bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analyzing the catalytic mechanism of MPtpA: A low molecular weight protein tyrosine phosphatase from Mycobacterium tuberculosis through site‐directed mutagenesis
Authors: Madhurantakam Chaithanya , Chavali Venkata Ramana Murthy , Das Amit Kumar 
Published: November 2007

AbstractMycobacterium tuberculosis adopts various measures to escape from the hostile environment of the host cells. A low molecular weight protein tyrosine phosphatase (LMWPTPase) MPtpA was found to be active in virulent mycobacterial forms during the phagocytosis process. To ascertain the importance of conserved residues Cys11, Arg17, and Asp126 in the catalytic mechanism of MPtpA, site‐directed mutagenesis was performed, namely C11S, R17A, D126A, and D126N. Kinetic characterization of wild‐type and the mutant MPtpAs using para‐nitrophenyl phosphate revealed the reaction mechanism followed by this LMWPTPase and it is similar to the other PTPases. All the LMWPTPases have a common signature motif, ‘C(X)5R(S/T)’ and an Asp as the general acid residue and the mechanism followed by MPtpA can be aptly attributed to other LMWPTPases as well, considering the similar three‐dimensional conformation. We have shown that the mutations caused major changes in the chemical environment surrounding the mutated residues and resulted in the decrease of catalytic activity significantly. Inhibition kinetics was performed with phosphate analogues: sodium molybdate, sodium orthovanadate, and sodium tungstate. Proteins 2008. © 2007 Wiley‐Liss, Inc.
The balance between the rates of incorporation and pyrophosphorolytic removal influences the HIV‐1 reverse transcriptase bypass of an abasic site with deoxy‐, dideoxy‐, and ribonucleotides
Authors: Sharma Bechan , Crespan Emmanuele , Villani Giuseppe , Maga Giovanni 
Published: November 2007

AbstractAbasic (AP) sites pose a potential danger to HIV‐1 replication. HIV‐1 RT has been shown to preferentially incorporate purines opposite an AP site, and subsequently extend from the lesion. While it is clear that AP sites are bypassed inefficiently and are major sites of RT pausing, detailed kinetic analysis of the relative contributions of both the incorporation and the pyrophosphorolytic reactions in translesion synthesis by HIV‐RT is still lacking. Investigation of the molecular basis of these processes is important, in light of the fact that HIV‐1 RT is the major target for anti‐HIV chemotherapy, and its low fidelity is an essential determinant of the extraordinary genetic variability of HIV‐1, which is important for the appearance of mutant viruses resistant to chemotherapy. Here, we analyzed the effects of the presence of an AP site on the template strand on the catalytic properties of the DNA‐dependent polymerization reaction as well as on the phosphorolytic activity of HIV‐1 RT, in the presence of deoxy‐, dideoxy,‐ and ribonucleotides. We find that AP sites can substantially influence the substrate specificity of HIV‐1 RT and that pyrophosphorolysis plays a significant role in determining the ability of HIV‐1 RT to (mis)incorporate nucleotides Proteins 2008. © 2007 Wiley‐Liss, Inc.
Problem of aspartimide formation in Fmoc‐based solid‐phase peptide synthesis using Dmab group to protect side chain of aspartic acid
Authors: Ruczyński JarosŁaw , Lewandowska Brygida , Mucha Piotr , Rekowski Piotr 
Published: November 2007

AbstractThe sequence‐dependent, acid‐ or base‐catalysed aspartimide formation is one of the most serious side reactions in solid‐phase synthesis of peptides containing aspartic acid. In the present work, we investigated the susceptibility of 4‐{N‐[1‐(4,4‐dimethyl‐2,6‐dioxocyclohexylidene)‐3‐methylbutyl]amino}benzyl (Dmab), an aspartic acid β‐carboxy side‐chain protecting group, for aspartimide formation. As a model, 15‐amino acid‐residue galanin fragment analogue containing the Asp‐Ala motif was used during Fmoc‐based solid‐phase synthesis. Our study showed a strong tendency of Dmab‐protected peptide to form aspartimide with unusual high efficiency. Furthermore, to investigate the susceptibility of Asp‐Ala motif for aspartimide formation during the synthesis using Asp(ODmab), a 5‐amino acid‐residue galanin fragment LGPDA, different types of resin linkers, variety of Fmoc‐deprotection conditions and coupling methods were applied. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Binding of nanoparticle receptors to peptide α‐helices using amino acid‐functionalized nanoparticles
Authors: Ghosh Partha S. , Han Gang , Erdogan Belma , Rosado Olga , Rotello Vincent M. 
Published: November 2007

AbstractNanoparticles provide large surface areas and controlled surface functionality and structure, making them excellent scaffolds for peptide recognition. A family of nanoparticles has been fabricated by amino acid functionalization to afford tailored surfaces. These particles are complementary to a tetraaspartate peptide (TAP) featuring cofacial anionic functionality when in the α‐helical conformation. The functional groups present on these nanoparticle surfaces provide a tool to investigate the contribution of various noncovalent interactions at the nanoparticle–peptide interface. The ability of these particles to enforce the folding of the peptide into an α‐helix was explored, demonstrating high helicity induction with particles featuring dicationic amino acids such as lysine or histidine, and little or no helix stabilization with hydrophobic amino acid termini. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Synthesis and antibody recognition of synthetic antigens from MUC1
Authors: Bánóczi Zoltán , Mezõ Gábor , Windberg Emõke , Uray Katalin , Majer Zsuzsa , Hudecz Ferenc 
Published: November 2007

AbstractIn the altered form of MUC1 mucin associated with breast cancer, the highly immunogenic sequence PDTRPAP is exposed, and may be an immunologically relevant target for the development of diagnostics or cancer immunotherapy. In this study, we report the preparation and antibody binding properties of monomeric and dimeric MUC1 peptides containing the epitope region recognized by monoclonal antibody (mAb) C595. Peptides contained a single or two copies of the whole 20‐mer repeat unit (VTSAPDTRPAPGSTAPPAHG) of MUC1 protein. MUC1 40‐mer peptides were prepared by the condensation of semi‐protected fragments of the repeat unit, in solution or by chemical ligation. In the first case, cyclohexyl‐type protecting groups were used for the synthesis of semi‐protected fragments by the Boc/Bzl strategy. Unprotected fragments were used in the chemical ligation to produce thioether linkages. In one of the fragments, a Gly residue was replaced by Cys at the C‐terminus and the other fragment was chloroacetylated at the N‐terminus. In addition, the short peptide APDTRPAPG, and its disulfide dimer, (APDTRPAPGC)2 were produced. The antibody binding properties of these MUC1 peptide constructs were tested by competition enzyme‐linked immunosorbent assay (ELISA). The short epitope region peptide, APDTRPAPG and its dimer (APDTRPAPGC)2 showed higher IC50 values (IC50 = 56.3 and 53.2 µmol/l, respectively). While the 20‐mer peptide (IC50 = 25.9 µmol/l) and more markedly its 40‐mer dimers (IC50 = 0.62 and 0.78 µmol/l) were recognized better. CD data obtained in water or in TFE indicated no significant conformational differences between the 20‐mer and 40‐mer peptides. We found a high level of similarity between the binding properties of the 40‐mer peptides with amide or thioether links, providing a new possibility to build up oligomeric MUC1 peptides by thioether bond formation. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
A study of the effect of pictorial markings and warning labels on handling of packages in the DHL single‐parcel environment
Authors: Singh J. , Singh S. P. , Voss T. , Saha K. 
Published: November 2007

AbstractOver the past two decades, there has been a heavy influx in the number of direct‐to‐consumer express shipments of packaged products. As a consequence, parcel delivery companies, such as DHL, FedEx and UPS, have strengthened their presence in air transport. This study measured and analysed the effect of moving single packages through air shipments in the USA using one of the newest service providers, DHL. The study also quantified the effect of placing pictorial markings and warning labels on mid‐sized and lightweight packages when using Next‐Day and 2nd Day services provided by the carrier DHL. Instrumented packages measuring 0.38  m × 0.34  m × 0.34  m and weighing 6.8  kg were shipped from Michigan to California and New York. A total of 48 trips were conducted to collect the data for this study.The results show that for the Next‐Day and 2nd Day service, packages with labels, as compared with those without labels, were subjected to approximately the same number of drops for shipment to California, and approximately 35% less drops for shipments to New York. The drop‐height data for the shipments are presented in terms of drop heights associated with the 90, 95 and 99th percentile of occurrence. Impact orientation is also discussed. Copyright © 2007 John Wiley & Sons, Ltd.
Quality of orange juice in barrier packaging material
Authors: Berlinet C. , Brat P. , Ducruet V. 
Published: November 2007

AbstractThe vitamin C content and the colour of orange juice made from concentrate were measured during 9 months of storage at 20°C either under artificial light or in darkness. The packaging materials used were glass, standard monolayer polyethylene terephthalate (PET) and multilayer PET (PET/nylon and oxygen scavenger/PET) containers. In this experiment, all bottles were sealed with aluminium foil in order to avoid any cap effect. The results showed that in plastic packaging materials, the loss of vitamin C was related to the oxygen permeability, and that glass provided the best preservation of ascorbic acid. No statistical difference (p < 0.05) was revealed between the vitamin C content in the juice stored under artificial light or in darkness, whatever the packaging used. The modification of colour was studied with the L, a* and b* values during storage at 20°C under artificial light. L and b* decreased, revealing a reduction of lightness and yellow colour of the juice, whereas a* increased, due to the formation of brown pigments. This change in colour was partly related to the oxygen permeability of the packaging used.The losses of aroma compounds by permeation through the bottle (PET) and the cap (high‐density polyethylene, HDPE) have also been investigated. The results showed that permeation mainly took place through the cap. The use of a multilayer cap [HDPE with internal barrier layer of low‐density polyethylene (LDPE)/EvOH/LDPE] considerably limited the permeation of the aroma compounds studied, whatever the PET bottle used. Copyright © 2007 John Wiley & Sons, Ltd.
Characterization of phenolic compounds in the crude extract of Hedysarum multijugum by high‐performance liquid chromatography with electrospray ionization tandem mass spectrometry
Authors: Yang Min , Wang Wei , Sun Jianghao , Zhao Yuying , Liu Yi , Liang Hong , Guo De‐an 
Published: November 2007

AbstractThe fragmentation behavior of four types of phenolic compounds: coumestans, pterocarpenes, benzofurans and isoflavones, were studied using electrospray ionization multistage mass spectrometry (ESI‐MSn) (n = 2–5) in negative ion mode. Losses of methyl (15 Da), CO (28 Da), CO2 (44 Da), isopropyl (43 Da) and isobutenyl (55 Da) were dominating fragmentation patterns. Different positions and numbers of the substituents also led to the different fragmentation behavior. These fragmentation rules were applied for the identification of constituents in methanolic extracts of Hedysarum multijugum, in which 29 compounds were characterized, including nine new compounds. The method established in this study could be applied to the comprehensive quality control of the herb and its formulations. It could also be applied to the biological and pharmacological research of traditional Chinese medicines. Copyright © 2007 John Wiley & Sons, Ltd.
Electron ionization mass spectra of aryl‐ and benzyl‐substituted 2,3‐dihydroimidazo[1,2‐a]pyrimidine‐5,7(1H,6H)‐diones
Authors: Martiskainen Olli , Kivelä Henri , Matosiuk Dariusz , Szacon Elzbieta , Rzadkowska Marzena , Pihlaja Kalevi 
Published: November 2007

AbstractThe electron ionization mass spectra of the 1‐phenyl‐, 1‐benzyl‐ and 6‐benzyl‐1‐phenyl‐2,3‐dihydroimidazo[1,2‐a]pyrimidine‐5,7(1H,6H)‐dione derivatives were recorded at 70 eV to find out the effects of substituents on their fragmentations. Fragmentation pathways were studied using B/E and B2/E scans. Some fragmentations involved the loss of C3HO2 or carbon suboxide. The possibility of keto‐enol tautomerism was also studied. For comparison selected compounds were studied using 1H and 13C NMR spectroscopy to reveal the presence of possible tautomerism. Some ions including [MOH]+ and [MHCO]+ and NMR results indicate that the enol form is predominant both in the gas and in the liquid phase. Copyright © 2007 John Wiley & Sons, Ltd.
Evaluation of propolis polyphenols absorption in humans by liquid chromatography/tandem mass spectrometry
Authors: Gardana Claudio , Simonetti Paolo , Berti Cristiana , Pietta Piergiorgio 
Published: November 2007

AbstractPropolis has various biological activities such as antibacterial, antiviral, antioxidant, immunostimulating and antiinflammatory, which are generally ascribed to the polyphenolic fraction. The aim of this study was to evaluate the absorption of the main polyphenols [caffeic acid (CA), pinobanksin‐5methyl ether (P‐5ME), pinobanksin (Pb), chrysin (C), pinocembrin (P), galangin (G), pinobanksin‐3‐acetate, pinobanksin esters and caffeic acid phenylethyl ester (CAPE)] from a dewaxed and standardized extract of propolis (EPID®). Fifteen healthy volunteers consumed 5 mL EPID® in water, corresponding to 125 mg of flavonoids. Blood samples were collected before, each hour for 8 h and 24 h after EPID® intake. After deconjugation byβ‐glucuronidase/sulfatase the plasma samples were analyzed by a selective liquid chromatography/tandem mass spectrometry (LC/MS/MS) method using morin as internal standard (I.S.). A kinetic profile characterized by two tmax, respectively at 1 h and about 5 h post‐ingestion, was observed in all the subjects. The two peaks may be due to enterohepatic cycling. Among the various polyphenols ingested, only P‐5ME, Pb, C, P and G were detected in plasma and Cmaxt1hwere 65.7 ± 13.3, 46.5 ± 12.7, 79.5 ± 18.6, 168.1 ± 16.3 and 113.7 ± 16.8 ng/mL, respectively. These levels decreased significantly after 8 h and were no longer detectable 24 h after EPID® intake. The recovery of the extraction for CA, Pb, C, P, G and I.S. from spiked plasma was 95.2 ± 3.1, 93.1 ± 3.6, 91 ± 2.5, 96.4 ± 4.2, 93.4 ± 2.4 and 85.5 ± 2.4%, respectively. The results of this study evidence that flavonoids from EPID® are absorbed, metabolized and Pb‐5ME and G seem to have apparent absorption, measured as (AUC/dose), higher than C, P and Pb. Copyright © 2007 John Wiley & Sons, Ltd.
Rapid determination of amino acid incorporation by stable isotope labeling with amino acids in cell culture (SILAC)
Authors: Schmidt Frank , Strozynski Margarita , Salus Sandra S. , Nilsen Hilde , Thiede Bernd 
Published: November 2007

AbstractStable isotope labeling with amino acids in cell culture (SILAC) has evolved to be a major technique for quantitative proteomics using cell cultures. We developed a rapid method to follow and determine the incorporation of arginine and lysine. Analysis of the heavy state is required to avoid quantification errors. Moreover, the mixture of light and heavy states can be exploited to normalize the protein amount for subsequent relative quantification experiments. Therefore, peptides from different cell lines were extracted with 0.1% trifluoroacetic acid and analyzed by matrix‐assisted laser desorption/ionization tandem time‐of‐flight (MALDI‐TOF/TOF) mass spectrometry (MS). This analysis was highly reproducible and was performed in less than 2 h, significantly faster than other methods for the same purpose. Similar peptide mass profiles were obtained for human EBV‐transformed B, Jurkat T, and HeLa cells as well as for mouse embryonic fibroblasts. Proteolytic fragments of 27 human proteins were identified with 56 peptides by MALDI‐MS/MS and can be used as a database for these kinds of experiments. Sequencing revealed that the peptides were predominantly amino‐ and carboxy‐terminal protein fragments displaying a specificity characteristic of the acidic proteases cathepsin D and E. Many of the identified peptides contained arginine and/or lysine, allowing determination of the incorporation rate of these amino acids. Furthermore, the rate of conversion of arginine into proline could be monitored easily. Copyright © 2007 John Wiley & Sons, Ltd.
Electrospray ionization mass spectral studies of N,N‐dialkylaminoethane‐2‐sulphonic acids
Authors: Lakshmi V. V. S. , Prabhakar S. , Murty M. R. V. S. , Vairamani M. 
Published: November 2007

AbstractOxidative reactions of VX type compounds and N,N‐dialkylaminoethane‐2‐thiols that are precursors for VX compounds produce N,N‐dialkylaminoethane‐2‐sulphonic acids, N(R1)(R2)‐CH2‐CH2SO3H (where R1 and R2 = methyl, ethyl, n‐propyl and isopropyl, 1–10), as the degradation products, and these degradation products are considered as markers for the detection of chemicals listed in the schedules of Chemical Weapons Convention (CWC) chemicals. Off‐site detection of such degradation products in aqueous samples is an important task in the verification of CWC‐related chemicals. Here we report a simple method involving the direct analysis of aqueous samples using positive and/or negative ion electrospray ionization (ESI) for the screening, detection and identification of N,N‐dialkylaminoethane‐2‐sulphonic acids, avoiding sample preparation and chromatographic steps. The positive ion ESI mass spectra of all the compounds result in abundant [M+Na]+ ions, and the negative ion spectra show abundant [M−H]− ions to confirm their molecular weight. The collision‐induced dissociation spectra of [M+Na]+ and [M−H]− give characteristic product ions by which it is easy to detect and identify all the studied N,N‐dialkylaminoethane‐2‐sulphonic acids including those of isomeric compounds. The method is successfully applied to detect the spiked chemical, N,N‐diisopropylaminoethane‐2‐sulphonic acid, present in a water sample received in a proficiency test. Copyright © 2007 John Wiley & Sons, Ltd.
Sequentially testing for a gene–drug interaction in a genomewide analysis
Authors: Kelly Patrick , Zhou Yinghui , Whitehead John , Stallard Nigel , Bowman Clive 
Published: November 2007

AbstractAssaying a large number of genetic markers from patients in clinical trials is now possible in order to tailor drugs with respect to efficacy. The statistical methodology for analysing such massive data sets is challenging. The most popular type of statistical analysis is to use a univariate test for each genetic marker, once all the data from a clinical study have been collected. This paper presents a sequential method for conducting an omnibus test for detecting gene–drug interactions across the genome, thus allowing informed decisions at the earliest opportunity and overcoming the multiple testing problems from conducting many univariate tests.We first propose an omnibus test for a fixed sample size. This test is based on combining F‐statistics that test for an interaction between treatment and the individual single nucleotide polymorphism (SNP). As SNPs tend to be correlated, we use permutations to calculate a global p‐value. We extend our omnibus test to the sequential case. In order to control the type I error rate, we propose a sequential method that uses permutations to obtain the stopping boundaries. The results of a simulation study show that the sequential permutation method is more powerful than alternative sequential methods that control the type I error rate, such as the inverse‐normal method. The proposed method is flexible as we do not need to assume a mode of inheritance and can also adjust for confounding factors. An application to real clinical data illustrates that the method is computationally feasible for a large number of SNPs. Copyright © 2007 John Wiley & Sons, Ltd.
A Bayesian approach for sample size determination in method comparison studies
Authors: Yin Kunshan , Choudhary Pankaj K. , Varghese Diana , Goodman Steven R. 
Published: November 2007

AbstractStudies involving two methods for measuring a continuous response are regularly conducted in health sciences to evaluate agreement of a method with itself and agreement between methods. Notwithstanding their wide usage, the design of such studies, in particular, the sample size determination, has not been addressed in the literature when the goal is the simultaneous evaluation of intra‐ and inter‐method agreement. We fill this need by developing a simulation‐based Bayesian methodology for determining sample sizes in a hierarchical model framework. Unlike a frequentist approach, it takes into account uncertainty in parameter estimates. This methodology can be used with any scalar measure of agreement available in the literature. We demonstrate this for four currently used measures. The proposed method is applied to an ongoing proteomics project, where we use pilot data to determine the number of individuals and the number of replications needed to evaluate the agreement between two methods for measuring protein ratios. We also apply our method to determine the sample size for an experiment involving measurement of blood pressure. Copyright © 2007 John Wiley & Sons, Ltd.
Predicting accrual in clinical trials with Bayesian posterior predictive distributions
Authors: Gajewski Byron J. , Simon Stephen D. , Carlson Susan E. 
Published: November 2007

AbstractInvestigators need good statistical tools for the initial planning and for the ongoing monitoring of clinical trials. In particular, they need to carefully consider the accrual rate—how rapidly patients are being recruited into the clinical trial. A slow accrual decreases the likelihood that the research will provide results at the end of the trial with sufficient precision (or power) to make meaningful scientific inferences. In this paper, we present a method for predicting accrual. Using a Bayesian framework we combine prior information with the information known up to a monitoring point to obtain a prediction. We provide posterior predictive distributions of the accrual. The approach is attractive since it accounts for both parameter and sampling distribution uncertainties. We illustrate the approach using actual accrual data and discuss practical points surrounding the accrual problem. Copyright © 2007 John Wiley & Sons, Ltd.
The intellectual structure of the strategic management field: an author co‐citation analysis
Authors: Nerur Sridhar P. , Rasheed Abdul A. , Natarajan Vivek 
Published: November 2007

AbstractThis paper complements a recent study by Ramos‐Rodriguez and Ruiz‐Navarro (2004) that investigated the intellectual structure of the strategic management field through co‐citation analysis. By using authors as the units of analysis and incorporating all the citations that are included in the Science Citation Index and the Social Science Citation Index, we trace the evolution of the intellectual structure of the strategic management field during the period 1980–2000. Using a variety of data analytic techniques such as multidimensional scaling, factor analysis, and Pathfinder analysis, we (1) delineate the subfields that constitute the intellectual structure of strategic management; (2) determine the relationships between the subfields; (3) identify authors who play a pivotal role in bridging two or more conceptual domains of research; and (4) graphically map the intellectual structure in two‐dimensional space in order to visualize spatial distances between intellectual themes. The analysis provides insights about the influence of individual authors as well as changes in their influence over time. Copyright © 2007 John Wiley & Sons, Ltd.