bluuebunny/crossref_metadata_2025_split huggingface dataset:
General and targeted statistical potentials for protein–ligand interactions
Authors: Mooij Wijnand T. M. , Verdonk Marcel L. 
Published: August 2005

AbstractWe present a novel atom–atom potential derived from a database of protein–ligand complexes. First, we clarify the similarities and differences between two statistical potentials described in the literature, PMF and Drugscore. We highlight shortcomings caused by an important factor unaccounted for in their reference states, and describe a new potential, which we name the Astex Statistical Potential (ASP). ASP's reference state considers the difference in exposure of protein atom types towards ligand binding sites. We show that this new potential predicts binding affinities with an accuracy similar to that of Goldscore and Chemscore. We investigate the influence of the choice of reference state by constructing two additional statistical potentials that differ from ASP only in this respect. The reference states in these two potentials are defined along the lines of Drugscore and PMF. In docking experiments, the potential using the new reference state proposed for ASP gives better success rates than when these literature reference states were used; a success rate similar to the established scoring functions Goldscore and Chemscore is achieved with ASP. This is the case both for a large, general validation set of protein–ligand structures and for small test sets of actives against four pharmaceutically relevant targets. Virtual screening experiments for these targets show less discrimination between the different reference states in terms of enrichment. In addition, we describe how statistical potentials can be used in the construction of targeted scoring functions. Examples are given for cdk2, using four different targeted scoring functions, biased towards increasingly large target‐specific databases. Using these targeted scoring functions, docking success rates as well as enrichments are significantly better than for the general ASP scoring function. Results improve with the number of structures used in the construction of the target scoring functions, thus illustrating that these targeted ASP potentials can be continuously improved as new structural data become available. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure
Authors: Garg Aarti , Kaur Harpreet , Raghava G.P.S. 
Published: August 2005

AbstractThe present study is an attempt to develop a neural network‐based method for predicting the real value of solvent accessibility from the sequence using evolutionary information in the form of multiple sequence alignment. In this method, two feed‐forward networks with a single hidden layer have been trained with standard back‐propagation as a learning algorithm. The Pearson's correlation coefficient increases from 0.53 to 0.63, and mean absolute error decreases from 18.2 to 16% when multiple‐sequence alignment obtained from PSI‐BLAST is used as input instead of a single sequence. The performance of the method further improves from a correlation coefficient of 0.63 to 0.67 when secondary structure information predicted by PSIPRED is incorporated in the prediction. The final network yields a mean absolute error value of 15.2% between the experimental and predicted values, when tested on two different nonhomologous and nonredundant datasets of varying sizes. The method consists of two steps: (1) in the first step, a sequence‐to‐structure network is trained with the multiple alignment profiles in the form of PSI‐BLAST‐generated position‐specific scoring matrices, and (2) in the second step, the output obtained from the first network and PSIPRED‐predicted secondary structure information is used as an input to the second structure‐to‐structure network. Based on the present study, a server SARpred (http://www.imtech.res.in/raghava/sarpred/) has been developed that predicts the real value of solvent accessibility of residues for a given protein sequence. We have also evaluated the performance of SARpred on 47 proteins used in CASP6 and achieved a correlation coefficient of 0.68 and a MAE of 15.9% between predicted and observed values. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Assembly of the hexameric Escherichia coli arginine repressor investigated by nano‐electrospray ionization time‐of‐flight mass spectrometry
Authors: Šamalíková Mária , Carey Jannette , Grandori Rita 
Published: August 2005

AbstractThe arginine repressor (ArgR) from Escherichia coli regulates genes for L‐arginine metabolism and is a required recombination factor for colE1 plasmid replication. Both functions require binding of L‐arginine to the protein. In this work, nano‐electrospray ionization time‐of‐flight mass spectrometry (nano‐ESI‐TOFMS) is used to study conformational and oligomeric states of intact ArgR and its isolated structural domains. In agreement with X‐ray diffraction studies, it is shown that ArgR oligomerizes to form hexamers in both the presence and absence of L‐arginine, and the basic unit of oligomerization appears to be the trimer. Higher‐order assembly into dodecamers is also detected. The isolated C‐terminal domain is found to associate into trimers and hexamers whereas the N‐terminal domain is detected in its monomeric form. The observed species distributions suggest a role for the N‐terminal domain in hexamer stabilization. Copyright © 2005 John Wiley & Sons, Ltd.
Tandem mass spectrometric analysis of cyclophosphamide, ifosfamide and their metabolites
Authors: Liu Zhongfa , Chan Kenneth K. , Wang Jeffrey J. 
Published: August 2005

AbstractA detailed multi‐stage (MSn) fragmentation study of cyclophosphamide (CP), ifosfamide (IF) and their major metabolites, using an ion‐trap mass spectrometer and a Q‐TOF mass spectrometer, was performed with the aid of specifically deuterium‐labeled analogs. The analytes showed good responses in positive‐ion electrospray mass spectrometry as [MH]+ ions. Tandem mass spectra revealed a wealth of structurally specific ions, allowing characterization of the fragmentation pathways of these analytes. The major fragmentation pathways of the protonated CP and IF are elimination of ethylene from C5 and C6 of 1,3,2‐oxazaphosphorine‐2‐oxide via a McLafferty rearrangement, and cleavage of the PN bond. However, their activated 4‐OOH and 4‐OH metabolites primarily underwent hydrogen peroxide elimination and dehydration, respectively, followed by fragmentation pathways similar to those of CP and IF. These results should prove useful in structural elucidation of future analogs of CP and IF, and/or of their metabolites. Copyright © 2005 John Wiley & Sons, Ltd.
Neither sustainable nor development: reconsidering sustainability in development
Authors: Luke Timothy W. 
Published: August 2005

AbstractThis paper questions the rhetorical workings of ‘sustainable development’ as an ideological construct in contemporary global society. It suggests that this term actually is increasingly used as a label to place over modes of existence that are neither sustainable nor developmental. Yet, the rhetoric is also now a material culture of being that is created, carried and continued in the everyday practices of design, exchange and production. Copyright ©; 2005 John Wiley & Sons, Ltd and ERP Environment.
Tripartite climate reversal in Central Europe 5600–5300 years ago
Authors: Magny Michel , Leuzinger Urs , Bortenschlager Sigmar , Haas Jean Nicolas 
Published: August 2005

AbstractThe history of variations in water level of Lake Constance, as reconstructed from sediment and pollen analysis of a sediment sequence from the archaeological site of Arbon-Bleiche 3, shows an abrupt rise in lake level dendrochronologically dated to 5375 yr ago (5320 yr relative to AD 1950). This event, paralleled by the destruction of the Neolithic village by fire, provoked the abandonment of this prehistoric lake-shore location established in the former shallow bay of Arbon-Bleiche, and was the last of a series of three episodes of successively higher lake level, the first occurring at 5600–5500 cal yr B.P. The dendrochronologically dated rise event was synchronous with an abrupt increase in atmospheric14C. This supports the hypothesis of an abrupt climate change forced by varying solar activity. Moreover, the three successive episodes of higher lake level between 5600 and 5300 cal yr B.P. at Arbon-Bleiche 3 coincided with climatic cooling and/or changes in moisture conditions in various regions of both hemispheres. This period corresponds to the mid-Holocene climate transition (onset of the Neoglaciation) and suggests inter-hemispheric linkages for the climate variations recorded at Arbon-Bleiche 3. This mid-Holocene climate reversal may have resulted from complex interactions between changes in orbital forcing, ocean circulation and solar activity. Finally, despite different seasonal hydrological regimes, the similarities between lake-level records from Lake Constance and from Jurassian lakes over the mid-Holocene period point to time scale as a crucial factor in considering the possible impact of climate change on environments.
Identify the reality: re‐build, manage and lead
Authors: Rabey Gordon 
Published: August 2005

PurposeTo show that the skills of managing and leading are both essential for those holding in‐charge positions wishing to generate the optimum contribution of employee effort. Organisational success and continuity lie in identifying the reality, clarifying the purpose, providing the resources, and working with and trusting people to achieve it.Design/methodology/approachThe outcome of literature research, organisational consultations, and a recognition of how the compartmentalisation of activities can blur the forward vision.FindingsMarketplace activities, business uncertainties and staff movements make planned implementation difficult and the needs of the moment will always receive priority attention.Practical implicationsThe coordination of the total activities of the organisation through the use of the senior team, improved communication and the recognition of special effort.Originality/valueImplementation of the points espoused here should increase operational effectiveness – the outcomes will confirm it.
Whatever happened to leadership?
Authors: Kearsley Mike 
Published: August 2005

PurposeProposes to provide a summary of ideas with regard to leadership and management with the author's interpretation of these and some of the issues these raise.Design/methodology/approachDiscussion of the manager versus leader debate followed by a discussion of organisational leadership (as opposed to individual leadership) with specific reference to the kaizen (Japanese) approach.FindingsThat leadership programs have frequently failed to produce leaders and that groups tasked with leadership development often do not produce leaders either for their organisation or within their own group.Research limitations/implicationsNo real statistics or research evidence is provided. The conclusions are subjective and anecdotal.Practical implicationsIt should cause readers to consider their own organisational development and whether leaders can be created.Originality/valueThe recent views of the CIPD and Prof. John Adair are included.
Thermo‐mechanical model to predict the tribological behaviour of the composite PEEK‐CF30/steel pair in dry sliding using multiple regression analysis
Authors: Paulo Davim J. , Cardoso Rosária 
Published: August 2005

PurposePEEK is an abbreviation for polyetheretherketone, a high performance engineering semicrystalline thermoplastic. This material can operate at higher temperatures and has excellent friction and wear properties, which are optimised in the specially formulated tribological grade PEEK‐CF30. The purpose of this work was to develop a thermo‐mechanical model to predict the tribological behaviour of the composite PEEK‐CF30/steel pair, in dry sliding, related to friction and wear with the pv factor, the temperature and the sliding distance, using multiple regression analysis (MRA).Design/methodology/approachThis paper presents a new thermo‐mechanical model to predict the tribological behaviour of the composite PEEK‐CF30/steel pair, in dry sliding, using MRA. A plan of experiments was performed on a pin‐on‐disc machine PLINT TE67HT®.FindingsThe objective was to establish a thermo‐mechanical model to predict the PEEK‐CF30 behaviour related to friction and wear with the pv factor (product of apparent pressure of contact and sliding velocity), the temperature and the sliding distance. This model was obtained by multiple linear regression. Finally, confirmation tests were performed to make a comparison between the obtained results from the mentioned model and the experimental results.Originality/valueThe novel element of this paper is the application of design experiments and MRA in tribological model behaviour in an advanced material – PEEK‐CF 30.
Research on experimentation of green cutting with water vapor as coolant and lubricant
Authors: Han Rongdi , Liu Junyan , Sun Yongfeng 
Published: August 2005

PurposeNowadays, green cutting has become the focus because of its ecological problem and the necessary environment protection, so that the research on experimentation of green cutting with water vapor as coolant and lubricant is studied because water vapor has many benefits of cheapness, no pollution, no harm and no recycling and handling.Design/methodology/approachThe vapor generator and the vapor feed system are manufactured, the distribution of temperature and velocity of vapor jet flow are simulated by MATLAB program, and under the conditions of compress air, oil water emulsion, water vapor as coolant and lubricant and dry cutting, respectively, the turning experimentation of comparison which the tool is YT15, and the working material is steel 45.FindingsWater vapor, as coolant and lubricant, the cutting force is reduced, respectively about 30‐40, 20‐30 and 10‐15 percent by comparing to dry cutting, compressed air and oil water emulsion. The cutting temperature is, respectively about 30, 40 and 50 percent with the other conditions of dry cutting, compressed air and oil water emulsion. The friction coefficient and the chip deformation coefficient are correspondingly decreased and the surface roughness value has been diminished too. Through analysis of the experimental results, water vapor as coolant and lubricant possesses better lubricating action because of the excellent penetration performance and the low lubrication layer shearing strength of water vapor.Originality/valueWater vapor as coolant and lubricant provides a novel method for realizing no contamination green cutting.
Two million dollars times three
Authors: Woodsworth Anne 
Published: August 2005

PurposeTo address the issue of using grant funding in the US public libraries. With reduced funding as in most public libraries, the three New York City library systems have partnered with the Urban Library Council (ULC), funded by The Wallace Foundation, to provide additional funds from these alternative sources of income.Design/methodology/approachExplores the current programs and services offered at Brooklyn Public Library (BPL) under the grant‐funded sources. In using the funds, this project gave the library a chance to directly connect its goals with the new funds, as well as meet new capacity‐building goals to set the library in new directions.FindingsThe new funding resulted in new staff, retooling positions and activities, task forces and committee work to give buy‐in from different interested parties, and results included expanded services and programs.Originality/valueBeyond evaluating the need for the funding at this system, much success can be found in the city‐wide collaboration found in this project with all three systems and the ULC working together on this project. These Tri‐Li (three library system) working groups are just one of the many valuable elements of reading this case.
Who's your donor?
Authors: Griffin Gregory J. 
Published: August 2005

PurposeTo show how the use of a database of potential donors may increase the success of fund‐raising activities.Design/methodology/approachExplains how a database was used to collect information on potential donors. Each donor was given a value reflecting the strength of their connection to the library. These rankings were based on past gifts, areas of interest, and career, to name a few.FindingsBy using a database to collect, maintain, and monitor fund‐raising activities at the Syracuse University Library, the library has been able to collaborate with other university units and has achieved more visibility and success in development activities.Originality/valueThis study suggests a practical model that could be adopted by other libraries in similar institutions. Early results from the Syracuse University Library experience have been positive, and the library is now positioned as an important partner in campus fund‐raising activities.
Preservation and metadata
Authors: Maxymuk John 
Published: August 2005

PurposeTo outline the various metadata schemes and digital initiatives undertaken by the library community to preserve material in digital formats.Design/methodology/approachSurveys a number of library metadata initiatives and digital repositories to illustrate that, even in the ever‐changing technological world, preservation is essential.FindingsDigital technology changes at an ever‐increasing rate, which makes it difficult to preserve digital information. Nonetheless, if information digitally created today is to be useful in the future, it is important to save it in many ways, and migrate it to modern formats when possible.Originality/valueThis review reminds us that preservation is key if we are to ensure that information created now is still accessible in the future.
Gran Centre Granollers – “city, culture and commerce”
Authors: Andres Coca‐Stefaniak J. , Parker Cathy , Barbany Amadeu , Garrell Xavier , Segovia Enric 
Published: August 2005

PurposeTown centre management (TCM) schemes in Spain have generally evolved primarily from a retail perspective, led by small and medium sized (SME) retailers. However, their development has often focused on business goals (e.g. profit, increase in footfall, etc). In doing so, they have often overlooked the very social issues that have embedded retail historically in the socio‐economic matrix of our towns and cities. This paper, adopting a case‐study approach, seeks to re‐address this imbalance by exploring some of the key success factors of Gran Centre Granollers (GCG) – one of Spain's most advanced retailer‐led TCM schemes located in Granollers (near Barcelona).Design/methodology/approachThis paper, adopting a case‐study approach, explores some of the key success factors ofGCC..FindingsGCG's visionary motto of “city, culture and commerce” and its inclusive approach to the management of the area's stakeholders have captured the imagination of the town's independent retailers (75 per cent of them are members of the scheme). It has also proved pivotal in engaging the town's residents with the scheme's vision, purpose and ethical values. This is reflected in the success of their customer loyalty credit card initiative and the steady growth of the scheme's membership from ten to three hundred businesses in the last ten years.Originality/valueThis case study should be of interest to town centre managers, SME retailers, researchers in the social sciences and students of urban regeneration and retail management.
Judging the quality of internet‐based health information
Authors: Childs Sue 
Published: August 2005

PurposeTo overview the topic of the quality assessment and quality control of health information on the internet, particularly information targeted at patients, carers and health consumers.Design/methodology/approachThe context and background of the issue are explained. A range of key quality initiatives is described. The debates on the topic are presented. A health consumer tool produced by the author is described. Items from the literature are used to support the arguments presented.FindingsA range of quality initiatives exists, but there is neither an internationally agreed set of criteria nor a quality assessment tool. Little evidence exists to demonstrate that the criteria are correlated with good quality web sites and that the quality assessment tools are valid.Research limitations/implicationsResearch is needed: to identify the positive or negative effects of the use of health information from the internet on health outcomes: to understand how health consumers use the internet and choose information sources and how this behaviour matches with existing quality initiatives; to explore how criteria correlate with good quality health sites.Practical implicationsThis paper is a useful overview of this topic for library and information professionals in both the health and non‐health fields.Originality/valueThis paper raises awareness of this topic with library and information professionals interested in performance measurement. Hopefully it will stimulate research activity on this topic from this professional group.
A coordination framework for supply chain inventory alignment
Authors: Piplani Rajesh , Fu Yonghui 
Published: August 2005

PurposeA traditional supply chain, all too often, is a sequence of weakly connected activities both within and outside the organization and leads to many misalignments. Tackling this inherent lack of coordination is a major value creation opportunity for supply chain managers. This paper aims to present a coordination framework, called ASCEND, to align the inventory decisions in decentralized supply chains.Design/methodology/approachThe framework rests on three pillars – multi‐agent technology, coordination theory, and optimization technology. Inventory alignment is transformed into a decentralized constraint satisfaction optimization problem, which is then solved using a genetic algorithm‐based coordination process. The guiding principle of this framework is the establishment of a proper incentive alignment mechanism through cost‐sharing and service level contracts, taking into account the associated dependencies.FindingsThe results of the pilot study indicate that the coordination framework reduces the supply chain inventory‐holding cost, compared with the “as‐is” scenario. Interestingly, the results also indicate that not all the supply chain partners will experience lower inventory costs in the absence of a proper incentive alignment mechanism. Only through cost sharing and service level contracts can the value of coordination be realized by each partner in a supply chain network!Practical implicationsThe coordination approach is applied to a pilot supply chain. The results of the case study lead to 10.4 percent (average) reduction in supply chain inventory‐holding costs, validating the efficacy of the coordination framework.Originality/valueThis research has resulted in the development of a supply chain coordination framework, which requires the establishment of a proper incentive alignment mechanism, based on cost‐sharing and service level contracts, and taking into account the associated dependencies.