bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved radiocarbon dating for contaminated archaeological bone collagen, silk, wool and hair samples via cross‐flow nanofiltrated amino acids
Authors: Boudin Mathieu , Boeckx Pascal , Vandenabeele Peter , Van Strydonck Mark 
Published: August 2013

RATIONALERadiocarbon dating and stable isotope analyses of bone collagen, wool, hair and silk contaminated with extraneous carbon (e.g. humic substances) does not yield reliable results if these materials are pre‐treated using conventional methods.METHODSA cross‐flow nanofiltration method was developed that can be applied to various protein materials like collagen, hair, silk, wool and leather, and should be able to remove low‐molecular and high‐molecular weight contaminants. To avoid extraneous carbon contamination via the filter a ceramic filter (molecular weight cut‐off of 200 Da) was used. The amino acids, released by hot acid hydrolysis of the protein material, were collected in the permeate and contaminants in the retentate (>200 Da).RESULTS14C‐dating results for various contaminated archaeological samples were compared for bulk material (pre‐treated with the conventional methods) and for cross‐flow nanofiltrated amino acids (permeate) originating from the same samples. Contamination and quality control of 14C dates of bulk and permeate samples were obtained by measuring C:N ratios, fluorescence spectra, and δ13C and δ15N values of the samples. Cross‐flow nanofiltration decreases the C:N ratio which means that contaminants have been removed.CONCLUSIONSCross‐flow nanofiltration clearly improved sample quality and 14C results. It is a quick and non‐labor‐intensive technique and can easily be implemented in any 14C and stable isotope laboratory for routine sample pre‐treatment analyses. Copyright © 2013 John Wiley & Sons, Ltd.
Liquid chromatography/mass spectrometry methods for measuring dipeptide abundance in non‐small‐cell lung cancer
Authors: Wu Manhong , Xu Yue , Fitch William L. , Zheng Ming , Merritt Robert E. , Shrager Joseph B. , Zhang Weiruo , Dill David L. , Peltz Gary , Hoang Chuong D. 
Published: August 2013

RATIONALEMetabolomic profiling is a promising methodology of identifying candidate biomarkers for disease detection and monitoring. Although lung cancer is among the leading causes of cancer‐related mortality worldwide, the lung tumor metabolome has not been fully characterized.METHODSWe utilized a targeted metabolomic approach to analyze discrete groups of related metabolites. We adopted a dansyl [5‐(dimethylamino)‐1‐naphthalene sulfonamide] derivatization with liquid chromatography/mass spectrometry (LC/MS) to analyze changes of metabolites from paired tumor and normal lung tissues. Identification of dansylated dipeptides was confirmed with synthetic standards. A systematic analysis of retention times was required to reliably identify isobaric dipeptides. We validated our findings in a separate sample cohort.RESULTSWe produced a database of the LC retention times and MS/MS spectra of 361 dansyl dipeptides. Interpretation of the spectra is presented. Using this standard data, we identified a total of 279 dipeptides in lung tumor tissue. The abundance of 90 dipeptides was selectively increased in lung tumor tissue compared to normal tissue. In a second set of validation tissues, 12 dipeptides were selectively increased.CONCLUSIONSA systematic evaluation of certain metabolite classes in lung tumors may identify promising disease‐specific metabolites. Our database of all possible dipeptides will facilitate ongoing translational applications of metabolomic profiling as it relates to lung cancer. Copyright © 2013 John Wiley & Sons, Ltd.
Capabilities and limitations of direct analysis in real time orbitrap mass spectrometry and tandem mass spectrometry for the analysis of synthetic and natural polymers
Authors: Bridoux Maxime C. , Machuron‐Mandard Xavier 
Published: August 2013

RATIONALEDespite the widespread use of direct analysis in real time mass spectrometry (DART‐MS), its capabilities in terms of accessible mass range and the types of polymers that can be analysed are not well known. The goal of this work was to evaluate the capabilities and limitations of this ionization technique combined with orbitrap mass spectrometry and tandem mass spectrometry, for the characterization (structural and polydispersity metrics) of various synthetic and natural polymers.METHODSThe capabilities and limitations of DART‐MS (and ‐MS2), using an orbitrap mass spectrometer, for polymer analysis were evaluated using various industrial synthetic polymers and biopolymers. Stainless steel mesh screens secured on a movable rail were used as the sampling surface, onto which 5 μL of various polymers dissolved in tetrahydrofuran were added. Assignment of spectral features and calculation of molecular weight and polydispersity metrics were performed using Polymerix™ software and the results were compared with those obtained by gel‐permeation chromatography (GPC).RESULTSProtonated oligomers and ammonium adducts were instantaneously detected as the major ionisation products in positive ion mode. Only perfluoropolyethers (PFPEs) were ionised in negative mode and detected as [M]–. ions. Only singly charged molecular species were observed for all oligomers under study, allowing for a rapid determination of the molecular weight and polydispersity metrics of polymers. At elevated DART gas temperatures (400–500°C) the molecular weight and polydispersity metrics compared fairly well with those obtained by GPC, with polymers whose masses ranged from 200 g.mol–1 to 4000 g.mol–1.CONCLUSIONSDART‐MS allowed the direct and rapid analysis (mass spectra and tandem mass spectra of all the polymers were acquired in seconds) based on the exact masses of their [M+H]+ and [M+NH4]+ ions (in the positive mode) or [M]–. ions (for polymers having a high sensitivity toward electron‐capture ionisation such as PFPEs), as well as the exact masses of their product ions, for both synthetic and natural polymers under ambient conditions without any sample pre‐treatment. Copyright © 2013 John Wiley & Sons, Ltd.
Plasma metabolome analysis by integrated ionization rapid‐resolution liquid chromatography/tandem mass spectrometry
Authors: Tian He , Bai Jinfa , An Zhuoling , Chen Yanhua , Zhang Ruiping , He Jiuming , Bi Xiaofeng , Song Yongmei , Abliz Zeper 
Published: August 2013

RATIONALEAcquiring global information on plasma‐endogenous metabolites challenges metabolomics. This study has been designed to investigate the suitability of integrated ionization rapid‐resolution liquid chromatography/tandem mass spectrometry (RRLC/MS/MS) for different kinds of metabolites in complex plasma, and provides an approach for plasma metabolomics in acquiring more comprehensive data of metabolites.METHODSIntegrated ionization of electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI), and atmospheric pressure photoionization (APPI) combined with RRLC/MS/MS has been carried out to perform analysis on the global plasma metabolome of healthy volunteers. The contributions to the total numbers of ion features by RRLC/MS with ESI, APCI, and APPI in positive and negative ion modes were calculated. Representative unique and identical ions were identified. The intensities of identical ions were compared.RESULTSEach of ESI, APCI, and APPI coupled with RRLC/MS has its own advantage over the other two techniques for certain types of metabolites in plasma. LC/ESI‐MS is very sensitive for detecting glycerophosphocholines, glycerophosphoethanolamines, acyl carnitines, bile acids, sulfate, etc. LC/APCI‐MS is suitable for analyzing cyclic alcohols, fatty acids, and linoleic acids. LC/APPI‐MS proves to be appropriate in detecting steroids, sphingolipids, some amino acids, nucleosides, and purines in plasma.CONCLUSIONSIt is suggested that the integrated ionization LC/MS approach should be applied for global plasma metabolomics. Moreover, the results obtained demonstrate that it is preferable to choose certain techniques from LC/ESI‐MS, LC/APCI‐MS, and LC/APPI‐MS for metabolite target analysis. Copyright © 2013 John Wiley & Sons, Ltd.
Chemically facilitating the generation of diagnostic ions from SUMO(2/3) remnant isopeptides
Authors: Chicooree Navin , Griffiths John R. , Connolly Yvonne , Smith Duncan L. 
Published: August 2013

RATIONALEMapping sites of wild‐type SUMO modification is a challenging endeavour. Here we postulate that a combination of chemical derivatistation and collision‐induced dissociation (CID) could be used to generate SUMO remnant diagnostic ions to aid both detection of these isopeptides and increase the analytical value of the product ion spectra required to characterize the nature and position of modification.METHODSSUMO(2/3)ylated proteins were digested with trypsin to generate isopeptides bearing TGG and QTGG isotags. The resulting digests were then dimethyl labelled followed by liquid chromatography/tandem mass spectrometry (LC/MS/MS) utilising CID in a data‐dependent acquisition on a QSTAR XL. Product ion spectra were interrogated for the presence of iso‐N‐terminal fragment ions in addition to backbone sequence ions. The ability to diagnostically detect these isopeptides was tested by generation of co‐XICs of the iso‐N‐terminal fragments in a semi‐complex background.REULTSDimethyl labelling facilitated the robust detection of a1', b2' & b3' (TGG isotag) and a1', b2' & b4' (QTGG isotag) ions. The abundance of both N‐terminal and iso‐N‐terminal fragment ions, supported by dimethyl labelling, facilitated the generation of information‐rich product ion spectra of these isopeptides to aid confident site assignment. Moreover, the diagnostic nature of the combined XICs of the iso‐N‐terminal fragments supported detection of the isopeptide signals from a semi‐complex background.CONCLUSIONSA combination of dimethyl labelling and CID does indeed lead to the generation of SUMO remnant isopeptide product ion spectra which are more analytically rich. This enables an improvement in characterization of both the isotag and backbone sequences and the site of modification. The diagnostic value of iso‐N‐terminal fragment ions allows for post‐acquisition XIC interrogation to detect putative isopeptides of interest. Copyright © 2013 John Wiley & Sons, Ltd.
Decentralized weighted control for a class of large‐scale systems with multi‐modes
Authors: Xiang Weiming , Xiao Jian , Han Lu 
Published: August 2013

SUMMARYIn this paper, the control synthesis problem for a class of large‐scale systems with multi‐modes that are called large‐scale switched systems is addressed. By introducing the concept of decentralized switching signal and the relevant decentralized average dwell time, the asymptotic stability and weighted ℓ2 gain performance are investigated. It should be noted that the decentralized switching covers general switching cases for large‐scale switched systems, namely, it admits both time‐dependent switching signal and arbitrary switching signal blended in the decentralized switching. Then, on the basis of the analysis results, the decentralized weighted control scheme including state feedback controller gains and switching signals is studied. Several design algorithms are proposed to meet different controller design problems. Finally, numerical examples are provided to illustrate theoretical findings within this paper. Copyright © 2013 John Wiley & Sons, Ltd.
Using LMIs to optimize robustness of observer‐based state‐feedback for a synchrotron
Authors: Gering Stefan , Grieser Jochen , Wahrburg Arne 
Published: August 2013

SUMMARYIn this article, a synthesis method for linear systems subject to uncertain time‐varying parameters is proposed. Starting with the given values for the nominal parameters, the first objective is to find a constant state feedback such that the controlled system is stabilized and given dynamic specifications, such as a minimal decay rate, are met. In a second step, the constant feedback is then locally optimized such that the uncertain system parameters are allowed to vary around their nominal point as much as possible, whereas stabilization and dynamic specifications still hold. In addition, the procedure is extended toward observer‐based state feedback. Finally, this approach is applied to a synchrotron example, where the particle beam in longitudinal direction is to be stabilized and the coherent synchrotron frequency as well as the damping rate are uncertain. Copyright © 2013 John Wiley & Sons, Ltd.
Behavior of moment‐resisting tall steel structures exposed to a vertically traveling post‐earthquake fire
Authors: Behnam Behrouz , Ronagh Hamid R. 
Published: August 2013

SUMMARYAn investigation is performed on a 10‐story moment‐resisting steel structure designed to the Life Safety level of performance of the Federal Emergency Management Agency (FEMA) 356 code by exposing it to post‐earthquake fire (PEF). The fire curve is accounted for using the natural fire method, and the fire is subjected to the floors vertically in three different scenarios: (a) fire initiated from the first floor, (b) fire initiated from the fourth floor and (c) fire initiated from the seventh floor. A delay of 5 minutes and 25 minutes are considered for spreading the fire between the floors. To make a comparison between the results, a concurrent fire is also considered for the fire analysis. The results indicate that the PEF resistance of the frame exposed to the concurrent fire and the 5 minutes delay is much lower than that with a delay of 25 minutes. The results also show that subjecting the frame to a delayed fire of 25 minutes leads to the collapse of the frame during cooling phase, whereas in the other scenarios, the frame collapses during heating phase. As a result, more considerations need to be implemented in the codes on top of that for the PEF itself and that is the appropriate rate of spread of fire between floors. Copyright © 2013 John Wiley & Sons, Ltd.
Flexible Polyurethane Foams: A Comparative Measurement of Toxic Vapors and Other Toxic Emissions in Controlled Combustion Environments of Foams With and Without Fire Retardants
Authors: Blais Matthew , Carpenter Karen 
Published: August 2013

Abstract
A series of experiments were performed to measure the toxic vapor emissions of fires involving flexible polyurethane foams (FPUF) with and without flame retardants (FR). FPUF were covered with FR and non-FR fabrics to simulate cushion conditions. Testing was performed to both maximize detection of gases in small scale testing and measurement of exposure concentrations in realistic fire conditions in a room sized enclosures. A standard smoke box with load cell, open flame ignition source and Fourier transform infra-red spectrometer (FTIR) fit with a 2 m gas cell was used to monitor gas emission real time during testing with filter samples analyzed for acid gases and chloro-dioxins and furans. An NFPA 286 room was used to measure realistic smoke emissions from three seat furniture mock-ups with non-combustible frames. Oxygen consumption calorimetry, smoke opacity and smoke toxicity were measured during these tests. FTIR and grab sampling were performed during the room fires. Grab sampling using evacuated metal canisters were used to collect combustion gasses at various stages of the fire followed by analysis using EPA method TO-15 indoor air pollutants. In addition chloro-dioxins and furans were measured using a particulate filter collection system. The results of the study indicated that both FR and non-FR FPUF gave very similar results for smoke toxicity and both were less than what would be produced by an equivalent mass of wood. Use of fire barrier materials increased the toxicity of smoke produced from non-FR FPUF due to the creation of oxygen limited conditions. Use of fire barrier materials with FR FPUF would not sustain ignition and ended up producing less toxic smoke for up to 19 kW ignition source.
‘Show me the money’: improving the economic evaluation of mental health services
Authors: Twomey C. , Byrne M. , McHugh P. 
Published: August 2013

BackgroundCompared with the United Kingdom, mental health services in Ireland are under-funded and under-developed. This may be partly due to the neglect of economic analyses concerning mental health services in Ireland, as few policy makers would invest in the sector without evidence that such investment represents ‘value-for-money’ economically.AimThe aim of this paper is to highlight how mental health services can conduct economic service evaluations that ultimately will drive the policy-making agenda and future governmental investment.MethodsA guide to the economic evaluation of mental health services, based on a narrative review of relevant policy documents and papers, in an Irish context.ResultsThree types of economic analyses that can be undertaken within mental health services are outlined: (a) cost-benefit analysis, (b) cost-utility analysis and (c) cost-minimisation analysis. In addition, a newly formulated questionnaire (i.e. the ‘EcoPsy 12’) is presented.ConclusionsEconomic evaluations of mental health services can provide re-assurances to policy-makers that (much-needed) investment in such services is economically viable.
Towards modular analysis of tropical-cyclone structure: the boundary layer
Authors: Fendell Francis , Mokhasi Paritosh 
Published: August 2013

AbstractIn the early 1970s, George Carrier and coworkers undertook a modular approach to modelling the internal thermofluid-dynamics of tropical cyclones of tropical-depression-or-greater intensity. A novel, relatively simplistic, approximate analysis of the vortex, idealized as axisymmetric, was carried out in the asymptotic limit of large Reynolds number, so that inviscid and diffusive subdomains of the structure were distinguished. Little subsequent work has followed this line of investigation. The indifference has proven problematic because accurate prediction of tropical-cycling intensity remains a challenge for operational forecasting, despite decades of effort at direct integration of comprehensive boundary/initial-value formulations. A contributing factor is that, to achieve solution in real time, such computational treatment of the entire vortex invariably resorts to coarse gridding, and key features remain inadequately resolved. Accordingly, here the modular approach is revisited, with the assistance of: recent observational insights; greatly enhanced computer-processing power; and convenient computational software, which facilitates implementation of a semi-analytic, semi-numerical methodology. Focus is largely, but not exclusively, on the dynamics and energetics occurring in the nominally kilometre-thick, ocean-surface-contiguous boundary layer, especially on influx to the boundary layer and efflux therefrom. The modular approach not only permits the boundary layer, which develops its own highly significant substructure under the high-speed portion of the inviscid vortex, to be well-resolved, but also allows the layer to be investigated in the context of the other tropical-cyclone-structure subdivisions.
On the quest for a hyperbolic effective-field model of disperse flows
Authors: Lhuillier Daniel , Chang Chih-Hao , Theofanous Theo G. 
Published: August 2013

AbstractThe cornerstone of multiphase flow applications in engineering practice is a scientific construct that translates the basic laws of fluid mechanics into a set of governing equations for effective interpenetrating continua, the effective-field (or two-fluid) model. Over more than half a century of development this model has taken many forms but all of them fail in a way that was known from the very beginning: mathematical ill-posedness. The aim of this paper is to refocus awareness of this problem from a unified fundamental perspective that clarifies the manner in which such failures took place and to suggest the means for a final closure.
Systemic administration of Follistatin288 increases muscle mass and reduces fat accumulation in mice
Authors: Gangopadhyay Samudra S. 
Published: August 2013

AbstractThe present study describes the physiological response associated with daily subcutaneous injection of mice with recombinant follistatin288. This systemic administration of follistatin288 increases the follistatin levels in serum, indicating that the protein enters the circulation. The data suggest that a dose-dependent increase in body lean mass also occurs, together with an increase in muscle mass, possibly as a result of an increase in the size of the muscle fibers. After thirteen weeks of treatment, metabolic changes were observed; additionally, the switching of muscle fiber types was also apparent through myosin heavy chain remodeling, implying that changes are occurring at the molecular level. Furthermore, an increase in the muscle mass was associated with a significant decrease in the body fat mass. Overall, this study raises the possibility for the use of follistatin288 as an agent to treat muscle wasting diseases and/or to restrict fat accumulation by systemic administration of the protein.
Replication stress-induced alternative mRNA splicing alters properties of the histone RNA-binding protein HBP/SLBP: a key factor in the control of histone gene expression
Authors: Rattray Alexander M. J. , Nicholson Pamela , Müller Berndt 
Published: August 2013

Animal replication-dependent histone genes produce histone proteins for the packaging of newly replicated genomic DNA. The expression of these histone genes occurs during S phase and is linked to DNA replication via S-phase checkpoints. The histone RNA-binding protein HBP/SLBP (hairpin-binding protein/stem-loop binding protein), an essential regulator of histone gene expression, binds to the conserved hairpin structure located in the 3′UTR (untranslated region) of histone mRNA and participates in histone pre-mRNA processing, translation and histone mRNA degradation. Here, we report the accumulation of alternatively spliced HBP/SLBP transcripts lacking exons 2 and/or 3 in HeLa cells exposed to replication stress. We also detected a shorter HBP/SLBP protein isoform under these conditions that can be accounted for by alternative splicing of HBP/SLBP mRNA. HBP/SLBP mRNA alternative splicing returned to low levels again upon removal of replication stress and was abrogated by caffeine, suggesting the involvement of checkpoint kinases. Analysis of HBP/SLBP cellular localization using GFP (green fluorescent protein) fusion proteins revealed that HBP/SLBP protein and isoforms lacking the domains encoded by exon 2 and exons 2 and 3 were found in the nucleus and cytoplasm, whereas HBP/SLBP lacking the domain encoded by exon 3 was predominantly localised to the nucleus. This isoform lacks the conserved region important for protein–protein interaction with the CTIF [CBP80/20 (cap-binding protein 80/20)]-dependent initiation translation factor and the eIF4E (eukaryotic initiation factor 4E)-dependent translation factor SLIP1/MIF4GD (SLBP-interacting protein 1/MIF4G domain). Consistent with this, we have previously demonstrated that this region is required for the function of HBP/SLBP in cap-dependent translation. In conclusion, alternative splicing allows the synthesis of HBP/SLBP isoforms with different properties that may be important for regulating HBP/SLBP functions during replication stress.