bluuebunny/crossref_metadata_2025_split huggingface dataset:
Membrane subproteomic analysis of Mycobacterium bovis bacillus Calmette‐Guérin
Authors: Zheng Jianhua , Wei Candong , Leng Wenchuan , Dong Jie , Li Rui , Li Weijun , Wang Jin , Zhang Zongde , Jin Qi 
Published: October 2007

AbstractMycobacterium bovis bacillus Calmette–Guérin (BCG) vaccine has been known for a long time to prevent tuberculosis (TB) worldwide since 1921. Nonetheless, we know little about BCG membrane proteome. In the present study, we utilized alkaline incubation and Triton X‐114‐based methods to enrich BCG membrane proteins and subsequently digested them using proteolytic enzyme. The recovered peptides were further separated by 2‐D LC and identified by ESI‐MS/MS. As a result, total 474 proteins were identified, including 78 integral membrane proteins (IMPs). Notably, 18 BCG IMPs were described for the first time in mycobacterium. Further analysis of the 78 IMPs indicated that the theoretical molecular mass distribution of them ranged from 8.06 to 167.86 kDa and pI scores ranged from 4.40 to 11.60. Functional classification revealed that a large proportion of the identified IMPs (67.9%, 53 out of 78) were involved in cell wall and cell processes functional group. In conclusion, here we reported a comprehensive profile of the BCG membrane subproteome. The present investigation may allow the identification of some valuable vaccine and drug target candidates and thus provide basement for future designing of preventive, diagnostic, and therapeutic strategies against TB.
Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences
Authors: Padliya Neerav D. , Garrett Wesley M. , Campbell Kimberly B. , Tabb David L. , Cooper Bret 
Published: October 2007

AbstractLC‐MS/MS has demonstrated potential for detecting plant pathogens. Unlike PCR or ELISA, LC‐MS/MS does not require pathogen‐specific reagents for the detection of pathogen‐specific proteins and peptides. However, the MS/MS approach we and others have explored does require a protein sequence reference database and database‐search software to interpret tandem mass spectra. To evaluate the limitations of database composition on pathogen identification, we analyzed proteins from cultured Ustilago maydis, Phytophthora sojae, Fusarium graminearum, and Rhizoctonia solani by LC‐MS/MS. When the search database did not contain sequences for a target pathogen, or contained sequences to related pathogens, target pathogen spectra were reliably matched to protein sequences from nontarget organisms, giving an illusion that proteins from nontarget organisms were identified. Our analysis demonstrates that when database‐search software is used as part of the identification process, a paradox exists whereby additional sequences needed to detect a wide variety of possible organisms may lead to more cross‐species protein matches and misidentification of pathogens.
Synthesis, characterization, and thermal degradation mechanism of fast biodegradable PPSu/PCL copolymers
Authors: Papadimitriou S. , Bikiaris D. N. , Chrissafis K. , Paraskevopoulos K. M. , Mourtas S. 
Published: October 2007

AbstractPoly(propylene succinate)/poly(ε‐caprolactone) (PPSu/PCL) 25/75, 50/50, and 75/25 w/w copolymers were prepared using a combination of polycondensation and ring opening polymerization. The randomness of copolymers was characterized using 1H NMR and 13C NMR spectroscopy. From molecular weights and DSC measurements it was observed that the molecular weight decreased with increasing the wt % content of PPSu, while the copolymers containing 50 and 75 wt % PPSu were completely amorphous. Enzymatic hydrolysis revealed that biodegradation rate was much enhanced compared with that of neat PCL and increased by increasing the PPSu content. From TGA analysis it was also found that the PPSu/PCL copolymers had similar thermal decomposition behaviour with the pure polyesters and exhibited their maximum decomposition rates at temperatures 400–420 °C. Two different mechanisms, which follow each other, were used to adequately describe their decomposition kinetics. The first one corresponded to the first stage taking place at 280–365 °C, where small mass loss was recorded and activation energies ranged between 94 and 156 kJ/mol. The second one took place at 370–460 °C and corresponded to the stage where the main polyester mass was decomposed. The activation energies for this stage ranged between 200 and 240 kJ/mol. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 5076–5090, 2007
Synthesis of novel asymmetric dendritic‐linear‐dendritic block copolymers via “living” anionic polymerization of ethylene oxide initiated by dendritic macroinitiators
Authors: Gitsov Ivan , Simonyan Arsen , Vladimirov Nikolay G. 
Published: October 2007

AbstractThe first synthesis of asymmetric dendritic‐linear‐dendritic ABC block copolymers, that contain a linear B block and dissimilar A and C dendritic fragments is reported. Third generation poly(benzyl ether) monodendrons having benzyl alcohol moiety at their “focal” point were activated by quantitative titration with organometallic anions and the resulting alkoxides were used as initiators in the “living” ring‐opening polymerization of ethylene oxide. The reaction proceeded in controlled fashion at 40–50 °C affording linear‐dendritic AB block copolymers with predictable molecular weights (Mw = 6000–13,000) and narrow molecular weight distributions (Mw/Mn = 1.02–1.04). The propagation process was monitored by size‐exclusion chromatography with multiple detection. The resulting “living” copolymers were terminated by reaction either with HCl/tetrahydrofuran or with a reactive monodendron that differed from the initiating dendron not only in size, but also in chemical composition. The asymmetric triblock copolymers follow a peculiar structure‐induced self‐assembly pattern in block‐selective solvents as evidenced by size‐exclusion chromatography in combination with multi‐angle light scattering. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 5136–5148, 2007
Rhythmic growth of ring‐banded spherulites in blends of liquid crystalline methoxy‐poly(aryl ether ketone) and poly(aryl ether ether ketone)
Authors: Chen Jian , Yang Decai 
Published: October 2007

AbstractRhythmic growth of ring‐banded spherulites in blends of liquid crystalline methoxy‐poly(aryl ether ketone) (M‐PAEK) and poly(aryl ether ether ketone) (PEEK) has been investigated by means of differential scanning calorimetry (DSC), polarized light microscopy (PLM), and scanning electron microscopy (SEM) techniques. The measurements reveal that the formation of the rhythmically grown ring‐banded spherulites in the M‐PAEK/PEEK blends is strongly dependent on the blend composition. In the M‐PAEK‐rich blends, upon cooling, an unusual ring‐banded spherulite is formed, which is ascribed to structural discontinuity caused by a rhythmic radial growth. For the 50:50 M‐PAEK/PEEK blend, ring‐banded spherulites and individual PEEK spherulites coexist in the system. In the blends with PEEK as the predominant component, M‐PAEK is rejected into the boundary of PEEK spherulites. The cooling rate and crystallization temperature have great effect on the phase behavior, especially the ring‐banded spherulite formation in the blends. In addition, the effects of M‐PAEK phase transition rate and phase separation rate on banded spherulite formation is discussed. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 3011–3024, 2007
Effect of temperature and membrane preparation parameters on gas permeation properties of polymethacrylates
Authors: Gülmüs Sergül Acikalin , Yilmaz Levent 
Published: October 2007

AbstractPermeabilities of N2, Ar, O2, CO2, and H2 gases in PEMA (Polyethylmethacrylate) membranes have been measured above and below glass transition in the temperature range of 25–70 °C. The permeabilities of the gases were observed increasing with temperature. Arrhenius plot of permeability versus temperature data showed that there is a slope discontinuity at near to Tg of PEMA. In addition, the effects of membrane preparation parameters by solvent casting method (percentage of polymer in solvent, annealing temperature, annealing time, evaporation temperature, and evaporation time) have been investigated by using homogenous dense membranes of PEMA. It is observed that membrane preparation parameters strongly affect the membrane performance and the reproducibility of the permeability measurements. On the other hand, the effect of polymer structure on membrane performance has been investigated. Comparison of the permeabilities of N2, Ar, O2, CO2, and H2 gases in PEMA and PMMA membranes shows that PMMA membranes have smaller permeabilities and higher selectivities than PEMA membranes because of their higher glass transition temperature, Tg. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 3025–3033, 2007
Assessing the reliability of sequence similarities detected through hydrophobic cluster analysis
Authors: Silva Pedro J. 
Published: October 2007

AbstractHydrophobic cluster analysis (HCA) has long been used as a tool to detect distant homologies between protein sequences, and to classify them into different folds. However, it relies on expert human intervention, and is sensitive to subjective interpretations of pattern similarities. In this study, we describe a novel algorithm to assess the similarity of hydrophobic amino acid distributions between two sequences. Our algorithm correctly identifies as misattributions several HCA‐based proposals of structural similarity between unrelated proteins present in the literature. We have also used this method to identify the proper fold of a large variety of sequences, and to automatically select the most appropriate structure for homology modeling of several proteins with low sequence identity to any other member of the protein data bank. Automatic modeling of the target proteins based on these templates yielded structures with TM‐scores (vs. experimental structures) above 0.60, even without further refinement. Besides enabling a reliable identification of the correct fold of an unknown sequence and the choice of suitable templates, our algorithm also shows that whereas most structural classes of proteins are very homogeneous in hydrophobic cluster composition, a tenth of the described families are compatible with a large variety of hydrophobic patterns. We have built a browsable database of every major representative hydrophobic cluster pattern present in each structural class of proteins, freely available at http://www2.ufp.pt/˜pedros/HCA_db/index.htm. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Observations of flame behavior during flame‐obstacle interaction
Authors: Fan Baochun , Ying Zhanfeng , Chen Zhihua , Ye Jingfang 
Published: October 2007

AbstractA series of experiments have been performed to investigate the premixed flame behavior during its propagation in a rectangle chamber with various obstacles mounted on its wall. A high speed shadowgraph system was used to visualize the flame front development. Three different obstacles were used, and their corresponding sequential images are presented and used to quantify the shape and location of the flame front during its propagation. Our experimental results for flame acceleration showed similar results as the literature: the flame accelerates as it passes over the obstacles and then decelerates due to the existence of a recirculation zone behind the obstacles. However, significant changes in flame structures and turbulent transitions were found for the three different obstacles. It is found that the passage, which is composed of the surface shape of the obstacle and the inner wall of chamber, is critical to the shape of the flame front and propagation of the flame. The obstacle with the largest volume results in the fastest flame acceleration. © 2007 American Institute of Chemical Engineers Process Saf Prog, 2008
Quantitative determination of lysozyme‐ligand binding in the solution and gas phases by electrospray ionisation mass spectrometry
Authors: Veros Christopher T. , Oldham Neil J. 
Published: October 2007

AbstractAffinity constants for the binding of a range of substrate and non‐substrate oligosaccharides to hen egg white lysozyme were determined by direct observation of the protein.ligand complexes using electrospray ionisation mass spectrometry (ESI‐MS) with a chip‐based nano‐ESI source. The values obtained for a series of β‐1,4‐N‐acetylglucosamine oligomers (NAGn) were found to be in good agreement with those determined by fluorescence measurement. Oligomers of α‐1,4‐glucose (Glcn), which are believed to bind to lysozyme non‐specifically, exhibited a 106‐ to 108‐fold lower affinity for the enzyme. Lysozyme.NAGn complexes displayed an increase in Ka from n = 2 to n = 4, but then reached a plateau. In contrast non‐specific lysozyme.Glcn complexes showed no such trend. Determination of gas‐phase complex stability was achieved by quantitative collision‐induced dissociation (CID) and infrared multiphoton dissociation (IRMPD) measurements. The collision energy (Ec50) or laser power (IRMPD50) required to dissociate precursor ions to 50% of their original intensity was determined for lysozyme.NAGn and Glcn complexes using the [M+8H]8+ charge state. An excellent correlation between trends in Ka and gas‐phase stability was seen for NAGn oligomers bound to lysozyme, whereas no such relationship was observed with the non‐specific, weaker lysozyme.Glcn complexes. These results illustrate that ESI‐MS can be used to quantify the interactions between lysozyme and oligosaccharides in both the solution and gas phase and that measurement of gas‐phase complex stability by CID or IRMPD can provide information about specific solution binding events. Copyright © 2007 John Wiley & Sons, Ltd.
Multi‐class confirmatory method for analyzing trace levels of tetracyline and quinolone antibiotics in pig tissues by ultra‐performance liquid chromatography coupled with tandem mass spectrometry
Authors: Shao Bing , Jia Xiaofei , Wu Yongning , Hu Jianying , Tu Xiaoming , Zhang Jing 
Published: October 2007

AbstractAn ultra‐performance liquid chromatography coupled with tandem mass spectrometry (UPLC/MS/MS) method was developed to screen and confirm multi‐class veterinary drug residues in pig tissues including pig kidney, liver and meat. Twenty‐one drugs of two different classes including seven tetracyclines and four types of quinolones (quinoline, naphthyridine, pyridopyrimidine and cinoline) were determined simultaneously in a single run. The homogenized sample tissues were extracted with EDTA–McIlvaine buffer solution and further purified using a polymer‐based Oasis HLB solid‐phase extraction (SPE) cartridge. An ACQUITY UPLC™ BEH C18 column was used to separate the analytes followed by tandem mass spectrometry using an electrospray ionization source. MS data acquisition was performed in the positive ion multiple reaction monitoring mode, selecting two ion transitions for each target compound. Recovery studies were performed at different fortification levels. The overall average recoveries from pig muscle, kidney, and liver fortified with quinolones and tetracyclines at three levels ranged from 80.2 to 117.8% based on the use of matrix‐fortified calibration with the coefficients of variation ranging from 2.1 to 17.8% (n = 6). The limits of quantitation (LOQs) of quinolones and tetracyclines in different tissues ranged from 0.03–4.50 µg/kg and 0.16–10.00 µg/kg, respectively. The effects of the extraction solvent, SPE cartridge, elution solvent and sample matrix on the analyte recovery as well as the effects of the mobile phase composition and column temperature on the chromatographic behavior were also studied. Copyright © 2007 John Wiley & Sons, Ltd.
The diameter of sparse random graphs
Authors: Fernholz Daniel , Ramachandran Vijaya 
Published: October 2007

AbstractWe derive an expression of the form c ln n + o(ln n) for the diameter of a sparse random graph with a specified degree sequence. The result holds asymptotically almost surely, assuming that certain convergence and supercriticality conditions are met, and is applicable to the classical random graph Gn,p with np = Θ(1) + 1, as well as certain random power law graphs. © 2007 Wiley Periodicals, Inc. Random Struct. Alg., 2007
Development and validation of time‐series synthesizers of rain attenuation for Ka‐band and Q/V‐band satellite communication systems
Authors: Lemorton Joël , Castanet Laurent , Lacoste Frédéric , Riva Carlo , Matricciani Emilio , Fiebig Uwe‐Carsten , Van de Kamp Max , Martellucci Antonio 
Published: October 2007

AbstractThe aim of this paper is to present recent developments in terms of propagation time‐series synthesizers, carried out in the framework of the ESA study 16865/03/NL/EC ‘Development of propagation models for telecommunication satellite systems’ (ONERA Final Report RF 4/07757/DEMR, 2004). The paper is composed of three parts: a review of the initial requirements related to propagation time series for system performance simulation, a description of a collection of rain attenuation time‐series synthesizers and of their related input parameters, and a comparative analysis of the output characteristics of these time‐series synthesizers as compared with experimental data collected during the OLYMPUS and ITALSAT propagation experiments. Copyright © 2007 John Wiley & Sons, Ltd.
Sequential causal inference: Application to randomized trials of adaptive treatment strategies
Authors: Dawson Ree , Lavori Philip W. 
Published: October 2007

AbstractClinical trials that randomize subjects to decision algorithms, which adapt treatments over time according to individual response, have gained considerable interest as investigators seek designs that directly inform clinical decision making. We consider designs in which subjects are randomized sequentially at decision points, among adaptive treatment options under evaluation. We present a sequential method to estimate the comparative effects of the randomized adaptive treatments, which are formalized as adaptive treatment strategies. Our causal estimators are derived using Bayesian predictive inference. We use analytical and empirical calculations to compare the predictive estimators to (i) the ‘standard’ approach that allocates the sequentially obtained data to separate strategy‐specific groups as would arise from randomizing subjects at baseline; (ii) the semi‐parametric approach of marginal mean models that, under appropriate experimental conditions, provides the same sequential estimator of causal differences as the proposed approach. Simulation studies demonstrate that sequential causal inference offers substantial efficiency gains over the standard approach to comparing treatments, because the predictive estimators can take advantage of the monotone structure of shared data among adaptive strategies. We further demonstrate that the semi‐parametric asymptotic variances, which are marginal ‘one‐step’ estimators, may exhibit significant bias, in contrast to the predictive variances. We show that the conditions under which the sequential method is attractive relative to the other two approaches are those most likely to occur in real studies. Copyright © 2007 John Wiley & Sons, Ltd.
Estimation of treatment effect adjusting for treatment changes using the intensity score method: Application to a large primary prevention study for coronary events (MEGA study)
Authors: Tanaka Yukari , Matsuyama Yutaka , Ohashi Yasuo 
Published: October 2007

AbstractThe MEGA study was a prospective, randomized, open‐labeled, blinded‐endpoints study conducted in Japan to evaluate the primary preventive effect of pravastatin against coronary heart disease (CHD), in which 8214 subjects were randomized to diet or diet plus pravastatin. The intention‐to‐treat (ITT) analysis showed that pravastatin reduced the incidence of CHD (hazard ratio=0.67; 95 per cent confidence interval (CI): 0.49–0.91) and of stroke events, which was the secondary endpoint in the MEGA study (hazard ratio=0.83; 95 per cent CI: 0.57–1.21). Owing to considerable treatment changes, it is also of interest to estimate the causal effect of treatment that would have been observed had all patients complied with the treatment to which they were assigned. In this paper, we present an intensity score method developed for clinical trials with time‐to‐event outcomes that correct for treatment changes during follow‐up. The proposed method can be easily extended to the estimation of time‐dependent treatment effects, where the technique of g‐estimation has been difficult to apply in practice. We compared the performances of the proposed method with other methods (as‐treated, ITT, and g‐estimation analysis) through simulation studies, which showed that the intensity score estimator was unbiased and more efficient. Applying the proposed method to the MEGA study data, several prognostic factors were associated with the process of treatment changes, and after adjusting for these treatment changes, larger treatment effects for pravastatin were observed for both CHD and stroke events. The proposed method provides a valuable and flexible approach for estimating treatment effect adjusting for non‐random non‐compliance. Copyright © 2007 John Wiley & Sons, Ltd.
Controlling the type 1 error rate in non‐inferiority trials
Authors: Snapinn Steven , Jiang Qi 
Published: October 2007

AbstractTwo different approaches have been proposed for establishing the efficacy of an experimental therapy through a non‐inferiority trial: The fixed‐margin approach involves first defining a non‐inferiority margin and then demonstrating that the experimental therapy is not worse than the control by more than this amount, and the synthesis approach involves combining the data from the non‐inferiority trial with the data from historical trials evaluating the effect of the control. In this paper, we introduce a unified approach that has both these approaches as special cases and show how the parameters of this approach can be selected to control the unconditional type 1 error rate in the presence of departures from the assumptions of assay sensitivity and constancy. It is shown that the fixed‐margin approach can be extremely inefficient and that it is always possible to achieve equivalent control of the unconditional type 1 error rate, with higher power, by using an appropriately chosen synthesis method. Copyright © 2007 John Wiley & Sons, Ltd.
Correction
Authors: Wu Yujun , Shih Weichung J. , Moore Dirk F. 
Published: October 2007

Abstract‘Estimating a survival curve with unlinked entry and failure times’, by Yujun Wu, Weichung J. Shih and Dirk F. Moore (Statistics in Medicine 2007; 26:3624–3638).(1) Equation (5) on page 3629 reads

which should read as

(2) Equation (7) on page 3630 reads

which should read as
The relationship between feminine gender role stress and disordered eating symptomatology in women
Authors: Mussap Alexander J. 
Published: October 2007

AbstractA questionnaire was administered to 124 women aged between 18 and 40 years (M = 24.49; SD = 4.9) to explore the relationship between feminine gender role stress and disordered eating symptomatology. Fear of being unattractive (a subscale of the Feminine Gender Role Stress scale) correlated with the dietary restraint, eating concern, bingeing and purging subscales of the Eating Disorder Examination‐Questionnaire, while fear of being assertive correlated with the eating concern subscale. These relationships were mediated primarily by body dissatisfaction and by a tendency towards overcontrol. Although interpretation is limited by the cross‐sectional design employed, these results add to evidence that the stress of conforming to the feminine role is associated with a range of unhealthy body change attitudes and behaviours. Copyright © 2007 John Wiley & Sons, Ltd.