to absorb the residual impact of variations (that cannot be contained through lower-level techniques). In this thesis, we address both these facets by developing robust and scalable variation-aware analysis and variation mitigation techniques at the system level. The first contribution of this thesis is a variation-aware system-level performance analysis framework. We address the key challenge of translating the per-component clock frequency distributions into a system-level application performance distribution. This task is particularly complex and challenging due to the inter-dependencies between components' execution, indirect effects of shared resources, and interactions between multiple system-level "execution paths". We argue that accurate variation-aware performance analysis requires Monte-Carlo based repeated system execution. Our proposed analysis framework leverages emulation to significantly speedup performance analysis without sacrificing the generality and accuracy achieved by Monte-Carlo based simulations. Our experiments show performance improvements of around 60x compared to state-of-the-art hardware-software co-simulation tools and also underscore the framework's potential to enable variation-aware design and exploration at the system level. Our second contribution addresses the problem of designing variation-tolerant SoCs using recovery based design, a popular circuit design paradigm that addresses variations by eliminating guard-bands and operating circuits at close to "zero margins" while detecting and recovering from timing errors. While previous efforts have demonstrated the potential benefits of recovery based design, we identify several challenges that need to be addressed in order to apply this technique to SoCs. We present a systematic design framework to apply recovery based design at the system level. We propose to partition SoCs into "recovery islands", wherein each recovery island consists of one or more SoC components that can recover independent of the rest of the SoC. We present a variation-aware design methodology that partitions a given SoC into recovery islands and computes the optimal operating points for each island, taking into account the various trade-offs involved. Our experiments demonstrate that the proposed design framework achieves an average of 32% energy savings over conventional worst-case designs, with negligible losses in performance. The third contribution of this thesis introduces disproportionate allocation of shared system resources as a means to combat the advers

Kozhikkottu, Vivek J.

267

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

268

The Schwinger Variational Method  

NASA Technical Reports Server (NTRS)

Variational methods have proven invaluable in theoretical physics and chemistry, both for bound state problems and for the study of collision phenomena. For collisional problems they can be grouped into two types: those based on the Schroedinger equation and those based on the Lippmann-Schwinger equation. The application of the Schwinger variational (SV) method to e-molecule collisions and photoionization has been reviewed previously. The present chapter discusses the implementation of the SV method as applied to e-molecule collisions.

Huo, Winifred M.

1995-01-01

269

Generalized quasi variational inequalities  

SciTech Connect

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

Noor, M.A. [King Saud Univ., Riyadh (Saudi Arabia)

1996-12-31

270

Complex Numbers  

NSDL National Science Digital Library

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

Mrs. Pierce

2010-11-16

271

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

272

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

273

Structural genomic variation in intellectual disability.  

PubMed

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

Pfundt, Rolph; Veltman, Joris A

2012-01-01

274

Quantum mechanical/molecular mechanical/continuum style solvation model: Linear response theory, variational treatment, and nuclear gradients  

NASA Astrophysics Data System (ADS)

Linear response and variational treatment are formulated for Hartree-Fock (HF) and Kohn-Sham density functional theory (DFT) methods and combined discrete-continuum solvation models that incorporate self-consistently induced dipoles and charges. Due to the variational treatment, analytic nuclear gradients can be evaluated efficiently for these discrete and continuum solvation models. The forces and torques on the induced point dipoles and point charges can be evaluated using simple electrostatic formulas as for permanent point dipoles and point charges, in accordance with the electrostatic nature of these methods. Implementation and tests using the effective fragment potential (EFP, a polarizable force field) method and the conductorlike polarizable continuum model (CPCM) show that the nuclear gradients are as accurate as those in the gas phase HF and DFT methods. Using B3LYP/EFP/CPCM and time-dependent-B3LYP/EFP/CPCM methods, acetone S0?S1 excitation in aqueous solution is studied. The results are close to those from full B3LYP/CPCM calculations.

Li, Hui

2009-11-01

275

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

276

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

Microsoft Academic Search

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

Christoph Bock; Jörn Walter; Martina Paulsen; Thomas Lengauer

2008-01-01

277

Mapping the Epigenetic Basis of Complex Traits  

E-print Network

Mapping the Epigenetic Basis of Complex Traits Sandra Cortijo,1 * René Wardenaar,2 * Maria Colomé Johannes2 Quantifying the impact of heritable epigenetic variation on complex traits is an emerging that several of these differentially methylated regions (DMRs) act as bona fide epigenetic quantitative trait

Napp, Nils

278

Complexity International  

NSDL National Science Digital Library

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

279

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

280

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

281

ORIGINAL ARTICLE The complex global pattern of genetic variation and  

E-print Network

with risk for various neuropsychiatric conditions such as schizophrenia, panic disorder, bipolar disorders Barta3 , SLB Kajuna4 and JR Kidd1* 1 Department of Genetics, Yale University School of Medicine, New region and in the 30 -untranslated region are responsible for the associations with disorders

Kidd, Kenneth

282

Complex chemical variation and the taxonomy of Hymenoxys scaposa (Compositae)  

Microsoft Academic Search

Over 30 flavonoids, some of which are unusual types of flavonols and flavones, occur in the taxaHymenoxys scaposa, H. acaulis, andH. ivesiana. The patterns of distributions of these compounds are correlated more closely with an east-west geographical range than with\\u000a the formally recognized identity of the plant, as deduced from its morphology. The exact significance of these observations\\u000a is not

Peter Seeligmann; R. E. Alston

1967-01-01

283

Variational Multiscale Modeling of Biomolecular Complexes , Xin Feng2  

E-print Network

pressure, and U denotes the solvent-solute non-electrostatic interactions, such as the van der Waals to singularity-free surface representation, curvature characterization, electrostatic mapping, solvation energy interaction. Here is the electrostatic potential, s and m are the dielectric constants of the solvent

284

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

285

Density Functional Theory: Toward Better Understanding of Complex Systems in Chemistry and Physics  

NASA Astrophysics Data System (ADS)

Density functional theory (DFT) has become the workhorse of computational chemistry and physics in the past two decades. The continuous developments of high-quality exchange-correlation functionals (xcFs) have enabled chemists and physicists to study complex as well as large systems with high accuracy at low-to-moderate computational expense. Although a wide range of normal systems have been well understood by DFT, there are still complex ones presenting particular challenges where most commonly used xcFs have failed due to the complex nature of the system, lack of or difficulty to obtain reliable reference data, or the practical limitations of the Kohn-Sham DFT (KS-DFT) formulation. This thesis presents studies with various exchange-correlation functionals on a wide selection of complex systems in chemistry and solid-state physics, including large organic molecules, adsorption on metallic surfaces, transition states, as well as transition metal atoms, ions, and compounds, to (i) draw conclusions upon recommendations of xcFs for important practical applications; (ii) understand the root of errors to help design better xcFs or propose new theoretical schemes of DFT; (iii) explore the utility of noncollinear spin orbitals in KS-DFT for better description of multi-reference systems.

Luo, Sijie

286

Variational Principles Relativistic SPH  

E-print Network

Variational Principles for Relativistic SPH J. J. Monaghan and D.J. Price Epsilon Laboratory Department of Mathematics and Statistics Monash University, Clayton 3800, Australia email: joe.monaghan see Monaghan 1992) is an ap- proximation to the continuum equations of uid dynamics which can

Price, Daniel

287

Geographic Variations in Risk  

PubMed Central

Background Chronic obstructive pulmonary disease (COPD) is an important cause of mortality with marked geographic variations in Great Britain. Additional factors beyond cigarette smoking are likely to influence these variations, but direct information on smoking by area is not readily available. We compared methods of jointly modeling the spatial distribution of mortality from COPD and lung cancer, using the latter as a proxy for smoking, to identify areas in which risk factors other than smoking may be important. Methods We obtained district-level mortality and population data for men aged 45 years or older in 1981–1999 in Great Britain. Three models were compared: Bayesian ecological regression using observed (model 1) or spatially smoothed (model 2) lung cancer standardized mortality ratio (SMR) as a smoking proxy, and bivariate regression (model 3) treating smoking as a spatial latent variable common to both diseases. Results Model selection criteria favored models 2 and 3 over model 1. Between 9% (model 3) and 25% (model 2) of spatial variation in COPD mortality was estimated to be unrelated to smoking. After adjustment for lung cancer as a proxy for smoking, both models showed similar geographic patterns of higher COPD mortality in conurbation and mining areas, historically associated with heavy industry and higher air pollution levels. Conclusions Joint modeling of multiple diseases can be used to investigate geographic variations in risk. These models reveal patterns that are adjusted for the effects of shared area-level risk factors for which no direct data are available. PMID:19318951

Best, Nicky; Hansell, Anna Louise

2010-01-01

288

Variation about the mean  

NSDL National Science Digital Library

This workshop session, part of a free online course developed for elementary and middle school teachers, explores the mean in depth. Participants work together to investigate the mean as the balancing point of a data set and come to understand how to measure variation from the mean. Video segments, interactive practice, problem sets, and discussion questions involve participants in active exploration.

Foundation, Wgbh E.

2008-03-06

289

Variational transition state theory  

SciTech Connect

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

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

1993-12-01

290

Mortality Variations in Sweden  

Microsoft Academic Search

The investigation of mortality variations has asttracted a great deal of interest in recent years. It is well known that, generally speaking, mortality rates have been continually decreasing during a long period. The detailed study of available experience concerning the structure of this movement, and the analysis of its relations to various factors of social and economic development and of

H. Cramér; H. Wold

1935-01-01

291

Seasonal Variation in Epidemiology  

ERIC Educational Resources Information Center

Seasonality analyses are important in medical research. If the incidence of a disease shows a seasonal pattern, then an environmental factor must be considered in its etiology. We discuss a method for the simultaneous analysis of seasonal variation in multiple groups. The nuts and bolts are explained using simple trigonometry, an elementary…

Marrero, Osvaldo

2013-01-01

292

Fluency Variation in Adolescents  

ERIC Educational Resources Information Center

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

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

2007-01-01

293

Nested biological variation and speciation  

PubMed Central

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

Foster, S. A.

1998-01-01

294

On Complexity  

NASA Astrophysics Data System (ADS)

Under the generic label "complexity", this chapter includes 3 related contributions of different natures. The first one (C1) is a synthetic exposition by Vincent Schächter of James P. Crutchfield's attempt [1] at a general computational representation of the notion of complexity; the second one (C2) is an account of a CeSEF-session devoted to a general discussion of this attempt; the third contribution (C3) consists of a brief note by Vincent Schächter, on the construction of complexity measures, within the framework of the method of relativized conceptualization exposed in the second part of this volume. Considered globally, the sequence indicated above should convey an illustration of the way in which, accordingly to the aim announced in the general introduction, we try to extract from modern scientific representations, methodological essences to be progressively incorporated in the researched formalized epistemology. In the following, Crutchfield is denoted by Cr.

Schächter, Vincent

295

Complex chimerism  

PubMed Central

Thousands of women with organ transplantation have undergone successful pregnancies, however little is known about how the profound immunologic changes associated with pregnancy might influence tolerance or rejection of the allograft. Pregnant women with a solid organ transplant are complex chimeras with multiple foreign cell populations from the donor organ, fetus, and mother of the pregnant woman. We consider the impact of complex chimerism and pregnancy-associated immunologic changes on tolerance of the allograft both during pregnancy and the postpartum period. Mechanisms of allograft tolerance are likely dynamic during pregnancy and affected by the influx of fetal microchimeric cells, HLA relationships (between the fetus, pregnant woman and/or donor), peripheral T cell tolerance to fetal cells, and fetal minor histocompatibility antigens. Further research is necessary to understand the complex immunology during pregnancy and the postpartum period of women with a solid organ transplant. PMID:23974274

Ma, Kimberly K.; Petroff, Margaret G.; Coscia, Lisa A.; Armenti, Vincent T.; Adams Waldorf, Kristina M.

2013-01-01

296

The Schwinger Variational Method  

NASA Technical Reports Server (NTRS)

Variational methods have proven invaluable in theoretical physics and chemistry, both for bound state problems and for the study of collision phenomena. The application of the Schwinger variational (SV) method to e-molecule collisions and molecular photoionization has been reviewed previously. The present chapter discusses the implementation of the SV method as applied to e-molecule collisions. Since this is not a review of cross section data, cross sections are presented only to server as illustrative examples. In the SV method, the correct boundary condition is automatically incorporated through the use of Green's function. Thus SV calculations can employ basis functions with arbitrary boundary conditions. The iterative Schwinger method has been used extensively to study molecular photoionization. For e-molecule collisions, it is used at the static exchange level to study elastic scattering and coupled with the distorted wave approximation to study electronically inelastic scattering.

Huo, Winifred M.

1995-01-01

297

Deinterlacing using variational methods.  

PubMed

We present a variational framework for deinterlacing that was originally used for inpainting and subsequently redeveloped for deinterlacing. From the framework, we derive a motion adaptive (MA) deinterlacer and a motion compensated (MC) deinterlacer and test them together with a selection of known deinterlacers. To illustrate the need for MC deinterlacing, the problem of details in motion (DIM) is introduced. It cannot be solved by MA deinterlacers or any simpler deinterlacers but only by MC deinterlacers. The major problem in MC deinterlacing is computing reliable optical flow [motion estimation (ME)] in interlaced video. We discuss a number of strategies for computing optical flows on interlaced video hoping to shed some light on this problem. We produce results on challenging real world video data with our variational MC deinterlacer that in most cases are indistinguishable from the ground truth. PMID:18854255

Keller, Sune Høgild; Lauze, François; Nielsen, Mads

2008-11-01

298

Variations and Adaptations  

NSDL National Science Digital Library

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

Consortium, The C.

2011-12-11

299

Genetic Variation and Atherosclerosis  

PubMed Central

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

Biros, Erik; Karan, Mirko; Golledge, Jonathan

2008-01-01

300

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

301

fimbriata complex  

Microsoft Academic Search

Ceratocystis fimbriata is a widely distributed, plant pathogenic fungus that causes wilts and cankers on many woody hosts. Earlier phylogenetic analyses of DNA sequences revealed three geographic clades within the C. fimbriata complex that are centered respectively in North America, Latin America and Asia. This study looked for cryptic species within the North American clade. The internal transcribed spacer regions

Jason A. Johnson; Thomas C. Harrington; C. J. B. Engelbrecht

302

Cellulose synthesis: a complex complex.  

PubMed

Cellulose is the world's most abundant biopolymer and a key structural component of the plant cell wall. Cellulose is comprised of hydrogen-bonded beta-1,4-linked glucan chains that are synthesized at the plasma membrane by large cellulose synthase (CESA) complexes. Recent advances in visualization of fluorescently labelled complexes have facilitated exploration of regulatory modes of cellulose production. For example, several herbicides, such as isoxaben and 2,6-dichlorobenzonitrile that inhibit cellulose production appear to affect different aspects of synthesis. Dual-labelling of cytoskeletal components and CESAs has revealed dynamic feedback regulation between cellulose synthesis and microtubule orientation and organization. In addition, fluorescently tagged CESA2 subunits may substitute for another subunit, CESA6, which suggests both plasticity and specificity for one of the components of the CESA complex. PMID:18485800

Mutwil, Marek; Debolt, Seth; Persson, Staffan

2008-06-01

303

Stroboscopic Variation Measurement  

E-print Network

A new procedure of the linear position measurement which allows to obtain sensitivity better than the Standard Quantum Limit and close to the Energetic Quantum Limit is proposed and analyzed in details. Proposed method is based on the principles of stroboscopic quantum measurement and variation quantum measurement and allows to avoid main disadvantages of both these procedures. This method can be considered as a good candidate for use as a local position meter in the ``intracavity'' topologies of the laser gravitational-wave antennae.

S. L. Danilishin; F. Ya. Khalili

2002-06-20

304

Evolution Variation Inequalities  

Microsoft Academic Search

\\u000a Chapter 5 is devoted to developing of the multi-valued penalty method for the proof of solvability for evolutional multivariational\\u000a inequalities with multi-valued maps of \\u000a wl<\\/font\\u000a>0{w}_{{\\\\lambda }_{0}}\\u000a -pseudomonotone type. These objects describe new classes of nonlinear problems with unilateral constraint. At first we consider\\u000a the equivalent representations for evolution variation inclusions with differential-operator inclusions. In Sect. 5.2 we consider\\u000a strong

Mikhail Z. Zgurovsky; Valery S. Mel’nik; Pavlo O. Kasyanov

305

Complex wounds.  

PubMed

Complex wound is the term used more recently to group those well-known difficult wounds, either chronic or acute, that challenge medical and nursing teams. They defy cure using conventional and simple "dressings" therapy and currently have a major socioeconomic impact. The purpose of this review is to bring these wounds to the attention of the health-care community, suggesting that they should be treated by multidisciplinary teams in specialized hospital centers. In most cases, surgical treatment is unavoidable, because the extent of skin and subcutaneous tissue loss requires reconstruction with grafts and flaps. New technologies, such as the negative pressure device, should be introduced. A brief review is provided of the major groups of complex wounds--diabetic wounds, pressure sores, chronic venous ulcers, post-infection soft-tissue gangrenes, and ulcers resulting from vasculitis. PMID:17187095

Ferreira, Marcus Castro; Tuma, Paulo; Carvalho, Viviane Fernandes; Kamamoto, Fábio

2006-12-01

306

Structure of complexes between aluminum chloride and other chlorides, 2: Alkali-(chloroaluminates). Gaseous complexes  

NASA Technical Reports Server (NTRS)

The structural chemistry of complexes between aluminum chloride and other metal chlorides is important both for practice and theory. Condensed-phase as well as vapor-phase complexes are of interest. Structural information on such complexes is reviewed. The first emphasis is given to the molten state because of its practical importance. Aluminum chloride forms volatile complexes with other metal chlorides and these vapor-phase complexes are dealt with in the second part. Finally, the variations in molecular shape and geometrical parameters are summarized.

Hargittai, M.

1980-01-01

307

Variational famework for Retinex  

NASA Astrophysics Data System (ADS)

Retinex theory addresses the problem of separating the illumination from the reflectance in a given image and thereby compensating for non-uniform lighting. This is in general an ill-posed problem. In this paper we propose a variational model for the Retinex problem that unifies previous methods. Similar to previous algorithms, it assumes spatial smoothness of the illumination field. In addition, knowledge of the limited dynamic range of the reflectance is used as a constraint in the recovery process. A penalty term is also included, exploiting a-priori knowledge of the nature of the reflectance image. The proposed formulation adopts a Bayesian view point of the estimation problem, which leads to an algebraic regularization term, that contributes to better conditioning of the reconstruction problem. Based on the proposed variational model, we show that the illumination estimation problem can be formulated as a Quadratic Programming optimization problem. An efficient multi-resolution algorithm is proposed. It exploits the spatial correlation in the reflectance and illumination images. Applications of the algorithm to various color images yield promising results.

Kimmel, Ron; Elad, Michael; Shaked, Doron; Keshet, Renato; Sobel, Irwin E.

2002-06-01

308

Variations in brain DNA  

PubMed Central

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

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

2014-01-01

309

Transitional lumbosacral osseous complex  

SciTech Connect

The weight of the head and trunk is transferred to the lower extremities through that segment of the spine articulating either directly or indirectly with the ilii. When a lumbosacral transitional vertebra is present the position of the weight-bearing platform usually changes. A bony entity is formed delineated superiorly by the top of the transitional vertebra and inferiorly by the lower level of the sacroiliac joints. This segment is designated as the transitional lumbosacral osseous complex. Measurements of its length in the three phylogenetic categories in man, including measurements of the articulating portion of the sacrum in the human mode, showed a range of 68 mm to 157 mm and variations from 2.0 to 3.7 in vertebral lengths.

Wigh, R.E.

1982-05-01

310

Genetic variation in social influence on mate preferences.  

PubMed

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

Rebar, Darren; Rodríguez, Rafael L

2013-07-22

311

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

312

Beyond Punnett Squares: Student Word Association and Explanations of Phenotypic Variation through an Integrative Quantitative Genetics Unit Investigating Anthocyanin Inheritance and Expression in "Brassica rapa" Fast Plants  

ERIC Educational Resources Information Center

Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question "What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev)," we developed a 4-wk unit for an inquiry-based laboratory…

Batzli, Janet M.; Smith, Amber R.; Williams, Paul H.; McGee, Seth A.; Dosa, Katalin; Pfammatter, Jesse

2014-01-01

313

Epigenetic variation in plant responses to defence hormones  

PubMed Central

Background and Aims There is currently much speculation about the role of epigenetic variation as a determinant of heritable variation in ecologically important plant traits. However, we still know very little about the phenotypic consequences of epigenetic variation, in particular with regard to more complex traits related to biotic interactions. Methods Here, a test was carried out to determine whether variation in DNA methylation alone can cause heritable variation in plant growth responses to jasmonic acid and salicylic acid, two key hormones involved in induction of plant defences against herbivores and pathogens. In order to be able to ascribe phenotypic differences to epigenetic variation, the hormone responses were studied of epigenetic recombinant inbred lines (epiRILs) of Arabidopsis thaliana – lines that are highly variable at the level of DNA methylation but nearly identical at the level of DNA sequence. Key Results Significant heritable variation was found among epiRILs both in the means of phenotypic traits, including growth rate, and in the degree to which these responded to treatment with jasmonic acid and salicylic acid. Moreover, there was a positive epigenetic correlation between the responses of different epiRILs to the two hormones, suggesting that plant responses to herbivore and pathogen attack may have a similar molecular epigenetic basis. Conclusions This study demonstrates that epigenetic variation alone can cause heritable variation in, and thus potentially microevolution of, plant responses to defence hormones. This suggests that part of the variation of plant defences observed in natural populations may be due to underlying epigenetic, rather than entirely genetic, variation. PMID:22543179

Latzel, Vít; Zhang, Yuanye; Karlsson Moritz, Kim; Fischer, Markus; Bossdorf, Oliver

2012-01-01

314

A modified variational approach to scattering  

E-print Network

. J. W. Henry, Phys. Rev. A 8, 572 (1973). 3 P. G. Burke, A. Hibbert, and W. D. Robb, J. Phys. B 4, 153 (1971). 4 P. G. Burke and W. D. Robb, J. Phys. B 5, 44 (1972). 5 M. J. Seaton, J. Phys. B 7, 1817 (1974). 6 F. E. Harris and I-I. I-I. Michels... that Jt" Ec; (e:, -k')+ azc;&4)L(@ + zhg&c &+ilLl(-) +&6"lL J&&) + ~6 b&f'IL I 4' A] + &, &F iL"fr). (3. 40) Applying the conditions due to Eq. (3. 11) we get the n equations found in the Kohn and Hulthen formulations 24 where the superscripts refer...

Parnell, Gregory Elliott

1978-01-01

315

Managing complexity  

Microsoft Academic Search

Physical analogs have shown considerable promise for understanding the\\u000abehavior of complex adaptive systems, including macroeconomics, biological\\u000asystems, social networks, and electric power markets. Many of today's most\\u000achallenging technical and policy questions can be reduced to a distributed\\u000aeconomic control problem. Indeed, economically-based control of large-scale\\u000asystems is founded on the conjecture that the price-based regulation (e.g.,\\u000aauctions, markets)

David P. Chassin; Christian POSSE; Joel MALARD

1998-01-01

316

Magnetic properties and electronic structure of neptunyl(VI) complexes: wavefunctions, orbitals, and crystal-field models.  

PubMed

The electronic structure and magnetic properties of neptunyl(VI), NpO2(2+), and two neptunyl complexes, [NpO2(NO3)3](-) and [NpO2Cl4](2-), were studied with a combination of theoretical methods: ab initio relativistic wavefunction methods and density functional theory (DFT), as well as crystal-field (CF) models with parameters extracted from the ab initio calculations. Natural orbitals for electron density and spin magnetization from wavefunctions including spin-orbit coupling were employed to analyze the connection between the electronic structure and magnetic properties, and to link the results from CF models to the ab initio data. Free complex ions and systems embedded in a crystal environment were studied. Of prime interest were the electron paramagnetic resonance g-factors and their relation to the complex geometry, ligand coordination, and nature of the nonbonding 5f orbitals. The g-factors were calculated for the ground and excited states. For [NpO2Cl4](2-), a strong influence of the environment of the complex on its magnetic behavior was demonstrated. Kohn-Sham DFT with standard functionals can produce reasonable g-factors as long as the calculation converges to a solution resembling the electronic state of interest. However, this is not always straightforward. PMID:24848696

Gendron, Frédéric; Páez-Hernández, Dayán; Notter, François-Paul; Pritchard, Ben; Bolvin, Hélène; Autschbach, Jochen

2014-06-23

317

Stratospheric condensation nuclei variations may relate to solar activity  

NASA Technical Reports Server (NTRS)

Observations of increases of stratospheric condensation nuclei suggest a photo-initiated sulphuric acid vapour formation process in spring in polar regions. It is proposed that the sulphuric acid rapidly forms condensation nuclei through attachment to negatively charged multi-ion complexes and that the process may be modulated through variations in solar activity.

Hofmann, D. J.; Rosen, J. M.

1982-01-01

318

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

319

Higher Education Earnings Premium: Value, Variation, and Trends  

ERIC Educational Resources Information Center

Much of the current skepticism about the financial payoff of higher education emerges from recent media focus on young college graduates struggling to enter a weak labor market. This brief highlights some of the complexities underlying discussions of the return to the investment in postsecondary education and describes some of the variation in…

Baum, Sandy

2014-01-01

320

Variation-Aware Resource Sharing and Binding in Behavioral Synthesis  

E-print Network

@mentor.com Abstract-- As technology scales, the delay uncertainty caused by process variations has become increasingly specifications. The effectiveness of the proposed algorithm is demonstrated with a set of industrial benchmark. However, as the complexity of the system grows, this labor intensive approach is both time consuming

Xie, Yuan

321

Stability of asynchronous variational integrators  

NASA Astrophysics Data System (ADS)

The adoption of multiple time step integrators can provide substantial computational savings for mechanical systems with multiple time scales. However, the scope of these savings may be limited by the range of allowable time step choices. In this paper we analyze the linear stability of the fully asynchronous methods termed AVI, for asynchronous variational integrators. We perform a detailed analysis for the case of a one-dimensional particle moving under the action of a soft and a stiff quadratic potential, integrated with two time steps in rational ratios. In this case, we provide sufficient conditions for the stability of the method. These generalize to the fully asynchronous AVI case the results obtained for synchronous multiple time stepping schemes, such as r-RESPA, which show resonances when the larger time step is a multiple of the effective half-period of the stiff potential. Additionally, we numerically investigate the appearance of instabilities. Based on the experimental observations, we conjecture the existence of a dense set of unstable time steps when arbitrary rational ratios of time steps are considered. In this way, unstable schemes for arbitrarily small time steps can be obtained. However, the vast majority of these instabilities are extremely weak and do not present an obstacle to the use of these integrators. We then applied these results to analyze the stability of multiple time step integrators in the more complex mechanical systems arising in molecular dynamics and solid dynamics. We explained why strong resonances are ubiquitously found in the former, while rarely encountered in the latter. Finally, in this paper we introduce a formulation of AVI that highlights the symplectic nature of the algorithm, complementing those introduced earlier by other authors.

Fong, William; Darve, Eric; Lew, Adrian

2008-09-01

322

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

E-print Network

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

Gill, Estelle

2008-01-01

323

Variational multiscale models for charge transport  

PubMed Central

This work presents a few variational multiscale models for charge transport in complex physical, chemical and biological systems and engineering devices, such as fuel cells, solar cells, battery cells, nanofluidics, transistors and ion channels. An essential ingredient of the present models, introduced in an earlier paper (Bulletin of Mathematical Biology, 72, 1562-1622, 2010), is the use of differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain from the microscopic domain, meanwhile, dynamically couple discrete and continuum descriptions. Our main strategy is to construct the total energy functional of a charge transport system to encompass the polar and nonpolar free energies of solvation, and chemical potential related energy. By using the Euler-Lagrange variation, coupled Laplace-Beltrami and Poisson-Nernst-Planck (LB-PNP) equations are derived. The solution of the LB-PNP equations leads to the minimization of the total free energy, and explicit profiles of electrostatic potential and densities of charge species. To further reduce the computational complexity, the Boltzmann distribution obtained from the Poisson-Boltzmann (PB) equation is utilized to represent the densities of certain charge species so as to avoid the computationally expensive solution of some Nernst-Planck (NP) equations. Consequently, the coupled Laplace-Beltrami and Poisson-Boltzmann-Nernst-Planck (LB-PBNP) equations are proposed for charge transport in heterogeneous systems. A major emphasis of the present formulation is the consistency between equilibrium LB-PB theory and non-equilibrium LB-PNP theory at equilibrium. Another major emphasis is the capability of the reduced LB-PBNP model to fully recover the prediction of the LB-PNP model at non-equilibrium settings. To account for the fluid impact on the charge transport, we derive coupled Laplace-Beltrami, Poisson-Nernst-Planck and Navier-Stokes equations from the variational principle for chemo-electro-fluid systems. A number of computational algorithms is developed to implement the proposed new variational multiscale models in an efficient manner. A set of ten protein molecules and a realistic ion channel, Gramicidin A, are employed to confirm the consistency and verify the capability. Extensive numerical experiment is designed to validate the proposed variational multiscale models. A good quantitative agreement between our model prediction and the experimental measurement of current-voltage curves is observed for the Gramicidin A channel transport. This paper also provides a brief review of the field. PMID:23172978

Wei, Guo-Wei; Zheng, Qiong; Chen, Zhan; Xia, Kelin

2012-01-01

324

RESULTS OF IPCS COLLABORATIVE STUDY ON COMPLEX MIXTURES  

EPA Science Inventory

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

325

Analysis of Haplotype Structure in the Bovine Major Histocompatibility Complex  

E-print Network

The goal of this project was to identify and characterize polymorphic markers spanning regions of the bovine major histocompatibility complex (BoLA) to analyze patterns of genetic variation and haplotype structure across diverse cattle breeds...

Fritz, Krista L.

2011-02-22

326

Getting a Handle on Variation  

NSDL National Science Digital Library

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

The Wisconsin Fast Plants Program

327

Periodic insolation variations on Mars.  

NASA Technical Reports Server (NTRS)

Previously unrecognized insolation variations on Mars are a consequence of periodic variations in eccentricity, first established by the theory of Brouwer and Van Woerkom (1950). Such annual insolation variations, characterized by both 95,000-year and 2,000,000-year periodicities, may actually be recorded in newly discovered layered deposits in the polar regions of Mars. An additional north-south variation in seasonal insolation, but not average annual insolation, exists with 51,000-year and 2,000,000-year periodicities.

Murray, B. C.; Ward, W. R.; Yeung, S. C.

1973-01-01

328

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 ...

329

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

E-print Network

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

Cai, PingGen

330

MHC standing genetic variation and pathogen resistance in wild Atlantic salmon  

E-print Network

critical to evaluate the influence of standing genetic variation on contemporary adaptation (see also involved in contemporary coevolution. MHC variability and bacterial infection rate were determined environment. Keywords: major histocompatibility complex; infection; local adaptation; myxozoa; bacteria

Bernatchez, Louis

331

CCMR: New Iridium Complexes for the Dehydrogenation of Alkanes  

NSDL National Science Digital Library

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

Wang, David

2004-08-17

332

Seasonal variations on Titan  

NASA Astrophysics Data System (ADS)

Eight years after Cassini's Saturn orbit insertion, we look at the evolution of the thermal and chemical composition of Titan's atmosphere by combining Cassini CIRS recordings and the related ground- and space- based observations The fulfillment of one Titanian year of observations provides us for the first time with the opportunity to evaluate the relative role of different physical processes in the long term evolution of this complex environment. By comparing V1 (1980), ISO (1997) and Cassini (2010) we find that a reversal of composition near the equator from automnal equinox to vernal equinox (1996 min -2009 max, half a year), as well as some differences in polar enhancement at the same era as Voyager.

Coustenis, A.; Bampasidis, G.; Vinatier, S.; Achterberg, R.; Lavvas, P.; Nixon, C.; Jennings, D.; Teanby, N.; Flasar, F. M.; Carlson, R.; Orton, G.; Romani, P.; Guandique, E. A.

2012-09-01

333

Propagation of genetic variation in gene regulatory networks  

NASA Astrophysics Data System (ADS)

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

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

2013-08-01

334

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

335

A variational principle for compressible fluid mechanics: Discussion of the multi-dimensional theory  

NASA Technical Reports Server (NTRS)

The variational principle for compressible fluid mechanics previously introduced is extended to two dimensional flow. The analysis is stable, exactly conservative, adaptable to coarse or fine grids, and very fast. Solutions for two dimensional problems are included. The excellent behavior and results lend further credence to the variational concept and its applicability to the numerical analysis of complex flow fields.

Prozan, R. J.

1982-01-01

336

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

Microsoft Academic Search

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

Peter S. White; Joan L. Walker

1997-01-01

337

Structural and functional impacts of copy number variations on the cattle genome  

Technology Transfer Automated Retrieval System (TEKTRAN)

Although there have been significant advances in resolving the pattern and nature of single nucleotide polymorphisms (SNPs), similar realizations for larger, more complex forms of genetic variation have just emerged. Several recent publications reveal that copy number variations (CNVs) are common an...

338

Research of Project Organization Variation Dynamics Based on the Theory of Organizational Behavior  

Microsoft Academic Search

A success project need a success project organization certainly, so the research on organization variation mechanism of Construction Project is important. The production shows the form mechanism and the motivity during the Life-Cycle variation in construction project organization and provides gists and references for construction project organization scheme and organization pattern choice. However, because of the dynamicity and complexity of

Jichu Lin; Jie Chen

2011-01-01

339

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

2005-01-01

340

Complex patterns and tip effect evolution  

E-print Network

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

Francisco Vera

2005-05-10

341

Evolution, robustness, and the cost of complexity  

Microsoft Academic Search

Evolutionary systems biology is the study of how regulatory networks evolve under the influence of natural selection, mutation, and the environment. It attempts to explain the dynamics, architecture, and variational properties of regulatory networks and how this relates to the origins, evolution and maintenance of complex and diverse functions. Key questions in the field of evolutionary systems biology ask how

Robert D. Leclerc

2009-01-01

342

Algorithms, complexity, and the sciences.  

PubMed

Algorithms, perhaps together with Moore's law, compose the engine of the information technology revolution, whereas complexity--the antithesis of algorithms--is one of the deepest realms of mathematical investigation. After introducing the basic concepts of algorithms and complexity, and the fundamental complexity classes P (polynomial time) and NP (nondeterministic polynomial time, or search problems), we discuss briefly the P vs. NP problem. We then focus on certain classes between P and NP which capture important phenomena in the social and life sciences, namely the Nash equlibrium and other equilibria in economics and game theory, and certain processes in population genetics and evolution. Finally, an algorithm known as multiplicative weights update (MWU) provides an algorithmic interpretation of the evolution of allele frequencies in a population under sex and weak selection. All three of these equivalences are rife with domain-specific implications: The concept of Nash equilibrium may be less universal--and therefore less compelling--than has been presumed; selection on gene interactions may entail the maintenance of genetic variation for longer periods than selection on single alleles predicts; whereas MWU can be shown to maximize, for each gene, a convex combination of the gene's cumulative fitness in the population and the entropy of the allele distribution, an insight that may be pertinent to the maintenance of variation in evolution. PMID:25349382

Papadimitriou, Christos

2014-11-11

343

Colony Variation in Staphylococcus lugdunensis  

PubMed Central

Staphylococcus lugdunensis is being increasingly reported as a pathogen with an outcome resembling that of S. aureus rather than coagulase-negative staphylococci. Recent local isolates exhibited colonial variation that delayed identification and interpretation of clinical significance. Until now previous descriptions have not emphasized colonial variation as an important identifying characteristic of S. lugdunensis. PMID:9738081

Leung, Michael J.; Nuttall, Nichalas; Pryce, Todd M.; Coombs, Geoffrey W.; Pearman, John W.

1998-01-01

344

Interpreting phenotypic variation in plants  

NSDL National Science Digital Library

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

345

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

346

Genetic variation, classification and 'race'  

Microsoft Academic Search

New genetic data has enabled scientists to re-examine the relationship between human genetic variation and 'race'. We review the results of genetic analyses that show that human genetic variation is geographically structured, in accord with historical patterns of gene flow and genetic drift. Analysis of many loci now yields reasonably accurate estimates of genetic similarity among individuals, rather than populations.

Stephen P Wooding; Lynn B Jorde

2004-01-01

347

Variational bayesian blind deconvolution using a total variation prior.  

PubMed

In this paper, we present novel algorithms for total variation (TV) based blind deconvolution and parameter estimation utilizing a variational framework. Using a hierarchical Bayesian model, the unknown image, blur, and hyperparameters for the image, blur, and noise priors are estimated simultaneously. A variational inference approach is utilized so that approximations of the posterior distributions of the unknowns are obtained, thus providing a measure of the uncertainty of the estimates. Experimental results demonstrate that the proposed approaches provide higher restoration performance than non-TV-based methods without any assumptions about the unknown hyperparameters. PMID:19095515

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

2009-01-01

348

Sea level variation  

NASA Technical Reports Server (NTRS)

Published values for the long-term, global mean sea level rise determined from tide gauge records range from about one to three mm per year. The scatter of the estimates appears to arise largely from the use of data from gauges located at convergent tectonic plate boundaries where changes of land elevation give fictitious sea level trends, and the effects of large interdecadal and longer sea level variations on short (less than 50+ years) or sappy records. In addition, virtually all gauges undergo subsidence or uplift due to isostatic rebound from the last deglaciation at a rate comparable to or greater than the secular rise of sea level. Modeling rebound by the ICE-3G model of Tushingham and Peltier (1990) and avoiding tide gauge records in areas of converging tectonic plates produces a highly consistent set of long sea level records. A global set of 21 such stations in nine oceanic regions with an average record length of 76 years during the period 1880-1980 yields the global sea level rise value 1.8 mm/year +/- 0.1. Greenhouse warming scenarios commonly forecast an additional acceleration of global sea level in the next 5 or 6+ decades in the range 0.1-0.2 mm/yr2. Because of the large power at low frequencies in the sea level spectrum, very long tide gauge records (75 years minimum) have been examined for past apparent sea level acceleration. For the 80-year period 1905-1985, 23 essentially complete tide gauge records in 10 geographic groups are available for analysis. These yielded the apparent global acceleration -0.011 (+/- 0.012) mm/yr2. A larger, less uniform set of 37 records in the same 10 groups with 92 years average length covering the 141 years from 1850-1991 gave 0.001 (+/- 0.008) mm/yr2. Thus there is no evidence for an apparent acceleration in the past 100+ years that is significant either statistically, or in comparison to values associated with global warming. Unfortunately, the large interdecadal fluctuations of sea level severely affect estimates of global sea level acceleration for time spans of less than about 50 years. This means that tide gauges alone cannot serve as a reliable leading indicator of climate change in less than many decades. This time required can be significantly reduced if the interdecadal fluctuations of sea level can be understood in terms of their forcing mechanisms, and then removed from the tide gauge records.

Douglas, Bruce C.

1992-01-01

349

Spatial Variation as a Tool for Inferring Temporal Variation and Diagnosing Types of Mechanisms in Ecosystems  

PubMed Central

Ecological processes, like the rise and fall of populations, leave an imprint of their dynamics as a pattern in space. Mining this spatial record for insight into temporal change underlies many applications, including using spatial snapshots to infer trends in communities, rates of species spread across boundaries, likelihood of chaotic dynamics, and proximity to regime shifts. However, these approaches rely on an inherent but undefined link between spatial and temporal variation. We present a quantitative link between a variable’s spatial and temporal variation based on established variance-partitioning techniques, and test it for predictive and diagnostic applications. A strong link existed between spatial and regional temporal variation (estimated as Coefficients of Variation or CV’s) in 136 variables from three aquatic ecosystems. This association suggests a basis for substituting one for the other, either quantitatively or qualitatively, when long time series are lacking. We further show that weak substitution of temporal for spatial CV results from distortion by specific spatiotemporal patterns (e.g., inter-patch synchrony). Where spatial and temporal CV’s do not match, we pinpoint the spatiotemporal causes of deviation in the dynamics of variables and suggest ways that may control for them. In turn, we demonstrate the use of this framework for describing spatiotemporal patterns in multiple ecosystem variables and attributing them to types of mechanisms. Linking spatial and temporal variability makes quantitative the hitherto inexact practice of space-for-time substitution and may thus point to new opportunities for navigating the complex variation of ecosystems. PMID:24586627

Hammond, Matthew P.; Kolasa, Jurek

2014-01-01

350

Variational formulation of high performance finite elements: Parametrized variational principles  

NASA Technical Reports Server (NTRS)

High performance elements are simple finite elements constructed to deliver engineering accuracy with coarse arbitrary grids. This is part of a series on the variational basis of high-performance elements, with emphasis on those constructed with the free formulation (FF) and assumed natural strain (ANS) methods. Parametrized variational principles that provide a foundation for the FF and ANS methods, as well as for a combination of both are presented.

Felippa, Carlos A.; Militello, Carmello

1991-01-01

351

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

352

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. PMID:23691014

Thompson, Matthew P.

2013-01-01

353

Integrative Genomics G -genetic variation  

E-print Network

Integrative Genomics G - genetic variation T - transcript levels P - protein concentrations M Model Single Data Analysis Single type + phenotype Analysis Multiple Data Types/ Integrated Analysis #12? Fromwikipedia Central Dogma DNA RNA Protein Metabolism & Cell Structure Organism Prokaryote 1010 atoms Eukaryote

Goldschmidt, Christina

354

Built for Speed: Pleistocene Climate Variation and the Origin of Human Culture  

E-print Network

. This hypothesis contrasts with the common idea that human language, tools, and culture represent a revolutionary adaptive complex--tool making, language, complex social organization, and other aspects of culture. MoreBuilt for Speed: Pleistocene Climate Variation and the Origin of Human Culture Peter J. Richerson

Richerson, Peter J.

355

Nonconvex functions and variational inequalities  

Microsoft Academic Search

In this paper, we study some properties of a class of nonconvex functions, called semipreinvex functions, which includes the classes of preinvex functions and arc-connected convex functions. It is shown that the minimum of an arcwise directionally differentiable semi-invex functions on a semi-invex set can be characterized by a class of variational inequalities, known as variational-like inequalities. We use the

M. A. Noor

1995-01-01

356

RFLP variation in diploid and tetraploid alfalfa.  

PubMed

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

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

1991-11-01

357

Copy Number Variation in Schizophrenia in Sweden  

PubMed Central

Schizophrenia is a highly heritable neuropsychiatric disorder of complex genetic etiology. Previous genome-wide surveys have revealed a greater burden of large, rare CNVs in schizophrenia cases and identified multiple rare recurrent CNVs that increase risk of schizophrenia although with incomplete penetrance and pleiotropic effects. Identification of additional recurrent CNVs and biological pathways enriched for schizophrenia CNVs requires greater sample sizes. We conducted a genome-wide survey for CNVs associated with schizophrenia using a Swedish national sample (4,719 cases and 5,917 controls). High-confidence CNV calls were generated using genotyping array intensity data and their effect on risk of schizophrenia was measured. Our data confirm increased burden of large, rare CNVs in schizophrenia cases as well as significant associations for recurrent 16p11.2 duplications, 22q11.2 deletions and 3q29 deletions. We report a novel association for 17q12 duplications (odds ratio=4.16, P=0.018), previously associated with autism and mental retardation but not schizophrenia. Intriguingly, gene set association analyses implicate biological pathways previously associated with schizophrenia through common variation and exome sequencing (calcium channel signaling and binding partners of the fragile X mental retardation protein). We found significantly increased burden of the largest CNVs (>500Kb) in genes present in the post-synaptic density, in genomic regions implicated via schizophrenia genome-wide association studies, and in gene products localized to mitochondria and cytoplasm. Our findings suggest that multiple lines of genomic inquiry – genome-wide screens for CNVs, common variation, and exonic variation – are converging on similar sets of pathways and/or genes. PMID:24776740

Szatkiewicz, Jin P.; O’Dushlaine, Colm; Chen, Guanhua; Chambert, Kimberly; Moran, Jennifer L.; Neale, Benjamin M; Fromer, Menachem; Ruderfer, Douglas; Akterin, Susanne; Bergen, Sarah E; Kähler, Anna; Magnusson, Patrik KE; Kim, Yunjung; Crowley, James J; Rees, Elliott; Kirov, George; O’Donovan, Michael C.; Owen, Michael J.; Walters, James; Scolnick, Edward; Sklar, Pamela; Purcell, Shaun; Hultman, Christina M.; McCarroll, Steven A.; Sullivan, Patrick F.

2014-01-01

358

45 CFR 156.420 - Plan variations.  

Code of Federal Regulations, 2013 CFR

...420 Plan variations. (a) Submission of silver plan variations. For each of its silver health plans that an issuer offers, or intends...certification prior to each benefit year the standard silver plan and three variations of the standard...

2013-10-01

359

45 CFR 156.420 - Plan variations.  

Code of Federal Regulations, 2014 CFR

...420 Plan variations. (a) Submission of silver plan variations. For each of its silver health plans that an issuer offers, or intends...certification prior to each benefit year the standard silver plan and three variations of the standard...

2014-10-01

360

A Simple Mechanism for Complex Social Behavior  

PubMed Central

The evolution of cooperation is a paradox because natural selection should favor exploitative individuals that avoid paying their fair share of any costs. Such conflict between the self-interests of cooperating individuals often results in the evolution of complex, opponent-specific, social strategies and counterstrategies. However, the genetic and biological mechanisms underlying complex social strategies, and therefore the evolution of cooperative behavior, are largely unknown. To address this dearth of empirical data, we combine mathematical modeling, molecular genetic, and developmental approaches to test whether variation in the production of and response to social signals is sufficient to generate the complex partner-specific social success seen in the social amoeba Dictyostelium discoideum. Firstly, we find that the simple model of production of and response to social signals can generate the sort of apparent complex changes in social behavior seen in this system, without the need for partner recognition. Secondly, measurements of signal production and response in a mutant with a change in a single gene that leads to a shift in social behavior provide support for this model. Finally, these simple measurements of social signaling can also explain complex patterns of variation in social behavior generated by the natural genetic diversity found in isolates collected from the wild. Our studies therefore demonstrate a novel and elegantly simple underlying mechanistic basis for natural variation in complex social strategies in D. discoideum. More generally, they suggest that simple rules governing interactions between individuals can be sufficient to generate a diverse array of outcomes that appear complex and unpredictable when those rules are unknown. PMID:21468302

Wolf, Jason B.; Thompson, Christopher R. L.

2011-01-01

361

Studies of the complexation of chloranilic acid with proguanil.  

PubMed

Studies on the complexation between chloranilic acid and proguanil has been carried out. The chloranilic acid acted as a pi-electron donor. The stoichiometric relationship in the complex was determined by employing the Job's method of continuous variation. The results indicate that the complex exhibits a purple colour and absorbs maximally at 520 nm. Spectrophotometric studies show that the method could be useful in the analysis of proguanil. PMID:11486609

Adikwu, M U; Builders, P F; Ofokansi, K C; Attama, A A

2001-01-01

362

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

363

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

364

Existence of evolutionary variational solutions via the calculus of variations  

NASA Astrophysics Data System (ADS)

In this paper we introduce a purely variational approach to time dependent problems, yielding the existence of global parabolic minimizers, that is ?0T ?? [u??t?+f(x,Du)] dx dt??0T ?? f(x,Du+D?) dx dt, whenever T>0 and ??C0?(?×(0,T),RN). For the integrand f:?×R?[0,?] we merely assume convexity with respect to the gradient variable and coercivity. These evolutionary variational solutions are obtained as limits of maps depending on space and time minimizing certain convex variational functionals. In the simplest situation, with some growth conditions on f, the method provides the existence of global weak solutions to Cauchy-Dirichlet problems of parabolic systems of the type ?tu-divD?f(x,Du)=0 in ?×(0,?).

Bögelein, Verena; Duzaar, Frank; Marcellini, Paolo

365

Is a Morphologically Complex Language Really that Complex in Full-Text Retrieval?  

Microsoft Academic Search

In this paper we show that keyword variation of a morphologically complex language, Finnish, can be handled effectively for IR purposes by generating only the textually most frequent forms of the keyword. Theoreti- cally Finnish nouns have about 2,000 different forms, but occurrences of most of the forms are rare. Corpus statistics showed that about 84 - 88 per cent

Kimmo Kettunen; Eija Airio

2006-01-01

366

System Complexity and Its Measures: How Complex Is Complex  

Microsoft Academic Search

\\u000a The last few decades of physics, chemistry, biology, computer science, engineering, and social sciences have been marked by\\u000a major developments of views on cognitive systems, dynamical systems, complex systems, complexity, self-organization, and emergent\\u000a phenomena that originate from the interactions among the constituent components (agents) and with the environment, without\\u000a any central authority. How can measures of complexity capture the intuitive

Witold Kinsner

367

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

368

Variation in 'Hayward' kiwifruit quality characteristics .  

E-print Network

??Quantify the magnitude, sources and distribution of variation in fruit quality traits within kiwifruit populations and identify opportunities for the management of this variation. Near-infrared… (more)

Woodward, Tim J.

2007-01-01

369

Magma rheology variation in sheet intrusions (Invited)  

NASA Astrophysics Data System (ADS)

The rheology of magma fundamentally controls igneous intrusion style as well as the explosivity and type of volcanic eruptions. Importantly, the dynamic interplay between the viscosity of magma and other processes active during intrusion (e.g., crystallisation, magma mixing, assimilation of crystal mushes and/or xenolith entrainment) will likely bear an influence on the temporal variation of magma rheology. Constraining the timing of rheological changes during magma transit therefore plays an important role in understanding the nuances of volcanic systems. However, the rheological evolution of actively emplacing igneous intrusions cannot be directly studied. While significant advances have been made via experimental modelling and analysis of lava flows, how these findings relate to intruding magma remains unclear. This has led to an increasing number of studies that analyse various characteristics of fully crystallised intrusions in an attempt to ';back-out' the rheological conditions governing emplacement. For example, it has long been known that crystallinity affects the rheology and, consequently, the velocity of intruding magma. This means that quantitative textural analysis of crystal populations (e.g., crystal size distribution; CSD) used to elucidate crystallinity at different stages of emplacement can provide insights into magma rheology. Similarly, methods that measure flow-related fabrics (e.g., anisotropy of magnetic susceptibility; AMS) can be used to discern velocity profiles, a potential proxy for the magma rheology. To illustrate these ideas, we present an integrated AMS and petrological study of several sheet intrusions located within the Ardnamurchan Central Complex, NW Scotland. We focus on the entrainment and transport dynamics of gabbroic inclusions that were infiltrated by the host magma upon entrainment. Importantly, groundmass magnetic fabrics within and external to these inclusions are coaxial. This implies that a deviatoric stress was transmitted into the inclusions during magma flow. We suggest that this represents a modification of the magma dynamics from Newtonian-like to Bingham-like behaviour. Furthermore, the spatial restriction of inclusions within the sheet intrusions suggest that subtle variations in magma rheology may partition apparently continuous intrusions, perhaps affecting lateral mixing and the longevity of discrete sheet segments. Detailed fabric analysis of other inclusion-free intrusions in the Ardnamurchan Central Complex supports this interpretation. Our results highlight that the crystalline cargo of a magma can result in temporal and spatial variations in magma rheology. This can partition coalesced magma bodies into ';zones' characterised by different magma properties, potentially affecting the location of magma flow pathways or even eruption sites.

Magee, C.; O'Driscoll, B.; Petronis, M. S.; Stevenson, C.

2013-12-01

370

Variational Principles in General Relativity  

E-print Network

This thesis details an effort to generate astrophysically interesting solutions to the two-body problem in General Relativity. The thesis consists of two main parts. The first part presents an analytical variational principle for describing binary neutron stars undergoing irrotational fluid flow. The variational principle is a powerful tool for generating accurate estimates of orbital parameters for neutron stars in quasi-equilibrium orbits. The second part of the thesis details the numerical application of the variational principle by solving the initial value problem for binary black holes in quasi- equilibrium circular orbits. The analysis draws from the novel ``puncture'' method of describing the black holes, and relies on nonlinear adaptive multigrid techniques for generating numerical results. We arrive at two important conclusions. First, the analytical variational principle describing binary neutron stars in irrotational motion provides a road map for future numerical simulations, and also lends credence to previous simulations by other authors. Second, the numerical application and description of binary black holes in quasi-equilibrium circular orbits simplifies the analyses of previous authors, and allows for the imposition of realistic boundary data in simulations with relatively high grid densities. Both the variational principle and its application are used to generate accurate estimates of the orbital parameters.

Brian D. Baker

2002-05-26

371

Solar flux and its variations  

NASA Technical Reports Server (NTRS)

Data on the solar irradiance as derived from a number of sources are presented. An attempt was made to bring these data onto a uniform scale. Summation of fluxes at all wavelengths yields a figure of 1357.826 per sq m for the solar constant. Estimates are made of the solar flux variations due to flares, active regions (slowly varying component), solar rotation and the 11-year cycle. Solar activity does not produce a significant variation in the value of the solar constant. Nevertheless, variations in the X-ray and extreme ultraviolet portions of the solar flux may be several orders of magnitude during solar activity, especially at times of major flares. It is well established that these short wavelength flux enhancements cause significant changes in the terrestrial ionosphere.

Smith, E. V. P.; Gottlieb, D. M.

1974-01-01

372

Diurnal variation of mesospheric ozone  

NASA Astrophysics Data System (ADS)

Four Petrel rockets were flown from South Uist on October 2, 1979, to investigate the ozone concentration variation predicted by photochemical models between day and night in the mesosphere by means of interference filters that defined an approximately 10 nm bandwidth. The first two rockets contained photometers with wavebands centered at 265 and 290 nm, while the last two employed a single waveband at 265 nm. Results show significant diurnal variation above 54 km, which exceeds a factor of 2 above 65 km and reaches a factor of 10 between night and sunrise at 90 km.

Vaughan, G.

1982-03-01

373

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

374

North Atlantic Sea Level Variations  

NASA Astrophysics Data System (ADS)

Sea Level trends are often studied as a direct effect of climate change, and considered an indicator of the global warming. Although a global Sea Level rise over the last decades is a well established fact, when we come to study regional variations some effort has to be paid in order to understand whether such trends are part of a longer cycle. In particular, relatively short time-span available from altimetry, combined with regional phenomenon influence, could lead to misleading conclusions. In order to illustrate this idea we have studied the North Atlantic sea level variations and how these are influenced by regional fenomena.

Vigo, I.; Belda, S.; Sanchez-Reales, J. M.

2013-12-01

375

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

PubMed

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

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

2011-09-01

376

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

377

Variations in Radiocarbon Concentration and Sunspot Activity  

Microsoft Academic Search

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

M. Stuiver

1961-01-01

378

Darwin's Finches: Population Variation and Natural Selection  

Microsoft Academic Search

Van Valen's model, which relates morphological variation to ecological variation in an adaptive scheme, was investigated with individually marked and measured Darwin's finches on two adjacent Galapagos islands, Santa Cruz and Daphne Major. Results show that environmental heterogeneity is correlated with large continuous, morphological variation: variation in bill dimensions of Geospiza fortis is greater on Santa Cruz than on Daphne,

P. R. Grant; B. R. Grant; J. N. M. Smith; I. J. Abbott; L. K. Abbott

1976-01-01

379

Spatiotemporal imaging of complexity.  

PubMed

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

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

2012-01-01

380

VARIATION IN CENTRAL AMERICAN FLICKERS  

Microsoft Academic Search

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

LESTER L. SHORT

381

Sociocultural Variation in Literacy Achievement  

ERIC Educational Resources Information Center

The purpose of this study was to describe the variations in literacy achievement among native and non-native upper primary school children (grades three to six) in the Netherlands. Various measures of word decoding, reading literacy and writing skill were collected from 1091 native Dutch children, 753 children with a former Dutch colonial…

Verhoeven, Ludo

2006-01-01

382

Variational Principles for Water Waves  

E-print Network

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

Boris Kolev; David H. Sattinger

2007-12-01

383

Reducing Information Variation in Text  

Microsoft Academic Search

We discuss the nature and the scope of linguistic (morphological,syntactic and semantic) variation of terms and its impact on twoinformation retrieval tasks: term acquisition and automatic indexing. Areview of natural language processing techniques existing in these twoareas is done, along with an in-depth presentation of FASTR, a corpusprocessor for the recognition, normalization, and acquisition of multi-word terms.

Agata Savary; Christian Jacquemin

2000-01-01

384

Cardioidal Variations Francesco De Comite  

E-print Network

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

Boyer, Edmond

385

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

386

Bayesianity of Ensemble Variational Assimilation  

NASA Astrophysics Data System (ADS)

Ensemble assimilation methods (EnKF, Particle Filters, Ensemble Variational Assimilation) are basically meant to produce a sample of the Bayesian probability distribution of the state of the observed system, conditional to the available data. We present a comparative evaluation of those methods, and in particular of Ensemble Variational Assimilation (Ens/4D-Var), considered as Bayesian estimators. Ensemble Variational Assimilation achieves bayesianity in the linear and gaussian case. It is implemented here on small dimensional chaotic systems (Lorenz '96, Kuramoto-Sivashinsky) in nonlinear and/non-gaussian situations. The bayesian character of a probability distribution cannot be in general objectively verified, and the weaker property of reliability (statistical consistency between predicted probabilities and observed frequencies of occurrence) is used instead. The general conclusions are, first, that non-gaussianity has no significant impact. Second, that Ens/4D-Var produces reliable and accurate ensembles. These conclusions remain valid for long assimilation periods, either through the use of Quasi-Static Variational Assimilation, in which the length of the assimilation window is progressively increased (in the case of a perfect model), or through weak-constraint assimilation (in the case of an imperfect model). Comparison with EnKF and Particle Filters shows that Ens/4D-Var is at least as good a bayesian estimator, although at a higher cost. The pros and cons of Ens/4D-Var are further discussed.

Jardak, Mohamed; Talagrand, Olivier

2013-04-01

387

Variation in Swedish Address Practices  

ERIC Educational Resources Information Center

This article explores variation in address in contemporary Swedish in Sweden-Swedish and Finland-Swedish. The research is part of a large-scale Australian project on changes in the address systems of French, German and Swedish. The present article focuses on results from 72 social network interviews conducted in Sweden (Gothenburg) and Finland…

Norrby, Catrin

2006-01-01

388

Forecasts of geomagnetic secular variation  

NASA Astrophysics Data System (ADS)

We attempt to forecast the geomagnetic secular variation based on stochastic models, non-parametric regression and singular spectrum analysis of the observed past field changes. Although this modelling approach is meant to be phenomenological, it may provide some insight into the mechanisms underlying typical time scales of geomagnetic field changes. We follow two strategies to forecast secular variation: Firstly, by applying time series models, and secondly, by using time-dependent kinematic models of the advected secular variation. These forecasts can span decades, to longer periods. This depends on the length of the past observations used as input, with different input models leading to different details in the forecasts. These forecasts become more uncertain over longer forecasting periods. One appealing reason is the disregard of magnetic diffusion in the kinematic modelling. But also the interactions of unobservable small scale core field with core flow at all scale unsettle the kinematic forecasting scheme. A further (obvious) reason is that geomagnetic secular variation can not be mimicked by linear time series models as the dynamo action itself is highly non-linear. Whether the dynamo action can be represented by a simple low-dimensional system requires further analysis.

Wardinski, Ingo

2014-05-01

389

Complexes of clusters and complexes of stars  

E-print Network

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

Yu. N. Efremov

2005-12-12

390

Aqueous and solid complexes of iron(III) with hyaluronic acid  

Microsoft Academic Search

The coordination of iron(III) ion to hyaluronic acid (Hyal) in aqueous solutions and solid state was accomplished by potentiometric titrations and infrared spectroscopy. The potentiometric titration studies provided the binding constants for the complexes found in the systems and the speciation of these species according to the variation of pH values. The complexes found presented a complexing ability through both

Ana Lucia Ramalho Mercê; Luiz Carlos Marques Carrera; Lilian Kelly Santos Romanholi; Mar??a Ángeles Lobo Recio

2002-01-01

391

Numerical Forward Modeling of Carbonate Platform Dynamics: An Evaluation of Complexity and Completeness in Carbonate Strata  

Microsoft Academic Search

It is clear that carbonate strata are complex and incom- plete, but the nature and origins of the complexity, and the origin and distribution of hiatuses remain poorly understood. A three-dimensional numerical forward model of carbonate platform systems has been used to investigate how variations in complexity and completeness arise in carbonate strata. The model includes depth-dependent carbonate pro- duction

PETER M. BURGESS; V. PAUL WRIGHT

2003-01-01

392

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

393

Hyper Space Complex Number  

E-print Network

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

Shanguang Tan

2007-04-23

394

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. PMID:22840197

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

2012-01-01

395

Oil Fingerprinting for Production Allocation: Exploiting the Natural Variations in Fluid Properties Encountered in Heavy Oil and Oil Sand Reservoirs  

Microsoft Academic Search

Summary The ability to allocate oil production along horizontal wells or in commingled production of heavy oilfields to reservoir location takes advantage of the natural variation in fluid composition in heavy oilfields that occurs over vertical and lateral reservoir scales. In the Peace River oil sands, variations in physical and chemical properties have developed via the complex interplay between biodegradation,

Barry Bennett; Jennifer J. Adams; Stephen R. Larter

396

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

Microsoft Academic Search

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

Joseph D Busch

2008-01-01

397

Structural genomic variation in ischemic stroke  

PubMed Central

Technological advances in molecular genetics allow rapid and sensitive identification of genomic copy number variants (CNVs). This, in turn, has sparked interest in the function such variation may play in disease. While a role for copy number mutations as a cause of Mendelian disorders is well established, it is unclear whether CNVs may affect risk for common complex disorders. We sought to investigate whether CNVs may modulate risk for ischemic stroke (IS) and to provide a catalog of CNVs in patients with this disorder by analyzing copy number metrics produced as a part of our previous genome-wide single-nucleotide polymorphism (SNP)-based association study of ischemic stroke in a North American white population. We examined CNVs in 263 patients with ischemic stroke (IS). Each identified CNV was compared with changes identified in 275 neurologically normal controls. Our analysis identified 247 CNVs, corresponding to 187 insertions (76%; 135 heterozygous; 25 homozygous duplications or triplications; 2 heterosomic) and 60 deletions (24%; 40 heterozygous deletions;3 homozygous deletions; 14 heterosomic deletions). Most alterations (81%) were the same as, or overlapped with, previously reported CNVs. We report here the first genome-wide analysis of CNVs in IS patients. In summary, our study did not detect any common genomic structural variation unequivocally linked to IS, although we cannot exclude that smaller CNVs or CNVs in genomic regions poorly covered by this methodology may confer risk for IS. The application of genome-wide SNP arrays now facilitates the evaluation of structural changes through the entire genome as part of a genome-wide genetic association study. PMID:18288507

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

2008-01-01

398

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

399

Simplifying complexity: a review of complexity theory  

Microsoft Academic Search

Complexity theory has captured the attention of the scientific community to the extent where its proponents tout it as a dominant scientific trend. Geographers, and environmental, human, and regional planners have applied complexity theory to topics ranging from cultural transmission and economic growth to the braiding of rivers. While such a wide array of applications is heartening because it speaks

Steven M. Manson

2001-01-01

400

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

401

Temporal variation of heat and moisture flux divergence in the FIFE atmospheric boundary layer during spring  

NASA Technical Reports Server (NTRS)

A one-day investigation of the atmospheric boundary layer (ABL) is reported in which an aircraft monitors the temporal and spatial variations of heat and moisture turbulent-flux divergences. Incoming solar radiation is similar over natural prairie land and agriculturally developed land although the heat and moisture values show significant differences over the surfaces. Other temporal variations are noted which demonstrate that ABL transport of sensible and latent heat is affected by complex variables even under simple synoptic conditions.

Grossman, Robert L.

1990-01-01

402

Respiratory variation and cardiopulmonary interactions.  

PubMed

It is often unclear whether or not a patient's stroke volume will increase following a fluid bolus. Volume responsiveness is defined by an increase in stroke volume following a fluid bolus. For patients being mechanically ventilated, the cardiopulmonary interactions associated with positive pressure ventilation create pulse pressure and stroke volume variation in the arterial pressure waveform that can be used to assess fluid responsiveness, so-called dynamic preload assessment. However, lung-protective ventilation is increasingly being used to avoid the adverse outcomes of higher tidal volume ventilation, and pulse pressure and stroke volume variation do not effectively predict volume responsiveness in the setting of lung-protective ventilation without using special techniques. Dynamic preload assessment is more effective at determining whether a patient will be fluid responsive than static measures of preload, but further studies are needed to more conclusively show that outcomes are improved with this approach to fluid management. PMID:25480770

Roberson, Russell S

2014-12-01

403

DIMENSIONAL VARIATION IN MIM COMPONENTS  

E-print Network

The aim of the present work was to evaluate process parameters influencing the dimensional variation of AISI 316L MIM components during manufacturing. 3D Finite Element (FE) models were used to reproduce thermal and mechanical stress/strain fields during molding of MIM components. In addition, experimental plans were used to reinforce outcomes of numerical simulations. The developed models predicted the thermal history of the injection molding process phase and temperature distributions for any position in the component. This research confirmed that FE simulations were an efficient method to assess the influence of process parameter variation on component manufacturability, suggesting adjustments to improve its quality. The use of the FE models allowed the process efficiency to be improved, as well as MIM component quality.

Donald F. Heaney; Roberto Spina; Donald F. Heaney; Roberto Spina

404

Variational method with staggered fermions  

E-print Network

The variational method is used widely for determining eigenstates of the QCD hamiltonian for actions with a conventional transfer matrix, e.g., actions with improved Wilson fermions. An alternative lattice fermion formalism, staggered fermions, does not have a conventional single-time-step transfer matrix. Nonetheless, with a simple modification, the variational method can also be applied to that formalism. In some cases the method also provides a mechanism for separating the commonly paired parity-partner states. We discuss the extension to staggered fermions and illustrate it by applying it to the calculation of the spectrum of charmed-antistrange mesons consisting of a clover charm quark and a staggered strange antiquark.

Carleton DeTar; Song-Haeng Lee

2014-11-17

405

A variational principle in optics.  

PubMed

We derive a new variational principle in optics. We first formulate the principle for paraxial waves and then generalize it to arbitrary waves. The new principle, unlike the Fermat principle, concerns both the phase and the intensity of the wave. In particular, the principle provides a method for finding the ray mapping between two surfaces in space from information on the wave's intensity there. We show how to apply the new principle to the problem of phase reconstruction from intensity measurements. PMID:15535374

Rubinstein, Jacob; Wolansky, Gershon

2004-11-01

406

Communication variations and aircrew performance  

NASA Technical Reports Server (NTRS)

Crew-related communication variations and their effects on performance are examined. The communication analysis involves evaluating the performance of 18 pilots to a high-fidelity full-mission simulation. Initiating speech consists of four categories: commands, questions, observations, and dysfluencies. Response speech is coded as: reply, acknowledgements, and zero response. A standard form of communication has been adopted which should aid in the coordination process and enhance crew performance.

Kanki, Barbara G.; Greaud, Valerie A.; Irwin, Cheryl M.

1989-01-01

407

Variational approach to image segmentation  

NASA Astrophysics Data System (ADS)

This paper deals with a class of variational problems rising from image segmentation. After introducing the mathematical model of this question, we analysis it's rationality in details. At the same time, two numerical methods will be proposed to solve it. Furthermore, the equivalence of these two equations will be proved briefly. At last, we shall apply this result to approximate a minimum problem that was introduced by D.Mumford and J.Shah to Study image Segmentation.

Tian, Yan; Xu, Hongbo; Liu, Jianguo

2001-09-01

408

Variational Integrators in Plasma Physics  

E-print Network

Variational integrators are a special kind of geometric discretisation methods applicable to any system of differential equations that obeys a Lagrangian formulation. In this thesis, variational integrators are developed for several important models of plasma physics: guiding centre dynamics (particle dynamics), the Vlasov-Poisson system (kinetic theory), and ideal magnetohydrodynamics (plasma fluid theory). Special attention is given to physical conservation laws like conservation of energy and momentum. Most systems in plasma physics do not possess a Lagrangian formulation to which the variational integrator methodology is directly applicable. Therefore the theory is extended towards nonvariational differential equations by linking it to Ibragimov's theory of integrating factors and adjoint equations. It allows us to find a Lagrangian for all ordinary and partial differential equations and systems thereof. Consequently, the applicability of variational integrators is extended to a much larger family of systems than envisaged in the original theory. This approach allows for the application of Noether's theorem to analyse the conservation properties of the system, both at the continuous and the discrete level. In numerical examples, the conservation properties of the derived schemes are analysed. In case of guiding centre dynamics, momentum in the toroidal direction of a tokamak is preserved exactly. The particle energy exhibits an error, but the absolute value of this error stays constant during the entire simulation. Therefore numerical dissipation is absent. In case of the kinetic theory, the total number of particles, total linear momentum and total energy are preserved exactly, i.e., up to machine accuracy. In case of magnetohydrodynamics, the total energy, cross helicity and the divergence of the magnetic field are preserved up to machine precision.

Michael Kraus

2014-12-05

409

Cyanobacterial NADPH dehydrogenase complexes  

SciTech Connect

Cyanobacteria possess functionally distinct multiple NADPH dehydrogenase (NDH-1) complexes that are essential to CO2 uptake, photosystem-1 cyclic electron transport and respiration. The unique nature of cyanobacterial NDH-1 complexes is the presence of subunits involved in CO2 uptake. Other than CO2 uptake, chloroplastic NDH-1 complex has similar role as cyanobacterial NDH-1 complexes in photosystem-1 cyclic electron transport and respiration (chlororespiration). In this mini-review we focus on the structure and function of cyanobacterial NDH-1 complexes and their phylogeny. The function of chloroplastic NDH-1 complex and characteristics of plants defective in NDH-1 are also described forcomparison.

Ogawa, Teruo; Mi, Hualing

2007-07-01

410

Variational principles for circle patterns  

NASA Astrophysics Data System (ADS)

A Delaunay cell decomposition of a surface with constant curvature gives rise to a circle pattern, consisting of the circles which are circumscribed to the facets. We treat the problem whether there exists a Delaunay cell decomposition for a given (topological) cell decomposition and given intersection angles of the circles, whether it is unique and how it may be constructed. Somewhat more generally, we allow cone-like singularities in the centers and intersection points of the circles. We prove existence and uniqueness theorems for the solution of the circle pattern problem using a variational principle. The functionals (one for the euclidean, one for the hyperbolic case) are convex functions of the radii of the circles. The analogous functional for the spherical case is not convex, hence this case is treated by stereographic projection to the plane. From the existence and uniqueness of circle patterns in the sphere, we derive a strengthened version of Steinitz' theorem on the geometric realizability of abstract polyhedra. We derive the variational principles of Colin de Verdière, Brägger, and Rivin for circle packings and circle patterns from our variational principles. In the case of Brägger's and Rivin's functionals. Leibon's functional for hyperbolic circle patterns cannot be derived directly from our functionals. But we construct yet another functional from which both Leibon's and our functionals can be derived. We present Java software to compute and visualize circle patterns.

Springborn, Boris A.

2003-12-01

411

Copy number variation and mutation  

NASA Astrophysics Data System (ADS)

Until very recently, the standard model of DNA included two genes for each trait. This dated model has given way to a model that includes copies of some genes well in excess of the canonical two. Copy number variations in the human genome play critical roles in causing or aggravating a number of syndromes and diseases while providing increased resistance to others. We explore the role of mutation, crossover, inversion, and reproduction in determining copy number variations in a numerical simulation of a population. The numerical model consists of a population of individuals, where each individual is represented by a single strand of DNA with the same number of genes. Each gene is initially assigned to one of two traits. Fitness of the individual is determined by the two most fit genes for trait one, and trait two genetic material is treated as a reservoir of junk DNA. After a sufficient number of generations, during which the genetic distribution is allowed to reach a steady-state, the mean numberof genes per trait and the copy number variation are recorded. Here, we focus on the role of mutation and compare simulation results to theory.

Clark, Brian; Weidner, Jacob; Wabick, Kevin

2009-11-01

412

Longitudinal Variations in Jupiter's Winds  

NASA Technical Reports Server (NTRS)

Long-term studies of Jupiter's zonal wind field revealed temporal variations on the order of 20 to 40 m/s at many latitudes, greater than the typical data uncertainties of 1 to 10 m/s. No definitive periodicities were evident, however, though some latitudinally-confined signals did appear at periods relevant to the Quasi- Quadrennial Oscillation (Simon-Miller & Gierasch, Icarus, in press). As the QQO appears, from vertical temperature profiles, to propagate downward, it is unclear why a signal is not more obvious, unless other processes dominate over possibly weaker forcing from the QQO. An additional complication is that zonal wind profiles represent an average over some particular set of longitudes for an image pair and most data sets do not offer global wind coverage. Lien avoiding known features, such as the large anticyclonic vortices especially prevalent in the south, there can be distinct variations in longitude. We present results on the full wind field from Voyager and Cassini data, showing apparent longitudinal variations of up to 60 m/s or more. These are particularly obvious near disruptions such as the South Equatorial Disturbance, even when the feature itself is not clearly visible. These two dates represent very different states of the planet for comparison: Voyagers 1 & 2 flew by Jupiter shortly after a global upheaval, while many regions were in a disturbed state, while the Cassini view is typical of a more quiescent period present during much of the 1990s and early 2000s.

Simon-Miller, Amy A.; Gierasch, P. J.; Tierney, G.

2010-01-01

413

The plume variation at Enceladus  

NASA Astrophysics Data System (ADS)

It has been nine years since the discovery of the Enceladus plume, while its variation within this time is still under debate. A recent study has proposed that the vent intensity depends on the moon-Saturn distance. In our study we use a different data set to investigate this variation, and also check its co-relationship with other orbital characters. Between 2005 and 2012, Cassini has made 20 close flybys around Enceladus. Its plasma instrument has recorded the ambient magnetospheric plasma density, while its magnetometers have recorded the change in magnetic field by particle pickup. Unlike particle detectors that measure the in situ density along the path, or imagers that measure the vent temperature, the magnetometer measures the magnetic field, which provides the total momentum exchange in the whole interaction region. We use the magnetometer data and ambient plasma data along these 20 flybys, assisted with our MHD model, to determine the time variation of the total plume ejecta during these 8 years.

Jia, Ying-Dong; Russell, Christopher; Khurana, Krishan

2014-05-01

414

Synthesis, Physicochemical Properties, and Antimicrobial Studies of Iron (III) Complexes of Ciprofloxacin, Cloxacillin, and Amoxicillin  

PubMed Central

Iron (III) complexes of ciprofloxacin, amoxicillin, and cloxacillin were synthesized and their aqueous solubility profiles, relative stabilities, and antimicrobial properties were evaluated. The complexes showed improved aqueous solubility when compared to the corresponding ligands. Relative thermal and acid stabilities were determined spectrophotometrically and the results showed that the complexes have enhanced thermal and acid stabilities when compared to the pure ligands. Antimicrobial studies showed that the complexes have decreased activities against most of the tested microorganisms. Ciprofloxacin complex, however, showed almost the same activity as the corresponding ligand. Job's method of continuous variation suggested 1?:?2 metals to ligand stoichiometry for ciprofloxacin complex but 1?:?1 for cloxacillin complex. PMID:25505991

Ajali, Uzoechi; Ukoha, Pius O.

2014-01-01

415

Tomography studies of volcanic complexes  

NASA Astrophysics Data System (ADS)

We present an overview of recent results of seismic tomography studies of different volcanic complexes performed in collaboration with different research teams. In first three examples corresponding to Central Andes, areas around Merapi volcano and Toba caldera, the tomographic images down to 100-200 km depth reveal the paths of fluids and melts which escape from the subducting plate and feed the arc volcanoes. In all these areas, the shapes of the paths are different depending on particular features of the subduction regimes, such as type of the overriding plate, age of the slab, rate of the subduction etc. Next group of studies covers detailed tomographic studies of local structures beneath selected volcanoes. Beneath the Spurr Volcano (Alaska) we clearly observe a thin vertical channel with anomalously high Vp/Vs ratio beneath the main cone. Beneath the volcanoes of Kluchevskoy group (Kamchatka) seismic images reveal complex structure of channels and intermediate magma reservoirs. In the mantle we detect an anomaly with very high Vp/Vs ratio reaching 2.2, which looks as a top of the mantle channel feeding the volcanoes of the group. For this group we observed the time variations of seismic structure based on more than 10 years of continuous data. We detect considerable variations in Vp/Vs ratio in the crust related to large eruptions of Kluchevskoy and Bezymyanny volcanoes in 2005. The last example is another time-lapse tomography model obtained for the El Hierro volcano in Canaries based on earthquake swarm occurred from July to October 2011. During this period we observe regular deepening of a large body with high Vp/Vs ratio, which is interpreted as a magma reservoir, together with lowering of seismicity.

Koulakov, I.; Gordeev, E. I.; West, M.; Yeguas, A. G.; Luehr, B.-G.; Jakovlev, A.

2012-04-01

416

Genetics of Complex Traits in Psychiatry.  

PubMed

Virtually all psychiatric traits are genetically complex. This article discusses the genetics of complex traits in psychiatry. The complexity is accounted for by numerous factors, including multiple risk alleles, epistasis, and epigenetic effects such as methylation. Risk alleles can individually be common or rare, and can include, for example, single nucleotide polymorphisms and copy number variants that are transmitted or are new mutations, and other kinds of variation. Many different kinds of variation can be important for trait risk, either together in various proportions or as different factors in different subjects. Until more recently, approaches to complex traits were limited, and consequently only a few variants, usually of individually minor effect, were identified. At the present time, a much richer armamentarium exists that includes the routine application of genome-wide association studies and next-generation high-throughput sequencing and the combination of this information with other biologically relevant information, such as expression data. We have also seen the emergence of large meta-analysis and mega-analysis consortia. These developments are extremely important for psychiatric genetics, have advanced the field substantially, and promise formidable gains in the years to come as they are applied more widely. PMID:25444161

Gelernter, Joel

2015-01-01

417

Complex Elliptic Pendulum  

E-print Network

This paper briefly summarizes previous work on complex classical mechanics and its relation to quantum mechanics. It then introduces a previously unstudied area of research involving the complex particle trajectories associated with elliptic potentials.

Carl M. Bender; Daniel W. Hook; Karta Kooner

2009-12-31

418

Oligocyclopentadienyl transition metal complexes  

SciTech Connect

Synthesis, characterization, and reactivity studies of oligocyclopentadienyl transition metal complexes, namely those of fulvalene, tercyclopentadienyl, quatercyclopentadienyl, and pentacyclopentadienyl(cyclopentadienyl) are the subject of this account. Thermal-, photo-, and redox chemistries of homo- and heteropolynuclear complexes are described.

de Azevedo, Cristina G.; Vollhardt, K. Peter C.

2002-01-18

419

Daunorubicin Lipid Complex Injection  

MedlinePLUS

Daunorubicin lipid complex is used to treat advanced Kaposi's sarcoma (a type of cancer that causes abnormal tissue to ... body) related to acquired immunodeficiency syndrome (AIDS). Daunorubicin lipid complex is in a class of medications called ...

420

Vincristine Lipid Complex Injection  

MedlinePLUS

Vincristine lipid complex is used to treat a certain type of acute lymphoblastic leukemia (ALL; a type of cancer ... least two different treatments with other medications. Vincristine lipid complex is in a class of medications called ...

421

Doxorubicin Lipid Complex Injection  

MedlinePLUS

Doxorubicin lipid complex is used to treat ovarian cancer that has not improved or that has worsened after treatment with other medications. Doxorubicin lipid complex is also used to treat Kaposi's sarcoma ( ...

422

Quantum Complex Minkowski Space  

E-print Network

The complex Minkowski phase space has the physical interpretation of the phase space of the scalar massive conformal particle. The aim of the paper is the construction and investigation of the quantum complex Minkowski space.

Grzegorz Jakimowicz; Anatol Odzijewicz

2005-05-06

423

GEMINI: integrative exploration of genetic variation and genome annotations.  

PubMed

Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical genetics. We have developed GEMINI (GEnome MINIng), a flexible software package for exploring all forms of human genetic variation. Unlike existing tools, GEMINI integrates genetic variation with a diverse and adaptable set of genome annotations (e.g., dbSNP, ENCODE, UCSC, ClinVar, KEGG) into a unified database to facilitate interpretation and data exploration. Whereas other methods provide an inflexible set of variant filters or prioritization methods, GEMINI allows researchers to compose complex queries based on sample genotypes, inheritance patterns, and both pre-installed and custom genome annotations. GEMINI also provides methods for ad hoc queries and data exploration, a simple programming interface for custom analyses that leverage the underlying database, and both command line and graphical tools for common analyses. We demonstrate GEMINI's utility for exploring variation in personal genomes and family based genetic studies, and illustrate its ability to scale to studies involving thousands of human samples. GEMINI is designed for reproducibility and flexibility and our goal is to provide researchers with a standard framework for medical genomics. PMID:23874191

Paila, Umadevi; Chapman, Brad A; Kirchner, Rory; Quinlan, Aaron R

2013-01-01

424

First evidence for heritable variation in cooperative breeding behaviour.  

PubMed

Understanding the evolution of complex social behaviours, such as cooperative breeding, is a fundamental problem in evolutionary biology, which has attracted much theoretical and empirical interest. Variation within and between species in the frequency of helping behaviour has been typically associated with variation in direct costs and benefits due to ecological constraints, or with indirect fitness payoffs (i.e. kin selection). Here, we provide the first evidence that individual variation in cooperative behaviour within a natural population also has a heritable component. Using a seven-generation pedigree in a wild population of western bluebirds (Sialia mexicana), we show significant heritable variation for the propensity to help rather than breed, as well as for the probability of having a helper at the nest. We also document a strong positive relationship between a bird's lifespan and its prospect of receiving help when breeding, in accordance with earlier comparative studies across species. These findings provide useful insights into the possible mechanisms which have led to the evolution of cooperative breeding and other social systems. PMID:17490945

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

2007-07-22

425

Genetically-Based Olfactory Signatures Persist Despite Dietary Variation  

PubMed Central

Individual mice have a unique odor, or odortype, that facilitates individual recognition. Odortypes, like other phenotypes, can be influenced by genetic and environmental variation. The genetic influence derives in part from genes of the major histocompatibility complex (MHC). A major environmental influence is diet, which could obscure the genetic contribution to odortype. Because odortype stability is a prerequisite for individual recognition under normal behavioral conditions, we investigated whether MHC-determined urinary odortypes of inbred mice can be identified in the face of large diet-induced variation. Mice trained to discriminate urines from panels of mice that differed both in diet and MHC type found the diet odor more salient in generalization trials. Nevertheless, when mice were trained to discriminate mice with only MHC differences (but on the same diet), they recognized the MHC difference when tested with urines from mice on a different diet. This indicates that MHC odor profiles remain despite large dietary variation. Chemical analyses of urinary volatile organic compounds (VOCs) extracted by solid phase microextraction (SPME) and analyzed by gas chromatography/mass spectrometry (GC/MS) are consistent with this inference. Although diet influenced VOC variation more than MHC, with algorithmic training (supervised classification) MHC types could be accurately discriminated across different diets. Thus, although there are clear diet effects on urinary volatile profiles, they do not obscure MHC effects. PMID:18974891

Kwak, Jae; Willse, Alan; Matsumura, Koichi; Curran Opiekun, Maryanne; Yi, Weiguang; Preti, George; Yamazaki, Kunio; Beauchamp, Gary K.

2008-01-01

426

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations  

PubMed Central

Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical genetics. We have developed GEMINI (GEnome MINIng), a flexible software package for exploring all forms of human genetic variation. Unlike existing tools, GEMINI integrates genetic variation with a diverse and adaptable set of genome annotations (e.g., dbSNP, ENCODE, UCSC, ClinVar, KEGG) into a unified database to facilitate interpretation and data exploration. Whereas other methods provide an inflexible set of variant filters or prioritization methods, GEMINI allows researchers to compose complex queries based on sample genotypes, inheritance patterns, and both pre-installed and custom genome annotations. GEMINI also provides methods for ad hoc queries and data exploration, a simple programming interface for custom analyses that leverage the underlying database, and both command line and graphical tools for common analyses. We demonstrate GEMINI's utility for exploring variation in personal genomes and family based genetic studies, and illustrate its ability to scale to studies involving thousands of human samples. GEMINI is designed for reproducibility and flexibility and our goal is to provide researchers with a standard framework for medical genomics. PMID:23874191

Paila, Umadevi; Chapman, Brad A.; Kirchner, Rory; Quinlan, Aaron R.

2013-01-01

427

Variation in trajectories of women's marital quality.  

PubMed

I examine variation in trajectories of women's marital quality across the life course. The analysis improves upon earlier research in three ways: (1) the analysis uses a sequential cohort design and data from the first 35years of marriage; (2) I analyze rich data from a national sample; (3) I examine multiple dimensions of marital quality. Latent class growth analyses estimated on data from women in the National Longitudinal Survey of Youth-1979 (N=2604) suggest multiple trajectories for each of three dimensions of marital quality, including two trajectories of marital happiness, two trajectories of marital communication, and three trajectories of marital conflict. Socioeconomic and demographic covariates are then used to illustrate how factors such as income, cohabitation, and race-ethnicity set individuals at risk of poor marital quality throughout the life course by differentiating between high and low trajectories of marital quality. Women on low marital quality trajectories are, as expected, at much greater risk of divorce. Taken together, these findings show how fundamental socioeconomic and demographic characteristics contribute to subsequent marital outcomes via their influence on trajectories of marital quality as well as providing a better picture of the complexity in contemporary patterns of marital quality. PMID:25432600

James, Spencer L

2015-01-01

428

GENETIC VARIATION IN BABOON CRANIOFACIAL SEXUAL DIMORPHISM  

PubMed Central

Sexual dimorphism is a widespread phenomenon and contributes greatly to intraspecies variation. Despite a long history of active research, the genetic basis of dimorphism for complex traits remains unknown. Understanding the sex-specific differences in genetic architecture for cranial traits in a highly dimorphic species could identify possible mechanisms through which selection acts to produce dimorphism. Using distances calculated from three-dimensional landmark data from CT scans of 402 baboon skulls from a known genealogy, we estimated genetic variance parameters in both sexes to determine the presence of gene-by-sex (G × S) interactions and X-linked heritability. We hypothesize that traits exhibiting the greatest degree of sexual dimorphism (facial traits in baboons) will demonstrate either stronger G × S interactions or X-linked effects. We found G × S interactions and X-linked effects for a few measures that span the areas connecting the face to the neurocranium but for no traits restricted to the face. This finding suggests that facial traits will have a limited response to selection for further evolution of dimorphism in this population. We discuss the implications of our results with respect to the origins of cranial sexual dimorphism in this baboon sample, and how the genetic architecture of these traits affects their potential for future evolution. PMID:19210535

Willmore, Katherine E.; Roseman, Charles C.; Rogers, Jeffrey; Richtsmeier, Joan T.; Cheverud, James M.

2010-01-01

429

Complexity, creativity and computers  

Microsoft Academic Search

Creativity, one of the hallmarks of the human spirit, has yet to travel deep into the domain of artificial intelligence and computers. We argue that creativity intrinsically requires and exploits complexity. The dynamic multilevel properties of complex systems give us a natural way of scaling creative solutions, from the everyday to the paradigm shift. In particular, the complexity model implies

T. R. J. Bossomaier; A. W. Snyder

430

Identification of structural variation in mouse genomes  

PubMed Central

Structural variation is variation in structure of DNA regions affecting DNA sequence length and/or orientation. It generally includes deletions, insertions, copy-number gains, inversions, and transposable elements. Traditionally, the identification of structural variation in genomes has been challenging. However, with the recent advances in high-throughput DNA sequencing and paired-end mapping (PEM) methods, the ability to identify structural variation and their respective association to human diseases has improved considerably. In this review, we describe our current knowledge of structural variation in the mouse, one of the prime model systems for studying human diseases and mammalian biology. We further present the evolutionary implications of structural variation on transposable elements. We conclude with future directions on the study of structural variation in mouse genomes that will increase our understanding of molecular architecture and functional consequences of structural variation. PMID:25071822

Keane, Thomas M.; Wong, Kim; Adams, David J.; Flint, Jonathan; Reymond, Alexandre; Yalcin, Binnaz

2014-01-01

431

An implicit method for mixed variational inequalities  

Microsoft Academic Search

In this paper, we suggest and analyze a new implicit method for solving mixed monotone variational inequalities. This method can be viewed as an extension of He's method [1] for solving monotone variational inequalities.

M. A. Noor

1998-01-01

432

Geochemistry and petrogenesis of the Laramie anorthosite complex, Wyoming  

USGS Publications Warehouse

A geochemical investigation of the Laramie anorthosite complex determined that monsonite associated with the complex are characterized by positive Eu anomalies and display a regular variation in composition with distance from the monzonite/county rock contact. Anorthositic rocks have major and trace element abundance typical of similar complexes. The internal variations in the m