bluuebunny/crossref_metadata_2025_split huggingface dataset:
A serial lectin approach to the mucin‐type O‐glycoproteome of Drosophila melanogaster S2 cells
Authors: Schwientek Tilo , Mandel Ulla , Roth Udo , Müller Stefan , Hanisch Franz‐Georg 
Published: August 2007

AbstractIdentification of mucin‐type O‐glycosylated proteins with known functions in model organisms like Drosophila could provide keys to elucidate functions of the O‐glycan moiety and proteomic analyses of O‐glycoproteins in higher eukaryotes remain a challenge due to structural heterogeneity and a lack of efficient tools for their specific isolation. Here we report a strategy to evaluate the O‐glycosylation potential of the embryonal hemocyte‐like Drosophila Schneider 2 (S2) cell line by expression of recombinant glycosylation probes derived from tandem repeats of the human mucin MUC1 or of the Drosophila salivary gland protein Sgs1. We obtained evidence that mucin‐type O‐glycosylation in S2 cells grown under serum‐free conditions is restricted to the Tn‐antigen (GalNAcα‐Ser/Thr) and the T‐antigen (Galβ1‐3GalNAcα‐Ser/Thr) and this structural homogeneity enables unique glycoproteomic strategies. We present a label‐free strategy for the isolation, profiling and analysis of O‐glycosylated proteins consisting of serial lectin affinity capture, 2‐DE‐based glycoprotein analysis by O‐glycan specific mAbs and protein identification by MALDI‐MS. Protein identity and O‐glycosylation was confirmed by ESI‐MS/MS with detection of diagnostic sugar oxonium‐ion fragments. Using this strategy, we established 2‐D reference maps and identified 21 secreted and intracellular mucin‐type O‐glycoproteins. Our results show that Drosophila S2 cells express O‐glycoproteins involved in a wide range of biological functions including proteins of the extracellular matrix (Laminin γ‐chain, Peroxidasin and Glutactin), pathogen recognition proteins (Gnbp1), stress response proteins (Glycoprotein 93), secreted proteases (Matrix‐metalloprotease 1 and various trypsin‐like serine proteases), protease inhibitors (Serpin 27A) and proteins of unknown function.
Implementation and application of a versatile clustering tool for tandem mass spectrometry data
Authors: Flikka Kristian , Meukens Jeroen , Helsens Kenny , Vandekerckhove Joël , Eidhammer Ingvar , Gevaert Kris , Martens Lennart 
Published: August 2007

AbstractHigh‐throughput proteomics experiments typically generate large amounts of peptide fragmentation mass spectra during a single experiment. There is often a substantial amount of redundant fragmentation of the same precursors among these spectra, which is usually considered a nuisance. We here discuss the potential of clustering and merging redundant spectra to turn this redundancy into a useful property of the dataset. To this end, we have created the first general‐purpose, freely available open‐source software application for clustering and merging MS/MS spectra. The application also introduces a novel approach to calculating the similarity of fragmentation mass spectra that takes into account the increased precision of modern mass spectrometers, and we suggest a simple but effective improvement to single‐linkage clustering. The application and the novel algorithms are applied to several real‐life proteomic datasets and the results are discussed. An analysis of the influence of the different algorithms available and their parameters is given, as well as a number of important applications of the overall approach.
Phosphorylation of human eukaryotic elongation factor 1Bγ is regulated by paclitaxel
Authors: Prado Miguel A. , Casado Pedro , Zuazua‐Villar Pedro , del Valle Eva , Artime Noelia , Cabal‐Hierro Lucía , Martínez‐Campa Carlos M. , Lazo Pedro S. , Ramos Sofía 
Published: August 2007

AbstractPaclitaxel (Ptx) is an antitumoural drug that inhibits microtubule dynamics, causes G2/M arrest and induces cell death. 2‐D PAGE and MALDI‐TOF‐MS analysis of HeLa cells extracts revealed that Ptx up‐regulates a form of the eukaryotic elongation factor 1Bγ (eEF1Bγ) and down‐regulates another one. This event, linked to the lack of Ptx effect over eEF1Bγ mRNA or protein levels suggested a PTM of this elongation factor. Further 2‐D PAGE analysis followed by a phosphospecific staining with PRO‐Q Diamond showed the staining of the Ptx up‐regulated form only. Moreover, this Ptx up‐regulated form of eEF1Bγ disappears upon treatment with protein phosphatase. Thus, we demonstrate that human eEF1Bγ phosphorylation is regulated by Ptx.
Combination of peptide OFFGEL fractionation and label‐free quantitation facilitated proteomics profiling of extraocular muscle
Authors: Fraterman Sven , Zeiger Ulrike , Khurana Tejvir S. , Rubinstein Neal A. , Wilm Matthias 
Published: August 2007

AbstractSeveral label‐free quantitation strategies have been introduced that obliterate the need for expensive isotopically labeled molecules. However label‐free approaches have considerably higher demands in respect of repeatability of sample preparation and fractionation than multiplexing isotope labeling‐based strategies. OFFGEL fractionation promises the necessary separation efficiency and repeatability. To test this platform, 12‐fraction peptide OFFGEL electrophoresis and online reversed‐phase LC connected to a quadrupole TOF mass spectrometer were used to determine differences of the physiological, pathological and biochemical distinct extraocular muscle allotype in comparison to hind‐limb muscle. Close to 70% of the peptides separated by OFFGEL electrophoresis were detected only in a single fraction. To determine the separation repeatability of four samples, we compared the ion volumes of multiple peptides deriving from the thick filament‐associated protein titin over several fractions and determined a coefficient of variation below 20%. Of the 474 proteins identified, 61 proteins were differently expressed between the two muscle allotypes and were involved in metabolism, muscle contraction, stress response, or gene expression. Several expression differences were validated using immunohistochemistry and Western blot analysis. We therefore consider peptide OFFGEL fractionation an effective and efficient addition to our label‐free quantitative proteomics workflow.
Exactness of simplified scalar optical approaches in modelling a threshold operation of possible nitride vertical‐cavity surface‐emitting diode lasers
Authors: Czyszanowski Tomasz , Wasiak Michał , Sarzała Robert P. , Nakwaski Włodzimierz 
Published: August 2007

AbstractModern small‐size vertical‐cavity surface‐emitting diode lasers (VCSELs) require principally fully vectorial optical modelling because their cavity sizes are of the order of the wavelength of emitted radiation. However, much simpler scalar approaches are often surprisingly exact even beyond the limits of their confirmed validity. Therefore, in the present paper, reasonable limits of an application of simplified scalar optical approaches (instead of more exact but also much more involved and time‐consuming rigorous vectorial ones) are determined to model threshold operation of possible nitride VCSELs equipped with tunnel junctions with the aid of a comparison of results of the scalar effective frequency method with those obtained using the fully vectorial three‐dimensional plane wave admittance method. Both these optical methods have been found to give usually quite close results for the fundamental transverse mode. Larger discrepancies between the results of both approaches have been found for first‐order transverse modes (and even larger are expected for higher‐order ones) and for larger (or very small) active regions. Some structural modifications of nitride VCSELs, which may enable their low‐threshold single‐fundamental‐mode room‐temperature continuous‐wave operation, are proposed. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Determination of activation energies from thermally stimulated currents: application to the CdS crystal containing cupric ions
Authors: Salehi S. M. A. 
Published: August 2007

AbstractTheoretical calculations which take into account thermally stimulated conductivity are presented. The model used has been established for the case of a single type of electron trap, a single type of recombination centre and in the presence of thermally disconnected deep traps. The conductivity relation has been derived and solved numerically in order to determine electron trap depths. It was then tested in the case of CdS single crystals doped with copper ions. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of hydrogenation, low energy ion irradiation and annealing on hydrogen bonding to polycrystalline diamond surface studied by high resolution electron energy loss spectroscopy
Authors: Michaelson Sh. , Ternyak O. , Akhvlediani R. , Lafosse A. , Bertin M. , Azria R. , Hoffman A. 
Published: August 2007

AbstractThe effects of different processes of hydrogenation, thermal treatment and ion irradiation of hydrogenated polycrystalline diamond surface have been investigated by means of high resolution electron energy loss spectroscopy (HR‐EELS). Analysis of the different contributions in the CH stretching, overtones and combination modes, as well as changes in relative intensities of the diamond CC and CHx related vibrations allowed us to identify the CHx adsorbed species on the diamond surface following the different treatments. Ex‐situ hydrogenation of diamond surface by means of exposure to H‐MW plasma results in a fully hydrogenated well‐ordered diamond surface and etching of the amorphous phase located on the grain boundaries present on the sample after CVD‐deposition. Annealing this surface to 600 °C results in some subtle changes in the HR‐EELS, probably associated with decomposition of CHx (x = 2, 3) adsorbed species. Ion irradiation on the surface induces partial desorption of hydrogen from the diamond phase and a large amount of amorphous defects, some of them of sp and the most of them of sp2 character. Annealing to 600–700 °C of the irradiated surface leads to hydrogen desorption. In‐situ hydrogenation of the irradiated and annealed sample does not restore the diamond structure, and results in hydrogenated amorphous surface, unstable with thermal annealing above 600–700 °C. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A theoretical study of Li as n‐type dopants for diamond: the role of aggregation
Authors: Goss J. P. , Eyre R. J. , Briddon P. R. 
Published: August 2007

AbstractThe formation of n‐type diamond has proved highly challenging, with the best species to date being the relatively deep phosphorus donor. Theory suggests that interstitial Li may be a superior donor species. In this paper we report the first principles modelling of Li as a donor, and report on the highly energetically favourable aggregation process that limits the likely success for Li‐based n‐type material. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electrical and optical properties of multivacancy centres in diamond
Authors: Jones Robert , Hounsome Luke S. , Fujita Naomi , Öberg Sven , Briddon Patrick R. 
Published: August 2007

AbstractRecent experiments have shown that vacancy clusters are common defects in all types of monocrystalline brown diamond. This is believed to be due to an enhanced stability of the bounding 〈111〉 or 〈110〉 surfaces, arising from the formation of π‐bonded chains. These chains lead to broad bands of gap states with acceptor and donor levels around Ev + 2 eV. They also are likely to be responsible for the broad absorption continuum extending from the NIR through the visible and into the UV region which is characteristic of brown diamonds. High temperature treatment removes or transforms the clusters in CVD and type IIa diamonds leaving the diamond colourless. In type Ia brown diamonds, heat treatments up to 2500 °C lead to the breakup of the clusters and the formation of specific vacancy‐nitrogen defects. We show that ab initio modelling of the interaction of nitrogen with the chains open a gap and leads to a threshold absorption energy in the 1–2 eV range. Finally, the calculations shed light on the identity of the vacancy‐nitrogen defects observed. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Differential theory of diffraction in cylindrical coordinates
Authors: Popov E. , Bonod N. 
Published: August 2007

AbstractThe principles of the differential theory of light diffraction are presented in cylindrical coordinates. Special attention is played to the factorisation rules necessary to obtain faster convergence with respect to the number of basic functions used in the field representation. A detailed description is given for diffracting objects having rotational symmetry and finite cylindrical length. Some properties of light diffracted by a single circular aperture piereced in a finitely conducting screen are discussed, including the excitation of surface plasmon wave and the enhanced beaming. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Light–matter interaction in photonic crystal slabs
Authors: Andreani Lucio Claudio , Gerace Dario 
Published: August 2007

AbstractA theoretical treatment of waveguide‐embedded photonic crystals based on a guided‐mode expansion method is reviewed. The following issues are discussed: (i) a formulation of the method for calculating photonic‐mode dispersion and intrinsic losses due to out‐of‐plane diffraction, (ii) modelling of disorder‐induced losses due to fabrication imperfections, and (iii) a quantum‐mechanical treatment of radiation‐matter interaction, with application to exciton‐polaritons in photonic crystal slabs. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Unusual temperature dependence of the positron lifetime in a polymer of intrinsic microporosity
Authors: Lima de Miranda Rodrigo , Kruse Jan , Rätzke Klaus , Faupel Franz , Fritsch Detlev , Abetz Volker , Budd Peter M. , Selbie James D. , McKeown Neil B. , Ghanem Bader S. 
Published: August 2007

AbstractThe performance of polymeric membranes for gas separation is mainly determined by the free volume. Polymers of intrinsic microporosity are interesting due to the high abundance of accessible free volume. We performed measurements of the temperature dependence of the positron lifetime, generally accepted for investigation of free volume, in two polymers of intrinsic microporosity (PIM‐1 and PIM‐7) in the range from 143 to 523 K. The mean value of the free volume calculated from the ortho‐positronium lifetime is in the range of typical values for high free volume polymers. However, the temperature dependence of the local free volume is non‐monotonous in contrast to the macroscopic thermal expansion. The explanation is linked to the spirocenters in the polymer. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interaction of a two‐level cyclic XY n‐spin model with a two‐mode cavity field in off‐resonant states
Authors: Grinberg Horacio 
Published: August 2007

AbstractThe interaction of the XY n‐spin cyclic model with a two‐mode cavity field in the rotating‐wave approximation is investigated in the framework of a generalized Jaynes–Cummings two‐level system consisting of the vacuum state and a thermally averaged manifold of excited sates. Computation of the energy of this manifold allows this interaction to be examined in off‐resonant states. Time evolution of the population inversion, photon distribution, and temperature distribution for an excited initial state are computed via second‐ and third‐order perturbation expansion of the time evolution operator matrix elements for the excited and ground states, respectively and for an ideal squeezed initial coherent state of the cavity field. It was assumed that the two modes have initially the same photon distribution. The pattern of the spin population inversion appears as a manifestation of multiple and complicated inerferences, which is mathematically reflected in a double discrete summation that appears in the calculation of the dynamics. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
3D‐quantitative structure activity analysis and quantum chemical analysis of pyrido‐di‐indoles
Authors: Pasha Farhan A. , Chung Hwan W. , Kang Soon B. , Cho Seung J. 
Published: August 2007

AbstractThe computational analyses of pyrido‐di‐indoles have been performed with various methods such as quantum mechanical studies (AM1, PM3, and DFT) and 3D‐QSAR analyses (CoMFA and CoMSIA). The electrophilicity index along with some other properties has been related with biological activities. Electrostatic field has been identified as an important descriptor from the 3D‐QSAR analyses. The AM1 geometry and Gasteiger–Marsili charged base CoMFA (r = 0.75) and CoMSIA (r = 0.62) give strong correlation and indicate that a substitution at sites 2 and 3 of Ring A might affect the activity. In addition, a plausible statistical model has been found with DFT‐based local philicity and negative Fukui function with a value of r2 = 0.82 and rcv2 = 0.60. The DFT analysis indicates that electron density of nitrogen atom of Ring B significantly contributes to activity. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Riccati differential equation for quantum mechanical bound states: Comparison of numerical integrators
Authors: Chou Chia‐Chun , Wyatt Robert E. 
Published: August 2007

AbstractComputational comparison is presented of several integrators for the Riccati differential equation for the one‐dimensional quantum mechanical bound state problem. The computational method for the quantum Hamilton‐Jacobi equation for stationary states is briefly reviewed. An interpolation formula for the quantum momentum function is proposed for the evaluation of the phase integral. The Möbius integrator, the R‐matrix propagation method, the log derivative method, and the symplectic integrator can accurately pass through singularities in the solution. These four integrators are actually Möbius transformations with different coefficients. Analytical analysis and numerical results demonstrate that the classical momentum is a good choice for the initial condition to obtain the bound state solution of the Riccati differential equation as long as the starting point of the propagation is far enough from the origin. The computational comparison is demonstrated for the harmonic oscillator. The numerical results indicate that the symplectic integrators achieve highest accuracy, and the simplicity of these algorithms shows an advantage over the other methods. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Many‐body Brillouin–Wigner second‐order perturbation theory: A robust and efficient approach to the multireference correlation problem
Authors: Papp P. , Mach P. , Hubač I. , Wilson S. 
Published: August 2007

AbstractThe multireference, state‐specific, second‐order, Brillouin–Wigner perturbation theory is presented as a robust approach to the electron correlation problem for systems demanding the use of a multireference function. A posteriori modifications are made which, in the case of a single reference function, recover the well known formula of second‐order many‐body perturbation theory (MBPT2), i.e. Møller–Plesset (MP2) theory, and in the multireference case can be shown to be equivalent to state‐specific multireference Rayleigh–Schrödinger‐like perturbation theory. It is shown that multireference many‐body Brillouin–Wigner perturbation theory when restricted to second‐order is a true many‐body theory, that is, it is a theory, which has the property of extensivity. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Single drop microextraction as a concentrating probe for rapid screening of low molecular weight drugs from human urine in atmospheric‐pressure matrix‐assisted laser desorption/ionization mass spectrometry
Authors: Shrivas Kamlesh , Wu Hui‐Fen 
Published: August 2007

AbstractThe present work reports the development of a new analytical procedure for simple and rapid screening of low molecular weight drugs (<500 Da) from human urine samples by atmospheric‐pressure matrix‐assisted laser desorption/ionization mass spectrometry (AP‐MALDI‐MS) combined with single drop microextraction (SDME). The success of the proposed method is due to the use of methyltrioctylammonium chloride (MTOAC) as additive to avoid the noise arising from the matrix ions (α‐cyano‐4‐hydroxycinnamic acid (CHCA)). SDME also aided in alleviating the interferences arising from other matrix ions present in the urine samples prior to AP‐MALDI‐MS analysis. Factors affecting the extraction efficiency of drugs, such as selection of solvent, stirring speed, extraction time, exposure volume of extraction phase and salt addition, have been optimized. The optimum molar ratio of CHCA/MTOAC that gave the minimum background noise of CHCA ions was 700:1. The limit of detection (LOD) and relative standard deviation (RSD) of the method were in the ranges 0.3–1.6 µM and 7.8–11.4%, respectively. The SDME method was compared with liquid‐liquid extraction (LLE) and hollow fiber liquid‐phase microextraction (HF‐LPME) to evaluate the compatibility of the present method in the extraction of drugs from urine samples. The role of MTOAC as matrix ion signal suppressor and SDME as analyte‐separating device in the rapid screening of low molecular weight drugs from human urine samples using AP‐MALDI/MS has been reported. Copyright © 2007 John Wiley & Sons, Ltd.
An illustrative example of refactoring object‐oriented source code with aspect‐oriented mechanisms
Authors: Monteiro Miguel P. , Fernandes João M. 
Published: August 2007

AbstractThis paper describes a refactoring process that transforms a Java source code base into a functionally equivalent AspectJ source code base. The process illustrates the use of a collection of refactorings for aspect‐oriented source code, covering the extraction of scattered implementation elements to aspects, the internal reorganization of the extracted aspects and the extraction of commonalities to super‐aspects. Copyright © 2007 John Wiley & Sons, Ltd.
A survey on approaches to gridification
Authors: Mateos Cristian , Zunino Alejandro , Campo Marcelo 
Published: August 2007

AbstractThe Grid shows itself as a globally distributed computing environment, in which hardware and software resources are virtualized to transparently provide applications with vast capabilities. Just like the electrical power grid, the Grid aims at offering a powerful yet easy‐to‐use computing infrastructure to which applications can be easily ‘plugged’ and efficiently executed. Unfortunately, it is still very difficult to Grid‐enable applications, since current tools force users to take into account many details when adapting applications to run on the Grid. In this paper, we survey some of the recent efforts in providing tools for easy gridification of applications and propose several taxonomies to identify approaches followed in the materialization of such tools. We conclude this paper by describing common features among the proposed approaches, and by pointing out open issues and future directions in the research and development of gridification methods. Copyright © 2007 John Wiley & Sons, Ltd.
An agent‐based perspective to handover management in 4G networks
Authors: Zafeiris Vassilis E. , Giakoumakis E. A. 
Published: August 2007

AbstractIn 3G or earlier generation networks handovers are usually initiated and decided by the base station, on the basis of measurements of RSS or SNR received by the terminal, cell congestion, terminal speed etc. In 4G, due to the diversity of available radio access services, additional factors, for example user profile, application requirements, and terminal device capabilities, need also to be taken into account. We propose an agent‐based architecture that determines the timing and target network for handovers in a 4G network setting. The capabilities of the architecture are provided as a value‐added service on top of network operators' wireless access infrastructure. Network selection spans both wireless access and core routing services and is performed by user agents executing in the network side. In order to deal with trust issues we study the integration of the regulatory authority in the architecture. A performance study of the architecture's impact on handover latency is provided through a simulation system. Copyright © 2007 John Wiley & Sons, Ltd.