bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate solution of multi‐region continuum biomolecule electrostatic problems using the linearized Poisson–Boltzmann equation with curved boundary elements
Authors: Altman Michael D. , Bardhan Jaydeep P. , White Jacob K. , Tidor Bruce 
Published: June 2008

AbstractWe present a boundary‐element method (BEM) implementation for accurately solving problems in biomolecular electrostatics using the linearized Poisson–Boltzmann equation. Motivating this implementation is the desire to create a solver capable of precisely describing the geometries and topologies prevalent in continuum models of biological molecules. This implementation is enabled by the synthesis of four technologies developed or implemented specifically for this work. First, molecular and accessible surfaces used to describe dielectric and ion‐exclusion boundaries were discretized with curved boundary elements that faithfully reproduce molecular geometries. Second, we avoided explicitly forming the dense BEM matrices and instead solved the linear systems with a preconditioned iterative method (GMRES), using a matrix compression algorithm (FFTSVD) to accelerate matrix–vector multiplication. Third, robust numerical integration methods were employed to accurately evaluate singular and near‐singular integrals over the curved boundary elements. Fourth, we present a general boundary‐integral approach capable of modeling an arbitrary number of embedded homogeneous dielectric regions with differing dielectric constants, possible salt treatment, and point charges. A comparison of the presented BEM implementation and standard finite‐difference techniques demonstrates that for certain classes of electrostatic calculations, such as determining absolute electrostatic solvation and rigid‐binding free energies, the improved convergence properties of the BEM approach can have a significant impact on computed energetics. We also demonstrate that the improved accuracy offered by the curved‐element BEM is important when more sophisticated techniques, such as nonrigid‐binding models, are used to compute the relative electrostatic effects of molecular modifications. In addition, we show that electrostatic calculations requiring multiple solves using the same molecular geometry, such as charge optimization or component analysis, can be computed to high accuracy using the presented BEM approach, in compute times comparable to traditional finite‐difference methods. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Nature of Stoner condition for metallic ferromagnetism
Authors: Seo Dong‐Kyun , Kim Sang‐Hwan 
Published: June 2008

AbstractFor proper applications of the Stoner condition, we describe the assumptions in its underlying theory and their implications that need to be considered in practice. The nature of Stoner exchange parameters is examined based on spin‐polarization perturbational orbital theory and a connection has been made in understanding the parameters with both local spin density and Hartree‐Fock approximations via a self‐interaction‐corrected local spin density (SIC‐LSD) exchange‐correlation functional. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Development of an in vitro cell culture assay system for measuring the activation of a neighbouring gene by the retroviral vector
Authors: Hong Youngtae , Yu Seung Shin , Yoon Nam‐Kyung , Kang Sung June , Lee Jun‐Tae , Kim Sujeong , Kim Jong‐Mook , Lee Karim , Jang Ji‐Won , Kim Sunyoung 
Published: June 2008

AbstractBackgroundThe use of retroviral vectors has shown an actual clinical benefit in a few inherited diseases. However, the occurrence of cases of leukemia after the X‐SCID gene therapy trial raised concerns about the safety of insertional mutagenesis inherent to the biology of the retrovirus. Although the retrovirus has long been known to integrate into the host chromosome, and thus have the potential to activate the nearby gene, there has been no convenient method of studying or assaying such a cis‐activation phenomenon.MethodsIn the present study, we report an in vitro assay system in which the effect of retroviral integration on the expression of the neighbouring gene can be studied. In this system, a retroviral vector and the neighbouring reporter gene were constructed in a single plasmid as if it had integrated into the chromosome.ResultsUsing this assay, we found that the full‐length long terminal repeat (LTR) could indeed activate the neighbouring gene expression from a distance and the magnitude of its activation was highly increased when this LTR was placed in the vicinity of the transcription start site of the gene, whereas the truncated LTR exerted little influence.ConclusionsThis assay system might provide a useful tool for selecting the appropriate vector structure, as well as for studying the molecular mechanism underlying the cis‐activation by the viral LTR. Copyright © 2008 John Wiley & Sons, Ltd.
Triple Dumbbell Polymer Nanolayer Frequency Response
Authors: Grisafi Steven 
Published: June 2008

AbstractA triple dumbbell sandwich model is developed to predict the frequency response of an interface created within nanolayer polymer films. One dumbbell different from two others is layered between the other two. The interactions among the macromolecules are modeled using Hooke's law for the intramolecular, intermolecular, and an applied external force. The external force is meant to describe incident electromagnetic radiation. The transient response of the system in the frequency domain is presented along with the steady‐state response. The frequency response for the central dumbbell differs from its two partners suggesting that birefringence of incident radiation is possible. The phase angle of the oscillations for the two different polymer species shows that the frequency of incident light would be shifted differently by the two when it traverses the polymer film.magnified image
Model reduction of interconnected linear systems
Authors: Sandberg H. , Murray R. M. 
Published: June 2008

AbstractThe problem of model reduction of linear systems with certain interconnection structure is considered in this paper. To preserve the interconnection structure between subsystems in the reduction, special care needs to be taken. This problem is important and timely because of the recent focus on complex networked systems in control engineering. Two different model reduction methods are introduced and compared in this paper. Both methods are extensions to the well‐known balanced truncation method. Compared with earlier work in the area these methods use a more general linear fractional transformation framework, and utilize linear matrix inequalities. Furthermore, new approximation error bounds that reduce to classical bounds in special cases are derived. The so‐called structured Hankel singular values are used in the methods, and indicate how important states in the subsystems are with respect to a chosen input–output map for the entire interconnected system. It is shown how these structured Hankel singular values can be used to select an approximation order. Finally, the two methods are applied to a model of a mechanical device. Copyright © 2008 John Wiley & Sons, Ltd.
A novel sodium carboxymethylcellulose/poly(N‐isopropylacrylamide)/Clay semi‐IPN nanocomposite hydrogel with improved response rate and mechanical properties
Authors: Ma Jinghong , Zhang Li , Fan Bing , Xu Yajing , Liang Borun 
Published: June 2008

AbstractA novel semi‐IPN nanocomposite hydrogel (CMC/PNIPA/Clay hydrogel) based on linear sodium carboxymethylcellulose (CMC) and poly(N‐isopropylacrylamide) (PNIPA) crosslinked by inorganic clay was prepared. The structure and morphology of these hydrogels were investigated and their swelling and deswelling kinetics were studied in detail. TEM images showed that the clay was substantially exfoliated to form nano‐dimension platelets dispersed homogeneously in the hydrogels and acted as a multifunctional crosslinker. The CMC/PNIPA/Clay hydrogels swell faster than the corresponding PNIPA/Clay hydrogels at pH 7.4, whereas they swell slower than the PNIPA/Clay hydrogels at pH 1.2. The CMC/PNIPA/Clay nanocomposite hydrogels showed much higher deswelling rates, which was ascribed to more passway formed in these hydrogels for water to diffuse in and out. The deswelling process of the hydrogels could be approximately described by the first‐order kinetic equation and the deswelling rate decreased with increasing clay content. The mechanical properties of the CMC/PNIPA/Clay nanocomposite hydrogels were analyzed based on the theory of rubber elasticity. It was found that with increasing clay content, the effective crosslink chain density, ve, increased whereas the molecular weight of the chains between crosslinks Mc decreased. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1546–1555, 2008
The crystal structure of the protein YhaK from Escherichia coli reveals a new subclass of redox sensitive enterobacterial bicupins
Authors: Gurmu Daniel , Lu Jun , Johnson Kenneth A. , Nordlund Pär , Holmgren Arne , Erlandsen Heidi 
Published: June 2008

AbstractYhaK is a protein of unknown function found in low abundance in the cytosol of Escherichia coli. DNA array studies have revealed that YhaK is strongly up‐regulated by nitroso‐glutathione (GSNO) and also displays a 12‐fold increase in expression during biofilm growth of E. coli 83972 and VR50 in human urine. We have determined the YhaK crystal structure and demonstrated that in vitro YhaK is a good marker for monitoring oxidative stresses in E. coli. The YhaK protein structure shows a bicupin fold where the two cupin domains are crosslinked with one intramolecular disulfide bond (Cys10 to Cys204). We found that the third cysteine in YhaK, Cys122, is oxidized to a sulfenic acid. Two chloride ions are found in the structure, one close to the reactive Cys122, and the other on a hydrophobic surface close to a symmetry‐related molecule. There are major structural differences at the N‐terminus of YhaK compared with similar structures that also display the bicupin fold (YhhW and hPirin). YhaK showed no quercetinase and peroxidase activity. However, reduced YhaK was very sensitive to reactive oxygen species (ROS). The complete, functional E. coli glutaredoxin or thioredoxin systems protected YhaK from oxidation. E. coli thioredoxin reductase and NADPH produced ROS and caused oxidation and oligomerization of reduced YhaK. Taken together, we propose that YhaK is the first of a new sub‐class of bicupins that lack the canonical cupin metal‐binding residues of pirins and may be involved in chloride binding and/or sensing of oxidative stress in enterobacteria. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Multicolour photochromic behaviour of silver nanoparticles in titanium dioxide matrix
Authors: Preclíková J. , Trojánek F. , Němec P. , Malý P. 
Published: June 2008

AbstractWe implemented photocatalytic technique of preparation of composite material consisting of silver nanoparticles embedded in nanoporous titanium dioxide matrix which has an unique property of multicolour photochromic behaviour. We report on the effect of preparation parameters on optical and photochromic properties of the material. In particular we investigate the role of the concentration of TiO2 nanoparticles in the ethanol solution used to produce the films for Ag deposition. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Studies of molecular docking between fibroblast growth factor and heparin using generalized simulated annealing
Authors: da Rocha Pita Samuel Silva , Fernandes Tácio Vinício Amorim , Caffarena Ernesto Raul , Pascutti Pedro Geraldo 
Published: June 2008

AbstractSince the middle 70s, the main molecular docking problem consists in limitations to treat adequately the degrees of freedom of protein (or a receptor) due to the energy landscape roughness and the high computational cost. Until recently, only few algorithms considering flexible simultaneously both ligand and receptor at low computational cost were developed. As a recent proposed Statistical Mechanics, generalized simulated annealing (GSA) has been employed at diverse works concerning global optimization problems. In this work, we used this method exploring the molecular docking problem taking into account the FGF‐2 and heparin complex. Since the requirements of an efficient docking algorithm are accuracy and velocity, we tested the influence of GSA parameters qA (new configuration acceptance index), qV (energy surface visiting index), and qT (temperature decreasing control) on the performance of GSADOCK program. Our simulations showed that as temperature parameter qT increases, qA parameter follows this behavior in the interval ranging from 1.1 to 2.3. We found that the GSA parameters have the best performance for the qA values ranging from 1.1 to 1.3, qV values from 1.3 to 1.5, and qT values from 1.1 to 1.7. Most of good qV values were equal or next the good qT values. Finally, the implemented algorithm is trustworthy and can be employed as a tool of molecular modeling methods. The final version of the program will be free of charge and will be accessible at our home‐page or could be requested to the authors for e‐mail. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Intra‐operative image update: first experiences with new software in computer‐assisted sinus surgery
Authors: Wurm Jochen , Bohr Christopher , Iro Heinrich , Bumm Klaus 
Published: June 2008

AbstractBackgroundSo far, conventional navigation systems do not provide the opportunity for any modification of acquired image datasets. In particular, the surgical progress in the operating field cannot be visualized unless new imaging scans are performed.MethodsIn a feasibility study, new software creating intra‐operative image updates by virtual means was tested in conjunction with conventional navigation. With this new software, surgically removed tissue volumes can be traced and viewed directly within the diagnostic image data.Results and ConclusionsThe new software represents an interesting and helpful amendment to conventional computer‐assisted surgery in selected cases. During surgical procedures around bony structures, the surgeon gets an accurate virtual image update of the surgical progress in the operating field and the amount of tissue removed. However, in cases where mobile structures are present or soft tissue shifts are expected, this feature seems to be suitable only to a limited extent. Copyright © 2008 John Wiley & Sons, Ltd.
Threshold to N-methyl-D-aspartate-induced seizures in mice undergoing chronic nutritional magnesium deprivation is lowered in a way partly responsive to acute magnesium and antioxidant administrations
Authors: Maurois Pierre , Pages Nicole , Bac Pierre , German-Fattal Michèle , Agnani Geneviève , Delplanque Bernadette , Durlach Jean , Poupaert Jacques , Vamecq Joseph 
Published: June 2008

Magnesium deficiency may be induced by a diet impoverished in magnesium. This nutritional deficit promotes chronic inflammatory and oxidative stresses, hyperexcitability and, in mice, susceptibility to audiogenic seizures. Potentiation by low-magnesium concentrations of the opening of N-methyl-d-aspartate (NMDA) receptor/calcium channel in in vitro and ex vivo studies, and responsiveness to magnesium of in vivo brain injury states are now well established. By contrast, little or no specific attention has been, however, paid to the in vivo NMDA receptor function/excitability in magnesium deficiency. The present work reports for the first time that, in mice undergoing chronic nutritional deprivation in magnesium (35 v. 930 parts per million for 27 d in OF1 mice), NMDA-induced seizure threshold is significantly decreased (38 % of normal values). The attenuation in the drop of NMDA seizure threshold (percentage of reversal) was 58 and 20 % upon acute intraperitoneal administrations of magnesium chloride hexahydrate (28 mg magnesium/kg) and the antioxidant ebselen (20 mg/kg), respectively. In nutritionally magnesium-deprived animals, audiogenic seizures are completely prevented by these compound doses. Taken as a whole, our data emphasise that chronic magnesium deprivation in mice is a nutritional in vivo model for a lowered NMDA receptor activation threshold. This nutritional model responds remarkably to acute magnesium supply and moderately to acute antioxidant administration.
Variability and genetic basis for migratory behaviour in a spring population of the aphid,Aphis gossypiiGlover in the Yangtze River Valley of China
Authors: Liu X.D. , Zhai B.P. , Zhang X.X. , Gu H.N. 
Published: June 2008

AbstractThe population dynamics, development of gonads, takeoff and flight behaviour ofAphis gossypiiGlover were investigated in order to test whether there was variation of migratory ability in the spring population. Field surveys showed that not all the aphids overwintering on hibiscus migrated to the secondary host plants, and the host-alternating and host-specific life-cycle forms coexisted in Nanjing, China. Substantial variation in flight capacity of winged individuals, development of gonads and takeoff behaviour were found within the spring population. The frequency distribution of flight duration and the number of ovarioles per individual alatae exhibited two peaks, representing the migratory and sedentary genotypes, respectively. Significant response to directional selection on takeoff behaviour demonstrated the additive genetic component of this variation. Selection for ‘takeoff’ individuals caused a significant increase in takeoff angle from 39.8° in the first selection to 68.7° in the fifth; and, hence, screened out the migratory genotype (M), while selection for the sedentary individuals increased the rate of non-takeoffs significantly, and screened out the sedentary genotype (S). The reciprocal cross, M♀×S♂, produced hybrid offspring performing significantly steeper takeoff angles compared with those from the cross S♀×M♂, suggesting the presence of a maternal effect. On the other hand, takeoff rate was ranked as M♀×S♂=S♀×M♂>M>S, involving no sex-linkage and maternal effect. The coexistence of host-alternating and host-specific life-cycle forms ofA. gossypiion the primary host has, as deduced from the present studies, a genetic basis.
Just for the hell of it: A comparison of two taboo-term constructions
Authors: HOEKSEMA JACK , JO NAPOLI DONNA 
Published: June 2008

The two English constructions exemplified inLet's get the hell out of here(type G) andThey beat the hell out of him(type B) differ both syntactically and semantically, but in both the taboo expression has the force of an intensifier. History (through a corpus investigation) reveals that the B-construction started as a literal exorcism (beat the devil out of someone), wherethe hellsubstituted forthe devil, and semantic bleaching ultimately made the literal sense give way to simple emphasis, with any taboo term jumping in. The G-construction may have developed simultaneously, always as an intensifier – or, perhaps, later, on analogy with B. Our analysis suggests that the use of taboo terms as intensifiers spread fromwh-constructions to these constructions and, finally, to degree intensifier constructions. These two uses of taboo terms as intensifiers are best characterized in terms of constructions and thus offer evidence against theories lacking any notion of constructions as basic building blocks. Further, they give us information about language change: a pragmatically unified but semantically disparate class of expressions (namely, taboo terms) can extend its distribution in parallel.Private Carr: God fuck old Bennett.He's a whitearsed bugger. I don't give a shit for him.(James Joyce,Ulysses)
Ambient fauna impairs parasite transmission in a marine parasite-host system
Authors: THIELTGES D. W. , BORDALO M. D. , CABALLERO HERNÁNDEZ A. , PRINZ K. , JENSEN K. T. 
Published: June 2008

SUMMARYTo understand possible factors controlling transmission of trematode larvae between first and second intermediate hosts we examined the impact of ambient fauna on parasite transmission in a marine intertidal parasite-host association. Cockle hosts (Cerastoderma edule) kept together with selected co-occurring macrozoobenthic species in mesocosms acquired a lower parasite load compared to cockles kept alone, when targeted by cercariae of the trematodeHimasthla elongata. The reduction of parasite load in the cockles differed between the 7 macrozoobenthic species tested and was between 35 and 91%. Three different types of reduction could be distinguished: (1) predators (Carcinus maenas, Crangon crangon) actively preying upon cercariae, (2) non-host filter feeders (Crepidula fornicata,Mya arenaria, Crassostrea gigas) filtering cercariae but not becoming infected and (3) alternative hosts (Mytilus edulis, Macoma balthica) becoming infected by the cercariae and thus distracting cercariae from the target hosts. In addition, interference competition may occur in the form of disturbance of cockles by ambient organisms resulting in lower filtration rates and subsequently lower parasite loads. Our results suggest that the species composition and relative abundance of the ambient fauna of parasite-host systems play an important role in controlling trematode transmission rates in benthic marine systems.
The Barthian heritage of Hans W. Frei
Authors: Knight John Allan 
Published: June 2008

AbstractHans Frei and the ‘Yale School’ of narrative theology are often understood to be Barthian in orientation, but only rarely have the origins and contours of Frei's engagement with Barth been treated in the secondary literature. Frei's dissertation itself remains unpublished, with the exception of an oddly edited abridgement that appeared ten years after Frei's untimely death. This lacuna is unfortunate, because Frei's dissertation on Barth, and especially his treatment of Barth's method, are of signal importance in that they set the agenda and orientation for much, if not all, of Frei's later work. Consequently, in this article I analyse Frei's dissertation on Barth, focusing primarily on his treatment of Barth's protest against ‘relationalism’. On Frei's reading, three moves constitute Barth's break with relationalism: the primacy of ontology over epistemology, the subordination of method to positive affirmations about God, and the conformance of interpretative method both to Barth's methodological commitments and to his affirmations about God. In his dissertation, Frei argues that Barth believed that, without these moves, theology would be vulnerable to Feuerbach's critique. Frei's construal of Barth's break with relationalism sets the agenda for Frei's own later work, in which he appropriates these Barthian moves by insisting on the primacy of biblical narratives in theological method. Similar to Barth, Frei takes twentieth-century hermeneutic theology to be vulnerable to deconstructionist critique. His insistence on the primacy of a literal reading of the biblical narratives is his attempt to rectify this vulnerability.