bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulating less‐than‐truckload terminal operations
Authors: Deshpande Pranav J. , Yalcin Ali , Zayas‐Castro José , Herrera Luis E.
Published: February 2007

Purpose

Recent surveys indicate that transportation companies are not utilizing technology in decision making despite growing complexity of transportation systems. This paper aims to present a discrete simulation approach to benchmarking performance measures of terminal operations of less‐than‐truckload (LTL) freight carriers.

Design/methodology/approach

The methodology involves design of heuristics for the dock assignment problem and uses discrete event simulation to evaluate performance of the various heuristics.

Findings

Intelligent dock assignment for incoming trailers can greatly improve performance of LTL terminals and simulation is an effective tool to determine the effects of various assignments on terminal performance.

Originality/value

The paper introduces a dock assignment heuristic and integrates the tactical level decision‐making process and operational aspects in LTL terminals to evaluate the performance of the system. A case study is used to demonstrate the use of the heuristic and performance improvements.
Elements of a business process management system: theory and practice
Authors: Shaw Duncan R. , Holland Christopher P. , Kawalek Peter , Snowdon Bob , Warboys Brian
Published: February 2007

Purpose

To construct, test and illustrate a sophisticated and theory‐based architecture for analyzing business process management systems (BPMS) used for business process change.

Design/methodology/approach

Exploration of business process modeling‐based BPMS via a meta‐survey of academic and business literatures. Two main dimensions are used based upon semiotics and a block‐based BPMS pyramid architecture. Each block is a core technology required for the functioning of the BPMS and include: the subject being modeled; the software formalism; the IT infrastructure; the modeling language and notation; and the underlying technical infrastructure.

Findings

Theoretically explains and empirically illustrates each core technology in the proposed architecture then does the same for the architecture, its arrangement as a whole and its interrelationships. Recognizes the lack of a theoretical basis for business process modeling constructs and the dangers that this generates. Explains why automatic BPMS require formal construct transmission from subject modeled to modeling hardware and software.

Research limitations/implications

The architecture's core technologies span numerous disciplines so each set of literatures introduces the component concepts and their bases but is not exhaustive.

Originality/value

This paper proposes a considerably more sophisticated framework for BPMS analysis than is currently available; it is theoretically and not just empirically based; it uses a novel method of theoretical justification concerned with the transmission of modeled properties and characteristics between several technological media; and it illustrates the innovative analytical use of this architecture and the practical use of BPMS with three different case vignettes.
An assessment of facilitators and inhibitors for the adoption of enterprise application integration technology
Authors: Bahli Bouchaib , Ji Fei
Published: February 2007

Purpose

Enterprise application integration (EAI) aims to integrate various enterprise applications, such as legacy systems, enterprise resource planning systems, and best‐of‐breed business applications, to aid in promoting organizational goals. EAI is a relatively new area of concern for researchers and practitioners and research on its adoption by organizations remain to be examined.

Design/methodology/approach

This paper extends prior research by providing a systematic examination of both generic and specific dimensions of facilitators and inhibitors for the adoption of EAI technology. A rigorous validation of these factors was established. A case study was conducted to refine the developed instrument.

Findings

The results indicate that EAI adoption is facilitated by generic as well as specific factors to this technology.

Research limitations/implications

Several limitations of the study need to be mentioned at this stage. First, the research design of this study has incorporated only one site to examine and enrich the list of facilitators and inhibitors of EAI adoption. It is not known whether these results would apply to other organizations, other technologies and whether the project size has some influence on the results. More empirical work is needed to increment the developed instrument. The results of this study have three specific implications for future research. First, this study can be replicated to examine the effect of these facilitators on EAI project performance. Second, more research can be conducted to validate dimensions identified in this study. A survey may strengthen the validation process of the developed instrument and the structure of the dimensions and constructs used. Finally, the results of this study and the developed instrument can be applied on other technologies such as web services, etc.

Practical implications

The paper extends King and Teo's list to include EAI‐specific factors. Second, it validates the instrument through the card sorting procedure and a case study. The identified dimensions can be used in future research on EAI adoption. The results have also important managerial implications. Managers who are planning to adopt EAI technology can use the developed instrument to assess systematically the facilitators and inhibitors of this technology in their organizational context.

Originality/value

This study extends and accumulates on Teo's framework for inhibitors and facilitators of IT adoption in the EAI context.
A model for analysing the success of adopting new technologies focusing on electronic commerce
Authors: Jackson Martin L. , Sloane Andy
Published: February 2007

Purpose

To provide an organisation or supply chain with the means to analyse their current business foundations prior to the adoption of a new technology for the assessment of successful adoption.

Design/methodology/approach

The objectives were to analyse and aid the successful adoption of new technology. This was achieved by the construction of three models from previously conducted research focusing on electronic commerce for application research.

Findings

The research clearly identified a link between an organisation's structure and ease of new technology adoption. This link is the bind between the categories developed for the models and reflects “best fit” for generic organisational analysis.

Research limitations/implications

A questionnaire was used to fuel the models. It included evenly weighted questions. This led to the category results being based on mid‐point scaling. Both the weighing and model scaling are to be addressed in further research assisted by the results from the application of the questionnaire, models, results and organisation follow‐up analysis.

Practical implications

The models provide a pre‐adoption analysis that can produce a general view towards success, with relatively no expenditure.

Originality/value

The three models are new. The target model is the main construction that has been developed over a number of years. The construction comprises of human resources, processes, organisational culture, and management styles, these elements have not been brought together in this way before to analyse the adoption of new technology in an organisation or supply chain. The models are generic and can be applied to all industries and types of business.
DRM, law and technology: an American perspective
Authors: Rosenblatt Bill
Published: February 2007

Purpose

The purpose of this paper is to provide a review of developments in the USA related to digital rights management (DRM) through legal, technological, and market developments in recent years.

Design/methodology/approach

This article summarizes recent developments in DRM in two areas. First is the legal landscape, including copyright law developments that apply to digital content and attempts to impose DRM technology through legislation and litigation. Second are recent advances in DRM‐related technology and developments in digital content markets that are based on DRM. In both cases, USA developments are compared with the situation in Europe.

Findings

Developments in American copyright law, DRM technology, and digital content markets exert heavy influences on the spread of DRM in Europe, but the legal and technological frameworks are not different, giving rise to incompatibilities.

Practical implications

DRM technologies need to evolve differently for European markets, because they need to exist in the context of fundamentally different copyright law frameworks (e.g., Private Copying) and incumbent technologies (e.g., Conditional Access television).

Originality/value

European readers of this paper should gain an understanding of American DRM technology and its legal context, and how they influence developments in Europe.
Clustering search results. Part I: web‐wide search engines
Authors: Jacsó Péter
Published: February 2007

Purpose

The purpose of this paper is to examine clustering search results. Traditionally, search results from professional online information services presented the results in reverse chronological order. Later, relevance ranking was introduced for ordering the display of the hits on the result list to separate the wheat from the chaff.

Design/methodology/approach

The need for better presentation of search results retrieved from millions, then billions, of highly unstructured and untagged Web pages became obvious. Clustering became a popular software tool to enhance relevance ranking by grouping items in the typically very large result list. The clusters of items with common semantic and/or other characteristics can guide the users in refining their original queries, to zoom in on smaller clusters and drill down through sub‐groups within the cluster.

Findings

Despite its proven efficiency, clustering is not available, except for Ask, in the primary Web‐wide search engines (Windows Live, Yahoo and Google).

Originality/value

Smaller, secondary Web‐wide search engines (WiseNut, Gigablast, and especially Exalead) offer good clustering options.
Integrating self‐managed work teams into project management
Authors: Roper Kathy O. , Phillips Deborah R.
Published: February 2007

Purpose

To present the advantages and possible deterrents of self‐managed work teams, and offer recommendations on ways to integrate these teams into project management.

Design/methodology/approach

A range of works, which provide a description and practical advice about self‐managed work teams, are reviewed in an effort to provide a thorough picture of self‐managed work teams. The information is sorted into sections: history of self‐managed work teams; self‐managed work teams: a definition; characteristics of self‐managed work teams; the role of emotional intelligence in self‐managed work teams; developing and empowering the team; barriers to successful self‐managed work teams; factors to consider before forming a self‐managed work team; and the longevity of self‐managed work teams.

Findings

Integrates theories and findings from other works to offer a holistic view of self‐managed work teams in today's workplace.

Research limitations/implications

Resources from USA, as well as European writings, were analyzed to bring global perspectives. Applications are not specific to FM or construction, but business in general.

Practical implications

A useful source for project managers or other managers considering implementing self‐managed work teams to increase productivity and employee morale.

Originality/value

Takes an integrated approach in exploring all areas of self‐managed work teams, including emotional intelligence. Provides useful information on integrating self‐managed work teams in project management.
Impact assessment and biodiversity considerations in Nigeria
Authors: Hamadina Mohammed K. , Otobotekere Dimie , Anyanwu Donald I.
Published: February 2007

Purpose

Niger Delta University (NDU) campus is located on the fringe of a Nun River Forest Reserve (NRFR) in Nigeria. The NRFR covers 97.15 km2 of humid tropical rainforest characterized by torrential rains, seasonal flooding, and multi‐layered vegetation. This paper aims to conduct a wildlife study, to assess the effects of the NDU campus project on NRFR.

Design/methodology/approach

The assessment was preceded by “scoping” to determine key wildlife issues. Thereafter a mix of methods, including literature search, reconnaissance visits, field exercises, and interviews with hunters, was adopted to gather information. These were augmented with diurnal and nocturnal forest expeditions to find evidence(s) of wildlife species existence.

Findings

There is a rich assemblage of wildlife species; of which 12 are enlisted in the 2006 IUCN Red List of threatened species, while 14 are protected by Nigeria's statutes; and they are threatened by human activities. The NDU campus project shall have significant adverse impacts on the wildlife: directly through habitat loss/fragmentation, nuisance, influx of people; and indirectly by exacerbating the existing threats.

Research limitations/implications

This work is limited to the NDU campus project and its impact on NRFR. The brevity of time spent in the field coupled with the generally inaccessible terrain and remote location of the NRFR constitute the limitations that must have influenced the findings in this paper.

Originality/value

This paper reports the results of an original work, discusses the impacts of NDU campus on NRFR, and highlights conservation‐friendly local beliefs/practices that could fit into a wildlife management plan, and fosters the debate on methodologies and field initiatives.
Designing a multimedia platform for emergency management
Authors: Nikolic Vesna , Savic Suzana , Stankovic Miomir
Published: February 2007

Purpose

The purpose of this paper is to describe research, the objective of which was the development of models, methodologies, and tools for the realization of the multimedia platform for emergency management in technological systems.

Design/methodology/approach

This objective was achieved through the operationalization of the following major tasks: the theoretical research on the specific characteristics of emergency management system structure and processes; definition of educational structures, processes, and subjects for emergency management; development of models and software tools for the analysis of emergency development; development of information (web) services to support the collaborative decision making.

Findings

A model of multimedia platform for emergency management in technological systems has been developed, which defines emergency services with appropriate information infrastructure, the structure and characteristics of the interoperability system and their mutual communication.

Research limitations/implications

Further research should result in: the concrete structure and processes of virtual organisation for emergency management in technological systems; software for the support of collaborative decision making; models for emergency management education and training based on multimedia technologies. The limitations are primarily related to model implementation, since there are no suitable emergency databases.

Practical implications

The platform can be used by: industrial companies, companies that provide building maintenance, public services, insurance companies, educational institutions, local authorities (by an adequate upgrade of models and software).

Originality/value

This paper presents the information flow identified in emergency management and the structure of a multimedia platform which, by creating favourable environment for collaborative decision making, enables effective and efficient emergency management in technological systems, as well as emergency management education and training.
Assessing social and economic impacts associated with changes in the coal mining industry in the Bowen Basin, Queensland, Australia
Authors: Ivanova Galina , Rolfe John , Lockie Stewart , Timmer Vanessa
Published: February 2007

Purpose

The coal mining industry makes a key contribution to the Queensland economy, and is the underlying driver of employment and economic conditions in many local and regional communities. This article aims to focus on how the social and economic impacts of mining should be assessed and negotiated with local and regional communities.

Design/methodology/approach

The following assessment tools were trialed to ascertain the impacts on communities of changes in the mining industry: extended stakeholder analysis of key community representatives; economic modeling of changes in the level of mining activity; a random survey of householders involving choice experiments to assess tradeoffs; and experimental workshops to assess how residents were prepared to prioritise different community development options.

Findings

The results showed that impact assessment should be addressed using different economic and social science tools to ensure regulatory approval as well as community acceptance.

Originality/value

This article suggests alternative social and economic impact assessment mechanisms that can be applied to any industry and any situation (e.g. growth, decline, new development, simultaneous changes).
A dynamic view on strategic resources and capabilities applied to an example from the manufacturing strategy literature
Authors: Größler Andreas
Published: February 2007

Purpose

The purpose of this paper is to demonstrate the usefulness of a dynamic analysis of the development and management of strategic capabilities and resources in manufacturing. It aims to present dynamic resource/capability systems as a means to understand an issue from manufacturing strategy.

Design/methodology/approach

A case study from a standard textbook on manufacturing strategy is used to illustrate the approach that is mainly based on Warren's strategy dynamics. Extensions to this approach are introduced.

Findings

Diagrams of dynamic resource/capability systems are valuable tools for understanding issues of interconnected and changing strategic resources and capabilities. Resources and capabilities can be interpreted as stocks in dynamic simulation models following ideas from system dynamics.

Research limitations/implications

The exact nature of strategic capabilities and their relationships needs to be further investigated. Approaches need to be developed to measure and to quantify these concepts. The connection between Hill's order winners/qualifiers and the inflows/outflows of capability and resource stocks should be further examined.

Practical implications

Static analyses of strategic issues are often difficult to interpret. The dynamic nature of strategic issues needs to be reflected in the tools used for analysing them.

Originality/value

Applies a dynamic analysis to manufacturing strategy and uses a textbook example in a new way to illustrate the relevance of the approach.
Improving factory layout under a mixed floor and overhead material handling condition
Authors: Djassemi Manocher
Published: February 2007

Purpose

In spite of having a number of general‐purpose algorithms for solving plant layout problems, facility planners may still face a challenging task to adjust these algorithms to handle special, but not uncommon, layout problems. The purpose of this study is to propose a new method for addressing the impact of overhead space utilization on a plant layout solution.

Design/methodology/approach

A new method for adjusting material flow under a mixed floor and overhead material handling condition is incorporated in an existing plant layout procedure. A case study involving the layout improvement in a lawn mower engine assembly facility is presented to illustrate the effectiveness of the proposed method.

Findings

The analysis of solutions for the case study shows that the layout generated by the proposed modified material flow approach is a more economical solution. The case also shows, when it is important to optimize the use of space, the overhead space should be considered as part of any methodology for designing a good layout.

Research limitations/implications

The proposed modified material flow approach can be applied to any facility where the use of overhead space for material handling is justifiable by limited floor space and/or by high cost of land. The proposed method can be applied to small to medium size problems with minimal computational effort. However, as the size of facility grows, the manual calculation becomes more time consuming and potentially erratic.

Originality/value

This paper should be useful to both researchers and practitioners who deal with overhead space utilization in designing facility layouts.
Model and approach of fuzzy bilevel decision making for logistics planning problem
Authors: Zhang Guangquan , Lu Jie
Published: February 2007

Purpose

This study aims to develop a decision making model and approach for logistics planning problem which naturally involves two or more decision units at a hierarchical structure. Such a decision problem in practice often involves uncertain and imprecise factors with the parameters of a bilevel decision model, either in the objective functions or constraints.

Design/methodology/approach

This paper proposes a fuzzy bilevel decision making model for a general logistics planning problem and develops a fuzzy number based Kth‐best approach to find an optimal solution for the proposed fuzzy bilevel decision problem.

Findings

The proposed approach illustrates an optimal solution in logistics management, which meets maximally/minimally the objectives of both supplier and distributor (or other parts of the logistics chain). The proposed fuzzy bilevel decision approach can have a wide range of logistics management applications.

Research limitations/implications

The decision model, approach and system will be further tested for some more complicated real cases in the future.

Originality/value

The proposed fuzzy bilevel decision model and approach are new, which offer theoretical and practice help to logistics management.
Prioritization of key performance indicators
Authors: Shahin Arash , Mahbod M. Ali
Published: February 2007

Purpose

The purpose of this paper is to provide an integrated approach that prioritizes organizational key performance indicators (KPIs) in terms of the criteria of SMART (Specific, Measurable, Attainable, Realistic, Time‐sensitive) goal setting.

Design/methodology/approach

The research was carried out using the analytical hierarchy process (AHP) technique as the basis for pairwise comparisons of SMART criteria, considering each KPI.

Findings

A new approach is outlined, encompassing step‐by‐step guidelines for decision makers to conduct the prioritization process of SMART KPIs. The results of the case study highlight the applicability of the proposed approach and the calculation process for prioritizing KPIs.

Research limitations/implications

The rating scales used in the AHP analysis are conceptual; although it identifies which dimensions require improvement, the proposed approach does not provide guidance on an appropriate action plan to address deficiencies; another limitation is that the framework adopted only the SERVQUAL service dimensions.

Originality/value

This paper gives a novel approach for prioritization of KPIs. The proposed approach has a holistic mechanism; it could empower decision‐making teams; it is capable of enhancing advanced quality engineering approaches; and provides great opportunities for future research.
Bonds of burden and bliss: the management of social relations in a peacekeeping organisation
Authors: Tallberg Teemu
Published: February 2007

Purpose

The purpose of this paper is to discuss the gendered social bonds and the everyday organisational practices and discourses of peacekeepers.

Design/methodology/approach

The paper is based on preliminary analysis of empirical material gathered through a seven‐month ethnography among Finnish peacekeeping officers in training and service.

Findings

In contrast to studies on homosociality, men's bonding and cohesion as a basis of optimal combat performance in military organisations, I suggest looking at the militarized social encounters, masculinities and collectives from the perspective of hybridity tensions and management. Peacekeepers' everyday practices and social structures can be interpreted as management of context‐specific power tensions.

Originality/approach

Offers a view to everyday life of peacekeeping and builds a basis for analysing men's social relations in organisations.
A study of factors affecting the success of private label brands in Chinese e‐market
Authors: Huei‐Chen Hsu
Published: February 2007

Purpose

The major objective of this study is to explore factors effect in purchasing preferences for foreign brands versus private label brands (PLB) in urban China on the internet.

Design/methodology/approach

In this paper, the research is designed to investigate the factors perception mentioned above how to affect consumers' online purchasing PLB intention. Along with literature review, an online survey is conducted to test the conceptual model. LISREL 8 is used to analyses the hypothesized model and a two‐step model‐building approach is used, in which the measurement models are tested prior to testing the structural model.

Findings

Using the data collected in GuangZhou, Shenzhen, Wuhan, Shanghai and Nanjing cities, it is found that both their direct and indirect effects. Interesting to find, that Chinese consumers' exposure to online products is relatively new, it appears that searching and experience online in reducing their perceived risk of quality concern, and it affects their choice of PLB. Price consciousness is very important to choose domestic PLB across all purchase situations, whereas the other types of factors have differential impact. It seems that Chinese respondents get used to surf on the internet, that is, their perceived risk is not low, which is different from other literatures studied.

Originality/value

The paper offers insights into the implications for e‐marketers' management of web sites in China.
An exploratory study on the environmental factors influencing the adoption of MAPs in Chinese SOEs and JVs
Authors: Wu Junjie , Drury Colin
Published: February 2007

Purpose

The purpose of this study is to analyze the environmental factors (either internal or external) that influence the adoption of management accounting practices (MAPs) in Chinese state ‐owned enterprises (SOEs) and foreign joint ventures (JVs) located in China.

Design/methodology/approach

A cross‐sectional survey and comparative study based on questionnaires from SOEs and JVs respondents.

Findings

The study finds a significant difference in the adoption levels of MAPs according to the ownership type of the enterprise (JVs and SOEs). This study provides some support for the findings from previous researches. It confirms that Chinese enterprises participating in foreign‐partnered JVs have made more changes to their management accounting systems when compared to similar Chinese enterprises that had no collaborative venture operation with foreign firms. This paper has also presented a detailed historic background and an in‐depth discussion to explore some environmental factors influencing the adoption of MAPs in SOEs and JVs and explain possible reasons.

Originality/value

This study is thought as one of the first attempts to systematically investigate of the benefits derived from traditional and contemporary practices of management accounting used in Chinese SOEs and JVs.
R&D team governance and R&D performance
Authors: Yunsheng Zhang , Deming Zeng , Lifei Zhang , Yang Lu Lucy
Published: February 2007

Purpose

With the clarification of three effective methods (share holding, decision participation and promotion of technical grade) to govern R&D teams in software enterprises, the purpose of this paper is to provide an empirical investigation of the application of these methods in Chinese software enterprises.

Design/methodology/approach

The research is based on a quantitative approach with 34 items designed in the questionnaire to measure the indicators. All items were rated by respondents on a five‐point Likert‐type scale. In order to testify the validity of the three methods of R&D team governance, a correlation analysis and a linear regression were made to examine the relationship between these methods of R&D team governance and R&D performance.

Findings

The evidence shows that decision participation and promotion of technical grades are the two most effective methods to govern R&D teams in Chinese software enterprises, while share holding is not conducive to R&D performance. The share holding level of R&D staffs is fairly low; even “no share.” What is more important is that many software enterprises regard it as a welfare institution but not an incentive method. Therefore, the shareholding mechanism cannot enhance R&D performance. In addition, relevant regulations have not been established completely. There are many deficiencies in the process of intellectual property management of Chinese enterprises. These factors have hindered the effective performance of R&D staff.

Practical implications

The research findings emphasize the importance of governance of R&D teams in the Chinese software industry and highlight the critical issues that need to be addressed in order to enhance the performance of R&D staff.

Originality/value

The concept of R&D team governance is examined and elaborated within the context of China, which points to the need of developing new direction of R&D team management.
Knowledge transfer in international educational collaboration programme
Authors: Li‐Hua Richard
Published: February 2007

Purpose

The purpose of this paper is to review the literature of international development strategy of high education and examine what is happening currently in terms of education collaboration between the UK and China and attempt to address various challenges in capacity building through knowledge transfer.

Design/methodology/approach

Theoretical analysis supported by observation and interviews.

Findings

The study has identified that there are a certain number of elements, which are crucial to the success of international educational collaboration, of which, the appropriateness and effectiveness of knowledge transfer/knowledge sharing is vital to the capacity building of higher educational institutions. The study examines on‐going Sino‐British education collaboration programme and fuelled the debate concerning knowledge transfer/knowledge sharing in high education between the developed and developing countries.

Originality/value

Based on a comprehensive examination and analysis of the process of knowledge transfer/knowledge sharing in a Sino‐British educational collaboration programme, this study emphasizes the significance of incorporating both cultural and organisational factors that play a role in the whole process. This paper describes the process of knowledge transfer between foreign and Chinese faculties when they work together on academic collaboration project in China. Furthermore, the paper addresses the appropriateness and effectiveness of knowledge transfer/knowledge sharing during the implementation of the international academic collaboration programme.
Digital B2B interactions in Romania
Authors: Gurău Călin
Published: February 2007

Purpose

The development of new information technology and telecommunication (ITT) devices has increased the complexity of business‐to‐business (B2B) interactions, forcing the service organisations to adopt a multi‐channel, customer‐oriented approach. The purpose of this study is to present an exploratory study of B2B interactions in Romania, which measures the preference of both service providers and client firms for various channels of interaction, and identifies the main dimensions of the interactive process.

Design/methodology/approach

The primary data were collected through an e‐mail questionnaire that was answered by 113 service providers and 102 client organisations, and then analysed using the SPSS statistical package.

Findings

Five main interaction dimensions have been identified as the framework used by client organisations to evaluate the quality of B2B interactions. These dimensions are complex constructs that have a double projection in the context of ITT systems and CRM procedures.

Originality/value

The process of B2B interactions is poorly documented for transition economies, such as Romania. After describing the dimensions of B2B interactions, the paper proposes a diagnostic procedure for evaluating the perception gaps between the service provider firm and the client organisation, concerning the quality level of each dimension. This diagnostic can be adapted and used by each service provider organisation to identify the possible areas of customer dissatisfaction and the requirements for future improvements.
Photo‐activity induced by amyloidogenesis
Authors: Tcherkasskaya Olga
Published: February 2007

Accumulation of chemically altered proteins is a noted characteristic of biological aging, and increasing evidence suggests a variety of deleterious cellular developments associated with senescence. Concomitantly, the “aging” of protein deposits associated with numerous neurological disorders may involve covalent modifications of their constituents. However, the link between disease‐related protein aggregation and chemical alterations of its molecular constituents has yet to be established. The present study of amyloidogenic α‐synuclein protein points to a decisive change in the biophysical behavior of growing protein aggregates with progressive photo‐activity in the visible range of the electromagnetic spectrum. I hypothesize that the photo‐activity induced by filament formation is governed by the same mechanism as seen for the intrinsic chromophore of 4‐(p‐hydroxybenzylidene)‐5‐imidazolinone‐type in the family of green fluorescent proteins. This type of the covalent alterations is initiated concurrently with amyloid elongation and involves a complex multi‐step process of chain cyclization, amino acid dehydration, and aerial oxidation. Given that different stages in filament formation yield distinct optical characteristics, the photo‐activity induced by amyloidogenesis may have application in molecular biology by enabling in vivo visualization of protein aggregation and its impact on cellular function.
The Abl SH2‐kinase linker naturally adopts a conformation competent for SH3 domain binding
Authors: Chen Shugui , Brier Sébastien , Smithgall Thomas E. , Engen John R.
Published: February 2007

The core of the Abelson tyrosine kinase (c‐Abl) is structurally similar to Src‐family kinases where SH3 and SH2 domains pack against the backside of the kinase domain in the down‐regulated conformation. Both kinase families depend upon intramolecular association of SH3 with the linker joining the SH2 and kinase domains for suppression of kinase activity. Hydrogen deuterium exchange (HX) and mass spectrometry (MS) were used to probe intramolecular interaction of the c‐Abl SH3 domain with the linker in recombinant constructs lacking the kinase domain. Under physiological conditions, the c‐Abl SH3 domain undergoes partial unfolding, which is stabilized by ligand binding, providing a unique assay for SH3:linker interaction in solution. Using this approach, we observed dynamic association of the SH3 domain with the linker in the absence of the kinase domain. Truncation of the linker before W254 completely prevented cis‐interaction with SH3, while constructs containing amino acids past this point showed SH3:linker interactions. The observation that the Abl linker sequence exhibits SH3‐binding activity in the absence of the kinase domain is unique to Abl and was not observed with Src‐family kinases. These results suggest that SH3:linker interactions may have a more prominent role in Abl regulation than in Src kinases, where the down‐regulated conformation is further stabilized by a second intramolecular interaction between the C‐terminal tail and the SH2 domain.
X‐ray crystallographic analysis of the sulfur carrier protein SoxY from Chlorobium limicola f. thiosulfatophilum reveals a tetrameric structure
Authors: Stout Jan , Van Driessche Gonzalez , Savvides Savvas N. , Van Beeumen Jozef
Published: February 2007

Dissimilatory oxidation of thiosulfate in the green sulfur bacterium Chlorobium limicola f. thiosulfatophilum is carried out by the ubiquitous sulfur‐oxidizing (Sox) multi‐enzyme system. In this system, SoxY plays a key role, functioning as the sulfur substrate‐binding protein that offers its sulfur substrate, which is covalently bound to a conserved C‐terminal cysteine, to another oxidizing Sox enzyme. Here, we report the crystal structures of a stand‐alone SoxY protein of C. limicola f. thiosulfatophilum, solved at 2.15 Å and 2.40 Å resolution using X‐ray diffraction data collected at 100 K and room temperature, respectively. The structure reveals a monomeric Ig‐like protein, with an N‐terminal α‐helix, that oligomerizes into a tetramer via conserved contact regions between the monomers. The tetramer can be described as a dimer of dimers that exhibits one large hydrophobic contact region in each dimer and two small hydrophilic interface patches in the tetramer. At the tetramer interface patch, two conserved redox‐active C‐terminal cysteines form an intersubunit disulfide bridge. Intriguingly, SoxY exhibits a dimer/tetramer equilibrium that is dependent on the redox state of the cysteines and on the type of sulfur substrate component bound to them. Taken together, the dimer/tetramer equilibrium, the specific interactions between the subunits in the tetramer, and the significant conservation level of the interfaces strongly indicate that these SoxY oligomers are biologically relevant.
Conformational stability and differential structural analysis of LcrV, PcrV, BipD, and SipD from type III secretion systems
Authors: Espina Marianela , Ausar S. Fernando , Middaugh C. Russell , Baxter M. Aaron , Picking William D. , Picking Wendy L.
Published: February 2007

Diverse Gram‐negative bacteria use type III secretion systems (T3SS) to translocate effector proteins into the cytoplasm of eukaryotic cells. The type III secretion apparatus (T3SA) consists of a basal body spanning both bacterial membranes and an external needle. A sensor protein lies at the needle tip to detect environmental signals that trigger type III secretion. The Shigella flexneri T3SA needle tip protein, invasion plasmid antigen D (IpaD), possesses two independently folding domains in vitro. In this study, the solution behavior and thermal unfolding properties of IpaD's functional homologs SipD (Salmonella spp.), BipD (Burkholderia pseudomallei), LcrV (Yersinia spp.), and PcrV (Pseudomonas aeruginosa) were examined to identify common features within this protein family. CD and FTIR data indicate that all members within this group are α‐helical with properties consistent with an intramolecular coiled‐coil. SipD showed the most complex unfolding profile consisting of two thermal transitions, suggesting the presence of two independently folding domains. No evidence of multiple folding domains was seen, however, for BipD, LcrV, or PcrV. Thermal studies, including DSC, revealed significant destabilization of LcrV, PcrV, and BipD after N‐terminal deletions. This contrasted with SipD and IpaD, which behaved like two‐domain proteins. The results suggest that needle tip proteins share significant core structural similarity and thermal stability that may be the basis for their common function. Moreover, IpaD and SipD possess properties that distinguish them from the other tip proteins.
An analysis of the molecular origin of osmolyte‐dependent protein stability
Authors: Rösgen Jörg , Pettitt B. Montgomery , Bolen David Wayne
Published: February 2007

Protein solvation is the key determinant for isothermal, concentration‐dependent effects on protein equilibria, such as folding. The required solvation information can be extracted from experimental thermodynamic data using Kirkwood‐Buff theory. Here we derive and discuss general properties of proteins and osmolytes that are pertinent to their biochemical behavior. We find that hydration depends very little on osmolyte concentration and type. Strong dependencies on both osmolyte concentration and type are found for osmolyte self‐solvation and protein–osmolyte solvation changes upon unfolding. However, solvation in osmolyte solutions does not involve complex concentration dependencies as found in organic molecules that are not used as osmolytes in nature. It is argued that the simple solvation behavior of naturally occurring osmolytes is a prerequisite for their usefulness in osmotic regulation in vivo.
Changes in element concentrations during Andosol formation on tephra in Japan
Authors: Nanzyo M. , Yamasaki S. , Honna T. , Yamada I. , Shoji S. , Takahashi T.
Published: February 2007

Andosol formation involves the rapid, abundant and in situ formation of non‐crystalline materials from tephra deposits. A large amount of humus complexed with Al also accumulates in the A horizons. As these materials are rich in Al or Fe compared to the parent tephra, the concentrations of the major and minor elements change significantly during Andosol formation. The objectives of this study were to examine how the rock type of the tephra and its weight loss during the formation process affect the changes in the element concentrations of Andosols. A total of 95 samples with different rock types from 18 pedons of Andosols in Japan were used to determine the total concentrations of 54 elements. Principal component analysis suggested that the degree of weathering and the rock types of parent tephra are the important factors in the variation of the element concentrations in Andosols. Three rock types, dacitic, andesitic and basaltic‐andesitic, were identified from the V and Zn contents of ferromagnetic minerals separated from the Andosol samples. Basaltic Andosols were identified from the abundant coloured volcanic glass and olivine in the sand fraction. Regarding concentrations of 41 elements, at least one group based on rock type was significantly different from one to three other groups at the P= 0.05 level. The content of oxalate‐extractable Si (Sio), Al (Alo) and Fe (Feo) was used as an index to show the extent of Andosol development. Relatively strong correlations between the element concentrations and Sio, Alo and Feo as well as other weathering indices were found in the andesitic samples. Among these elements, at least 27 (Be, Al, Ti, Fe, Y, Zr, Nb, La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Hf, Ta, Tl, Pb, Th and U) were enriched in the Andosols and the increases in these concentrations were related to total weight loss due to soil formation processes.
The effect of the El Niño Southern Oscillation on the reproductive frequency of eastern Pacific leatherback turtles
Authors: SABA VINCENT S. , SANTIDRIÁN‐TOMILLO PILAR , REINA RICHARD D. , SPOTILA JAMES R. , MUSICK JOHN A. , EVANS DAVID A. , PALADINO FRANK V.
Published: February 2007

Pacific leatherback turtle Dermochelys coriacea populations have been declining precipitously. It has been suggested that fishery‐associated mortality is the leading factor causing the decline; however, the sensitivity of leatherbacks to climate variability relative to their population ecology is unknown.

We investigated the effects of interannual climate variability, as governed by the El Niño Southern Oscillation (ENSO), on leatherback nesting ecology. We used equatorial Pacific sea surface temperature (SST) anomaly data over various time scales derived from both moored buoys and remote satellites as signals of ENSO. We then incorporated these data into a remigration probability model for the largest nesting population of eastern Pacific leatherbacks at Parque Nacional Marino Las Baulas (PNMB), Costa Rica.

Our results showed that nesting females of PNMB exhibited a strong sensitivity to ENSO, as reflected in their nesting remigration probabilities. Cool La Niña events corresponded with a higher remigration probability and warm El Niño events corresponded with a lower remigration probability.

We suggest that productivity transitions at leatherback foraging areas in the eastern equatorial and south‐eastern Pacific in response to El Niño/La Niña events result in variable remigration intervals and thus variable annual egg production. This phenomenon may render the eastern Pacific leatherback population more vulnerable to anthropogenic mortality than other populations.

Synthesis and applications. Physical indices of environmental variation can be used to estimate the probability of leatherbacks remigrating to nest at PNMB. This type of modelling approach can be extremely useful for understanding the effects of climatic variation on the population dynamics of sea turtles. Our remigration probability model can be applied to any monitored sea turtle nesting population where nesting site fidelity and beach monitoring coverage remains high. This modelling approach can help nesting beach monitoring programmes forecast remigrant numbers based on prior climate data, and can further quantify anthropogenic mortality by validating survival estimates.
Realized climatic niches of deciduous trees: comparing western Eurasia and eastern North America
Authors: Manthey Michael , Box Elgene O.
Published: February 2007

Aim  Assessment of cross‐continental similarities and differences in climatic limiting values for deciduous tree species and of the possible deterministic influence of past and present climatic differences on the modern tree flora in two regions.

Location  The deciduous forest regions of western Eurasia and eastern North America.

Methods  Based on species distribution data (range maps) and climate site data, the realized climatic niches of 137 deciduous tree species from the two regions were quantified using climatic envelopes. To compare these envelopes on the two continents, a hierarchical cluster analysis was performed, and principal components analysis was used to check cluster consistency.

Results  Significant differences do exist for upper limits of winter temperatures and for lower limits of summer temperatures between Western Eurasia and eastern North America. Lower limits for the annual water balance also appear different, suggesting that the deciduous trees may be more drought‐tolerant in western Eurasia than in eastern North America. Climatic range types generated by the cluster analysis can be characterized, according to the distribution of the species, as boreal‐temperate, northern temperate, temperate, southern temperate, and Appalachian. Five of the eight clusters contain trees from both regions, but three groups consist only of American species that have no European counterparts.

Main conclusions  Differences in temperature limitations can be explained by location on the east versus west side of the continents and by the almost complete lack of warm moist areas in western Eurasia. The difference in drought tolerance, on the other hand, is more likely to be the product of a deterministic sorting process that occurred during the Plio‐Pleistocene.