bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selenolthiol and Dithiol C‐Terminal Tetrapeptide Motifs for One‐Step Purification and Labeling of Recombinant Proteins Produced in E. coli
Authors: Cheng Qing , Johansson Linda , Thorell Jan‐Olov , Fredriksson Anna , Samén Erik , Stone‐Elander Sharon , Arnér Elias S. J. 
Published: October 2006

AbstractWe have previously shown that a redox‐active selenocysteine‐containing tetrapeptide—Sel‐tag (Gly‐Cys‐Sec‐Gly)—can be used as a C‐terminal fusion motif for recombinant proteins produced in Escherichia coli. This Sel‐tag allows selenolate‐targeted one‐step purification, as well as fluorescent labeling or radiolabeling either with gamma emitters (75Se) or with positron‐emitting radionuclides (11C). Here we have analyzed four different redox‐active C‐terminal motifs, carrying either dithiol (Gly‐Cys‐Cys‐Gly or Ser‐Cys‐Cys‐Ser) or selenolthiol (Gly‐Cys‐Sec‐Gly or Ser‐Cys‐Sec‐Ser) motifs. Utilizing these different functional motifs with the same recombinant protein (Fel d 1), we were able to assess their relative reactivities and potential usefulness for biotechnological applications. We found that all four redox‐active tags could be utilized for efficient one‐step purification to provide pure protein from a crude bacterial lysate through reversible binding to phenylarsine oxide sepharose, with yields and purities comparable to those obtained for a His‐tagged protein purified by the more common approach with use of a Ni2+ column. For labeling with electrophilic fluorescent or radioactive compounds, however, the selenolthiol motifs were considerably more efficient than their dithiol counterparts. The results thus show that both the selenolthiol‐ and the dithiol‐containing tags can serve as efficient alternatives to His‐tags for protein purification, while the selenolthiol motifs offer additional and unique potential for Sec‐targeted labeling. It should therefore be possible to utilize these multifunctional tetrapeptide motifs to develop a wide range of novel biotechnological applications based on Sec targeting with electrophilic compounds.
Component‐based iterative methods for sparse linear systems
Authors: Jones J. , Sosonkina M. , Saad Y. 
Published: October 2006

AbstractIterative methods play an important role in solving large‐scale systems of linear equations that arise in real‐world applications. Due to numerous linear system properties that may affect the solution, it is rather difficult for a user to develop a good sparse linear system solver from scratch. Thus, various collections of solution methods are made available to the user. One such software package is SPARSKIT, which is well known in the scientific community. Written in FORTRAN77 and provided with a cumbersome interface, it is considered, however, a legacy code. Our objective is to enable its wider usage in modern applications and to facilitate further SPARSKIT enhancements. Applying a ‘peer‐component’ design, we have created a set of SPARSKIT components that: (a) incorporate both original and new iterative methods; (b) are readily extensible with more methods; (c) may be connected to applications in a component framework; and (d) provide access from a variety of programming languages. Tools available from the Common Component Architecture (CCA) Forum enabled our component design of SPARSKIT. Copyright © 2006 John Wiley & Sons, Ltd.
High‐speed network and Grid computing for high‐end computation: application in geodynamics ensemble simulations
Authors: Zhou S. , Kuang W. , Jiang W. , Gary P. , Palencia J. , Gardner G. 
Published: October 2006

AbstractHigh‐speed network and Grid computing have been actively investigated, and their capabilities are being demonstrated. However, their application to high‐end scientific computing and modeling is still to be explored. In this paper we discuss the related issues and present our prototype work on applying XCAT3 framework technology to geomagnetic data assimilation development with distributed computers, connected through an up to 10 Gigabit Ethernet network. Copyright © 2006 John Wiley & Sons, Ltd.
Component‐oriented application construction for a Web service‐based Grid
Authors: Schmidt Rainer , Benkner Siegfried , Brandic Ivona , Engelbrecht Gerhard 
Published: October 2006

AbstractWe present the architecture and prototype implementation of a component‐oriented programming environment for a Web service based computational Grid. As middleware, we utilize the Vienna Grid Environment (VGE), a framework that enables the provision of compute‐intensive parallel applications as configurable, QoS‐aware Grid services. Our component model follows the Common Component Architecture (CCA) and models application Web services as distributed components. We describe a component framework that integrates VGE services with a component model allowing to express and dynamically manage application and performance meta‐data as well as dependencies on the infrastructure or other components. Furthermore, we show how the client programming interface is used to compose Grid applications from abstract application components that are mapped against available Grid services by the component framework at runtime. Copyright © 2006 John Wiley & Sons, Ltd.
Design and implementation issues for distributed CCA framework interoperability
Authors: Govindaraju Madhusudhan , Lewis Michael J. , Chiu Kenneth 
Published: October 2006

AbstractComponent frameworks, including those that support the Common Component Architecture (CCA), represent a promising approach to addressing the challenge of building and deploying high‐performance scientific applications in Grid environments, one that is being realized, for example, in our LegionCCA and XCAT‐C++ frameworks. The next step beyond building independent individual frameworks is making them interoperate. Component‐based applications should be able to transparently span multiple disjoint component frameworks with low overhead as compared with the same applications running within a single framework. Interoperable frameworks enable applications to take advantage of more resources, and to better match constituent parts to the underlying resources that best support them. The CCA specification does not prescribe a wire format for inter‐component calls in distributed frameworks, thereby promoting considerable flexibility and customization for the framework developer. This approach thus requires an additional specific strategy outside of the CCA to support interoperability between distributed frameworks. Mandating one common wire format, however, risks choosing the wrong format. We discuss in detail five underlying component framework interoperability requirements, and three general approaches to addressing them. We then discuss how the approaches can be applied to meet the requirements, and address the advantages, issues, and implications of doing so. This effectively defines a design space for framework interoperability approaches. We then address the communication interoperability in detail via a single multi‐protocol communication library called Proteus, and discuss how we have incorporated it into two distinct distributed framework implementations of the CCA specification: LegionCCA and XCAT‐C++. Copyright © 2006 John Wiley & Sons, Ltd.
Cross‐organization interoperability experiments of weather and climate models with the Earth System Modeling Framework
Authors: Zhou Shujia , Balaji V. , Cruz Carlos , da Silva Arlindo , Hill Chris , Kluzek Erik , Smithline Shep , Trayanov Atanas , Yang Weiyu 
Published: October 2006

AbstractTypical weather and climate models need a software tool to couple sub‐scale model components. The high‐performance computing requirements and a variety of model interfaces make the development of such a coupling tool very challenging. In this paper, we describe the approach of the Earth System Modeling Framework, in particular its component and coupling mechanism, and present the results of three cross‐organization model interoperability experiments. Copyright © 2006 John Wiley & Sons, Ltd.
Synthesis, Characterization, and Crystal Structure of Two Manganese Metallacrowns: 30‐Metallacrown‐10 and 18‐Metallacrown‐6 with Ligands Derived from 3‐Hydroxy‐2‐naphthalenecarbohydrazide
Authors: Dou Jianmin , Liu Mingli , Li Dacheng , Wang Daqi 
Published: October 2006

AbstractTwo manganese metallacrowns [Mn10(pnhz)10(DMF)4(H2O)6]·10.5H2O·MeOH·DMF (1) and [Mn6(anhz)6(DMF)2(H2O)4]·6DMF (2), (H3pnhz = 3‐hydroxy‐N‐phenyl‐2‐naphthalenecarbohydrazide, H3anhz = N‐acyl‐3‐hydroxy‐2‐naphthalenecarbohydrazide) have been prepared by the reactions of two pentadentate ligands, H3anhz and H3pnhz, with the corresponding manganese(II) salt, respectively, and characterized by elemental analysis, IR spectra, and X‐ray single‐crystal diffraction analysis. Complex 1 has an [Mn–N–N]10 skeleton with two kinds of MnIII centers in an ···AABAB··· alignment, and the metallic centers exhibit a ···ΔΛΔΛ··· chiral configuration alignment. Adjacent molecules are linked by four intermolecular H bonds to form a 1D infinite chain structure. This is the first 1D supramolecular sample of a metallacrown formed by weak interactions. Complex 2 shows an [Mn–N–N]6 skeleton with two kinds of MnIII centers in a ···BAA··· alignment. The successive manganese centers possess a ···ΔΛΔΛ··· chiral configuration alignment. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Intramolecular Apical C–H···M Interactions in Square‐Planar Nickel(II) Complexes with Dianionic Tridentate Ligands and 2‐Phenylimidazole
Authors: Mukhopadhyay Abhik , Pal Samudranil 
Published: October 2006

AbstractTwo square‐planar ternary nickel(II) complexes [Ni(bhac)(phim)] (1) and [Ni(ahac)(phim)] (2) with O,N,O‐donor Schiff bases [acetylacetone benzoylhydrazone (H2bhac) and acetylacetone acetylhydrazone (H2ahac)] and sp2N‐donor 2‐phenylimidazole (phim) as the ancillary ligand have been synthesised and characterised by analytical, spectroscopic, magnetic and electrochemical methods. The solid‐state structures of both complexes have been determined by X‐ray crystallography. The asymmetric unit of1contains a single complex molecule while that of2contains four complex molecules with different conformations. The molecular structures of both complexes reveal that one of the twoorthoC–H groups of the pendant phenyl ring of the phim ligand is very close to the metal centre at the apical site indicating the presence of an intramolecular C–H···Ni interaction. In the structures of1and2, the shape of the C–H···Ni interaction is determined by the twisting of the phim ligand and the extent of orthogonality between the planes containing the chelate rings formed by the tridentate ligand and the imidazole ring. A survey of the reported X‐ray structures of similar d8metal ion complexes containing intramolecular C–H···M interactions has been performed for comparison with the structural features of1and2. The optimised molecular structures of1and2generated by calculations based on the density functional method are compared with the experimental structures. Calculations also reveal that the four molecules present in the asymmetric unit of2are very close in energy. Theoretical studies and the down‐field shift of the proton resonance on cooling in the NMR spectra suggest three‐centre four‐electron hydrogen‐bond character of the observed apical C–H···Ni interaction in1and2. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
A high‐order accurate method for two‐dimensional incompressible viscous flows
Authors: De Arnab Kumar , Eswaran Vinayak 
Published: October 2006

AbstractA high‐order accurate solution method for complex geometries is developed for two‐dimensional flows using the stream function–vorticity formulation. High‐order accurate spectrally optimized compact schemes along with appropriate boundary schemes are used for spatial discretization while a two‐level backward Euler implicit scheme is used for the time integration. The linear system of equations for stream function and vorticity are solved by an inner iteration while contravariant velocities constitute outer iterations. The effect of curvilinear grids on the solution accuracy is studied. The method is used to compute Cartesian and inclined driven cavity, flow in a triangular cavity and viscous flow in constricted channel. Benchmark‐like accuracy is obtained in all the problems with fewer grid points compared to reported studies. Copyright © 2006 John Wiley & Sons, Ltd.
A hybrid immersed‐boundary and multi‐block lattice Boltzmann method for simulating fluid and moving‐boundaries interactions
Authors: Sui Yi , Chew Yong‐Tian , Roy Partha , Low Hong‐Tong 
Published: October 2006

AbstractA numerical method is developed for modelling the interactions between incompressible viscous fluid and moving boundaries. The principle of this method is introducing the immersed‐boundary concept in the framework of the lattice Boltzmann method, and improving the accuracy and efficiency of the simulation by refining the mesh near moving boundaries. Besides elastic boundary with a constitutive law, the method can also efficiently simulate solid moving‐boundary interacting with fluid by employing the direct forcing technique. The method is validated by the simulations of flow past a circular cylinder, two cylinders moving with respect to each other and flow around a hovering wing. The versatility of the method is demonstrated by the numerical studies including elastic filament flapping in the wake of a cylinder and fish‐like bodies swimming in quiescent fluid. Copyright © 2006 John Wiley & Sons, Ltd.
Microrough titanium surface affects biologic response in MG63 osteoblast‐like cells
Authors: Kim Myung‐Joo , Kim Chang‐Whe , Lim Young‐Jun , Heo Seong‐Joo 
Published: October 2006

AbstractThe purpose of this study was to define the surface properties of prepared titanium (Ti) disks, which served as a model system, and to contrast the biologic response of MG63 cells exposed to Ti disks with different levels of surface roughness. The surface properties interact with each other, resulting in a change of other surface qualities in addition to roughness due to the surface roughening procedure. The machined Ti disks were roughened by sandblasting and electric glow discharging. The surface properties of the Ti specimens were inspected through a comprehensive surface analysis. MG63 cell behaviors were compared along with cell number, alkaline phosphatase (ALP) activity, Runx2 gene expression, and type I collagen production. Statistics were evaluated, using analysis of variance (ANOVA). The sandblasted Ti disks demonstrated well‐controlled surface roughness features and meaningful average roughness ranges, including the surface roughness of the “modern” microrough implant, used clinically. With increasing Ti surface roughness, the cell number decreased, while the ALP activity, type I collagen production, and Runx2 gene expression increased significantly. The rougher the Ti surface was, the sooner the Runx2 gene was expressed. Based on these results, we suggest that the microrough Ti surfaces of the 1–3 μm range may contribute effectively to osteogenic differentiation and proliferation in MG63 cells. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res, 2006
Effect of oxygen inhibition on composite repair strength over time
Authors: Dall'Oca Susanna , Papacchini Federica , Goracci Cecilia , Cury Álvaro H. , Suh Byoung I. , Tay Franklin R. , Polimeni Antonella , Ferrari Marco 
Published: October 2006

AbstractThe study was aimed at examining whether an oxygen inhibition layer is required for bonding a repairing to a pre‐existing composite, and to determine the time required for free radicals within a composite substrate to decay to the extent that the composite repair strength drops significantly. Ten slabs of Gradia Direct Anterior (GC Corp.) were divided into (1) control group: an interfacial oxygen inhibition layer was created by applying and light‐curing two layers of bonding resin (D/E Resin, Bisco) to the slabs surface in atmospheric air; (2) experimental group: the absence of an interfacial oxygen inhibition layer was obtained by light‐curing the second bonding resin layer in a nitrogen atmosphere. After 1 and 2 h, 1, 14, and 30 days of air storage, a composite repair was layered over the bonding resin. Microtensile bond strengths were measured and statistically analyzed. The curing atmosphere was not a significant factor for bond strength (p = 0.82), and time and curing atmosphere‐time interaction were significant (p < 0.001). The 30 day‐strengths were the lowest (p < 0.05). An oxygen‐inhibited layer is not initially required for bonding to resin composite, and it takes more than 14 days before the bond strength between a pre‐existing and a fresh composite drops. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2006
CO2 laser‐induced zonation in dental enamel: A Raman and IR microspectroscopic study
Authors: Klocke Arndt , Mihailova Boriana , Zhang Shengqiang , Gasharova Biliana , Stosch Rainer , Güttler Bernd , Kahl‐Nieke Bärbel , Henriot Peter , Ritschel Bodo , Bismayer Ulrich 
Published: October 2006

AbstractThe gradient of structural alteration and molecular exchange across CO2 laser‐irradiated areas in dental enamel was analyzed by Raman and attenuated total reflectance infrared microspectroscopy. The type and the degree of structural changes in morphologically distinguishable zones within the laser spot vary depending on the laser‐irradiation parameters—power (1 and 3 W), treatment time (5 and 10 s), and operational mode (super pulse and continuous wave). Using higher power, irrespective of the operation mode, the enamel tissue ablates and a crater is formed. The prevalent phase at the bottom of the crater is dehydrated O‐bearing apatite, that is, the fundamental framework topology is preserved. Additional nonapatite calcium phosphate phases are located mainly at the slope of the laser crater. No structural transformation of mineral component was detected aside the crater rim, only a CO3–CO2 exchange, which decays with the radial distance. A lower‐power laser irradiation slightly roughens the enamel surface and the structural modification of enamel apatite is considerably weaker for continuous wave than for super pulse mode. Prolonged low‐power laser treatment results in recrystallization, and thus structural recovering of apatite might be of clinical relevance for enamel surface treatments. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2006
Environmental degradation of glass‐ionomer cements: A depth‐sensing microindentation study
Authors: Wang X. Y. , Yap Adrian U. J. , Ngo H. C. , Chung S. M. 
Published: October 2006

AbstractThis study investigated the effects of various environmental conditions on the hardness and elastic modulus of restorative glass‐ionomer cements (GICs). Two resin‐modified GICs (RMGICs) (Fuji II LC [FL]; Photac‐Fil Quick [PQ]) and three highly viscous GICs (HVGICs) (Fuji IX Fast [FN]; KetacMolar [KM]; KetacMolar Quick [KQ]) were evaluated in this study. Specimens were fabricated according to the manufacturers' instructions and stored under a variety of conditions (n = 7): 100% humidity, distilled water, pH 5 demineralization solution, and pH 7 remineralization solution. The hardness and elastic modulus were measured using a depth‐sensing microindentation test after 4 weeks. The results were analyzed using the independent samples T‐test and ANOVA/Scheffe's post hoc test (p < 0.05). HVGICs showed significantly higher hardness and elastic modulus than RMGICs under all storage conditions. Storage in distilled water significantly increased the hardness and elastic modulus of FN, but decreased that of PQ. All HVGICs and RMGICs stored in remineralization solution had hardness values and elastic moduli comparable to those stored in water. Compared to remineralization solution, demineralization solution had no significant effects on the modified GICs with the exception of KQ. The results suggest that the mechanical properties of glass‐ionomer restoratives are material‐type and storage condition dependent. Therefore, the clinical selection of a glass‐ionomer material should be based on the oral environment to which it will be subjected. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2006
Computer assisted Koeppen climate classification: a case study for Brazil
Authors: Sparovek Gerd , De Jong Van Lier Quirijn , Dourado Neto Durval 
Published: October 2006

AbstractKoeppen's climate classification, developed one century ago, is still used as a reference for large‐scale climate mapping and useful for climatologic research (climate shift, climate model testing, and ecological research). This paper describes a software that was developed to allow non‐assisted Koeppen climate classification based on a simple database (monthly mean temperatures and rainfall) as input. The software follows, as strictly as possible, the original concepts suggested by Koeppen, but does not include climates that cannot be defined by simple input parameters. Combined with GIS tools, the software was used to produce the first comprehensive climate map of Brazil using a large database. The map showed 21 Climate Equations in three climate zones (A = tropical moist; B = dry; C = moist with mild winter). This map was compared with an existing climate map of Brazil (FAO/SDRN). The two maps showed good agreement only in the less detailed information (climate zone and type). The complete Climate Equations were not comparable in relation to spatial distribution and class coincidence. Improvements were made for Koeppen's climate classification, avoiding computational or database errors, and it increased the details for climate classification of Brazil. Copyright © 2006 Royal Meteorological Society
Trends in snow ablation over North America
Authors: Dyer Jamie L. , Mote Thomas L. 
Published: October 2006

AbstractA substantial decrease in snow cover extent (SCE) and snow depth over North America has been observed over the 1960–2000 period. One explanation for the changes in North American snow cover is a change in the frequency and/or intensity of snow ablation. This study uses a gridded dataset of United States and Canadian surface observations from 1960 to 2000 to examine patterns of snow ablation over North America. An ablation event is defined as an interdiurnal snow depth change exceeding a critical value. Results show a significant positive trend in the frequency of ablation events during March (p < 0.05) and a significant negative trend in May (p < 0.05), indicating an earlier onset of ablation. This pattern is consistent for ablation of varying intensity. Surface energy budget components and air mass frequencies are examined in relation to the observed trends in snow ablation. Changes in March ablation frequency were shown to be dominated by increases in the sensible heat flux. A higher frequency of dry moderate instead of moist polar air masses during high ablation years may explain the increase in sensible heat flux and ablation over the study period. Copyright © 2006 Royal Meteorological Society