bluuebunny/crossref_metadata_2025_split huggingface dataset:
A mariner transposon vector adapted for mutagenesis in oral streptococci
Authors: Nilsson Martin , Christiansen Natalia , Høiby Niels , Twetman Svante , Givskov Michael , Tolker‐Nielsen Tim 
Published: April 2014

AbstractThis article describes the construction and characterization of a mariner‐based transposon vector designed for use in oral streptococci, but with a potential use in other Gram‐positive bacteria. The new transposon vector, termed pMN100, contains the temperature‐sensitive origin of replication repATs‐pWV01, a selectable kanamycin resistance gene, a Himar1 transposase gene regulated by a xylose‐inducible promoter, and an erythromycin resistance gene flanked by himar inverted repeats. The pMN100 plasmid was transformed into Streptococcus mutans UA159 and transposon mutagenesis was performed via a protocol established to perform high numbers of separate transpositions despite a low frequency of transposition. The distribution of transposon inserts in 30 randomly picked mutants suggested that mariner transposon mutagenesis is unbiased in S. mutans. A generated transposon mutant library containing 5000 mutants was used in a screen to identify genes involved in the production of sucrose‐dependent extracellular matrix components. Mutants with transposon inserts in genes encoding glycosyltransferases and the competence‐related secretory locus were predominantly found in this screen.
Overview of low molecular weight heparin for preventative treatment of adverse obstetric outcomes related to abnormal placentation
Authors: Ghidini Alessandro 
Published: April 2014

ABSTRACTDifferent proportions of cases of preterm and severe preeclampsia, placental abruption, fetal growth restriction, and fetal death share a common causal pathway of abnormal placental implantation. Documentation of an association between the risk of such adverse pregnancy outcomes (APOs) and inherited thrombophilias prompted initial studies to evaluate the benefit of anticoagulants for the prevention of recurrences both in patients with and without inherited thrombophilias. Prenatal administration of low molecular weight heparin (LMWH) has been evaluated in case control, cohort and randomized clinical trials. The evidence suggests a benefit of LMWH in the reduction of recurrences of APOs, with a number needed to treat of 6 (95% confidence interval: 4–10) to prevent one case of recurrent APOs. Such benefit is independent of the presence of inherited thrombophilias or the administration of low dose aspirin. Further studies are needed to establish the optimal duration for the prophylaxis, to better delineate the mechanism of action of LMWH and to explore the role, if any, of maternal serum markers and uterine artery Doppler findings in the modulation of the LMWH prophylaxis. © 2014 John Wiley & Sons, Ltd.
Theoretical description of unconstrained thermally induced shape‐memory recovery in crosslinked polyethylenes
Authors: Kolesov Igor , Dolynchuk Oleksandr , Radusch Hans‐Joachim 
Published: April 2014

ABSTRACTA new theoretical approach based on the modified three‐element Eyring‐Halsey model was developed for the derivation of an equation describing the thermally induced recovery of predeformed and crystallized crosslinked polymers. The proposed approach takes into account the influence of crystallizable covalent network and of entangled slipped molecular chains. Modeling of thermally induced shape‐memory (SM) recovery strain and SM recovery rate detected at constant heating rate has been successfully performed for nearly linear and two short‐chain branched polyethylenes, which were crosslinked by peroxide. The values of material constants determined by fitting agree with the estimations existing in literature. Fitting results have shown that increase of degree of branching and crosslink density accompanied with reducing crystallinity results in increasing contribution of the entangled slipped chains to the total stored SM strain. The physical sense of main fitting parameters and their dependences on the material constants such as crystallinity are discussed. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014, 52, 815–822
Phosphine resistance in Australian Cryptolestes species (Coleoptera: Laemophloeidae): perspectives from mitochondrial DNA cytochrome oxidase I analysis
Authors: Tay Wee Tek , Beckett Stephen J , De Barro Paul J 
Published: April 2014

AbstractBACKGROUNDThe flat grain beetle (FGB) species Cryptolestes ferrugineus, C. pusillus, C. pusilloides and C. turcicus are major stored‐product pests worldwide, of which the first three are present in Australia. C. ferrugineus is also a species with high phosphine resistance status in various countries. Morphological identification of Cryptolestes species is difficult and represents an additional barrier to effective management of phosphine resistance in FGBs.RESULTMitochondrial DNA cytochrome oxidase I (mtDNA COI) gene characterisation enabled differentiation of the four major FGB pest species through direct sequence comparison, and enabled the development of a PCR‐RFLP method for rapid species differentiation. We detected two mtDNA haplotypes (Cunk‐01, 02) present at low frequencies with an average nucleotide divergence rate of 0.079 ± 0.011 (SE) from C. pusillus. This nucleotide divergence rate is similar to that between C. ferrugineus and C. pusilloides (0.088 ± 0.012). Male and female genitalia morphologies of the Cunk‐02 individuals indicated they were consistent with C. pusillus, yet DNA sequence analyses suggested species‐level divergence. The mtDNA COI gene of phosphine‐bioassayed, lab‐reared F1 generation survivors supported the presence of strong phosphine resistance in C. ferrugineus, but unexpectedly also in C. pusilloides and C. pusillus F1 survivors.CONCLUSIONWe demonstrated the utility of molecular DNA techniques for differentiating closely related insect species, and its usefulness in assisting the management of pest insect species. The likely presence of a cryptic C. pusillus species in Australia and the possible development of strong phosphine resistance in Australian FGB pest species require further investigation. © 2014 Society of Chemical Industry
High‐precision determination of 13C–18O bonds in CO2 using multicollector peak hopping
Authors: Petrizzo Daniel A. , Young Edward D. 
Published: April 2014

RATIONALERapid development of the CO2 'clumped‐isotope' temperature proxy (Δ47) has involved both resource‐ and labor‐intensive analytical methods. We report strategies for measuring Δ47 on a conventional mass spectrometer, with the usual CO2 set of three Faraday collectors while reducing the time devoted to standardization with temperature‐equilibrated CO2.METHODSWe measured Δ47 in CO2 on a mass spectrometer using only three Faraday cups by 'multicollector peak hopping', directing 46CO2+ and 47CO2+ ion beams into the Faraday cups normally used for m/z 44 and 45. Δ47 was calculated from the previously measured δ13C and δ18O values and we then measured 47CO2+/46CO2+. We invoke a protocol for correcting ion‐beam intensities for secondary electrons to address common problems with compositional non‐linearity and both long‐ and short‐term measurement stability.RESULTSOur method eliminates the need for six Faraday cups for measuring Δ47, a possible advantage for many laboratories. In addition, by using a correction based on removing the effects of secondary electrons, we remove the Δ47 dependence on δ47CO2. As a result, our methods are robust against mass spectrometer operating conditions.CONCLUSIONSΔ47 can be precisely measured on mass spectrometers currently employed for measuring δ13C and δ18O values without significant resource investment. Accounting for ion scatter during measurements of CO2 results in improved external precision and long‐term stability, while significantly increasing the machine time available for sample analysis. Copyright © 2014 John Wiley & Sons, Ltd.
Direct detection of brominated flame retardants from plastic e‐waste using liquid extraction surface analysis mass spectrometry
Authors: Paine Martin R. L. , Rae Ian D. , Blanksby Stephen J. 
Published: April 2014

RATIONALEThe worldwide generation of plastic electronic waste (e‐waste) is reaching epic proportions. The presence of toxic brominated flame retardants (BFRs) within these materials limits their ability to be recycled, resulting in large amounts of e‐waste reaching landfills.METHODSLiquid extraction surface analysis mass spectrometry (LESA‐MS) employing a chip‐based nanoelectrospray coupled to a triple quadrupole mass spectrometer represents a novel control technology for directing e‐waste streams for recycling. LESA‐MS allows direct sampling and analysis of solid material, capable of detecting BFRs including polybrominated diphenyl ethers (PBDEs) and tetrabromobisphenol A (TBBP‐A), the two most common flame retardant additives currently in circulation.RESULTSAuthentic PBDE congeners and TBBP‐A were deposited on glass and characterised by LESA‐MS analysis. PBDEs are notoriously difficult to detect via electrospray; however, they were detected with ease by utilising a combination of nanoelectrospray and solvent doped with ammonium acetate. In situ detection of TBBP‐A within plastic e‐waste was also possible by performing LESA‐MS on the surface of granulated material provided by a commercial waste depot. E‐waste sample analysis was completely automated, with each sample analysed in less than 1 min.CONCLUSIONSLESA‐MS is fast, simple, and robust allowing unambiguous detection of a range of additives through tandem mass spectrometry. LESA‐MS does not require dissolution of the solid matrix nor the sample to be present under vacuum and the use of separative techniques prior to analysis is not necessary. Copyright © 2014 John Wiley & Sons, Ltd.
Identification of multiple constituents from seed of Vaccaria segetalis with an adsorbent‐separation strategy based on liquid chromatography coupled to quadrupole time‐of‐flight mass spectrometry
Authors: Qi Peng , Zhang Feng , Xue Rui , Li Zhixiong , Chen Mingcang , Sun Zhaolin , Zhu Kaicheng , Huang Chenggang 
Published: April 2014

RATIONALESeeds of Vaccaria segetalis (Wang‐Bu‐Liu‐Xing in Chinese) are mainly used in traditional Chinese medicine for the treatment of amenorrhea, breast infections, and edema. The study was designed to identify the components and metabolites of Wang‐Bu‐Liu‐Xing.METHODSA novel methodology combining an adsorbent‐separation strategy with analysis by liquid chromatography/quadrupole time‐of‐flight tandem mass spectrometry (LC/QTOF‐MS/MS) was established to identify the components of Wang‐Bu‐Liu‐Xing. The adsorbent‐separation technique was applied on macroporous resin (adsorbents). Different concentrations of ethanol (30%, 60%, and 95%), which covered high‐to‐low polarity ranges, were chosen as the elution solvent, respectively. The QTOF mass spectrometer was operated in negative ion mode with an electrospray ionization source.RESULTSA total of 52 components were successfully identified in the Wang‐Bu‐Liu‐Xing decoction based on the fragmentation pathways and QTOF high‐accuracy mass spectral analysis. To the best of our knowledge, several new saponins were reported for the first time. A total of 20 compounds, which included 10 prototypes and 10 metabolites, were also identified in rat plasma and urine after oral administration of Wang‐Bu‐Liu‐Xing decoction.CONCLUSIONSAn integrated adsorbent‐separation strategy is powerful and reliable for global detection and identification of complex components in herbal prescriptions. The components identified in rat biofluids may also provide helpful chemical information for further pharmacology and active mechanism study on this herb. Copyright © 2014 John Wiley & Sons, Ltd.
Analysis of trace organic pollutants in wastewater to assess biodegradation using wrong‐way‐round ionization in liquid chromatography/tandem mass spectrometry
Authors: Su Lijuan , Khunjar Wendell O. , Aga Diana S. 
Published: April 2014

RATIONALEMonitoring the concentrations of pharmaceuticals and personal care products (PPCPs) in wastewater is an integral step toward understanding the fate of these contaminants in wastewater treatment plants (WWTPs). This paper aims to develop a method that allows for the simultaneous analysis of multiple classes of PPCPs that can be used as tracers to assess the performance of WWTPs.METHODSFive PPCP tracers – carbamazepine (CBZ), 17α‐ethinylestradiol (EE2), nonylphenol (NP), salicylic acid (SA), and trimethoprim (TMP) – were analyzed by liquid chromatography/triple quadrupole mass spectrometry (LC/MS/MS) using a highly basic mobile phase (pH 10.3). Conventionally, TMP (pKa 7.12) and CBZ (pKa 13.94) are analyzed in positive ion mode using an acidic mobile phase. However, the high pH mobile phase allowed the quantification of all the tracers by polarity switching, with TMP undergoing wrong‐way‐round (WWR) ionization.RESULTSThe instrument limits of detection for the five tracers, without solid‐phase extraction, were in the range of 1.3 to 5.9 ng/mL, except for NP, which was 238 ng/mL. The signal‐to‐noise (S/N) ratios for TMP and CBZ with the mobile phase at pH 10.3 were higher than the S/N ratios observed at pH 2.7 under positive electrospray ionization. The mechanism of WWR ionization for TMP was investigated, and we propose that a charge transfer from solvent clusters to TMP molecules due to electrolytic reactions at the surface of the droplet leads to WWR ionization in electrospray.CONCLUSIONSA method to simultaneously analyze five representative PPCP tracers with a wide range of pKa values using WWR ionization in LC/MS/MS with polarity switching was developed. The method was successfully used to monitor the selected PPCPs in samples from full‐scale WWTPs to assess their biodegradation under various treatment conditions. Copyright © 2014 John Wiley & Sons, Ltd.
Internal energy distribution in electrospray ionization: Towards the evaluation of a thermal‐like distribution from the multiple‐collision model
Authors: Rondeau David , Drahos László , Vékey Károly 
Published: April 2014

RATIONALEThe internal energy deposition in ions that cross the desolvation region of an electrospray ionization (ESI) source affects the mass spectra that are obtained using in‐source collision‐induced dissociation (CID) or in tandem mass spectrometry (MS/MS) mode. It is thus important to evaluate the internal energy distributions of the ions in different parts of an ESI mass spectrometer.METHODSThe desolvation region is considered as a collision zone and a partially elastic multiple‐collision model is used to account for the accumulation of internal energy in the ions. The ion survival yields (SYTheo) of the theoretical mass spectra calculated by MassKinetics software are fitted with the experimental ion survival yields (SYExp) of the substituted benzylpyridinium cations that have been obtained with an ESI source interfaced with a quadrupole mass spectrometer. The theoretical parameters used for fitting the calculation data with the experimental results are the center‐of‐mass collision energy (Ecom) of the colliding ions and a term related to the pressure of the desolvation area of the ESI interface.RESULTSIn the proposed model, an average number of 'effective' collisions of close to 30 in the desolvation area is employed. The voltages applied to the orifice of this interface are correlated to a theoretical initial kinetic energy (Einit,Kin) in the laboratory frame of the ions. In the present case, these theoretical initial kinetic energies range from 5.5 to 9 eV. The internal energy distributions evaluated from this model resemble the thermal distributions of ions having 'characteristic temperatures' between 1020 and 1550 K, and the results of calculations show that the mean internal energy of the ions increases linearly with the orifice voltage.CONCLUSIONSThe model used in this study can account for the energy build‐up of the ions in an ESI interface and allows the change in the internal energy distribution of the electrosprayed ions in different regions of a mass spectrometer to be evaluated. Copyright © 2014 John Wiley & Sons, Ltd.
Identification of alcohol‐dependent clopidogrel metabolites using conventional liquid chromatography/triple quadrupole mass spectrometry
Authors: Hu Zhe‐Yi , Laizure S. Casey , Herring Vanessa L. , Parker Robert B. 
Published: April 2014

RATIONALEClopidogrel (CLO) is a prodrug used to prevent ischemic events in patients undergoing percutaneous coronary intervention or with myocardial infarction. A previous study found ethyl clopidogrel (ECLO) is formed by transesterification of CLO when incubated with alcohol in human liver microsomes. We hypothesize that ECLO will be subject to further metabolism and developed an assay to identify its metabolites.METHODSA liquid chromatography/triple quadrupole mass spectrometry (LC/MS/MS) method was developed to identify metabolites of ECLO. According to the predicted metabolic pathway of ECLO, precursor–product ion pairs were used to screen the possible metabolites of ECLO in human liver S9 fractions. Subsequently, the detected metabolites were characterized by the results of product ion scan.RESULTSIn the presence of alcohol, CLO was tranesterified to ECLO, which was further oxidized to form ethylated 2‐oxo‐clopidogrel and several ethylated thiol metabolites including the ethylated form of the H4 active metabolite.CONCLUSIONSThe ECLO formed by transesterification with alcohol is subject to metabolism by CYP450 enzymes producing ethylated forms of 2‐oxo‐clopidogrel and the active H4 thiol metabolite. Copyright © 2014 John Wiley & Sons, Ltd.
Joint longitudinal and survival‐cure models in tumour xenograft experiments
Authors: Pan Jianxin , Bao Yanchun , Dai Hongsheng , Fang Hong‐Bin 
Published: April 2014

AbstractIn tumour xenograft experiments, treatment regimens are administered, and the tumour volume of each individual is measured repeatedly over time. Survival data are recorded because of the death of some individuals during the observation period. Also, cure data are observed because of a portion of individuals who are completely cured in the experiments. When modelling these data, certain constraints have to be imposed on the parameters in the models to account for the intrinsic growth of the tumour in the absence of treatment. Also, the likely inherent association of longitudinal and survival‐cure data has to be taken into account in order to obtain unbiased estimators of parameters. In this paper, we propose such models for the joint modelling of longitudinal and survival‐cure data arising in xenograft experiments. Estimators of parameters in the joint models are obtained using a Markov chain Monte Carlo approach. Real data analysis of a xenograft experiment is carried out, and simulation studies are also conducted, showing that the proposed joint modelling approach outperforms the separate modelling methods in the sense of mean squared errors. Copyright © 2014 John Wiley & Sons, Ltd.
Nuchal Translucency Quality Review (NTQR) program: first one and half million results
Authors: Cuckle H. , Platt L. D. , Thornburg L. L. , Bromley B. , Fuchs K. , Abuhamad A. , Benacerraf B. , Copel J. A. , Depp R. , D'Alton M. , Goldberg J. , O'Keeffe D. , Spitz J. , Toland G. , Wapner R. ,   for the Nuchal Translucency Quality Review Program of the Perinatal Quality Foundation
Published: April 2014

ABSTRACTObjectiveTo evaluate the performance of first‐trimester nuchal translucency (NT) measurement by providers (physician‐sonologists and sonographers) within the Nuchal Translucency Quality Review (NTQR) program.MethodsAfter training and credentialing providers, the NTQR monitored performance of NT measurement by the extent to which an individual's median multiple of the normal median (MoM) for crown–rump length (CRL) was within the range 0.9–1.1 MoM of a published normal median curve. The SD of log10 MoM and regression slope of NT on CRL were also evaluated. We report the distribution between providers of these performance indicators and evaluate potential sources of variation.ResultsAmong the first 1.5 million scans in the NTQR program, performed between 2005 and 2011, there were 1 485 944 with CRL in the range 41–84 mm, from 4710 providers at 2150 ultrasound units. Among the 3463 providers with at least 30 scans in total, the median of the providers' median NT‐MoMs was 0.913. Only 1901 (55%) had a median NT‐MoM within the expected range; there were 89 above 1.1 MoM, 1046 at 0.8–0.9 MoM, 344 at 0.7–0.8 MoM and 83 below 0.7 MoM. There was a small increase in the median NT‐MoM according to providers' length of time in the NTQR program and number of scans entered annually. On average, physician‐sonologists had a higher median NT‐MoM than did sonographers, as did those already credentialed before joining the program. The median provider SD was 0.093 and the median slope was 13.5%. SD correlated negatively with the median NT‐MoM (r = −0.34) and positively with the slope (r = 0.22).ConclusionEven with extensive training, credentialing and monitoring, there remains considerable variability between NT providers. There was a general tendency towards under‐measurement of NT compared with expected values, although more experienced providers had performance closer to that expected. Copyright © 2014 ISUOG. Published by John Wiley & Sons Ltd.
Computational models reveal genotype–phenotype associations in Saccharomyces cerevisiae
Authors: Franco‐Duarte Ricardo , Mendes Inês , Umek Lan , Drumonde‐Neves João , Zupan Blaz , Schuller Dorit 
Published: April 2014

AbstractGenome sequencing is essential to understand individual variation and to study the mechanisms that explain relations between genotype and phenotype. The accumulated knowledge from large‐scale genome sequencing projects of Saccharomyces cerevisiae isolates is being used to study the mechanisms that explain such relations. Our objective was to undertake genetic characterization of 172 S. cerevisiae strains from different geographical origins and technological groups, using 11 polymorphic microsatellites, and computationally relate these data with the results of 30 phenotypic tests. Genetic characterization revealed 280 alleles, with the microsatellite ScAAT1 contributing most to intrastrain variability, together with alleles 20, 9 and 16 from the microsatellites ScAAT4, ScAAT5 and ScAAT6. These microsatellite allelic profiles are characteristic for both the phenotype and origin of yeast strains. We confirm the strength of these associations by construction and cross‐validation of computational models that can predict the technological application and origin of a strain from the microsatellite allelic profile. Associations between microsatellites and specific phenotypes were scored using information gain ratios, and significant findings were confirmed by permutation tests and estimation of false discovery rates. The phenotypes associated with higher number of alleles were the capacity to resist to sulphur dioxide (tested by the capacity to grow in the presence of potassium bisulphite) and the presence of galactosidase activity. Our study demonstrates the utility of computational modelling to estimate a strain technological group and phenotype from microsatellite allelic combinations as tools for preliminary yeast strain selection. Copyright © 2014 John Wiley & Sons, Ltd.