bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lipid a from lipopolysaccharide recognition: Structure, dynamics and cooperativity by molecular dynamics simulations
Authors: Garate Jose Antonio , Oostenbrink Chris 
Published: January 2013

AbstractMolecular dynamics simulations of Lipid A and its natural precursor Lipid IVA from E.coli have been carried out free in solution, bound to the myeliod differentiation protein 2 (MD2) and in the complex of MD2 with the toll like receptor 4 (TLR4). In addition, simulations of the ligand free MD2 and MD2‐TLR4 complex were performed. A structural and energetic characterization of the bound and unbound states of Lipid A/IVA was generated. As the crystal structures depict, the main driving force for MD2‐Lipid A/IVA are the hydrophobic interactions between the aliphatic tails and the MD2 cavity. The charged phosphate groups do strongly interact with positively charged residues, located at the surface of MD2. However, they are not essential for keeping the lipids in the cavity, indicating a more prominent role in binding recognition and ionic interactions with TLR4 at the MD2/TLR4 interface. Interestingly, in the absence of any ligand MD2 rapidly closes, blocking the binding cavity. The presence of TLR4, though changing the dynamics, was not able to impede the aforementioned closing event. We hypothesize that fluctuations of the H1 region are essential for this phenomenon, and it is plausible that an equilibrium between the open and closed states exists, although the lengths of our simulations are not sufficient to encompass the reversible process. The MD2/Lipid A‐TLR4 complex simulations show that the presence of the ligand energetically stabilizes the complex relative to the ligand‐free structures, indicating cooperativity in the binding process. © Proteins 2013. © 2012 Wiley Periodicals, Inc.
Hydrophobic environment is a key factor for the stability of thermophilic proteins
Authors: Gromiha M. Michael , Pathak Manish C. , Saraboji Kadhirvel , Ortlund Eric A. , Gaucher Eric A. 
Published: January 2013

AbstractThe stability of thermophilic proteins has been viewed from different perspectives and there is yet no unified principle to understand this stability. It would be valuable to reveal the most important interactions for designing thermostable proteins for such applications as industrial protein engineering. In this work, we have systematically analyzed the importance of various interactions by computing different parameters such as surrounding hydrophobicity, inter‐residue interactions, ion‐pairs and hydrogen bonds. The importance of each interaction has been determined by its predicted relative contribution in thermophiles versus the same contribution in mesophilic homologues based on a dataset of 373 protein families. We predict that hydrophobic environment is the major factor for the stability of thermophilic proteins and found that 80% of thermophilic proteins analyzed showed higher hydrophobicity than their mesophilic counterparts. Ion pairs, hydrogen bonds, and interaction energy are also important and favored in 68%, 50%, and 62% of thermophilic proteins, respectively. Interestingly, thermophilic proteins with decreased hydrophobic environments display a greater number of hydrogen bonds and/or ion pairs. The systematic elimination of mesophilic proteins based on surrounding hydrophobicity, interaction energy, and ion pairs/hydrogen bonds, led to correctly identifying 95% of the thermophilic proteins in our analyses. Our analysis was also applied to another, more refined set of 102 thermophilic–mesophilic pairs, which again identified hydrophobicity as a dominant property in 71% of the thermophilic proteins. Further, the notion of surrounding hydrophobicity, which characterizes the hydrophobic behavior of residues in a protein environment, has been applied to the three‐dimensional structures of elongation factor‐Tu proteins and we found that the thermophilic proteins are enriched with a hydrophobic environment. The results obtained in this work highlight the importance of hydrophobicity as the dominating characteristic in the stability of thermophilic proteins, and we anticipate this will be useful in our attempts to engineering thermostable proteins. © Proteins 2013. © 2012 Wiley Periodicals, Inc.
Using an ultrahigh‐resolution regional climate model to predict local climatology
Authors: Wang Changgui , Jones Richard , Perry Matthew , Johnson Catrina , Clark Peter 
Published: January 2013

AbstractMany applications of risk assessment and Environmental Impact Assessments (EIA) require information about the local mesoscale climate at a very fine spatial scale. Current regional climate models (RCMs) with grid resolutions that normally range between 10 and 50 km cannot resolve the local physiographic features that influence the small‐scale features of local climate. This article presents a local climate model (LCM) system with an ultrahigh resolution and demonstrates its application to study the local climatology in a coastal zone where details of orography and coastline are important influences on the climate. The LCM has been developed from the Met Office Unified Model (MetUM) based on the concept of very high‐resolution numerical weather prediction. The ultrahigh‐resolution regional climate modelling is achieved through operating multiple nesting from a spatial resolution of 12 km down to ∼500 m. In this pilot study of the LCM, RCMs were run at 12, 4, 1.5 and 0.5 km grid resolutions to simulate the mesoscale climate of Weymouth Bay and Portland Harbour along the south coast of the United Kingdom. The period simulated was July‐August of the years 1993 to 2002, with model results validated against meteorological station time series. The results demonstrated the added value of the 500 m resolution model compared with the 1.5 km resolution model in modelling very fine local mesoscale climate patterns over the inner domain, including diurnal variations of temperature and winds, such as southwesterly flows, and the effect of wind channelling between the Isle of Portland and the mainland. Lower mean wind speeds are also found along the south‐facing coast to the east and in the shelter of Portland in the 500 m resolution model, particularly showing a sheltering zone between Portland and Weymouth Bay.
D‐Lactate production as a function of glucose metabolism in Saccharomyces cerevisiae
Authors: Stewart Benjamin J. , Navid Ali , Kulp Kristen S. , Knaack Jennifer L. S. , Bench Graham 
Published: January 2013

AbstractMethylglyoxal, a reactive, toxic dicarbonyl, is generated by the spontaneous degradation of glycolytic intermediates. Methylglyoxal can form covalent adducts with cellular macromolecules, potentially disrupting cellular function. We performed experiments using the model organism Saccharomyces cerevisiae, grown in media containing low, moderate and high glucose concentrations, to determine the relationship between glucose consumption and methylglyoxal metabolism. Normal growth experiments and glutathione depletion experiments showed that metabolism of methylglyoxal by log‐phase yeast cultured aerobically occurred primarily through the glyoxalase pathway. Growth in high‐glucose media resulted in increased generation of the methylglyoxal metabolite d‐lactate and overall lower efficiency of glucose utilization as measured by growth rates. Cells grown in high‐glucose media maintained higher glucose uptake flux than cells grown in moderate‐glucose or low‐glucose media. Computational modelling showed that increased glucose consumption may impair catabolism of triose phosphates as a result of an altered NAD+:NADH ratio. Copyright © 2013 John Wiley & Sons, Ltd.
Design and performance analysis of deterministic learning of sampled-data nonlinear systems
Authors: Yuan ChengZhi , Wang Cong 
Published: January 2013

Abstract
In this paper, we extend the deterministic learning theory to sampled-data nonlinear systems. Based on the Euler approximate model, the adaptive neural network identifier with a normalized learning algorithm is proposed. It is proven that by properly setting the sampling period, the overall system can be guaranteed to be stable and partial neural network weights can exponentially converge to their optimal values under the satisfaction of the partial persistent excitation (PE) condition. Consequently, locally accurate learning of the nonlinear dynamics can be achieved, and the knowledge can be represented by using constant-weight neural networks. Furthermore, we present a performance analysis for the learning algorithm by developing explicit bounds on the learning rate and accuracy. Several factors that influence learning, including the PE level, the learning gain, and the sampling period, are investigated. Simulation studies are included to demonstrate the effectiveness of the approach.
Incidence of adverse outcomes associated with gestational diabetes mellitus in low‐ and middle‐income countries
Authors: Wang Zheng , Kanguru Lovney , Hussein Julia , Fitzmaurice Ann , Ritchie Katherine 
Published: January 2013

AbstractBackgroundThe contribution of medical conditions such as diabetes mellitus to maternal and neonatal ill‐health in low‐ and middle‐income countries is not well documented.ObjectivesTo ascertain the incidence of adverse outcomes associated with gestational diabetes mellitus (GDM) in these countries.Search strategyElectronic databases were searched between 1990 and 2011.Selection criteriaObservational, experimental, and quasi‐experimental studies reporting adverse outcomes associated with GDM in mothers and their infants in low‐ and middle‐income countries were included.Data collection and analysisTitles and abstracts were screened, and full‐text articles were independently assessed by at least 2 reviewers. Characteristics of studies were tabulated and quality assessment performed. Median and interquartile range (IQR) were computed for each adverse outcome.Main results25 articles were included from an initial 1282 citations. High median incidences of cesarean (43.8%; IQR, 34.9%–65.9%), neonatal jaundice (17.1%; IQR, 8.5%–22.9%), and macrosomia (17.0%; IQR, 8.3%–32.5%) were reported in women with GDM.ConclusionsThe high incidence of some complications of GDM is a concern and may indicate poorer care for women with GDM in low‐resource settings. The wide IQRs found indicate uncertainty about the burden of GDM in these settings.
Attachment–aversion (AA) model of customer–brand relationships
Authors: Park C. Whan , Eisingerich Andreas B. , Park Jason Whan 
Published: January 2013

AbstractThe present paper proposes a customer–brand relationships model and empirically tests the following: (1) brand–self distance and brand prominence as representing customers' attachment–aversion relationships (AA Relationships) with a brand, (2) key distinguishing differences between the AA Relationships measure and other alternative relationship measures (i.e., brand attachment, emotional valence and brand attitude strength) based on a set of dependent variables, (3) three key determinants of the AA Relationships and the underlying process between the AA Relationships and behavioral intentions and actual brand behaviors, and (4) customer age as moderating the customer–brand relationships specified in the nomological model of the AA Relationships. The results offer strong support for the unique and important contribution of the AA Relationships model as representing consumers' relationship valence with a brand and its salience.
Long-term talus flatirons formation in the hyperarid northeastern Negev, Israel
Authors: Boroda Ronen , Matmon Ari , Amit Rivka , Haviv Itai , Porat Naomi ,   ASTERTeam, Rood Dylan , Eyal Yehuda , Enzel Yehuda 
Published: January 2013

AbstractColluvial sediments of talus relicts (“talus flatirons”) around mesas preserve a record that sheds light on slope-forming processes at temporal scales > 103yr. The sedimentology and soil stratigraphy of two groups of talus flatirons in the northeastern hyperarid Negev desert reveal four deposition events in the younger talus and at least two in the older one. Numerical modeling of high-resolution10Be depth profiles suggests that these taluses were deposited during the middle Pleistocene; the younger talus group first depositional event occurred at 551− 142+ 80ka and its abandonment occurred at 270− 38+ 17ka. The abandonment of the older talus group and stabilization of its surface occurred at 497− 114+ 176ka. These ages indicate that the development of the studied talus sequence is not specifically associated with Pleistocene glacial–interglacial cycles. The10Be modeled concentrations indicate significant differences in the average inheritance of talus flatirons of different groups. These differences can be attributed to variability in the transport distance and duration of gravel exposure during transport but could also reflect some temporal variability in cliff retreat. Our results also demonstrate that talus slopes in hyperarid areas, despite their steepness, can store sediment for long periods (~ 500 ka) and thus constitute a valuable archive.
Why nature really chose phosphate
Authors: Kamerlin Shina C. L. , Sharma Pankaz K. , Prasad Ram B. , Warshel Arieh 
Published: January 2013

AbstractPhosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and maintaining the integrity of the genetic material. On the surface, it would appear to be a simple nucleophile displacement reaction. However, this simplicity is deceptive, as, even in aqueous solution, the low-lying d-orbitals on the phosphorus atom allow for eight distinct mechanistic possibilities, before even introducing the complexities of the enzyme catalyzed reactions. To further complicate matters, while powerful, traditional experimental techniques such as the use of linear free-energy relationships (LFER) or measuring isotope effects cannot make unique distinctions between different potential mechanisms. A quarter of a century has passed since Westheimer wrote his seminal review, ‘Why Nature Chose Phosphate’ (Science 235 (1987), 1173), and a lot has changed in the field since then. The present review revisits this biologically crucial issue, exploring both relevant enzymatic systems as well as the corresponding chemistry in aqueous solution, and demonstrating that the only way key questions in this field are likely to be resolved is through careful theoretical studies (which of course should be able to reproduce all relevant experimental data). Finally, we demonstrate that the reason that naturereallychose phosphate is due to interplay between two counteracting effects: on the one hand, phosphates are negatively charged and the resulting charge-charge repulsion with the attacking nucleophile contributes to the very high barrier for hydrolysis, making phosphate esters among the most inert compounds known. However, biology is not only about reducing the barrier to unfavorable chemical reactions. That is, the same charge-charge repulsion that makes phosphate ester hydrolysis so unfavorable also makes it possible to regulate, by exploiting the electrostatics. This means that phosphate ester hydrolysis can not only be turned on, but also be turned off, by fine tuning the electrostatic environment and the present review demonstrates numerous examples where this is the case. Without this capacity for regulation, it would be impossible to have for instance a signaling or metabolic cascade, where the action of each participant is determined by the fine-tuned activity of the previous piece in the production line. This makes phosphate esters the ideal compounds to facilitate life as we know it.
Remaking the past: Tamil sacred landscape and temple renovations
Authors: Branfoot Crispin 
Published: January 2013

AbstractThis article explores the repeated renovation of south Indian temples over the past millennium and the conception of the Tamil temple-city. Though the requirement for renovation is unremarkable, some “renovations” have involved the wholesale replacement of the central shrine, in theory the most sacred part of the temple. Rather than explaining such radical rebuilding as a consequence of fourteenth-century iconoclasm, temple renovation is considered in this article as an ongoing process. Several periods of architectural reconstruction from the tenth to the early twentieth centuries demonstrate the evolving relationship between building, design and sacred geography over one millennium of Tamil temple history. The conclusion explores the widespread temple “renovations” by the devout Nakarattar (Nattukottai Chettiar) community in the early twentieth century, and the consequent dismay of colonial archaeologists at the perceived destruction of South India's monumental heritage, in order to reassess the lives and meanings of Tamil sacred sites.
XIX.—The Late-glacial History of the Highlands and Islands of Scotland
Authors: Charlesworth J. K. 
Published: January 2013

SynopsisFrom the abounding moraines, drainage features (fig. 21) and other marginal indications an attempt has been made to reconstruct the successive phases of the ice in its retreat into the corries of the Highlands and Islands (Pl. I). Two late-glacial stages are recognised. During the first, the Highland Glaciation, an ice-margin ran from the Orkney Islands across the mouth of the Moray Firth to the Buchan and out to sea north of Aberdeen. Twelve substages (A–L) of retreat, arbitrarily selected, have been traced through the country, except in the Moraineless West where they are unrepresented.At the maximum of the second stage, the Moraine Glaciation, the ice readvanced to the line stage M (beaded line in Pl. I). The retreat from this line, the inner boundary of the Moraineless West and of the 100-foot raised beach (Pl. I), is divided into nine substages (N–V), based upon a consideration of snowlines. Substage N corresponds to the 50-foot raised beach, substage P to an important readvance.The snowline throughout the late-glacial period ran in the west parallel with the meridians and rose eastwards. The disposition of the snowlines for stage M is given in fig. 22, p. 900.The distribution of the ice in the British Isles during the North British, Highland and Moraine Glaciations is represented in fig. 23, p. 923.
X. —The Structure, Bionomics, and Forest Importance of Myelophilus minor Hart
Authors: Ritchie Walter 
Published: January 2013

The two beetles Myelophilus minor Hart, and Myelophilus piniperda Linn, belong to the family Scolytidæ (the Ipidæ of Hagedorn), of the series Rhynchophora or snouted beetles.The genus Myelophilus Eichhoff has the following characters: (1) the biting edges of the maxillæ are beset with spines, (2) third basal tarsal joint broadened out, (3) head with rostrum visible, (4) funiculus of antenna six-jointed, (5) club of antennæ not quite round but somewhat pointed at the apex, (6) head and thorax with outstanding hairs, (7) front edge of thorax not depressed in the middle.
8.—A Stratigraphical Revision of the Old Red Sandstone of North-eastern Caithness
Authors: Donovan R. Nowell , Foster Richard J. , Westoll T. Stanley 
Published: January 2013

SynopsisThe stratigraphy of the Old Red Sandstone between Latheron and Brough in north-eastern Caithness has been revised. Stratigraphical subdivision in this area is primarily based on variations in lithology but is supported by the recognition of distinct faunal assemblages. The terms Wick Flagstone and Thurso Flagstone are discarded both as Group and Formation names and in their place type sequences different from those given by the Survey are proposed on the basis of the more continuous exposure seen between Ellens Goe and Latheron in eastern Caithness and in the Ham/Scarfskerry area of northern Caithness. The revision has been facilitated by an analysis of the structure of the area which suggests that a variablec. east-west compression has been the dominant controlling factor in the development of the structure of Caithness.As a result of the revision the position of the Achanarras Fish Bed is now clear. The Passage Beds Group is no longer considered a meaningful subdivision as it is partly overlain by and partly overlies this Fish Bed. The John o' Groats Sandstone Group is thought to probably overlie the Caithness Flagstones conformably.The following major stratigraphical subdivisions are recognised:D. John o' Groats Sandstone Group.C. Upper Caithness Flagstone Group(c) Mey Subgroup(b) Ham-Scarfskerry Subgroup(a) Latheron Subgroup.B. Lower Caithness Flagstone Group (position of Achanarras Fish Bed)(d) Robbery Head Subgroup(c) Lybster Subgroup(b) Hillhead Red Bed Subgroup(a) Clyth Subgroup.A. Sarclet Group.A typographical device is used for formal description of formations and groups whose boundaries are truncated by faults.
11.—Some Observations on the Fertile Parts of Zosterophyllum myretonianum Penhallow from the Lower Old Red Sandstone of Scotland
Authors: Edwards Dianne 
Published: January 2013

SynopsisNew collections of Zosterophyllum myretonianum Penhallow have been made at a number of localities in the Lower Old Red Sandstone of Scotland. For the first time, details of the fructification are recorded and incorporated into an emended diagnosis of the species. A comparison with the remaining species of Zosterophyllum indicates that sporangial and stalk characteristics are most important in delimiting Z. myretonianum. Tentative explanations for the wide variation in the overall morphology of the fructifications are put forward.
I.—The Glacial Geology of the Southern Uplands of Scotland, West of Annandale and Upper Clydesdale
Authors: Charlesworth J. Kaye 
Published: January 2013

The present paper embodies the results of an investigation into the glacial phenomena of the Southern Uplands of Scotland, west of Annandale and Upper Clydesdale.The literature dealing with the glaciation of this extensive region is very meagre. Apart from the Memoirs of the Geological Survey of Scotland, only a few and scattered papers and occasional references bear upon the subject. These will be noted in the course of the paper as occasion arises.
XX.—Geology of the Outer Hebrides. Part IV.—South Harris
Authors: Jehu T. J. , Craig R. M. 
Published: January 2013

Harris is supposed to derive its name from the Gaelic “na hardibh,” a designation signifying “the heights.” The term is appropriate in that the most mountainous parts of the Long Island lie within its boundaries.South Harris forms a natural geographical division for it is divided, from North Harris by a narrow neck of iand at Tarbert separating the eastern from the western seas. This isthmus is less than half a mile across. In addition to South Harris proper, this memoir deals also with the Isle of Scalpay and neighbouring islets off the north-east coast, the Isle of Taran-say on the north-west, and several islands off the south-west coast in the Sound of Harris, of which the principal ones are Ensay, Killegray, Groay, Lingay, and Gilsay.