bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid knowledge: ‘Bridging research and policy’ at the Overseas Development Institute
Authors: Stone Diane 
Published: July 2009

AbstractNumerous organizations advocate the need to ‘bridge research and policy’. Philanthropic foundations, national social science funding regimes and international organizations have sought to improve knowledge utilization. Similarly, research consumers such as NGOs and government departments complain of research irrelevance for policy purposes. The concern of this article is with ‘evidence informed policy’ within the field of international development in which the Overseas Development Institute (ODI), a London‐based think tank, forms the case study. Most think tanks are driven by the need to influence immediate political agendas but ODI has also developed organizational strategies of policy entrepreneurship that extend to longer term influence through creating human capital, building networks and engaging policy communities. Copyright © 2009 John Wiley & Sons, Ltd.
Using action research to develop a model of patient‐centred day care
Authors: Bothe Janine , Donoghue Judith 
Published: July 2009

AbstractThe objective of this study was to develop a model of care that was patient centred, safe and effective for day surgery patients undergoing complex surgical procedures. The research team used Habermas' (1987) theory of communicative action to guide a process that enabled honest communication and equality within the group necessary to obtain sustained technical and emancipatory change. An action research method was used to make changes based on the best available evidence. Three criteria were used as a basis for change – the effectiveness of care, patient safety and patient‐centeredness. Prior to the study, no patient had had complex day surgery at this hospital. During the study, 55 patients underwent complex day surgery in an effective, safe and patient‐centred way. Improved communication and increased confidence enabled the research team to achieve significant technical outcomes. The group matured into autonomous, accountable and engaged clinicians that demonstrated emancipation. Copyright © 2009 John Wiley & Sons, Ltd.
Optimal analysis of complex protein mass spectra
Authors: Dijkstra Martijn , Jansen Ritsert C. 
Published: July 2009

AbstractDue to physical and chemical phenomena, a simple sample can give rise to a complex mass spectrum with many more peaks than the number of molecular species present in the sample. We link peaks within and between different spectra, and come up with an advanced analysis approach to produce reliable estimates of the molecule masses and abundances. By linking peaks, we can locate multiple‐charge peaks at the correct position in the spectrum, we can deconvolute complex regions with many overlapping peaks by including information from related regions with lower complexity and higher resolution, and we reduce the total number of observed peaks in a spectrum to a much smaller number of underlying molecular species. In this paper we properly model 29 952 peaks in 64 spectra, using only 39 location parameters and one shape parameter. This major reduction from many different molecules to a limited set of molecular species reduces the statistical test multiplicity for biomarker discovery and therefore we imply that the reduction should eventually increase the biomarker discovery power significantly, too.
Proteomic analysis of β‐catenin activation in mouse liver by DIGE analysis identifies glucose metabolism as a new target of the Wnt pathway
Authors: Chafey Philippe , Finzi Laetitia , Boisgard Raphael , Caüzac Michèle , Clary Guillem , Broussard Cédric , Pégorier Jean‐Paul , Guillonneau François , Mayeux Patrick , Camoin Luc , Tavitian Bertrand , Colnot Sabine , Perret Christine 
Published: July 2009

AbstractThe Wnt/β‐catenin signaling pathway has been increasingly implicated in liver development and physiology. Aberrant activation of this pathway is one of the major genetic events observed during the process of human HCC development. To gain insight into the mechanism underlying β‐catenin action in the liver, we conducted a quantitative differential proteomic analysis using 2‐D DIGE combined with MS, in mice with liver‐specific deletion of Apc resulting in acute activation of β‐catenin signaling (ApcKOliv mice). We identified 94 protein spots showing differential expression between mutant ApcKOliv and control mice, corresponding to 56 individual proteins. Most of the proteins identified were associated with metabolic pathways, such as ammonia and glucose metabolism. Our analysis showed an increase in lactate dehydrogenase activity together with a downregulation of two mitochondrial ATPase subunits (ATP5a1 and ATP5b). These observations indicate that β‐catenin signaling may induce a shift in the glucose metabolism from oxidative phosphorylation to glycolysis, known as the “Warburg effect”. Imaging with 18F‐fluoro‐2‐deoxy‐D‐glucose‐positron emission tomography suggests that the specific metabolic reprogramming induced by β‐catenin in the liver does not imply the first step of glycolysis. This observation may explain why some HCCs are difficult to assess by fluoro‐2‐deoxy‐D‐glucose‐positron emission tomography imaging.
The plasma membrane proteome of germinating barley embryos
Authors: Hynek Radovan , Svensson Birte , Jensen Ole Nørregaard , Barkholt Vibeke , Finnie Christine 
Published: July 2009

AbstractCereal seed germination involves a complex coordination between different seed tissues. Plasma membranes must play crucial roles in coordination and execution of germination; however, very little is known about seed plasma membrane proteomes due to limited tissue amounts combined with amphiphilicity and low abundance of membrane proteins. A fraction enriched in plasma membranes was prepared from embryos dissected from 18 h germinated barley seeds using aqueous two‐phase partitioning. Reversed‐phase chromatography on C4 resin performed in micro‐spin columns with stepwise elution by 2‐propanol was used to reduce soluble protein contamination and enrich for hydrophobic proteins. Sixty‐one proteins in 14 SDS‐PAGE bands were identified by LC‐MS/MS and database searches. The identifications provide new insight into the plasma membrane functions in seed germination.
OMSSA Parser: An open‐source library to parse and extract data from OMSSA MS/MS search results
Authors: Barsnes Harald , Huber Steffen , Sickmann Albert , Eidhammer Ingvar , Martens Lennart 
Published: July 2009

AbstractProtein identification by MS is an important technique in both gel‐based and gel‐free proteome studies. The Open Mass Spectrometry Search Algorithm (OMSSA) (http://pubchem.ncbi.nlm.nih.gov/omssa) is an open‐source search engine that can be used to identify MS/MS spectra acquired in these experiments. We here present a lightweight, open‐source Java software library, OMSSA Parser (http://code.google.com/p/omssa‐parser), which parses OMSSA omx result files into easy accessible and fully functional object models. In addition, we also provide examples illustrating the usage of our library.
iTRAQ‐coupled 2‐D LC‐MS/MS analysis of protein profile associated with HBV‐modulated DNA methylation
Authors: Niu Dandan , Sui Jianjun , Zhang Jianhua , Feng Huixing , Chen Wei Ning 
Published: July 2009

AbstractThe development of hepatocellular carcinoma (HCC) is believed to be associated with multiple risk factors, including the infection of hepatitis B virus (HBV). Based on the analysis of individual genes, evidence has indicated the association between HCC and HBV and has also been expanded to epigenetic regulation, with an involvement of HBV in the DNA methylation of the promoter of cellular target genes leading to changes in their expression. Proteomic study has been widely used to map a comprehensive protein profile, which in turn could provide a better understanding of underlying mechanisms of disease onset. In the present study, we performed a proteomic profiling by using iTRAQ‐coupled 2‐D LC/MS‐MS analysis to identify cellular genes down‐regulated in HBV‐producing HepG2.2.15 cells compared with HepG2 cells. A total of 15 proteins including S100A6 and Annexin A2 were identified by our approach. The significance of these cellular proteins as target of HBV‐mediated epigenetic regulation was supported by our validation assays, including their reactivation in cells treated with 5‐aza‐2′‐deoxycytidine (a DNA methyltransferase inhibitor) by real‐time RT‐PCR and Western blot analysis, as well as the DNA methylation status analysis by bisulfite genome sequencing. Our approach provides a comprehensive analysis of cellular target proteins to HBV‐mediated epigenetic regulation and further analysis should facilitate a better understanding of its involvement in HCC development.
Sol–gel transparent nano‐glass‐ceramics comprising rare‐earth‐doped NaYF4 nanocrystals
Authors: Santana‐Alonso A. , Yanes A. C. , Méndez‐Ramos J. , del‐Castillo J. , Rodríguez V. D. 
Published: July 2009

AbstractTransparent nano‐glass‐ceramics containing rare‐earth‐doped NaYF4 nanocrystals (Eu3+ single‐doped and Yb3+–Er3+ co‐doped) have been successfully developed for the first time by thermal treatment of precursor bulk glasses obtained by sol–gel technique. X‐ray diffraction and high‐resolution transmission electron microscopy measurements reveal the precipitation of NaYF4 nanocrystals during the heat treatment and their corresponding sizes have been calculated. Luminescence measurements confirm the partition of rare‐earth ions in NaYF4 nanocrystals. In Eu3+‐doped samples, changes in the local environment of these rare‐earth ions have been investigated by site‐selective emission and excitation spectra. In Yb3+–Er3+ co‐doped samples, efficient visible up‐conversion luminescence has been obtained under infrared excitation at 980 nm. The red to green up‐conversion emission ratio can be varied as a function of temperature of heat treatment, resulting in colour tuneable up‐conversion phosphors with applications in optical integrated devices. Colour tuneability has been analysed and quantified in terms of Comission Internationale d'Eclairage standard chromaticity diagram.magnified image
Infrared spectrum of potassium‐cationized triethylphosphate generated using tandem mass spectrometry and infrared multiple photon dissociation
Authors: Groenewold Gary S. , Leavitt Christopher M. , Dain Ryan P. , Oomens Jos , Steill Jeffrey D. , van Stipdonk Michael J. 
Published: July 2009

AbstractTandem mass spectrometry and wavelength‐selective infrared photodissociation were used to generate an infrared spectrum of gas‐phase triethylphosphate cationized by attachment of K+. Prominent absorptions were observed in the region of 900 to 1300 cm−1 that are characteristic of phosphate PO and POR stretches. The relative positions and intensities of the IR absorptions were reproduced well by density functional theory (DFT) calculations performed using the B3LYP functional and the 6‐31+G(d), 6‐311+G(d,p) and 6‐311++G(3df,2pd) basis sets. Because of good correspondence between experiment and theory for the cation, DFT was then used to generate a theoretical spectrum for neutral triethylphosphate, which in turn accurately reproduces the IR spectrum of the neat liquid when solvent effects are included in the calculations. Copyright © 2009 John Wiley & Sons, Ltd.
Can density functional theory (DFT) be used as an aid to a deeper understanding of tandem mass spectrometric fragmentation pathways?
Authors: Alex Alexander , Harvey Sophie , Parsons Teresa , Pullen Frank S. , Wright Patricia , Riley Jo‐Anne 
Published: July 2009

AbstractPrediction of tandem mass spectrometric (MS/MS) fragmentation for non‐peptidic molecules based on structure is of immense interest to the mass spectrometrist. If a reliable approach to MS/MS prediction could be achieved its impact within the pharmaceutical industry could be immense. Many publications have stressed that the fragmentation of a molecular ion or protonated molecule is a complex process that depends on many parameters, making prediction difficult. Commercial prediction software relies on a collection of general heuristic rules of fragmentation, which involve cleaving every bond in the structure to produce a list of ‘expected’ masses which can be compared with the experimental data. These approaches do not take into account the thermodynamic or molecular orbital effects that impact on the molecule at the point of protonation which could influence the potential sites of bond cleavage based on the structural motif. A series of compounds have been studied by examining the experimentally derived high‐resolution MS/MS data and comparing it with the in silico modelling of the neutral and protonated structures. The effect that protonation at specific sites can have on the bond lengths has also been determined. We have calculated the thermodynamically most stable protonated species and have observed how that information can help predict the cleavage site for that ion. The data have shown that this use of in silico techniques could be a possible way to predict MS/MS spectra. Copyright © 2009 John Wiley & Sons, Ltd.
An integrated serum proteomic approach capable of monitoring the low molecular weight proteome with sequencing of intermediate to large peptides
Authors: Merrell Karen , Thulin Craig D. , Esplin M. Sean , Graves Steven W. 
Published: July 2009

AbstractThe low‐abundance, low molecular weight serum proteome has high potential for the discovery of new biomarkers using mass spectrometry (MS). Because the serum proteome is large and complex, defining relative quantitative differences for a molecular species between comparison groups requires an approach with robust separation capability, high sensitivity, as well as high mass resolution. Capillary liquid chromatography (cLC)/MS provides both the necessary separation technique and the sensitivity to observe many low‐abundance peptides. Subsequent identification of potential serum peptide biomarkers observed in the cLC/MS step can in principle be accomplished by in series cLC/MS/MS without further sample preparation or additional instrumentation. In this report a novel cLC/MS/MS method for peptide sequencing is described that surpasses previously reported size limits for amino acid sequencing accomplished by collisional fragmentation using a tandem time‐of‐flight MS instrument. As a demonstration of the approach, two low‐abundance peptides with masses of ∼4000–5000 Da were selected for MS/MS sequencing. The multi‐channel analyzer (MCA) was used in a novel way that allowed for summation of 120 fragmentation spectra for each of several customized collision energies, providing more thorough fragmentation coverage of each peptide with improved signal to noise. The peak list from this composite analysis was submitted to Mascot for identification. The two index peptides, 4279 Da and 5061 Da, were successfully identified. The peptides were a 39 amino acid immunoglobulin G heavy chain variable region fragment and a 47 amino acid fibrin alpha isoform C‐terminal fragment. The method described here provides the ability both to survey thousands of serum molecules and to couple that with markedly enhanced cLC/MS/MS peptide sequencing capabilities, providing a promising technique for serum biomarker discovery. Copyright © 2009 John Wiley & Sons, Ltd.
Identification of active compounds and their metabolites by high‐performance liquid chromatography/electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry from Xiao‐xu‐ming decoction (XXMD)
Authors: Wang Yilin , Ding Chunguang , Du Kehe , Xiao Yao , Wu Caisheng , Zhang Jinlan , Qin Hailin , Du Guanhua 
Published: July 2009

AbstractXiao‐xu‐ming decoction (XXMD) prescription is a traditional Chinese prescription that has been widely used to treat theoplegia and the sequela of theoplegia. Modern pharmacological research has also indicated that the active fraction from XXMD is able to treat cardiovascular diseases and Alzheimer's disease. In the study reported here, high‐performance liquid chromatography coupled with Fourier transform ion cyclotron resonance mass spectrometry (HPLC/FTICR‐MS) was developed to identify active compounds and their metabolites after oral administration of active fraction from Xiao‐xu‐ming decoction to rats, using parent mass list triggered data‐dependent multiple‐stage mass analysis at a resolving power of 100 000 in the external calibration mode. The mass accuracies obtained for full‐scan MS were within 2 ppm in most cases. Fifteen constituents were identified in the active fraction from XXMD and the biological samples of rats. The fragmentation behaviors of these constituents were summarized which would be helpful for structural characterization. The profiles of the constituents in the active fraction and biological samples of rats were obtained which provided us with much information for a better understanding of the chemical basis of the pharmacologic actions of XXMD. Copyright © 2009 John Wiley & Sons, Ltd.
Mass spectrometry study of PRL‐3 phosphatase inactivation by disulfide bond formation and cysteine into glycine conversion
Authors: Orsatti Laura , Innocenti Federica , Surdo Paola Lo , Talamo Fabio , Barbato Gaetano 
Published: July 2009

AbstractThe Phosphatase of Regenerating Liver‐3 (PRL‐3) is a cysteine‐based phosphatase (CBP) that is highly over‐expressed in liver metastasis in colorectal cancer and suspected to be involved in the progression from tumor to metastasis. During substrate‐specificity studies based on the screening of PRL‐3 phosphatase activity on several phosphorylated synthetic peptides, we observed a decrease in activity depending on sample aging and storage conditions. By liquid chromatography combined with selective alkylation and mass spectrometry, we found two main PRL‐3 inactivation pathways: a disulfide bond formation between the catalytic C104 and C49, blocking the enzyme in an inactive oxidized form, or the conversion of the catalytic C104 into glycine. We also found that the disulfide formation and the cysteine into glycine conversion are catalyzed by cations present in the sample after protein purification through a nickel column. By adding a cation chelator such as EDTA and de‐oxygenating the sample with argon, PRL‐3 phosphatase activity was preserved. These findings suggest that PRL‐3, like other CBPs, is sensitive to inactivation by catalytic cysteine oxidation and this has implications for future studies of its activity and specificity. Copyright © 2009 John Wiley & Sons, Ltd.
Mass spectrometric analysis of carbohydrates labeled with a biotinylated tag
Authors: Kapková Petra 
Published: July 2009

AbstractA derivatization method for mass spectrometric analysis of oligosaccharides is presented. Small saccharides, complex, high‐mannose‐type oligosaccharides and oligosaccharides released from hen ovalbumin were converted into their biotin derivatives by incubating them with biotinamidocaproyl hydrazide (BACH). Improved sensitivity of mass spectrometric analysis of labeled glycans in comparison with their natural counterparts was achieved after derivatization. The labeling reagent contains a biotin handle at one end and a hydrazide group at the other. Hence, the key feature of biotinylated sugars is that in addition to their usefulness in functional studies (e.g. analysis of the interaction between lectins and biotin‐derivatized oligosaccharides) they might be utilized also for structural analysis of oligosaccharides. Mass spectrometric studies were performed by matrix‐assisted laser desorption/ionization time‐of‐flight and electrospray ionization mass spectrometry. Copyright © 2009 John Wiley & Sons, Ltd.
Structure and end‐group analysis of complex hexanediol‐neopentylglycol‐adipic acid copolyesters by matrix‐assisted laser desorption/ionization collision‐induced dissociation tandem mass spectrometry
Authors: Weidner Steffen M. , Falkenhagen Jana , Knop Karin , Thünemann Andreas 
Published: July 2009

AbstractSequences and end groups of complex copolyesters were determined by fragmentation analysis by means of matrix‐assisted laser desorption/ionization collision‐induced dissociation tandem mass spectrometry (MALDI CID MS/MS). The complexity of the crude copolyester mixture was reduced by a chromatographic separation followed by a MALDI time‐of‐flight (TOF) investigation of fractions. Due to overlapping compositional and end‐group information a clear assignment of end groups was very difficult. However, the fragmentation of suitable precursor ions resulted in typical fragment ion patterns and, therefore, enabled a fast and unambiguous determination of the end groups and composition of this important class of polymers. Copyright © 2009 John Wiley & Sons, Ltd.
Chewing gum, stress and health
Authors: Smith Andrew Paul 
Published: July 2009

AbstractHollingworth described chewing gum as ‘a technique of relaxation’. Recent research has examined this issue and there is evidence that chewing gum can prevent the adverse effects of acute stress. There are also plausible biological mechanisms that could explain such effects. It is now important to examine chewing gum and chronic stress and the present study involved a survey of this topic. The survey covered the ‘stress process’, collecting data on exposure to stressful events, levels of perceived stress and health outcomes. Frequency of chewing gum was also recorded. Potential confounding factors (demographics, personality and health‐related behaviours) were also recorded. The web‐based survey was completed by a community sample of 2,248 full‐time workers (68% female. Mean age: 35 years, range 18–74 years). Sixty‐one per cent of the sample were gum chewers. The results showed that chewing gum was associated with lower levels of perceived stress (both at work and life in general). Gum chewers were also less likely to be depressed and to have seen their doctor for high blood pressure or high cholesterol. Chewing gum was associated with lower levels of alcohol consumption and with cigarette smoking. Gum chewers were also more likely to be neurotic extraverts. Those who chewed gum were also more likely to be exposed to negative factors at work. Logistic regression analyses showed that the effects of chewing gum on stress and health remained significant when these confounding factors were controlled for. These results suggest that chewing gum may be a simple way of preventing stress and the negative health outcomes that are often associated with it. Intervention studies are now required and the mechanisms underlying the effects reported here need further investigation. Copyright © 2009 John Wiley & Sons, Ltd.
Reliability comparison of direct‐drive and geared‐drive wind turbine concepts
Authors: Arabian‐Hoseynabadi H. , Tavner P. J. , Oraee H. 
Published: July 2009

AbstractThis paper proposes for wind turbines (WTs) an analytical reliability method, used on other engineering systems, to compare the reliability of different turbine concepts. The main focus of the paper is to compare the reliability of geared generator and direct‐drive concept WTs. Modification methods are also recommended for improving the availability of WTs and geared generator concept incorporating doubly fed induction generator. Copyright © 2009 John Wiley & Sons, Ltd.