Two human valyl-tRNA synthetase-encoding cDNA sequences deposited in GenBank display extensive differences

Five blocks of significant differences exist between two published sequences of the cDNA encoding human valyl-tRNA synthetase (GenBank X59303 and M98326). By comparison with the partial sequence of rat valyl-tRNA synthetase (GenBank M98327) the correct sequence can be deduced for two such blocks. The possible origin of the diversity for the two sequences is discussed.     

Physiological variation in metabolic phenotyping and functional genomic studies: use of orthogonal signal correction and PLS-DA

Metabolic phenotyping, or metabotyping, is increasingly being used as a probe in functional genomics studies. However, such profiling is subject to intrinsic physiological variation found in all animal populations. Using a nuclear magnetic resonance-based metabonomic approach, we show that diurnal variations in metabolism can obscure the interpretation of strain-related metabolic differences in two phenotypically normal mouse strains (C57BL10J and Alpk:ApfCD). To overcome this problem, diurnal-related metabolic variation was removed from these spectral data by application of orthogonal signal correction (OSC), a data filtering method. Interpretation of the removed orthogonal variation indicated that diurnal-related variation had been removed and that the AM samples contained higher levels of creatine, hippurate, trimethylamine, succinate, citrate and 2-oxo-glutarate and lower levels of taurine, trimethylamine-N-oxide, spermine and 3-hydroxy-iso-valerate relative to the PM samples. We propose OSC will have great potential removing confounding variation obscuring subtle changes in metabolism in functional genomic studies and will be of benefit to optimising interpretation of proteomic and genomic datasets.     

Global Positioning System (GPS) location accuracy improvement due to selective availability removal

Global Positioning System (GPS) is an important new technology for spatio-temporal behaviour studies of animals. Differential correction improves location accuracy. Previously, it mostly removed partially the influence of Selective Availability (SA). SA was deactivated in May 2000. The aim of this study was to quantify the influence of SA cancellation on location accuracy of various GPS receivers. We tested the accuracy of locations obtained from non-differential and differential GPS animal collars before and after SA removal. We found a significant improvement in accuracy for both types of GPS collars. However, differential GPS still provides more accurate locations.     

Some general points in estimating heterogeneity variance with the DerSimonian-Laird estimator

In this paper we consider estimating heterogeneity variance with the DerSimonian-Laird (DSL) estimator as typically used in meta-analysis. In its general form the DSL estimator requires inverse population-averaged study-specific variances as weights, in which case the estimator is unbiased. It has become common practice, however, to use estimates of the study-specific variances instead of their population-averaged versions. This can lead to considerable bias. Simulations illustrate these findings.     

Small-sample bias and corrections for conditional maximum-likelihood odds-ratio estimators

A number of small-sample corrections have been proposed for the conditional maximum-likelihood estimator of the odds ratio for matched pairs with a dichotomous exposure. I here contrast the rationale and performance of several corrections, specifically those that generalize easily to multiple conditional logistic regression. These corrections or Bayesian analyses with informative priors may serve as diagnostics for small-sample problems. Points are illustrated with a small exact performance comparison and with an example from a study of electrical wiring and childhood leukemia. The former comparison suggests that small-sample bias may be more prevalent than commonly realized.     

Ab Initio and DFT Study of the Structures,Vibrations and Energetics of the Urea Dimer and Trimer

Stable structures and electronic properties of small urea clusters are investigated with ab initio calculations. We optimized the cluster geometries and calculated the vibrational frequencies with Hartree–Fock (HF), second-order Møller-Plesset perturbation theory (MP2), and Density Functional Theory (DFT) methods using different basis sets. The most stable dimer was found to consist of two nonplanar urea molecules which are connected by two N–-H...O bonds in a common plane, and the most stable trimer has a flat structure of complex and planar C2 form for each urea molecule, like in the crystal. The interaction energies were corrected for the basis set superposition error (BSSE) using the full Boys*ndash;Bernardi counterpoise correction scheme. The stability of different dimer and trimer structures, the features of formation of H-bonds and presented here are compared to the available experimental data.     

Tests for Genetic Differentiation

When testing for genetic differentiation the joint null hypothesis that there is no allele frequency difference at any locus is of interest. Common approaches to test this hypothesis are based on the summation of χ² statistics over loci and on the Bonferroni correction, respectively. Here, we also consider the Simes adjustment and a recently proposed truncated product method (TPM) to combine P‐values. The summation and the TPM (using a relatively large truncation point) are powerful when there are differences in many or all loci. The Simes adjustment, however, is powerful when there are differences regarding one or a few loci only. As a compromise between the different approaches we introduce a combination between the Simes adjustment and the TPM, i.e. the joint null hypothesis is rejected if at least one of the two methods, Simes and TPM, is significant at the α/2‐level. Simulation results indicate that this combination is a robust procedure with high power over the different types of alternatives.     

Estimating and Correcting for Bias in Population Assessments of Sooty Shearwaters

Abstract: We investigated the precision and accuracy of an infrared burrowscope for detecting sooty shearwater (Pufffinus griseus) chicks at 13 plots from 3 islands in southern New Zealand in 2003. We partially excavated burrows systems to reveal the entire burrow contents after 2 teams of observers had prospected all burrow entrances. Accuracy was similar between islands and observer teams at approximately 85%. The majority of the inaccuracy stemmed from failure to detect some chicks. Logistic regression modeling identified 4 burrow characteristics occurring between the entrance and the nest-site that influenced detection of burrow occupants. Detection was lower at nest-sites further from burrow entrances, in burrows with a high rate of burrow division, and in burrows with a high level of curvature. There was a positive relationship between the interaction of rate of division and curvature and detection of chicks. Distance from the burrow entrance was the only parameter that could be reliably used as a predictor of detection rate, so a reduced model containing only this variable was constructed to correct for burrowscope bias. The correction factor performed well on The Snares and Bench Island where predicted bias was very similar to observed levels (within 5%), but bias was overestimated on Putauhinu by up to 19.1%. Consistent bias, lack of damage to burrows from excavation, and the successful application of a correction factor all indicate the value of further testing burrowscope accuracy on other burrow-nesting seabird species.