bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of gender differences in rat lens proteins using 2‐D‐DIGE
Authors: Guest Paul C. , Skynner Heather A. , Salim Kamran , Tattersall F. David , Knowles Michael R. , Atack John R. 
Published: December 2005

AbstractThe glass‐like transparency of the human eye lens is achieved by the tight packing of abundant crystallin proteins. However, the precise role of the accessory non‐crystallin proteins is not well understood. We have carried out 2‐DE mapping of these proteins in rat lens. This showed the presence of the high molecular weight filamentous structural proteins spectrin, filensin, tubulin, vimentin, actin and phakinin as well as several forms of potential crystallin oligomers comprised of αA, βB1, βA1 and βA4 chains. Other proteins that were present include, heat shock protein 71, WD repeat protein 1, and several enzymes including α‐enolase, pyruvate kinase, transketolase and aldose reductase. 2‐D‐DIGE analysis revealed several expression differences between the lens proteomes of male and female rats. Female rat lenses contained lower levels of aldose reductase, increased proteolyic fragments of the structural proteins filensin, vimentin and phakinin and higher levels of potential αA, βB1 and βA1 crystallin oligomers. Taken together these findings suggest that there are potential differences in oxidative stress regulation between male and female rat lenses, which may have implications on susceptibility to cataract formation. Future studies aimed at elucidating pre‐cataractic changes in the non‐crystallin proteins described here may facilitate identification of novel markers involved in cataractogenesis.
Phosphopeptide detection using automated online IMAC‐capillary LC‐ESI‐MS/MS
Authors: Wang Jinglan , Zhang Yangjun , Jiang Hong , Cai Yun , Qian Xiaohong 
Published: December 2005

AbstractIMAC has become a commonly used technique in phosphoprotein analysis because of its affinity for phosphopeptides. However, the commonly used strategy combining offline IMAC enrichment with desalting procedures prior to MS/MS makes this method laborious. Here we report the development of a robust and automatic IMAC‐capillary RP HPLC‐ESI MS/MS technology platform, by which all procedures needed in phosphopeptide analysis including IMAC enrichment, RP HPLC separation and nanospray MS/MS can be done automatically controlled by the MassLynx program. The platform was optimized by analyzing standard phosphopeptide, and was then applied to the identification of phosphorylation sites of recombinant human telomeric repeat binding factor 1 treated with kinase in vitro, and two phosphorylation sites are defined.
Proteomics‐based generation and characterization of monoclonal antibodies against human liver mitochondrial proteins
Authors: Gao Jianen , Gao Yuan , Ju Yanfang , Yang Jinju , Wu Qiong , Zhang Jinchao , Du Xuemei , Wang Zhaoqing , Song Yingbo , Li Hui , Luo Xiaotong , Ren Feiyao , Li Jian , Chen Yong , Wang Lihong , Xu Han , Liu Xiaolan , Wang Jinlan , Zhang Yangjun , Cai Yun , Cui Yufang , Qian Xiaohong , He Fuchu , Li Ming , Sun Qi‐Hong 
Published: December 2005

AbstractMonoclonal antibodies (mAbs) have the potential to be a very powerful tool in proteomics research to determine protein expression, quantification, localization and modification, as well as protein‐protein interactions, especially when combined with microarray technology. Thus, a large amount of well‐characterized and highly qualified antibodies are needed in proteomics. Purified antigen, which is not always available, has proven to be one of the rate‐limiting steps in mAb large‐scale generation. Here we describe our strategies to establish a murine hybridoma cell bank for human liver mitochondria using unknown native proteins as the immunogens. The antibody‐recognized mitochondrial proteins were identified by MS following immunoprecipitation (IP), and by screening of human liver cDNA expression library. We found that the established antibodies reacted specifically with a number of important enzymes in mitochondria. The subcellular localization of these antigens in mitochondria was further confirmed by immunohistocytochemistry. A panel of antibodies was also tested for their ability to capture and deplete the targeting proteins and complexes from the total mitochondrial proteins. We believe these well‐characterized antibodies would be useful in various applications for Human Liver Proteome Project (HLPP) when the scale of this hybridoma cell bank is enlarged significantly in the near future.
Type II photoreaction of benzoyl‐ and (benzoylmethyl)cyclohexanones: cyclohexanone ring inversion and other factors determining their photoreactivities
Authors: Hasegawa Tadashi , Yang Yiming , Kikuchi Shuichi , Nakamura Takayuki , Maeda Yutaka 
Published: December 2005

AbstractX‐ray crystallographic structure analysis showed that a molecule of 2‐benzoylcyclohexanone (2), which undergoes an efficient Type II reaction in solution but not in the crystalline state, is in a keto and chair form with an equatorial benzoyl group. Irradiation of 3‐benzoylcyclohexanone (3) gives 7‐phenylhepten‐4,7‐dione (4, 61%) and a mixture of cyclization products 5 (25%). High photoreactivity of 2 and 3 is caused by the efficient cyclohexanone ring inversion. Upon irradiation, 2‐(benzoylmethyl)cyclohexanone (6) gives acetophenone (7), 2‐cyclohexenone (8) and the cyclobutanol 9 in 59, 59 and 35% yield, respectively, and 1‐phenyl‐3‐propylpentan‐1,4‐dione (10) gives 7 and the cyclobutanol 11 in 73 and 4% yield, respectively. The quantum yields for the disappearance of 6 and 10 are 0.68 and 0.67, respectively. Irradiation of 2‐(benzoylmethyl)‐2‐ethoxycarbonylcyclohexanone (12) gives 7 and the cyclobutanol 13 in 46 and 51% yield, respectively. The quantum yield for the disappearance of 12 is 1.00, so that reverse hydrogen transfer is suppressed by intramolecular hydrogen bonding in the 1,4‐biradical intermediate. When 6 is irradiated on a dry silica gel surface, the Type II reaction occurs to give 7, 8 and 9 in 38, 38 and 43% yield, respectively. The cyclization in the photoreaction of (benzoylmethyl)cyclohexane also increases from 68% in benzene to 81% on a dry silica gel surface. Restriction of conformational change in the 1,4‐biradical is an important factor for the cyclization. Copyright © 2005 John Wiley & Sons, Ltd.
Mutations in α‐helical solvent‐exposed sites of eglin c have long‐range effects: Evidence from molecular dynamics simulations
Authors: Fetrow Jacquelyn S. , Knutson Stacy T. , Edgell Marshall Hall 
Published: December 2005

AbstractEglin c is a small protease inhibitor whose structural and thermodynamic properties have been well studied. Previous thermodynamic measurements on mutants at solvent‐accessible positions in the protein's helix have shown the unexpected result that the data could be best fit by the inclusion of residue‐ and position‐specific parameters to the model. To explore the origins of this surprising result, long molecular dynamics simulations in explicit solvent have been performed. These simulations indicate specific long‐range interactions between the solvent‐exposed residues in the eglin c α‐helix and binding loop, an unexpected observation for such a small protein. The residues involved in the interaction are on opposite sides of the protein, about 25 Å apart. Simulations of alanine substitutions at the solvent‐exposed helix positions, arginine 22, glutamic acid 23, threonine 26, and leucine 27, show both small and large perturbations of eglin c dynamics. Two mutations exhibit large impacts on the long‐range helix‐loop interactions. Previous stability measurements (Yi et al., Biochemistry 2003;42:7594–7603) had indicated that an alanine substitution at position 27 was less stabilizing than at other solvent‐exposed positions in the helix. The L27A mutation effects observed in these simulations suggest that the position‐dependent loss of stability measured in wet bench experiments is derived from changes in dynamics that involve long‐range interactions; thus, these simulations support the hypothesis that solvent‐exposed positions in helices are not always equivalent. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Evaluating the quality of NMR structures by local density of protons
Authors: Ban Yih‐En Andrew , Rudolph Johannes , Zhou Pei , Edelsbrunner Herbert 
Published: December 2005

AbstractEvaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high‐resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z‐scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z‐scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711–1733) generated by all atom contact analysis. Local density Z‐scores for NMR structures exhibit a significantly wider range of values than for X‐ray structures and demonstrate a combination of potentially problematic inflation and compression. Water‐refined NMR structures show improved packing quality. Our analysis of a high‐quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Folding and amyloid‐fibril formation for a series of human stefins' chimeras: Any correlation?
Authors: Kenig Manca , Jenko‐Kokalj Saša , Tušek‐Žnidarič Magda , Pompe‐Novak Maruša , Gunčar Gregor , Turk Dušan , Waltho Jonathan P. , Staniforth Rosemarie A. , Avbelj Franc , Žerovnik Eva 
Published: December 2005

AbstractTo study the influence of whole secondary structure elements to the process of folding and amyloid‐fibril formation, chimeras of stefins have been prepared. GdnHCl denaturation curves and folding rates (chevron plots) have been analyzed based on a two‐state mechanism. The order of stability is: stefin A > aAbbbb > bAbbbb > stefin B = aBaaaa > bBaaaa, where the make up of chimeric proteins is designated by small letters representing the source of individual strands (a for stefin A, b for stefin B) and a capital letter representing the source of the helix (A for stefin A and B for stefin B). Only the fast folding reactions were included in the analysis and it has been found that stefin B folds the fastest (657 s−1). Similarly, fast folders are the chimeric proteins aBaaaa and bBaaaa, both of which contain the α‐helix of stefin B. Unfolding rates correlate very well with protein stability, with the slowest rate for the most stable protein, stefin A. Amyloid‐fibril growth was measured for each protein by monitoring thioflavin T fluorescence and was visualized using electron microscopy. The propensity to form amyloid‐fibrils is in the order: stefin B > bAbbbb > aAbbbb > bBaaaa > aBaaaa > stefin A. This order does not correlate with stability, or with the folding or unfolding rates. Instead, the propensity to fibrillize is related to selected parts of structure, such as the β‐sheet of stefin B, and can be predicted reasonably well by calculating the β‐strand propensity of the denatured states. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Cost‐effective connections
Authors: Steenhuis C M , Stark J W B , Gresnigt A M 
Published: December 2005

AbstractThis review highlights some of the recent developments in steel design and construction, and its associated research. In recent decades, labour costs have increased considerably while material costs have remained constant. Therefore, there is a tendency to simplify the most labour‐intensive parts of a steel structure: the connections, thus cutting labour costs. Simplifying the fabrication process is of considerably more importance than minimizing the use of materials. Research has been carried out to support the process of simplification. This review reports on some of the practical outcomes of this research. Special attention is given to fabrication and erection‐friendly connections, the application of preloaded fasteners, and unstiffened moment connections (including base plates). Finally, in the conclusions, the review identifies future research needs.
High strength steels
Authors: Gresnigt A M , Steenhuis C M 
Published: December 2005

AbstractIn recent decades, the ductility and weldability of structural steels has improved considerably. Also, the developments in modern welding technology have led to a decrease in the fabrication costs of steel structures, especially when higher strength steels are used. This has created new opportunities for more economical applications of steel in the construction industry. The choice of higher strength steels has become increasingly attractive, eg grade S355 (specified minimum yield strength 355 N/mm2) instead of S235 or S275, or grade S460 instead of S355.This review surveys the possibilities for the cost‐effective application of high strength steels in buildings, bridges, cranes, etc. Some developments in research and drafting of codes are also highlighted.The review focuses mainly on developments in Europe, but in other parts of the world, such as Japan and the USA, similar trends can be observed.
Steel bridges
Authors: Kuhlmann U 
Published: December 2005

AbstractWith recent developments, structural engineers are realizing that the quality of their structures is not only bound by economics, function and feasibility, but also aesthetics. The special quality of steel to allow high forces in very slender members is able to meet these new aesthetic requirements.Tough economic competition between the concrete and steel industries has led to a decrease in the number of small and medium‐size steel bridges compared with concrete bridges. The bridges which have been built recently as steel structures, in spite of economic competition, are typically those which span a very long distance with an especially light structure. Examples are the Akashi‐Kaikyo Bridge in Japan, the Storebaelt East Bridge in Denmark and the Normandy Bridge in France. Other recently built steel bridges have been those which have to carry especially high loads over a long span since steel structures combine relatively light weight with high stiffness.Steel bridges worldwide have been growing old. Deciding whether to replace or repair them, mainly depends on their physical condition, especially the degree of fatigue and their state of corrosion. Increasing traffic demands are the main reason for modifications and extensions to existing steel bridges. Seismic evaluation studies recommend the retrofitting of bridges that are at risk. Besides these functional considerations, some bridges are repaired because of their historical and architectural significance; this is a sign of a new perception of bridges as part of our cultural environment.
Seismic‐resistant steel moment connections: developments since the 1994 Northridge earthquake
Authors: Engelhardt Michael D , Sabol Thomas A 
Published: December 2005

AbstractSince the 1994 Northridge earthquake, major changes have occurred in US design and construction practice for seismic‐resistant steel moment connections. These changes, motivated by the widespread failure of welded moment‐resisting beam‐to‐column connections in the Northridge earthquake, hold the promise of significantly better connection performance in future strong earthquakes. While the debate and discussion on these connection failures continues, intensive research and testing efforts have led to major advances in diagnosing the causes of the failures, and in developing improved connections. This paper presents a summary of key US developments in seismic‐resistant steel moment connections since the Northridge earthquake. A description of the typical moment connection detail in use prior to the earthquake is provided first, together with a description of damage observed at these connections after the earthquake. This is followed by a discussion of some of the major causes of the failures. Finally, some of the approaches currently being used in the US for the design and construction of improved moment connections are presented.
Seismic damage indices for RC buildings: evaluation of concepts and procedures
Authors: Kappos A J 
Published: December 2005

AbstractThis review clarifies the basic concepts involved in defining seismic damage indices for reinforced concrete buildings, and critically reviews the different schemes for classifying these indices. Typical examples are given for each class of indices, with emphasis on more recent studies. The available analytical procedures for the determination of damage indices are evaluated and the associated problems discussed. A brief reference is also made to empirical procedures for damage assessment. The most commonly used damage indices are evaluated in quantitative terms, using data from very recent comparative studies. Finally, conclusions are drawn, focusing on the practical use of these indices, and some directions for future research efforts are identified.
Seismic design of masonry structures
Authors: Tomaževič Miha 
Published: December 2005

AbstractAs a result of experimental and analytical research in seismic behaviour of masonry structures in the last few decades, new methods for seismic resistance analysis and design, as well as new, seismic resistant technologies and construction systems have been developed. After many centuries of traditional use, and decades of allowable stresses verification, clear concepts for limit states verification of seismic resistance of masonry structures have been introduced in the seismic codes. In this review, some basic aspects of seismic resistance verification of masonry walls and buildings are discussed, and some suggestions for future research are given.
Fatigue of tubular joints and fatigue improvement methods
Authors: Haagensen P J 
Published: December 2005

AbstractThis paper reviews important parameters and conditions that determine the life of welded joints, and summarizes recent research developments in the fatigue design of welded structures, with an emphasis on offshore tubular structures. Two of the factors that strongly affect fatigue life, the environment and plate thickness, have been the subject of several large research programs in recent years. With the increasing use of higher strength steels much interest has also been taken in various methods for improving the fatigue life of welded joints. Developments in these areas of research are reviewed. Examples of approaches to fatigue life prediction in design codes are given. Recent changes to design codes are evaluated, and examples of significant changes in design codes are given. Progress in the implementation of techniques for fatigue life improvement and life extension of fatigue‐damaged structures are discussed.
Fractures in seismically loaded bridges
Authors: Miki Chitoshi 
Published: December 2005

AbstractDuring the Hanshin‐Awaji earthquake near Kobe, Japan, in January 1995, many civil structures suffered various kinds of damage which had never before been seen. Subsequently, many research programs have been undertaken which are related to the Hanshin‐Awaji earthquake and the associated damage. This paper reviews the currently conceived causes of the damage, particularly the fracture of steel bridge members. Related matters which should be given consideration in the future are also reviewed.
Creep and shrinkage analysis of composite beams
Authors: Dezi L , Leoni G , Tarantino A M 
Published: December 2005

AbstractThe principal aspects concerning long‐term behaviour of steel–concrete composite beams are illustrated by analysing separately the effects of static and geometrical actions, shrinkage and prestressing of the concrete slab. After having qualitatively described the time‐dependent phenomena which occur in composite beams, the most important methods of creep analysis are discussed. An accurate numerical solution can be obtained by means of the step‐by‐step procedure of the general method, that must necessarily be computer processed. Alternatively, single‐step solutions can be found by using approximated algebraic methods. The effectiveness of these simplified methods is subsequently estimated with reference to each single action. Finally, some practical design rules are provided in order to perform simplified creep analyses by means of pseudo‐elastic analyses.
Seismic isolation of civil buildings in Europe
Authors: Martelli A , Forni M 
Published: December 2005

AbstractThis review outlines the present state of applications of seismic isolation to civil buildings in Europe (with particular reference to Italy), including the countries formerly belonging to the USSR. Some information is also given on the use of other passive innovative antiseismic devices, like energy dissipators and shock transmitters, as well as on applications to bridges, viaducts and industrial plants. The adopted innovative antiseismic systems are described. Research projects, mainly in the framework of Programmes funded by the European Commission, which have been completed recently or are in progress, are briefly outlined. The available or proposed design rules and guidelines and statistics of applications (based on the outcome of recent international seminars) are included. Some examples of applications are briefly illustrated. Finally, the perspectives for future applications are discussed, highlighting the issues which have so far restrained a wider use of innovative antiseismic techniques in Europe.
Structural health monitoring of civil engineering structures
Authors: Culshaw B 
Published: December 2005

AbstractContinuous monitoring to highlight the performance of major civil engineering structures is a process which to date has received relatively little attention. However, emerging legislation, the farreaching economic consequences of decay in the civil infrastructure, increasing social pressures and the changes in the contractual relationships between builder and user, all highlight the potential benefits which may accrue from the use of appropriate instrumentation. This article briefly examines the type of measurements which may be useful in civil engineering monitoring and some of the means whereby these measurements may be realized using the current and emerging instrumentation packages. The need for measurement functions over large areas, at very large numbers of sampling points, highlights the necessity for new instrumentation approaches, and of these, the global positioning system (GPS) and optical fibre sensor technology appear to offer particular promise. Signal processing and event recognition are also critical to the success of a monitoring system so this article provides a very basic introduction to the implicit requirements for data analysis.
Buckling analysis of thin‐walled structures: Analytical developments and applications
Authors: Rasmussen Kim J R , Hancock Gregory J 
Published: December 2005

AbstractThis article is the first part of a review of recent research in buckling analysis of thin‐walled structures. It covers fundamental developments in new methods of analysis and their applications. The second part of the review will be published in April 1999 and will focus on numerical developments based mainly on the finite element and finite strip methods, and applied research on specific types of thin‐walled structures, including stiffened panels, girders, shear panels and coldformed structural members.