987 resultados para sheath fold


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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.

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Motivation: In order to enhance genome annotation, the fully automatic fold recognition method GenTHREADER has been improved and benchmarked. The previous version of GenTHREADER consisted of a simple neural network which was trained to combine sequence alignment score, length information and energy potentials derived from threading into a single score representing the relationship between two proteins, as designated by CATH. The improved version incorporates PSI-BLAST searches, which have been jumpstarted with structural alignment profiles from FSSP, and now also makes use of PSIPRED predicted secondary structure and bi-directional scoring in order to calculate the final alignment score. Pairwise potentials and solvation potentials are calculated from the given sequence alignment which are then used as inputs to a multi-layer, feed-forward neural network, along with the alignment score, alignment length and sequence length. The neural network has also been expanded to accommodate the secondary structure element alignment (SSEA) score as an extra input and it is now trained to learn the FSSP Z-score as a measurement of similarity between two proteins. Results: The improvements made to GenTHREADER increase the number of remote homologues that can be detected with a low error rate, implying higher reliability of score, whilst also increasing the quality of the models produced. We find that up to five times as many true positives can be detected with low error rate per query. Total MaxSub score is doubled at low false positive rates using the improved method.

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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.

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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?

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Coronal mass ejections (CMEs) can be continuously tracked through a large portion of the inner heliosphere by direct imaging in visible and radio wavebands. White light (WL) signatures of solar wind transients, such as CMEs, result from Thomson scattering of sunlight by free electrons and therefore depend on both viewing geometry and electron density. The Faraday rotation (FR) of radio waves from extragalactic pulsars and quasars, which arises due to the presence of such solar wind features, depends on the line-of-sight magnetic field component B ∥ and the electron density. To understand coordinated WL and FR observations of CMEs, we perform forward magnetohydrodynamic modeling of an Earth-directed shock and synthesize the signatures that would be remotely sensed at a number of widely distributed vantage points in the inner heliosphere. Removal of the background solar wind contribution reveals the shock-associated enhancements in WL and FR. While the efficiency of Thomson scattering depends on scattering angle, WL radiance I decreases with heliocentric distance r roughly according to the expression Ir –3. The sheath region downstream of the Earth-directed shock is well viewed from the L4 and L5 Lagrangian points, demonstrating the benefits of these points in terms of space weather forecasting. The spatial position of the main scattering site r sheath and the mass of plasma at that position M sheath can be inferred from the polarization of the shock-associated enhancement in WL radiance. From the FR measurements, the local B ∥sheath at r sheath can then be estimated. Simultaneous observations in polarized WL and FR can not only be used to detect CMEs, but also to diagnose their plasma and magnetic field properties.

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There has been recent interest in sensory systems that are able to display a response which is proportional to a fold change in stimulus concentration, a feature referred to as fold-change detection (FCD). Here, we demonstrate FCD in a recent whole-pathway mathematical model of Escherichia coli chemotaxis. FCD is shown to hold for each protein in the signalling cascade and to be robust to kinetic rate and protein concentration variation. Using a sensitivity analysis, we find that only variations in the number of receptors within a signalling team lead to the model not exhibiting FCD. We also discuss the ability of a cell with multiple receptor types to display FCD and explain how a particular receptor configuration may be used to elucidate the two experimentally determined regimes of FCD behaviour. All findings are discussed in respect of the experimental literature.

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Purpose We study particular structural and organisational factors affecting the formality of human resource management (HRM) practices in small and medium-sized enterprises (SMEs) in South-Eastern European (SEE) post-communist countries, in particular Serbia, Romania, Bulgaria and the Former Yugoslav Republic of Macedonia (FYROM) in order to understand the antecedents of formalization in such settings. Design/methodology/approach Adopting a quantitative approach, this study analyses data gathered through a survey of 168 managers of SMEs from throughout the region. Findings The results show that HRM in SMEs in the SEE region can be understood through a three-fold framework which includes: degree of internationalisation of SMEs, sector of SMEs and organisational size of SMEs. These three factors positively affect the level of HRM formalisation in SEE SMEs. These findings are further attributed to the particular political and economic context of the post-communist SEE region. Research limitations/implications Although specific criteria were set for SME selection, we do not suggest that the study reflects a representative picture of the SEE region because we used a purposive sampling methodology. Practical implications This article provides useful insights into the factors which influence HRM in SMEs in a particular context. The findings can help business owners and managers understand how HRM can be applied in smaller organisations, particularly in post-communist SEE business contexts. Originality/value HRM in SMEs in this region has hardly been studied at all despite their importance. Therefore, this exploratory research seeks to expand knowledge relating to the application of HRM in SMEs in SEE countries which have their business environments dominated by different dynamics in comparison to western European ones.

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Precise repositioning of a fractured zygoma is difficult. The traditional approach is through an eyebrow incision, but it can produce a scar that causes aesthetic and psychological problems for the patient. We describe the supratarsal fold approach to expose the frontozygomatic suture and to reduce small displacements of frontal sinus anterior wall; it gives good access and excellent aesthetic results. (C) 2007 The British Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

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This paper explores the structural continuum in CATH and the extent to which superfamilies adopt distinct folds. Although most superfamilies are structurally conserved, in some of the most highly populated superfamilies (4% of all superfamilies) there is considerable structural divergence. While relatives share a similar fold in the evolutionary conserved core, diverse elaborations to this core can result in significant differences in the global structures. Applying similar protocols to examine the extent to which structural overlaps occur between different fold groups, it appears this effect is confined to just a few architectures and is largely due to small, recurring super-secondary motifs (e.g., alpha beta-motifs, alpha-hairpins). Although 24% of superfamilies overlap with superfamilies having different folds, only 14% of nonredundant structures in CATH are involved in overlaps. Nevertheless, the existence of these overlaps suggests that, in some regions of structure space, the fold universe should be seen as more continuous.

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The South-American continent is constituted of three major geologic-geotectonic entities the homonym platform (consolidated at the end of the Cambrian) the Andean chain (essentially Meso-Cenozoic) and the Patagonian terrains affected by tectonism and magmatism through almost all of the Phanerozoic The platform is constituted by a series of cratonic nuclei (pre-Tonian fragments of the Rodinia fission) surrounded by a complex fabric of Neoproterozoic structural provinces Two major groups of orogenic processes (plate interaction cycles) constitute the evolution of these provinces the older occurred in the Tonian (smaller in area) and the younger Brasiliano that is present in all provinces The Tonian cycles (pre-Rodinia fission?) are still being sorted out and many questions still need to be answered The Brasiliano orogenic collage events (post-Rodinia fission?) developed in three main stages in part coeval from a province to another and are 650-600 580-560 and 540-500 Ma respectively (the late event reaching the Ordovician) The first group of orogenies is recorded in practically all provinces The third group is restricted to part of the Mantiqueira Province (southeast of the platform Buzios Orogeny) and present in the Pampean province (SW of the platform) For all these groups of orogenic events there are considerable records of rock assemblages related to processes of convergent plate interaction opening accretion collision and further extrusion There is a good correlation between the geologic and geotectonic data and geochemical and isotopic data The late tectonic processes (post-orogenic magmatism foreland basins etc) of the first two groups compete in time in distinct spaces with the peak of orogenic processes in the third group The introduction of the SHRIMP U-Pb methodology was fundamental to separate the Tonian and post-Tonian orogenic groups and their respective divisions in time and space Thus there are still many open points/problems which lead to expectations of addressing these issues in the near future with the more Intense use of this methodology (C) 2010 Elsevier B V All rights reserved

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Elemental and Sr-Nd isotopic data on metatexites, diatexites, orthogneisses and charnockites from the central Ribeira Fold Belt indicate that they are LILE-enriched weakly peraluminous granodiorites. Harker and Th-Hf-La correlation trends suggest that these rocks represent a co-genetic sequence, whereas variations on CaO, MnO, Y and HREE for charnockites can be explained by garnet consumption during granulitic metamorphism. Similar REE patterns and isotopic results of epsilon(565)(Nd) = -5.4 to -7.3 and (87)Sr/(86)Sr(565) = 0.706-0.711 for metatexites, diatexites, orthogneisses and charnockites, as well as similar T(DM) ages between 2.0 and 1.5 Ga are consistent with evolution from a relatively homogeneous and enriched common crustal (metasedimentary) protolith. Results suggest a genetic link between metatexites, diatexites, orthogneisses and charnockites and a two-step process for charnockite development: (a) generation of the hydrated igneous protoliths by anatexis of metasedimentary rocks; (b) continuous high-grade metamorphism that transformed the ""S-type granitoids"" (leucosomes and diatexites) into orthogneisses and, as metamorphism and dehydration progressed, into charnockites. (C) 2011 Elsevier Ltd. All rights reserved.

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The studied sector of the central Ribeira Fold Belt (SE Brazil) comprises metatexites, diatexites, charnockites and blastomylonites. This study integrates petrological and thermochronological data in order to constrain the thermotectonic and geodynamic evolution of this Neoproterozoic-Ordovician mobile belt during Western Gondwana amalgamation. New data indicate that after an earlier collision stage at similar to 610 Ma (zircon, U-Pb age), peak metamorphism and lower crust partial melting, coeval with the main regional high grade D(1) thrust deformation, occurred at 572-562 Ma (zircon, U-Pb ages). The overall average cooling rate was low (<5 degrees C/Ma) from 750 to 250 degrees C (at similar to 455 Ma; biotite-WR Rb-Sr age), but disparate cooling paths indicate differential uplift between distinct lithotypes: (a) metatexites and blastomylonites show a overall stable 3-5 degrees C/Ma cooling rate; (b) charnockites and associated rocks remained at T>650 degrees C during sub-horizontal D(2) shearing until similar to 510-470 Ma (garnet-WR Sm-Nd ages) (1-2 degrees C/Ma), being then rapidly exhumed/cooled (8-30 degrees C/Ma) during post-orogenic D(3) deformation with late granite emplacement at similar to 490 Ma (zircon, U-Pb age). Cooling rates based on garnet-biotite Fe-Mg diffusion are broadly consistent with the geochronological cooling rates: (a) metatexites were cooled faster at high temperatures (6 degrees C/Ma) and slowly at low temperatures (0.1 degrees C/Ma), decreasing cooling rates with time; (b) charnockites show low cooling rates (2 degrees C/Ma) near metamorphic peak conditions and high cooling rates (120 degrees C/Ma) at lower temperatures, increasing cooling rates during retrogression. The charnockite thermal evolution and the extensive production of granitoid melts in the area imply that high geothermal gradients were sustained fora long period of time (50-90 Ma). This thermal anomaly most likely reflects upwelling of asthenospheric mantle and magma underplating coupled with long-term generation of high HPE (heat producing elements) granitoids. These factors must have sustained elevated crustal geotherms for similar to 100 Ma, promoting widespread charnockite generation at middle to lower crustal levels. (C) 2010 Elsevier B.V. All rights reserved.

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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.

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Combined fluid inclusion (FI) microthermometry, Raman spectroscopy, X-ray diffraction, C-O-H isotopes and oxygen fugacities of granulites from central Ribeira Fold Belt, SE Brazil, provided the following results: i) Magnetite-Hematite fO(2) estimates range from 10(-11.5) bar (QFM + 1) to 10(-18.3) bar (QFM - 1) for the temperature range of 896 degrees C-656 degrees C, implying fO(2) decrease from metamorphic peak temperatures to retrograde conditions; ii) 5 main types of fluid inclusions were observed: a) CO(2) and CO(2)-N(2) (0-11 mol%) high to medium density (1.01-0.59 g/cm(3)) FI; b) CO(2) and CO(2)-N(2) (0-36 mol%) low density (0.19-0.29 g/cm(3)) FI; c) CO(2) (94-95 mol%)-N(2) (3 mol%)-CH(4) (2-3 mol%)-H(2)O (water phi(v) (25 degrees C) = 0.1) FI; d) low-salinity H(2)O-CO(2) FI; and e) late low-salinity H(2)O FI; iii) Raman analyses evidence two graphite types in khondalites: an early highly ordered graphite (T similar to 450 degrees C) overgrown by a disordered kind (T similar to 330 degrees C); iv) delta(18)O quartz results of 10.3-10.7 parts per thousand, imply high-temperature CO(2) delta(18)O values of 14.4-14.8 parts per thousand, suggesting the involvement of a metamorphic fluid, whereas lower temperature biotite delta(18)O and delta D results of 7.5-8.5 parts per thousand and -54 to -67 parts per thousand respectively imply H(2)O delta(18)O values of 10-11 parts per thousand and delta D(H2O) of -23 to -36 parts per thousand suggesting delta(18)O depletion and increasing fluid/rock ratio from metamorphic peak to retrograde conditions. Isotopic results are compatible with low-temperature H(2)O influx and fO(2) decrease that promoted graphite deposition in retrograde granulites, simultaneous with low density CO(2), CO(2)-N(2) and CO(2)-N(2)-CH(4)-H(2)O fluid inclusions at T = 450-330 degrees C. Graphite delta(13)C results of -10.9 to -11.4 parts per thousand imply CO(2) delta(13)C values of -0.8 to -1.3 parts per thousand suggesting decarbonation of Cambrian marine carbonates with small admixture of lighter biogenic or mantle derived fluids. Based on these results, it is suggested that metamorphic fluids from the central segment of Ribeira Fold Belt evolved to CO(2)-N(2) fluids during granulitic metamorphism at high fO(2), followed by rapid pressure drop at T similar to 400-450 degrees C during late exhumation that caused fO(2) reduction induced by temperature decrease and water influx, turning carbonic fluids into CO(2)-H(2)O (depleting biotite delta(18)O and delta D values), and progressively into H(2)O. When fO(2) decreased substantially by mixture of carbonic and aqueous fluids, graphite deposited forming khondalites. (C) 2010 Elsevier Ltd. All rights reserved.