bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformation and dynamics of the three‐helix bundle UBA domain of p62 from experiment and simulation
Authors: Evans Clare‐Louise , Long Jed E. , Gallagher Thomas R. A. , Hirst Jonathan D. , Searle Mark S. 
Published: October 2007

AbstractThe ubiquitin associated domain of p62 is a small three‐helix bundle of ∼50 residues that mediates the recognition of polyubiquitin chains and ubiquitylated substrates. The solution structure of a 52 residue construct containing this domain has been characterized using heteronuclear nuclear magnetic resonance (NMR) methods. The resulting ensemble of NMR‐derived structures was used in molecular dynamics (MD) simulations to investigate the equilibrium conformation and dynamics of this domain. NOE and 15N relaxation data have been used to validate the structural ensemble produced by the MD simulations and show a good correlation for residues in regions of secondary structure. A similar approach was taken using an ensemble of structures from the MD simulations to calculate electronic circular dichroism (CD) and IR spectra from first principles with an encouraging correlation with the experimental CD and IR data. Proteins 2008. © 2007 Wiley‐Liss, Inc.
An asymmetric dimer of β‐lactoglobulin in a low humidity crystal form—Structural changes that accompany partial dehydration and protein action
Authors: Vijayalakshmi L. , Krishna R. , Sankaranarayanan R. , Vijayan M. 
Published: October 2007

AbstractDimeric lactoglobulin molecules exist in the open conformation at basic pH, whereas they exist in the closed conformation at acidic pH, after undergoing the Tanford transition around neutral pH. Orthorhombic crystals consisting of molecules in the open conformation, grown close to neutral pH, undergo a water‐mediated transformation when the relative humidity around the crystals is reduced. The two subunits in the dimer are related by a crystallographic twofold axis in the native crystals while the dimer is asymmetric in the low humidity form. Interestingly, one of the subunits in the dimer in the low humidity form is in an open conformation while the other is in a closed conformation. This is the first observation of such an asymmetric dimer. A hydrogen bond between the side chains of Gln35 and Tyr42 exists and the side chain of Glu89 is substantially buried in the closed subunit of the asymmetric unit, as in other structures with molecules in the closed conformation. However, the closure of the EF loop is not complete; its conformation can be described as half‐closed. A comparison of different crystal structures of β‐lactoglobulin indicates that the conformation of the loops in the molecule is substantially influenced by other factors such as crystal packing, the pH, and the composition of the medium, while the change in the conformation of the EF loop follows the Tanford transition. The mutual disposition of the two subunits in the low humidity form is halfway between those in the open and closed structures. The present work further demonstrates that structural changes that occur during partial dehydration could mimic those that occur during the action of proteins. Proteins 2008. © 2007 Wiley‐Liss, Inc.
QMEAN: A comprehensive scoring function for model quality assessment
Authors: Benkert Pascal , Tosatto Silvio C. E. , Schomburg Dietmar 
Published: October 2007

AbstractIn protein structure prediction, a considerable number of alternative models are usually produced from which subsequently the final model has to be selected. Thus, a scoring function for the identification of the best model within an ensemble of alternative models is a key component of most protein structure prediction pipelines. QMEAN, which stands for Qualitative Model Energy ANalysis, is a composite scoring function describing the major geometrical aspects of protein structures. Five different structural descriptors are used. The local geometry is analyzed by a new kind of torsion angle potential over three consecutive amino acids. A secondary structure‐specific distance‐dependent pairwise residue‐level potential is used to assess long‐range interactions. A solvation potential describes the burial status of the residues. Two simple terms describing the agreement of predicted and calculated secondary structure and solvent accessibility, respectively, are also included. A variety of different implementations are investigated and several approaches to combine and optimize them are discussed. QMEAN was tested on several standard decoy sets including a molecular dynamics simulation decoy set as well as on a comprehensive data set of totally 22,420 models from server predictions for the 95 targets of CASP7. In a comparison to five well‐established model quality assessment programs, QMEAN shows a statistically significant improvement over nearly all quality measures describing the ability of the scoring function to identify the native structure and to discriminate good from bad models. The three‐residue torsion angle potential turned out to be very effective in recognizing the native fold. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Local interactions in protein folding determined through an inverse folding model
Authors: Bastolla Ugo , Porto Markus , Ortíz Angel R. 
Published: October 2007

AbstractWe adopt a model of inverse folding in which folding stability results from the combination of the hydrophobic effect with local interactions responsible for secondary structure preferences. Site‐specific amino acid distributions can be calculated analytically for this model. We determine optimal parameters for the local interactions by fitting the complete inverse folding model to the site‐specific amino acid distributions found in the Protein Data Bank. This procedure reduces drastically the influence on the derived parameters of the preference of different secondary structures for buriedness, which affects local interaction parameters determined through the standard approach based on amino acid propensities. The quality of the fit is evaluated through the likelihood of the observed amino acid distributions given the model and the Bayesian Information Criterion, which indicate that the model with optimal local interaction parameters is strongly preferable to the model where local interaction parameters are determined through propensities. The optimal model yields a mean correlation coefficient r = 0.96 between observed and predicted amino acid distributions. The local interaction parameters are then tested in threading experiments, in combination with contact interactions, for their capacity to recognize the native structure and structures similar to the native against unrelated ones. In a challenging test, proteins structurally aligned with the Mammoth algorithm are scored with the effective free energy function. The native structure gets the highest stability score in 100% of the cases, a high recognition rate comparable to that achieved against easier decoys generated by gapless threading. We then examine proteins for which at least one highly similar template exists. In 61% of the cases, the structure with the highest stability score excluding the native belongs to the native fold, compared to 60% if we use local interaction parameters derived from the usual amino acid propensities and 52% if we use only contact interactions. A highly similar structure is present within the five best stability scores in 82%, 81%, and 76% of the cases, for local interactions determined through inverse folding, through propensity, and set to zero, respectively. These results indicate that local interactions improve substantially the performances of contact free energy functions in fold recognition, and that similar structures tend to get high stability scores, although they are often not high enough to discriminate them from unrelated structures. This work highlights the importance to apply more challenging tests, as the recognition of homologous structures, for testing stability scores for protein folding. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Sequence‐based protein domain boundary prediction using BP neural network with various property profiles
Authors: Ye Lei , Liu Ting , Wu Zhaohui , Zhou Ruhong 
Published: October 2007

AbstractGiven the rapid growth in the number of sequences without known structures, it is becoming increasingly important to not only accurately define protein structural domains but also predict domain boundaries from the amino‐acid sequence alone. In this article, we present a Back‐Propagation (BP) neural network method using 9 different sequence profiles, based on chemical, physical, and statistical properties, to predict the domain boundary of two‐domain proteins from one dimensional sequences. We have achieved an accuracy of 69% with a 10‐fold cross validation on a 238 nonredundant two‐domain protein dataset that we built based on a common set from both SCOP and CATH classifications. The method has also been applied to a larger third‐party dataset with 522 proteins; and an accuracy of 62% has been achieved. Our prediction results on both datasets are found to be significantly better than those from some other methods, such as DomCut and DGS on the same datasets, and also comparable to that from the PPRODO method, upon which the larger dataset was based. Our cross validation results are also noticeably better than previous ones from other BP neural network methods, probably because we have used more property descriptors with significantly more training nodes in our neural network. The integration with PPRODO method also indicates that the information obtained from our current approach is complementary to that available through multiple sequence alignments. Moreover, the relative importance of each property profile has been analyzed in detail. Proteins 2008. © 2007 Wiley‐Liss, Inc.
MALIDUP: A database of manually constructed structure alignments for duplicated domain pairs
Authors: Cheng Hua , Kim Bong‐Hyun , Grishin Nick V. 
Published: October 2007

AbstractWe describe MALIDUP (manual alignments of duplicated domains), a database of 241 pairwise structure alignments for homologous domains originated by internal duplication within the same polypeptide chain. Since duplicated domains within a protein frequently diverge in function and thus in sequence, this would be the first database of structurally similar homologs that is not strongly biased by sequence or functional similarity. Our manual alignments in most cases agree with the automatic structural alignments generated by several commonly used programs. This carefully constructed database could be used in studies on protein evolution and as a reference for testing structure alignment programs. The database is available at http://prodata.swmed.edu/malidup. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Self‐assembly of the octapeptide lanreotide and lanreotide‐based derivatives: the role of the aromatic residues
Authors: Pandit Anjali , Fay Nicolas , Bordes Luc , Valéry Céline , Cherif‐Cheikh Roland , Robert Bruno , Artzner Franck , Paternostre MaÏté 
Published: October 2007

AbstractWe investigated the spectroscopic properties of the aromatic residues in a set of octapeptides with various self‐assembly properties. These octapeptides are based on lanreotide, a cyclic peptide analogue of somatostatin‐14 that spontaneously self‐assembles into very long and monodisperse hollow nanotubes. A previous study on these lanreotide‐based derivatives has shown that the disulfide bridge, the peptide hairpin conformation and the aromatic residues are involved in the self‐assembly process and that modification of these properties either decreases the self‐assembly propensity or modifies the molecular packing resulting in different self‐assembled architectures. In this study we probed the local environment of the aromatic residues, naphthyl‐alanine, tryptophan and tyrosine, by Raman and fluorescence spectroscopy, comparing nonassembled peptides at low concentrations with the self‐assembled ones at high concentrations. As expected, the spectroscopic characteristics of the aromatic residues were found to be sensitive to the peptide–peptide interactions. Among the most remarkable features we could record a very unusual Raman spectrum for the tyrosine of lanreotide in relation to its propensity to form H‐bonds within the assemblies. In Lanreotide nanotubes, and also in the supramolecular architectures formed by its derivatives, the tryptophan side chain is water‐exposed. Finally, the low fluorescence polarization of the peptide aggregates suggests that fluorescence energy transfer occurs within the nanotubes. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Thermoelectric effect in laser annealed printed nanocrystalline silicon layers
Authors: Lechner Robert , Wiggers Hartmut , Ebbers André , Steiger Jürgen , Brandt Martin S. , Stutzmann Martin 
Published: October 2007

AbstractNanocrystalline boron and phosphorus doped silicon particles were produced in a microwave reactor, collected, and dispersed in ethanol. Pulsed laser annealing of spin‐coated films of these particles resulted in p‐ and n‐type conductive layers on flexible substrates if a threshold laser energy density of 60 mJ/cm2 was exceeded. The thermopower of the laser sintered layers exhibits a distinct maximum at a doping concen‐ tration around 1019 cm–3 for both boron and phosphorus doping with an absolute value of the Seebeck coefficient of about 300 µV/K. Since the thermal conductivity of the layers is reduced by nearly the same factor compared to bulk crystalline silicon as the electrical conductivity, these results are promising for the application of such nanocrystalline layers in thin film thermoelectric devices. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
9. Sorting out pelvic inflammatory disease
Authors: von Knorring N. , Wilson Janet 
Published: October 2007

AbstractPelvic inflammatory disease is a major threat to the reproductive health of young women and has a large impact on healthcare resources. Immediate treatment is necessary to prevent long‐term complications such as tubal factor infertility and ectopic pregnancy. The authors emphasise the importance of a pragmatic approach to management. Copyright © 2007 Wiley Interface Ltd
Decomposition and nitrogen release from the foliage litter of fir (Abies sachalinensis) and oak (Quercus crispula) under different forest canopies in Hokkaido, Japan
Authors: Miyamoto Toshizumi , Hiura Tsutom 
Published: October 2007

AbstractWhen two tree species co‐occur, decomposition and nitrogen (N) release from the foliage litter depend on two factors: the forest floor conditions under each canopy type and the species composition of the litter. We conducted an experiment using fir and oak to answer several questions regarding decomposition beneath canopies of the two species and the effects of litter species composition on decomposition. We compared the rates of decomposition and N release from three different litters (fir needle, oak leaf, and a mixture of the two) in 1‐mm‐mesh litterbags on the forest floor under three different canopies (a 40‐year‐old fir plantation, large oak trees, and mixed fir and oak trees) in Hokkaido, Japan, over a 2‐year period. Beneath each of these canopy types, the litter decomposition rate and percentage of N remaining in the litterbags containing a mixture of fir and oak litter were not significantly different from the expected values calculated for litterbags containing litter from a single tree species. Oak leaf litter decomposed significantly faster than fir needle litter beneath each canopy type. The litter decomposition rate was significantly higher beneath the fir canopy than under the oak canopy, and was intermediate under the mixed canopy of fir and oak. No net N release, that is, a decrease in the total N compared to the original amount, was detected from fir litter under each canopy type or from oak leaf litter beneath the oak canopy. N increased over the original amount in the fir litter beneath the oak canopy and the mixed canopy of fir and oak, but N was released from the oak litter under the fir canopy and the mixed canopy of fir and oak. These results suggest that oak leaf litter blown onto fir forest floor enhances nutrient cycling, and this might be a positive effect of a mixed stand of conifer and broad‐leaved trees.
Adsorption of Anionic–Cationic Surfactant Mixtures on Metal oxide Surfaces
Authors: Upadhyaya A. , Acosta E. J. , Scamehorn J. F. , Sabatini D. A. 
Published: October 2007

AbstractThis research evaluates the adsorption of anionic and cationic surfactant mixtures on charged metal oxide surfaces (i.e., alumina and silica). For an anionic‐rich surfactant mixture below the CMC, the adsorption of anionic surfactant was found to substantially increase with the addition of low mole fractions of cationic surfactant. Two anionic surfactants (sodium dodecyl sulfate and sodium dihexyl sulfosuccinate) and two cationic surfactants (dodecyl pyridinium chloride and benzethonium chloride) were studied to evaluate the effect of surfactant tail branching. While cationic surfactants were observed to co‐adsorb with anionic surfactants onto positively charged surfaces, the plateau level of anionic surfactant adsorption (i.e., at or above the CMC) did not change significantly for anionic–cationic surfactant mixtures. At the same time, the adsorption of anionic surfactants onto alumina was dramatically reduced when present in cationic‐rich micelles and the adsorption of cationic surfactants on silica was substantially reduced in the presence of anionic‐rich micelles. This demonstrates that mixed micelle formation can effectively reduce the activity of the highly adsorbing surfactant and thus inhibit the adsorption of the surfactant, especially when the highly adsorbing surfactant is present at a low mole fraction in the mixed surfactant system. Thus surfactant adsorption can be either enhanced or inhibited using mixed anionic–cationic surfactant systems by varying the concentration and composition.
Why Work in Perioperative Nursing? Baby Boomers and Generation Xers Tell All
Authors: Thompson Julia A. 
Published: October 2007

ABSTRACTTHIS QUANTITATIVE AND QUALITATIVE study explored factors that influence nurses of different age groups to choose to work in and remain in the specialty of OR nursing, including the effect of work environment perceptions.BABY BOOMER NURSES (n = 130) and Generation X nurses (n = 117) were surveyed, and seven RNs from each group also participated in semistructured interviews.RESULTS SHOWED THAT NURSES of both age groups were more alike than different in the factors that influence them to choose and remain in OR nursing and in their perceptions of their work environment. Baby Boomers indicated a higher level of commitment to their jobs than did Generation Xers.
Verbal Medication Orders in the OR
Authors: Hendrickson Thomas 
Published: October 2007

ABSTRACTMEDICATION ERRORS are the fourth most commonly reported sentinel event, and changes in practice are needed to provide a safe environment for patients in the OR.EXISTING MEASURES for preventing medication errors in the OR have focused on labeling medication containers on and off the sterile field. Very little attention, however, has been given to the potential for errors caused by verbal orders in the OR or to developing processes to prevent such errors.SIMPLE SOLUTIONS for improving the safety of verbal medication orders include instituting a read‐back system in which verbal orders are written on a dry‐erase board and verified by the ordering physician, requesting clarification of questionable orders, and reducing distractions in the OR.
On Call: Alert or Unsafe? A Report of the AORN On‐Call Electronic Task Force
Authors: Kenyon Trudy A.G. , Gluesing Rebecca E. , White Karen Y. , Dunkel Wanda L. , Burlingame Byron L. 
Published: October 2007

ABSTRACTRESEARCH HAS LINKED health care providers' long work hours with patient care errors. Perioperative staff members often work extended hours because of long shifts and being on call.AORN's ON‐CALL ELECTRONIC TASK FORCE conducted a survey of nurses to determine their work load, call scheduling, and experiences related to fatigue. Of the 1,013 respondents, 67.7% said they had experienced effects of sleep deprivation.A FOLLOW‐UP SURVEY revealed that few call programs are in compliance with AORN's recommended practices. Compliant call programs are detailed for adaptation in other perioperative settings.
Translating Research on Venous Thromboembolism into Practice
Authors: Cantrell Shirley W. , Ward Karen S. , Van Wicklin Sharon A. 
Published: October 2007

ABSTRACTEVIDENCE‐BASED NURSING PRACTICE incorporates the best research available with clinical expertise. It can be difficult, however, for nurses to integrate use of evidence into their everyday work.THIS ARTICLE PROVIDES an example of using research findings to implement best nursing practice for patients at risk for venous thromboembolism (VTE). Remaining current on methods to prevent and treat VTE is essential for nurses throughout the hospital but is especially important in the perioperative environment.NURSES CAN USE THIS EXAMPLE as a basis for establishing evidence‐based practice in other patient care situations.
Knee Joint Preservation With Autologous Cartilage Implantation
Authors: Nagle Judith A. 
Published: October 2007

ABSTRACTDAMAGE TO THE BODY'S JOINT CARTILAGE is becoming a disabling problem for Americans as they live longer and remain active.TRADITIONALLY, ARTICULAR DAMAGE has been treated with arthroscopic debridement and microfracture, abrasion arthroplasty, and osteochondral autograft. Orthopedic surgeons now can offer patients a new option: autologous cartilage implantation (ACI), in which cultured autologous cartilage cells are used to repair and promote growth in cartilage defects.USE OF ACI PRESERVES the articular surfaces of the knee in patients with early onset osteoarthritis, decreases pain, maintains patients' quality of life, and delays possible total joint replacement.
Antecedents and consequences of social capital on buyer performance improvement
Authors: Lawson Benn , Tyler Beverly B. , Cousins Paul D. 
Published: October 2007

AbstractThe ability to leverage social capital within strategic buyer–supplier relationships is increasingly cited as a key driver of value creation. Despite the importance of strategic partnerships, the process by which social capital accumulates within buyer–supplier relationships and contributes to buyer performance improvements is not well understood. Drawing on social capital theory, we develop a model linking positive relational capital, and its antecedents, supplier integration and supplier closeness, to buyer performance improvements. Further, we hypothesize that structural capital, as reflected in managerial communication and technical exchanges, is also positively related to buyer performance improvements. Using data provided by 111 procurement executives from the United Kingdom, we find support for our hypotheses. The study extends the supply chain management and social capital literature and suggests important implications for both research and practice.