bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystallization of poly(butylene adipate) in the presence of nucleating agents
Authors: Kai Weihua , Zhu Bo , He Yong , Inoue Yoshio 
Published: July 2005

AbstractThe effect of nucleating agents on the polymorphic crystallization behavior of poly(butylene adipate) (PBA) was studied with four kinds of commercially available nucleating agents, such as talc and boron nitride. The crystal structures of the α and β forms were studied with wide‐angle X‐ray diffraction. The β‐to‐α‐crystal transformation of PBA in the absence and presence of the nucleating agents in isothermal crystallization and nonisothermal crystallization processes was studied with differential scanning calorimetry and polarized optical microscopy. In both isothermal and nonisothermal crystallization, the introduction of nucleating agents selectively initiated the nucleation of the α‐form crystal, which was relatively slow in the absence of nucleating agents. The nucleating activity of the four kinds of nucleating agents in the crystallization of the PBA α‐form crystal was determined by the study of the nonisothermal crystallization, spherulite morphology, and isothermal kinetics. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2340–2351, 2005
Loop‐closure events during protein folding: Rationalizing the shape of Φ‐value distributions
Authors: Weikl Thomas R. 
Published: July 2005

AbstractIn the past years, the folding kinetics of many small single‐domain proteins has been characterized by mutational Φ‐value analysis. In this article, a simple, essentially parameter‐free model is introduced which derives folding routes from native structures by minimizing the entropic loop‐closure cost during folding. The model predicts characteristic folding sequences of structural elements such as helices and β‐strand pairings. Based on few simple rules, the kinetic impact of these structural elements is estimated from the routes and compared to average experimental Φ‐values for the helices and strands of 15 small, well‐characterized proteins. The comparison leads on average to a correlation coefficient of 0.62 for all proteins with polarized Φ‐value distributions, and 0.74 if distributions with negative average Φ‐values are excluded. The diffuse Φ‐value distributions of the remaining proteins are reproduced correctly. The model shows that Φ‐value distributions, averaged over secondary structural elements, can often be traced back to entropic loop‐closure events, but also indicates energetic preferences in the case of a few proteins governed by parallel folding processes. Proteins 2005. © 2005 Wiley‐Liss, Inc.
How well are protein structures annotated in secondary databases?
Authors: Rother Kristian , Michalsky Elke , Leser Ulf 
Published: July 2005

AbstractWe investigated to what extent Protein Data Bank (PDB) entries are annotated with second‐party information based on existing cross‐references between PDB and 15 other databases. We report 2 interesting findings. First, there is a clear “annotation gap” for structures less than 7 years old for secondary databases that are manually curated. Second, the examined databases overlap with each other quite well, dividing the PDB into 2 well‐annotated thirds and one poorly annotated third. Both observations should be taken into account in any study depending on the selection of protein structures by their annotation. Proteins 2005. © 2005 Wiley‐Liss, Inc.
The Gō model revisited: Native structure and the geometric coupling between local and long‐range contacts
Authors: Faísca Patrícia F. N. , Telo da Gama Margarida M. , Nunes Ana 
Published: July 2005

AbstractMonte Carlo simulations show that long‐range interactions play a major role in determining the folding rates of 48‐mer three‐dimensional lattice polymers modeled by the Gō potential. For three target structures with different native geometries we found a sharp increase in the folding time when the relative contribution of the long‐range interactions to the native state's energy is decreased from ∼50% towards zero. However, the dispersion of the simulated folding times is strongly dependent on native geometry and Gō polymers folding to one of the target structures exhibits folding times spanning three orders of magnitude. We have also found that, depending on the target geometry, a strong geometric coupling may exist between local and long‐range contacts, which means that, when this coupling exists, the formation of long‐range contacts is forced by the previous formation of local contacts. The absence of a strong geometric coupling results in a kinetics that is more sensitive to the interaction energy parameters; in this case, the formation of local contacts is not capable of promoting the establishment of long‐range ones when the latter are strongly penalized energetically and this results in longer folding times. Proteins 2005. © 2005 Wiley‐Liss, Inc.
The “first in–last out” hypothesis on protein folding revisited
Authors: Pintar Alessandro , Pongor Sándor 
Published: July 2005

AbstractWe calculated profiles for mean residue depth, contact order, and number of contacts in the native structure of a series of proteins for which folding has been studied extensively, the chymotrypsin inhibitor 2, the SH3 module from the src tyrosine kinase, the small ribonuclease barnase, the bacterial immunity protein Im7, and apomyoglobin. We compared these profiles with experimental data from equilibrium or pulse labeling hydrogen‐deuterium exchange obtained from NMR and ϕ values obtained from the protein engineering approach. We find a good qualitative agreement between the hierarchy of formation of topological elements during the folding process and the ranking of secondary structure elements in terms of residue depth. Residues that are most deeply buried in the core of the native protein usually belong to stretches of secondary structure elements that are formed early in the folding pathway. Residue depth can thus provide a useful and simple tool for the design of folding experiments. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily
Authors: Liger Dominique , Quevillon‐Cheruel Sophie , Sorel Isabelle , Bremang Michael , Blondeau Karine , Aboulfath Ilham , Janin Joël , van Tilbeurgh Herman , Leulliot Nicolas 
Published: July 2005

AbstractIn the Pseudomonas bacterial genomes, the PhzF proteins are involved in the production of phenazine derivative antibiotic and antifungal compounds. The PhzF superfamily however also encompasses proteins in all genomes from bacteria to eukaryotes, for which no function has been assigned. We have determined the three dimensional crystal structure at 2.05 Å resolution of YHI9, the yeast member of the PhzF family. YHI9 has a fold similar to bacterial diaminopimelate epimerase, revealing a bimodular structure with an internal symmetry. Residue conservation identifies a putative active site at the interface between the two domains. Evolution of this protein by gene duplication, gene fusion and domain swapping from an ancestral gene containing the “hot dog” fold, identifies the protein as a “kinked double hot dog” fold. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Fibre composite structures in Australia's civil engineering market: an anatomy of innovation
Authors: Van Erp Gerard , Cattell Craig , Heldt Tim 
Published: July 2005

AbstractDuring the last 5–10 years there has been considerable activity in research and development of fibre composites in the Australian civil engineering market. Areas of activity have included; bridge systems, replacement of large‐section hardwood girders, waterfront structures and railway sleepers. The work has involved not only the initial concept development, but also the construction and deployment of full‐scale prototypes. Through close involvement of major asset owners, including state road and rail authorities and city councils, these technologies have evolved from initial technology demonstrators to become viable commercial alternatives to traditional structural solutions. This paper presents a review of these developments and examines the process involved in taking these new systems from a novelty to a viable and credible alternative for local asset owners.
Method for the analysis of nonselective spectra of optically stimulated electron emission from irradiated dielectrics
Authors: Zatsepin A. F. , Biryukov D. Yu. , Kortov V. S. 
Published: July 2005

AbstractA method has been proposed and substantiated for processing of nonselective optically stimulated electron emission (OSEE) spectra of irradiated crystalline and amorphous dielectrics. This method allows the separation of the emission contribution of discrete centers taking into account effects of radiation‐induced electrization of materials and the unsteady state of the electron emission. Separation of OSEE selective bands facilitates the establishment of the origin of discrete emission‐active centers and makes it possible to estimate the concentration and parameters of radiation defects localized in surface layers. The quantum yields of OSEE and ionization barriers of optically excited defects are calculated using kinetic and corrected isochronal temperature dependences of the emission current. Some capabilities of the method have been demonstrated by an example of glassy SiO2 and crystalline Be2SiO4. Oxygen‐deficient centers (ODCs), bulk and surface E′‐centers, and also non‐bridging oxygen hole centers (NBOHCs) have been recorded. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Growth Parameters and Substrate Treatment for the MOCVD Growth of ZnO
Authors: Wang Jinzhong , Sallet Vincent , Amiri Gaëlle , Rommeluère Jean‐François , Lusson Alain , Rzepka E. , Lewis John E. , Galtier Pierre , Gorochov Ouri 
Published: July 2005

AbstractZnO films were grown on sapphire substrates using vertical MOCVD system with DEZn and tertiary‐butanol as precursors, respectively. The benefits of substrate treatment on the microstructure and morphology of the film were shown. The influences of growth temperature and partial pressure ratio RVI/II on crystal quality were investigated in detail. XRD, Electron Channeling Pattern and Raman spectra indicated that the highest crystal quality film was grown at 425 °C when the partial pressure ratio of tertiary‐butanol (t‐Bu) to diethylzinc (DEZn) was 8. X‐ray rocking curves exhibit Full Width at Half Maximum (FWHM) of 607 arcsec. A strong exciton emission peak appears in the photoluminescence (PL) spectra. Furthermore, the peak position has a slight shift to low energy with increase of the growth temperature. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Vertical chip of GaN‐based light‐emitting diode formed on sapphire substrate
Authors: Kim Seong‐Jin , Choi Yong‐Seok , Han Young‐Heon , Kim Chang‐Yeon , Yu Soon‐Jae , Kim Song‐Gang 
Published: July 2005

AbstractIn order to improve GaN‐based light‐emitting diode (LED) performance, a sapphire‐etched vertical‐electrode nitride semiconductor (SEVENS) LED is fabricated by a chemical wet etching technique. The light‐output power, heat dissipation, and reverse electrostatic discharge (ESD) characteristics of SEVENS‐LED are improved compared to those of the conventional NiAu lateral‐electrode (LE) GaN‐based LED formed on the sapphire substrate. The 20 mA light‐output power and reverse ESD pulse amplitude of SEVENS‐LED are approximately 4.5 mW and 2000 V, respectively. The improved LED performance is attributed to changing a lateral electrode to a vertical electrode although the sapphire substrate is not transferred to a conducting substrate. The device fabrication method will be useful for providing us high‐brightness and high‐power GaN‐based LEDs for future solid‐state general lighting applications. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Structural and electro‐optical characteristics of Ga‐doped ZnO films prepared by thermal oxidation of metallic Zn100–xGax films
Authors: Mohamed S. H. 
Published: July 2005

AbstractGa‐doped ZnO thin films have been obtained by thermal oxidation of electron beam evaporated metallic Zn100–xGax thin films. The structural, optical, and electrical resistivity of the oxidized films depend on Ga content. The value of oxidation temperature shifts to higher temperatures with increasing Ga content. After oxidation, polycrystalline ZnO phase is formed and no Ga2O3 peaks are found. The Ga content is found to affect transmittance strongly and the optical bandgap slightly. The optical bandgap values of the oxidized Ga‐doped films are comparable at higher oxidation temperatures. Depending on the Ga content, the electrical resistivity increases with increasing oxidation temperature. At 550 °C all the Ga‐doped films have electrical resistivity values around 105 Ω cm. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Density functional theory study of the relative energies and structures of the chair, twist, and boat conformations of stannacyclohexane, 1‐methylstannacyclohexane, and 1,1‐dimethylstannacyclohexane
Authors: Freeman Fillmore , Fang Christine , Hoang David V. , Trinh Khue M. 
Published: July 2005

AbstractThe relative energies and structures of the chair, twist, and boat conformations of stannacyclohexane, 1‐methylstannacyclohexane, and 1,1‐dimethylstannacyclohexane have been investigated using density functional theory (DFT) (BLYP, B3LYP, B3P86, B3PW91) and hybrid Hartree–Fock/DFT (BH and HLYP) methods with the SDD basis set. The five levels of theory predicted similar energy differences (Erel) among the respective conformations of the stannacyclohexanes. Similar equilibrium geometries were also predicted at the five theoretical levels, with BLYP giving the longest bonds and BH and HLYP giving the shortest bonds. B3LYP predicted the chair conformer of stannacyclohexane to be 3.09, 3.47, and 4.27 kcal/mol, respectively, more stable than the 1,4‐twist and 2,5‐twist conformers and the 2,5‐boat transition state. The chair conformer of axial 1‐methylstannacyclohexane is 2.85, 3.40, and 4.46 kcal/mol, respectively, more stable than the 1,4‐twist and 2,5‐twist conformers and the 2,5‐boat transition state and the chair conformer of equatorial 1‐methylstannacyclohexane is 3.05, 3.52, and 4.56 kcal/mol, respectively, more stable than the 1,4‐twist and 2,5‐twist conformers and the 2,5‐boat transition state. The chair conformer of axial 1‐methylstannacyclohexane is 0.19 kcal/mol less stable than the equatorial chair conformer, and the chair conformer of 1,1‐dimethylstannacyclohexane is 2.94, 3.49, and 4.21 kcal/mol, respectively, more stable than the 1,4‐twist and 2,5‐twist conformers and the 2,5‐boat transition state. The relative energies (Erel) of the conformers of the stannacyclohexanes are also compared with the available experimental and theoretical relative energies of the corresponding cyclohexanes and silacyclohexanes. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Quantum study of the structure of the active site of methylamine dehydrogenase
Authors: Pierdominici‐Sottile Gustavo , Echave Julián , Palma Juliana 
Published: July 2005

AbstractIn this article we present the results of a quantum study performed on different models of the active site of methylamine dehydrogenase (MADH). This enzyme catalyzes the oxidation of methylamine to produce formaldehyde and ammonia. During the rate‐determinant step of the reaction, a proton is transferred from the methyl group of the substrate to one of the bases of the active site. We performed calculations on three different models of the active site. The number of atoms of the models ranges from 68 to 95. Minimizations and optimizations were performed at the PM3 level of theory. The energies of the optimized structures were then recalculated at the B3LYP 6‐31G(d) level. From these energies, we calculated the barriers for H+ transfer toward the putative acceptors of the proton Asp76 and Thr122. By comparing the results of different models against each other, we drew some conclusions about the role of different residues. We found that the H+ transfer from the substrate toward Thr122 requires that this residue be ionized. The estimated barrier for this ionization was found to be >19 kcal/mol. The barrier for H+ transfer from the substrate toward Asp76 is significantly smaller. Our best estimates indicate that this barrier is 9.7 kcal/mol, when the imino group of the substrate is unprotonated and 7.7 kcal/mol when it is protonated. We thoroughly discussed the agreement and disagreement of these values with the results reported in previous theoretical and experimental studies. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Electrospray ionization mass spectrometric studies of nucleophilic carbenes derived from pyrazolium and indazolium carboxylates
Authors: Schmidt Andreas , Habeck Tobias , Merkel Lars , Mäkinen Marko , Vainiotalo Pirjo 
Published: July 2005

AbstractPyrazolium‐3‐carboxylate and indazolium‐3‐carboxylate, which belong to the class of pseudo‐cross‐conjugated mesomeric betaines and which represent the electronically relevant partial structures of the betaine alkaloid Nigellicin, were examined by electrospray ionization mass spectrometry. These compounds decarboxylate to pyrazol‐3‐ylidene and indazol‐3‐ylidene. The formation of adducts of these new nucleophilic carbenes under the measurement conditions was examined. Copyright © 2005 John Wiley & Sons, Ltd.
Matrix‐assisted laser desorption/ionisation mass spectrometry for the direct analysis of enzymatically digested kappa‐ iota‐ and hybrid iota/nu‐carrageenans
Authors: Antonopoulos Aristotelis , Hardouin Julie , Favetta Patrick , Helbert William , Delmas Agnès F. , Lafosse Michel 
Published: July 2005

AbstractEnzymatically digested oligosaccharides of kappa‐, iota‐ and hybrid iota/nu‐carrageenans were analysed using matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry in the negative‐ion mode. nor‐Harmane was used as matrix. Depending on the stock concentration and the laser intensity applied, the oligosaccharides exhibited losses of sulphate units (neutralised by the Na+ ion, and thus non‐stable), leaving the primary backbone structure in most cases with only the deprotonated sulphate groups (carrying the negative charge, stable). This meant that kappa‐ and iota‐oligosaccharides could not be easily distinguished from one another since they share the same primary backbone structure. However, for the hybrid iota/nu‐oligosaccharides the primary backbone structure could be identified since the nu‐carrageenan repeating unit differs from that of the kappa/iota‐carrageenan unit. For all types of oligosaccharides, the results indicated cleavage of an anhydrogalactose unit from the non‐reducing end. Specifically, for the hybrid oligosaccharides of iota/nu‐carrageenans, this type of fragmentation means that the nu‐carrageenan unit is not positioned on the non‐reducing end of the hybrid oligosaccharides. Dehydration reactions, and exchange reactions of Na+ with K+ and Ca2+, were also observed. Copyright © 2005 John Wiley & Sons, Ltd.
Relative quantification of erythropoietin receptor‐dependent phosphoproteins using in‐gel 18O‐labeling and tandem mass spectrometry
Authors: Körbel Sandra , Schümann Michael , Bittorf Thomas , Krause Eberhard 
Published: July 2005

AbstractOn examining different proteomics approache for the investigation of structure‐function relationships of erythropoietin (EPO) receptor signaling, it was found that two‐dimensional gel electrophoresis/mass spectrometry procedures are clearly limited in their ability to detect low‐expressed signaling proteins. Instead it was found that a strategy involving anti‐phosphotyrosine immunoprecipitation, one‐dimensional gel electrophoresis (1DE), and capillary liquid chromatography/tandem mass spectrometry (LC/MS/MS) provides the sensitivity required for identification of signaling proteins. In the present work the immunoprecipitation/1DE/LC/MS approach was combined with an in‐gel 18O‐labeling technique to analyze EPO receptor‐dependent proteins. Identification and relative quantification of more than 180 EPO receptor‐dependent proteins were achieved directly based on the in‐gel 18O‐labeling approach. Copyright © 2005 John Wiley & Sons, Ltd.
Tandem mass spectrometry of deprotonated iodothyronines
Authors: Couldwell Alison M. , Thomas Michael C. , Mitchell Todd W. , Hulbert Anthony J. , Blanksby Stephen J. 
Published: July 2005

AbstractIn order to assist with the development of more selective and sensitive methods for thyroid hormone analysis the [M–H]− anions of the iodothyronines T4, T3, rT3, (3,5)‐T2 and the non‐iodinated thyronine (T0) have been generated by negative ion electrospray mass spectrometry. Tandem mass spectra of these ions were recorded on a triple‐quadrupole mass spectrometer and show a strong analogy with the fragmentation pathways of the parent compound, tyrosine. All iodothyronines also show significant abundances of the iodide anion in their tandem mass spectra, which represents an attractive target for multiple reaction monitoring (MRM) analysis, given that iodothyronines are the only iodine bearing endogenous molecules. Characteristic fragments are observed at m/z 359.7 and 604.5 for rT3 but are absent in the spectrum of T3, thus differentiating the two positional isomers. The striking difference in the fragmentation patterns of these regioisomeric species is attributed to the increased acidity of the phenol moiety in rT3 compared with T3. Copyright © 2005 John Wiley & Sons, Ltd.
Development of a liquid chromatography/tandem mass spectrometry assay for the quantification of rabeprazole in human plasma
Authors: Huang Jinchang , Xu Yu , Gao Shu , Rui Lei , Guo Qingxiang 
Published: July 2005

AbstractA simple and sensitive liquid chromatography/tandem mass spectrometry method, employing electrospray ionization, has been developed and validated to quantify rabeprazole in human plasma using omeprazole as the internal standard. The method was validated to demonstrate the specificity, lower limit of quantification, accuracy, and precision of measurements. Selected reaction monitoring was specific for rabeprazole and omeprazole (the internal standard, IS); no endogenous materials interfered with the analysis of rabeprazole and IS from blank plasma. The assay was linear over the concentration range 0.2–200 ng/mL using a 2 µL aliquot of plasma. The correlation coefficients for the calibration curves ranged from 0.9988–0.9994. The intra‐ and inter‐day precision, calculated from quality control samples, were less than 6.65%. A mixture of methanol and water (50:50) was used as the isocratic mobile phase, with 0.1% of formic acid in water, that did not affect the stability of rabeprazole or IS. A simple sample preparation method of protein precipitation with methanol was chosen. The method was employed in a pharmacokinetic study after oral administration of 20 mg rabeprazole to 24 healthy volunteers. Copyright © 2005 John Wiley & Sons, Ltd.
Webs of significance: the work of Geoffrey Vickers
Authors: Checkland Peter 
Published: July 2005

AbstractThis paper is a personal account by Peter Checkland of his correspondence with Geoffrey Vickers in the years before Vickers' death and the discussions they had about the relationship between systems ideas and real‐world experience. Professor Checkland demonstrates how the model he created of the appreciative process reflects those discussions, and how it may be used as a basis for making sense of the world we live in. He provides numerous examples to demonstrate the way in which the model may be applied in very different situations. Copyright © 2005 John Wiley & Sons, Ltd.