bluuebunny/crossref_metadata_2025_split huggingface dataset:
Holocene Chemical Weathering, Surface Lowering and Rock Weakening Rates on Glacially Eroded Bedrock Surfaces in an Alpine Periglacial Environment, Jotunheimen, Southern Norway
Authors: Matthews John A. , Owen Geraint 
Published: August 2010

ABSTRACTIndices of the rate of Holocene chemical weathering of pyroxene‐granulite gneiss and peridotite are estimated from bedrock surfaces deglaciated c. 9700 years ago. A mean surface lowering rate for pyroxene‐granulite gneiss of 4.8 ± 1.0 mm ka−1 is estimated from the mean height of upstanding quartz veins, and Schmidt hammer R‐values are used to validate the reference‐surface method. Microrelief development and crack‐widening rates for peridotite are 2.6 ± 1.1 mm ka−1 and 1.8 ± 0.4 mm ka−1, respectively. Well‐developed weathering rinds indicate a mean rind development rate for peridotite of 0.6 ± 0.1 mm ka−1. New indices of rock surface weakening (IRW) and the rock surface weakening rate (WR) are defined in relation to Schmidt hammer mean R‐values. IRW values from weathered and unweathered surfaces of known age are 38.7 per cent for gneiss and 34.1–59.2 per cent (depending on the texture of the weathered rock surface) for peridotite: corresponding WR values are 2.7 R‐units ka−1 and 2.1–3.7 R‐units ka−1, respectively. Our methods and results are evaluated, particularly in relation to previous research and other rock types in Scandinavia. The various indices, being affected in different ways by biochemical and biological mechanical weathering and micro‐erosion, are regarded as complementary aids in the investigation of both the effects of chemical weathering and its rate. Copyright © 2010 John Wiley & Sons, Ltd.
Some observations on the formation of an active pronival rampart at Grunehogna Peaks, Western Dronning Maud Land, Antarctica
Authors: Hedding D. W. , Meiklejohn K. I. , Le Roux J. J. , Loubser M. , Davis J. K. 
Published: August 2010

AbstractSummer observations of the morphology and the debris accumulation processes at an actively forming pronival rampart at Grunehogna Peaks, Western Dronning Maud Land, Antarctica demonstrate that rockfall debris accumulation is causing downslope (outward) rampart extension even though the distal slope is not at the angle of repose. Field experiments show that the vast majority of rocks can traverse a stable firn surface to reach the proximal slope of the rampart and more than half end up on the distal slope or beyond. The formation processes indicate that the morphological characteristics and environmental conditions under which such features develop may be more varied than conceived in current models. Consequently, caution must be employed when fossil ramparts are used to infer palaeo‐environmental conditions. Copyright © 2010 John Wiley & Sons, Ltd.
A general model of autochthonous blockfield evolution
Authors: Ballantyne Colin K. 
Published: August 2010

AbstractTwo competing models have been invoked to explain the evolution of autochthonous blockfields: the Neogene model, which envisages that blockfield debris was produced by pre‐Quaternary chemical weathering; and the periglacial model, which explains autochthonous blockfields as the product of weathering and frost sorting under cold conditions during the Quaternary. This paper proposes that the evidence favouring both models can be accommodated within a single evolutionary framework. Research demonstrating tor emergence during the Pleistocene and rates of long‐term regolith production indicate lowering of blockfield‐mantled surfaces by at least several metres during the Quaternary. Such lowering implies that regolith covers have undergone continuous or intermittent renewal as surface losses are offset by lowering of the weathering front at the regolith‐rockhead boundary. Depending on initial (pre‐Quaternary) regolith depth and the surface lowering rate, some blockfields may retain inherited Neogene characteristics, but if lowering exceeds pre‐Quaternary regolith depth, a blockfield dominated by the products of mechanical weathering develops. It is proposed that the dominant mechanism operating in the later stages of blockfield evolution has been frost wedging of jointed bedrock at the base of the active layer, a process favoured by saturation of the lower parts of blockfields during seasonal freezeback and possibly by upwards freezing from ‘cold’ permafrost. Copyright © 2010 John Wiley & Sons, Ltd.
Isotopic composition and thermal regime of ice wedges in northern Victoria Land, East Antarctica
Authors: Raffi R. , Stenni B. 
Published: August 2010

AbstractIce wedges, with tops located 27 to 55 cm below the ground surface, were studied over several summers between 1998 and 2006 at three sites with differing elevations in northern Victoria Land, East Antarctica. The thermal regime, based on data‐logger measurements over five years, exhibits very low temperatures, an inferred absence of snow, and high temperature gradients between the ground surface and the top of the ice wedge that may trigger cracking. A co‐isotopic study of the wedge‐ice oxygen (δ18O) and hydrogen (δD) isotopic values shows extremely negative deuterium excess values and a strong divergence from the expected precipitation. These values and observations of hoarfrost crystals in ice‐wedge cracks during summer field surveys indicate that sublimation processes control the formation of ice in wedges, especially at high elevations within this region. Copyright © 2010 John Wiley & Sons, Ltd.
HandTutorTM enhanced hand rehabilitation after stroke — a pilot study
Authors: Carmeli Eli , Peleg Sara , Bartur Gadi , Elbo Enbal , Vatine Jean‐Jacques 
Published: August 2010

AbstractBackground and Purpose. This study assessed the potential therapeutic benefit of using HandTutorTM in combination with traditional rehabilitation in a post‐stroke sub‐acute population. The study compares an experimental group receiving traditional therapy combined with HandTutorTM treatment, against a control group receiving only traditional therapy. Method. An assessor‐blinded, randomized controlled pilot trial, was conducted in the Reuth rehabilitation unit in Israel. Thirty‐one stroke patients in the sub‐acute phase, were randomly assigned to one of the two groups (experimental or control) in sets of three. The experimental group (n = 16) underwent a hand rehabilitation programme using the HandTutorTM combined with traditional therapy. The control group (n = 15) received only traditional therapy. The treatment schedules for both groups were of similar duration and frequency. Improvements were evaluated using three indicators: 1) The Brunnström‐Fugl‐Meyer (FM) test, 2) the Box and Blocks (B&B) test and 3) improvement parameters as determined by the HandTutorTM software. Results. Following 15 consecutive treatment sessions, a significant improvement was observed within the experimental group (95% confidence intervals) compared with the control group: B&B p = 0.015; FM p = 0.041, HandTutorTM performance accuracy on x axis and performance accuracy on y axis p < 0.0003. Conclusion. The results from this pilot study support further investigation of the use of the HandTutorTM in combination with traditional occupational therapy and physiotherapy during post stroke hand function rehabilitation. Copyright © 2010 John Wiley & Sons, Ltd.
The lambda spanin components Rz and Rz1 undergo tertiary and quaternary rearrangements upon complex formation
Authors: Berry Joel , Savva Christos , Holzenburg Andreas , Young Ry 
Published: August 2010

AbstractPhage holins and endolysins have long been known to play key roles in lysis of the host cell, disrupting the cytoplasmic membrane and peptidoglycan (PG) layer, respectively. For phages of Gram‐negative hosts, a third class of proteins, the spanins, are involved in disrupting the outer membrane (OM). Rz and Rz1, the components of the lambda spanin, are, respectively, a class II inner membrane protein and an OM lipoprotein, are thought to span the entire periplasm by virtue of C‐terminal interactions of their soluble domains. Here, the periplasmic domains of Rz and Rz1 have been purified and shown to form dimeric and monomeric species, respectively, in solution. Circular dichroism analysis indicates that Rz has significant alpha‐helical character, but much less than predicted, whereas Rz1, which is 25% proline, is unstructured. Mixture of the two proteins leads to complex formation and an increase in secondary structure, especially alpha‐helical content. Moreover, transmission electron‐microscopy reveals that Rz–Rz1 complexes form large rod‐shaped structures which, although heterogeneous, exhibit periodicities that may reflect coiled‐coil bundling as well as a long dimension that matches the width of the periplasm. A model is proposed suggesting that the formation of such bundles depends on the removal of the PG and underlies the Rz–Rz1 dependent disruption of the OM.
The apicomplexan Cryptosporidium parvum possesses a single mitochondrial‐type ferredoxin and ferredoxin:NADP+ reductase system
Authors: Lei Cheng , Rider S. Dean , Wang Cai , Zhang Haili , Tan Xiangshi , Zhu Guan 
Published: August 2010

AbstractWe have successfully expressed recombinant mitochondrial‐type ferredoxin (mtFd) and ferredoxin:NADP+ reductase (mtFNR) from Cryptosporidium parvum and characterized their biochemical features for the first time for an apicomplexan. Both C. parvum mtFd (CpmtFd) and FNR (CpmtFNR) were obtained and purified as holo‐proteins, in which the correct assembly of [2Fe–2S] cluster in Fd and that of FAD in FNR were confirmed and characterized by UV/vis and electron paramagnetic resonance. These proteins were fully functional and CpmtFNR was capable of transferring electrons from NADPH to CpmtFd in a cytochrome c‐coupled assay that followed a typical Michaelis‐Menten kinetics. Apicomplexan mtFd and mtFNR proteins were evolutionarily divergent from their counterparts in humans and animals and could be explored as potential drug targets in Cryptosporidium and other apicomplexans.
Blind predictions of protein interfaces by docking calculations in CAPRI
Authors: Lensink Marc F. , Wodak Shoshana J. 
Published: August 2010

AbstractReliable prediction of the amino acid residues involved in protein–protein interfaces can provide valuable insight into protein function, and inform mutagenesis studies, and drug design applications. A fast‐growing number of methods are being proposed for predicting protein interfaces, using structural information, energetic criteria, or sequence conservation or by integrating multiple criteria and approaches. Overall however, their performance remains limited, especially when applied to nonobligate protein complexes, where the individual components are also stable on their own. Here, we evaluate interface predictions derived from protein–protein docking calculations. To this end we measure the overlap between the interfaces in models of protein complexes submitted by 76 participants in CAPRI (Critical Assessment of Predicted Interactions) and those of 46 observed interfaces in 20 CAPRI targets corresponding to nonobligate complexes. Our evaluation considers multiple models for each target interface, submitted by different participants, using a variety of docking methods. Although this results in a substantial variability in the prediction performance across participants and targets, clear trends emerge. Docking methods that perform best in our evaluation predict interfaces with average recall and precision levels of about 60%, for a small majority (60%) of the analyzed interfaces. These levels are significantly higher than those obtained for nonobligate complexes by most extant interface prediction methods. We find furthermore that a sizable fraction (24%) of the interfaces in models ranked as incorrect in the CAPRI assessment are actually correctly predicted (recall and precision ≥50%), and that these models contribute to 70% of the correct docking‐based interface predictions overall. Our analysis proves that docking methods are much more successful in identifying interfaces than in predicting complexes, and suggests that these methods have an excellent potential of addressing the interface prediction challenge. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Noncellulosomal cohesin from the hyperthermophilic archaeon Archaeoglobus fulgidus
Authors: Voronov‐Goldman Milana , Lamed Raphael , Noach Ilit , Borovok Ilya , Kwiat Moria , Rosenheck Sonia , Shimon Linda J. W. , Bayer Edward A. , Frolow Felix 
Published: August 2010

AbstractThe increasing numbers of published genomes has enabled extensive survey of protein sequences in nature. During the course of our studies on cellulolytic bacteria that produce multienzyme cellulosome complexes designed for efficient degradation of cellulosic substrates, we have investigated the intermodular cohesin–dockerin interaction, which provides the molecular basis for cellulosome assembly. An early search of the genome databases yielded the surprising existence of a dockerin‐like sequence and two cohesin‐like sequences in the hyperthermophilic noncellulolytic archaeon, Archaeoglobus fulgidus, which clearly contradicts the cellulosome paradigm. Here, we report a biochemical and biophysical analysis, which revealed particularly strong‐ and specific‐binding interactions between these two cohesins and the single dockerin. The crystal structure of one of the recombinant cohesin modules was determined and found to resemble closely the type‐I cohesin structure from the cellulosome of Clostridium thermocellum, with certain distinctive features: two of the loops in the archaeal cohesin structure are shorter than those of the C. thermocellum structure, and a large insertion of 27‐amino acid residues, unique to the archaeal cohesin, appears to be largely disordered. Interestingly, the cohesin module undergoes reversible dimer and tetramer formation in solution, a property, which has not been observed previously for other cohesins. This is the first description of cohesin and dockerin interactions in a noncellulolytic archaeon and the first structure of an archaeal cohesin. This finding supports the notion that interactions based on the cohesin–dockerin paradigm are of more general occurrence and are not unique to the cellulosome system. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Structural, functional, and bioinformatics studies reveal a new snake venom homologue phospholipase A2 class
Authors: dos Santos Juliana I. , Cintra‐Francischinelli Mariana , Borges Rafael J. , Fernandes Carlos A. H. , Pizzo Paola , Cintra Adélia C. O. , Braz Antonio S. K. , Soares Andreimar M. , Fontes Marcos R. M. 
Published: August 2010

AbstractPhospholipases A2 (PLA2s) are enzymes responsible for membrane disruption through Ca2+‐dependent hydrolysis of phospholipids. Lys49‐PLA2s are well‐characterized homologue PLA2s that do not show catalytic activity but can exert a pronounced local myotoxic effect. These homologue PLA2s were first believed to present residual catalytic activity but experiments with a recombinant toxin show they are incapable of catalysis. Herein, we present a new homologue Asp49‐PLA2 (BthTX‐II) that is also able to exert muscle damage. This toxin was isolated in 1992 and characterized as presenting very low catalytic activity. Interestingly, this myotoxic homologue Asp49‐PLA2 conserves all the residues responsible for Ca2+ coordination and of the catalytic network, features thought to be fundamental for PLA2 enzymatic activity. Previous crystallographic studies of apo BthTX‐II suggested this toxin could be catalytically inactive since a distortion in the calcium binding loop was observed. In this article, we show BthTX‐II is not catalytic based on an in vitro cell viability assay and time‐lapse experiments on C2C12 myotube cell cultures, X‐ray crystallography and phylogenetic studies. Cell culture experiments show that BthTX‐II is devoid of catalytic activity, as already observed for Lys49‐PLA2s. Crystallographic studies of the complex BthTX‐II/Ca2+ show that the distortion of the calcium binding loop is still present and impairs ion coordination even though Ca2+ are found interacting with other regions of the protein. Phylogenetic studies demonstrate that BthTX‐II is more phylogenetically related to Lys49‐PLA2s than to other Asp49‐PLA2s, thus allowing Crotalinae subfamily PLA2s to be classified into two main branches: a catalytic and a myotoxic one. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Why are polar residues within the membrane core evolutionary conserved?
Authors: Illergård Kristoffer , Kauko Anni , Elofsson Arne 
Published: August 2010

AbstractHere, we present a study of polar residues within the membrane core of alpha‐helical membrane proteins. As expected, polar residues are less frequent in the membrane than expected. Further, most of these residues are buried within the interior of the protein and are only rarely exposed to lipids. However, the polar groups often border internal water filled cavities, even if the rest of the sidechain is buried. A survey of their functional roles in known structures showed that the polar residues are often directly involved in binding of small compounds, especially in channels and transporters, but other functions including proton transfer, catalysis, and selectivity have also been attributed to these proteins. Among the polar residues histidines often interact with prosthetic groups in photosynthetic‐ and oxidoreductase‐related proteins, whereas prolines often are required for conformational changes of the proteins. Indeed, the polar residues in the membrane core are more conserved than other residues in the core, as well as more conserved than polar residues outside the membrane. The reason is twofold; they are often (i) buried in the interior of the protein and (ii) directly involved in the function of the proteins. Finally, a method to identify which polar residues are present within the membrane core directly from protein sequences was developed. Applying the method to the set of all human membrane proteins the prediction indicates that polar residues were most frequent among active transporter proteins and GPCRs, whereas infrequent in families with few transmembrane regions, such as non‐GPCR receptors. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Ferromagnetism in Fe‐doped ZnO bulk samples with additional Cu doping
Authors: Wang Y. Q. , Su L. , Liu L. , Tian Z. M. , Chang T. Q. , Wang Z. , Yin S. Y. , Yuan S. L. 
Published: August 2010

AbstractRoom‐temperature (RT) ferromagnetism (FM) has been observed in Fe‐doped ZnO bulk samples fabricated by a coprecipitation method, and the effect of additional Cu doping on magnetic properties of the samples has been investigated. The results of XRD show that all doping samples are single‐phase with a wurtzite structure. X‐ray photoelectron spectroscopy reveals that Fe is in 3+ state substituting for Zn in the sample without Cu doping, however, Fe shows a mixed oxidation state of 2+ or 3+ in the sample with additional Cu doping, where Cu is 1+ valence. Magnetic measurements indicate that additional Cu doping enhances the FM of the system, and the magnetization increases gradually with the increasing Cu content x up to 1%. The observed RT FM was attributed to the ferromagnetic coupling between Fe3+ ions mediated by holes.
High‐surface‐quality nanocrystalline InN layers deposited on GaN templates by RF sputtering
Authors: Valdueza‐Felip Sirona , Naranjo Fernando B. , González‐Herráez Miguel , Lahourcade Lise , Monroy Eva , Fernández Susana 
Published: August 2010

AbstractWe report a detailed study of the effect of deposition parameters on optical, structural, and morphological properties of InN films grown by reactive radio‐frequency (RF) sputtering on GaN‐on‐sapphire templates in a pure nitrogen atmosphere. Deposition parameters under study are substrate temperature, RF power, and sputtering pressure. Wurtzite crystallographic structure with c‐axis preferred growth orientation is confirmed by X‐ray diffraction measurements. For the optimized deposition conditions, namely at a substrate temperature of 450 °C and RF power of 30 W, InN films present a root‐mean‐square surface roughness as low as ∼0.4 nm, comparable to the underlying substrate. The apparent optical bandgap is estimated at 720 nm (1.7 eV) in all cases. However, the InN absorption band tail is strongly influenced by the sputtering pressure due to a change in the species of the plasma.
Mechanisms of doping graphene
Authors: Pinto H. , Jones R. , Goss J. P. , Briddon P. R. 
Published: August 2010

AbstractWe distinguish three mechanisms of doping graphene. Density functional theory is used to show that electronegative molecules like tetrafluoro‐tetracyanoquinodimethane (F4‐TCNQ) and electropositive metals like K dope graphene p‐ and n‐ type, respectively. These dopants are expected to lead to a decrease in carrier mobility arising from Coulomb scattering but without any hysteresis effects. Secondly, a novel doping mechanism is exhibited by Au which dopes bilayer graphene but not single layer. Thirdly, electrochemical doping is effected by redox reactions and can result in p‐doping by humid atmospheres and n‐doping by NH3 and toluene.
Optically active point defects in high quality single crystal diamond
Authors: Goss J. P. , Briddon P. R. , Pinto H. , Jones R. 
Published: August 2010

AbstractWe use density functional theory to investigate the optical properties of vacancy di‐nitrogen, vacancy–nitrogen–hydrogen and vacancy di‐hydrogen defects. The first is a common defect found in irradiated natural type IaA diamonds while the second is found in as‐grown CVD diamond. The last has not yet been detected. We find that these defects possess at least two charge states which can lead to photochromic behaviour. In the neutral and negative states, the three defects have optical bands due to internal transitions and two weaker optical absorption bands coming from charge state changes. Thus at least four absorption bands are expected for these defects. Vibrational modes of the hydrogen defects are reported.
Room temperature ferromagnetism in Cr doped chalcopyrite type Cu–Zn–Se compound
Authors: Joseph D. Paul , Venkateswaran C. 
Published: August 2010

AbstractConsidering the well‐established CuInSe2 as a prototype system, a new compound of the chalcopyrite type, by replacing In with Zn, has been attempted by metallurgical method. The X‐ray diffraction pattern of the ordered defect compound Cu1‐xZn1−ySe2−δ with the characteristic peaks of a chalcopyrite phase, such as (112), (204) and (312) confirm the tetragonal structure. On doping with ‘Cr’ the band gap blue shifted to 4.09 from 3.4 eV indicating possibility of band gap tailoring. Cu1−xZn1−ySe2−δ magnetically doped with Cr shows ferromagnetic ordering at room temperature. The results are discussed.
Calculation of semiconductor band structures and defects by the screened exchange density functional
Authors: Clark S. J. , Robertson J. 
Published: August 2010

AbstractThe screened exchange (SX) density functional is a hybrid density functional which has been developed to improve the description of the band gaps of semiconductors and insulators in the local density approximation. It is accurate enough to reduce the band gap error to 7%, and efficient enough to be used variationally for total energy minimization in defects for supercells of 100 atoms. It also gives the correct localization of trapped hole states. Calculations of band structures and defects by SX for several materials are given as examples.