bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thioredoxin and peptide methionine sulfoxide reductase: Convergence of similar structure and function in distinct structural folds
Authors: Gladyshev Vadim N. 
Published: August 2002

AbstractThioredoxin (Trx) and peptide methionine sulfoxide reductase (PMSR) are small thiol oxidoreductases implicated in antioxidant defense and redox regulation of cellular processes. Here we show that the structures of Trx and PMSR exhibit resemblance in their αβ core regions and that the active site cysteines in two proteins occupy equivalent positions downstream of a central β‐strand and at the N‐terminus of an α‐helix. Moreover, we identified a PMSR subfamily that contains an active site CxxC motif (two cysteines separated by two other amino acids) positioned similarly to the catalytic redox active CxxC motif in Trx. However, Trx and PMSR are characterized by distinct ancient folds that differ in both orientation of secondary structures and their patterns. Trx is a member of the Trx‐fold superfamily, whereas PMSR has a unique fold not found in other proteins. The data suggest that similar structures and functions of Trx and PMSR were acquired independently during evolution and point to a general strategy of identifying new redox regulatory proteins. Proteins 2002;46:149–152. © 2001 Wiley‐Liss, Inc.
Threading with chemostructural restrictions method for predicting fold and functionally significant residues: Application to dipeptidylpeptidase IV (DPP‐IV)
Authors: Reva Boris , Finkelstein Alexei , Topiol Sid 
Published: August 2002

AbstractWe present a new method for more accurate modeling of protein structure, called threading with chemostructural restrictions. This method addresses those cases in which a target sequence has only remote homologues of known structure for which sequence comparison methods cannot provide accurate alignments. Although remote homologues cannot provide an accurate model for the whole chain, they can be used in constructing practically useful models for the most conserved—and often the most interesting—part of the structure. For many proteins of interest, one can suggest certain chemostructural patterns for the native structure based on the available information on the structural superfamily of the protein, the type of activity, the sequence location of the functionally significant residues, and other factors. We use such patterns to restrict (1) a number of possible templates, and (2) a number of allowed chain conformations on a template. The latter restrictions are imposed in the form of additional template potentials (including terms acting as sequence anchors) that act on certain residues. This approach is tested on remote homologues of α/β‐hydrolases that have significant structural similarity in the positions of their catalytic triads. The study shows that, in spite of significant deviations between the model and the native structures, the surroundings of the catalytic triad (positions of Cα atoms of 20–30 nearby residues) can be reproduced with accuracy of 2–3 Å. We then apply the approach to predict the structure of dipeptidylpeptidase IV (DPP‐IV). Using experimentally available data identifying the catalytic triad residues of DPP‐IV (David et al., J Biol Chem 1993;268:17247–17252); we predict a model structure of the catalytic domain of DPP‐IV based on the 3D fold of prolyl oligopeptidase (Fulop et al., Cell 1998;94:161–170) and use this structure for modeling the interaction of DPP‐IV with inhibitor. Proteins 2002;47:180–193. © 2002 Wiley‐Liss, Inc.
Automated multiple structure alignment and detection of a common substructural motif
Authors: Leibowitz Nathaniel , Fligelman Zipora Y. , Nussinov Ruth , Wolfson Haim J. 
Published: August 2002

AbstractWhile a number of approaches have been geared toward multiple sequence alignments, to date there have been very few approaches to multiple structure alignment and detection of a recurring substructural motif. Among these, none performs both multiple structure comparison and motif detection simultaneously. Further, none considers all structures at the same time, rather than initiating from pairwise molecular comparisons. We present such a multiple structural alignment algorithm. Given an ensemble of protein structures, the algorithm automatically finds the largest common substructure (core) of Cαatoms that appears in all the molecules in the ensemble. The detection of the core and the structural alignment are done simultaneously. Additional structural alignments also are obtained and are ranked by the sizes of the substructural motifs, which are present in the entire ensemble. The method is based on the geometric hashing paradigm. As in our previous structural comparison algorithms, it compares the structures in an amino acid sequence order‐independent way, and hence the resulting alignment is unaffected by insertions, deletions and protein chain directionality. As such, it can be applied to protein surfaces, protein–protein interfaces and protein cores to find the optimally, and suboptimally spatially recurring substructural motifs. There is no predefinition of the motif. We describe the algorithm, demonstrating its efficiency. In particular, we present a range of results for several protein ensembles, with different folds and belonging to the same, or to different, families. Since the algorithm treats molecules as collections of points in three‐dimensional space, it can also be applied to other molecules, such as RNA, or drugs. Proteins 2001;43:235–245. © 2001 Wiley‐Liss, Inc.
A refined accuracy index to evaluate algorithms of protein secondary structure prediction
Authors: Zhang Chun‐Ting , Zhang Ren 
Published: August 2002

AbstractNowadays even a 1% increase of the accuracy for the secondary structure prediction is considered remarkable progress. In this case, we have to consider the reasonableness of the accuracy index Q3, which is used widely. A refined accuracy index, called Q8, is proposed to evaluate algorithms of secondary structure prediction. It is shown that Q8 is superior to the widely used index Q3 in that the former carries more information of the predictive accuracy matrix than does the latter. Therefore, algorithms are evaluated more objectively by Q8 than Q3. Based on 396 nonhomologous proteins, five currently available algorithms of secondary structure prediction were evaluated and compared using the new index Q8. Of the five algorithms, PHD turned out to be the unique algorithm, with Q8 accuracy better than 70%. It is suggested that Q3 should be replaced by Q8 in evaluating secondary structure prediction in future studies. Proteins 2001;43:520–522. © 2001 Wiley‐Liss, Inc.
Molecular mapping of thrombin‐receptor interactions
Authors: Ayala Youhna M. , Cantwell Angelene M. , Rose Thierry , Bush Leslie A. , Arosio Daniele , Di Cera Enrico 
Published: August 2002

AbstractIn addition to its procoagulant and anticoagulant roles in the blood coagulation cascade, thrombin works as a signaling molecule when it interacts with the G‐protein coupled receptors PAR1, PAR3, and PAR4. We have mapped the thrombin epitopes responsible for these interactions using enzymatic assays and Ala scanning mutagenesis. The epitopes overlap considerably, and are almost identical to those of fibrinogen and fibrin, but a few unanticipated differences are uncovered that help explain the higher (90‐fold) specificity of PAR1 relative to PAR3 and PAR4. The most critical residues for the interaction with the PARs are located around the active site where mutations affect recognition in the order PAR4 > PAR3 > PAR1. Other important residues for PAR binding cluster in a small area of exosite I where mutations affect recognition in the order PAR1 > PAR3 > PAR4. Owing to this hierarchy of effects, the mutation W215A selectively compromises PAR4 cleavage, whereas the mutation R67A abrogates the higher specificity of PAR1 relative to PAR3 and PAR4. 3D models of thrombin complexed with PAR1, PAR3, and PAR4 are constructed and account for the perturbations documented by the mutagenesis studies. Proteins 2001;45:107–116. © 2001 Wiley‐Liss, Inc.
A new method for assessing foliar uptake of fungicides using Congo Red as a tracer
Authors: Yu Ju‐Hyun , Lim He‐Kyoung , Choi Gyung‐Ja , Cho Kwang‐Yun , Kim Jeong‐Han 
Published: August 2002

AbstractIn order to develop a new method for measuring foliar uptake of fungicides, Congo Red was selected as a tracer, and optimum procedures were established for washing, extracting and analyzing it and fungicides from leaf surfaces. Congo Red, a water‐soluble dye, was not absorbed into cucumber or rice leaf, even in the presence of various surfactants, and was completely washable from leaf surfaces by aqueous acetonitrile solutions. Congo Red and fungicides in washings were quantified to calculate the amount of foliar uptake of the latter, by comparing the ratio to Congo Red. The optimum concentration of Congo Red in a formulation should be established in order to minimize its influence on fungicide uptake. Although Congo Red has proved to be useful with a conventional droplet application method, it will give more realistic and practical results with the spraying method used in the present study.© 2001 Society of Chemical Industry
Identification of a 2,6‐dichloroisonicotinic‐acid‐sensitive protein kinase from tobacco by affinity chromatography on benzothiadiazole‐sepharose and NIM‐metal chelate adsorbent
Authors: Pillonel Christian 
Published: August 2002

AbstractIn the search for the target site of inducers of systemic acquired resistance (SAR), a BTH‐binding protein kinase (BBPK) has been identified from tobacco by affinity chromatography on benzothiadiazole‐sepharose (CGA 324041‐sepharose) and NIM‐metal chelate affinity resin. The substrate selectivity of the isolated enzyme (phosphorylation of histone type III‐S, IκBα,IkBα S32A/S36A and NIM1) suggested a possible BBPK‐mediated regulation of NIM1 in tobacco. The measurement of the effect of different SAR‐inducers showed an inhibition of BBPK by 2,6‐dichloroisonicotinic acid (INA) and, to a lower extent, by benzothiadiazoles and salicylic acid. Comparison between BBPK cell‐free inhibition and in vivo PR‐1 induction revealed that BBPK could be the target site of INA.© 2001 Society of Chemical Industry
Evaluation of propargyl bromide for control of barnyardgrass and Fusarium oxysporum in three soils
Authors: Ma Qingli , Gan Jianying , Becker J Ole , Papiernik Sharon K , Yates Scott R 
Published: August 2002

AbstractWith the scheduled phasing out of methyl bromide, there is an urgent need for alternatives. We evaluated the efficacy of propargyl bromide as a potential replacement for methyl bromide for the control of barnyardgrass (Echinochloa crus‐galli) and Fusarium oxysporum in an Arlington sandy loam, a Carsitas loamy sand and a Florida muck soil. Soil was mixed with barnyardgrass seeds or F oxysporum colonized on millet seeds, and treated with propargyl bromide at a range of concentrations. The mortality of the fungi and weed seeds was determined after 24 h of exposure at 30 °C. The concentrations required to inhibit 50% barnyard seed germination (LC50) were 2.8, 2.4 and 48.5 µg g−1 in the sandy loam, loamy sand and muck soil, respectively. In contrast, the LC50 values for F oxysporum were 11.2, 10.8 and 182.1 µg g−1 in the sandy loam, loamy sand and muck soil, respectively. The low efficacy of propargyl bromide in the muck soil was a result of the rapid degradation and high adsorption of the compound in the soil. The degradation half‐life (t1/2) was only 7 h in the muck soil at an initial concentration of 6.8 µg g−1, compared to 60 and 67 h in the sandy loam and loamy sand, respectively. The adsorption coefficients (Kd) were 0.96, 0.87 and 5.6 cm3 g−1 in the sandy loam, loamy sand and muck soil, respectively. These results suggest that registration agencies should consider site‐specific properties in recommending application rates for propargyl bromide.© 2001 Society of Chemical Industry
Structure–function relationships in the tryptophan‐rich, antimicrobial peptide indolicidin
Authors: Staubitz Petra , Peschel Andreas , Nieuwenhuizen Willem F. , Otto Michael , Götz Friedrich , Jung Günther , Jack Ralph W. 
Published: August 2002

AbstractIndolicidin is a cationic 13 amino acid peptide amide produced in the granules of bovine neutrophils with the sequence H‐ILPWKWPWWPWRR‐NH2. Indolicidin is both antimicrobial and, to a lesser extent, haemolytic. In order to systematically investigate structure–function relationships, the solid‐phase synthesis of indolicidin and 48 distinct analogues are reported, as well as the characterization of their respective biological properties. Peptides synthesized and characterized include analogues with modified terminal functions, truncations from either terminus, an alanine scan to determine the role of each individual amino acid, specific amino acid exchanges of aromatic, charged and structural residues and several retro‐, inverso‐ and retroinverso‐analogues. Together, characterization of these analogues identifies specific residues involved in antimicrobial or haemolytic activity and suggests a core structure that may form a scaffold for the further development of peptidomimetic analogues of indolicidin. Copyright © 2001 European Peptide Society and John Wiley & Sons, Ltd.
Effects of Shilajit on the development of tolerance to morphine in mice
Authors: Tiwari P , Ramarao P , Ghosal S 
Published: August 2002

AbstractEffects of concomitant administration of Processed Shilajit (PS, 0.1 and 1 mg/kg, i.p.), in Swiss mice were evaluated on the development of tolerance to morphine induced analgesia in the hot plate test. Chronic administration of morphine (10 mg/kg, i.p., b.i.d.) to mice over a duration of 10 days resulted in the development of tolerance to the analgesic effect of morphine. Concomitant administration of PS with morphine, from day 6 to day 10, resulted in a significant inhibition of the development of tolerance to morphine (10 mg/kg, i.p.) induced analgesia. Processed Shilajit per se, in the doses used, did not elicit any significant analgesia in mice; nor did the chronic concomitant administration of Processed Shilajit alter the morphine‐induced analgesia. These findings with Processed Shilajit indicate its potential as a prospective modifier of analgesic tolerance to morphine. Copyright © 2001 John Wiley & Sons, Ltd.
Optimal portion control using variable cutter‐blade spacing in can‐filling
Authors: Omar F. , de Silva C. W. 
Published: August 2002

AbstractIn the present context, optimal portion control refers to the process of preparing can‐filling portions so that the deviation of the portion weight from a specified target weight is minimized. An approach has been developed for achieving this where a batch of objects is placed in a linearly overlapped optimal arrangement and then cut into portions using a series of parallel blades. The parameters of optimization are the arrangement order, orientation and degree of overlap of the objects. The approach has been demonstrated to produce impressive improvements in the application of fish canning. For this application, two approaches of optimal cutting are compared in the present paper. In one approach, the blade spacing is kept fixed and constant at a predetermined value. In the second approach, the blade spacing is varied for each portion after the objects are placed according to the optimal arrangement, where the target weight distribution is allowed to vary within a tolerance interval. The results presented in this paper indicate that the second approach produces a significantly higher percentage of acceptable portions than the first approach. What is presented are results from computer simulations, utilizing true data as measured from actual batches of fish. The paper demonstrates the potential benefit of the optimal portion control approach when applied in an industrial fish‐canning process. Copyright © 2001 John Wiley & Sons, Ltd.
Exploring the suitability of the European Foundation for Quality Management (EFQM) Excellence Model as a framework for delivering clinical governance in the UK National Health Service
Authors: Jackson Sue 
Published: August 2002

AbstractIn December 1997 the United Kingdom (UK) government publicized its vision for the National Health Service (NHS) to become the best health care system in the world. In line with this vision a number of consultative and directive documents were circulated, one of which was Clinical Governance: in the new NHS. This particular document provided insight into the principles and proposed framework for delivering clinical governance. However, the document suggested that health care organizations create mechanisms for delivering clinical governance which implied that the government had failed to recognize that suitable mechanisms were already available. The author suggests that one such suitable mechanism/framework is the EFQM Excellence Model. The article therefore examines the similarities of the principles behind clinical governance and the EFQM Excellence Model and recommends the latter as a suitable tool for ensuring that the country's people have the best health care system in the world. Copyright © 2001 John Wiley & Sons, Ltd.
Standard operating procedures for clinical research personnel—part 6
Authors: Bohaychuk Wendy , Ball Graham 
Published: August 2002

AbstractThis is the sixth in a series of articles containing proposals for wording and content of standard operating procedures (SOPs) for clinical research activities conducted by sponsors and Contract Research Organisations (CROs). The procedures include those required by the International Conference on Harmonisation (ICH), the Food and Drug Administration (FDA), many other guidelines and regulations, and ‘best practice’ observed by the authors. The model forms require modification for actual use. In this article, three SOPs for the management of investigator brochures including preparation (SOP 301), review, approval and amendment (SOP 302) and distribution (SOP 303) are addressed. A sample of the format and contents of an investigator brochure is also included. (The full text of all 101 SOPs is available from the authors.) Copyright © 2001 John Wiley & Sons, Ltd.
GCP auditors: hard to find—hard to develop—hard to keep: part III. Continuous education and further development
Authors: Hattemer‐Apostel Rita 
Published: August 2002

AbstractClinical research is a dynamic and constantly changing discipline. Continuous education of good clinical practice (GCP) auditors is required to guarantee consistent and dependable audit results during their careers. Ongoing training should strive to increase the auditor's capabilities and skills, even beyond GCP. This should not only maintain the quality assurance (QA) auditor in a position to conduct audits according to state‐of‐the‐art methodologies and regulations, but also promote her/his further career development. To be ‘fit for purpose’ does not only characterize processes meeting defined requirements, but also implies that QA auditors must be continuously trained (hence, ‘be fit’) to perform high‐quality audit services (hence, ‘the purpose’). Copyright © 2001 John Wiley & Sons, Ltd.
Standard operating procedures for clinical research personnel—Part 7
Authors: Bohaychuk Wendy , Ball Graham 
Published: August 2002

AbstractThis is the seventh in a series of articles containing proposals for wording and content of standard operating procedures (SOPs) for clinical research activities conducted by sponsors and Contract Research Organizations (CROs). The procedures include those required by the International Conference on Harmonization (ICH), the Food and Drug Administration (FDA), many other guidelines and regulations, and ‘best practice’ observed by the authors. The model forms require modification for actual use. In this article, SOPs are presented for the management of protocols and protocol amendments including preparation and format (SOPs 304 and 307), review, approval and amendment (SOPs 305 and 308) and distribution (SOPs 306 and 309). (The full text of all 101 SOPs is available from the authors.) Copyright © 2001 John Wiley & Sons, Ltd.
Use and limitations of checklists. Other strategies for audits and inspections
Authors: Seoane Pedro J. Gris 
Published: August 2002

AbstractChecklists are tools commonly used by quality assurance (QA) unit professionals in inspections and audits as they perform their customary tasks of verifying and checking compliance with various applicable standards. An analysis of the advantages and disadvantages of checklist use is discussed in this article. Excessive dependence on these auxiliary‐checking systems can cause certain problems, and in some cases their real usefulness is called into question. Alternative or complementary strategies are proposed in order to optimise the rational use of checklists. Copyright © 2001 John Wiley & Sons, Ltd.
Standard operating procedures for clinical research personnel ‐ Part 12
Authors: Bohaychuk Wendy , Ball Graham 
Published: August 2002

AbstractThis is the 12th in a series of articles containing proposals for wording and content of standard operating procedures (SOPs) for clinical research activities conducted by sponsors and Contract Research Organisations (CROs). The procedures include those required by the International Conference on Harmonisation (ICH), the Food and Drug Administration (FDA), many other guidelines and regulations, and 'best practice' observed by the authors. The model forms require modification for actual use. In this article, a SOP is presented for selection of clinical laboratories (SOP 327). (The full text of all 101 SOPs is available from the authors). Copyright © 2002 John Wiley & Sons, Ltd.
A forecast‐based monitoring methodology for process transitions
Authors: Nembhard Harriet Black , Kao Ming Shu 
Published: August 2002

AbstractNonconforming parts are often produced when a process moves from one level to another due to transition events. Control charting, when applied to a stable state process, is an effective monitoring tool to continuously check for process shifts or upsets. However, the presence of transition events can impede the normal performance of traditional control chart with increased false alarms. The presence of autocorrelation also requires modification to the control charting procedure. We present a methodology for characterizing the process transition which involves a tracking signal statistic, based on the forecast‐based exponentially weighted moving average (EWMA). This test will supplement the forecast‐based EWMA control charting as a means of detecting when the transition event is complete. Such a procedure facilitates smooth application of the appropriate control chart by knowing when the transition is over. The transition characterization methodology also carries benefits in cost and material savings. We use a color transition process in plastic extrusion to illustrate a transition event and demonstrate our proposed methodology. Simulation is employed to evaluate the performance of the methodology. Copyright © 2001 John Wiley & Sons, Ltd.