Prediction of novel and analogous folds using fragment assembly and fold recognition

A number of new and newly improved methods for predicting protein structure developed by the Jones–University College London group were used to make predictions for the CASP6 experiment. Structures were predicted with a combination of fold recognition methods (mGenTHREADER, nFOLD, and THREADER) and a substantially enhanced version of FRAGFOLD, our fragment assembly method. Attempts at automatic domain parsing were made using DomPred and DomSSEA, which are based on a secondary structure parsing algorithm and additionally for DomPred, a simple local sequence alignment scoring function. Disorder prediction was carried out using a new SVM-based version of DISOPRED. Attempts were also made at domain docking and “microdomain” folding in order to build complete chain models for some targets.

Benchmarking secondary structure prediction for fold recognition

If secondary structure predictions are to be incorporated into fold recognition methods, an assessment of the effect of specific types of errors in predicted secondary structures on the sensitivity of fold recognition should be carried out. Here, we present a systematic comparison of different secondary structure prediction methods by measuring frequencies of specific types of error. We carry out an evaluation of the effect of specific types of error on secondary structure element alignment (SSEA), a baseline fold recognition method. The results of this evaluation indicate that missing out whole helix or strand elements, or predicting the wrong type of element, is more detrimental than predicting the wrong lengths of elements or overpredicting helix or strand. We also suggest that SSEA scoring is an effective method for assessing accuracy of secondary structure prediction and perhaps may also provide a more appropriate assessment of the “usefulness” and quality of predicted secondary structure, if secondary structure alignments are to be used in fold recognition.

What are the baselines for protein fold recognition?

What constitutes a baseline level of success for protein fold recognition methods? As fold recognition benchmarks are often presented without any thought to the results that might be expected from a purely random set of predictions, an analysis of fold recognition baselines is long overdue. Given varying amounts of basic information about a protein—ranging from the length of the sequence to a knowledge of its secondary structure—to what extent can the fold be determined by intelligent guesswork? Can simple methods that make use of secondary structure information assign folds more accurately than purely random methods and could these methods be used to construct viable hierarchical classifications?

The accuracy of students' predictions of their GCSE grades

The paper reports a study that investigated the relationship between students’ self-predicted and actual General Certificate of Secondary Education results in order to establish the extent of over- and under-prediction and whether this varies by subject and across genders and socio-economic groupings. It also considered the relationship between actual and predicted attainment and attitudes towards going to university. The sample consisted of 109 young people in two schools being followed up from an earlier study. Just over 50% of predictions were accurate and students were much more likely to over-predict than to under-predict. Most errors of prediction were only one grade out and may reflect examination unreliability as well as student misperceptions. Girls were slightly less likely than boys to over-predict but there were no differences associated with social background. Higher levels of attainment, both actual and predicted, were strongly associated with positive attitudes to university. Differences between predictions and results are likely to reflect examination errors as well as pupil errors. There is no evidence that students from more advantaged social backgrounds over-estimate themselves compared with other students, although boys over-estimate themselves compared with girls.

First order k-th moment finite element analysis of nonlinear operator equations with stochastic data

We develop and analyze a class of efficient Galerkin approximation methods for uncertainty quantification of nonlinear operator equations. The algorithms are based on sparse Galerkin discretizations of tensorized linearizations at nominal parameters. Specifically, we consider abstract, nonlinear, parametric operator equations J(\alpha ,u)=0 for random input \alpha (\omega ) with almost sure realizations in a neighborhood of a nominal input parameter \alpha _0. Under some structural assumptions on the parameter dependence, we prove existence and uniqueness of a random solution, u(\omega ) = S(\alpha (\omega )). We derive a multilinear, tensorized operator equation for the deterministic computation of k-th order statistical moments of the random solution's fluctuations u(\omega ) - S(\alpha _0). We introduce and analyse sparse tensor Galerkin discretization schemes for the efficient, deterministic computation of the k-th statistical moment equation. We prove a shift theorem for the k-point correlation equation in anisotropic smoothness scales and deduce that sparse tensor Galerkin discretizations of this equation converge in accuracy vs. complexity which equals, up to logarithmic terms, that of the Galerkin discretization of a single instance of the mean field problem. We illustrate the abstract theory for nonstationary diffusion problems in random domains.

The accuracy of SST retrievals from AATSR: An initial assessment through geophysical validation against in situ radiometers, buoys and other SST data sets

The Advanced Along-Track Scanning Radiometer (AATSR) was launched on Envisat in March 2002. The AATSR instrument is designed to retrieve precise and accurate global sea surface temperature (SST) that, combined with the large data set collected from its predecessors, ATSR and ATSR-2, will provide a long term record of SST data that is greater than 15 years. This record can be used for independent monitoring and detection of climate change. The AATSR validation programme has successfully completed its initial phase. The programme involves validation of the AATSR derived SST values using in situ radiometers, in situ buoys and global SST fields from other data sets. The results of the initial programme presented here will demonstrate that the AATSR instrument is currently close to meeting its scientific objectives of determining global SST to an accuracy of 0.3 K (one sigma). For night time data, the analysis gives a warm bias of between +0.04 K (0.28 K) for buoys to +0.06 K (0.20 K) for radiometers, with slightly higher errors observed for day time data, showing warm biases of between +0.02 (0.39 K) for buoys to +0.11 K (0.33 K) for radiometers. They show that the ATSR series of instruments continues to be the world leader in delivering accurate space-based observations of SST, which is a key climate parameter.

Type-1 error inflation in the traditional by-participant analysis to metamemory accuracy: a generalized mixed-effects model perspective

In order to examine metacognitive accuracy (i.e., the relationship between metacognitive judgment and memory performance), researchers often rely on by-participant analysis, where metacognitive accuracy (e.g., resolution, as measured by the gamma coefficient or signal detection measures) is computed for each participant and the computed values are entered into group-level statistical tests such as the t-test. In the current work, we argue that the by-participant analysis, regardless of the accuracy measurements used, would produce a substantial inflation of Type-1 error rates, when a random item effect is present. A mixed-effects model is proposed as a way to effectively address the issue, and our simulation studies examining Type-1 error rates indeed showed superior performance of mixed-effects model analysis as compared to the conventional by-participant analysis. We also present real data applications to illustrate further strengths of mixed-effects model analysis. Our findings imply that caution is needed when using the by-participant analysis, and recommend the mixed-effects model analysis.

Determination of the absolute accuracy of UK chamber facilities used in measuring methane emissions from livestock

Respiration chambers are one of the primary sources of data on methane emissions from livestock. This paper describes the results from a coordinated set of chamber validation experiments which establishes the absolute accuracy of the methane emission rates measured by the chambers, and for the first time provides metrological traceability to international standards, assesses the impact of both analyser and chamber response times on measurement uncertainty and establishes direct comparability between measurements made across different facilities with a wide range of chamber designs. As a result of the validation exercise the estimated combined uncertainty associated with the overall capability across all facilities reduced from 25.7% (k = 2, 95% confidence) before the validation to 2.1% (k = 2, 95% confidence) when the validation results are applied to the facilities’ data.

Ex Vivo Accuracy of an Apex Locator Using Digital Signal Processing in Primary Teeth

The purpose of this study was to evaluate ex vivo the accuracy an electronic apex locator during root canal length determination in primary molars. Methods: One calibrated examiner determined the root canal length in 15 primary molars (total=34 root canals) with different stages of root resorption. Root canal length was measured both visually, with the placement of a K-file 1 mm short of the apical foramen or the apical resorption bevel, and electronically using an electronic apex locator (Digital Signal Processing). Data were analyzed statistically using the intraclass correlation (ICC) test. Results: Comparing the actual and electronic root canal length measurements in the primary teeth showed a high correlation (ICC=0.95) Conclusions: The Digital Signal Processing apex locator is useful and accurate for apex foramen location during root canal length measurement in primary molars. (Pediatr Dent 200937:320-2) Received April 75, 2008 vertical bar Lost Revision August 21, 2008 vertical bar Revision Accepted August 22, 2008

Ex vivo evaluation of the accuracy of two electronic apex locators during root canal length determination in primary teeth

Aim To evaluate ex vivo the accuracy of two electronic apex locators during root canal length determination in primary incisor and molar teeth with different stages of physiological root resorption. Methodology One calibrated examiner determined the root canal length in 17 primary incisors and 16 primary molars (total of 57 root canals) with different stages of root resorption based on the actual canal length and using two electronic apex locators. Root canal length was measured both visually, with the placement of a K-file 1 mm short of the apical foramen or the apical resorption bevel, and electronically using two electronic apex locators (Root ZX II - J. Morita Corp. and Mini Apex Locator - SybronEndo) according to the manufacturers` instructions. Data were analysed statistically using the intraclass correlation (ICC) test. Results Comparison of the actual root canal length and the electronic root canal length measurements revealed high correlation (ICC = 0.99), regardless of the tooth type (single-rooted and multi-rooted teeth) or the presence/absence of physiological root resorption. Conclusions Root ZX II and Mini Apex Locator proved useful and accurate for apex foramen location during root canal length measurement in primary incisors and molars.

Accuracy of the iPex multi-frequency electronic apex locator in primary molars: an ex vivo study

P>Aim To evaluate ex vivo the accuracy of the iPex multi-frequency electronic apex locator (NSK Ltd, Tokyo, Japan) for working length determination in primary molar teeth. Methodology One calibrated examiner determined the working length in 20 primary molar teeth (total of 33 root canals). Working length was measured both visually, with the placement of a K-file 1 mm short of the apical foramen or the most coronal limit of root resorption, and electronically using the electronic apex locator iPex, according to the manufacturers` instructions. Data were analysed statistically using the intraclass correlation (ICC) test. Results Comparison of the actual and the electronic measurements revealed high correlation (ICC = 0.99) between the methods, regardless of the presence or absence of physiological root resorption. Conclusions In this laboratory study, the iPex accurately identified the apical foramen or the apical opening location for working length measurement in primary molar teeth.

Photometric redshifts and k-corrections for the Sloan Digital Sky Survey Data Release 7

We present a catalogue of galaxy photometric redshifts and k-corrections for the Sloan Digital Sky Survey Data Release 7 (SDSS-DR7), available on the World Wide Web. The photometric redshifts were estimated with an artificial neural network using five ugriz bands, concentration indices and Petrosian radii in the g and r bands. We have explored our redshift estimates with different training sets, thus concluding that the best choice for improving redshift accuracy comprises the main galaxy sample (MGS), the luminous red galaxies and the galaxies of active galactic nuclei covering the redshift range 0 < z < 0.3. For the MGS, the photometric redshift estimates agree with the spectroscopic values within rms = 0.0227. The distribution of photometric redshifts derived in the range 0 < z(phot) < 0.6 agrees well with the model predictions. k-corrections were derived by calibration of the k-correct_v4.2 code results for the MGS with the reference-frame (z = 0.1) (g - r) colours. We adopt a linear dependence of k-corrections on redshift and (g - r) colours that provide suitable distributions of luminosity and colours for galaxies up to redshift z(phot) = 0.6 comparable to the results in the literature. Thus, our k-correction estimate procedure is a powerful, low computational time algorithm capable of reproducing suitable results that can be used for testing galaxy properties at intermediate redshifts using the large SDSS data base.

Metamorphic P-T evolution of granulites in the central Ribeira Fold Belt, SE Brazil

Pseudosections, geothermobarometric estimates and careful petrographic observations of gneissic migmatites and granulites from Neoproterozoic central Ribeira Fold Belt (SE Brazil) were performed in order to quantify the metamorphic P-T conditions during prograde and retrograde evolution of the Brasiliano Orogeny. Results establish a prograde metamorphic trajectory from amphibolite facies conditions to metamorphic peak (T = 850 +/- 50 A degrees C; P = 8 +/- 1 kbar) that promoted widespread dehydrationmelting of 30 to 40% of the gneisses and high-grade granitization. After the metamorphic peak, migmatites evolved with cooling and decompression to T a parts per thousand 500 A degrees C and P a parts per thousand 5 kbar coupled with aH2O increase, replacing the high-grade paragenesis plagioclase-quartz-K-feldspar-garnet by quartz-biotite-sillimanite-(muscovite). Cordierite absence, microtextural observations and P-T results constrain the migmatite metamorphic evolution in the pseudosections as a clockwise P-T path with retrograde cooling and decompression. High-temperature conditions further dehydrated the lower crust with biotite and amphibole-dehydration melting and granulite formation coupled with 10% melt generation. Granulites can thus be envisaged as middle to lower crust dehydrated restites. Granulites were slowly (nearly isobarically) cooled, followed by late exhumation/retrograde rapid decompression and cooling, reflecting a two step P-T path. This retrograde evolution, coupled with water influx, chemically reequilibrated the rocks from granulite to amphibolite/greenschist facies, promoting the replacement of the plagioclase-quartz-garnet-hypersthene peak assemblage by quartz-biotite- K-feldspar symplectites.