The development of a ligase mediated PCR with potential for the differentiation of serovars within Leptospira interrogans

A ligase mediated polymerase chain reaction (LMPCR) was developed to amplify between the repetitive element, IS1533, of Leptospira and adjacent chromosomally located BglII restriction endonuclease enzyme sites. To do this, complimentary oligonucleotide linkers designed to anneal together with an overhanging BglII end were ligated to BglII digested DNA from 35 leptospiral reference strains and field isolates, This ligated DNA was used as template for PCR with oligonucleotide primers specific for the linker and for the repetitive element IS1533. The resultant amplicon profile hybridised a 102 hp region derived from the terminus of IS1533 thus confirming that amplicons generated by LMPCR contained part of IS1533. The number of fragments generated containing IS1533 was significantly fewer than that generated by RFLP but the LMPCR method has the potential to use far less template DNA and be quicker than standard RFLP. Obvious and reproducible interserovar differences were demonstrated by LMPCR whereas for 20 of 21 L. hardjo-bovis isolates tested no intraserovar differences were observed. Of those serovars known to possess IS1533 homologues and tested here by LMPCR, each produced a unique amplicon profile which hybridised the IS1533 terminus probe. The limited heterogeneity amongst hardjo-bovis isolates is discussed as is the potential contribution of this method to diagnosis, differentiation and the phylogenetics of the Leptospires.

Trefftz discontinuous Galerkin methods for acoustic scattering on locally refined meshes

We extend the a priori error analysis of Trefftz-discontinuous Galerkin methods for time-harmonic wave propagation problems developed in previous papers to acoustic scattering problems and locally refined meshes. To this aim, we prove refined regularity and stability results with explicit dependence of the stability constant on the wave number for non convex domains with non connected boundaries. Moreover, we devise a new choice of numerical flux parameters for which we can prove L2-error estimates in the case of locally refined meshes near the scatterer. This is the setting needed to develop a complete hp-convergence analysis.

Optimal convergence estimates for the trace of the polynomial L2-projection operator on a simplex

In this paper we study convergence of the L2-projection onto the space of polynomials up to degree p on a simplex in Rd, d >= 2. Optimal error estimates are established in the case of Sobolev regularity and illustrated on several numerical examples. The proof is based on the collapsed coordinate transform and the expansion into various polynomial bases involving Jacobi polynomials and their antiderivatives. The results of the present paper generalize corresponding estimates for cubes in Rd from [P. Houston, C. Schwab, E. Süli, Discontinuous hp-finite element methods for advection-diffusion-reaction problems. SIAM J. Numer. Anal. 39 (2002), no. 6, 2133-2163].

High-throughput root phenotyping screens identify genetic loci associated with root architectural traits in Brassica napus under contrasting phosphate availabilities

Background and Aims: Phosphate (Pi) deficiency in soils is a major limiting factor for crop growth worldwide. Plant growth under low Pi conditions correlates with root architectural traits and it may therefore be possible to select these traits for crop improvement. The aim of this study was to characterize root architectural traits, and to test quantitative trait loci (QTL) associated with these traits, under low Pi (LP) and high Pi (HP) availability in Brassica napus. Methods: Root architectural traits were characterized in seedlings of a double haploid (DH) mapping population (n = 190) of B. napus 'Tapidor' x 'Ningyou 7' (TNDH) using high-throughput phenotyping methods. Primary root length (PRL), lateral root length (LRL), lateral root number (LRN), lateral root density (LRD) and biomass traits were measured 12 d post-germination in agar at LP and HP. Key Results: In general, root and biomass traits were highly correlated under LP and HP conditions. 'Ningyou 7' had greater LRL, LRN and LRD than 'Tapidor', at both LP and HP availability, but smaller PRL. A cluster of highly significant QTL for LRN, LRD and biomass traits at LP availability were identified on chromosome A03; QTL for PRL were identified on chromosomes A07 and C06. Conclusions: High-throughput phenotyping of Brassica can be used to identify root architectural traits which correlate with shoot biomass. It is feasible that these traits could be used in crop improvement strategies. The identification of QTL linked to root traits under LP and HP conditions provides further insights on the genetic basis of plant tolerance to P deficiency, and these QTL warrant further dissection.

Meta-analysis of the INSIG2 association with obesity including 74,345 individuals: does heterogeneity of estimates relate to study design?

The INSIG2 rs7566605 polymorphism was identified for obesity (BMI> or =30 kg/m(2)) in one of the first genome-wide association studies, but replications were inconsistent. We collected statistics from 34 studies (n = 74,345), including general population (GP) studies, population-based studies with subjects selected for conditions related to a better health status ('healthy population', HP), and obesity studies (OB). We tested five hypotheses to explore potential sources of heterogeneity. The meta-analysis of 27 studies on Caucasian adults (n = 66,213) combining the different study designs did not support overall association of the CC-genotype with obesity, yielding an odds ratio (OR) of 1.05 (p-value = 0.27). The I(2) measure of 41% (p-value = 0.015) indicated between-study heterogeneity. Restricting to GP studies resulted in a declined I(2) measure of 11% (p-value = 0.33) and an OR of 1.10 (p-value = 0.015). Regarding the five hypotheses, our data showed (a) some difference between GP and HP studies (p-value = 0.012) and (b) an association in extreme comparisons (BMI> or =32.5, 35.0, 37.5, 40.0 kg/m(2) versus BMI<25 kg/m(2)) yielding ORs of 1.16, 1.18, 1.22, or 1.27 (p-values 0.001 to 0.003), which was also underscored by significantly increased CC-genotype frequencies across BMI categories (10.4% to 12.5%, p-value for trend = 0.0002). We did not find evidence for differential ORs (c) among studies with higher than average obesity prevalence compared to lower, (d) among studies with BMI assessment after the year 2000 compared to those before, or (e) among studies from older populations compared to younger. Analysis of non-Caucasian adults (n = 4889) or children (n = 3243) yielded ORs of 1.01 (p-value = 0.94) or 1.15 (p-value = 0.22), respectively. There was no evidence for overall association of the rs7566605 polymorphism with obesity. Our data suggested an association with extreme degrees of obesity, and consequently heterogeneous effects from different study designs may mask an underlying association when unaccounted for. The importance of study design might be under-recognized in gene discovery and association replication so far.

Effects of temporal resolution of input precipitation on the performance of hydrological forecasting

Flood prediction systems rely on good quality precipitation input data and forecasts to drive hydrological models. Most precipitation data comes from daily stations with a good spatial coverage. However, some flood events occur on sub-daily time scales and flood prediction systems could benefit from using models calibrated on the same time scale. This study compares precipitation data aggregated from hourly stations (HP) and data disaggregated from daily stations (DP) with 6-hourly forecasts from ECMWF over the time period 1 October 2006–31 December 2009. The HP and DP data sets were then used to calibrate two hydrological models, LISFLOOD-RR and HBV, and the latter was used in a flood case study. The HP scored better than the DP when evaluated against the forecast for lead times up to 4 days. However, this was not translated in the same way to the hydrological modelling, where the models gave similar scores for simulated runoff with the two datasets. The flood forecasting study showed that both datasets gave similar hit rates whereas the HP data set gave much smaller false alarm rates (FAR). This indicates that using sub-daily precipitation in the calibration and initiation of hydrological models can improve flood forecasting.

Ordered-defect sulfides as thermoelectric materials

The thermoelectric behaviour of the transition-metal disulphides n-type NiCr2S4 and p-type CuCrS2 is investigated. Materials prepared by high-temperature reaction were consolidated using cold-pressing and sintering, hot-pressing (HP) in graphite dies or spark-plasma sintering (SPS) in tungsten carbide dies. The consolidation conditions have a marked influence on the electrical transport properties. In addition to the effect on sample density, altering the consolidation conditions results in changes to the sample composition, including the formation of impurity phases. Maximum room-temperature power factors are 0.18 mW m-1 K-2 and 0.09 mW m-1 K-2 for NiCr2S4 and CuCrS2, respectively. Thermal conductivities of ca. 1.4 and 1.2 W m-1 K-1 lead to figures of merit of 0.024 and 0.023 for NiCr2S4 and CuCrS2, respectively.

A frequency-independent boundary element method for scattering by two-dimensional screens and apertures

We propose and analyse a hybrid numerical–asymptotic hp boundary element method (BEM) for time-harmonic scattering of an incident plane wave by an arbitrary collinear array of sound-soft two-dimensional screens. Our method uses an approximation space enriched with oscillatory basis functions, chosen to capture the high-frequency asymptotics of the solution. We provide a rigorous frequency-explicit error analysis which proves that the method converges exponentially as the number of degrees of freedom N increases, and that to achieve any desired accuracy it is sufficient to increase N in proportion to the square of the logarithm of the frequency as the frequency increases (standard BEMs require N to increase at least linearly with frequency to retain accuracy). Our numerical results suggest that fixed accuracy can in fact be achieved at arbitrarily high frequencies with a frequency-independent computational cost, when the oscillatory integrals required for implementation are computed using Filon quadrature. We also show how our method can be applied to the complementary ‘breakwater’ problem of propagation through an aperture in an infinite sound-hard screen.

Effect of different bleaching systems on the ultrastructure of bovine dentin

The aim of this study was to evaluate in vitro the effect of different in-office bleaching systems on the surface morphology of bovine dentin. Thirty tooth fragments measuring 4 x 4mm, containing enamel and dentin, were obtained from the crowns of extracted bovine incisors. Samples were subjected to simulated intracoronal bleaching techniques using conventional (Opalescence Endo (R) and Whiteness Super Endo (R)) and light-activated systems (Opalescence Xtra (R) and Whiteness HP Maxx (R)). Controls were treated with either sodium perborate mixed with 10% hydrogen peroxide or no bleaching agent. The samples were observed under SEM and the recorded images were evaluated for topographic alterations. The ultrastructural alterations of dentin observed in this study varied greatly between groups according to the products used. Higher pH products (Whiteness HP Maxx (R) and Opalescence Xtra (R)) associated with in-office techniques yielded better maintenance of dentin ultrastructure. Apparently, both low pH and hydrogen peroxide oxidation play a role in altering the ultrastructure of dentin during internal dental bleaching. The use of alkaline products with reduced time of application (in-office techniques) may decrease such morphological alterations.

Additive genetic relationships between scrotal circumference, heifer pregnancy, and stayability in Nellore cattle

Scrotal circumference data from 47,605 Nellore young bulls, measured at around 18 mo of age (SC18), were analyzed simultaneously with 27,924 heifer pregnancy (HP) and 80,831 stayability (STAY) records to estimate their additive genetic relationships. Additionally, the possibility that economically relevant traits measured directly in females could replace SC18 as a selection criterion was verified. Heifer pregnancy was defined as the observation that a heifer conceived and remained pregnant, which was assessed by rectal palpation at 60 d. Females were exposed to sires for the first time at about 14 mo of age (between 11 and 16 mo). Stayability was defined as whether or not a cow calved every year up to 5 yr of age, when the opportunity to breed was provided. A Bayesian linear-threshold-threshold analysis via Gibbs sampler was used to estimate the variance and covariance components of the multitrait model. Heritability estimates were 0.42 +/- 0.01, 0.53 +/- 0.03, and 0.10 +/- 0.01, for SC18, HP, and STAY, respectively. The genetic correlation estimates were 0.29 +/- 0.05, 0.19 +/- 0.05, and 0.64 +/- 0.07 between SC18 and HP, SC18 and STAY, and HP and STAY, respectively. The residual correlation estimate between HP and STAY was -0.08 +/- 0.03. The heritability values indicate the existence of considerable genetic variance for SC18 and HP traits. However, genetic correlations between SC18 and the female reproductive traits analyzed in the present study can only be considered moderate. The small residual correlation between HP and STAY suggests that environmental effects common to both traits are not major. The large heritability estimate for HP and the high genetic correlation between HP and STAY obtained in the present study confirm that EPD for HP can be used to select bulls for the production of precocious, fertile, and long-lived daughters. Moreover, SC18 could be incorporated in multitrait analysis to improve the prediction accuracy for HP genetic merit of young bulls.

A FOSSIL BULGE GLOBULAR CLUSTER REVEALED BY VERY LARGE TELESCOPE MULTI-CONJUGATE ADAPTIVE OPTICS

The globular cluster HP 1 is projected on the bulge, very close to the Galactic center. The Multi-Conjugate Adaptive Optics Demonstrator on the Very Large Telescope allowed us to acquire high-resolution deep images that, combined with first epoch New Technology Telescope data, enabled us to derive accurate proper motions. The cluster and bulge fields` stellar contents were disentangled through this process and produced an unprecedented definition in color-magnitude diagrams of this cluster. The metallicity of [Fe/H] approximate to -1.0 from previous spectroscopic analysis is confirmed, which together with an extended blue horizontal branch imply an age older than the halo average. Orbit reconstruction results suggest that HP 1 is spatially confined within the bulge.

Novel endogenous peptide agonists of cannabinoid receptors

Hemopressin (Hp), a 9-residue alpha-hemoglobin-derived peptide, was previously reported to function as a CB(1) cannabinoid receptor antagonist (1). In this study, we report that mass spectrometry (MS) data from peptidomics analyses of mouse brain extracts identified N-terminally extended forms of Hp containing either three (RVD-Hp alpha) or two (VD-Hp alpha) additional amino acids, as well as a beta-hemoglobinderived peptide with sequence similarity to that of hemopressin (VD-Hp beta). Characterization of the alpha-hemoglobin-derived peptides using binding and functional assays shows that in contrast to Hp, which functions as a CB(1) cannabinoid receptor antagonist, both RVD-Hp alpha and VD-Hp alpha function as agonists. Studies examining the increase in the phosphorylation of ERK1/2 levels or release of intracellular Ca(2+) indicate that these peptides activate a signal transduction pathway distinct from that activated by the endo-cannabinoid, 2-arachidonoylglycerol, or the classic CB(1) agonist, Hu-210. This finding suggests an additional mode of regulation of endogenous cannabinoid receptor activity. Taken together, these results suggest that the CB(1) receptor is involved in the integration of signals from both lipid-and peptide-derived signaling molecules.-Gomes, I., Grushko, J. S., Golebiewska, U., Hoogendoorn, S., Gupta, A., Heimann, A. S., Ferro, E. S., Scarlata, S., Fricker, L. D., Devi, L. A. Novel endogenous peptide agonists of cannabinoid receptors. FASEB J. 23, 3020-3029 (2009). www.fasebj.org

Conversion coefficients from air kerma to personal dose equivalent in mammography

In this work, the scattered X-ray beams produced by a mammography unit with a Mo/Mo, Mo/Rh and W/Rh anode/filter combinations were applied in the evaluation of the Hp(10, 0) and mean conversion coefficients from air kerma to the personal dose equivalent ((C) over barH(p(10,0 degrees))). The higher values of H(p)(10,0 degrees) are related to the Mo/Rh combination whereas the lower ones are for the W/Rh target/filter. (C) over barH(p(10,0 degrees)) values are in the range 0.19-0.54 Sv/Gy, where the higher values comprise the W/Rh combination. (C) 2009 Elsevier Ltd. All rights reserved.

Performance of GEANT4 in dosimetry applications: Calculation of X-ray spectra and kerma-to-dose equivalent conversion coefficients

In order to validate the Geant4 toolkit for dosimetry applications, simulations were performed to calculate conversion coefficients h(10, alpha) from air kerma free-in-air to personal dose equivalent Hp(10, a). The simulations consisted of two parts: the production of X-rays with radiation qualities of narrow and wide spectra, and the interaction of radiation with ICRU tissue-equivalent and ISO water slab phantoms. The half-value layers of the X-ray spectra obtained by simulation were compared with experimental results. Mean energy, spectral resolution, half-value layers and conversion coefficients were compared with ISO reference values. The good agreement between results from simulation and reference data shows that the Geant4 is suitable for dosimetry applications which involve photons with energies in the range of ten to a few hundreds of keV. (C) 2008 Elsevier Ltd. All rights reserved.

Polymethine cyanine dyes in beta-cyclodextrin solution: multiple equilibria and chemical oxidation

Absorption and fluorescence spectroscopy, electrochemical techniques, and semiempirical calculations were employed to characterize the multiple complexation equilibria between two polymethine cyanine dyes (IR-786 and Indocyanine green-ICG, 5) and beta-cyclodextrin (beta-CD, L), as well as the chemical reactivity of the complexed and uncomplexed species against the oxidizing agents hypochlorite (HC) and hydrogen peroxide (HP). IR-786 dimerization is favored with the increase in beta-CD concentration in the form of (SL)(2) complexes. In the case of ICG, free dimers (D) and SL complexes are favored. Both IR-786 and ICG react and discolor in the presence of HC and HP. For IR-786, the reaction with HP and HC proceeds with observed rate constants of 10(-3) and 0.28 s(-1) and second-order rate constants (k(2)) of similar to 10(-3) and 10(4) M(-1) s(-1), respectively. The intermediate species observed in the bleaching reactions of IR-786 and ICG were shown, by cyclic voltammetry and VIS absorption, to result from one electron oxidation. IR-786 complexed with beta-CD is protected against bleaching in the presence of HP and HC by factors of 20 and 4, respectively. This protection was not observed in ICG complexes. Superdelocalizability profile of both dyes and frontier orbital analysis indicates that beta-CD does not protect ICG from oxidation by HP or HC, whereas the 2:2 IR-786/beta-Cd complex is able to avoid the oxidation of IR-786. We concluded that the decrease in the chemical reactivity of the dyes against oxidant agents in the presence of beta-CD is due to the formation of (SL)(2) complexes. Copyright (C) 2010 John Wiley & Sons, Ltd.