bluuebunny/crossref_metadata_2025_split huggingface dataset:
Membrane proteins from the cyanobacterium Synechocystis sp. PCC 6803 interacting with thioredoxin
Authors: Mata‐Cabana Alejandro , Florencio Francisco J. , Lindahl Marika 
Published: October 2007

AbstractCysteine dithiol/disulphide exchange forms the molecular basis for regulation of a wide variety of enzymatic activities and for transduction of cellular signals. Thus, the search for proteins with reactive, accessible cysteines is expected to contribute to the unravelling of new molecular mechanisms for enzyme regulation and signal transduction. Several methods have been designed for this purpose taking advantage of the interactions between thioredoxins and their protein substrates. Thioredoxins comprise a family of redox‐active enzymes, which catalyse reduction of protein disulphides and sulphenic acids. Due to the inherent practical difficulties associated with studies of membrane proteins these have been largely overlooked in the many proteomic studies of thioredoxin‐interacting proteins. In the present work, we have developed a procedure to isolate membrane proteins interacting with thioredoxin by binding in situ to a monocysteinic His‐tagged thioredoxin added directly to the intact membranes. Following fractionation and solubilisation of the membranes, thioredoxin target proteins were isolated by Ni‐affinity chromatography and 2‐DE SDS‐PAGE under nonreducing/reducing conditions. Applying this method to total membranes, including thylakoid and plasma membranes, from the cyanobacterium Synechocystis sp. PCC 6803 we have identified 50 thioredoxin‐interacting proteins. Among the 38 newly identified thioredoxin targets are the ATP‐binding subunits of several transporters and members of the AAA‐family of ATPases.
Evidences of phase separation in moisture‐cured poly(urethane urea)s by means of temperature modulated differential scanning calorimetry
Authors: Daniel‐da‐Silva Ana Luísa , Bordado João Carlos Moura , Martín‐Martínez José Miguel 
Published: October 2007

AbstractThe degree of phase separation in several moisture‐cured poly(urethane urea)s (PUUs) was studied by FTIR spectroscopy, wide angle X‐ray diffraction (WAXD), and temperature‐modulated differential scanning calorimetry (TMDSC). This latter technique was shown to be particularly useful in analysing the degree of phase separation in PUU polymers. Both phase mixing and phase segregation coexisted in the PUUs and the degree of phase separation increased as the urea hard segment (HS) content in the PUU increased. The maximum solubility of urea HSs into the polyol soft segments (SSs) was achieved for 50 wt % urea HS content in diol‐based PUUs, whereas for triol‐based PUUs the highest solubility between HS and SS was reached for lower urea HS amount. Finally, the higher the urea HS content the higher the extent of phase separation in the PUU. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 3034–3045, 2007
Chemical denudation rates and carbon dioxide drawdown in an ice‐free polar karst catchment: Londonelva, Svalbard
Authors: Krawczyk Wiesława Ewa , Pettersson Lars‐Evan 
Published: October 2007

AbstractChemical denudation rates and carbon dioxide withdrawal were calculated for the Londonelva basin, an ice‐free karst catchment on Svalbard. Runoff was recorded 12 June to 11 October 2000 and water samples were collected daily in August. The chemical denudation rate that month amounted to 2.2 m3 km−2. The estimated chemical denudation rate for 2000 was 5.8 m3 km−2 yr−1 or 303 Σ meq+ m−2 yr−1, but this rate may be unusually low because basin runoff was only 158 × 103 m3, the lowest since recording began in 1992. For other discharge years estimated chemical denudation rates range from 5.8 to 13.3 m3 km−2 yr−1 or 300–690 Σ meq+ m−2 yr−1. The CO2 withdrawal in August 2000 amounted to 560 kg C km−2 and for the hydrological year 2000 it was 1560 kg C km−2 yr−1. In 1993, the highest recorded runoff year, withdrawal of CO2 may have reached 3800 kg C km−2 yr−1. Copyright © 2007 John Wiley & Sons, Ltd.
A relict sand‐wedge polygon site in north‐central Hungary
Authors: Kovács János , Fábián Szabolcs Ákos , Schweitzer Ferenc , Varga Gábor 
Published: October 2007

AbstractRelict sand‐wedge polygons are described from palaeosol and gravel deposits in the Mogyoród area, Hungary. Based on previously reported periglacial features, the local glacial history and optically stimulated luminescence (OSL) dates, these features suggest that the Pannonian Basin was underlain by permafrost during the Late Pleniglacial (22 000–18 000 years ago) and that the permafrost may have been continuous. Copyright © 2007 John Wiley & Sons, Ltd.
Hydrophobic interactions and ionic networks play an important role in thermal stability and denaturation mechanism of the porcine odorant‐binding protein
Authors: Stepanenko Olesya V. , Marabotti Anna , Kuznetsova Irina M. , Turoverov Konstantin K. , Fini Carlo , Varriale Antonio , Staiano Maria , Rossi Mose' , D'Auria Sabato 
Published: October 2007

AbstractDespite the fact that the porcine odorant‐binding protein (pOBP) possesses a single tryptophan residue (Trp 16) that is characterized by a high density microenvironment (80 atoms in a sphere with radius 7 Å) with only one polar group (Lys 120) and three bound water molecules, pOBP displayed a red shifted fluorescence emission spectrum (λmax = 340 nm). The protein unfolding in 5M GdnHCl was accompanied by the red shift of the fluorescence emission spectrum (λmax = 353 nm), by the increase of fluorescence quantum yield, and by the decrease of lifetime of the excited state (from 4.25 ns in native state to 3.15 ns in the presence of 5M GdnHCl). Taken together these data indicate the existence of an exciplex complex (Trp 16 with Lys 120 and/or with bound molecules of water) in the protein native state. Heat‐induced denaturation of pOBP resulted in significant red shifts of the fluorescence emission spectra: the value of the ratio (I320/I365) upon excitation at λex = 297 nm (parameter A) decreases from 1.07 to 0.64 passing from 60 to 85°C, and the calculated midpoint of transition was centered at 70°C. Interestingly, even at higher temperature, the values of the parameter A both in the absence and in the presence of GdnHCl did not coincide. This suggests that a portion of the protein structure is still preserved upon the temperature‐induced denaturation of the protein in the absence of GdnHCl. CD experiments performed on pOBP in the absence and in the presence of GdnHCl and at different temperatures were in agreement with the fluorescence results. In addition, the obtained experimental data were corroborated by the analysis of the 3D structure of pOBP which revealed the amino acid residues that contribute to the protein dynamics and stability. Finally, molecular dynamics simulation experiments pointed out the important role of ion pair interactions as well as the molecular motifs that are responsible for the high thermal stability of pOBP, and elucidated the reasons of the protein aggregation that occurred at high temperature. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Docking and scoring protein complexes: CAPRI 3rd Edition
Authors: Lensink Marc F. , Méndez Raúl , Wodak Shoshana J. 
Published: October 2007

AbstractThe performance of methods for predicting protein–protein interactions at the atomic scale is assessed by evaluating blind predictions performed during 2005–2007 as part of Rounds 6–12 of the community‐wide experiment on Critical Assessment of PRedicted Interactions (CAPRI). These Rounds also included a new scoring experiment, where a larger set of models contributed by the predictors was made available to groups developing scoring functions. These groups scored the uploaded set and submitted their own best models for assessment. The structures of nine protein complexes including one homodimer were used as targets. These targets represent biologically relevant interactions involved in gene expression, signal transduction, RNA, or protein processing and membrane maintenance. For all the targets except one, predictions started from the experimentally determined structures of the free (unbound) components or from models derived by homology, making it mandatory for docking methods to model the conformational changes that often accompany association. In total, 63 groups and eight automatic servers, a substantial increase from previous years, submitted docking predictions, of which 1994 were evaluated here. Fifteen groups submitted 305 models for five targets in the scoring experiment. Assessment of the predictions reveals that 31 different groups produced models of acceptable and medium accuracy‐but only one high accuracy submission‐for all the targets, except the homodimer. In the latter, none of the docking procedures reproduced the large conformational adjustment required for correct assembly, underscoring yet again that handling protein flexibility remains a major challenge. In the scoring experiment, a large fraction of the groups attained the set goal of singling out the correct association modes from incorrect solutions in the limited ensembles of contributed models. But in general they seemed unable to identify the best models, indicating that current scoring methods are probably not sensitive enough. With the increased focus on protein assemblies, in particular by structural genomics efforts, the growing community of CAPRI predictors is engaged more actively than ever in the development of better scoring functions and means of modeling conformational flexibility, which hold promise for much progress in the future. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Vinyl chloride monomer explosion
Authors: Long Lisa A. , Lay James , Leskin Katherine , McClure Randy , Smith Allen 
Published: October 2007

AbstractOn April 23, 2004, an explosion and fire at the Formosa Plastics Corporation, Illiopolis, Illinois (Formosa‐IL) polyvinyl chloride (PVC) manufacturing facility killed five and severely injured three workers. The explosion and fire destroyed most of the reactor facility and adjacent warehouse and ignited PVC resins stored in the warehouse. The plume of smoke from the smoldering fire drifted over the community and resulted in an evacuation that lasted 48 h. Vinyl chloride (VCM), a highly flammable chemical and known carcinogen, and the major component in the facility's manufacturing process, was the primary fuel for the initial fire and explosion. Formosa‐IL used VCM to manufacture a variety of PVC resins in 24 heated and pressurized reactors. Formosa‐IL, a wholly owned subsidiary of Formosa Plastics Corporation, USA (FPC USA), purchased the Illiopolis facility from Borden Chemical and operated it for ∼2 years before the incident. This article includes the incident's root and contributing causes, and CSB recommendations to prevent recurrence. This paper represents the views of the authors. The full CSB report on this incident can be found at www.csb.gov. © 2007 American Institute of Chemical Engineers Process Saf Prog, 2008
Differentiation of diastereomeric N‐aryltetrahydropyrano/tetrahydrofuranochromenylamines under electron ionization and chemical ionization conditions
Authors: Ramanjaneyulu G. S. , Prabhakar S. , Bhaskar G. , Venkatesham A. , Nagaiah K. , Rao R. Nageswara , Soujanya Y. , Sastry G. Narahari 
Published: October 2007

AbstractA series of diastereomeric 4S,5S,6R/S‐tetrahydropyrano‐ and 3S,4S,5R/S‐tetrahydrofuranochromenylamine derivatives (a/b isomers; 1–26) has been studied under electron ionization (EI) and chemical ionization (CI) conditions. The EI mass spectra of all diastereomeric compounds show two characteristic fragment ions, of which one is formed by retro‐Diels‐Alder (RDA) reaction from the molecular ion, retaining the charge on the diene fragment, and the other [M–(HNAr)]+ ion by a simple radical loss. The RDA process is more favorable in all b isomers, whereas the radical loss is dominant in all a isomers; based on these two ions it is easy to differentiate the two diastereomers. The collision‐induced dissociation (CID) spectra of all the molecular ions also show the same trend, which reflects the stereoselectivity in the formation of the two characteristic fragment ions. The results of theoretical calculations performed are in accordance with the experimental observations. The CI experiments (methane and isobutane) on all the diastereomeric compounds also enabled the differentiation of the isomers. Copyright © 2007 John Wiley & Sons, Ltd.
A generic fast solid‐phase extraction high‐performance liquid chromatography/mass spectrometry method for high‐throughput drug discovery
Authors: Gao Lan , Cheng Xueheng , Zhang Jun , Burns David J. 
Published: October 2007

AbstractHigh‐performance liquid chromatography/mass spectrometry (HPLC/MS) is increasingly perceived to be an essential tool in drug discovery at many key steps, like drug screening, lead identification, ADME profiling, and drug metabolism and pharmacology studies. High‐throughput screenings in the early phase for metabolic stability, protein binding, permeability (ADME) and bioavailability are widely used to weed out compounds that do not exhibit the necessary characteristics. For such high‐throughput LC/MS studies, a generic LC/MS method that can be used for a variety of compounds is desired. In this study, we used a small set of compounds with a wide range of properties to guide method development, and achieved a sample throughput of 1.7 min/sample. Here, we present a generic fast method that achieves good peak separation and peak shape on conventional HPLC systems using a column‐switching mechanism for on‐line solid‐phase extraction (SPE)‐HPLC/MS analysis. The method has a linear response range from 1 to 500 nM for the tested compounds. When a larger set of 658 randomly picked small molecules were analyzed using this method, 612 were observed with good signal intensity and HPLC peak shapes. This generic fast SPE‐LC/MS method has been used to screen more than 1.5 million compounds repetitively against over 200 protein targets for hit confirmation and semi‐quantitation of binding constants from biological assays. Over 7000 different compounds for a variety of protein‐binding assays have been studied using this method for quantitative analysis as well. Copyright © 2007 John Wiley & Sons, Ltd.
Mass spectrometry characterization of Escherichia coli K4 oligosaccharides from 2‐mers to more than 20‐mers
Authors: Volpi Nicola 
Published: October 2007

AbstractThe separation and characterization of oligosaccharides obtained by hyaluronidase [E.C. 3.2.1.35] digestion of Escherichia coli K4 polysaccharide using online high‐performance liquid chromatography/electrospray ionization mass spectrometry (HPLC/ESI‐MS) are presented. Complete identification and structural information for oligosaccharides containing 2–24 monomers (from 2‐ to 24‐mers) were obtained. In particular, smaller K4 species, from 2‐mers to 4‐mers, exhibited mainly [M–H]−1 anions, whereas the 6‐ to 8‐mers existed predominantly at the charge state of −2. The K4 oligomers from 10‐mers to 14‐mers were mainly represented by [M–3H]−3 anions while species from 16‐ to 20‐mers were characterized by a charge state of −4. K4 oligosaccharides from 22‐ to 24‐mers existed as [M–4H]−4 and [M–5H]−5 anions and, for this latter species, ions having a charge state of −6 appeared. For smaller K4 species, in particular from 6‐mers to 10‐mers, ESI‐MS revealed anions related to the loss of one monosaccharide unit from the oligomers due to apparent collisional activation and ion source fragmentation. However, no odd‐numbered anions were produced for K4 2/4‐mer species or for oligosaccharides greater than 12‐mers, while for K4 species 8/10‐mer, ESI‐MS revealed odd‐numbered anions generally in low relative abundance making the interpretation of the spectra easier. The ESI‐MS spectra of oligosaccharides separated by online HPLC were applied to the evaluation of the K4 polymerization process, confirming that the addition of fructose units is not critical for chain elongation as variously fructosylated oligomer species were detected directly on the K4 carbohydrate backbone. Copyright © 2007 John Wiley & Sons, Ltd.
Study of the end‐group contribution to ToF‐SIMS and G‐SIMS spectra of poly (lactic acid) using deuterium labelling
Authors: Ogaki R. , Green F. M. , Gilmore I. S. , Shard A. G. , Luk S. , Alexander M. R. , Davies M. C. 
Published: October 2007

AbstractIn this study, polymeric (MW 50 000) and oligomeric (MW 2000) poly (lactic acid) (PLA), both with and without end‐group deuterium exchange, were analysed using static secondary ion mass spectrometry (SSIMS) to investigate the contribution of end‐group‐derived secondary ions to the SSIMS spectra. By monitoring the SSIMS intensities between the non‐deuterated and deuterated PLA, it is evident that the only significant end‐group‐derived secondary ions are [nM + H]+ (n > 1) and C4H9O2+. The gentle‐SIMS (G‐SIMS) methodology was employed to establish that deuterated fragments were produced through low energy processes and were not the result of substantial rearrangements. It was noted that end‐group‐derived secondary ions had higher G‐SIMS intensities for oligomeric PLA than polymeric PLA, showing that these secondary ions are simple fragment products that are not the result of rearrangement or degraded product ions. Copyright © 2007 John Wiley & Sons, Ltd.
Electron Rutherford back‐scattering case study: oxidation and ion implantation of aluminium foil
Authors: Went M. R. , Vos M. 
Published: October 2007

AbstractElectron Rutherford back scattering (ERBS) is a new spectroscopy for determining the composition of surfaces. In this work the surface sensitivity of ERBS was investigated by changing the entrance and exit angle of the electron beam while keeping the scattering angle constant. It was found that in this way the surface sensitivity of the technique can be varied considerably. We use aluminium as a test case for ERBS, as it is well studied. The technique has been used to investigate the oxide film of aluminium foil as manufactured and the native oxide (Al2O3) film formed on a clean aluminium surface exposed to air. We have also used ERBS to investigate the presence of Xe, implanted during the sputter cleaning process, at a variety of depths within an aluminium matrix. Copyright © 2007 John Wiley & Sons, Ltd.
Study on the anodic reaction of Ni in an alkaline solution by transient pH detection based on scanning electrochemical microscopy (SECM)
Authors: Kang Jianqiang , Yang Yifu , Jiang Fengshan , Shao Huixia 
Published: October 2007

AbstractThe anodic reaction of Ni in an alkaline solution was studied by the tip–substrate voltammetry mode of scanning electrochemical microscopy (SECM) and cyclic voltammetry (CV). A platinum microdisc electrode was selected as the tip electrode, which functioned as a pH sensor with transient response capability. The pH value of the solution near the Ni electrode surface varied while the Ni substrate oxidation reaction occurred, and the pH variation could be detected by the tip faradic current. The cyclic voltammogram results showed that two types of hydroxides: i.e. α‐Ni(OH)2 and β‐Ni(OH)2 were formed during Ni oxidation in the lower potential region. In the proceedings of α‐Ni(OH)2 → γ‐NiOOH and β‐Ni(OH)2 → β‐NiOOH, the process of OH− concentration decrease in the solution was ahead and behind of electron transfer in the solid phase, respectively. These results indicate that the OH− adsorption process occurs as an elementary step in the former reaction and the H+ diffusion process from the inner to the outer layer of the solid phase occurs as a subsequent step in the latter reaction. The results also revealed that the oxide film on the Ni surface has a two‐layer structure. The real potential of the oxygen evolution reaction (OER) on the Ni surface with different cycles is also analyzed in the paper. Copyright © 2007 John Wiley & Sons, Ltd.
A comparison of methods for combining quality and efficiency performance measures: Profiling the value of hospital care following acute myocardial infarction
Authors: Timbie Justin W. , Normand Sharon‐Lise T. 
Published: October 2007

AbstractHealth plans have begun to combine data on the quality and cost of medical providers in an attempt to identify and reward those that offer the greatest ‘value.’ The analytical methods used to combine these measures in the context of provider profiling have not been rigorously studied. We propose three methods to measure and compare the value of hospital care following acute myocardial infarction by combining a single measure of quality, in‐hospital survival, and the cost of an episode of acute care. To illustrate these methods, we use administrative data for heart attack patients treated at 69 acute care hospitals in Massachusetts in fiscal year 2003. In the first method we reproduce a common approach to value profiling by modeling the two case mix‐standardized outcomes independently. In the second approach, survival is regressed on patient risk factors and the average cost of care at each hospital. The third method models survival and cost for each hospital jointly and combines the outcomes on a common scale using a cost‐effectiveness framework. For each method we use the resulting parameter estimates or functions of the estimates to compute posterior tail probabilities, representing the probability of being classified in the upper or lower quartile of the statewide distribution. Hospitals estimated to have the highest and lowest value according to each method are compared for consistency, and the advantages and disadvantages of each approach are discussed. Copyright © 2007 John Wiley & Sons, Ltd.
Experimental investigation of transient and thermal effects on lubricated non‐conformal contacts
Authors: Bassani R. , Ciulli E. , Carli M. , Stadler K. 
Published: October 2007

AbstractIn this work, thermal and transient effects on non‐conformal lubricated contacts are investigated through experimental analyses. Experiments between a ball and a plane surface of a disc are described. Friction coefficients and film thicknesses are measured (the film thickness only for the glass‐on‐steel contact). A paraffin base mineral oil is used as a lubricant.First experiments are carried out under steady‐state conditions. To include effects due to different thermal properties of contacting materials, a steel‐on‐steel and a glass‐on‐steel contact with different slide‐to‐roll ratios are tested. If the contacting materials have different thermal properties, as in the case of a glass‐on‐steel contact, thermal effects like the temperature–viscosity wedge action could clearly be shown. It is found that the friction coefficients are influenced by the slide‐to‐roll ratio and the thermal properties of the contacting materials.Under transient conditions, the entraining velocity is varied with a sinusoidal law. Squeeze effects explain ‘loops’ of friction and film thickness found also in previous works. The formation of friction loops is related to the measured film thickness differences. However, also under non‐steady‐state conditions, thermal effects, like the temperature–viscosity wedge action, influence the friction coefficients. Copyright © 2007 John Wiley & Sons, Ltd.