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1

Elise C. Kohn, MD  

Cancer.gov

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

2

A Rigorous Extension of the Kohn-Sham Equation for Strongly Correlated Electron Systems  

Microsoft Academic Search

By introducing a set of auxiliary equations representing a many-body system, we have derived an extension of the Kohn-Sham scheme for the density functional theory. These equations consist of a Kohn-Sham-type equation determining single-particle orbitals and an eigen-value equation for an effective many-body problem. A variational method similar to the Kohn-Sham technique was utilized to derive effective interactions as well

Koichi Kusakabe

2001-01-01

3

Variational Multiscale Modeling of Biomolecular Complexes , Xin Feng2  

E-print Network

Variational Multiscale Modeling of Biomolecular Complexes Kelin Xia1 , Xin Feng2 , Yiying Tong2 and Molecular Biology, Michigan State University, MI 48824, USA Introduction Multiscale modeling is of paramount discuss our variational multiscale models and associated geometric modeling of biomolecular complexes

4

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

5

Chromosome Variation in the Heleocharis palustris-uniglumis Complex  

Microsoft Academic Search

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

Lise H. Saunte

1958-01-01

6

Are Kohn-Sham conductances accurate?  

PubMed

We use Fermi-liquid relations to address the accuracy of conductances calculated from the single-particle states of exact Kohn-Sham (KS) density functional theory. We demonstrate a systematic failure of this procedure for the calculation of the conductance, and show how it originates from the lack of renormalization in the KS spectral function. In certain limits this failure can lead to a large overestimation of the true conductance. We also show, however, that the KS conductances can be accurate for single-channel molecular junctions and systems where direct Coulomb interactions are strongly dominant. PMID:21231333

Mera, H; Niquet, Y M

2010-11-19

7

Human genetic variation and its contribution to complex traits  

Microsoft Academic Search

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

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

2009-01-01

8

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

9

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, Agnes; Albuisson, Juliette; Heredia, Fabiana; Audigier, Pascal; Bouchez, David; Dillmann, Christine; Guerche, Philippe; Hospital, Frederic; Colot, Vincent

2009-01-01

10

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

11

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

12

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

PubMed Central

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

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

2014-01-01

13

Kohn-Sham potentials for fullerenes and spherical molecules  

SciTech Connect

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

Pavlyukh, Y.; Berakdar, J. [Institut fuer Physik, Martin-Luther-Universitaet Halle-Wittenberg, Heinrich-Damerow-Strasse 4, D-06120 Halle (Germany)

2010-04-15

14

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

15

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

16

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

17

Magnetism and homogenization of micro-resonators Robert V. Kohn  

E-print Network

the same scattering data as the micro-structured composite. Keywords: homogenization; meta-material; micro of the individual components of the micro-structured composite material, D = E, B = µH, (1) give rise to bulkMagnetism and homogenization of micro-resonators Robert V. Kohn Courant Institute Stephen P

18

Major histocompatibility complex class II sequence variation in cetaceans: DQ? and DR? variation in beluga (Delphinapterus leucas) and DQ? variation in North Atlantic right whales (Eubalaena glacialis)  

Microsoft Academic Search

Allelic variation at the Major Histocompatibility Complex (Mhc) class II loci DQ? and DR? was assessed in a large sample (~300) of beluga (Delphinapterus leucas) and a sample (~12) of narwhal (Monodon monoceros) in order to study the evolutionary significance of the Mhc in cetaceans and to compare levels of variation among beluga populations. Mhc class II DQ? allelic variation

Brent William Murray

1997-01-01

19

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

SciTech Connect

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

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

1991-12-31

20

Exact Kohn-Sham potential of strongly correlated finite systems.  

PubMed

The dissociation of molecules, even the most simple hydrogen molecule, cannot be described accurately within density functional theory because none of the currently available functionals accounts for strong on-site correlation. This problem led to a discussion of properties that the local Kohn-Sham potential has to satisfy in order to correctly describe strongly correlated systems. We derive an analytic expression for the nontrivial form of the Kohn-Sham potential in between the two fragments for the dissociation of a single bond. We show that the numerical calculations for a one-dimensional two-electron model system indeed approach and reach this limit. It is shown that the functional form of the potential is universal, i.e., independent of the details of the two fragments. PMID:20001022

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

2009-12-14

21

Exact Kohn-Sham potential of strongly correlated finite systems  

SciTech Connect

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

Helbig, N. [Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Dpto. Fisica de Materiales, Universidad del Pais Vasco, Centro de Fisica de Materiales CSIC-UPV/EHU-MPC and DIPC, Av. Tolosa 72, San Sebastian E-20018 (Spain); Tokatly, I. V. [Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Dpto. Fisica de Materiales, Universidad del Pais Vasco, Centro de Fisica de Materiales CSIC-UPV/EHU-MPC and DIPC, Av. Tolosa 72, San Sebastian E-20018 (Spain); IKERBASQUE, Basque Foundation for Science, Bilbao E-48011 (Spain); Rubio, A. [Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Dpto. Fisica de Materiales, Universidad del Pais Vasco, Centro de Fisica de Materiales CSIC-UPV/EHU-MPC and DIPC, Av. Tolosa 72, San Sebastian E-20018 (Spain); Fritz-Haber-Institut, Max-Planck-Gesellschaft, Berlin D-14195 (Germany)

2009-12-14

22

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

23

Complex biogeographical distribution of genetic variation within Podarcis wall lizards across the  

E-print Network

Complex biogeographical distribution of genetic variation within Podarcis wall lizards across To examine the effect of a known geological barrier on genetic variation within a wall lizard species complex. Location The Iberian Peninsula and North Africa. Methods Sequencing of partial 12S rRNA and cytochrome b mtDNA

Carranza, Salvador

24

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

25

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

26

Kohn-Sham calculations with the exact functional  

E-print Network

As a proof of principle, self-consistent Kohn-Sham calculations are performed with the exact exchange-correlation functional. The systems calculated are one-dimensional real-space interacting fermions with more than two electrons. To find the exact functional for trial densities requires solving the interacting Schroedinger equation multiple times, a much more demanding task than direct solution of the Schr\\"odinger equation. The density matrix renormalization group method makes this possible. We illustrate and explore the convergence properties of the exact KS scheme for both weakly and strongly correlated systems. We also explore the spin-dependent generalization and densities for which the functional is ill defined.

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

2014-01-01

27

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

28

Towards a Kohn-Sham potential via the optimized effective-potential method  

NASA Astrophysics Data System (ADS)

The optimized effective-potential (OEP) method is applied to a self-interaction-corrected local-spin-density (SIC-LSD) energy functional. The local potential which results has the useful properties of being both self-interaction free and orbital independent, and it can thus be regarded as a good approximation to the exact Kohn-Sham potential. A number of atomic systems are examined in the exchange-only and in the Ceperley-Alder exchange-correlation approximations. The resulting total energies are very close to those obtained by previous applications of the LSD-SIC functional. The resultant potentials are structurally similar to those derived by applying the OEP method to a Hartree-Fock Hamiltonian: showing much improved behavior over the local-spin-density approximation in both large- and small-r regions as well as the characteristic intershell cusplike structure. The eigenvalues have less formal significance than the more standard approaches, especially those for unoccupied orbitals which seem to have no significance whatsoever. Nonetheless, the highest occupied eigenvalue agrees closely with the conventional LSD-SIC value. However, for the deeper levels, each eigenvalue lies higher than the comparable eigenvalue of the conventional SIC, although lower than the eigenvalue of the LSD potential-the deeper the level, the larger the difference. This property follows from the nonvariational character of the eigenvalues, and it is shown that one can obtain realistic excitation spectra from this formalism by utilizing the appropriate variational quantity. The results obtained illustrate some of the less understood issues in the application of the Kohn-Sham procedure within density-functional theory. Based on observations made here using atomic calculations, we can offer a plausible explanation of the underestimation by LSD calculations of the experimental band gaps in insulators.

Norman, M. R.; Koelling, D. D.

1984-11-01

29

Complex Variation in Measures of General Intelligence and Cognitive Change  

PubMed Central

Combining information from multiple SNPs may capture a greater amount of genetic variation than from the sum of individual SNP effects and help identifying missing heritability. Regions may capture variation from multiple common variants of small effect, multiple rare variants or a combination of both. We describe regional heritability mapping of human cognition. Measures of crystallised (gc) and fluid intelligence (gf) in late adulthood (64–79 years) were available for 1806 individuals genotyped for 549,692 autosomal single nucleotide polymorphisms (SNPs). The same individuals were tested at age 11, enabling us the rare opportunity to measure cognitive change across most of their lifespan. 547,750 SNPs ranked by position are divided into 10, 908 overlapping regions of 101 SNPs to estimate the genetic variance each region explains, an approach that resembles classical linkage methods. We also estimate the genetic variation explained by individual autosomes and by SNPs within genes. Empirical significance thresholds are estimated separately for each trait from whole genome scans of 500 permutated data sets. The 5% significance threshold for the likelihood ratio test of a single region ranged from 17–17.5 for the three traits. This is the equivalent to nominal significance under the expectation of a chi-squared distribution (between 1df and 0) of P<1.44×10?5. These thresholds indicate that the distribution of the likelihood ratio test from this type of variance component analysis should be estimated empirically. Furthermore, we show that estimates of variation explained by these regions can be grossly overestimated. After applying permutation thresholds, a region for gf on chromosome 5 spanning the PRRC1 gene is significant at a genome-wide 10% empirical threshold. Analysis of gene methylation on the temporal cortex provides support for the association of PRRC1 and fluid intelligence (P?=?0.004), and provides a prime candidate gene for high throughput sequencing of these uniquely informative cohorts. PMID:24349040

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

2013-01-01

30

Variations in recollection: The effects of complexity on source recognition  

PubMed Central

Whether recollection is a threshold or signal detection process is highly controversial. U-shaped zROCs observed in tests thought to rely heavily on recollection, such as source memory tests, have provided evidence in favor of the threshold assumption, but zROCs are not always as U-shaped as threshold theory predicts. Source zROCs have been shown to become more linear when the contribution of familiarity to source discriminations is increased, and this may account for the existing results. However, another way in which source zROCs may become more linear is if recollection can become more graded under certain conditions. We tested the ‘graded recollection’ account in the current study. We found that increasing stimulus complexity (i.e., changing from single words to sentences), or increasing source complexity (i.e., changing the sources from audio to videos of speakers), resulted in flatter source zROCs. In addition, conditions expected to reduce recollection (i.e., divided attention and amnesia) had comparable effects on source memory in simple and complex conditions, suggesting that differences between simple and complex conditions were due to differences in the nature of recollection, rather than differences in the utility of familiarity. The results suggest that under conditions of high complexity recollection can appear more graded and it can produce curved ROCs. The results have implications for measurement models and for current theories of recognition memory. PMID:21417513

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

2011-01-01

31

Compositional variations in monomeric trimethylsilylated allyl lanthanide complexes  

Microsoft Academic Search

Treatment of three equivalents of the potassium salt of the bis(1,3-trimethylsilyl)allyl anion with various late lanthanide triflates (M=Dy, Ho, Er, Tm, Lu) produces the unsolvated triallyllanthanide complexes LnA3? (A?=1,3-(SiMe3)2C3H3). The use of lanthanide halides (Cl, I) with the potassium allyl also generates neutral complexes, but when lanthanide iodides and the corresponding lithium allyl are combined, the lanthanate species Li(thf)4[LnA3?I] are

Rosemary E. White; Timothy P. Hanusa; Benjamin E. Kucera

2007-01-01

32

Stock Identification of Fraser River Sockeye Salmon Using Microsatellites and Major Histocompatibility Complex Variation  

Microsoft Academic Search

The utility of DNA-based variation for stock identification was evaluated for Fraser River sockeye salmon Oncorhynchus nerka. For this evaluation, the variation at 14 microsatellite loci and one major histocompatibility complex (MHC) locus was determined from approximately 13,000 fish from 47 populations in the drainage. Genetic differentiation among the populations was observed, the overall FST value for the 14 microsatellite

Terry D. Beacham; Michael Lapointe; John R. Candy; Brenda McIntosh; Cathy MacConnachie; Amy Tabata; Karia Kaukinen; Langtuo Deng; Kristina M. Miller; Ruth E. Withler

2004-01-01

33

Genetic Variants Associated with Complex Human Diseases Show Wide Variation across Multiple Populations  

Microsoft Academic Search

Background: The wide use of genome wide association studies (GWAS) has led to the successful identification of multiple genetic susceptibility variants to several complex human diseases. Given the limited amount of data on genetic variation at these loci in populations of non-European origin, we investigated population variation among 11 population groups for loci showing strong and consistent association from GWAS

A. Adeyemo; C. Rotimi

2010-01-01

34

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

35

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

36

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

37

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

E-print Network

Restricted open-shell Kohn-Sham (ROKS) theory provides a powerful computational tool for calculating singlet excited state energies and dynamics. However, the possibility of multiple solutions to the ROKS equations — with ...

Kowalczyk, Tim

38

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

E-print Network

Variation of large elastodynamic earthquakes on complex fault systems Bruce E. Shaw Lamont, and a source of some of the biggest uncertainties in earthquake hazard estimation is the role of fault segmentation in controlling large earthquake ruptures. Here we apply a new model which produces sequences

Shaw, Bruce E.

39

Resolution of identity Dirac-Kohn-Sham method using the large component only: Calculations of g-tensor and hyperfine tensor.  

PubMed

A new relativistic two-component density functional approach, based on the Dirac-Kohn-Sham method and an extensive use of the technique of resolution of identity (RI), has been developed and is termed the DKS2-RI method. It has been applied to relativistic calculations of g and hyperfine tensors of coinage-metal atoms and some mercury complexes. The DKS2-RI method solves the Dirac-Kohn-Sham equations in a two-component framework using explicitly a basis for the large component only, but it retains all contributions coming from the small component. The DKS2-RI results converge to those of the four-component Dirac-Kohn-Sham with an increasing basis set since the error associated with the use of RI will approach zero. The RI approximation provides a basis for a very efficient implementation by avoiding problems associated with complicated integrals otherwise arising from the elimination of the small component. The approach has been implemented in an unrestricted noncollinear two-component density functional framework. DKS2-RI is related to Dyall's [J. Chem. Phys. 106, 9618 (1997)] unnormalized elimination of the small component method (which was formulated at the Hartree-Fock level and applied to one-electron systems only), but it takes advantage of the local Kohn-Sham exchange-correlation operators (as, e.g., arising from local or gradient-corrected functionals). The DKS2-RI method provides an attractive alternative to existing approximate two-component methods with transformed Hamiltonians (such as Douglas-Kroll-Hess [Ann. Phys. 82, 89 (1974); Phys. Rev. A 33, 3742 (1986)] method, zero-order regular approximation, or related approaches) for relativistic calculations of the structure and properties of heavy-atom systems. In particular, no picture-change effects arise in the property calculations. PMID:16512709

Komorovský, Stanislav; Repiský, Michal; Malkina, Olga L; Malkin, Vladimir G; Malkin, Irina; Kaupp, Martin

2006-02-28

40

Further exploration of the Fukui function, hardness, and other reactivity indices and its relationships within the Kohn-Sham scheme  

NASA Astrophysics Data System (ADS)

The Fukui function, hardness, and other reactivity indices defined in the context of the Kohn-Sham scheme have been further examined following up previous developments. An equation analogue to the Berkowitz-Parr relationship among the noninteracting linear response function and a new Kohn-Sham softness hierarchy can be derived as defined in the present study. The thermodynamic-like structure of the mathematical equations is retained among the global, local, and nonlocal hierarchies of descriptors, yielding equations that present fewer approximations. In particular, it is stressed that the Kohn-Sham hardness is better approximated by the Kohn-Sham energy gap and, as previously emphasized, that the Kohn-Sham Fukui function is precisely equal to the square of the frontier orbital. The higher-order perturbational extensions have been outlined, and the analogue of a Fukui response function within the Kohn-Sham context has been derived.

Fuentealba, P.; Chamorro, E.; Cárdenas, C.

41

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

42

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

PubMed Central

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

McIntyre, Patrick J.

2012-01-01

43

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

44

Genotypic and phenotypic variation in transmission traits of a complex life cycle parasite  

PubMed Central

Characterizing genetic variation in parasite transmission traits and its contribution to parasite vigor is essential for understanding the evolution of parasite life-history traits. We measured genetic variation in output, activity, survival, and infection success of clonal transmission stages (cercaria larvae) of a complex life cycle parasite (Diplostomum pseudospathaceum). We further tested if variation in host nutritional stage had an effect on these traits by keeping hosts on limited or ad libitum diet. The traits we measured were highly variable among parasite genotypes indicating significant genetic variation in these life-history traits. Traits were also phenotypically variable, for example, there was significant variation in the measured traits over time within each genotype. However, host nutritional stage had no effect on the parasite traits suggesting that a short-term reduction in host resources was not limiting the cercarial output or performance. Overall, these results suggest significant interclonal and phenotypic variation in parasite transmission traits that are not affected by host nutritional status. PMID:23919156

Louhi, Katja-Riikka; Karvonen, Anssi; Rellstab, Christian; Jokela, Jukka

2013-01-01

45

Natural variation for drought-response traits in the Mimulus guttatus species complex  

Microsoft Academic Search

Soil moisture is a key factor affecting plant abundance and distribution, both across and within species. In response to water\\u000a limitation, plants have evolved numerous morphological, physiological, and phenological adaptations. In both well-watered\\u000a and water-limited conditions, we identified considerable natural variation in drought-related whole-plant and leaf-level traits\\u000a among closely related members of the Mimulus guttatus species complex that occupy a

Carrie A. Wu; David B. Lowry; Laura I. Nutter; John H. Willis

2010-01-01

46

Using CAD geometric variation approach machining complex workpiece by a 3SPR parallel machine tool  

Microsoft Academic Search

A novel CAD geometric variation approach is proposed for machining the complex workpiece, caving letter on a 3D free-form surface, and milling cam by a 3-SPR parallel machine tool. First, a simulation mechanism of the 3-SPR parallel manipulator is created, and a workspace of the moving platform is constructed by the 3-SPR simulation mechanism. Second, the tool path guiding plane

Yi Lu; Jiayin Xu; Jianping Yu

2010-01-01

47

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

ERIC Educational Resources Information Center

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

Kuiken, Folkert; Vedder, Ineke

2012-01-01

48

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

49

Identification of a common docking topology with substantial variation among different TCR-peptide-MHC complexes.  

PubMed

Whether T-cell receptors (TCRs) recognize antigenic peptides bound to major histocompatability complex (MHC) molecules through common or distinct docking modes is currently uncertain. We report the crystal structure of a complex between the murine N15 TCR [1-4] and its peptide-MHC ligand, an octapeptide fragment representing amino acids 52-59 of the vesicular stomatitis virus nuclear capsid protein (VSV8) bound to the murine H-2Kb class I MHC molecule. Comparison of the structure of the N15 TCR-VSV8-H-2Kb complex with the murine 2C TCR-dEV8-H-2Kb [5] and the human A6 TCR-Tax-HLA-A2 [6] complexes revealed a common docking mode, regardless of TCR specificity or species origin, in which the TCR variable Valpha domain overlies the MHC alpha2 helix and the Vbeta domain overlies the MHC alpha1 helix. As a consequence, the complementary determining regions CDR1 and CDR3 of the TCR Valpha and Vbeta domains make the major contacts with the peptide, while the CDR2 loops interact primarily with the MHC. Nonetheless, in terms of the details of the relative orientation and disposition of binding, there is substantial variation in TCR parameters, which we term twist, tilt and shift, and which define the variation of the V module of the TCR relative to the MHC antigen-binding groove. PMID:9545202

Teng, M K; Smolyar, A; Tse, A G; Liu, J H; Liu, J; Hussey, R E; Nathenson, S G; Chang, H C; Reinherz, E L; Wang, J H

1998-03-26

50

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

51

A taxonomic study of selected European taxa of the Tortula muralis (Pottiaceae, Musci) complex: variation in morphology and ploidy level  

E-print Network

A taxonomic study of selected European taxa of the Tortula muralis (Pottiaceae, Musci) complex study of selected European taxa of the Tortula muralis (Pottiaceae, Musci) complex: variation in morphology and ploidy level. ­ Preslia 81: 399­421. Four European taxa of the Tortula muralis complex (T

Kucera, Jan

52

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

53

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

PubMed Central

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

Ansel, Juliet; Bottin, Helene; Rodriguez-Beltran, Camilo; Damon, Christelle; Nagarajan, Muniyandi; Fehrmann, Steffen; Francois, Jean; Yvert, Gael

2008-01-01

54

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

55

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

ERIC Educational Resources Information Center

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

Weininger, Elliot B.; Lareau, Annette

2009-01-01

56

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

57

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

NASA Astrophysics Data System (ADS)

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

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

2012-02-01

58

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

59

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

PubMed

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; Baliga, Nitin S

2014-03-01

60

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

61

Learned Vocal Variation Is Associated with Abrupt Cryptic Genetic Change in a Parrot Species Complex  

PubMed Central

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

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

2012-01-01

62

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

PubMed

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

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

1995-07-01

63

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

PubMed

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

64

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

65

N-density representability and the optimal transport limit of the Hohenberg-Kohn functional.  

PubMed

We derive and analyze a hierarchy of approximations to the strongly correlated limit of the Hohenberg-Kohn functional. These "density representability approximations" are obtained by first noting that in the strongly correlated limit, N-representability of the pair density reduces to the requirement that the pair density must come from a symmetric N-point density. One then relaxes this requirement to the existence of a representing symmetric k-point density with k < N. The approximate energy can be computed by simulating a fictitious k-electron system. We investigate the approximations by deriving analytically exact results for a 2-site model problem, and by incorporating them into a self-consistent Kohn-Sham calculation for small atoms. We find that the low order representability conditions already capture the main part of the correlations. PMID:24182006

Friesecke, Gero; Mendl, Christian B; Pass, Brendan; Cotar, Codina; Klüppelberg, Claudia

2013-10-28

66

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

PubMed Central

Despite considerable excitement over the potential functional significance of copy-number variants (CNVs), we still lack knowledge of the fine-scale architecture of the large majority of CNV regions in the human genome. In this study, we used a high-resolution array-based comparative genomic hybridization (aCGH) platform that targeted known CNV regions of the human genome at approximately 1 kb resolution to interrogate the genomic DNAs of 30 individuals from four HapMap populations. Our results revealed that 1020 of 1153 CNV loci (88%) were actually smaller in size than what is recorded in the Database of Genomic Variants based on previously published studies. A reduction in size of more than 50% was observed for 876 CNV regions (76%). We conclude that the total genomic content of currently known common human CNVs is likely smaller than previously thought. In addition, approximately 8% of the CNV regions observed in multiple individuals exhibited genomic architectural complexity in the form of smaller CNVs within larger ones and CNVs with interindividual variation in breakpoints. Future association studies that aim to capture the potential influences of CNVs on disease phenotypes will need to consider how to best ascertain this previously uncharacterized complexity. PMID:18304495

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

2008-01-01

67

Continuous corrections to the molecular Kohn-Sham gap and virtual orbitals  

Microsoft Academic Search

We use projector operators to correct the Kohn-Sham Hamiltonian of density functional theory (KS-DFT) so that the resulting mean-field scheme yields, in finite systems, virtual orbitals and energy gaps in better agreement with those predicted by quasiparticle theory. The proposed correction term is a scissors-like operator of the form $(\\\\hat{I}-\\\\hat{\\\\rho})\\\\delta \\\\hat{H}(\\\\hat{I}-\\\\hat{\\\\rho})$, where $\\\\hat{I}$ is the identity operator, $\\\\hat{\\\\rho}$ the density

Hector Mera

2008-01-01

68

Using Kohn-Sham density functional theory to describe charged excitations in finite systems  

Microsoft Academic Search

We use projector operators to correct the Kohn-Sham Hamiltonian of density functional theory (KS-DFT) so that, in finite systems, the resulting mean-field scheme yields virtual orbitals and energy gaps in better agreement with those predicted by quasiparticle theory. The proposed correction term is a scissorslike operator of the form (Î-rhoˆ)deltaH(Î-rhoˆ) , where Î is the identity operator, rhoˆ is the

Héctor Mera; Kurt Stokbro

2009-01-01

69

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

70

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)] 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

71

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

NASA Astrophysics Data System (ADS)

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

Li, Yong

72

Localising Loci underlying Complex Trait Variation Using Regional Genomic Relationship Mapping  

PubMed Central

The limited proportion of complex trait variance identified in genome-wide association studies may reflect the limited power of single SNP analyses to detect either rare causative alleles or those of small effect. Motivated by studies that demonstrate that loci contributing to trait variation may contain a number of different alleles, we have developed an analytical approach termed Regional Genomic Relationship Mapping that, like linkage-based family methods, integrates variance contributed by founder gametes within a pedigree. This approach takes advantage of very distant (and unrecorded) relationships, and this greatly increases the power of the method, compared with traditional pedigree-based linkage analyses. By integrating variance contributed by founder gametes in the population, our approach provides an estimate of the Regional Heritability attributable to a small genomic region (e.g. 100 SNP window covering ca. 1 Mb of DNA in a 300000 SNP GWAS) and has the power to detect regions containing multiple alleles that individually contribute too little variance to be detectable by GWAS as well as regions with single common GWAS-detectable SNPs. We use genome-wide SNP array data to obtain both a genome-wide relationship matrix and regional relationship (“identity by state" or IBS) matrices for sequential regions across the genome. We then estimate a heritability for each region sequentially in our genome-wide scan. We demonstrate by simulation and with real data that, when compared to traditional (“individual SNP") GWAS, our method uncovers new loci that explain additional trait variation. We analysed data from three Southern European populations and from Orkney for exemplar traits – serum uric acid concentration and height. We show that regional heritability estimates are correlated with results from genome-wide association analysis but can capture more of the genetic variance segregating in the population and identify additional trait loci. PMID:23077511

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

2012-01-01

73

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

74

Variation in the major histocompatibility complex [MHC] gene family in schizophrenia: associations and functional implications.  

PubMed

Schizophrenia is a chronic debilitating neuropsychiatric disorder with a complex genetic contribution. Although multiple genetic, immunological and environmental factors are known to contribute to schizophrenia susceptibility, the underlying neurobiological mechanism(s) is yet to be established. The immune system dysfunction theory of schizophrenia is experiencing a period of renewal due to a growth in evidence implicating components of the immune system in brain function and human behavior. Current evidence indicates that certain immune molecules such as Major Histocompatibility Complex (MHC) and cytokines, the key regulators of immunity and inflammation are directly involved in the neurobiological processes related to neurodevelopment, neuronal plasticity, learning, memory and behavior. However, the strongest support in favor of the immune hypothesis has recently emerged from on-going genome wide association studies advocating MHC region variants as major determinants of one's risk for developing schizophrenia. Further identification of the interacting partners and receptors of MHC molecules in the brain and their role in down-stream signaling pathways of neurotransmission have implicated these molecules as potential schizophrenia risk factors. More recently, combined brain imaging and genetic studies have revealed a relationship between genetic variations within the MHC region and neuromorphometric changes during schizophrenia. Furthermore, MHC molecules play a significant role in the immune-infective and neurodevelopmental pathogenetic pathways, currently hypothesized to contribute to the pathophysiology of schizophrenia. Herein, we review the immunological, genetic and expression studies assessing the role of the MHC in conferring risk for developing schizophrenia, we summarize and discuss the possible mechanisms involved, making note of the challenges to, and future directions of, immunogenetic research in schizophrenia. PMID:22813842

Debnath, Monojit; Cannon, Dara M; Venkatasubramanian, Ganesan

2013-04-01

75

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

PubMed

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

2013-10-22

76

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

PubMed Central

The genetic architecture of plant defense against microbial pathogens may be influenced by pathogen lifestyle. While plant interactions with biotrophic pathogens are frequently controlled by the action of large-effect resistance genes that follow classic Mendelian inheritance, our study suggests that plant defense against the necrotrophic pathogen Botrytis cinerea is primarily quantitative and genetically complex. Few studies of quantitative resistance to necrotrophic pathogens have used large plant mapping populations to dissect the genetic structure of resistance. Using a large structured mapping population of Arabidopsis thaliana, we identified quantitative trait loci influencing plant response to B. cinerea, measured as expansion of necrotic lesions on leaves and accumulation of the antimicrobial compound camalexin. Testing multiple B. cinerea isolates, we identified 23 separate QTL in this population, ranging in isolate-specificity from being identified with a single isolate to controlling resistance against all isolates tested. We identified a set of QTL controlling accumulation of camalexin in response to pathogen infection that largely colocalized with lesion QTL. The identified resistance QTL appear to function in epistatic networks involving three or more loci. Detection of multilocus connections suggests that natural variation in specific signaling or response networks may control A. thaliana–B. cinerea interaction in this population. PMID:18845849

Rowe, Heather C.; Kliebenstein, Daniel J.

2008-01-01

77

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

78

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

NASA Astrophysics Data System (ADS)

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

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

2012-02-01

79

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

80

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

81

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

PubMed Central

Mutualistic relationships are beneficial for both partners and are often studied within a single environment. However, when the range of the partners is large, geographical differences in selective pressure may shift the relationship outcome from positive to negative. The marine bryozoan Bugula neritina is a colonial invertebrate common in temperate waters worldwide. It is the source of bioactive polyketide metabolites, the bryostatins. Evidence suggests that an uncultured vertically transmitted symbiont, “Candidatus Endobugula sertula”, hosted by B. neritina produces the bryostatins, which protect the vulnerable larvae from predation. Studies of B. neritina along the North American Atlantic coast revealed a complex of two morphologically similar sibling species separated by an apparent biogeographic barrier: the Type S sibling species was found below Cape Hatteras, North Carolina, while Type N was found above. Interestingly, the Type N colonies lack “Ca. Endobugula sertula” and, subsequently, defensive bryostatins; their documented northern distribution was consistent with traditional biogeographical paradigms of latitudinal variation in predation pressure. Upon further sampling of B. neritina populations, we found that both host types occur in wider distribution, with Type N colonies living south of Cape Hatteras, and Type S to the north. Distribution of the symbiont, however, was not restricted to Type S hosts. Genetic and microscopic evidence demonstrates the presence of the symbiont in some Type N colonies, and larvae from these colonies are endowed with defensive bryostatins and contain “Ca. Endobugula sertula”. Molecular analysis of the symbiont from Type N colonies suggests an evolutionarily recent acquisition, which is remarkable for a symbiont thought to be transmitted only vertically. Furthermore, most Type S colonies found at higher latitudes lack the symbiont, suggesting that this host-symbiont relationship is more flexible than previously thought. Our data suggest that the symbiont, but not the host, is restricted by biogeographical boundaries. PMID:25275632

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

2014-01-01

82

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

PubMed

Mutualistic relationships are beneficial for both partners and are often studied within a single environment. However, when the range of the partners is large, geographical differences in selective pressure may shift the relationship outcome from positive to negative. The marine bryozoan Bugula neritina is a colonial invertebrate common in temperate waters worldwide. It is the source of bioactive polyketide metabolites, the bryostatins. Evidence suggests that an uncultured vertically transmitted symbiont, "Candidatus Endobugula sertula", hosted by B. neritina produces the bryostatins, which protect the vulnerable larvae from predation. Studies of B. neritina along the North American Atlantic coast revealed a complex of two morphologically similar sibling species separated by an apparent biogeographic barrier: the Type S sibling species was found below Cape Hatteras, North Carolina, while Type N was found above. Interestingly, the Type N colonies lack "Ca. Endobugula sertula" and, subsequently, defensive bryostatins; their documented northern distribution was consistent with traditional biogeographical paradigms of latitudinal variation in predation pressure. Upon further sampling of B. neritina populations, we found that both host types occur in wider distribution, with Type N colonies living south of Cape Hatteras, and Type S to the north. Distribution of the symbiont, however, was not restricted to Type S hosts. Genetic and microscopic evidence demonstrates the presence of the symbiont in some Type N colonies, and larvae from these colonies are endowed with defensive bryostatins and contain "Ca. Endobugula sertula". Molecular analysis of the symbiont from Type N colonies suggests an evolutionarily recent acquisition, which is remarkable for a symbiont thought to be transmitted only vertically. Furthermore, most Type S colonies found at higher latitudes lack the symbiont, suggesting that this host-symbiont relationship is more flexible than previously thought. Our data suggest that the symbiont, but not the host, is restricted by biogeographical boundaries. PMID:25275632

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

2014-01-01

83

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

SciTech Connect

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

2013-11-15

84

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

NASA Astrophysics Data System (ADS)

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

Zeller, Rudolf

2014-09-01

85

Effect of discontinuities in Kohn-Sham-based chemical reactivity theory  

NASA Astrophysics Data System (ADS)

We provide a new derivation of a formula for the Fukui function of density functional chemical reactivity theory which incorporates the discontinuities in the Kohn-Sham reference system. Orbital relaxations are described in terms of the exchange-correlation (XC) kernel, i.e., the derivative of the XC potential with respect to the density and it is shown that in order to correctly measure the reactivity toward a nucleophilic reagent a discontinuity of the XC kernel has to be taken into account. The importance of this finding is illustrated in model molecular systems.

Hellgren, Maria; Gross, E. K. U.

2012-03-01

86

A unifying geometric solution framework and complexity analysis for variational inequalities  

Microsoft Academic Search

In this paper, we propose a concept of polynomiality for variational inequality problems and show how to find a near optimal solution of variational inequality problems in a polynomial number of iterations. To establish this result, we build upon insights from several algorithms for linear and nonlinear programs (the ellipsoid algorithm, the method of centers of gravity, the method of

Thomas L. Magnanti; Georgia Perakis

1995-01-01

87

GENETIC DIFFERENTIATION, GEOGRAPHIC VARIATION AND HYBRIDIZATION IN GULLS OF THE LARUS GLA UCESCENS-OCCIDENTALIS COMPLEX  

Microsoft Academic Search

Survey of morphometric, calorimetric, and allozymic variation in the Glau- cous-winged Gull (Larus glaucescens), the Western Gull (L. occidentalis) and their hybrids is based on 706 specimens taken from 33 colony areas located throughout the breeding range of both species. Whereas most morphometric characters overlap between taxa, col- orimetric characters exhibited significant intraspecific and interspecific clinal variation. Ca- nonical discriminant

DOUGLAS A. BELLY

88

Heritability of variation in glycaemic response to metformin: a genome-wide complex trait analysis  

PubMed Central

Summary Background Metformin is a first-line oral agent used in the treatment of type 2 diabetes, but glycaemic response to this drug is highly variable. Understanding the genetic contribution to metformin response might increase the possibility of personalising metformin treatment. We aimed to establish the heritability of glycaemic response to metformin using the genome-wide complex trait analysis (GCTA) method. Methods In this GCTA study, we obtained data about HbA1c concentrations before and during metformin treatment from patients in the Genetics of Diabetes Audit and Research in Tayside Scotland (GoDARTS) study, which includes a cohort of patients with type 2 diabetes and is linked to comprehensive clinical databases and genome-wide association study data. We applied the GCTA method to estimate heritability for four definitions of glycaemic response to metformin: absolute reduction in HbA1c; proportional reduction in HbA1c; adjusted reduction in HbA1c; and whether or not the target on-treatment HbA1c of less than 7% (53 mmol/mol) was achieved, with adjustment for baseline HbA1c and known clinical covariates. Chromosome-wise heritability estimation was used to obtain further information about the genetic architecture. Findings 5386 individuals were included in the final dataset, of whom 2085 had enough clinical data to define glycaemic response to metformin. The heritability of glycaemic response to metformin varied by response phenotype, with a heritability of 34% (95% CI 1–68; p=0·022) for the absolute reduction in HbA1c, adjusted for pretreatment HbA1c. Chromosome-wise heritability estimates suggest that the genetic contribution is probably from individual variants scattered across the genome, which each have a small to moderate effect, rather than from a few loci that each have a large effect. Interpretation Glycaemic response to metformin is heritable, thus glycaemic response to metformin is, in part, intrinsic to individual biological variation. Further genetic analysis might enable us to make better predictions for stratified medicine and to unravel new mechanisms of metformin action. Funding Wellcome Trust. PMID:24731673

Zhou, Kaixin; Donnelly, Louise; Yang, Jian; Li, Miaoxin; Deshmukh, Harshal; Van Zuydam, Natalie; Ahlqvist, Emma; Spencer, Chris C; Groop, Leif; Morris, Andrew D; Colhoun, Helen M; Sham, Pak C; McCarthy, Mark I; Palmer, Colin N A; Pearson, Ewan R

2014-01-01

89

Kohn's theorem, Larmor's equivalence principle and the Newton-Hooke group  

SciTech Connect

Highlights: > We show that non-relativistic electrons moving in a magnetic field with trapping potential admits as relativity group the Newton-Hooke group. > We use this fact to give a group theoretic interpretation of Kohn's theorem and to obtain the spectrum. > We obtain the lightlike lift of the system exhibiting showing it coincides with the Nappi-Witten spacetime. - Abstract: 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-Inoenue 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.

Gibbons, G.W., E-mail: gwg1@amtp.cam.ac.uk [DAMTP, Centre for Mathematical Sciences, Cambridge University, Wilberforce Road, Cambridge CB3 OWA (United Kingdom); Pope, C.N. [DAMTP, Centre for Mathematical Sciences, Cambridge University, Wilberforce Road, Cambridge CB3 OWA (United Kingdom); George P. and Cynthia W. Mitchell Institute for Fundamental Physics and Astronomy, Texas A and M University, College Station, TX 77843-4242 (United States)

2011-07-15

90

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

NASA Astrophysics Data System (ADS)

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

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

2013-08-01

91

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

NASA Astrophysics Data System (ADS)

We present for the first time an efficient iterative method to directly solve the four-component Dirac-Kohn-Sham (DKS) density functional theory. Due to the existence of the negative energy continuum in the DKS operator, the existing iterative techniques for solving the Kohn-Sham systems cannot be efficiently applied to solve the DKS systems. The key component of our method is a novel filtering step (F) which acts as a preconditioner in the framework of the locally optimal block preconditioned conjugate gradient (LOBPCG) method. The resulting method, dubbed the LOBPCG-F method, is able to compute the desired eigenvalues and eigenvectors in the positive energy band without computing any state in the negative energy band. The LOBPCG-F method introduces mild extra cost compared to the standard LOBPCG method and can be easily implemented. We demonstrate our method in the pseudopotential framework with a planewave basis set which naturally satisfies the kinetic balance prescription. Numerical results for Pt2, Au2, TlF, and Bi2Se3 indicate that the LOBPCG-F method is a robust and efficient method for investigating the relativistic effect in systems containing heavy elements.

Lin, Lin; Shao, Sihong; E, Weinan

2013-07-01

92

Comparison of Dyson, Hartree-Fock, Kohn-Sham, natural, and natural-bond orbitals: electron momentum spectroscopy of CH4  

NASA Astrophysics Data System (ADS)

The Dyson, Hartree-Fock, Kohn-Sham, natural, and natural-bond orbitals of methane (CH4) were compared with the experimental electron momentum distributions. The Dyson, Hartree-Fock, Kohn-Sham theories can present a direct concise interpretation and well reproduce the experimental results, but the natural-bond orbital cannot.

Ning, Chuangang; Miao, Yurun; Deng, Jingkang; Zhu, Jingsheng

2014-04-01

93

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

94

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

PubMed

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

Miller, Hilary C; Lambert, David M

2004-12-01

95

Age- and gender-related regional variations of human brain cortical thickness, complexity, and gradient in the third decade.  

PubMed

Brain functional and cytoarchitectural maturation continue until adulthood, but little is known about the evolution of the regional pattern of cortical thickness (CT), complexity (CC), and intensity or gradient (CG) in young adults. We attempted to detect global and regional age- and gender-related variations of brain CT, CC, and CG, in 28 healthy young adults (19-33 years) using a three-dimensional T1 -weighted magnetic resonance imaging sequence and surface-based methods. Whole brain interindividual variations of CT and CG were similar to that in the literature. As a new finding, age- and gender-related variations significantly affected brain complexity (P?

Creze, Maud; Versheure, Leslie; Besson, Pierre; Sauvage, Chloe; Leclerc, Xavier; Jissendi-Tchofo, Patrice

2014-06-01

96

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.

97

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

Microsoft Academic Search

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

Kelly W. Allred

1984-01-01

98

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

SciTech Connect

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

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

2011-01-15

99

Recent advances and perspectives in four-component Dirac-Kohn-Sham calculations.  

PubMed

We review recent theoretical and computational advances in the full relativistic four-component Dirac-Kohn-Sham (DKS) approach and its application to the calculation of the electronic structure of chemical systems containing many heavy atoms. We describe our implementation of an all-electron DKS approach based on the use of G-spinor basis sets, Hermite Gaussian functions, state-of-the-art density-fitting techniques and memory distributed parallelism. This approach has enormously extended the applicability of the DKS method, including for example large clusters of heavy atoms, and opens the way for future key developments. We examine the current limitations and future possible applications of the DKS approach, including the implementation of four-current density functionals and real-time propagation schemes. This would make possible to describe molecules in strong fields, accurately accounting for relativistic kinematic effects and spin-orbit coupling. PMID:21670843

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

2011-07-21

100

Fundamental Gaps in Finite Systems from Eigenvalues of a Generalized Kohn-Sham Method  

NASA Astrophysics Data System (ADS)

We present a broadly applicable, physically motivated, first-principles approach to determining the fundamental gap of finite systems from single-electron orbital energies. The approach is based on using a range-separated hybrid functional within the generalized Kohn-Sham approach to density functional theory. Its key element is the choice of a range-separation parameter such that Koopmans’ theorem for both neutral and anion is obeyed as closely as possible. We demonstrate the validity, accuracy, and advantages of this approach on first, second and third row atoms, the oligoacene family of molecules, and a set of hydrogen-passivated silicon nanocrystals. This extends the quantitative usage of density functional theory to an area long believed to be outside its reach.

Stein, Tamar; Eisenberg, Helen; Kronik, Leeor; Baer, Roi

2010-12-01

101

Fundamental gaps in finite systems from the eigenvalues of generalized kohn-sham method  

NASA Astrophysics Data System (ADS)

We present a broadly-applicable, physically-motivated first-principles approach to determining the fundamental gap of finite systems. The approach is based on using a range-separated hybrid functional within the generalized Kohn-Sham approach to density functional theory. Its key element is the choice of a range-separation parameter such that Koopmans' theorem for both neutral and anion is obeyed as closely as possible. We demonstrated the validity, accuracy, and advantages of this approach on first, second and third row atoms, the oligoacene family of molecules, and a set of hydrogen-passivated silicon nanocrystals. This extends the quantitative usage of density functional theory to an area long believed to be outside its reach.

Stein, Tamar; Eisenberg, Helen; Kronik, Leeor; Baer, Roi

2011-03-01

102

Local reduced density matrix functional theory: incorporating static correlation effects in the Kohn-Sham equations  

E-print Network

We propose a novel scheme to bring reduced density matrix functional theory (RDMFT) into the realm of density functional theory (DFT) that preserves the accurate density functional description at equilibrium, while incorporating accurately static and left-right correlation effects in molecules and keeping the good computational performance of DFT-based schemes. The key ingredient is to relax the requirement that the local potential is the functional derivative of the energy with respect to the density. Instead, we propose to restrict the search for the approximate natural orbitals within a domain where these orbitals are eigenfunctions of a single-particle hamiltonian with a local effective potential. In this way, fractional natural occupation numbers are accommodated into Kohn-Sham equations allowing for the description of molecular dissociation without breaking spin symmetry. Additionally, our scheme provides a natural way to connect an energy eigenvalue spectrum to the approximate natural orbitals and this...

Lathiotakis, Nektarios N; Rubio, Angel; Gidopoulos, Nikitas I

2014-01-01

103

Quadratic response functions in the relativistic four-component Kohn-Sham approximation.  

PubMed

A formulation and implementation of the quadratic response function in the adiabatic four-component Kohn-Sham approximation is presented. The noninteracting reference state is time-reversal symmetric and formed from Kramers pair spinors, and the energy density is gradient corrected. Example calculations are presented for the optical properties of disubstituted halobenzenes in their meta and ortho conformations. It is demonstrated that correlation and relativistic effects are not additive, and it is shown that relativity alone reduces the mubeta-response signal by 62% and 75% for meta- and ortho-bromobenzene, respectively, and enhances the same response by 17% and 21% for meta- and ortho-iodobenzene, respectively. Of the employed functionals, CAM-B3LYP shows the best performance and gives hyperpolarizabilities beta distinctly different from B3LYP. PMID:18205441

Henriksson, Johan; Saue, Trond; Norman, Patrick

2008-01-14

104

The Korringa-Kohn-Rostoker Method Applied to Warm Dense Matter  

NASA Astrophysics Data System (ADS)

The electronic structure, EOS and transport properties of warm electrons in an amorphous or disordered configuration of ions is not well described by either solid-state or plasma models. Such warm, dense systems share the characteristic of the solid state that multi-center scattering effects are of paramount importance in forming bands of valence states. Theoretical treatment of the EOS of warm, dense matter therefore requires a way to include significant occupation of higher energy and angular momentum channel continuum states. We are extending the Green's function Kohn-Korringa-Rostoker code MECCA as an all-electron (non-pseudo potential) method that treats arbitrary mixtures of atoms on an ab-initio basis over a broad range of conditions, from cold, solid matter up to hot plasmas at extreme (ICF) compression. Specific examples of Aluminum and Boron-Nitride will be discussed.

Finkenstadt, Daniel; Newnam, Charles E.; Wilson, Brian G.

2012-02-01

105

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

106

Kohn-Luttinger effect and the instability of a repulsive Fermi-liquid at T = 0  

SciTech Connect

The author considers the possibility for a pairing instability in a 2D repulsive Fermi-liquid due to the singularity in the scattering amplitude {Gamma}(q) at the momentum transfer q {approx} 2p{sub F} (Kohn-Luttinger effect). For arbitrary Fermi-liquid, {Gamma}(q) for the particles at the Fermi surface is found to have a singular part. For large 2D orbital momentum l, this term gives a dominant attractive contribution to the scattering amplitude and leads to a pairing instability in a 2D Fermi-liquid with arbitrary short-range repulsion. In the dilute limit, numerical studies show that the effect survives down to l = 1 and gives rise to a p-wave pairing. 12 refs.

Chubukov, A.V. [Univ. of Illinois, Urbana (United States)]|[P.L. Kapitza Inst. for Physical Problems, Moscow (Russian Federation)

1992-11-01

107

Numerical methods for a Kohn-Sham density functional model based on optimal transport  

E-print Network

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

Huajie Chen; Gero Friesecke; Christian B. Mendl

2014-05-27

108

Numerical methods for a Kohn-Sham density functional model based on optimal transport  

E-print Network

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

Chen, Huajie; Mendl, Christian B

2014-01-01

109

Optimized local basis set for Kohn-Sham density functional theory  

NASA Astrophysics Data System (ADS)

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

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

2012-05-01

110

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

111

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

112

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

PubMed Central

The rate of recombination is a key genomic parameter that displays considerable variation among taxa. Species comparisons have demonstrated that the rate of evolution in recombination rate is strongly dependent on the physical scale of measurement. Individual recombination hotspots are poorly conserved among closely related taxa, whereas genomic-scale recombination rate variation bears a strong signature of phylogenetic history. In contrast, the mode and tempo of evolution in recombination rates measured on intermediate physical scales is poorly understood. Here, we conduct a detailed statistical comparison between two whole-genome F2 genetic linkage maps constructed from experimental intercrosses between closely related house mouse subspecies (Mus musculus). Our two maps profile a common wild-derived inbred strain of M. m. domesticus crossed to distinct wild-derived inbred strains representative of two other house mouse subspecies, M. m. castaneus and M. m. musculus. We identify numerous orthologous genomic regions with significant map length differences between these two crosses. Because the genomes of these recently diverged house mice are highly collinear, observed differences in map length (centimorgans) are suggestive of variation in broadscale recombination rate (centimorgans per megabase) within M. musculus. Collectively, these divergent intervals span 19% of the house mouse genome, disproportionately aggregating on the X chromosome. In addition, we uncover strong statistical evidence for a large effect, sex-linked, site-specific modifier of recombination rate segregating within M. musculus. Our findings reveal considerable variation in the megabase-scale recombination landscape among recently diverged taxa and underscore the continued importance of genetic linkage maps in the post-genome era. PMID:20978138

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

2011-01-01

113

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

NASA Astrophysics Data System (ADS)

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.

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

2010-09-01

114

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

115

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

NASA Technical Reports Server (NTRS)

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

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

1989-01-01

116

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

PubMed

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

Grunst, Melissa L; Grunst, Andrea S

2014-05-01

117

Genetic variation of the mitochondrial complex I subunit NDUFV2 and Parkinson’s disease  

Microsoft Academic Search

NADH dehydrogenase ubiquinone flavoprotein 2 (NDUFV2), encoding a subunit of mitochondrial complex I, is a candidate gene for several neuronal diseases; schizophrenia, bipolar disorder and Parkinson disease (PD). We screened the entire coding region of NDUFV2 in 33 familial PD patients of North African Arab-Berber ethnicity in which all known genetic forms of PD had been excluded. We detected one

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

2010-01-01

118

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

ERIC Educational Resources Information Center

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

Blankenbaker, E. Keith

119

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

PubMed

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

Johnson, Darren W

2006-05-01

120

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

PubMed

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

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

2014-10-01

121

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

122

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

PubMed Central

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

Green, Tim; Rosen, Stuart

2013-01-01

123

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

124

Disparity in population differentiation of sex-linked and autosomal variation in sibling species of the Jaera albifrons (Isopoda) complex.  

PubMed

The genetic variation at four enzyme loci is described for 22 populations of three Jaera species--J. albifrons, J. ischiosetosa, and J. praehirsuta--in the J. albifrons complex (Crustacea, Isopoda) in Denmark. The variation at three of the loci is similar, with the allele frequency spectra close to each other in all three species. An evolutionary tree based on the variation at these three loci revealed that the populations from the different species are completely intermixed in the tree. This was supported by hierarchical F-statistics where the between-species component was zero. At a fourth locus, Gpi (glucose phosphate isomerase), the species differ substantially. This locus is sex linked in J. ischiosetosa, but in the two other species, J. albifrons and J. praehirsuta, it is either found on autosomes or is sex linked with a high recombination rate between the locus and the centromere. An evolutionary tree for this locus partitions the populations into separate groups and a hierarchical F-statistic has a between-species component of about 50%. The results are attributed to introgression with a higher rate for autosomes than for sex chromosomes. PMID:12642644

Siegismund, H R

2002-01-01

125

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

126

The Children's Hospitals Neonatal Database: an overview of patient complexity, outcomes and variation in care.  

PubMed

The Children's Hospitals Neonatal Consortium is a multicenter collaboration of leaders from 27 regional neonatal intensive care units (NICUs) who partnered with the Children's Hospital Association to develop the Children's Hospitals Neonatal Database (CHND), launched in 2010. The purpose of this report is to provide a first summary of the population of infants cared for in these NICUs, including representative diagnoses and short-term outcomes, as well as to characterize the participating NICUs and institutions. During the first 2 1/2 years of data collection, 40910 infants were eligible. Few were born inside these hospitals (2.8%) and the median gestational age at birth was 36 weeks. Surgical intervention (32%) was common; however, mortality (5.6%) was infrequent. Initial queries into diagnosis-specific inter-center variation in care practices and short-term outcomes, including length of stay, showed striking differences. The CHND provides a contemporary, national benchmark of short-term outcomes for infants with uncommon neonatal illnesses. These data will be valuable in counseling families and for conducting observational studies, clinical trials and collaborative quality improvement initiatives. PMID:24603454

Murthy, K; Dykes, F D; Padula, M A; Pallotto, E K; Reber, K M; Durand, D J; Short, B L; Asselin, J M; Zaniletti, I; Evans, J R

2014-08-01

127

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

PubMed

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

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

2006-03-01

128

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

129

Variation of electronic transitions and reduction potentials of cerium(iv) complexes.  

PubMed

The trivalent compound K[Ce[N(SiHMe2)2]4] was synthesized and oxidized, providing a convenient route to the reported cerium(iv) compound Ce[N(SiHMe2)2]4. Protonolysis reactions of Ce[N(SiHMe2)2]4 with tert-butanol, substituted benzyl alcohols, and 2,6-diphenylphenol yielded the neutral tetravalent compounds Ce(O(t)Bu)4(py)2, Ce2(OCH2C6R5)8(thf)2 (R = Me, F), and Ce(Odpp)4 (dpp = 2,6-(C6H5)2-C6H3). Spectroscopic and electrochemical characterization of the monometallic cerium(iv) silylamide, alkoxide, and aryloxide compounds revealed variable ligand-to-metal charge transfer transitions and metal-based reduction potentials. Computational bonding analyses were performed to complement the physical characterization of the complexes. PMID:25148646

Williams, Ursula J; Schneider, David; Dorfner, Walter L; Maichle-Mössmer, Cäcilia; Carroll, Patrick J; Anwander, Reiner; Schelter, Eric J

2014-10-14

130

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

131

Population differentiation and genetic variation in performance on eight hosts in the pea aphid complex.  

PubMed

Phytophagous insects frequently use multiple host-plant species leading to the evolution of specialized host-adapted populations and sometimes eventually to speciation. Some insects are confronted with a large number of host-plant species, which may provide complex routes of gene flow between host-adapted populations. The pea aphid (Acyrthosiphon pisum) attacks a broad range of plants in the Fabaceae and it is known that populations on Trifolium pratense and Medicago sativa can be highly specialized at exploiting these species. To find out whether adaptation to a broad range of co-occurring hosts has occurred, we tested the performance of pea aphid clones collected from eight host-plant genera on all of these plants in a reciprocal transfer experiment. We provide evidence for pervasive host-plant specialization. The high performance of all aphid clones on Vicia faba suggests that this host plant could be a site of gene flow between different populations that could limit further host-associated divergence. The genetic variance in host-plant usage was partitioned into within- and among-population components, which represent different levels of host adaptation. Little evidence of within-population trade-offs in performance on different plant species was found. PMID:18647340

Ferrari, Julia; Via, Sara; Godfray, H Charles J

2008-10-01

132

Molecular Variation and Distribution of Anopheles fluviatilis (Diptera: Culicidae) Complex in Iran  

PubMed Central

Anopheles fluviatilis James (Diptera: Culicidae) is one of the known malaria vectors in south and southeastern Iran. Earlier ITS2 sequences analysis of specimens from Iran demonstrated only a single genotype that was identical to species Y in India, which is also the same as species T. We identified 2 haplotypes in the An. fluviatilis populations of Iran based on differences in nucleotide sequences of D3 domain of the 28S locus of ribosomal DNA (rDNA). Comparison of sequence data from 44 Iranian specimens with those publicly available in the Genbank database showed that all of the 28S-D3 sequences from Kazeroun and Khesht regions in Fars Province were identical to the database entry representing species U in India. In other regions, all the individuals showed heterozygosity at the single nucleotide position, which identifies species U and T. It is argued that the 2 species may co-occur in some regions and hybridize; however, the heterozygosity in the 28S-D3 locus was not reflected in ITS2 sequences and this locus for all individuals was identical to species T. This study shows that in a newly diverged species, like members of An. fluviatilis complex, a single molecular marker may not be sufficiently discriminatory to identify all the taxa over a vast geographical area. In addition, other molecular markers may provide more reliable information for species discrimination. PMID:20877502

Razavi, Mohammad Reza; Bahramali, Golnaz

2010-01-01

133

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

Maki-Tanila, Asko; Hill, William G.

2014-01-01

134

Influence of gene interaction on complex trait variation with multilocus models.  

PubMed

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

2014-09-01

135

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

PubMed Central

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

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

2013-01-01

136

Local reduced-density-matrix-functional theory: Incorporating static correlation effects in Kohn-Sham equations  

NASA Astrophysics Data System (ADS)

We propose a scheme to bring reduced-density-matrix-functional theory into the realm of density functional theory (DFT) that preserves the accurate density functional description at equilibrium, while incorporating accurately static and left-right correlation effects in molecules and keeping the good computational performance of DFT-based schemes. The key ingredient is to relax the requirement that the local potential is the functional derivative of the energy with respect to the density. Instead, we propose to restrict the search for the approximate natural orbitals within a domain where these orbitals are eigenfunctions of a single-particle Hamiltonian with a local effective potential. In this way, fractional natural occupation numbers are accommodated into Kohn-Sham equations allowing for the description of molecular dissociation without breaking spin symmetry. Additionally, our scheme provides a natural way to connect an energy eigenvalue spectrum to the approximate natural orbitals and this spectrum is found to represent accurately the ionization potentials of atoms and small molecules.

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

2014-09-01

137

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

NASA Astrophysics Data System (ADS)

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

Schauer, Volker; Linder, Christian

2013-10-01

138

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

E-print Network

Self-consistency based Kohn-Sham density functional theory (KS-DFT) electronic structure calculations with Gaussian basis sets are reported for a set of 17 protein-like molecules with geometries obtained from the protein data bank. It is found that in many cases such calculations do not converge due to vanishing HOMO-LUMO gaps. A sequence of polyproline I helix molecules is also studied, and it is found that self-consistency calculations using pure functionals fail to converge for helices longer than six proline units. Since the computed gap is strongly correlated to the fraction of Hartree-Fock exchange, test calculations using both pure and hybrid density functionals are reported. The tested methods include the pure functionals BLYP, PBE, and LDA, as well as Hartree-Fock and the hybrid functionals BHandHLYP, B3LYP, and PBE0. The effect of including solvent molecules in the calculations is studied, and it is found that the inclusion of explicit solvent molecules around the protein fragment in many cases give...

Rudberg, Elias

2011-01-01

139

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

SciTech Connect

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

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

2013-10-01

140

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

NASA Astrophysics Data System (ADS)

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

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

2012-01-01

141

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

142

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

143

Variation in the Complex Carbohydrate Biosynthesis Loci of Acinetobacter baumannii Genomes  

PubMed Central

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

Kenyon, Johanna J.; Hall, Ruth M.

2013-01-01

144

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

NASA Astrophysics Data System (ADS)

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

Hooke, J. M.

2007-11-01

145

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

146

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

NASA Astrophysics Data System (ADS)

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

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

2010-12-01

147

Genetic variation and haplotype structure of the gene Vitamin K epoxide reductase complex, subunit 1 in the Tamilian population  

PubMed Central

Objective: To study the genetic variation and haplotype structure of Vitamin K epoxide reductase complex, subunit 1 (VKORC1) gene in the Tamilian population. Materials And Methods: The study was performed on 210 unrelated, healthy volunteers of the Tamilian population, of either sex between the age group of 18-60 years. Five ml of venous blood sample was collected using sodium ethylene diamine tetra acetic acid (EDTA) as anticoagulant. DNA was extracted using phenol-chloroform extraction method. Eight single nucleotide polymorphisms (SNPs) VKORC1 rs9923231 (G), rs7196161 (T), rs2884737 (T), rs17708472 (C), rs9934438 (C), rs8050894 (G), rs23596121 (C), and rs7294 (A) were studied using real-time quantitative Polymerase Chain Reaction (qPCR) method and they were included for constructing five-major haplotype blocks of VKORC1 gene. Results: The major alleles of VKORC1 rs9923231 (G), rs7196161 (T), rs2884737 (T), rs17708472 (C), rs9934438 (C), rs8050894 (G), and rs23596121 (C), were found to be at frequencies of 90.0%, 89.2%, 90.9%, 94.1%, 90.7%, 89.5% and 91.2%, respectively. The variant allele of VKORC1 rs7294 (A) was more frequent (83.6%) in the Tamilian population. The frequencies of haplotypes HAP1 (GTTCCGCA), HAP2 (ACGCTCTG), HAP3 (GTTTCGCG), HAP4 (GTTCCGCG) and HAP5 (GCTCCCCG) were found to be 80.0%, 7.4%, 4.7%, 1.5% and 1.1%, respectively. Conclusion: In the present study the allele- frequency distributions, genotype and haplotype frequencies of the VKORC1 gene was considered. The findings of this study provide the genetic information required for learning the association of VKORC1 genetic variation and oral anticoagulant dose variability among patients receiving oral anticoagulants in the Tamilian population. PMID:23662025

Kumar, Dhakchinamoorthi Krishna; Shewade, Deepak Gopal; Surendiran, Adithan; Adithan, Chandrasekaran

2013-01-01

148

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

149

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

150

Extreme Nd isotopic variation in the Trinity Ophiolite Complex and the role of melt\\/rock reactions in the oceanic lithosphere  

Microsoft Academic Search

.  ?Peridotites, dykes and gabbros from the 470–420 Ma Trinity Ophiolite Complex of northern California exhibit large geochemical\\u000a rare earth element (REE) and Nd isotopic variations on the small scales which are indicative of a complex history. The Trinity\\u000a Ophiolite, which covers an area of ?1600 km2, consists of three distinct units: (1) a ?2–4 km-thick sheet of plastically deformed peridotites,

G. Gruau; J. Bernard-Griffiths; C. Lécuyer; O. Henin; J. Macé; M. Cannat

1995-01-01

151

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

PubMed

The mean radiant temperature, T(mrt), which sums up all shortwave and longwave radiation fluxes (both direct and reflected) to which the human body is exposed is one of the key meteorological parameters governing human energy balance and the thermal comfort of man. In this paper, a new radiation model (SOLWEIG 1.0), which simulates spatial variations of 3D radiation fluxes and T(mrt) in complex urban settings, is presented. The T(mrt) is derived by modelling shortwave and longwave radiation fluxes in six directions (upward, downward and from the four cardinal points) and angular factors. The model requires a limited number of inputs, such as direct, diffuse and global shortwave radiation, air temperature, relative humidity, urban geometry and geographical information (latitude, longitude and elevation). The model was evaluated using 7 days of integral radiation measurements at two sites with different building geometries--a large square and a small courtyard in Göteborg, Sweden (57 degrees N)--across different seasons and in various weather conditions. The evaluation reveals good agreement between modelled and measured values of T(mrt), with an overall good correspondence of R (2) = 0.94, (p < 0.01, RMSE = 4.8 K). SOLWEIG 1.0 is still under development. Future work will incorporate a vegetation scheme, as well as an improvement of the estimation of fluxes from the four cardinal points. PMID:18523814

Lindberg, Fredrik; Holmer, Björn; Thorsson, Sofia

2008-09-01

152

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

PubMed Central

Background The Lysiphlebus fabarum group is a taxonomically poorly resolved complex of aphid parasitoids, presently split into three described species that comprise sexual (arrhenotokous) and asexual (thelytokous) lineages of unknown relationship. Specifically, it is unclear how asexuals evolved from sexuals in this system, to what extent reproductive modes are still connected by genetic exchange, how much the complex is structured by geography or by host-associated differentiation, and whether species designations are valid. Using a combination of population genetic and phylogenetic approaches, we addressed these issues in a comprehensive sample of parasitoid wasps from across Europe. Results Asexual reproduction predominated in parasitoids of the L. fabarum group, with asexual populations exhibiting high genotypic diversity. Sexual populations were only common in southern France; elsewhere sexual reproduction was restricted to specific aphid hosts. Although reproductive modes were aggregated on the mitochondrial genealogy and significantly differentiated at nuclear microsatellite loci, there was clear evidence for genetic exchange, especially on hosts attacked by sexual and asexual parasitoids. The microsatellite data further revealed that parasitoids collected from certain host aphids were significantly differentiated, yet the mitochondrial sequence variation across the entire L. fabarum group did not exceed 1.32% and exhibited a very shallow topology. Morphological characters used for delineation of described species were found to be phylogenetically non-conservative. Conclusions Our results suggest that the sexual-asexual L. fabarum group represents a young complex of lineages with incomplete isolation between reproductive modes. We propose three mechanisms of genetic exchange that may jointly explain the high genotypic diversity observed in asexual parasitoids: (i) the formation of new asexual lineages via 'contagious parthenogenesis', (ii) introgression from sexual lineages through matings between sexual males and thelytokous females, and (iii) 'cryptic sex' within asexuals, mediated by rare males that thelytokous lines are known to produce spontaneously. The partially strong differentiation among wasps collected from different aphids suggests that host specialization can evolve readily in these parasitoids. Finally, we conclude that in the light of our data, the current taxonomic division of the L. fabarum group into three species cannot be upheld. PMID:22132834

2011-01-01

153

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

SciTech Connect

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

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

2012-01-01

154

Generalization of internal Density Functional Theory and Kohn-Sham scheme to multicomponent systems, and link with traditional DFT  

E-print Network

We generalize the recently developped "internal" Density Functional Theory (DFT) and Kohn-Sham scheme to multicomponent systems. We obtain a general formalism, applicable for the description of multicomponent self-bound systems (as molecules where the nuclei are treated explicitely, atomic nuclei and mix of 3He and 4He droplets), where the fundamental translational symmetry has been treated correctly. The main difference with traditional DFT is the explicit inclusion of center-of-mass correlations in the functional. A large part of the paper is dedicated to the application to molecules, which permits among other to clarify the approximations that underly traditional DFT.

Jeremie Messud

2011-07-22

155

Both Naturally Occurring Insertions of Transposable Elements and Intermediate Frequency Polymorphisms at the achaete-scute Complex Are Associated With Variation in Bristle Number in Drosophila melanogaster  

Microsoft Academic Search

A restriction enzyme survey of a 110-kb region including the achaete scute complex (ASC) examined 14 polymorphic molecular markers in a sample of 56 naturally occurring chromosomes. Large insertions as a class were associated with a reduction in both sternopleural and abdominal bristle number, supporting deleterious mutation-selection equilibrium models for the maintenance of quantitative genetic variation. Two polymorphic sites were

Anthony D. Long; Richard F. Lyman; Alison H. Morgan; Charles H. Langley; Trudy F. C. Mackay

2000-01-01

156

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

SciTech Connect

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

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

1999-09-01

157

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

PubMed Central

Background Hop (Humulus lupulus L.) is cultivated for its cones, the secondary metabolites of which contribute bitterness, flavour and aroma to beer. Molecular breeding methods, such as marker assisted selection (MAS), have great potential for improving the efficiency of hop breeding. The success of MAS is reliant on the identification of reliable marker-trait associations. This study used quantitative trait loci (QTL) analysis to identify marker-trait associations for hop, focusing on traits related to expediting plant sex identification, increasing yield capacity and improving bittering, flavour and aroma chemistry. Results QTL analysis was performed on two new linkage maps incorporating transferable Diversity Arrays Technology (DArT) markers. Sixty-three QTL were identified, influencing 36 of the 50 traits examined. A putative sex-linked marker was validated in a different pedigree, confirming the potential of this marker as a screening tool in hop breeding programs. An ontogenetically stable QTL was identified for the yield trait dry cone weight; and a QTL was identified for essential oil content, which verified the genetic basis for variation in secondary metabolite accumulation in hop cones. A total of 60 QTL were identified for 33 secondary metabolite traits. Of these, 51 were pleiotropic/linked, affecting a substantial number of secondary metabolites; nine were specific to individual secondary metabolites. Conclusions Pleiotropy and linkage, found for the first time to influence multiple hop secondary metabolites, have important implications for molecular selection methods. The selection of particular secondary metabolite profiles using pleiotropic/linked QTL will be challenging because of the difficulty of selecting for specific traits without adversely changing others. QTL specific to individual secondary metabolites, however, offer unequalled value to selection programs. In addition to their potential for selection, the QTL identified in this study advance our understanding of the genetic control of traits of current economic and breeding significance in hop and demonstrate the complex genetic architecture underlying variation in these traits. The linkage information obtained in this study, based on transferable markers, can be used to facilitate the validation of QTL, crucial to the success of MAS. PMID:23718194

2013-01-01

158

Phenotypic consequences of genetic variation in a gynogenetic complex of Phoxinus eos-neogaeus clonal fish (Pisces: Cyprinidae) inhabiting a heterogeneous environment.  

PubMed

We examined the genetic composition, habitat use, and morphological variation of a Phoxinus eos-neogaeus unisexual hybrid complex and its sexually reproducing progenitor species inhabiting beaver-modified drainages of Voyageurs National Park, Minnesota. In addition to the single diploid P. eos-neogaeus gynogenetic clone, triploid and diploid-triploid mosaic biotypes were present at our study sites. Both P. eos and P. neogaeus, and all three hybrid biotypes were ubiquitous throughout one intensively surveyed drainage, but abundances and relative frequencies of the parental species and hybrids varied considerably within and among successional environments. Data from a large number of additional sites indicated that the proportion of polyploid hybrids within an environment was negatively related to hybrid relative frequency, implying that the genomic constitution of hybrids is an important determinant of clonal fitness among successional environments. Statistical comparisons of variation along size-free multivariate body shape axes indicated that despite its genetic uniformity, the P. eos-neogaeus clone is no less variable than its sexual progenitors, suggesting that a single genotype may actually respond to environmental variation with as much phenotypic variation as a genetically variable sexual population. The incorporation and expression of a third genome in triploid and diploid-triploid mosaic biotypes derived from the gynogenetic clone significantly expanded phenotypic variation of the clone. This additional variation results in greater similarities in habitat use and morphological overlap with the parental species, primarily P. eos, the predominant sperm donor for gynogenetic hybrid females in this complex. Polyploid augmentation of a diploid gynogenetic clone appears to be typical in the P. eos-neogaeus complex, and the additional genetic and phenotypic variation that it generates has potentially significant ecological and evolutionary consequences for the success and persistence of a single genotype in highly variable environments. PMID:15266975

Doeringsfeld, Matthew R; Schlosser, Isaac J; Elder, John F; Evenson, Donald P

2004-06-01

159

Both naturally occurring insertions of transposable elements and intermediate frequency polymorphisms at the achaete-scute complex are associated with variation in bristle number in Drosophila melanogaster.  

PubMed

A restriction enzyme survey of a 110-kb region including the achaete scute complex (ASC) examined 14 polymorphic molecular markers in a sample of 56 naturally occurring chromosomes. Large insertions as a class were associated with a reduction in both sternopleural and abdominal bristle number, supporting deleterious mutation-selection equilibrium models for the maintenance of quantitative genetic variation. Two polymorphic sites were independently associated with variation in bristle number measured in two genetic backgrounds as assessed by a permutation test. A 6-bp deletion near sc alpha is associated with sternopleural bristle number variation in both sexes and a 3.4-kb insertion between sc beta and sc gamma is associated with abdominal bristle number variation in females. Under an additive genetic model, the small deletion polymorphism near sc alpha accounts for 25% of the total X chromosome genetic variation in sternopleural bristle number, and the 3.4 kb insertion accounts for 22% of the total X chromosome variation in female abdominal bristle number. The observation of common polymorphisms associated with variation in bristle number is more parsimoniously explained by models that incorporate balancing selection or assume variants affecting bristle number are neutral, than mutation-selection equilibrium models. PMID:10757767

Long, A D; Lyman, R F; Morgan, A H; Langley, C H; Mackay, T F

2000-03-01

160

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

PubMed Central

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

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

2013-01-01

161

Isoallergen variations contribute to the overall complexity of effector cell degranulation: effect mediated through differentiated IgE affinity.  

PubMed

Most allergens exist in several variants (isoallergens), each of which may be recognized differently by patient IgE. We have previously shown that several properties of the IgE repertoire, including IgE affinity and IgE clonality, are important factors determining degranulation responses of effector cells involved in type I allergic reactions. However, less is known about how the repertoire of naturally occurring isoallergens may affect this response. Thus, in this study, we investigated how individual rIgE Ab clones derived from a human subject are able to distinguish among variants of Der p 2 isoallergens and assessed the impact on basophil degranulation. Biacore analyses showed that individual rIgE clones cloned from an individual allergic to house dust mites recognized Der p 2 with binding affinities varying up to 100-fold between different Der p 2 isoforms. In a well-defined biological system consisting of human basophils sensitized with low rIgE clonality, degranulation responses were directly related to rIgE affinity toward particular rDer p 2 isoallergens. However, basophils sensitized with polyclonal patients' sera showed no differences in degranulation responses toward the different rDer p 2 isoallergens. In conclusion, our study shows that individual IgE Abs are able to bind single allergens with a broad range of affinities due to natural isoallergen variations, contributing further to the overall complexity of IgE-allergen interactions at the effector cell surface, which is, however, blurred by the polyclonal nature of patients' IgE repertoires. PMID:20348423

Christensen, Lars H; Riise, Erik; Bang, Laerke; Zhang, Chunqing; Lund, Kaare

2010-05-01

162

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

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

163

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

Microsoft Academic Search

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

Donelle M. Robinson; Molly R. Morris

2010-01-01

164

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

165

Artificial symmetry breaking in radicals is avoided by the use of the Ensemble-Referenced Kohn Sham (REKS) method  

NASA Astrophysics Data System (ADS)

The computational scheme, termed spin-restricted ensemble-referenced Kohn-Sham (REKS) method (M. Filatov, S. Shaik, Chem. Phys. Lett. 304 (1999) 429; M. Filatov, S. Shaik, J. Phys. Chem. A 104 (2000) 6628), developed earlier to treat the strong non-dynamic correlation in singlet diradicals is extended for doublet states of triradicals. The energy and the density in the REKS method are represented as weighted sums of energies and densities of several KS determinants. The new method, dubbed REKS(3,3), is applied to calculation of several model problems where the conventional spin-unrestricted density functional calculations break the spatial symmetry. The results of the REKS(3,3) calculations show that the method avoids an artificial symmetry breaking in open-shell systems.

Filatov, Michael; Shaik, Sason

2000-12-01

166

Mitochondrial-DNA variation and the evolutionary affinities of the Peromyscus maniculatus complex from western North America  

E-print Network

. Mitochondrial DNA (mtDNA) fits these criteria and was thereby ideal for analyzing genetic variation within and among the youngest taxonomic members of the Peromyscus maniculatus species group, P. sejugis (restricted to two islands in the Sea of Cort���©s), P...

Walker, Mindy Lynn

2006-04-12

167

Between-Year Variation in Population Sex Ratio Increases with Complexity of the Breeding System in Hymenoptera.  

E-print Network

, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive occurs in social Hymenoptera, long-term studies have revealed substantial un- explained between-year variation in population sex ratio in multiple-queen eu- social species, which supports the view

Alvarez, Nadir

168

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

NASA Technical Reports Server (NTRS)

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

Leith, Andrew C.; Mckinnon, William B.

1991-01-01

169

[Variation of microsatellites BM224 and Bcal7 in populations of green toads (Bufo viridis complex) with various nuclear DNA content and ploidy].  

PubMed

We studied variation of microsatellites BM224 and Bcal7 in three species of the Bufo viridis diploid-polyploid complex. We found that locus Bcal7 in all examined samples was monomorphic. Three alleles of microsatellite BM224 were found. Among tetraploid toads, the western species B. oblongus had only one allele variant, whereas the eastern species B. pewzowi had two other alleles. Similar distribution of alleles was observed in triploid specimens, collected in the area borders of tetraploid and diploid species. Among samples of diploid toad B. viridis, we found all three allele variants of microsatellite BM224. Their distribution was geographically determined. A comparison of allele distribution with genome size variation in diploid toads showed very similar patterns. PMID:16841495

Litvinchuk, S N; Rozanov, Iu M; Usmanova, N M; Borkin, L Ia; Mazanaeva, L F; Kazakov, V I

2006-01-01

170

Extreme Nd isotopic variation in the Trinity Ophiolite Complex and the role of melt/rock reactions in the oceanic lithosphere  

NASA Astrophysics Data System (ADS)

Peridotites, dykes and gabbros from the 470 420 Ma Trinity Ophiolite Complex of northern California exhibit large geochemical rare earth element (REE) and Nd isotopic variations on the small scales which are indicative of a complex history. The Trinity Ophiolite, which covers an area of ?1600 km2, consists of three distinct units: (1) a ˜2 4 km-thick sheet of plastically deformed peridotites, including various ultrabasic lithologies (plagioclase and spinel lherzolite, harzburgite, wherlite and dunite); the peridotite unit is a fragment of mantle lithosphere of oceanic affinity; (2) a series of small (˜1 km diameter) undeformed gabbroic massifs; (3) several generations of basic dykes. The peridotites display the largest geochemical and isotopic variations, with ?Nd( T) values ranging from +10 down to 0. In the gabbroic massifs and intrusive dykes, the variation in model ?Nd( T) values is reduced to 7 ?Nd units: 0 to +7. As a general rule, peridotites, gabbros and dykes with ?Nd( T) values around 0 or +3 give less depleted L(light)REE patterns than do those with ?Nd( T) values in the range +7 to +10. In the peridotites, the Nd isotopic variations take place over very short distances, with jumps as large as 7 ?Nd units occurring on scales of less than 20 m. Comparison with available age data indicates that the peridotites with ?Nd( T)?+10 could be slightly older than the intrusive gabbro massifs and basic dykes (470 Ma vs. 420 Ma). Strontium isotopic data used in connection with Sm-Nd results demonstrate that the 10 ?Nd units variation displayed by the Trinity Peridotite is a primary feature and not an artefact due to REE mobility during seawater interaction. The variable Nd isotopic signatures and variable LREE patterns in the Trinity Peridotite cannot represent mantle source characteristics as there is evidence that this unit was partially melted when it rose as part of the upwelling convecting mantle. Field, petrographic, geochemical and isotopic data rather suggest that the observed heterogeneity is due to local reactions between a 470 Ma proto-peridotite with ?Nd( T)=+10 and younger (420 Ma) basaltic melts with lower ?Nd( T) values (i.e. the gabbroic massifs and the dykes). The gabbros and basic dykes of the Trinity Complex have geochemical and isotopic compositions similar to the arc basalts from the adjacent Copley Formation, so it is proposed that the younger melts are related to arc magmatism.

Gruau, G.; Bernard-Griffiths, J.; Lécuyer, C.; Henin, O.; Macé, J.; Cannat, M.

1995-10-01

171

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

PubMed Central

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

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

2014-01-01

172

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

USGS Publications Warehouse

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

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

2014-01-01

173

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

E-print Network

.S.A.) (ANSP), Museum of Comparative Zoology (Cambridge, U.S.A.) (MCZ), Museum of Vertebrate Zoology (Berke- ley, U.S.A.) (MVZ), Yale Peabody Museum (New Haven, U.S.A.) (YPM), Royal ontario Museum (Toronto, Canada) (RoM), University of Kansas Natural History... poliocephalus from Tolokiwa Island in the Bismarck Archipelago. emu 89:58-60. Galbraith, I. C. J. 1956. Variation, relationships and evolution in the Pachycephala pectoralis superspecies (Aves, Muscicapidae). Bulletin of the British Museum (Natural History...

Peterson, A. Townsend

2007-09-12

174

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

PubMed

The role of the static Kohn-Sham (KS) response function describing the response of the electron density to a change of the local KS potential is discussed in both the theory of the optimized effective potential (OEP) and the so-called inverse Kohn-Sham problem involving the task to find the local KS potential for a given electron density. In a general discussion of the integral equation to be solved in both cases, it is argued that a unique solution of this equation can be found even in case of finite atomic orbital basis sets. It is shown how a matrix representation of the response function can be obtained if the exchange-correlation potential is expanded in terms of a Schmidt-orthogonalized basis comprising orbitals products of occupied and virtual orbitals. The viability of this approach in both OEP theory and the inverse KS problem is illustrated by numerical examples. PMID:25296783

Kollmar, Christian; Neese, Frank

2014-10-01

175

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

NASA Astrophysics Data System (ADS)

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

Kollmar, Christian; Neese, Frank

2014-10-01

176

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

PubMed Central

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

Duchoslav, Martin; Safarova, Lenka; Jandova, Michaela

2013-01-01

177

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

178

The complex global pattern of genetic variation and linkage disequilibrium at Catechol-O-methyl transferase (COMT)  

PubMed Central

Genetic variation at the Catechol-O-metyltransferase (COMT) gene has been significantly associated with risk for various neuropsychiatric conditions such as schizophrenia, panic disorder, bipolar disorders, anorexia nervosa, and others. It has also been associated with nicotine dependence, sensitivity to pain, and cognitive dysfunctions especially in schizophrenia. The non-synonymous SNP in exon 4 - Val108/158Met - is the most studied SNP at COMT and the basis for most associations. It is not, however, the only variation in the gene; several haplotypes exist across the gene. Some studies indicate that the haplotypic combinations of alleles at the Val108/158Met SNP with those in the promoter region and in the 3' untranslated region are responsible for the associations with disorders and not the non-synonymous SNP by itself. We have now studied DNA samples from 45 populations for 63 SNPs in a region of 172kb across the region of 22q11.2 encompassing the COMT gene. We focused on 28 SNPs spanning the COMT coding region and immediately flanking DNA, and found that the haplotypes are from diverse evolutionary lineages that could harbor as yet undetected variants with functional consequences. Future association studies should be based on SNPs that define the common haplotypes in the population(s) being studied. PMID:18574484

Mukherjee, N; Kidd, KK; Pakstis, AJ; Speed, WC; Li, H; Tarnok, Z; Barta, C; Kajuna, SLB; Kidd, JR

2009-01-01

179

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

PubMed Central

The planar NNN-pincer complexes [MII(pyN Me2)(OH)]1? (MII = Ni, Cu) fix CO2 in ?1-OCO2H complexes; results for the copper system are described. MnII, FeII, CoII, and ZnII behave differently, forming [MII(pyN2Me)2]2? with N4O2 coordination. Incorporation of the NiII pincer into binucleating macrocycle 2 containing a triamino MII locus connected by two 1,3-biphenylene groups affords proximal NiII and MII sites for investigation of the synthesis, structure, and reactivity of Ni-X-M bridge units. This ligand structure is taken as a reference for variations in MII atoms and binding sites and bridges X = OH? and CN? to produce additional members of the macrocyclic family with improved properties. Macrocycle 2 with a 22-membered ring is shown to bind MII = Mn, Fe, and Cu with hydroxo bridges. Introduction of the 4-BuiO group (macrocycle 3) improves the solubility of neutral complexes such as those with NiII-OH-CuII and NiII-CN-FeII bridges. The syntheses of macrocycle 5 with a 7-Me-[12]aneSN3 and macrocycle 6 with a 1,8-Me2-[14]aneN4 MII binding site are described to together with hydoxo-bridged Ni-Cu and cyano-bridged Ni-Fe complexes. This work was motivated by the presence of a Ni?(HO)-Fe bridge grouping in a reactive state of carbon monoxide dehydrogenase. Attempted decrease in Ni-(OH)-M distances (3.70-3.87 Å) to smaller values observed in the enzyme by use of macrocycle 4 having 1,2-biphenylene connectors led to a mononuclear octahedral NiII complex. Bridge structural units are summarized and the structures of fourteen macrocyclic complexes including eight with bridges are described. PMID:23030366

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

2012-01-01

180

Seismic Velocity Variation within the Footwall of an Oceanic Core Complex - Atlantis Massif, Mid-Atlantic Ridge 30?N  

Microsoft Academic Search

The Atlantis Massif, an oceanic core complex (OCC) at 30ºN on the Mid-Atlantic Ridge, is hypothesized to have formed via long-lived slip on a detachment fault. Due to unroofing that results from this sustained slip, the domal core of the OCC is predicted to comprise lower crustal and\\/or upper mantle rock. Seafloor mapping and deep drilling confirm that this is

Ashlee S. Henig; Donna K. Blackman; Alistair J. Harding; Graham M. Kent; Juan-Pablo Canales

181

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

PubMed

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

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

2012-07-01

182

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

PubMed Central

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

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

2012-01-01

183

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

PubMed

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

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

2014-05-22

184

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

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

185

Chebyshev-filtered subspace iteration method free of sparse diagonalization for solving the Kohn-Sham equation  

NASA Astrophysics Data System (ADS)

First-principles density functional theory (DFT) calculations for the electronic structure problem require a solution of the Kohn-Sham equation, which requires one to solve a nonlinear eigenvalue problem. Solving the eigenvalue problem is usually the most expensive part in DFT calculations. Sparse iterative diagonalization methods that compute explicit eigenvectors can quickly become prohibitive for large scale problems. The Chebyshev-filtered subspace iteration (CheFSI) method avoids most of the explicit computation of eigenvectors and results in a significant speedup over iterative diagonalization methods for the DFT self-consistent field (SCF) calculations. However, the original formulation of the CheFSI method utilizes a sparse iterative diagonalization at the first SCF step to provide initial vectors for subspace filtering at latter SCF steps. This diagonalization is expensive for large scale problems. We develop a new initial filtering step to avoid completely this diagonalization, thus making the CheFSI method free of sparse iterative diagonalizations at all SCF steps. Our new approach saves memory usage and can be two to three times faster than the original CheFSI method.

Zhou, Yunkai; Chelikowsky, James R.; Saad, Yousef

2014-10-01

186

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

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

2009-01-01

187

Analysis of the Effect of Natural Sequence Variation in Tat and in Cyclin T on the Formation and RNA Binding Properties of Tat-Cyclin T Complexes  

PubMed Central

The biological activity of the human immunodeficiency virus type 1 (HIV-1) Tat (Tat1) transcriptional activator requires the recruitment of a Tat1-CyclinT1 (CycT1) complex to the TAR RNA target encoded within the viral long terminal repeat (LTR). While other primate immunodeficiency viruses, such as HIV-2 and mandrill simian immunodeficiency virus (SIVmnd), also encode Tat proteins that activate transcription via RNA targets, these proteins differ significantly, both from each other and from Tat1, in terms of their ability to activate transcription directed by LTR promoter elements found in different HIV and SIV isolates. Here, we show that CycT1 also serves as an essential cofactor for HIV-2 Tat (Tat2) and SIVmnd Tat (Tat-M) function. Moreover, the CycT1 complex formed by each Tat protein displays a distinct RNA target specificity that accurately predicts the level of activation observed with a particular LTR. While Tat2 and Tat-M share the ability of Tat1 to bind to CycT1, they differ from Tat1 in that they are also able to bind to the related but distinct CycT2. However, the resultant Tat-CycT2 complexes fail to bind TAR and are therefore abortive. Surprisingly, mutation of a single residue in CycT2 (asparagine 260 to cysteine) rescues the ability of CycT2 to bind Tat1 and also activates not only TAR binding by all three Tat-CycT2 complexes but also Tat function. Therefore, the RNA target specificity of different Tat-CycT1 complexes is modulated by natural sequence variation in both the viral Tat transcriptional activator and in the host cell CycT molecule recruited by Tat. Further, the RNA target specificity of the resultant Tat-CycT1 complex accurately predicts the ability of that complex to activate transcription from a given LTR promoter element. PMID:10364329

Bieniasz, Paul D.; Grdina, Therese A.; Bogerd, Hal P.; Cullen, Bryan R.

1999-01-01

188

Human interleukin-27: wide individual variation in plasma levels and complex inter-relationships with interleukin-17A.  

PubMed

Although it is widely believed that interleukin (IL)-27 is anti-inflammatory, its role in controlling human immune responses is not fully established. In particular, its interactions with T helper type 17 (Th)17 cytokines are unclear. Our aims were to establish the relationships between IL-27 and proinflammatory cytokines, including IL-17A, in human sera and cultures of peripheral blood mononuclear cells. Plasma IL-27 levels in 879 healthy humans from 163 families varied widely, but with relatively low heritability (19%). Despite IL-27 including a subunit encoded by Epstein-Barr virus-induced gene 3 (EBI3), there was no correlation of levels with serological evidence of infection with the virus. Although IL-27 has been reported to inhibit IL-17A production, we demonstrated a strong positive correlation in sera, but lower correlations of IL-27 with other proinflammatory cytokines. We verified that IL-27 inhibited IL-17A production by human peripheral blood T cells in vitro, but not that it stimulated IL-10 secretion. Importantly, addition of IL-17A decreased IL-27 production by stimulated T cells but had the opposite effect on resting T cells. Together, these data suggest a model whereby IL-27 and IL-17A exerts complex reciprocal effects to boost inflammatory responses, but restrain resting cells to prevent inappropriate activation. PMID:24975574

Forrester, M A; Robertson, L; Bayoumi, N; Keavney, B D; Barker, R N; Vickers, M A

2014-11-01

189

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

190

Variation in the organization and subunit composition of the mammalian pyruvate dehydrogenase complex E2/E3BP core assembly.  

PubMed

Crucial to glucose homoeostasis in humans, the hPDC (human pyruvate dehydrogenase complex) is a massive molecular machine comprising multiple copies of three distinct enzymes (E1-E3) and an accessory subunit, E3BP (E3-binding protein). Its icosahedral E2/E3BP 60-meric 'core' provides the central structural and mechanistic framework ensuring favourable E1 and E3 positioning and enzyme co-operativity. Current core models indicate either a 48E2+12E3BP or a 40E2+20E3BP subunit composition. In the present study, we demonstrate clear differences in subunit content and organization between the recombinant hPDC core (rhPDC; 40E2+20E3BP), generated under defined conditions where E3BP is produced in excess, and its native bovine (48E2+12E3BP) counterpart. The results of the present study provide a rational basis for resolving apparent differences between previous models, both obtained using rhE2/E3BP core assemblies where no account was taken of relative E2 and E3BP expression levels. Mathematical modelling predicts that an 'average' 48E2+12E3BP core arrangement allows maximum flexibility in assembly, while providing the appropriate balance of bound E1 and E3 enzymes for optimal catalytic efficiency and regulatory fine-tuning. We also show that the rhE2/E3BP and bovine E2/E3BP cores bind E3s with a 2:1 stoichiometry, and propose that mammalian PDC comprises a heterogeneous population of assemblies incorporating a network of E3 (and possibly E1) cross-bridges above the core surface. PMID:21627584

Vijayakrishnan, Swetha; Callow, Philip; Nutley, Margaret A; McGow, Donna P; Gilbert, David; Kropholler, Peter; Cooper, Alan; Byron, Olwyn; Lindsay, J Gordon

2011-08-01

191

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

192

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

PubMed Central

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

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

2012-01-01

193

"Kohn-Shamification" of the classical density-functional theory of inhomogeneous polar molecular liquids with application to liquid hydrogen chloride  

E-print Network

The Gordian knot of density-functional theories for classical molecular liquids remains finding an accurate free-energy functional in terms of the densities of the atomic sites of the molecules. Following Kohn and Sham, we show how to solve this problem by considering noninteracting molecules in a set of effective potentials. This shift in perspective leads to an accurate and computationally tractable description in terms of simple three-dimensional functions. We also treat both the linear- and saturation- dielectric responses of polar systems, presenting liquid hydrogen chloride as a case study.

Johannes Lischner; T. A. Arias

2008-06-27

194

Generalization of internal density-functional theory and Kohn-Sham scheme to multicomponent self-bound systems, and link with traditional density-functional theory  

SciTech Connect

We generalize the recently developed ''internal'' density-functional theory (DFT) and Kohn-Sham scheme to multicomponent systems. We obtain a general formalism, applicable for the description of multicomponent self-bound systems (such as molecular systems where the nuclei are treated explicitly, atomic nuclei and mixtures of {sup 3}He and {sup 4}He droplets), where the fundamental translational symmetry has been treated correctly. The main difference with traditional DFT is the explicit inclusion of center-of-mass correlations in the functional. A large part of the paper is dedicated to the application to molecular systems, which permits us to clarify the approximations that underly traditional DFT.

Messud, Jeremie [Universite Bordeaux, CNRS/IN2P3, Centre d'Etudes Nucleaires de Bordeaux Gradignan, UMR5797, F-33175 Gradignan (France) and Conseil Regional d'Aquitaine, F-33077 Bordeaux (France)

2011-11-15

195

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

196

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

197

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

198

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

PubMed

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

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

2013-01-01

199

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

NASA Astrophysics Data System (ADS)

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

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

2014-08-01

200

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

NASA Astrophysics Data System (ADS)

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

Levy, Mel; Zahariev, Federico

2014-09-01

201

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

202

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

E-print Network

We present a subspace projection technique to conduct large-scale Kohn-Sham density functional theory calculations using spectral finite-element discretization. The proposed method treats both metallic and insulating materials in a single framework, and is applicable to both pseudopotential as well as all-electron calculations. The key ideas involved in the method include: (i) employing a higher-order spectral finite-element basis that is amenable to mesh adaption; (ii) using a Chebyshev filter to construct a subspace which is an approximation to the occupied eigenspace in a given self-consistent field iteration; (iii) using a localization procedure to construct a non-orthogonal localized basis spanning the Chebyshev filtered subspace; (iv) using a Fermi-operator expansion in terms of the subspace-projected Hamiltonian represented in the non-orthogonal localized basis to compute relevant quantities like the density matrix, electron density and band energy. We demonstrate the accuracy and efficiency of the app...

Motamarri, Phani

2014-01-01

203

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

PubMed

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

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

2010-11-01

204

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

205

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

206

Downscaling Climate over Complex Terrain: High Finescale (<1000 m) Spatial Variation of Near-Ground Temperatures in a Montane Forested Landscape (Great Smoky Mountains)  

Microsoft Academic Search

Landscape-driven microclimates in mountainous terrain pose significant obstacles to predicting the re- sponse of organisms to atmospheric warming, but few if any studies have documented the extent of such finescale variation over large regions. This paper demonstrates that ground-level temperature regimes in Great Smoky Mountains National Park (Tennessee and North Carolina) vary considerably over fine spatial scales and are only

Jason D. Fridley

2009-01-01

207

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

NASA Astrophysics Data System (ADS)

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

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

1996-11-01

208

A biometrical analysis of morphological variation within a section of genusEuplotes (ciliata, hypotrichida), with special reference to theE. vannus complex of sibling species  

NASA Astrophysics Data System (ADS)

Some 50 clones belonging to a rather homogeneous, presumably monophyletic, section of genusEuplotes proved to be distributed between two clear-cut subgroups on the basis of cell size and relative peristome length. These subgroups are referred to asvannus andminuta morphotypes. Withinvannus morphotype, theE. vannus complex of 5 sibling species was previously defined on the basis of interfertility criterion. Electrophoretical studies revealed clear-cut biochemical differences between theE. vannus complex and theminuta morphotype. A multivariate analysis concerning 6 characters shows that the 5 species in the complex are closely similar. Nevertheless, the results of discriminant analysis suggest that a morphological discrimination could be possible. The status of one peculiar clone remains somewhat obscure. It belongs undoubtedly to thevannus morphotype, but shows no mating reaction with any of the 5 species ofE. vannus complex and is electrophoretically related tominuta morphotype. The following interpretation is suggested. In this section of genusEuplotes, two stable adaptive zones are available, corresponding to the two morphotypes. Speciation and change of adaptive zone are more or less independent evolutionary events. For example, the 5 species of thevannus complex have been generated by speciation without change of adaptive zone. Conversely, the exceptional clone may be phyletically related to theminuta morphotype through a rather recent jump from one adaptive zone to the other.

Machelon, Véronique; Génermont, Jean; Dattée, Yvette

1984-03-01

209

A fully relativistic method for calculation of nuclear magnetic shielding tensors with a restricted magnetically balanced basis in the framework of the matrix Dirac-Kohn-Sham equation.  

PubMed

A new relativistic four-component density functional approach for calculations of NMR shielding tensors has been developed and implemented. It is founded on the matrix formulation of the Dirac-Kohn-Sham (DKS) method. Initially, unperturbed equations are solved with the use of a restricted kinetically balanced basis set for the small component. The second-order coupled perturbed DKS method is then based on the use of restricted magnetically balanced basis sets for the small component. Benchmark relativistic calculations have been carried out for the (1)H and heavy-atom nuclear shielding tensors of the HX series (X=F,Cl,Br,I), where spin-orbit effects are known to be very pronounced. The restricted magnetically balanced basis set allows us to avoid additional approximations and/or strong basis set dependence which arises in some related approaches. The method provides an attractive alternative to existing approximate two-component methods with transformed Hamiltonians for relativistic calculations of chemical shifts and spin-spin coupling constants of heavy-atom systems. In particular, no picture-change effects arise in property calculations. PMID:18345871

Komorovský, Stanislav; Repiský, Michal; Malkina, Olga L; Malkin, Vladimir G; Malkin Ondík, Irina; Kaupp, Martin

2008-03-14

210

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

NASA Astrophysics Data System (ADS)

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

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

2012-01-01

211

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

NASA Astrophysics Data System (ADS)

The quadratic response function has been derived and implemented at the adiabatic four-component Kohn-Sham density functional theory level with inclusion of noncollinear spin magnetization and gradient corrections in the exchange-correlation functional-a work that is an extension of our previous report where magnetization dependencies in the exchange-correlation functional were ignored [J. Henriksson, T. Saue, and P. Norman, J. Chem. Phys. 128, 024105 (2008)]. The electric-field induced second-harmonic generation experiments on CF3Cl and CF3Br are addressed by a determination of ?(-2??,?) for a wavelength of 694.3 nm, and the same property is also determined for CF3I. The relativistic effects on the static hyperpolarizability for the series of molecules amount to 1%, 5%, and 9%, respectively. At the experimental wavelength, the contributions to ? due to the magnetization dependence in the exchange-correlation functional are negligible for CF3Cl and CF3Br and small for CF3I. The noticeable effect of magnetization in the latter case is attributed to a near two-photon resonance with the excited state 1 3E (nonrelativistic notation). It is emphasized, however, that the effect of magnetization on ? for CF3I is negligible both in comparison to the total relativistic correction as well as to the effects of electron correlation. It is concluded that, in calculations of hyperpolarizabilities under nonresonant conditions, the magnetization dependence in the exchange-correlation functional may be ignored.

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

2009-01-01

212

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

PubMed Central

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

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

2010-01-01

213

Natural crossbreeding between sympatric species of the phyllosoma complex (Insecta: Hemiptera: Reduviidae) indicate the existence of only one species with morphologic and genetic variations.  

PubMed

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

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

2010-01-01

214

Direct Variation  

NSDL National Science Digital Library

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

2012-01-01

215

Tunable self-assembly properties of amphiphilic phosphole alkynylgold(I) complexes through variation of the extent of the aromatic ?-surface at the alkynyl moieties.  

PubMed

A new class of amphiphilic phosphole alkynylgold(I) complexes was synthesized and was demonstrated to display sheet-like nanostructures in aqueous DMSO solution. Modulation of the extent of the aromatic ?-surface at the alkynyl ligands was found to affect the self-assembly properties as well as the stability of the aggregates as revealed by the nucleation-elongation model. PMID:25229073

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

2014-11-11

216

Different crystal morphologies lead to slightly different conformations of light-harvesting complex II as monitored by variations of the intrinsic fluorescence lifetime  

Microsoft Academic Search

In 2005, it was found that the fluorescence of crystals of the major light-harvesting complex LHCII of green plants is significantly quenched when compared to the fluorescence of isolated LHCII (A. A. Pascal et al., Nature, 2005, 436, 134-137). The Raman spectrum of crystallized LHCII was also found to be different from that of isolated LHCII but very similar to

Bart van Oort; Amandine Maréchal; Alexander V. Ruban; Bruno Robert; Andrew A. Pascal; Norbert C. A. de Ruijter; Rienk van Grondelle; Herbert van Amerongen

2011-01-01

217

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

218

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

219

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

PubMed

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

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

2003-05-01

220

C3v versus C2v Cd(1S,3P,1P)- CH4 van der Waals complexes: A variational and perturbational multireference configuration interaction study  

NASA Astrophysics Data System (ADS)

The Cd(1S,3,1P)-CH4 interaction is studied for the C3v vertex-on Cd(1S,3,1P)-HCH3 and face-on Cd(1S,3,1P)-H3CH approaches as well as the C2v Cd(1S,3,1P)-H2CH2 edge-on approach of the metal atom to methane using extensive ab initio multireference configuration interaction plus second order multireference Møller-Plesset calculations. The ground state Cd(1S)-CH4 is totally repulsive for the C3v vertex-on and C2v edge-on approaches. Only a stable face-on Cd(1S)-H3CH complex was found. Although vertex-on and edge-on minima were found for the Cd(3P)-CH4 excited complexes, they are less attractive than the corresponding Cd(3P)-H3CH face-on exciplexes. The optimal orientation of the face-on occupied 5p orbital of Cd(5s5p) is that which minimizes the overlap with C-H bonds leading to a ``3?y'' exciplex. For the Cd(1P)-CH4 interaction, two face-on and two edge-on very stable complexes (all with De?1300 cm-1) were found. The Cd(1S)-H3CH (1A1) complex was found to have a 185 cm-1 well at 8.03 a.u. Both excited P states present shorter equilibrium distances—the Cd(3P)-H3CH (3E) exciplex has a 799 cm-1 well at 6.08 a.u., while the Cd(1P)-H3CH exciplex (1E) has a 1337 cm-1 well at 5.57 a.u. These results are in good agreement with the recent experimental values X 1O+(1S)—(De=121 cm-1, Re=7.9 a.u.); A 3O+(3P)—(De=677 cm-1, Re=5.80 a.u.); and 1P—(De?1300 cm-1, Re=5.59 a.u.) obtained by Wallace and Breckenridge [J. Chem. Phys. 97, 2318 (1992)]. The present work confirms the C3v facial nature of the observed (1S) ground and (3P) excited complexes. The present results are inconclusive as to the facial or edge-on nature of the Cd(1P)-CH4 exciplex, but they preclude the C3v vertex-on possibility.

Ramírez-Solís, Alejandro; Castillo A., Sidonio

1993-05-01

221

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

SciTech Connect

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

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

1993-05-01

222

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

SciTech Connect

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

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

1993-01-01

223

Macro-array and bioinformatic analyses reveal mycobacterial 'core' genes, variation in the ESAT-6 gene family and new phylogenetic markers for the Mycobacterium tuberculosis complex.  

PubMed

To better understand the biology and the virulence determinants of the two major mycobacterial human pathogens Mycobacterium tuberculosis and Mycobacterium leprae, their genome sequences have been determined recently. In silico comparisons revealed that among the 1439 genes common to both M. tuberculosis and M. leprae, 219 genes code for proteins that show no similarity with proteins from other organisms. Therefore, the latter 'core' genes could be specific for mycobacteria or even for the intracellular mycobacterial pathogens. To obtain more information as to whether these genes really were mycobacteria-specific, they were included in a focused macro-array, which also contained genes from previously defined regions of difference (RD) known to be absent from Mycobacterium bovis BCG relative to M. tuberculosis. Hybridization of DNA from 40 strains of the M. tuberculosis complex and in silico comparison of these genes with the near-complete genome sequences from Mycobacterium avium, Mycobacterium marinum and Mycobacterium smegmatis were undertaken to answer this question. The results showed that among the 219 conserved genes, very few were not present in all the strains tested. Some of these missing genes code for proteins of the ESAT-6 family, a group of highly immunogenic small proteins whose presence and number is variable among the genomically highly conserved members of the M. tuberculosis complex. Indeed, the results suggest that, with few exceptions, the 'core' genes conserved among M. tuberculosis H37Rv and M. leprae are also highly conserved among other mycobacterial strains, which makes them interesting potential targets for developing new specific anti-mycobacterial drugs. In contrast, the genes from RD regions showed great variability among certain members of the M. tuberculosis complex, and some new specific deletions in Mycobacterium canettii, Mycobacterium microti and seal isolates were identified and further characterized during this study. Together with the distribution of a particular 6 or 7 bp micro-deletion in the gene encoding the polyketide synthase pks15/1, these results confirm and further extend the revised phylogenetic model for the M. tuberculosis complex recently presented. PMID:14766927

Marmiesse, Magali; Brodin, Priscille; Buchrieser, Carmen; Gutierrez, Christina; Simoes, Nathalie; Vincent, Veronique; Glaser, Philippe; Cole, Stewart T; Brosch, Roland

2004-02-01

224

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

225

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

NASA Astrophysics Data System (ADS)

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

Neese, Frank

2001-12-01

226

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

227

Robust Understanding of Statistical Variation  

ERIC Educational Resources Information Center

This paper presents a framework that captures the complexity of reasoning about variation in ways that are indicative of robust understanding and describes reasoning as a blend of design, data-centric, and modeling perspectives. Robust understanding is indicated by integrated reasoning about variation within each perspective and across…

Peters, Susan A.

2011-01-01

228

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

PubMed

Species in the genus Oncorhynchus 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 are considered isoloci because the most common allele at one of these loci cannot be separated electrophoretically from the most common allele of the other. Over 12 electrophoretically detectable alleles are segregating at the two sIDHP* loci in chinook salmon. Careful electrophoretic comparisons of the sIDHP isozyme patterns of muscle, eye, and liver extracts of heterozygotes reveal marked differences between the tissues with regard to both relative isozyme staining and the expression of several common alleles. Presumed single-dose heterozygotes at the sIDHP isolocus isozyme system exhibit approximate 9:6:1 ratios of staining intensity in liver and eye, while they exhibit approximate 1:2:1 ratios in skeletal muscle. The former proportions are consistent with the equal expression of two loci (isolocus expression), while the latter are consistent with the expression of a single locus. Screening of over 10,000 fish from spawning populations and mixed-stock fishery samples revealed that certain variant alleles (*127, *50) are detectable only in liver and eye, while other alleles (*129, *94, and *74) are strongly expressed in muscle, eye, and liver. The simplest explanation for these observations is that the "isolocus" sIDHP system of chinook salmon (and that of steelhead and rainbow trout) results from the expression of two distinct loci (sIDHP-1* and sIDHP-2*) that have the same common allele (as defined by electrophoretic mobility). IDHP expression in skeletal muscle is due to the nearly exclusive expression of the sIDHP-1* locus, while IDHP expression in eye and liver tissues is due to high levels of expression of both sIDHP-1* and sIDHP-2*--giving rise to the isolocus situation in these latter tissues. Direct inheritance studies confirm this model of two genetically independent (disomic) loci encoding sIDHP in chinook salmon. Extensive geographic surveys of chinook salmon populations from California to British Columbia reveal marked differences in allele frequencies at both sIDHP-1* and sIDHP-2* and considerably more interpopulation differentiation than was recognized previously when sIDHP was treated as an isolocus system with only five recognized alleles.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:1445187

Shaklee, J B; Phelps, S R

1992-10-01

229

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

NASA Astrophysics Data System (ADS)

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 raised that the KS orbital basis used in the calculation provides only approximate potential energy surfaces [J. Chem. Phys. 125, 014110 (2006)]. While this approximation does exist in our method, we show here that FSSH-TDKS is a viable option for computationally efficient calculations in large systems with straightforward excited state dynamics. We demonstrate that the potential energy surfaces and nonadiabatic transition probabilities obtained within the TDKS and linear response (LR) time-dependent density functional theories (TDDFT) agree semiquantitatively for three different systems, including an organic chromophore ligating a transition metal, a quantum dot, and a small molecule. Further, in the latter case the FSSH-TDKS procedure generates results that are in line with FSSH implemented within LR-TDDFT. The FSSH-TDKS approach is successful for several reasons. First, single-particle KS excitations often give a good representation of LR excitations. In this regard, DFT compares favorably with the Hartree-Fock theory, for which LR excitations are typically combinations of multiple single-particle excitations. Second, the majority of the FSSH-TDKS applications have been performed with large systems involving simple excitations types. Excitation of a single electron in such systems creates a relatively small perturbation to the total electron density summed over all electrons, and it has a small effect on the nuclear dynamics compared, for instance, with thermal nuclear fluctuations. In such cases an additional, classical-path approximation can be made. Third, typical observables measured in time-resolved experiments involve averaging over many initial conditions. Such averaging tends to cancel out random errors that may be encountered in individual simulated trajectories. Finally, if the flow of energy between electronic and nuclear subsystems is insignificant, the ad hoc FSSH procedure is not required, and a straightforward mean-field, Ehrenfest approach is sufficient. Then, the KS representation provides rigorously a convenient and efficient basis for numerically solving the TDDFT equations of motion.

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

2011-01-01

230

Variation Game  

NSDL National Science Digital Library

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

Science, Lawrence H.

1980-01-01

231

Complex poles and oscillatory screened potential in QED plasmas  

E-print Network

We discuss the mechanism for the oscillatory behavior of the static interparticle potential in a degenerate electron plasma. This behavior, observed in metallic alloys, is commonly referred to as 'Friedel oscillations', and its origin associated to the Kohn singularity. We show that, although this interpretation is adequate for large distances, the oscillations at short distances originate from a complex pole of the in-medium photon propagator in the complex q-plane, which exists aside the (purely imaginary) Debye pole. Such short-range oscillations can be physically discriminated if they remain at temperatures for which Friedel oscillations have already disappeared. This is suggested by finite temperature calculations in non-electromagnetic plasma models showing a similar pole structure.

H. D. Sivak; A. Perez; Joaquin Diaz-Alonso

2001-06-04

232

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

233

Infrared Variation of Blazars  

E-print Network

In this paper, the historical infrared (JHK) data compiled from the published literature are presented here for 30 blazars. Maximum near-IR variations are found and compared with the optical ones. For the color-magnitude relation, some objects show that the color index increases with magnitude while 1253-055 shows complex behaviour, which perhaps suggests that the emission mechanism consists of, at least, two parts. The spectral indexes are in the range of $\\alpha_{IR}$ = 0.77 to 2.37.

J. H. Fan

1999-10-14

234

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

235

Causes and Consequences of Chromatin Variation between Inbred Mice  

PubMed Central

Variation at regulatory elements, identified through hypersensitivity to digestion by DNase I, is believed to contribute to variation in complex traits, but the extent and consequences of this variation are poorly characterized. Analysis of terminally differentiated erythroblasts in eight inbred strains of mice identified reproducible variation at approximately 6% of DNase I hypersensitive sites (DHS). Only 30% of such variable DHS contain a sequence variant predictive of site variation. Nevertheless, sequence variants within variable DHS are more likely to be associated with complex traits than those in non-variant DHS, and variants associated with complex traits preferentially occur in variable DHS. Changes at a small proportion (less than 10%) of variable DHS are associated with changes in nearby transcriptional activity. Our results show that whilst DNA sequence variation is not the major determinant of variation in open chromatin, where such variants exist they are likely to be causal for complex traits. PMID:23785304

Hosseini, Mona; Goodstadt, Leo; Hughes, Jim R.; Kowalczyk, Monika S.; de Gobbi, Marco; Otto, Georg W.; Copley, Richard R.; Mott, Richard; Higgs, Douglas R.; Flint, Jonathan

2013-01-01

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

Dimension variation prediction and control for composites  

NASA Astrophysics Data System (ADS)

This dissertation presents a systematic study on the dimension variation prediction and control for polymer matrix fiber reinforced composites. A dimension variation model was developed for process simulation based on thermal stress analysis and finite element analysis (FEA). This model was validated against the experimental data, the analytical solutions and the data from literature. Using the FEA-based dimension variation model, the deformations of typical composite structures were studied and the regression-based dimension variation model was developed. The regression-based dimension variation model can significantly reduce computation time and provide a quick design guide for composite products with reduced dimension variations. By introducing the material modification coefficient, this comprehensive model can handle various fiber/resin types and stacking sequences. It eliminates the complicated, time-consuming finite element meshing and material parameter defining process. The deformation compensation through tooling design was investigated using the FEA-based and the regression-based dimension variation models. The structural tree method (STM) was developed to compute the assembly deformation from the deformations of individual components, as well as the deformation of general shape composite components. The STM enables rapid dimension variation analysis/synthesis for complex composite assemblies with the regression-based dimension variation model. Using the STM and the regression-based dimension variation model, design optimization and tolerance analysis/synthesis were conducted. The exploring work presented in this research provides a foundation to develop practical and proactive dimension control techniques for composite products.

Dong, Chensong

238

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

Microsoft Academic Search

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

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

2006-01-01

239

A density functional study of the electronic structure and spin Hamiltonian parameters of mononuclear thiomolybdenyl complexes.  

PubMed

The electron paramagnetic resonance spin Hamiltonian parameters of mononuclear thiomolybdenyl complexes based upon the tris(pyrazolyl)borate ligand, together with their molybdenyl analogues, are calculated using density functional theory. The electronic g matrix and 95Mo hyperfine matrix are calculated as second-order response properties from the coupled-perturbed Kohn-Sham equations. The scalar relativistic zero-order regular approximation (ZORA) is used with an all-electron basis and an accurate mean-field spin-orbit operator which includes all one- and two-electron terms. The principal values and relative orientations of the g and A interaction matrices obtained from the experimental spectra in a previous EPR study are compared with those obtained from unrestricted Kohn-Sham calculations at the BP86 and B3LYP level, and the latter are found to be in good quantitative agreement. A quasi-restricted approach is used to analyze the influence of the various molecular orbitals on g and A. In all complexes the ground state magnetic orbital is dX2-Y2-based and the orientation of the A matrix is directly related to the orientation of this orbital. The largest single contribution to the orientation of the g matrix arises from the spin-orbit coupling of the dYZ-based lowest-unoccupied molecular orbital into the ground state. A number of smaller, cumulative charge-transfer contributions augment the d-d contributions. A comparison of the theoretical EPR parameters obtained using both crystallographic and gas-phase geometry-optimized structures of Tp*MoO(bdt) (Tp* = hydrotris(3,5-dimethylpyrazol-1-yl)borate, bdt = 1,2-benzenedithiolate) suggests a correspondence between the metal-dithiolate fold angle and the angle of noncoincidence between g and A. PMID:17305330

Drew, Simon C; Young, Charles G; Hanson, Graeme R

2007-04-01

240

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

241

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

242

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

PubMed

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

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

2014-06-01

243

December, 2012. CURRICULUM VITAE: Melvin L. Kohn  

E-print Network

on Family Relations, for the research reported in "Social Class and the Exercise of Parental Authority of Birth: October 19, 1928; New York, New York. Education: 1944-46 Deep Springs Jr. College, Deep Springs-52 Cornell University, Ph.D. in sociology, with minors in social psychology and industrial relations

244

Variation of fundamental constants  

E-print Network

We present a review of recent works devoted to the variation of the fine structure constant alpha, strong interaction and fundamental masses. There are some hints for the variation in quasar absorption spectra, Big Bang nucleosynthesis, and Oklo natural nuclear reactor data. A very promising method to search for the variation of the fundamental constants consists in comparison of different atomic clocks. Huge enhancement of the variation effects happens in transition between accidentally degenerate atomic and molecular energy levels. A new idea is to build a ``nuclear'' clock based on the ultraviolet transition between very low excited state and ground state in Thorium nucleus. This may allow to improve sensitivity to the variation up to 10 orders of magnitude! Huge enhancement of the variation effects is also possible in cold atomic and molecular collisions near Feschbach resonance.

Flambaum, V V

2006-01-01

245

Variation of fundamental constants  

E-print Network

We present a review of recent works devoted to the variation of the fine structure constant alpha, strong interaction and fundamental masses. There are some hints for the variation in quasar absorption spectra, Big Bang nucleosynthesis, and Oklo natural nuclear reactor data. A very promising method to search for the variation of the fundamental constants consists in comparison of different atomic clocks. Huge enhancement of the variation effects happens in transition between accidentally degenerate atomic and molecular energy levels. A new idea is to build a ``nuclear'' clock based on the ultraviolet transition between very low excited state and ground state in Thorium nucleus. This may allow to improve sensitivity to the variation up to 10 orders of magnitude! Huge enhancement of the variation effects is also possible in cold atomic and molecular collisions near Feschbach resonance.

V. V. Flambaum

2006-08-25

246

Cultural Complexity  

Microsoft Academic Search

This paper is divided into four parts. The first section (I.) consists of definitions which center on the concept of complexity. As a minimum, the terms, system, complexity, and adaptation as used in this paper need an explanation. The second section (II.) is a sketch of cultural complexity in the real world. I will use Pueblo tribal laws and other

Wolfgang Fikentscher

1998-01-01

247

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

248

Scales of mussel bed complexity: structure, associated biota and recruitment  

Microsoft Academic Search

Hierarchically scaled surveys were carried out on beds of the brown mussel Perna perna (Linnaeus) on the South coast of South Africa. The object was to assess spatial and temporal variations in the complexity of mussel beds and to investigate relationships between mussel bed complexity and mussel recruitment. Complexity was divided into three components: physical complexity; demographic complexity; associated biota.

S. M. Lawrie; C. D. McQuaid

2001-01-01

249

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

250

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

251

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

252

Atomic dipole polarization in charge-transfer complexes with halogen bonding.  

PubMed

The polarization effects associated with halogen bonding for the series of charge-transfer complexes D(m)···X-Y, where donor molecules D(m) = NH(3), H(2)O, H(2)S, C(2)H(4), CO and X-Y = Cl(2), ClF, Br(2), BrCl, ICl, I(2), are characterized in terms of the quantum theory of atoms in molecules using the B3LYP/6-311** Kohn-Sham wave functions. We study the electrostatic potential features of separate donor and acceptor molecules, the change in atomic charges as well as the atomic electric dipole moments and their components, and the intra-atomic electron density dipole polarization and the bonding dipole moments resulting from the electron density redistribution between the molecules in the charge-transfer complexes. The equation linking the most negative electrostatic potential values in the donor molecules and the most positive values in dihalogen molecules with the stretching force constants was found using two-factor regression. It is demonstrated that the dipole polarization of the acceptor atom mirrors the strength of halogen bonding in complexes in a series of different donors and acceptors. An exponential relationship between the magnitude of the total atomic electric dipole moment of the acceptor atom and the intermolecular stretching force constant is established for weakly bounded complexes. PMID:23322002

Bartashevich, E V; Tsirelson, V G

2013-02-21

253

Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli  

E-print Network

Individual genetic variation affects gene responsiveness to stimuli, often by influencing complex molecular circuits. Here we combine genomic and intermediate-scale transcriptional profiling with computational methods to ...

Gat-Viks, Irit

254

Total Variation Electrocardiogram Filtering.  

National Technical Information Service (NTIS)

We examine the performance of Total Variation (TV) smoothing for processing of noisy Electrocardiogram (ECG) recorded by an ambulatory device. The TV smoothing is compared with traditionally-used bandpass filtering using ECG with artificially added noise ...

A. Gribok, M. Buller, R. Hoyt, W. Rumpler

2011-01-01

255

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

256

Direct and Inverse Variation  

NSDL National Science Digital Library

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

Media, Annenberg

2009-12-23

257

Chromatic variations suppress suprathreshold brightness variations.  

PubMed

Most objects in natural scenes are suprathreshold in both color (chromatic) and luminance contrast. How salient is each dimension? We have developed a novel method employing a stimulus similar to that used by B. C. Regan and J. D. Mollon (1997) who studied the relative saliencies of the two chromatic cardinal directions. Our stimuli consist of left- and right-oblique modulations of color and/or luminance defined within a lattice of circles. In the "separated" condition, the two modulations were presented separately as forced-choice pairs, and the task was to indicate which was more salient. In the "combined" condition, the two orthogonal-in-orientation modulations were added, and the task was to indicate the more salient orientation. The ratio of color to luminance contrast at the PSE was calculated for both conditions. Across color directions, 48% more luminance contrast relative to color contrast was required to achieve a PSE in the "combined" compared to the "separated" condition. A second experiment showed that the PSE difference was due to the luminance being masked by the color, rather than due to superior color grouping. We conclude that suprathreshold brightness variations are masked by suprathreshold color variations. PMID:20884478

Kingdom, Frederick A A; Bell, Jason; Gheorghiu, Elena; Malkoc, Gokhan

2010-01-01

258

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

NASA Astrophysics Data System (ADS)

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

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

2009-12-01

259

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.

260

Variation ontology: annotator guide  

PubMed Central

Background Systematic representation of information related to genetic and non-genetic variations is required to allow large scale studies, data mining and data integration, and to make it possible to reveal novel relationships between genotype and phenotype. Although lots of variation data is available it is often difficult to use due to lack of systematics. Results A novel ontology, Variation Ontology (VariO http://variationontology.org), was developed for annotation of effects, consequences and mechanisms of variations. In this article instructions are provided on how VariO annotations are made. The major levels for description are the three molecules, namely DNA, RNA and protein. They are further divided to four major sublevels: variation type, function, structure, and property, and further up to eight sublevels. VariO annotation summarizes existing knowledge about a variation and its effects and formalizes it so that computational analyses are efficient. The annotations should be made on as many levels as possible. VariO annotations are made in reference to normal states, which vary for each data item including e.g. reference sequences, wild type properties, and activities. Conclusions Detailed instructions together with examples are provided to indicate how VariO can be used for annotation of variations and their effects. A dedicated tool has been developed for annotation and will be further developed to cover also evidence for the annotations. VariO is suitable for annotation of data in many types of databases. As several different kinds of databases are in a process of adapting VariO annotations it is important to have guidelines to guarantee consistent annotation. PMID:24533660

2014-01-01

261

Complex variation of spectral line widths observed in polar corona  

NASA Astrophysics Data System (ADS)

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

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

2012-07-01

262

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

263

Variational nodal transport methods with heterogeneous nodes  

SciTech Connect

The variational nodal transport method is generalized for the treatment of heterogeneous nodes while maintaining nodal balances. Adapting variational methods to heterogeneous nodes requires the ability to integrate over a node with discontinuous cross sections. Integrals are evaluated using composite Gaussian quadrature rules, which permit accurate integration while yielding acceptable computing times. Allowing structure within a nodal solution scheme avoids some of the necessity of cross-section homogenization and more accurately defines the intranodal flux shape. Ideally, any desired heterogeneity can be constructed within the node, but in reality, the finite set of basis functions limits the intranodal complexity that can be modeled. Comparison tests show that the heterogeneous variational nodal method provides accurate results for moderate heterogeneities, even if some improvements are needed for very difficult configurations.

Fanning, T.H. [Univ. of Wisconsin, Madison, WI (United States). Dept. of Nuclear Engineering and Engineering Physics; Palmiotti, G. [Argonne National Lab., IL (United States). Reactor Analysis Div.

1997-10-01

264

Variations in the rotation of the Earth.  

PubMed

Variations in the earth's rotation (UT1) and length of day have been tracked at the submillisecond level by astronomical radio interferometry and laser ranging to the LAGEOS satellite. Three years of regular measurements reveal complex patterns of variations including UT1 fluctuations as large as 5 milliseconds in a few weeks. Comparison of the observed changes in length of day with variations in the global atmospheric angular momentum indicates that the dominant cause of changes in the earth's spin rate, on time scales from a week to several years, is the exchange of angular momentum between the atmosphere and the mantle. The unusually intense El Niño of 1982-1983 was marked by a strong peak in the length of day. PMID:17731980

Carter, W E; Robertson, D S; Pettey, J E; Tapley, B D; Schutz, B E; Eanes, R J; Lufeng, M

1984-06-01

265

Variations in the rotation of the earth  

NASA Astrophysics Data System (ADS)

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

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

266

Brane Variation Dirac Style  

E-print Network

Dirac's method for variations of a brane embedded in co-dimension one is demonstrated. The variation in the location of the brane invokes a rest frame formulation of the 'sandwiched' brane action. We first demonstrate the necessity of this method by re-deriving Snell's law. Second, we apply the method to a general $N$-dimensional brane embedded in co-dimension one bulk in the presence of gravity. We re-derive the brane equations: (i) Israel junction condition, (ii) Energy/momentum conservation on the brane, and (iii) Geodetic-type equation for the brane.

David Karasik; Aharon Davidson

2002-02-04

267

MORPHOLOGIC VARIATION IN PNEUMOCOCCUS  

PubMed Central

The problem of morphologic variation in pneumococcus has been reviewed and the desirability of studying such variation through an examination of bacterial cells rather than of bacterial colonies has been pointed out. To further this objective, a new terminology to describe the morphologic variants of pneumococcus, potentially applicable to other bacterial species, has been proposed. A hitherto undefined morphologic variant of pneumococcus, the filamentous capsulated (fil+ S+) variant, has been defined and its relationship to the three previously recognized non-filamentous capsulated (fil- S+), nonfilamentous non-capsulated (fil- S-), and filamentous non-capsulated (fil+ S-) variants has been presented. PMID:13069647

Austrian, Robert

1953-01-01

268

KNOWLEDGE COMPLEXITY VERSUS COMPUTATIONAL COMPLEXITY  

E-print Network

, and Rafi Ostrovsky, with whom I had the opportunity to work closely. Each of them contributed in his own to thank Mihir and Rafi for collaborating with us in the research of knowledge complexity versus

Goldreich, Oded

269

Tonotopic cortical representation of periodic complex sounds  

Microsoft Academic Search

Most of the sounds that are biologically relevant are complex periodic sounds, i.e., they are made up of harmonics, whose frequencies are integer multiples of a fundamental frequency (Fo). The Fo of a complex sound can be varied by modifying its periodicity frequency; these variations are perceived as the pitch of the voice or as the note of a musical

Selene Cansino; Antoine Ducorps; Richard Ragot

2003-01-01

270

Algebra Lab: Inverse Variation  

NSDL National Science Digital Library

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

2012-01-01

271

Variations in NHL Attendance  

Microsoft Academic Search

In recent years the National Hockey League (NHL) has put policies in place to boost attendance. Specifically, these changes have been to curb violence, increase scoring, and move to an unbalanced schedule featuring more games against regional rivals. This research looks at variations in game-to-game attendance in the NHL, focusing on these policy changes. It is found that violence, specifically

Rodney J. Paul

2003-01-01

272

Variation in Okra  

Microsoft Academic Search

A study of the variation of 29 characteristics of 585 varieties or seedlings of okra revealed that 17 West African varieties could be distinguished from all others on the basis of 5 discriminating characteristics. In addition, seedlings of the 3rd outcrossing generation of a population differed from a varietal collection in several characteristics, the most important of which were more

Franklin W. Martin; A. M. Rhodes; Manuel Ortiz; Félix Díaz

1981-01-01

273

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

274

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

275

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

276

Deinterlacing Using Variational Methods  

Microsoft Academic Search

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.

Sune Høgild Keller; François Lauze; Mads Nielsen

2008-01-01

277

Dissociative electron attachment to the H2O molecule. I. Complex-valued potential-energy surfaces for the 2B1, 2A1, and 2B2 metastable states of the water anion  

E-print Network

We present the results of calculations defining global, three-dimensional representations of the complex-valued potential-energy surfaces of the doublet B1, doublet A1, and doublet B2 metastable states of the water anion that underlie the physical process of dissociative electron attachment to water. The real part of the resonance energies is obtained from configuration-interaction calculations performed in a restricted Hilbert space, while the imaginary part of the energies (the widths) is derived from complex Kohn scattering calculations. A diabatization is performed on the 2A1 and 2B2 surfaces, due to the presence of a conical intersection between them. We discuss the implications that the shapes of the constructed potential-energy surfaces will have upon the nuclear dynamics of dissociative electron attachment to H2O. This work originally appeared as Phys Rev A 75, 012710 (2007). Typesetting errors in the published version have been corrected here.

Haxton, Daniel J; Rescigno, T N

2007-01-01

278

The nonholonomic variational principle  

NASA Astrophysics Data System (ADS)

A variational principle for mechanical systems and fields subject to nonholonomic constraints is found, providing Chetaev-reduced equations as equations for extremals. Investigating nonholonomic variations of the Chetaev type and their properties, we develop foundations of the calculus of variations on constraint manifolds, modelled as fibred submanifolds in jet bundles. This setting is appropriate to study general first-order 'nonlinear nonitegrable constraints' that locally are given by a system of first-order ordinary or partial differential equations. We obtain an invariant constrained first variation formula and constrained Euler-Lagrange equations both in intrinsic and coordinate forms, and show that the equations are the same as Chetaev equations 'without Lagrange multipliers', introduced recently by other methods. We pay attention to two possible settings: first, when the constrained system arises from an unconstrained Lagrangian system defined in a neighbourhood of the constraint, and second, more generally, when an 'internal' constrained system on the constraint manifold is given. In the latter case a corresponding unconstrained system need not be a Lagrangian, nor even exist. We also study in detail an important particular case: nonholonomic constraints that can be alternatively modelled by means of (co)distributions in the total space of the fibred manifold; in nonholonomic mechanics this happens whenever constraints affine in velocities are considered. It becomes clear that (and why) if the distribution is completely integrable (= the constraints are semiholonomic), the principle of virtual displacements holds and can be used to obtain the constrained first variational formula by a more or less standard procedure, traditionally used when unconstrained or holonomic systems are concerned. If, however, the constraint is nonintegrable, no significant simplifications are available. Among others, some properties of nonholonomic systems are clarified that without a deeper insight seem rather mysterious.

Krupková, Olga

2009-05-01

279

Measuring temporal gravitational variations using SLR data  

NASA Technical Reports Server (NTRS)

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

Nerem, Robert S.

1994-01-01

280

A computational model of teeth and the developmental origins of morphological variation  

E-print Network

LETTERS A computational model of teeth and the developmental origins of morphological variation variation of real teeth. To model the full range of develop- mentally possible morphologies, we used the complexity of development and teeth, there may be a simple basis for dental variation. Changes in single

Jernvall, Jukka

281

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

282

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

283

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

284

Sampling and variation  

SciTech Connect

The objective of geochemical soil surveys is to gather surface and near-surfaced data that, when combined with conventional information, may provide information concerning type and distribution of hydrocarbons in the subsurface. A well-planned sample arrangement is necessary if the resulting information is to be confidently applied throughout the sampled area. No amount of later statistical analysis or other sophisticated mathematical manipulation can overcome inadequate or improper sampling. Better estimates of probabilities of hydrocarbon potential and a more reliable depiction of probable regions for hydrocarbon reservoirs within a basin result when sampling design is coordinated with project goals. In contrast to subsurface exploration, surface methods allow for a totally programmed sample design. Grids and various random arrangements are sample designs that estimate subsurface processes in three dimensions. Non-grid linear sample patterns, including selected locations along roads, fence lines, or seismic survey lines, estimate variance along these lines and, therefore, are limited to estimating subsurface processes in two dimensions. Accurate interpretation of survey data requires accurate estimation of the relative contributions from each of three sources of variation: the surface environment, operational error, and the subsurface. Data can be related to the geologic framework, as determined by conventional subsurface methods, only within the limitations established by the magnitude of unwanted variation. Several pilot study designs that are useful for determining the relative magnitude of unwanted variation resulting from both operational error and from surface environmental effects are suggested, and should be planned as part of any large-scale program.

Gevirtz, J.L.; Curtis, J.B.; Gorody, T.W.; Brown, S.W.

1988-01-01

285

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

PubMed Central

Proton transport plays an important role in biological energy transduction and sensory systems. Therefore it has attracted much attention in biological science and biomedical engineering in the past few decades. The present work proposes a multiscale/multiphysics model for the understanding of the molecular mechanism of proton transport in transmembrane proteins involving continuum, atomic and quantum descriptions, assisted with the evolution, formation and visualization of membrane channel surfaces. We describe proton dynamics quantum mechanically via a new density functional theory based on the Boltzmann statistics, while implicitly model numerous solvent molecules as a dielectric continuum to reduce the number of degrees of freedom. The density of all other ions in the solvent is assumed to obey the Boltzmann distribution in a dynamic manner. The impact of protein molecular structure and its charge polarization on the proton transport is considered explicitly at the atomic scale. A variational solute-solvent interface is designed to separate the explicit molecule and implicit solvent regions. We formulate a total free energy functional to put proton kinetic and potential energies, the free energy of all other ions, the polar and nonpolar energies of the whole system on an equal footing. The variational principle is employed to derive coupled governing equations for the proton transport system. Generalized Laplace-Beltrami equation, generalized Poisson-Boltzmann equation and generalized Kohn-Sham equation are obtained from the present variational framework. The variational solvent-solute interface is generated and visualized to facilitate the multiscale discrete/continuum/quantum descriptions. Theoretical formulations for the proton density and conductance are constructed based on fundamental laws of physics. A number of mathematical algorithms, including the Dirichlet to Neumann mapping (DNM), matched interface and boundary (MIB) method, Gummel iteration, and Krylov space techniques are utilized to implement the proposed model in a computationally efficient manner. The Gramicidin A (GA) channel is used to validate the performance of the proposed proton transport model and demonstrate the efficiency of the proposed mathematical algorithms. The proton channel conductances are studied over a number of applied voltages and reference concentrations. A comparison with experimental data verifies the present model predictions and confirms the proposed model. PMID:22328970

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

2011-01-01

286

Complex networks created by aggregation  

NASA Astrophysics Data System (ADS)

We study aggregation as a mechanism for the creation of complex networks. In this evolution process vertices merge together, which increases a number of highly connected hubs. We study a range of complex network architectures produced by the aggregation. Fat-tailed (in particular, scale-free) distributions of connections are obtained for both networks with a finite number of vertices and growing networks. We observe a strong variation of a network structure with growing density of connections and find the phase transition of the condensation of edges. Finally, we demonstrate the importance of structural correlations in these networks.

Alava, M. J.; Dorogovtsev, S. N.

2005-03-01

287

Accurate finite-element multi-grid (FEM-MG) description for angular momentum and spin dependences of Kohn–Sham density functionals for axially restricted calculations on first-row atoms and dimers  

Microsoft Academic Search

A comparative study of various combinations of exchange and correlation density functionals was made possible by the finite element multi-grid method which has a controlled accuracy and became fast enough for large-scale applications on atoms and diatomic molecules under axial symmetry. The open-shell atoms B, C and O exhibit particularly interesting behaviour on occupation number variation, differing strongly in a

A. V. Kopylow; D. Kolb

1998-01-01

288

Complex Systems  

PubMed Central

Physiologic systems in health and disease display an extraordinary range of temporal behaviors and structural patterns that defy understanding based on linear constructs, reductionist strategies, and classical homeostasis. Application of concepts and computational tools derived from the contemporary study of complex systems, including nonlinear dynamics, fractals and “chaos theory,” is having an increasing impact on biology and medicine. This presentation provides a brief overview of an emerging area of biomedical research, including recent applications to cardiopulmonary medicine and chronic obstructive lung disease. PMID:16921107

Goldberger, Ary L.

2006-01-01

289

variational analysis in psychological modeling  

E-print Network

considerations are based on the recent “variational rationality approach” that unifies ..... e.g., anchoring, status quo, sunk costs, confirming evidence, framing, esti- ...... in a variational trap, which is a goal system habit for agents or a bundle of.

2013-11-06

290

The coefficient of cyclic variation: a novel statistic to measure the magnitude of cyclic variation  

PubMed Central

Background Periodic or cyclic data of known periodicity are frequently encountered in epidemiological and biomedical research: for instance, seasonality provides a useful experiment of nature while diurnal rhythms play an important role in endocrine secretion. There is, however, little consensus on how to analysis these data and less still on how to measure association or effect size for the often complex patterns seen. Results A simple statistic, readily derived from Fourier regression models, provides a readily-understood measure cyclic variation in a wide variety of situations. Conclusion The coefficient of cyclic variation or similar statistics derived from the variance of a Fourier series could provide a universal means of summarising the magnitude of periodic variation. PMID:25342954

2014-01-01

291

Social complexity can drive vocal complexity: group size influences vocal information in Carolina chickadees.  

PubMed

One hypothesis to explain variation in vocal communication in animal species is that the complexity of the social group influences the group's vocal complexity. This social-complexity hypothesis for communication is also central to recent arguments regarding the origins of human language, but experimental tests of the hypothesis are lacking. This study investigated whether group size, a fundamental component of social complexity, influences the complexity of a call functioning in the social organization of Carolina chickadees, Poecile carolinensis. In unmanipulated field settings, calls of individuals in larger groups had greater complexity (more information) than calls of individuals in smaller groups. In aviary settings manipulating group size, individuals in larger groups used calls with greater complexity than individuals in smaller groups. These results indicate that social complexity can influence communicative complexity in this species. PMID:16866738

Freeberg, Todd M

2006-07-01

292

Anisotropic Total Variation Filtering  

SciTech Connect

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

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

2010-12-15

293

Comprehensive variation discovery in single human genomes.  

PubMed

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

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

2014-12-01

294

Gene Transposition Causing Natural Variation for Growth in Arabidopsis thaliana  

PubMed Central

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

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

2010-01-01

295

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

296

Variations on tremor parameters  

NASA Astrophysics Data System (ADS)

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

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

1995-03-01

297

[Variation and evolution of meiosis].  

PubMed

Meiosis arose in the evolution of primitive unicellular organisms as a part of sexual process. One type of meiosis, the so-called classical type, predominates in all kingdoms of eukaryotes. Meiosis is controlled by hundreds of genes, both shared with mitosis and specifically meiotic ones. In a wide range of taxa, which in some cases include kingdoms, meiotic genes and features obey Vavilov's law of homologous variation series. Synaptonemal complexes (SCs) temporarily binding homologous chromosomes at prophase I, ensure precise and equal crossing over and interference. SC proteins have 60-80% homology within the class of mammals but differ from the corresponding proteins in fungi and plants. Thus, nonhomologous SC proteins perform similar functions in different taxa. Some recombination enzymes in fungi and insects have common epitopes. The molecular mechanism of recombination is inherited by eukaryotes from prokaryotes and operates in special compartments: SC recombination nodules. Chiasmata, i.e., physical crossovers of nonsister chromatids, are preserved in bivalents until metaphase I due to local cohesion of sister chromatids in the remaining SC fragments. Owing to chiasmata, homologous chromosomes participate in meiosis I in pairs rather than individually, which, along with unipolarity of kinetochores (only in meiosis 1), ensures segregation of homologous chromosomes. The appearance of SC and chiasmata played a key role in the evolution of unicellular organisms since it promoted the development of a progressive type of meiosis. Some lower eukaryotes retain primitive meiosis types. These primitive modes of meiosis also occur in the sex of some insects that is heterozygous for sex chromosomes. I suggest an explanation for these cases. Mutations at meiotic genes impair meiosis; however, due to the preservation of archaic meiotic genes in the genotype, bypass metabolic pathways arise, which provide partial rescue of the traits damaged by mutations. Individual blocks of genetic program of meiotic regulation have probably evolved independently. PMID:12760244

Bogdanov, Iu F

2003-04-01

298

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, Vit; Zhang, Yuanye; Karlsson Moritz, Kim; Fischer, Markus; Bossdorf, Oliver

2012-01-01

299

Saturn chorus intensity variations  

NASA Astrophysics Data System (ADS)

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

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

2013-09-01

300

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

301

PERSPECTIVE Copy-number variation and association studies of  

E-print Network

to be associated with several complex disease phenotypes, including HIV acquisition and progression6,lupus glomerulonephritis7 and three systemic autoimmune diseases: systemic lupus erythemato- sus,microscopic polyangiitisPERSPECTIVE Copy-number variation and association studies of human disease Steven A Mc

McCarroll, Steve

302

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

303

Variations of the sea level in the Amazon Estuary  

Microsoft Academic Search

We analyze the Geosat altimeter data off the mouth of the Amazon river. Variations of the sea level of up to 6 m are observed, which are correlated with bathymetry, and dominated by a complex tidal pattern. M2, N2 and O1 altimetric cotidal maps are constructed. Their amplitudes decrease strongly off the river mouth, probably by dissipation in the estuary.

J.-F. Minster; M.-L. Genco; C. Brossier

1995-01-01

304

Gene Transposition Causing Natural Variation for Growth in Arabidopsis thaliana  

E-print Network

recombinant inbred line set was decomposed into several QTLs. Nearly-isogenic lines generated from the residual heterozygosity segregating among lines revealed an even more complex picture, with major variation (Shoot Growth-3), as well as epistasis with SG3i (SG3-interactor). Using principally a fine-mapping

305

Variational Delaunay Approach to the Generation of Tetrahedral  

E-print Network

Variational Delaunay Approach to the Generation of Tetrahedral Finite Element Meshes Petr Krysl of arbitrarily complex three-dimensional solids into tetrahe- dral finite elements (tetrahedrization) is a very is easy to achieve), lack of robustness in three-dimensional geometries is a serious impediment

Krysl, Petr

306

Mitochondrial DNAsequence variation in single cells from leukemia patients  

Microsoft Academic Search

cells, in patients compared to controls. Patients with similar clinical leukemia types, particularly acute myeloid leuke- mia (AML), did not show a uniform pattern of sequence variation in single blasts. Some patients at relapse presented a complex shift of major haplotypes in single cells. Four patients showed high frequencies of cells containing mutations 189, 260, 16150, and 16488, respectively, as

Yong-Gang Yao; Yoji Ogasawara; Sachiko Kajigaya; Jeffrey J. Molldrem; Roberto P. Falcao; Maria-Carolina Pintao; J. Philip McCoy Jr; Edgar Gil Rizzatti; Neal S. Young

2007-01-01

307

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

308

The influence of variation in litter habitats on spider communities  

Microsoft Academic Search

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

George W. Uetz

1979-01-01

309

Variations in Myth: How Manipulations of Topos Create Morality  

Microsoft Academic Search

The Homeric epics have inspired the Western world for three thousand years. The Iliad especially is complex and compelling, while the author himself is enigmatic. Both poem and poet have sparked several libraries worth of scholarship. The poem is traditionally considered to be transmitted orally with numerous extant variations within the text itself. In the 6th century BC, by tradition,

Joel Huber

2012-01-01

310

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."

Program, The W.

311

Variational multiscale models for charge transport.  

PubMed

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

312

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

313

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

314

What constrains directional selection on complex traits in the wild?  

E-print Network

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

Mojica, Julius Penalba

2011-08-31

315

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

316

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

317

Variational Bounds for Creeping Composites  

Microsoft Academic Search

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

Petr Procházka

2010-01-01

318

Variational Bounds for Creeping Composites  

NASA Astrophysics Data System (ADS)

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

Procházka, Petr

2010-05-01

319

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.

320

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

321

Genetic Variation in Political Participation  

Microsoft Academic Search

The decision to vote has puzzled scholars for decades. Theoretical models predict little or no variation in participation in large population elections and empirical models have typically accounted for only a relatively small portion of individual-level variance in turnout behavior. However, these models have not considered the hypothesis that part of the variation in voting behavior can be attributed to

JAMES H. FOWLER; LAURA A. BAKER; CHRISTOPHER T. DAWES

2008-01-01

322

Contextual Variations in Implicit Evaluation  

Microsoft Academic Search

In the present research, the authors examined contextual variations in automatic attitudes. Using 2 measures of automatic attitudes, the authors demonstrated that evaluative responses differ qualitatively as perceivers focus on different aspects of a target's social group membership (e.g., race or gender). Contextual variations in automatic attitudes were obtained when the manipulation involved overt categorization (Experiments 1–3) as well as

Jason P. Mitchell; Brian A. Nosek; Mahzarin R. Banaji

2003-01-01

323

Seasonal Variations in Soudan 2  

Microsoft Academic Search

Seasonal Variations in an underground detector may be a signature for Dark Matter. 1 The Soudan 2 detector searches for nucleon decay and atmospheric neutrinos. The trigger rate is about 0.5 Hertz. It is dominated by approximately equal numbers of atmospheric muons and low level radioactivity. The muon rate has a seasonal variation of +-2°, which is consistent with a

Maury Goodman

1999-01-01

324

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

325

Copy number variation in schizophrenia in Sweden.  

PubMed

Schizophrenia (SCZ) is a highly heritable neuropsychiatric disorder of complex genetic etiology. Previous genome-wide surveys have revealed a greater burden of large, rare copy number variations (CNVs) in SCZ cases and identified multiple rare recurrent CNVs that increase risk of SCZ although with incomplete penetrance and pleiotropic effects. Identification of additional recurrent CNVs and biological pathways enriched for SCZ CNVs requires greater sample sizes. We conducted a genome-wide survey for CNVs associated with SCZ using a Swedish national sample (4719 cases and 5917 controls). High-confidence CNV calls were generated using genotyping array intensity data, and their effect on risk of SCZ was measured. Our data confirm increased burden of large, rare CNVs in SCZ cases as well as significant associations for recurrent 16p11.2 duplications, 22q11.2 deletions and 3q29 deletions. We report a novel association for 17q12 duplications (odds ratio=4.16, P=0.018), previously associated with autism and mental retardation but not SCZ. Intriguingly, gene set association analyses implicate biological pathways previously associated with SCZ through common variation and exome sequencing (calcium channel signaling and binding partners of the fragile X mental retardation protein). We found significantly increased burden of the largest CNVs (>500?kb) in genes present in the postsynaptic density, in genomic regions implicated via SCZ genome-wide association studies and in gene products localized to mitochondria and cytoplasm. Our findings suggest that multiple lines of genomic inquiry--genome-wide screens for CNVs, common variation and exonic variation--are converging on similar sets of pathways and/or genes. PMID:24776740

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

2014-07-01

326

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

327

M-Theory on Complex Spacetime  

E-print Network

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

Abdul Rouf Samurah

2012-09-26

328

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

329

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

NASA Astrophysics Data System (ADS)

At crustal conditions, the fluid-melt partitioning of Sr is mainly controlled by the salinity of the fluid and the composition of the melt (Borchert et al., 2010). The data show a sharp increase in the Sr partition coefficient with the alumina saturation index (ASI) to a maximum of 0.3 at an ASI of 1.05. Because fluid-melt partitioning of a given element depends on its complexation in the fluid and its incorporation in the melt, these data imply a change in the Sr speciation at least one of the two phases. For silicate melts, Kohn et al. (1990) found only small changes in the first coordination shell of Sr in a suite of melts with various degrees of polymerization, and argued that incorporation of Sr in the melt should not play a major role in controlling Sr partitioning. For the aqueous fluid, Bai and Koster van Groos (1999) and Webster et al. (1989) suggested a control of the Sr partition coefficient by SrCl2 complexes based on the correlation between partition coefficient and Cl concentration in the fluid after quenching. Both hypotheses cannot explain our partitioning data. Thus, new information on Sr complexation is required. Here, we studied the complexation of Sr in peraluminous or peralkaline melt dissolved in aqueous fluids in-situ at elevated PT conditions using hydrothermal diamond-anvil cells (HDAC) and X-ray absorption near edge structure (XANES) spectroscopy. The starting materials were peraluminous or peralkaline glass and H2O or a chloridic solution. The glass was doped with high concentrations of 5000 or 10000 ppm Sr. We used bulk compositions with 10 to 15 wt.% glass to ensure that the melt was completely dissolved in the fluid at high PT conditions. For qualitative evaluation, we analyzed the starting glasses and various crystalline compounds and standard solutions. The experiments were performed at beamline ID26 at ESRF (Grenoble, France) using a high resolution emission spectrometer and Si(311) monochromator crystals for high resolution and Si(111) for low resolution measurements. An overall resolution of 1.98 eV (Si(311)) and 3 eV (Si(111)) was achieved using a beamsize of 120x400 ?m, Si(777) analyzer crystals and a Rowland circle diameter of 1 m. Strontium XANES spectra of peraluminous and peralkaline starting glasses show distinct differences in pre-edge, main edge and position of the first EXAFS maximum which is directly correlated to the distance of Sr and its nearest neighbor. Therefore, the spectra indicate an effect of the ASI on the local structure around Sr. Spectra of standard solution at various PT conditions indicate detectable temperature-dependent changes in the intensity and peak width of the white line. The XANES spectra of chloridic solutions with peraluminous or peralkaline melt dissolved differ significantly from each other. The latter are similar to the one of the peralkaline starting glass, while this is not the case for solutions with peraluminous melt. The spectra of water with dissolved peralkaline melt distinctly differ from those using chloridic fluids. In conclusion, the first spectroscopic evidence on Sr complexation at elevated PT condition indicates significant speciation changes in both fluid and melt, and suggest ASI-dependent formation of Sr-Si complexes in the fluids. Literature Bai and Koster van Groos (1999), GCA 63, 1117-1131. Borchert et al. (2010), GCA 74, 1057-1076. Kohn et al. (1990), CMP 105, 359-368. Webster et al. (1989), Econ. Geol. 84, 116-134.

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

2010-05-01

330

Complex dynamics of text analysis  

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

331

Mid Vowels and Mute e: A Discussion of Phonological Variations in French.  

ERIC Educational Resources Information Center

Discusses two phonological features of standard French, mid-vowels and mute e, with respect to their formal description. The wide variation involved in the use of these features by native speakers is presented, and the way that this variation adds to the complexities of language learning and teaching is examined. (JL/Author)

Dumenil, Annie

1990-01-01

332

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

333

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

Microsoft Academic Search

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

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

2012-01-01

334

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

335

Complex Systems and Human Complexity in Medicine  

Microsoft Academic Search

Concepts taken from complex systems theory, such as ‘agents’ and ‘attractors’, have been proposed as metaphors in medical practice.This proposal is assessed by a comparison of the notions of complex adaptive systems (CAS) and human complexity. CAS are characterized by the emergence of sophisticated output features of rule-governed non-linear systems. Human complexity is the result of higher mental capacities and

Roger Strand; Guri Rortveit; Edvin Schei

2005-01-01

336

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

337

COMPLEX TRAUMA, COMPLEX REACTIONS: ASSESSMENT AND TREATMENT  

Microsoft Academic Search

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

Christine A. Courtois

2004-01-01

338

Complex Trauma, Complex Reactions: Assessment and Treatment  

Microsoft Academic Search

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

Christine A. Courtois

2008-01-01

339

Variational MCMC Nando de Freitas  

E-print Network

-1776 USA fjfgf,jordan,russellg@cs.berkeley.edu Pedro H#28;jen-S#28;rensen y Michael I. Jordan Stuart (Jaakkola and Jordan 1999, Jordan, Ghahramani, Jaakkola and Saul 1999). However, variational approx

Jordan, Michael I.

340

Variational Principles in Potential Theory.  

National Technical Information Service (NTIS)

Although the theoretical and practical importance of variational techniques in potential theory has long been secure, fresh instances of their utility are not without interest. Two cases in point are detailed, one relating to the capacitance of a condense...

H. Levine

1965-01-01

341

Copy number variation and susceptibility to human disorders (Review).  

PubMed

A large number of analyses of a new form of genetic variation, known as copy number variation (CNV), have been published recently as a new tool for understanding the genetic basis of complex traits such as diabetes, asthma, Crohn's disease, autism and bipolar disorder. Through the use of different types of genome-wide scanning procedures, CNVs have been shown to be associated with several complex and common disorders, including nervous system disorders. One of the common features of the regions associated with the complex and common disorders identified thus far is the presence of CNVs and segmental duplications. Segmental duplications lead to genome instability. Because of their location and nature (several contain genes), many CNVs have functional consequences, such as gene dosage alteration, the disruption of genes and the modulation of the activities of other genes. Therefore, these genetic variations have an influence on phenotypes, the susceptibility of an individual to disease, drug response and human genome evolution. These types of variants (gain and loss of DNA) are not restricted to humans, having also been identified in other organisms. Our current knowledge regarding CNVs and their heritability is still rudimentary, due to their location in regions of complex genomic structure and to the technical limitations of association studies. Future advances in the technology will aid in the construction of a new CNV map, used to find the genes underlying common diseases and to understand familial genetic conditions, severe developmental defects in humans and other organisms, and genome evolution. PMID:21475803

Shastry, Barkur S

2009-01-01

342

Coupled dark energy field variation  

NASA Astrophysics Data System (ADS)

The variation of the dark energy field is found under the assumption that the dark energy is parametric and interacts with the cold dark matter. Considering that the variation of the field could not exceed the Planck mass, we obtain bounds on the coupling and adiabatic coefficients. Three parametrizations of the adiabatic coefficients are considered and two coupling terms where the energy flows from dark energy to dark matter, or the other way around.

García-Zúñiga, Roberto Carlos; Izquierdo, Germán

2014-10-01

343

Theory of solar luminosity variations  

E-print Network

The theory of stellar structure can be used to identify the most plausible mechanisms for the irradiance variations associated with the solar cycle. Changes in surface emissivity, i.e. the reduced cooling in spots and enhanced emission by small scale magnetic fields, are the most effective mechanisms and account for most of the observed variation. Helioseismology will soon be able to test the consequences of changes in surface emissivity, and distinguish them from other scenarios for irradiance variability.

H. C. Spruit

2000-03-03

344

The theory of facilitated variation.  

PubMed

This theory concerns the means by which animals generate phenotypic variation from genetic change. Most anatomical and physiological traits that have evolved since the Cambrian are, we propose, the result of regulatory changes in the usage of various members of a large set of conserved core components that function in development and physiology. Genetic change of the DNA sequences for regulatory elements of DNA, RNAs, and proteins leads to heritable regulatory change, which specifies new combinations of core components, operating in new amounts and states at new times and places in the animal. These new configurations of components comprise new traits. The number and kinds of regulatory changes needed for viable phenotypic variation are determined by the properties of the developmental and physiological processes in which core components serve, in particular by the processes' modularity, robustness, adaptability, capacity to engage in weak regulatory linkage, and exploratory behavior. These properties reduce the number of regulatory changes needed to generate viable selectable phenotypic variation, increase the variety of regulatory targets, reduce the lethality of genetic change, and increase the amount of genetic variation retained by a population. By such reductions and increases, the conserved core processes facilitate the generation of phenotypic variation, which selection thereafter converts to evolutionary and genetic change in the population. Thus, we call it a theory of facilitated phenotypic variation. PMID:17494755

Gerhart, John; Kirschner, Marc

2007-05-15

345

Parameters in Dynamic Models of Complex Traits are Containers of Missing Heritability  

Microsoft Academic Search

Polymorphisms identified in genome-wide association studies of human traits rarely explain more than a small proportion of the heritable variation, and improving this situation within the current paradigm appears daunting. Given a well-validated dynamic model of a complex physiological trait, a substantial part of the underlying genetic variation must manifest as variation in model parameters. These parameters are themselves phenotypic

Yunpeng Wang; Arne B. Gjuvsland; Jon Olav Vik; Nicolas P. Smith; Peter J. Hunter; Stig W. Omholt

2012-01-01

346

Effort variation regularization in sound field reproduction.  

PubMed

In this paper, active control is used in order to reproduce a given sound field in an extended spatial region. A method is proposed which minimizes the reproduction error at a number of control positions with the reproduction sources holding a certain relation within their complex strengths. Specifically, it is suggested that the phase differential of the source driving signals should be in agreement with the phase differential of the desired sound pressure field. The performance of the suggested method is compared with that of conventional effort regularization, wave field synthesis (WFS), and adaptive wave field synthesis (AWFS), both under free-field conditions and in reverberant rooms. It is shown that effort variation regularization overcomes the problems associated with small spaces and with a low ratio of direct to reverberant energy, improving thus the reproduction accuracy in the listening room. PMID:20707444

Stefanakis, Nick; Jacobsen, Finn; Sarris, John

2010-08-01

347

Variation Ontology for annotation of variation effects and mechanisms.  

PubMed

Ontology organizes and formally conceptualizes information in a knowledge domain with a controlled vocabulary having defined terms and relationships between them. Several ontologies have been used to annotate numerous databases in biology and medicine. Due to their unambiguous nature, ontological annotations facilitate systematic description and data organization, data integration and mining, and pattern recognition and statistics, as well as development of analysis and prediction tools. The Variation Ontology (VariO) was developed to allow the annotation of effects, consequences, and mechanisms of DNA, RNA, and protein variations. Variation types are systematically organized, and a detailed description of effects and mechanisms is possible. VariO is for annotating the variant, not the normal-state features or properties, and requires a reference (e.g., reference sequence, reference-state property, activity, etc.) compared to which the changes are indicated. VariO is versatile and can be used for variations ranging from genomic multiplications to single nucleotide or amino acid changes, whether of genetic or nongenetic origin. VariO annotations are position-specific and can be used for variations in any organism. PMID:24162187

Vihinen, Mauno

2014-02-01

348

Variation Ontology for annotation of variation effects and mechanisms  

PubMed Central

Ontology organizes and formally conceptualizes information in a knowledge domain with a controlled vocabulary having defined terms and relationships between them. Several ontologies have been used to annotate numerous databases in biology and medicine. Due to their unambiguous nature, ontological annotations facilitate systematic description and data organization, data integration and mining, and pattern recognition and statistics, as well as development of analysis and prediction tools. The Variation Ontology (VariO) was developed to allow the annotation of effects, consequences, and mechanisms of DNA, RNA, and protein variations. Variation types are systematically organized, and a detailed description of effects and mechanisms is possible. VariO is for annotating the variant, not the normal-state features or properties, and requires a reference (e.g., reference sequence, reference-state property, activity, etc.) compared to which the changes are indicated. VariO is versatile and can be used for variations ranging from genomic multiplications to single nucleotide or amino acid changes, whether of genetic or nongenetic origin. VariO annotations are position-specific and can be used for variations in any organism. PMID:24162187

Vihinen, Mauno

2014-01-01

349

Heat transfer variations of bicycle helmets.  

PubMed

Bicycle helmets exhibit complex structures so as to combine impact protection with ventilation. A quantitative experimental measure of the state of the art and variations therein is a first step towards establishing principles of bicycle helmet ventilation. A thermal headform mounted in a climate-regulated wind tunnel was used to study the ventilation efficiency of 24 bicycle helmets at two wind speeds. Flow visualization in a water tunnel with a second headform demonstrated the flow patterns involved. The influence of design details such as channel length and vent placement was studied, as well as the impact of hair. Differences in heat transfer among the helmets of up to 30% (scalp) and 10% (face) were observed, with the nude headform showing the highest values. On occasion, a negative role of some vents for forced convection was demonstrated. A weak correlation was found between the projected vent cross-section and heat transfer variations when changing the head tilt angle. A simple analytical model is introduced that facilitates the understanding of forced convection phenomena. A weak correlation between exposed scalp area and heat transfer was deduced. Adding a wig reduces the heat transfer by approximately a factor of 8 in the scalp region and up to one-third for the rest of the head for a selection of the best ventilated helmets. The results suggest that there is significant optimization potential within the basic helmet structure represented in modern bicycle helmets. PMID:16882634

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

2006-09-01

350

MHC variation in birds and reptiles.  

PubMed

The major histocompatibility complex (MHC) has been studied in a multitude of mammals by now, but much less is known about its organisation and variation in other vertebrate species. The mammalian MHC is organised as a single gene cluster, but recent studies on birds suggest that this paradigm of MHC organisation has to be supplemented. The domestic chicken thus possesses two separate gene clusters which both contain MHC class I and class II B genes, and we have shown that the ring-necked pheasant Phasianus colchicus also has two unlinked clusters of class II B genes. We are studying the effect of the MHC on mate choice, survival and reproductive success in natural populations of birds and reptiles. For this reason, we are developing DNA techniques to determine the animals' MHC genotype. The amplification of the hypervariable exon 3 of the class I gene from songbirds and reptiles has provided us with species specific probes that can be used in Southern blot analysis. The first results indicate very extensive variation in all studied species, that is starlings Sturnus vulgaris, great reed warblers Acrocephalus arundinaceus and water pythons Liasis fuscus. The restriction fragment length polymorphism (RFLP) analysis also suggests that the number of MHC genes is significantly larger in these species than in pheasants and domestic chickens. PMID:10386396

Wittzell, H; Madsen, T; Westerdahl, H; Shine, R; von Schantz, T

351

Understanding and using quantitative genetic variation  

PubMed Central

Quantitative genetics, or the genetics of complex traits, is the study of those characters which are not affected by the action of just a few major genes. Its basis is in statistical models and methodology, albeit based on many strong assumptions. While these are formally unrealistic, methods work. Analyses using dense molecular markers are greatly increasing information about the architecture of these traits, but while some genes of large effect are found, even many dozens of genes do not explain all the variation. Hence, new methods of prediction of merit in breeding programmes are again based on essentially numerical methods, but incorporating genomic information. Long-term selection responses are revealed in laboratory selection experiments, and prospects for continued genetic improvement are high. There is extensive genetic variation in natural populations, but better estimates of covariances among multiple traits and their relation to fitness are needed. Methods based on summary statistics and predictions rather than at the individual gene level seem likely to prevail for some time yet. PMID:20008387

Hill, William G.

2010-01-01

352

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

353

Are Observed Variations of Topography of The '660' Influenced By Lateral Variations of An Underlying Interface ?  

NASA Astrophysics Data System (ADS)

Most global studies of lateral variations of topography of the '660' have been per- formed so far with long-period data. This presentation assess the seismic signature of this region when studied with broadband data in the frequency range 0.1-1 Hz. When sampled with P-to-s converted phases, this region shows a complex pattern, associat- ing 3 interfaces at the average depths of 600, 650 and 715 km. First results indicate that lateral topography variations of the '650' fit previous observations by long-period data (Gu et al., 1998), except in some subduction zones, especially in East Asia, where vari- ation trends appear to behave in an opposite way. In such regions, better correlations are found with the behaviour of the '715'. We propose that the seismic signature of long-period waves generated at the bottom of the transition zone may be influenced by both interfaces. Because of the lateral variations of their thickness and velocity jump as a function of thermal context, the signature of one interface could prevail against the other. The transformation of garnet into perovskite, and dissociation of ringwood- ite are tested as possible candidates for the '715' and '650', respectively (Vacher et al., 1998), using available thermoelastic data. Synthetic modelling of converted phases on the velocity profiles computed in different thermal contexts can explain our broadband observations. References : Gu et al., EPSL, 157, 57-67, 1998 ; Vacher et al., PEPI, 106, 275-298, 1998.

Castillo, J.; Mocquet, A.; Vacher, P.; Sotin, C.

354

Variational Lie derivative and cohomology classes  

E-print Network

We relate cohomology defined by a system of local Lagrangian with the cohomology class of the system of local variational Lie derivative, which is in turn a local variational problem; we show that the latter cohomology class is zero, since the variational Lie derivative `trivializes' cohomology classes defined by variational forms. As a consequence, conservation laws associated with symmetries ensuring the vanishing of the second variational derivative of a local variational problem are globally defined.

Marcella Palese; Ekkehart Winterroth

2011-03-02

355

Effective permittivity of saline ice under thermal variation  

NASA Technical Reports Server (NTRS)

A model for calculating the effective permittivity of saline ice under thermal variation is presented. The model includes multiphase inhomogeneities with multiple species characterized by orientation, size and shape distributions. The model is used to derive the effective permittivity as a function of temperature under the strong fluctuation theory which is extended to account for the complexity. The results calculated from the model are compared with experimental data at 4.8 GHz for saline ice grown at the US Army Cold Regions Research and Engineering Laboratory (CRREL). The comparison between measured and calculated complex permittivities is good for the imaginary part, and the difference is within 10 percent for the real part.

Nghiem, S. V.; Kwok, R.; Kong, J. A.; Shin, R. T.; Gow, A. J.; Arcone, S. A.

1992-01-01

356

A Variational Approach to Enhanced Sampling and Free Energy Calculations  

E-print Network

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

Valsson, Omar

2014-01-01

357

Variational Approach to Enhanced Sampling and Free Energy Calculations  

NASA Astrophysics Data System (ADS)

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

Valsson, Omar; Parrinello, Michele

2014-08-01

358

Variational approach to enhanced sampling and free energy calculations.  

PubMed

The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo simulations, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to alleviate this problem. Many are based on the introduction of a bias potential which is a function of a small number of collective variables. However constructing such a bias is not simple. Here we introduce a functional of the bias potential and an associated variational principle. The bias that minimizes the functional relates in a simple way to the free energy surface. This variational principle can be turned into a practical, efficient, and flexible sampling method. A number of numerical examples are presented which include the determination of a three-dimensional free energy surface. We argue that, beside being numerically advantageous, our variational approach provides a convenient and novel standpoint for looking at the sampling problem. PMID:25215968

Valsson, Omar; Parrinello, Michele

2014-08-29

359

A Variational Approach to Enhanced Sampling and Free Energy Calculations  

E-print Network

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

Omar Valsson; Michele Parrinello

2014-07-02

360

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

361

Simplicial complexes Further ideas  

E-print Network

Graphs Simplicial complexes Further ideas Critical Groups of Simplicial Complexes Art Duval1, Martin Critical Groups of Simplicial Complexes #12;Graphs Simplicial complexes Further ideas Sandpiles and chip-firing Algebra Reduced Laplacian and spanning trees Sandpiles and chip-firing Motivation Think

Duval, Art

362

Spatiotemporal imaging of complexity  

PubMed Central

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

2013-01-01

363

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

364

VARIATION IN EYESPOT ULTRASTRUCTURE IN CHLAMYDOMONAS REINHARDI (ac-31)  

Microsoft Academic Search

SUMMARY Several morphological variations in eyespot complex fine structure were exhibited in some cells of the pale-green mutant strain ac-31 of Chlamydomonas reinhardi. The cells were grown in minimal medium supplemented with 0-2 % sodium acetate and were harvested by centrifuga- tion and prepared for electron-microscopic examination. Microtubules were seen near the flagella, confirming previous observations. Microtubules were also seen

HELEN E. GRUBER; BENJAMIN ROSARIO

365

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

366

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

2007-03-23

367

Mapping the Epistatic Network Underlying Murine Reproductive Fatpad Variation  

PubMed Central

Genome-wide mapping analyses are now commonplace in many species and several networks of interacting loci have been reported. However, relatively few details regarding epistatic interactions and their contribution to complex trait variation in multicellular organisms are available and the identification of positional candidate loci for epistatic QTL (epiQTL) is hampered, especially in mammals, by the limited genetic resolution inherent in most study designs. Here we further investigate the genetic architecture of reproductive fatpad weight in mice using the F10 generation of the LG,SM advanced intercross (AI) line. We apply multiple mapping techniques including a single-locus model, locus-specific composite interval mapping (CIM), and tests for multiple QTL per chromosome to the 12 chromosomes known to harbor single-locus QTL (slQTL) affecting obesity in this cross. We also perform a genome-wide scan for pairwise epistasis. Using this combination of approaches we detect 199 peaks spread over all 19 autosomes, which potentially contribute to trait variation including all eight original F2 loci (Adip1-8), novel slQTL peaks on chromosomes 7 and 9, and several novel epistatic loci. Extensive epistasis is confirmed involving both slQTL confidence intervals (C.I.) as well as regions that show no significant additive or dominance effects. These results provide important new insights into mapping complex genetic architectures and the role of epistasis in complex trait variation. PMID:21115969

Jarvis, Joseph P.; Cheverud, James M.

2011-01-01

368

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

369

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 t...

Efremov, Yu N

2005-01-01

370

Natural Variation in Drosophila Stressed Locomotion Meets or Exceeds Variation Caused by Hsp70 Mutation: Analysis of Behavior and Performance  

Microsoft Academic Search

Thermotolerance involves more than life or death. Investigating the complexity of this trait will aid identification of its\\u000a genetic contributors. We examined variation in thermally stressed walking behavior and performance in natural Drosophila melanogaster strains and strains mutant for the heat shock protein Hsp70, to determine which aspects of locomotion are affected by heat shock and genotype. We developed software

Brian R. Bettencourt; Brian W. Drohan; Andrea T. Ireland; Mahalakshmi Santhanam; Mary Beth Smrtic; Erin M. Sullivan

2009-01-01

371

Sensory deprivation versus sensory variation  

Microsoft Academic Search

Compared verbal and physiological reactions to sensory deprivation (SD) and extreme sensory variation (SV). 22 male undergraduates were confined to a cubicle for 8 hr. in each condition on 2 different occasions. 2 other 8-hr sessions were spent in a relatively normal, nonconfined condition. Ss found SD more boring, dislikable, and anxiety and depression provoking than SV. More unreality stress

Marvin Zuckerman; Harold Persky; Lynne Miller; Bernard Levine

1970-01-01

372

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

373

VARIATION IN PEREGRINE FALCON EGGS  

Microsoft Academic Search

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

WILLIAM A. BURNHAM; JAMES H. ENDERSON

1984-01-01

374

Variational Calculation for Muonic Molecules  

Microsoft Academic Search

Adopting the spheroidal variables to describe the muon coordinates, variational calculations are carried out for the ground and the excited states of the homo-nuclear muonic hydrogen molecular ion (ppmu)+ and its isotopes with total angular momentum J{=}0 and 1. The best binding energies among those so far reported are obtained for several states.

Shunsuke Hara; Takeshi Ishihara; Nobuyuki Toshima

1986-01-01

375

Regularization of Nonmonotone Variational Inequalities  

SciTech Connect

In this paper we extend the Tikhonov-Browder regularization scheme from monotone to rather a general class of nonmonotone multivalued variational inequalities. We show that their convergence conditions hold for some classes of perfectly and nonperfectly competitive economic equilibrium problems.

Konnov, Igor V. [Department of Applied Mathematics, Kazan University, ul. Kremlevskaya 18, Kazan 420008 (Russian Federation)], E-mail: Igor.Konnov@ksu.ru; Ali, M.S.S. [Department of Mathematics, Faculty of Education, Ain Shams University, Cairo (Egypt); Mazurkevich, E.O. [Informatics Problems Institute of AS RT, Kazan 420012 (Russian Federation)

2006-05-15

376

Research Focus Glutamate receptors: variation  

E-print Network

Research Focus Glutamate receptors: variation in structure­function coupling Anders S. Kristensen1 transmission in the CNS relies almost entirely on the neurotransmitter glutamate and its family of ion channel different mechanisms to translate agonist binding into channel opening. Working hypotheses for glutamate

Traynelis, Stephen F.

377

Somatic variation in Lolium perenne  

Microsoft Academic Search

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

Y Shimamoto; M D Hayward

1975-01-01

378

Observer variation in skeletal radiology  

Microsoft Academic Search

The factors that affect observer variation in bone radiology are analysed from data in the literature and on the basis of studies carried out at McMaster University on the hands and sacroiliac joints. A plea is made for presenting results in terms of Kappa statistics so that agreement due purely to chance is eliminated. In the conclusions the main variables

W. Peter Cockshott; William M. Park

1983-01-01

379

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

380

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

381

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

382

Theory of cosmic ray variations  

NASA Technical Reports Server (NTRS)

The initial anisotropic and isotropic spaces of solar cosmic ray spreading in interplanetary space are compared with the results of direct observations in the region adjacent to the earth's orbit and with the results of explorations of the eleven-year and twenty-seven-day variations of the cosmic rays in more distant regions.

Dorman, L. I.

1975-01-01

383

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

384

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

385

Mitochondrial DNA Sequence Variation in Saugers  

Microsoft Academic Search

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

Matthew M. White

2012-01-01

386

Short-period geomagnetic secular variation  

Microsoft Academic Search

In this paper, the main problems of the theory of the short period geomagnetic secular variation are described. An approximate analytical representation of the observational data on both the geomagnetic field variations and the associated variations in the length of the day, the kinematics of the generation of geomagnetic variations in the skin layer at the core-mantle boundary, and the

S. I. Braginskii

1984-01-01

387

Mapping and sequencing of structural variation from eight human genomes  

PubMed Central

Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale—particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence map of human structural variation—a standard for genotyping platforms and a prelude to future individual genome sequencing projects. PMID:18451855

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

2008-01-01

388

Variation in emission metrics due to variation in CO2 and temperature impulse response functions  

NASA Astrophysics Data System (ADS)

Emission metrics are used to compare the climate effect of the emission of different species, such as carbon dioxide (CO2) and methane (CH4). The most common metrics use linear impulse response functions (IRFs) derived from a single more complex model. There is currently little understanding on how IRFs vary across models, and how the model variation propagates into the metric values. In this study, we first derive CO2 and temperature IRFs for a large number of complex models participating in different intercomparison exercises, synthesizing the results in distributions representing the variety in behaviour. The derived IRF distributions differ considerably, which is partially related to differences among the underlying models, and partially to the specificity of the scenarios used (experimental setup). In a second part of the study, we investigate how differences among the IRFs impact the estimates of global warming potential (GWP), global temperature change potential (GTP) and integrated global temperature change potential (iGTP) for time horizons between 20 and 500 yr. Within each derived CO2 IRF distribution, underlying model differences give similar spreads on the metrics in the range of -20 to +40% (5-95% spread), and these spreads are similar among the three metrics. GTP and iGTP metrics are also impacted by variation in the temperature IRF. For GTP, this impact depends strongly on the lifetime of the species and the time horizon. The GTP of black carbon shows spreads of up to -60 to +80% for time horizons to 100 yr, and even larger spreads for longer time horizons. For CH4 the impact from variation in the temperature IRF is still large, but it becomes smaller for longer-lived species. The impact from variation in the temperature IRF on iGTP is small and falls within a range of ±10% for all species and time horizons considered here. We have used the available data to estimate the IRFs, but we suggest the use of tailored intercomparison projects specific for IRFs in emission metrics. Intercomparison projects are an effective means to derive an IRF and its model spread for use in metrics, but more detailed analysis is required to explore a wider range of uncertainties. Further work can reveal which parameters in each IRF lead to the largest uncertainties, and this information may be used to reduce the uncertainty in metric values.

Olivié, D. J. L.; Peters, G. P.

2013-08-01

389

Simplicial Structure on Complexes.  

E-print Network

While chain complexes are equipped with a differential $d$ satisfying $d^2 = 0$, their generalizations called $N$-complexes have a differential $d$ satisfying $d^N = 0$. In this paper we show that the lax nerve of the category of chain complexes is pointwise adjoint equivalent to the décalage of the simplicial category of $N$-complexes. This reveals additional simplicial structure on the lax nerve of the category of chain complexes which provides a categorfication of the triangulated homotopy category of chain complexes. We study this phenomena in general and present evidence that the axioms of triangulated categories have simplicial origin.

Djalal Mirmohades

390

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

391

Variations of the sciatic nerve anatomy and blood supply in the gluteal region: a review of the literature.  

PubMed

Variations of the sciatic nerve anatomy and blood supply are complex and largely not dealt with in common anatomy texts. Variations of the sciatic nerve anatomy can be divided into the height of division of its branches, relation of the branches to the piriformis muscle, and its blood supply. These variations should be well known to any surgeon operating in this anatomical region. It is unknown whether these variations increase the risk of surgical injury and consequent morbidity. This paper will review the current knowledge regarding anatomical variations of the sciatic nerve and its blood supply. PMID:24842563

Kanawati, Andrew James

2014-11-01

392

Montani, Kohn, Smith and Schultz (2006), Supplemental Material Supplemental Material  

E-print Network

, this would correspond to the assumption that the probability distribution of response words at a fixed spike 1996). Consider the problem of estimating the Shannon entropy for a given probability distribution p estimator It is well known that the naïve or "plugin" estimator of entropy tends toward underestimation (it

Smith, Matthew A.

393

The Mathematics of Wrinkles and Folds Robert V. Kohn  

E-print Network

hold for all unit vectors v in R2 . Facts from geometry: A surface in R3 has 2 principal curvatures 1). For arbitary "creases" (violating angle condition) there is no way to fold paper flat using them

394

Iron under pressure: "Kohn tweezers" and remnant magnetism.  

PubMed

In this work we investigate the magnetic and structural properties of bulk Fe and Fe nanoparticles under pressure with x-ray absorption and emission spectroscopies providing answers to two fundamental questions: (a) the chicken-or-egg problem for the magnetic and structural transitions and (b) magnetism in the high pressure hcp phase. The two transitions, inextricably linked in the bulk, are clearly decoupled in the nanoparticles, with the magnetic collapse preceding the structural transition. Ultrafast x-ray emission spectroscopy detects remnant magnetism, probably antiferromagnetic fluctuations, up to pressures of about 40 GPa in the hcp phase. This could be of direct relevance to the superconductivity in ?-Fe [K. Shimizu et al., Nature (London) 412, 316 (2001)] through the existence of a quantum critical point and associated magnetic fluctuations. PMID:21770592

Monza, A; Meffre, A; Baudelet, F; Rueff, J-P; d'Astuto, M; Munsch, P; Huotari, S; Lachaize, S; Chaudret, B; Shukla, Abhay

2011-06-17

395

On the Occasion of the Birthday of Walter Kohn  

E-print Network

to theoretical physics � it is indeed wonderful to see that "age" has not changed his radiant lifestyle. He still Germany had uprooted. Eventually he managed to be accepted at Toronto University. His first pub- lication

Geller, Michael R.

396

Robin M. Kohn, MSW, LCSW University of Central Florida  

E-print Network

Practice with Loss and Life's Transitions BSW Courses Developed: o Social Work in Health Settings o Social Work Practice with Loss and Life's Transitions o Field Education Seminar Media Enhanced #12;2 MSW competencies and content into the BSW curriculum. The expectation is to plan, implement, evaluate, and sustain

Wu, Shin-Tson

397

Metal ion complexation by ionizable crown ethers  

SciTech Connect

During the report period a variety of new lipophilic ionizable crown ethers with pendent proton-ionizable groups has been synthesized. In addition a series of proton-ionizable crown ethers without lipophilic groups was prepared to study how structural variations within the ligand influence metal ion complexation in homogeneous media as assessed by NMR spectroscopy or titration calorimetry. A third class of new metal ion-complexing agents is a series of lipophilic acyclic polyether dicarboxylic acids. Competitive solvent extractions of alkali metal and alkaline earth cations and of the mixed species have been conducted to reveal the influence of ring size, nature and attachment site of the lipophilic group, sidearm length, and proton-ionizable group identity and location upon the selectivity and efficiency of metal ion complexation. In addition to such studies of structural variation within the lipophilic proton-ionizable crown ether, the effect of changing the organic solvent and variation of the stripping conditions have been assessed. The ability of proton- ionizable crown ethers to function as selective metal ion carriers in liquid membrane transport processes has been examined in both bulk liquid membrane and polymer-supported liquid membrane transport systems. New acyclic and cyclic polyether carboxylic acid resins have been prepared by condensation polymerization and characterized.

Bartsch, R.A.

1990-06-01

398

Macrocyclic ligands for uranium complexation  

SciTech Connect

A highly preorganized 24-macrocycle containing biuret, thiobiuret and pyridine subunits has been prepared by high dilution ring-closure procedures. Intermediate products to this macrocycle have been utilized to extend this synthetic route to include further representatives where solubility and stability will be influenced by substituent variation. A 1:1 complex has been formed from uranyl acetate and a quinquepyridine derivative, this representing a new type of ligand for the uranyl ion. A very convenient synthetic procedure that will allow the incorporation of these macrocycles into polymeric systems has been developed for the introduction of a vinyl substituent into the 4-position of the pyridine ring. Using triflate, vinyltributyltin and Pd{sup 0} chemistry, this procedure should make a variety of substituted 4-vinylpyridines available for the first time. 3 refs.

Potts, K.T.

1991-04-01

399

Complex regional pain syndrome  

MedlinePLUS

Complex regional pain syndrome (CRPS) is a chronic pain condition that can affect any area of the ... Bailey A, Audette JF. Complex regional pain syndrome. In: Frontera ... of Physical Medicine and Rehabilitation. 2nd ed. Philadelphia, ...

400

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 ( ...

401

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 ...

402

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 ...

403

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

404

Dispersion in microchannels with temporal temperature variations  

NASA Astrophysics Data System (ADS)

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

Tripathi, Anubhav; Bozkurt, Ozgur; Chauhan, Anuj

2005-10-01

405

Complex systems: An introduction  

Microsoft Academic Search

The characteristic feature of complex systems is the emergence of unexpected properties or behaviour. Complexity, beyond a certain threshold, may even lead to the emergence of new principles. It is\\u000a a one-way traffic: The new principles and features may be sometimes deducible from, but are not reducible to, those operating\\u000a at the lower levels of complexity. Reductionism stands discounted. Complexity

V. K. Wadhawan

2009-01-01

406

Photo- and electroluminescence of mixed-ligand Eu(III) complexes  

NASA Astrophysics Data System (ADS)

Spectral and luminescent properties of mixed-ligand Eu(III) complexes were studied in solutions and in polyvinylcarbazole (PVC) thin films. Trends in their variations were found depending on the complex structure and excitation mode. The electroluminescence was observed in ITO/PEDOT/Eu complex:PVC/CaMg/Al devices. Their current-voltage and voltage-brightness characteristics were investigated.

Eremina, N. S.; Meshkova, S. B.; Degtyarenko, K. M.; Kopylova, T. N.; Topilova, Z. M.; Gadirov, R. M.; Samsonova, L. G.

2012-05-01

407

Coastal eutrophication and temperature variation  

SciTech Connect

A 3-D hydroecological model has been developed to simulate the impact of climate-change-induced daily temperature variation on coastal water quality and eutrophication. Historical daily temperature time series over a thirty-year period have been used to link local meteorological variables to large-scale atmospheric circulation patterns (CPs). Then, CPs generated under a 2{times}CO{sub 2} scenario have been used to simulate climate-change-induced local daily temperature variations. Both historical and climate-change-induced temperature time series have been introduced as inputs into the hydroecological model to simulate coastal water quality and eutrophication. Subject to model validation with available data, a case study in the bay of Thessaloniki (N. Greece) indicates a risk of increasing eutrophication and oxygen depletion in coastal areas due to possible climate change.

Ganoulis, J.; Rafailidis, S. [Aristotle Univ. of Thessaloniki (Greece). Civil Engineering Dept.; Bogardi, I. [Univ. of Nebraska, Lincoln, NE (United States). Civil Engineering Dept.; Duckstein, L. [Univ. of Arizona, Tucson, AZ (United States). Systems and Industrial Engineering Dept.; Matyasovszky, I. [Eotvos-Lorand Univ., Budapest (Hungary). Dept. of Meteorology

1994-12-31

408

Helioseismic Limits on Irradiance Variations  

NASA Astrophysics Data System (ADS)

Changes in the frequencies of solar oscillations are the most precise probe of irradiance variations over the solar cycle. Using MDI data, Dziembowski and Goode (2005) showed that f-mode changes arise from the direct effect of the evolving magnetic activity, while p-mode changes are due to small, activity induced changes in convective flows very near to the solar surface (turbulent pressure). The f-modes also sharply limit the allowed field growth with activity, and the limit is consistent with the observations of Lin and Rimmele (1999). Combining MDI data with BBSO Ca II K, we find the Sun is smooth at activity minimum and becomes increasingly corrugated with rising activity. The overall physical picture is one in which the Sun is hottest and smoothest at activity minimum, and becomes cooler, more corrugated and irradiant with rising activity. These results place a lower limit on irradiance variations and are roughly consistent with a picture of Spruit (2000).

Goode, P. R.

2005-05-01

409

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

2013-07-22

410

Scalable Variational Bayesian Matrix Factorization  

E-print Network

.9175/ 4 0.9217/ 4 0.9314/ 4 0.9431/ 3 Netflix probe10 RMSE/optimal number of epohcs of the BRSIMF(V) Likelihood P(X |U,V) Posterior P(U,V |X) MCMC on Netflix Approximate the posterior by MCMC (Salakhutdinov 12 Element-wisely factorized variational distribution K=100 O((I+J)(K+K2)) O(2(I+J)K) Netflix I = 480

Choi, Seungjin

411

UVIS PSF Spatial & Temporal Variations  

NASA Astrophysics Data System (ADS)

Observations of the globular cluster ? Centauri in the filter F606W were used to characterize the impact of telescope breathing on the UVIS PSF as a function of position across the detector. Our study suggests that these variations can be well characterized using data from the archive and that it is possible to correct empirical and/or theoretical PSF models by taking into account the value of the telescope focus at the moment of the observations.

Sabbi, E.; Bellini, A.

2013-06-01

412

Dyslexia: Anomaly or normal variation?  

Microsoft Academic Search

This paper is an interim report on a large-scale survey. The background to the authors’ research into dyslexia is briefly\\u000a outlined. Next comes an explication of the contrast between “anomaly” and “normal variation.” Some details are then provided\\u000a of a survey of 12,905 children, age ten, who were given a variety of educational and cognitive tests relevant to a diagnosis

T. R. Miles; Mary N. Haslum

1986-01-01

413

Understanding Cancer Series: Genetic Variation  

Cancer.gov

This tutorial explains tiny variations in the human genome called Single Nucleotide Polymorphisms (SNPs) that can influence a person's health. Shows how SNPs occur in both coding and noncoding regions and can cause silent, harmless, harmful, or latent effects. Shows how SNPs can be markers for cancer. Suggests that SNPs may also be involved in the different levels of individual cancer risk observed. Suggests that in the future, SNPs databases may be used to improve cancer diagnosis and treatment planning.

414

Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme.  

PubMed

Cryptic variation is caused by the robustness of phenotypes to mutations. Cryptic variation has no effect on phenotypes in a given genetic or environmental background, but it can have effects after mutations or environmental change. Because evolutionary adaptation by natural selection requires phenotypic variation, phenotypically revealed cryptic genetic variation may facilitate evolutionary adaptation. This is possible if the cryptic variation happens to be pre-adapted, or "exapted", to a new environment, and is thus advantageous once revealed. However, this facilitating role for cryptic variation has not been proven, partly because most pertinent work focuses on complex phenotypes of whole organisms whose genetic basis is incompletely understood. Here we show that populations of RNA enzymes with accumulated cryptic variation adapt more rapidly to a new substrate than a population without cryptic variation. A detailed analysis of our evolving RNA populations in genotype space shows that cryptic variation allows a population to explore new genotypes that become adaptive only in a new environment. Our observations show that cryptic variation contains new genotypes pre-adapted to a changed environment. Our results highlight the positive role that robustness and epistasis can have in adaptive evolution. PMID:21637259

Hayden, Eric J; Ferrada, Evandro; Wagner, Andreas

2011-06-01

415

Conundrum of Combinatorial Complexity  

Microsoft Academic Search

This paper examines fundamental problems underlying difficulties encountered by pattern recognition algorithms, neural networks, and rule systems. These problems are manifested as combinatorial complexity of algorithms, of their computational or training requirements. The paper relates particular types of complexity problems to the roles of a priori knowledge and adaptive learning. Paradigms based on adaptive learning lead to the complexity of

Leonid I. Perlovsky

1998-01-01

416

Linguistic Complexity and Performance.  

ERIC Educational Resources Information Center

An experimental study investigating the interaction of linguistic complexity and performance in child language acquisition tests the hypothesis that children learning a first language acquire relatively complex sentences somewhat later than less complex sentences. In one of three tests, the subjects, 44 children aged 3.6 to 6 years, were presented…

Smith, Carlota S.; van Kleeck, Anne

417

Simply Complex by Design  

ERIC Educational Resources Information Center

Reality--real life--is complex, more complex than can be imagined. The majority of our most pressing issues confronted in the management of organizations are overwhelmingly complex. I make the case for a systems design approach as a remedy. Examples introduced in this paper illuminate conceptual tools that advance how people transform their…

Nelson, Harold G.

2007-01-01

418

Complex fuzzy soft multisets  

NASA Astrophysics Data System (ADS)

In this paper we combine two definitions, namely fuzzy soft multiset and complex fuzzy set to construct the definition of a complex fuzzy soft multiset and study its properties. In other words, we study the extension of a fuzzy soft multiset from real numbers to complex numbers. We also introduce its basic operations, namely complement, union and intersection. Some examples are given.

Alkouri, Abd Ulazeez M.; Salleh, Abdul Razak

2014-09-01