bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enzymatic characterization and crystal structure analysis of the D‐alanine‐D‐alanine ligase from Helicobacter pylori
Authors: Wu Dalei , Zhang Liang , Kong Yunhua , Du Jiamu , Chen Shuai , Chen Jing , Ding Jianping , Jiang Hualiang , Shen Xu 
Published: March 2008

AbstractD‐Alanine‐D‐alanine ligase is the second enzyme in the D‐Ala branch of bacterial cell wall peptidoglycan assembly, and recognized as an attractive antimicrobial target. In this work, the D‐Ala‐D‐Ala ligase of Helicobacter pylori strain SS1 (HpDdl) was kinetically and structurally characterized. The determined apparent Km of ATP (0.87 μM), the Km1 (1.89 mM) and Km2 of D‐Ala (627 mM), and the kcat (115 min−1) at pH 8.0 indicated its relatively weak binding affinity and poor catalytic activity against the substrate D‐Ala in vitro. However, by complementary assay of expressing HpDdl in Escherichia coli Δddl mutant, HpDdl was confirmed to be capable of D‐Ala‐D‐Ala ligating in vivo. Through sequence alignment with other members of the D‐Ala‐D‐X ligase superfamily, HpDdl keeps two conservatively substituted residues (Ile16 and Leu241) and two nonconserved residues (Leu308 and Tyr311) broadly located in the active region of the enzyme. Kinetic analyses against the corresponding HpDdl mutants (I16V, L241Y, L241F, L308T, and Y311S) suggested that these residues, especially Leu308 and Tyr311, might partly contribute to the unique catalytic properties of the enzyme. This was fairly proved by the crystal structure of HpDdl, which revealed that there is a 310‐helix (including residues from Gly306 to Leu312) near the D‐Ala binding region in the C‐terminal domain, where HpDdl has two sequence deletions compared with other homologs. Such 310‐helix may participate in D‐Ala binding and conformational change of the enzyme. Our present work hopefully provides useful information for understanding the D‐Ala‐D‐Ala ligase of Helicobacter pylori. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Effects of external interactions on protein sequence‐structure relations of beta‐trefoil fold
Authors: Li Mingfeng , Huang Yanzhao , Xiao Yi 
Published: March 2008

AbstractProteins with symmetric structures are ideal models to investigate the sequence‐structure relations. We investigate proteins with β‐trefoil fold and find they have different degrees of sequence symmetries although they show similar symmetric structures. To understand this, we calculate the strength of interactions of the β‐trefoil folds with surrounding environments and find the low degrees of sequence symmetries are often correlated with large external interactions. Our results give an additional confirmation of Anfinsen's thermodynamic hypothesis that protein structures are not only determined by their sequences but also by their surrounding environments. We suggest the external interactions should be considered additionally in protein structure prediction through ab initio folding. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Metabolism of olaquindox in rat liver microsomes: structural elucidation of metabolites by high‐performance liquid chromatography combined with ion trap/time‐of‐flight mass spectrometry
Authors: Liu Zhaoying , Huang Lingli , Dai Menghong , Chen Dongmei , Wang Yulian , Tao Yanfei , Yuan Zonghui 
Published: March 2008

AbstractOlaquindox (N‐(2‐hydroxyethyl)‐3‐methyl‐2‐quinoxalincarboxamide‐1,4‐dioxide) is a growth‐promoting feed additive for food‐producing animals. Its toxicity is closely related to the metabolism. The complete metabolic pathways of olaquindox are not revealed. To improve studies of the metabolism and toxicity of olaquindox, its biotransformation in rat liver microsomes and the structure of its metabolites using high‐performance liquid chromatography combined with ion trap/time‐of‐flight mass spectrometry (LC/MS‐ITTOF) were investigated. When olaquindox was incubated with an NADPH‐generating system and rat liver microsomes, ten metabolites (M1–M10) were detected. The structures of these metabolites were identified from mass spectra and comparison of their changes in their accurate molecular masses and fragment ions with those of the parent drug. With the high resolution and good mass accuracy achieved by this technique, the elemental compositions of the metabolites and their fragment ions were exactly determined. The results indicate that the N → O group reduction is the main metabolic pathway of olaquindox metabolism in rat liver microsomes, because abundant 1‐desolaquindox (M2), 4‐desolaquindox (M1) and bisdesoxyolaquindox (M9) were produced during the incubation step. Seven other minor metabolites were revealed which were considered to be hydroxylation metabolites, based on the position of the quinoxaline ring or 3‐methyl group and a carboxylic acid derivative on the side chain at position 2 of the quinoxaline ring. Among the identified metabolites, five new hydroxylated metabolites (M3–M7) were found for the first time in rat liver microsomes. This work will conduce to complete clarification of olaquindox metabolism, and improve the in vivo metabolism of olaquindox in food animals. Copyright © 2008 John Wiley & Sons, Ltd.
Quantitative determination of progesterones and corticosteroids in human urine using gas chromatography/mass spectrometry: application to pelvic organ prolapse patients
Authors: Shama Naz , Bai Sang Wook , Chung Bong Chul , Jung Byung Hwa 
Published: March 2008

AbstractA quantitative analytical method using gas chromatography/mass spectrometry (GC/MS) to determine urinary concentrations of eight progesterones and corticosteroids has been developed. After enzymatic hydrolysis with β‐glucouronidase/arylsulfatase, urine samples were extracted by simple one‐step solid‐phase extraction. Obtained extracts were derivatized with a mixture of N‐methyl‐N‐(trimethylsilyl)trifluoroacetamide/ammonium iodide/dithiothreitol and determined by GC/MS in selected ion monitoring mode to increase the sensitivity. d4‐Cortisol and d9‐progesterone were used as internal standards for two different steroid groups. The linear correlation coefficient was in the range of 0.9913 to 0.9998 and recoveries were over 80% for all compounds. Precision and accuracy were in the range of 0.9–18.1 and 84.1–118.7%, respectively. The limit of quantitation (LOQ) was 10 ng/mL for 11‐deoxycorticosterone and 21‐deoxycortisol and 5 ng/mL for all other analytes. The developed method was successfully applied on pelvic organ prolapsed patients (n = 10, age: 67.9 ± 4.9) and post‐menopausal (n = 10, age: 63.6 ± 5.5) control women. Urinary levels of most progesterones and corticosteroids except 11‐deoxycorticosterone decreased but only that of 17α‐hydroxyprogesterone significantly decreased in patients compared with the control groups. Thus, it is concluded that progesterones could be a factor in the pathogenesis of pelvic organ prolapse, and, among them, 17α‐hydroxyprogesterone could be a biomarker for pelvic organ prolapse. Copyright © 2008 John Wiley & Sons, Ltd.
Gas chromatography/mass spectrometry analysis of triacetone triperoxide (TATP) degradation products
Authors: Armitt David , Zimmermann Peter , Ellis‐Steinborner Simon 
Published: March 2008

AbstractInterest in the analysis and detection of triacetone triperoxide (TATP) and other organic peroxides has increased in recent years. Also of interest is the degradation and decomposition of the peroxides, not only to gain more detailed chemical information from organic peroxide samples, but also to investigate possible new procedures or mechanisms for chemical neutralisation. This report investigates the chemical degradation products of TATP after it has been treated with different acids within a sealed system over a period of 14 days. The samples were collected and analysed by solid‐phase microextraction (SPME) and direct liquid injection gas chromatography/mass spectrometry (GC/MS). The results of the experiments indicate that the rate of chemical degradation of TATP and the products formed are dependent on the type of acid. The observed differences enables the type of acid used in the degradation process to be determined, provide complementary information to identify the presence of TATP, and possibly indicate new pathways that may be used to chemically neutralise TATP. Copyright © 2008 Commonwealth of Australia. Published by John Wiley & Sons, Ltd.
Chemical derivatization of peptides containing phosphorylated serine/threonine for efficient ionization and quantification in matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry
Authors: Tsumoto Hiroki , Ra Moonjin , Samejima Keijiro , Taguchi Ryo , Kohda Kohfuku 
Published: March 2008

AbstractWe describe a useful method for the efficient ionization and relative quantification of peptides containing serine/threonine phosphorylation sites. This method is based on β‐elimination of the phosphate group from serine/threonine phosphorylation sites under alkaline conditions, followed by Michael addition reaction with N‐(2‐mercaptoethyl)‐6‐methylnicotinamide (MEMN). As a result of the derivatization reaction, the negatively charged phosphate group is substituted with the nicotinoyl moiety to improve the ionization efficiency of the derivatized peptide. The combination of d3‐labeled MEMN (d3‐MEMN) and MEMN (d0‐MEMN) generates a 3 Da mass difference between d3‐MEMN‐labeled and d0‐MEMN‐labeled peptides, which is a useful signature for the identification of peptides containing serine/threonine phosphorylation sites in the matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrum. Moreover, the mass difference is useful for the quantitative analysis of serine/threonine phosphorylation in proteins. In this paper, we describe the synthesis of d0/d3‐labeled MEMN and an application of our approach to model peptides and proteins. Copyright © 2008 John Wiley & Sons, Ltd.
Dual negative precursor ion scan approach for rapid detection of glutathione conjugates using liquid chromatography/tandem mass spectrometry
Authors: Mahajan Mukesh K. , Evans Christopher A. 
Published: March 2008

AbstractScreening for conjugates formed by the tripeptide glutathione with new chemical entities is an essential step during the drug discovery process, as the formation of these conjugates serves as an indicator for the presence of reactive electrophilic intermediates. To increase the selectivity and throughput of this analysis, various mass spectral scan types have evolved over time. Historically, samples were analyzed under positive ionization conditions for the neutral loss ofm/z129 (loss of the pyroglutamic acid moiety from glutathione); however, more recently, negative precursor ion scanning for the loss ofm/z272 (deprotonatedγ‐glutamyl‐dehydroalanyl‐glycine from glutathione) has emerged as a more selective tool. Further increasing the selectivity, we report on an extension of this methodology by incorporating a simultaneous dual negative precursor ion scan for two commonly observed ion fragments from glutathione conjugates,m/z272 and 254 (the dehydrated form ofm/z272). This negative dual precursor ion scan methodology was first validated using substrates known to undergo metabolic bioactivation (diclofenac, carbamazepine, and 3‐methyl indole) and has then been applied to the routine analysis of proprietary compounds undergoing active lead optimization. In comparison to alternative scan methodologies, the increased selectivity offered by this simultaneous dual precursor method results in a reduction in the generation of false positive results as well as reduced data interpretation time. Copyright © 2008 John Wiley & Sons, Ltd.
Classification of vegetable oils according to their botanical origin using sterol profiles established by direct infusion mass spectrometry
Authors: Lerma‐García María J. , Ramis‐Ramos Guillermo , Herrero‐Martínez José M. , Simó‐Alfonso Ernesto F. 
Published: March 2008

AbstractA simple and quick method to classify vegetable oils according to their botanical origin, based on direct infusion of sterol extracts into a mass spectrometer, was developed. Using mass spectrometry (MS) with either an electrospray ionization or an atmospheric pressure photoionization source, followed by linear discriminant analysis of the mass spectral data, oil samples corresponding to eight different botanical origins were perfectly classified with an excellent resolution among all the categories. An excellent correlation between the sterol profiles obtained by MS and by the official gas chromatography (with flame ionization detection) method was obtained. Thus, the proposed method is a promising alternative for sterol fingerprinting of vegetable oils, with the advantage that prior chromatographic separation is not required. Copyright © 2008 John Wiley & Sons, Ltd.
Direct analysis of illicit drugs by desorption atmospheric pressure photoionization
Authors: Kauppila Tiina J. , Arvola Ville , Haapala Markus , Pól Jaroslav , Aalberg Laura , Saarela Ville , Franssila Sami , Kotiaho Tapio , Kostiainen Risto 
Published: March 2008

AbstractThe feasibility of desorption atmospheric pressure photoionization (DAPPI) in the direct analysis of illicit drugs was demonstrated by the analysis of confiscated drug samples of various forms such as tablets, blotter paper, and plant resin and bloom. 3,4‐Methylenedioxymethamphetamine (MDMA), amphetamine, phenazepam, and buprenorphine were detected from the analyzed tablets, lysergic acid diethylamide (LSD) and bromobenzodifuranylisopropylamine (bromo‐Dragonfly, ABDF) from blotter paper, and Δ9‐tetrahydrocannabinol (THC) and cannabinol from Cannabis Sativa bloom and resin. The amphetamines, phenazepam and ABDF showed protonated molecules independent of the solvent used, whereas buprenorphine, LSD and the cannabinoids showed molecular ions with toluene and protonated molecules with acetone as the solvent. Copyright © 2008 John Wiley & Sons, Ltd.
Robotic system for no‐scar gastrointestinal surgery
Authors: Phee S. J. , Low S. C. , Sun Z. L. , Ho K. Y. , Huang W. M. , Thant Z. M. 
Published: March 2008

AbstractIntroductionFlexible endoscopy allows diagnostic and therapeutic interventions on the gastrointestinal (GI) tract. Simple procedures can be performed endoscopically using currently available tools. More advanced endoscopic surgical interventions are much desired and anticipated, yet they await improvements in instrumentation.MethodsPresented here is a master–slave robotic system designed for use with flexible endoscopy. The slave is a cable‐driven flexible robotic manipulator that can be attached to an endoscope, allowing two‐handed endoscopic manipulation with 9–12 degrees of freedom (DOF).ResultsFeasibility has been demonstrated in a porcine intragastric model.ConclusionsFurther studies should determine whether this novel device can overcome some of the instrumentation‐related challenges that have heretofore limited the development of natural orifice transluminal endoscopic surgery (NOTES). Copyright © 2008 John Wiley & Sons, Ltd.
Dynamic Variations in Adhesion of Self‐Assembled Monolayers on Nanoasperities Probed by Atomic Force Microscopy
Authors: Xu Chang , Jones Ryan L. , Batteas James D. 
Published: March 2008

AbstractOctadecyltriethoxysilane (OTE) self‐ assembled monolayers (SAMs) and their effects on friction and adhesion have been investigated on various combinations of functionalized and unfunctionalized silicon oxide surfaces including the oxidized surface of crystalline Si(100), silica nanoparticle films, and oxidized Si atomic force microscopy (AFM) tips. Force‐distance spectroscopy was utilized to probe and compare the properties of the OTE SAMs on silica asperities with nanoscale curvature against these same monolayers on surfaces with sub‐1 nm roughness (flat surfaces). It was found that adhesion between SAMs and silicon oxide surfaces can vary significantly when assembly takes place on surfaces with nanoscopic curvature as compared to flat surfaces. Observations indicate that the SAM structure present during force measurements is dynamic in nature, which yields different adhesion values when measured with variations of both tip‐sample contact time and tip‐approach/retract rates. These results point the need in reporting a number of measurement parameters when probing adhesion by SAM functionalized tips. SCANNING 30: 000–000, 2008. © 2008 Wiley Periodicals, Inc.
Morphology and Amine Accessibility of (3‐Aminopropyl) Triethoxysilane Films on Glass Surfaces
Authors: Wang Wei , Vaughn Mark. W. 
Published: March 2008

Abstract3‐Aminopropyl) triethoxysilane (APTES) is commonly used to functionalize glass substrates because it can form an amine‐reactive film that is tightly attached to the surface. In this study, we investigated the morphology and chemical reactivity of APTES films prepared on glass substrates using common deposition techniques. Films were prepared using concentrated vapor‐phase deposition, dilute vapor‐phase deposition, anhydrous organic‐phase deposition and aqueous‐phase deposition. All films were annealed, or cured, at 150 °C. The morphology of the films was quantified by fluorescence and by atomic force microscopy (AFM). The optical equivalent of the AFM images was computed and then used to directly compare optical and AFM images. Reactive amine density was determined by a picric acid assay and by a method that employed N‐succinimidyl 3‐[2‐pyridyldithio]‐propionamido (SPDP) cross‐linked rhodamine. Fluorescence and AFM images showed that silane films prepared from dilute vapor‐phase and aqueous‐phase deposition were more uniform and had fewer domains than those deposited by the other methods. The ratio of picric acid‐accessible amino groups to SPDP cross‐linked rhodamine‐accessible groups varied with the preparation method, suggesting reactant size‐dependent difference in amine accessibility. We found a larger number of accessible amino groups on films prepared by vapor‐phase deposition than on those prepared from solution deposition. The dilute vapor‐phase deposition technique produced relatively few domains, and it should be a good choice for bioconjugation applications. There were appreciable differences in the films produced by each method. We suggest that these differences originate from differences in film rearrangement during annealing. SCANNING 30: 000–000, 2008. © 2008 Wiley Periodicals, Inc.
PISA test items and school textbooks related to science: A textual comparison
Authors: Hatzinikita Vassilia , Dimopoulos Kostas , Christidou Vasilia 
Published: March 2008

AbstractThe paper compares the nature of the textual construction of the Programme for International Student Assessment (PISA) science test items and the Greek school science textbooks. This nature is determined by the interplay of the notions of classification (content specialization) and formality (code specialization) modulated by both the linguistic and the visual expressive modes. The results of the relevant analysis showed that the textual materials employed in PISA and in school textbooks are oppositional in nature. Specifically, while the linguistic mode of the PISA items tends to resemble texts falling within the public domain (nonspecialized content and code), the corresponding visual mode tends to resemble texts of the esoteric domain (specialized content and code) thus familiarizing students with the specialized conventions and ways of representing entities falling within the realm of technoscientific knowledge. On the other hand, school science textbooks tend to employ the linguistic and the visual mode in exactly the opposite way. These differences between PISA science items and school science textbooks could contribute to a disorientation of the students in relation to what is expected in each specific context. This disparity could potentially be one of the factors explaining the low level of Greek students' attainment in PISA. © 2008 Wiley Periodicals, Inc. Sci Ed 92:664–687, 2008
A more powerful exact test of noninferiority from binary matched‐pairs data
Authors: Lloyd Chris J. , Moldovan Max V. 
Published: March 2008

AbstractAssessing the therapeutic noninferiority of one medical treatment compared with another is often based on the difference in response rates from a matched binary pairs design. This paper develops a new exact unconditional test for noninferiority that is more powerful than available alternatives. There are two new elements presented in this paper. First, we introduce the likelihood ratio statistic as an alternative to the previously proposed score statistic of Nam (Biometrics 1997; 53:1422–1430). Second, we eliminate the nuisance parameter by estimation followed by maximization as an alternative to the partial maximization of Berger and Boos (Am. Stat. Assoc. 1994; 89:1012–1016) or traditional full maximization. Based on an extensive numerical study, we recommend tests based on the score statistic, the nuisance parameter being controlled by estimation followed by maximization. Copyright © 2008 John Wiley & Sons, Ltd.
Assessing the association between environmental impacts and health outcomes: A case study from Florida
Authors: Young Linda J. , Gotway Carol A. , Yang Jie , Kearney Greg , DuClos Chris 
Published: March 2008

AbstractThe Centers for Disease Control and Prevention (CDC) created the Environmental Public Health Tracking (EPHT) program to integrate hazard monitoring, exposure, and health effects surveillance into a cohesive tracking network. Part of Florida's effort to move toward implementation of EPHT is to develop models of the spatial and temporal association between myocardial infarctions (MIs) and ambient ozone levels in Florida. Existing data were obtained from Florida's Agency for Health Care Administration, Florida's Department of Environmental Protection, the U.S. Census Bureau, and CDC's Behavioral Risk Factor Surveillance System. These data were linked by both ignoring spatial support and using block kriging, a support‐adjusted approach. The MI data were indirectly standardized by age, race/ethnicity, and sex. The state of Florida was used as the comparison standard to compute the MI standardized event ratio (SER) for each county and each month. After the data were linked, global models were used initially to relate MIs to ambient ozone levels, adjusting for covariates. The global models provide an estimated relative MI SER for the state. Realizing that the association in MIs and ozone might change across locations, local models were used to estimate the relative MI SER for each county, again adjusting for covariates. Results differed, depending on whether the spatial support was ignored or accounted for in the models. The opportunities and challenges associated with EPHT analyses are discussed and future directions highlighted. Copyright © 2008 John Wiley & Sons, Ltd.
In situ EDXRF analyses on Renaissance plaquettes and indoor bronzes patina problems and provenance clues
Authors: Bonizzoni Letizia , Galli Anna , Poldi Gianluca 
Published: March 2008

AbstractThe preliminary work for the edition of the complete catalogs of Civic collections of Vicenza (Italy) was an occasion to study by energy dispersive x‐ray fluorescence (EDXRF) about 30 small bronzes and plaquettes of Italian Renaissance. It was necessary to perform in situ analyses directly in the museum without any possibility of sampling or cleaning the objects. We report the results of quantitative analysis on principal and trace elements; moreover, patina problems and the possible clues for raw materials provenance are faced. Copyright © 2008 John Wiley & Sons, Ltd.