The electronic structure of pyrazine. Configuration interaction calculations using an extended basis

Extensive ab initio double zeta basis set configuration interaction calculations have been carried out on the nπ^∗ and ππ^∗ states of pyrazine as well as on the low‐lying n and π cations. The calculations corroborate the validity of the valence bond (VB) model for the interaction of lone pair excitations proposed earlier by Wadt and Goddard. Good agreement (errors of ∼0.2 eV) with experiment is obtained (except for the higher‐lying 1ππ∗ states that possess significant ionic character). The calculations indicate that the order of increasing ionization potentials is ^2A_g(n), 2B_(1g)(π), 2B_(1u)(n), and ^2B_(2g)(π). The forbidden 1 ^1B_(2g)(nπ^∗) state is predicted to be 1.30 eV above the allowed 1^ 1B_(3u)(nπ^∗) state. Finally, the calculations indicate that the adiabatic excitation energies to the 1^ 3B_1(nπ^∗) and 1^ 3A_1(ππ^∗) states in pyridine should be nearly degenerate at ∼3.6 eV

3+1 Approach to the Long Wavelength Iteration Scheme

Large-scale inhomogeneities and anisotropies are modeled using the Long Wavelength Iteration Scheme. In this scheme solutions are obtained as expansions in spatial gradients, which are taken to be small. It is shown that the choice of foliation for spacetime can make the iteration scheme more effective in two respects: (i) the shift vector can be chosen so as to dilute the effect of anisotropy on the late-time value of the extrinsic curvature of the spacelike hypersurfaces of the foliation; and (ii) pure gauge solutions present in a similar calculation using the synchronous gauge vanish when the spacelike hypersurfaces have extrinsic curvature with constant trace. We furthermore verify the main conclusion of the synchronous gauge calculation which is large-scale inhomogeneity decays if the matter--considered to be that of a perfect-fluid with a barotropic equation of state--violates the strong-energy condition. Finally, we obtain the solution for the lapse function and discuss its late-time behaviour. It is found that the lapse function is well-behaved when the matter violates the strong energy condition.Comment: 21 pages, TeX file, already publishe

On the coset duals of extended higher spin theories

We study the holographic duality between the M x M matrix extension of Vasiliev higher spin theories on AdS3 and the large N limit of SU(N+M)/SU(N) x U(1) type cosets. We present a simplified proof for the agreement of the spectra and clarify the relation between this duality and the version in which the cosets are replaced by Kazama-Suzuki models of Grassmannian type.Comment: 27 pages, 1 tabl

Supersymmetric holography on AdS3

The proposed duality between Vasiliev's supersymmetric higher spin theory on AdS3 and the 't Hooft limit of the 2d superconformal Kazama-Suzuki models is analysed in detail. In particular, we show that the partition functions of the two theories agree in the large N limit.Comment: 25 pages, 3 figures, improved fig.

Higher spin AdS_3 holography with extended supersymmetry

We propose a holographic duality between a higher spin AdS_3 gravity with so(p) extended supersymmetry and a large N limit of a 2-dimensional Grassmannian-like model with a specific critical level k=N and a non-diagonal modular invariant. As evidence, we show the match of one-loop partition functions. Moreover, we construct symmetry generators of the coset model for low spins which are dual to gauge fields in the supergravity. Further, we discuss a possible relation to superstring theory by noticing an N=3 supersymmetry of critical level model at finite k,N. In particular, we examine BPS states and marginal deformations. Inspired by the supergravity side, we also propose and test another large N CFT dual obtained as a Z_2 automorphism truncation of a similar coset model, but at a non-critical level.Comment: 44 pages, published versio

An inverse for the Jaumann derivative and some applications to the rheology of viscoelastic fluids

By using a generalization of the matrizant of matrix calculus, it is shown how one can construct formally an inverse, or integral, for the well-known Jaumann derivative of continuum mechanics. Some applications to fluid rheology are then considered. First, it is shown that this integral provides, via the Boltzmann super-position principle, a generalization of Oldroyd's quasi-linear fluid model, which is related to the molecular model of Bueche . Explicit expressions for the stresses arising in a general laminar shear flow are then derived for this model. Secondly, it is indicated how the operation can be used with rheological equations which are nonlinear in the deformation-rate, but quasi-linear in stress, to solve explicitly for the stress in terms of kinematic quantities. As an example, a rheological equation for suspensions of viscoelastic spheres in a Newton ian fluid is treated.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47218/1/397_2005_Article_BF01982423.pd

A two-domain elevator mechanism for sodium/proton antiport

Sodium/proton (Na+/H+) antiporters, located at the plasma membrane in every cell, are vital for cell homeostasis1. In humans, their dysfunction has been linked to diseases, such as hypertension, heart failure and epilepsy, and they are well-established drug targets2. The best understood model system for Na+/H+ antiport is NhaA from Escherichia coli1, 3, for which both electron microscopy and crystal structures are available4, 5, 6. NhaA is made up of two distinct domains: a core domain and a dimerization domain. In the NhaA crystal structure a cavity is located between the two domains, providing access to the ion-binding site from the inward-facing surface of the protein1, 4. Like many Na+/H+ antiporters, the activity of NhaA is regulated by pH, only becoming active above pH 6.5, at which point a conformational change is thought to occur7. The only reported NhaA crystal structure so far is of the low pH inactivated form4. Here we describe the active-state structure of a Na+/H+ antiporter, NapA from Thermus thermophilus, at 3 Å resolution, solved from crystals grown at pH 7.8. In the NapA structure, the core and dimerization domains are in different positions to those seen in NhaA, and a negatively charged cavity has now opened to the outside. The extracellular cavity allows access to a strictly conserved aspartate residue thought to coordinate ion binding1, 8, 9 directly, a role supported here by molecular dynamics simulations. To alternate access to this ion-binding site, however, requires a surprisingly large rotation of the core domain, some 20° against the dimerization interface. We conclude that despite their fast transport rates of up to 1,500 ions per second3, Na+/H+ antiporters operate by a two-domain rocking bundle model, revealing themes relevant to secondary-active transporters in general

The importance of anaemia in diagnosing colorectal cancer: a case–control study using electronic primary care records

Although anaemia is recognised as a feature of colorectal cancer, the precise risk is unknown. We performed a case–control study using electronic primary care records from the Health Improvement Network database, UK. A total of 6442 patients had a diagnosis of colorectal cancer, and were matched to 45 066 controls on age, sex, and practice. We calculated likelihood ratios and positive predictive values for colorectal cancer in both sexes across 1 g dl−1 haemoglobin and 10-year age bands, and examined the features of iron deficiency.In men, 178 (5.2%) of 3421 cases and 47 (0.2%) of 23 928 controls had a haemoglobin <9.0 g dl−1, giving a likelihood ratio (95% confidence interval) of 27 (19, 36). In women, the corresponding figures were 227 (7.5%) of 3021 cases and 58 (0.3%) of 21 138 controls, a likelihood ratio of 41 (30, 61). Positive predictive values increased with age and for each 1 g dl−1 reduction in haemoglobin. The risk of cancer for current referral guidance was quantified. For men over 60 years with a haemoglobin <11 g dl−1 and features of iron deficiency, the positive predictive value was 13.3% (9.7, 18) and for women with a haemoglobin <10 g dl−1 and iron deficiency, the positive predictive value was 7.7% (5.7, 11). Current guidance for urgent investigation of anaemia misses some patients with a moderate risk of cancer, particularly men

African tropical rainforest net carbon dioxide fluxes in the twentieth century

The African humid tropical biome constitutes the second largest rainforest region, significantly impacts global carbon cycling and climate, and has undergone major changes in functioning owing to climate and land-use change over the past century. We assess changes and trends in CO2 fluxes from 1901 to 2010 using nine land surface models forced with common driving data, and depict the inter-model variability as the uncertainty in fluxes. The biome is estimated to be a natural (no disturbance) net carbon sink (−0.02 kg C m−2 yr−1 or −0.04 Pg C yr−1, p < 0.05) with increasing strength fourfold in the second half of the century. The models were in close agreement on net CO2 flux at the beginning of the century (σ1901 = 0.02 kg C m−2 yr−1), but diverged exponentially throughout the century (σ2010 = 0.03 kg C m−2 yr−1). The increasing uncertainty is due to differences in sensitivity to increasing atmospheric CO2, but not increasing water stress, despite a decrease in precipitation and increase in air temperature. However, the largest uncertainties were associated with the most extreme drought events of the century. These results highlight the need to constrain modelled CO2 fluxes with increasing atmospheric CO2 concentrations and extreme climatic events, as the uncertainties will only amplify in the next century

Array CGH Phylogeny: How accurate are Comparative Genomic Hybridization-based trees?

<p>Abstract</p> <p>Background</p> <p>Array-based Comparative Genomic Hybridization (CGH) data have been used to infer phylogenetic relationships. However, the reliability of array CGH analysis to determine evolutionary relationships has not been well established. In most CGH work, all species and strains are compared to a single reference species, whose genome was used to design the array. In the accompanying work, we critically evaluated CGH-based phylogeny using simulated competitive hybridization data. This work showed that a limited number of conditions, principally the tree topology and placement of the reference taxon in the tree, had a strong effect on the ability to recover the correct tree topology. Here, we add to our simulation study by testing the use of CGH as a phylogenetic tool with experimental CGH data from competitive hybridizations between <it>N. crassa </it>and other <it>Neurospora </it>species. In the discussion, we add to our empirical study of <it>Neurospora </it>by reanalyzing of data from a previous CGH phylogenetic analysis of the yeast <it>sensu stricto </it>complex.</p> <p>Results</p> <p>Array ratio data for <it>Neurospora </it>and related species were normalized with loess, robust spline, and linear ratio based methods, and then used to construct Neighbor-Joining and parsimony trees. These trees were compared to published phylogenetic analyses for <it>Neurospora </it>based on multilocus sequence analysis (MLSA). For the <it>Neurospora </it>dataset, the best combination of methods resulted in recovery of the MLSA tree topology less than half the time. Our reanalysis of a yeast dataset found that trees identical to established phylogeny were recovered only by pruning taxa - including the reference taxon - from the analysis.</p> <p>Conclusion</p> <p>Our results indicate that CGH data can be problematic for phylogenetic analysis. Success fluctuates based on the methods utilized to construct the tree and the taxa included. Selective pruning of the taxa improves the results - an impractical approach for normal phylogenetic analysis. From the more successful methods we make suggestions on the normalization and post-normalization methods that work best in estimating genetic distance between taxa.</p