bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spectroscopic investigations on polypropylene‐carbon nanofiber composites. I. Raman and electron spin resonance spectroscopy
Authors: Chipara Mircea , Villarreal John R. , Chipara Magdalena Dorina , Lozano Karen , Chipara Alin Cristian , Sellmyer David J. 
Published: July 2009

AbstractIsotactic polypropylene‐vapor grown carbon nanofiber composites containing various fractions of carbon nanofibers, ranging from 0 to 20 wt %, have been prepared. Raman spectroscopy was used to analyze the effect of the dispersion of carbon nanofibers within polypropylene and the interactions between carbon nanofibers and macromolecular chains. The as‐recorded Raman spectra have been successfully fitted by a linear convolution of Lorentzian lines. Changes of the Raman lines parameters (position, intensity, width, and area) of polypropylene and carbon nanofibers were analyzed in detail. The Raman spectra of the polymeric matrix—at low concentrations of nanofibers—show important modifications that indicate strong interactions between carbon nanofibers and the polymeric matrix reflecting by vibrational dephasing of macromolecular chains. The Raman spectrum of carbon nanofibers is sensitive to the loading with carbon nanofibers, showing changes of the resonance frequencies, amplitudes, and width for both D‐ and G‐bands. Raman data reveals the increase of the disorder, as the concentration of carbon nanofibers is increased. The presence of the typical ESR line assigned to conducting electrons delocalized over carbon nanofibers is confirmed and the presence of a spurious magnetic line due to catalyst's residues is reported. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 1644–1652, 2009
Molecular weight dependence of fiber structure development in the laser drawing of poly(ethylene terephthalate) fibers
Authors: Kim Kyoung Hou , Yamaguchi Takayoshi , Ohkoshi Yutaka , Gotoh Yasuo , Nagura Masanobu , Urakawa Hiroshi , Kotera Masaru , Kikutani Takeshi 
Published: July 2009

AbstractThe effect of molecular weight on fiber structure development during the continuous neck‐drawing of the amorphous poly(ethylene terephthalate) (PET) fiber was investigated by fiber temperature measurements and online WAXD analysis. The fiber temperature was also simulated using the energy balance equation. The simulated temperature increased differently with molecular weight immediately after the neck point, while the measured temperature showed no difference. The difference in the simulated temperature was caused by the potential energy increase with increasing molecular weight, which would result in a retardation effect in the initial stage of fiber structure development. Online X‐ray measurements were carried out with a time resolution of 0.5 ± 0.06 ms. A two‐dimensionally ordered mesophase was formed within 1 ms after the neck point and developed into a microfibrillar structure. The time required for the disappearance of the two‐dimensionally ordered structure increased with increasing molecular weight, leading to a retardation effect. No molecular weight dependence was observed in the rate of transformation from the two‐dimensionally ordered structure to the PET crystal. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 1653–1665, 2009
Study of Nanoparticles Formation in a Pulsed Magnetron Discharge in Acetylene
Authors: De Vriendt Valérie , Maseri Fabrizio , Nonet Aurélien , Lucas Stéphane 
Published: July 2009

AbstractThe aim of this work is to study in a pulsed magnetron discharge of acetylene at 10−1 Torr, the influence of tOFF parameter on roughness and morphology of films deposited on silicon substrates. By using a low power discharge (long tOFF and short tON for a given power), a coating with unique morphology is deposited. This film is formed of nanoparticles and particular agglomerates called ‘flowers’ of micrometric size. To the best of our knowledge, it's the first time that such ‘flowers’ structures have been observed for a pulsed plasma polymerization of acetylene. According to the obtained results in mass spectrometry of plasma, nanoparticles and ‘flowers’ are probably formed in gas phase. A growth mechanism in several steps is proposed.
PO4046‐Hard Coatings with High Film Thickness Prepared by PVD
Authors: Zimmer Otmar , Kaulfuß Frank 
Published: July 2009

AbstractClassical hard coatings such as nitrides, oxides, or carbon coatings are normally used in a thickness range of under 10 µm. The preparation of such coatings can properly be handled in the industry and their coating properties can be well adjusted. Such coatings are used for wear resistant coatings of tools and components. For example, specific cutting applications are only possible by using a high performance hard coating. The preparation of thicker coatings is a demanding task, among others, for the following reasons. Most of the coating materials have a high level of intrinsic stress. At elevated coating thicknesses, the coatings tend to form cracks or to delaminate. Also an inhomogeneous film structure can be observed in many cases. Furthermore, the preparation of thicker films by PVD is a very time‐consuming operation. Nevertheless, thicker films are very interesting for many applications. One can, for example, achieve a remarkable longer lifetime of coated components. Another possibility is the mechanical post‐treatment of a coated part to sharpen a coated cutting edge or to create a special geometry. Precondition is a thick coating without growth defects and sufficient mechanical properties such as hardness, toughness, and temperature stability. This paper contributes to clarifying the problem and to discuss the possibilities to face the task.
Properties of (Ti,Al,Si)N coatings for high demanding metal cutting applications deposited by HPPMS in an industrial coating unit
Authors: Bobzin Kirsten , Bagcivan Nazlim , Immich Philipp , Bolz Stephan , Fuß Hans Gerd , Cremer Rainer 
Published: July 2009

AbstractHard and smooth coatings with high oxidation resistance and thermal stability are used for economical machining. In this regard, nc‐(Ti,Al)N/a‐Si3N4 films were sputtered on tungsten carbide cutting inserts and WC/Co samples by using an industrial CC800/9 high power pulse magnetron sputtering (HPPMS) coating unit. Coating composition and mechanical properties were investigated by scanning electron microscopy (EDS) and nano‐indentation. Hardness was about 36 GPa for a silicon content of about 9.6 at%. Optical emission spectroscopy (OES) was done to detect the ionization fraction of deposition species and to compare it to direct current (dc). Deposition rate of the HPPMS coatings was 1.6 times higher on areas positioned orthogonal to the target compared to dc sputtered coatings. Finally cutting performance was compared to a state‐of‐the‐art coating in turning HSS (high speed steel) under severe conditions. After the cutting tests SEM pictures were taken at the flank side of the cutting inserts to detect the wear. Cutting results show enhanced cutting performance due to the application of the HPPMS‐technology resulting in denser structure, higher hardness, smoother surface and better thickness uniformity compared to dc.
Microstructural Characterization of In‐flight Particles in Plasma Spray Process
Authors: Tekmen Cagri , Tsunekawa Yoshiki , Yoshida Masashi , Okumiya Masahiro 
Published: July 2009

AbstractOxidation behavior of in‐flight particle in plasma spray process significantly affects the coating properties and performance. Therefore, understanding the relationship between in‐flight particle characteristics and oxidation phenomena is essential to improve the coating properties. This paper presents the oxidation behavior of in‐flight aluminum particles and its relationship between in‐flight particle temperature and velocity. Aluminum powder was injected into the plasma flame at different spray conditions and collected at different stand‐off distances by using a specially designed equipment. It has been observed that in‐flight particle velocity is the main parameter that affects the oxidation of aluminum particles.
Combining crystallography and molecular dynamics: The case of Schistosoma mansoni phospholipid glutathione peroxidase
Authors: Dimastrogiovanni Daniela , Anselmi Massimiliano , Miele Adriana Erica , Boumis Giovanna , Petersson Linn , Angelucci Francesco , Nola Alfredo Di , Brunori Maurizio , Bellelli Andrea 
Published: July 2009

AbstractOxidative stress is a widespread challenge for living organisms, and especially so for parasitic ones, given the fact that their hosts can produce reactive oxygen species (ROS) as a mechanism of defense. Thus, long lived parasites, such as the flatworm Schistosomes, have evolved refined enzymatic systems capable of detoxifying ROS. Among these, glutathione peroxidases (Gpx) are a family of sulfur or selenium‐dependent isozymes sharing the ability to reduce peroxides using the reducing equivalents provided by glutathione or possibly small proteins such as thioredoxin. As for other frontline antioxidant enzymatic systems, Gpxs are localized in the tegument of the Schistosomes, the outermost defense layer. In this article, we present the first crystal structure at 1.0 and 1.7 Å resolution of two recombinant SmGpxs, carrying the active site mutations Sec43Cys and Sec43Ser, respectively. The structures confirm that this enzyme belongs to the monomeric class 4 (phospholipid hydroperoxide) Gpx. In the case of the Sec to Cys mutant, the catalytic Cys residue is oxidized to sulfonic acid. By combining static crystallography with molecular dynamics simulations, we obtained insight into the substrate binding sites and the conformational changes relevant to catalysis, proposing a role for the unusual reactivity of the catalytic residue. Proteins 2010. © 2009 Wiley‐Liss, Inc.
gCOMBINE: A graphical user interface to perform structure‐based comparative binding energy (COMBINE) analysis on a set of ligand‐receptor complexes
Authors: Gil‐Redondo Rubén , Klett Javier , Gago Federico , Morreale Antonio 
Published: July 2009

AbstractWe present gCOMBINE, a Java‐written graphical user interface (GUI) for performing comparative binding energy (COMBINE) analysis (Ortiz et al. J Med Chem 1995; 38:2681–2691) on a set of ligand‐receptor complexeswith the aim of deriving highly informative quantitative structure‐activity relationships. The essence of the method is to decompose the ligand‐receptor interaction energies into a series of terms, explore the origins of the variance within the set using Principal Component Analysis, and then assign weights to selected ligandresidue interactions using partial least squares analysis to correlate with the experimental activities or binding affinities. The GUI allows plenty of interactivity and provides multiple plots representing the energy descriptors entering the analysis, scores, loadings, experimental versus predicted regression lines, and the evolution of parameterssuch as r2 (correlation coefficient), q2 (cross‐validated r2), and prediction errors as the number of extracted latent variables increases. Other representative features include the implementation of a sigmoidal dielectric function for electrostatic energy calculations, alternative cross‐validation procedures (leave‐N‐out and random groups), drawing of confidence ellipses, and the possibility to carry out several additional tasks such as optional truncation of positive interaction energy values and generation of ready‐to‐use PDB files containing information related to the importance for activity of individual protein residues. This information can be displayed and color‐coded using a standard molecular graphics program such as PyMOL. It is expected that this user‐friendly tool will expand the applicability of the COMBINE analysis method and encourage more groups to use it in their drug design research programs. Proteins 2010. © 2009 Wiley‐Liss, Inc.
RigidFinder: A fast and sensitive method to detect rigid blocks in large macromolecular complexes
Authors: Abyzov Alexej , Bjornson Robert , Felipe Mihali , Gerstein Mark 
Published: July 2009

AbstractAdvances in structure determination have made possible the analysis of large macromolecular complexes (some with nearly 10,000 residues, such as GroEL). The large‐scale conformational changes associated with these complexes require new approaches. Historically, a crucial component of motion analysis has been the identification of moving rigid blocks from the comparison of different conformations. However, existing tools do not allow consistent block identification in very large structures. Here, we describe a novel method, RigidFinder, for such identification of rigid blocks from different conformations—across many scales, from large complexes to small loops. RigidFinder defines rigidity in terms of blocks, where inter‐residue distances are conserved across conformations. Distance conservation, unlike the averaged values (e.g., RMSD) used by many other methods, allows for sensitive identification of motions. A further distinguishing feature of our method, is that, it is capable of finding blocks made from nonconsecutive fragments of multiple polypeptide chains. In our implementation, we utilize an efficient quasi‐dynamic programming search algorithm that allows for real‐time application to very large structures. RigidFinder can be used at a dedicated web server (http://rigidfinder.molmovdb.org). The server also provides links to examples at various scales such as loop closure, domain motions, partial refolding, and subunit shifts. Moreover, here we describe the detailed application of RigidFinder to four large structures: Pyruvate Phosphate Dikinase, T7 RNA polymerase, RNA polymerase II, and GroEL. The results of the method are in excellent agreement with the expert‐described rigid blocks. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Conformational selection and collagenolysis in Type III collagen
Authors: Salsas‐Escat Ramon , Stultz Collin M. 
Published: July 2009

AbstractMatrix metalloproteases (MMPs) cleave native collagen at a single site despite the fact that collagen contains more than one scissile bond that can, in principle, be cleaved. For peptide bond hydrolysis to occur at one specific site, MMPs must (1) localize to a region near the unique scissile bond, (2) bind residues at the catalytic site that form the scissile bond, and (3) hydrolyze the corresponding peptide bond. Prior studies suggest that for some types of collagen, binding of noncatalytic MMP domains to amino acid sequences in the vicinity of the true cleavage site facilitates the localization of collagenases. In the present study, our goal was to determine whether binding to the catalytic site also plays a role in determining MMP specificity. To investigate this, we computed the conformational free energy landscape of Type III collagen at each potential cleavage site. The free energy profiles suggest that although all potential cleavage sites sample unfolded states at relatively low temperatures, the true cleavage site samples structures that are complementary to the catalytic site. By contrast, potential cleavage sites that are not cleaved sample states that are relatively incompatible with the MMP active site. Furthermore, our findings point to a specific role for arginine residues in modulating the structural stability of collagen near the collagenase cleavage site. These data imply that locally unfolded potential cleavage sites in Type III collagen sample distinct unfolded ensembles, and that the region about the true collagenase cleavage site samples states that are most complementary to the MMP active site. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Structural features of the Nostoc punctiforme debranching enzyme reveal the basis of its mechanism and substrate specificity
Authors: Dumbrepatil Arti Baban , Choi Ji‐Hye , Park Jong Tae , Kim Myo‐Jeong , Kim Tae Jip , Woo Eui‐Jeon , Park Kwan Hwa 
Published: July 2009

AbstractThe debranching enzyme Nostoc punctiforme debranching enzyme (NPDE) from the cyanobacterium Nostoc punctiforme (PCC73102) hydrolyzes the α‐1,6 glycosidic linkages of malto‐oligosaccharides. Despite its high homology to cyclodextrin/pullulan (CD/PUL)‐hydrolyzing enzymes from glycosyl hydrolase 13 family (GH‐13), NPDE exhibits a unique catalytic preference for longer malto‐oligosaccharides (>G8), performing hydrolysis without the transgylcosylation or CD‐hydrolyzing activities of other GH‐13 enzymes. To investigate the molecular basis for the property of NPDE, we determined the structure of NPDE at 2.37‐Å resolution. NPDE lacks the typical N‐terminal domain of other CD/PUL‐hydrolyzing enzymes and forms an elongated dimer in a head‐to‐head configuration. The unique orientation of residues 25–55 in NPDE yields an extended substrate binding groove from the catalytic center to the dimeric interface. The substrate binding groove with a lengthy cavity beyond the −1 subsite exhibits a suitable architecture for binding longer malto‐oligosaccharides (>G8). These structural results may provide a molecular basis for the substrate specificity and catalytic function of this cyanobacterial enzyme, distinguishing it from the classical neopullulanases and CD/PUL‐hydrolyzing enzymes. Proteins 2010. © 2009 Wiley‐Liss, Inc.
PIE—Efficient filters and coarse grained potentials for unbound protein–protein docking
Authors: Ravikant D. V. S. , Elber Ron 
Published: July 2009

AbstractIdentifying correct binding modes in a large set of models is an important step in protein–protein docking. We identified protein docking filter based on overlap area that significantly reduces the number of candidate structures that require detailed examination. We also developed potentials based on residue contacts and overlap areas using a comprehensive learning set of 640 two‐chain protein complexes with mathematical programming. Our potential showed substantially better recognition capacity compared to other publicly accessible protein docking potentials in discriminating between native and nonnative binding modes on a large test set of 84 complexes independent of our training set. We were able to rank a near‐native model on the top in 43 cases and within top 10 in 51 cases. We also report an atomic potential that ranks a near‐native model on the top in 46 cases and within top 10 in 58 cases. Our filter+potential is well suited for selecting a small set of models to be refined to atomic resolution. Proteins 2010. © 2009 Wiley‐Liss, Inc.
The other 90% of the protein: Assessment beyond the Cαs for CASP8 template‐based and high‐accuracy models
Authors: Keedy Daniel A. , Williams Christopher J. , Headd Jeffrey J. , Arendall W. Bryan , Chen Vincent B. , Kapral Gary J. , Gillespie Robert A. , Block Jeremy N. , Zemla Adam , Richardson David C. , Richardson Jane S. 
Published: July 2009

AbstractFor template‐based modeling in the CASP8 Critical Assessment of Techniques for Protein Structure Prediction, this work develops and applies six new full‐model metrics. They are designed to complement and add value to the traditional template‐based assessment by the global distance test (GDT) and related scores (based on multiple superpositions of Cα atoms between target structure and predictions labeled “Model 1”). The new metrics evaluate each predictor group on each target, using all atoms of their best model with above‐average GDT. Two metrics evaluate how “protein‐like” the predicted model is: the MolProbity score used for validating experimental structures, and a mainchain reality score using all‐atom steric clashes, bond length and angle outliers, and backbone dihedrals. Four other new metrics evaluate match of model to target for mainchain and sidechain hydrogen bonds, sidechain end positioning, and sidechain rotamers. Group‐average Z‐score across the six full‐model measures is averaged with group‐average GDT Z‐score to produce the overall ranking for full‐model, high‐accuracy performance. Separate assessments are reported for specific aspects of predictor‐group performance, such as robustness of approximately correct template or fold identification, and self‐scoring ability at identifying the best of their models. Fold identification is distinct from but correlated with group‐average GDT Z‐score if target difficulty is taken into account, whereas self‐scoring is done best by servers and is uncorrelated with GDT performance. Outstanding individual models on specific targets are identified and discussed. Predictor groups excelled at different aspects, highlighting the diversity of current methodologies. However, good full‐model scores correlate robustly with high Cα accuracy. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Key safety roles in organizational changes
Authors: Davidson Paul A. , Mooney S.D. 
Published: July 2009

AbstractAs, business moves to lean manufacture to minimize costs, it inherently leads to reduced staff and a flatter management structure. During these organizational changes, it is important that safety is not compromised by the removal of key people. A number of layers of controls and defenses are put in place, to both prevent an event and to mitigate the consequences if an event occurs. There are many competing techniques for assessing the impact of organizational change, each of which has its pros and cons.This article discusses a technique based on the use of the Bow Tie methodology to analyze major accident scenarios for a high‐hazard site, and presents an example from a real life case study. Controls identified in the analysis have a responsible person assigned to them and a summary of these roles is used to define the impact of removing a role. Key roles for safety controls are maintained and any eliminated roles have their responsibilities reassigned. After the change, final role descriptions would specifically include descriptions of key safety control responsibilities.Within this article, we have discussed the application of the Bow Tie technique to Organizational Change on a site during a 15% staff reduction. This application and technique is easily followed, leading to identification and correction of gaps in the management systems. © 2009 American Institute of Chemical Engineers Process Saf Prog, 2010
A comparison of aircraft‐based surface‐layer observations over Denmark Strait and the Irminger Sea with meteorological analyses and QuikSCAT winds
Authors: Renfrew I. A. , Petersen G. N. , Sproson D. A. J. , Moore G. W. K. , Adiwidjaja H. , Zhang S. , North R. 
Published: July 2009

AbstractA compilation of aircraft observations of the atmospheric surface layer is compared with several meteorological analyses and QuikSCAT wind products. The observations are taken during the Greenland Flow Distortion Experiment, in February and March 2007, during cold‐air outbreak conditions and moderate to high wind speeds. About 150 data points spread over six days are used, with each data point derived from a 2‐min run (equivalent to a 12 km spatial average). The observations were taken 30–50 m above the sea surface and are adjusted to standard heights. Surface‐layer temperature, humidity and wind, as well as sea‐surface temperature (SST) and surface turbulent fluxes are compared against co‐located data from the ECMWF operational analyses, NCEP Global Reanalyses, NCEP North American Regional Reanalyses (NARR), Met Office North Atlantic European (NAE) operational analyses, two MM5 hindcasts, and two QuikSCAT products.In general, the limited‐area models are better at capturing the mesoscale high wind speed features and their associated structure; often the models underestimate the highest wind speeds and gradients. The most significant discrepancies are: a poor simulation of relative humidity by the NCEP global and MM5 models, a cold bias in 2 m air temperature near the sea‐ice edge in the NAE model, and an overestimation of wind speed above 20 m s−1in the QuikSCAT wind products. In addition, the NCEP global, NARR and MM5 models all have significant discrepancies associated with the parametrisation of surface turbulent heat fluxes. A high‐resolution prescription of the SST field is crucial in this region, although these were not generally used at this time. Copyright © 2009 Royal Meteorological Society