bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thaw‐Consolidation Effects on the Stability of Alpine Talus Slopes in Permafrost
Authors: Bommer Christian , Fitze Philipp , Schneider Hansruedi 
Published: September 2012

ABSTRACTThe relative contributions of thaw consolidation and slope‐parallel seepage to the generation of overall porewater pressure and resultant potential changes in slope stability are determined in two case studies of thawing soils. The first study concerns experimental slopes of frozen silt inclined at 12° and 24° that thawed during scaled centrifuge modelling reported by Harris et al. (2008). The second study concerns a natural slope near Pontresina, eastern Swiss Alps, of coarse‐grained talus inclined at 37° and overlying fine‐grained soil that contains the permafrost table. In both cases, seepage parallel to the slope was found to contribute much more to the excess porewater pressures in the thawing soils than did thaw consolidation. This suggests that the effects of thaw consolidation on the stability of alpine talus slopes in mountain permafrost may have only minor significance. Copyright © 2012 John Wiley & Sons, Ltd.
The crystal structure of the Rv0301‐Rv0300 VapBC‐3 toxin—antitoxin complex from M. tuberculosis reveals a Mg2+ ion in the active site and a putative RNA‐binding site
Authors: Min Andrew B. , Miallau Linda , Sawaya Michael R. , Habel Jeff , Cascio Duilio , Eisenberg David 
Published: September 2012

AbstractVapBC pairs account for 45 out of 88 identified toxin‐antitoxin (TA) pairs in the Mycobacterium tuberculosis (Mtb) H37Rv genome. A working model suggests that under times of stress, antitoxin molecules are degraded, releasing the toxins to slow the metabolism of the cell, which in the case of VapC toxins is via their RNase activity. Otherwise the TA pairs remain bound to their promoters, autoinhibiting transcription. The crystal structure of Rv0301‐Rv0300, an Mtb VapBC TA complex determined at 1.49 Å resolution, suggests a mechanism for these three functions: RNase activity, its inhibition by antitoxin, and its ability to bind promoter DNA. The Rv0301 toxin consists of a core of five parallel beta strands flanked by alpha helices. Three proximal aspartates coordinate a Mg2+ ion forming the putative RNase active site. The Rv0300 antitoxin monomer is extended in structure, consisting of an N‐terminal beta strand followed by four helices. The last two helices wrap around the toxin and terminate near the putative RNase active site, but with different conformations. In one conformation, the C‐terminal arginine interferes with Mg2+ ion coordination, suggesting a mechanism by which the antitoxin can inhibit toxin activity. At the N‐terminus of the antitoxin, two pairs of Ribbon‐Helix‐Helix (RHH) motifs are related by crystallographic twofold symmetry. The resulting hetero‐octameric complex is similar to the FitAB system, but the two RHH motifs are about 30 Å closer together in the Rv0301‐Rv0300 complex, suggesting either a different span of the DNA recognition sequence or a conformational change.
Regulation of the activities of the mammalian transglutaminase family of enzymes
Authors: Klöck Cornelius , Khosla Chaitan 
Published: September 2012

AbstractMammalian transglutaminases catalyze post‐translational modifications of glutamine residues on proteins and peptides through transamidation or deamidation reactions. Their catalytic mechanism resembles that of cysteine proteases. In virtually every case, their enzymatic activity is modulated by elaborate strategies including controlled gene expression, allostery, covalent modification, and proteolysis. In this review, we focus on our current knowledge of post‐translational regulation of transglutaminase activity by physiological as well as synthetic allosteric agents. Our discussion will primarily focus on transglutaminase 2, but will also compare and contrast its regulation with Factor XIIIa as well as transglutaminases 1 and 3. Potential structure–function relationships of known mutations in human transglutaminases are analyzed.
Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures
Authors: Bermejo Guillermo A. , Clore G. Marius , Schwieters Charles D. 
Published: September 2012

AbstractStatistical potentials that embody torsion angle probability densities in databases of high‐quality X‐ray protein structures supplement the incomplete structural information of experimental nuclear magnetic resonance (NMR) datasets. By biasing the conformational search during the course of structure calculation toward highly populated regions in the database, the resulting protein structures display better validation criteria and accuracy. Here, a new statistical torsion angle potential is developed using adaptive kernel density estimation to extract probability densities from a large database of more than 106 quality‐filtered amino acid residues. Incorporated into the Xplor‐NIH software package, the new implementation clearly outperforms an older potential, widely used in NMR structure elucidation, in that it exhibits simultaneously smoother and sharper energy surfaces, and results in protein structures with improved conformation, nonbonded atomic interactions, and accuracy.
Side‐chain hydrophobicity and the stability of Aβ16–22 aggregates
Authors: Berhanu Workalemahu M. , Hansmann Ulrich H. E. 
Published: September 2012

AbstractRecent mutagenesis studies using the hydrophobic segment of Aβ suggest that aromatic π‐stacking interactions may not be critical for fibril formation. We have tested this conjecture by probing the effect of Leu, Ile, and Ala mutation of the aromatic Phe residues at positions 19 and 20, on the double‐layer hexametric chains of Aβ fragment Aβ16–22 using explicit solvent all‐atom molecular dynamics. As these simulations rely on the accuracy of the utilized force fields, we first evaluated the dynamic and stability dependence on various force fields of small amyloid aggregates. These initial investigations led us to choose AMBER99SB‐ILDN as force field in multiple long molecular dynamics simulations of 100 ns that probe the stability of the wild‐type and mutants oligomers. Single‐point and double‐point mutants confirm that size and hydrophobicity are key for the aggregation and stability of the hydrophobic core region (Aβ16–22). This suggests as a venue for designing Aβ aggregation inhibitors the substitution of residues (especially, Phe 19 and 20) in the hydrophobic region (Aβ16–22) with natural and non‐natural amino acids of similar size and hydrophobicity.
LacZ β‐galactosidase: Structure and function of an enzyme of historical and molecular biological importance
Authors: Juers Douglas H. , Matthews Brian W. , Huber Reuben E. 
Published: September 2012

AbstractThis review provides an overview of the structure, function, and catalytic mechanism of lacZ β‐galactosidase. The protein played a central role in Jacob and Monod's development of the operon model for the regulation of gene expression. Determination of the crystal structure made it possible to understand why deletion of certain residues toward the amino‐terminus not only caused the full enzyme tetramer to dissociate into dimers but also abolished activity. It was also possible to rationalize α‐complementation, in which addition to the inactive dimers of peptides containing the “missing” N‐terminal residues restored catalytic activity. The enzyme is well known to signal its presence by hydrolyzing X‐gal to produce a blue product. That this reaction takes place in crystals of the protein confirms that the X‐ray structure represents an active conformation. Individual tetramers of β‐galactosidase have been measured to catalyze 38,500 ± 900 reactions per minute. Extensive kinetic, biochemical, mutagenic, and crystallographic analyses have made it possible to develop a presumed mechanism of action. Substrate initially binds near the top of the active site but then moves deeper for reaction. The first catalytic step (called galactosylation) is a nucleophilic displacement by Glu537 to form a covalent bond with galactose. This is initiated by proton donation by Glu461. The second displacement (degalactosylation) by water or an acceptor is initiated by proton abstraction by Glu461. Both of these displacements occur via planar oxocarbenium ion‐like transition states. The acceptor reaction with glucose is important for the formation of allolactose, the natural inducer of the lac operon.
Environmental Awareness and Sustainable Development in the Russian Federation
Authors: Crotty Jo , Hall Sarah Marie 
Published: September 2012

ABSTRACTDrawing on empirical research from a qualitative study in the Russian Federation, this paper contributes to the limited academic literature on environmental awareness and sustainable development in Russia. Using data from nearly 100 interviews with firms, NGOs and environmental regulators, we explore current barriers to public environmental awareness and the avenues to sustainable development, in the context of a transition country. We conclude by calling for further research that investigates the possibilities for environmental education and sustainability in contemporary Russian society and the institutional barriers thereto. Copyright © 2012 John Wiley & Sons, Ltd and ERP Environment.
‘Sustainable Development’: the ‘Unsustainable’ Development of a Concept in Political Discourse
Authors: Kambites Carol Jill 
Published: September 2012

ABSTRACTThis article uses critical discourse analysis to analyse national level discourses of sustainable development in the UK through the 1990s and 2000s, as revealed in five documents produced by successive national governments during this period. After briefly reviewing the concept of sustainable development and its interpretations, national sustainable development discourses are analysed in the context of the wider political discourses that have arisen around the political ideologies of neo‐liberalism, Thatcherism and New Labour. A critical discourse analysis, using the concept of ‘discursive techniques’, reveals the way in which the concept of sustainable development has been adapted to conform to the dominant political discourses of neo‐liberalism, Thatcherism and New Labour. In this process, the term has been used to emphasize the compatibility of economic growth and environmental protection, and hence, arguably, has been used to avoid rather than to facilitate radical action. Copyright © 2012 John Wiley & Sons, Ltd and ERP Environment.
An overview of the Amber biomolecular simulation package
Authors: Salomon‐Ferrer Romelia , Case David A. , Walker Ross C. 
Published: September 2012

AbstractMolecular dynamics (MD) allows the study of biological and chemical systems at the atomistic level on timescales from femtoseconds to milliseconds. It complements experiment while also offering a way to follow processes difficult to discern with experimental techniques. Numerous software packages exist for conducting MD simulations of which one of the widest used is termed Amber. Here, we outline the most recent developments, since version 9 was released in April 2006, of the Amber and AmberTools MD software packages, referred to here as simply the Amber package. The latest release represents six years of continued development, since version 9, by multiple research groups and the culmination of over 33 years of work beginning with the first version in 1979. The latest release of the Amber package, version 12 released in April 2012, includes a substantial number of important developments in both the scientific and computer science arenas. We present here a condensed vision of what Amber currently supports and where things are likely to head over the coming years. Figure 1 shows the performance in ns/day of the Amber package version 12 on a single‐core AMD FX‐8120 8‐Core 3.6GHz CPU, the Cray XT5 system, and a single GPU GTX680. © 2012 John Wiley & Sons, Ltd.This article is categorized under:

Software > Molecular Modeling
Isolation and characterization of a novel Rhodococcus strain with switchable carbonyl reductase and para-acetylphenol hydroxylase activities
Authors: Zhang Rui , Ren Jie , Wang Yu , Wu Qiaqing , Wang Min , Zhu Dunming 
Published: September 2012

Abstract
In the search for an effective biocatalyst for the reduction of acetophenones with unprotected hydroxy group on the benzene ring, a microorganism, which reduced para-acetylphenol to S-(−)-1-(para-hydroxyphenyl)ethanol under anaerobic conditions, was isolated from soil samples and the 16S rDNA study showed that it was phylogenetically affiliated with species of the genus Rhodococcus and was most similar to Rhodococcus pyridinivorans. Unexpectedly, this strain also hydroxylated para-acetylphenol to give 4-acetylcatechol in presence of oxygen, possessing para-acetylphenol hydroxylase activity. While the reduction of para-acetylphenol had an optimal reaction pH at 7 and a broad optimal temperature range (35–45 °C), the hydroxylation reached the maximum conversion at the pH range of 7–8 and 35 °C. This study identified for the first time a Rhodococcus strain with para-acetylphenol hydroxylase activity, which also contains highly enantioselective carbonyl reductase activity with potential applications for the asymmetric reduction of these less-explored but important ketones such as α-aminoacetophenone, 3′-hydroxyacetophenone and 4′-hydroxyacetophenone. The para-acetylphenol hydroxylase and carbonyl reductase activity are switchable by the reaction conditions.
Fast Transmethylation of Serum Lipids Using Microwave Irradiation
Authors: Lin Yu Hong , Loewke James D. , Hyun Duk Y. , Leazer Jay , Hibbeln Joseph R. 
Published: September 2012

AbstractMicrowave irradiation as the energy source for one‐step direct transesterification of fatty acids in human serum lipids was examined in a solvent system of methanol: hexane: acetyl chloride based on a Lepage & Roy assay. Innovative and explosion proof single‐mode or multimode microwave accelerated reaction system was employed. Recoveries were calculated as the percentage of fatty acid concentrations measured by microwave assay to those by the reference method of the Lepage & Roy assay that utilized conductive heating at 100 °C for 60 min. Under conditions of 100 °C for 1 min in Single‐mode (S4–100 × 1), or 125 °C for 5 min in Multimode (M5–125 × 5), the recoveries were 100–103 % for the total fatty acids and 96–106 % for each categorized fatty acid, including saturates, monounsaturates, n‐6 PUFA, and n‐3 PUFA. For individual PUFA, the mean recoveries were 102–105 % for 18:2n‐6 and 18:3n‐3; 99, 109, and 95 % for 20:4n‐6, 20:5n‐3, and 22:6n‐3, respectively. Thus, fatty acid concentrations determined by microwave fatty acid assay were accurate to those results by the reference method, when the microwave conditions were optimal. In summary, the microwave irradiation could replace conductive heating in one‐step direct transesterification, and reduce the duration from 60 min to 5 min or less. This methodology may be applied in both the absolute and relative quantification of serum total fatty acids.
A Visual Titration Method for the Determination of the Acid Number of Oils and Fats: a Green Alternative
Authors: Aricetti J. A. , Tubino M. 
Published: September 2012

AbstractA visual and green titrimetric method is proposed for the determination of the acid number of oils and fats. The sample is dissolved in a water–ethanol mixture (1:1 v/v) and titrated with a 0.02 mol L−1 aqueous NaOH solution. Phenolphthalein is used as acid‐basic indicator. Oils of canola, sunflower, linseed, castor, corn and soy as well as swine lard, a total of twelve real samples, were analyzed. The results obtained were compared with those from the application of the AOCS Cd 3d‐63 method, through a statistical linear regression procedure at the 95 % confidence level and no evidence for systematic differences between the two sets of results was observed. The mean RSD (relative standard deviation) for the proposed procedure is 4.8 %, whereas that of the official method was found to be 5.4 %.
Synthesis and Characterization of Allyl Fatty Acid Derivatives as Reactive Coalescing Agents for Latexes
Authors: Barbosa Joana V. , Oliveira Fernanda , Moniz Jorge , Magalhães Fernão D. , Bastos Margarida M. S. M. 
Published: September 2012

AbstractThis work evaluated the use of allyl fatty acid esters derived from vegetable oil (palmitic acid, soybean and sunflower oils) as reactive coalescing agents in a waterborne latex system. Allyl fatty acid derivatives (AFAD) from vegetable oils were synthesized by two different processes. The synthesis was monitored by IR‐spectroscopy and the final product characterized by FT‐IR, GC–MS, 1H and 13C NMR. The presence of conjugated double bonds in the aliphatic chain was confirmed, which is a determinant for the proposed autoxidative latexes drying mechanism. Each of the AFAD were subsequently added to a standard acrylic emulsion, in order to study its potential as reactive coalescing agent. The minimum film‐forming temperature (MFT), glass transition temperature (Tg), drying time and rubbing resistance to solvents were evaluated. The results showed that, when added to water‐borne acrylic resins, an AFAD acts as a non‐volatile plasticizer capable of autoxidative crosslinking with itself.
Prebiotic Chemistry: What We Know, What We Don't
Authors: Cleaves H. James 
Published: September 2012

AbstractHow life on Earth began remains an unexplained scientific problem. This problem is nuanced in its practical details and the way attempted explanations feedback with questions and developments in other areas of science, including astronomy, biology, and planetary science. Prebiotic chemistry attempts to address this issue theoretically, experimentally, and observationally. The ease of formation of bioorganic compounds under plausible prebiotic conditions suggests that these molecules were present in the primitive terrestrial environment. In addition to synthesis in the Earth's primordial atmosphere and oceans, it is likely that the infall of comets, meteorites, and interplanetary dust particles, as well as submarine hydrothermal vent synthesis, may have contributed to prebiotic organic evolution. The primordial organic soup may have been quite complex, but it did not likely include all of the compounds found in modern organisms. Regardless of their origin, organic compounds would need to be concentrated and complexified by environmental mechanisms. While this review is by no means exhaustive, many of the issues central to the state of the art of prebiotic chemistry are reviewed here.
Lava Channel of Khedrai Dam, Northeast of Nasik in Western Deccan Volcanic Province: Detailed Morphology and Evidences of Channel Reactivation
Authors: Sen Bibhas , Sabale A. B. , Sukumaran P.V. 
Published: September 2012

Abstract
The 120 m-wide Khedrai Dam lava channel is one of the widest recorded in the Deccan Volcanic Province. Like many recent ones, this channel also has a pair of linear marginal levees made of breccia and confines the channel-fill lava. It is resting over a pahoehoe flow (substrate) of basalt studded with plagioclase megacrysts, also known as the Giant Plagioclase Basalt (GPB). The channel-fill lava, which makes the lining at the edges and basal portion of the channel, is a comb-layered basalt (Cl-B) characterized by alternating layers rich in curved, branching augite crystals and laths of plagioclase – a texture indicative of high order of supercooling and rapid cooling rates. The dominant and centrally filling lava of this channel is a plagioclase-phyric basalt (Pp-B) that has a wide variation in phenocryst number from megacryst-poor to megacryst-rich. Occurrence of centimetre to decimetre size angular fragments of Cl-B within Pp-B fill indicates mechanical dislodgements of channel-lining by flowing lava. This also suggests that the channel was reactivated before it finally lost its hydraulic gradient and solidified.
Application of Universal Soil Loss Equation (USLE) to Recently Reclaimed Badlands along the Adula and Mahalungi Rivers, Pravara Basin, Maharashtra
Authors: Sinha Debasree , Joshi Veena U. 
Published: September 2012

Abstract
The rapid erosion of soil by wind and water has been a problem since man began cultivating the land. Moreover soil erosion, as a hazard, has always been associated mainly with agriculture in the tropical and semi-arid areas. Soil loss through rill, gully and sheet erosion is a major environmental problem in India. Among all the predictive equations developed to estimate soil loss, the most accepted, used, convenient and suitable technique, for smaller areas like hillslopes and fields, is the Universal Soil Loss Equation (USLE). This method has been applied to the cultivated fields on either side of the gullied banks of the Adula and Mahalungi rivers, to estimate soil loss from fields under different crops. Rainfall data from the IMD has been used for the purpose. Field slope measurements, textural analysis of soil and determination of soil organic matter have also been carried out. Finally the soil loss has been computed from the generated data. The results have been used to ascertain whether the soil loss in the area is within or beyond the tolerance limit. It has been found that the soil loss in these areas have exceeded the tolerance limit and hence require due attention.
Earthquake Forerunner as Probable Precursor – An Example from North Burma Subduction Zone
Authors: Dasgupta Sujit , Mukhopadhyay Basab , Mukhopadhyay Manoj 
Published: September 2012

Abstract
The Burmese Arc seismic activity is not uniform for its ~ 1100 km length; only the Northern Burmese Arc (NBA) is intensely active. Six large earthquakes in the magnitude range 6.1 – 7.4 have originated from the NBA Benioff zone between 1954 -2011, within an area of 200 x 300 km2 where the Indian plate subducts eastward to depths beyond 200 km below the Burma plate. An analysis on seismogenesis of this interplate region suggests that while the subducting lithosphere is characterized by profuse seismicity, seismicity in the overriding plate is rather few. Large earthquakes occurring in the overriding plate are associated with the backarc Shan-Sagaing Fault (SSF) further east. The forecasting performance of the Benioff zone earthquakes in NBA as forerunner is analysed here by: (i) spatial earthquake clustering, (ii) seismic cycles and their temporal quiescence and (iii) the characteristic temporal b-value changes. Three such clusters (C1- C3) are identified from NBA Benioff Zones I & II that are capable of generating earthquakes in the magnitude ranges of 7.38 to 7.93. Seismic cycles evidenced for the Zone I displayed distinct quiescence (Q1, Q2 and Q3) prior to the 6th August 1988 (M 6.6) earthquake. Similar cycles were used to forecast an earthquake (Dasgupta et al. 2010) to come from the Zone I (cluster C1); which, actually struck on 4 February 2011 (M 6.3). The preparatory activity for an event has already been set in the Zone II and we speculate its occurrence as a large event (M &gt; 6.0) possibly within the year 2012, somewhere close to cluster C3. Temporal analysis of b-value indicates a rise before an ensuing large earthquake.