bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of immunoglobulin glycosylation by LC‐ESI‐MS of glycopeptides and oligosaccharides
Authors: Stadlmann Johannes , Pabst Martin , Kolarich Daniel , Kunert Renate , Altmann Friedrich 
Published: July 2008

AbstractTwo LC‐ESI‐MS methods for the analysis of antibody glycosylation are presented. In the first approach, tryptic glycopeptides are separated by RP chromatography and analyzed by ESI‐MS. This “glycopeptide strategy” allows a protein‐ and subclass‐specific quantitation of both neutral and sialylated glycan structures. Additional information about under‐ or deglycosylation and the protein backbone, e.g., termini, can be extracted from the same data. In the second LC‐ESI‐MS method, released oligosaccharides are separated on porous graphitic carbon (PGC). A complete structural assignment of neutral and sialylated oligosaccharides occurring on antibodies is thereby achieved in one chromatographic run. The two methods were applied to polyclonal human IgG, to commercial mAb expressed in CHO cells (Rituximab, Xolair, and Herceptin), in SP2/0 (Erbitux and Remicade) or NS0 cells (Zenapax) and the anti‐HIV antibody 4E10 produced either in CHO cells or in a human cell line. Both methods require comparably little sample preparation and can be applied to SDS‐PAGE bands. They both outperform non‐MS methods in terms of reliability of peak assignment and MALDI‐MS of underivatized glycans with regard to the recording of sialylated structures. Regarding fast and yet detailed structural assignment, LC‐MS on graphitic carbon supersedes all other current methods.
O‐acetylation of sialic acids in N‐glycans of Atlantic salmon (Salmo salar) serum is altered by handling stress
Authors: Liu Xin , Afonso Luis , Altman Eleonora , Johnson Stewart , Brown Laura , Li Jianjun 
Published: July 2008

AbstractO‐acetylation is one of the major modifications of sialic acids that significantly alters biological properties of the parent molecule. These O‐acetylated forms are components of the cellular membrane and can affect physiological and pathological responses. Understanding the role of N‐glycans in physiology is of increasing relevance to cellular biologists in various disciplines who study glycoproteomics yet lack information regarding the function of the attached glycans. It is well known that stress may decrease immune function in fish; however, there are only few suitable biomarkers available to monitor the physiological responses under the stress conditions. This study is the first report on the effect of stress on the profile of O‐acetylation of sialic acids in fish serum. In order to preserve the relevant structural characteristics as much as possible, native N‐glycans were directly analyzed using CE‐MS. We have characterized the N‐glycans in serum of salmon (Salmo salar) exposed to long‐term handling stress (15 s out of the water, daily for 4 wk) and compared with the results obtained from sera of control fish. The results indicated that major N‐glycans in salmon serum contained mono‐acetylated sialic acids (83%), and that the O‐acetylation pattern of sialic acids could be altered by long‐term stress.
Increasing information from shotgun proteomic data by accounting for misassigned precursor ion masses
Authors: Scherl Alexander , Tsai Yihsuan Shannon , Shaffer Scott A. , Goodlett David R. 
Published: July 2008

AbstractAlthough mass spectrometers are capable of providing high mass accuracy data, assignment of true monoisotopic precursor ion mass is complicated during data‐dependent ion selection for LC‐MS/MS analysis of complex mixtures. The complication arises when chromatographic peak widths for a given analyte exceed the time required to acquire a precursor ion mass spectrum. The result is that many measured monoisotopic masses are misassigned due to calculation from a single mass spectrum with poor ion statistics based on only a fraction of the total available ions for a given analyte. Such data in turn produces errors in automated database searches, where precursor m/z value is one search parameter. We propose here a postacquisition approach to correct misassigned monoisotopic m/z values that involves peak detection over the entire elution profile and correction of the precursor ion monoisotopic mass. As a result of using this approach to reprocess shotgun proteomic data we increased peptide sequence assignments by 10% while reducing the estimated false positive ratio from 1 to 0.2%. We also show that 4% of the salvaged identifications may be accounted for by correction of mixed tandem mass spectra resulting from fragmentation of multiple peptides simultaneously, a situation which we refer to as accidental CID.
Proteomic analysis of hypoxia‐induced tube breakdown of an in vitro capillary model composed of HUVECs: Potential role of p38‐regulated reduction of HSP27
Authors: Eguchi Ryoji , Naitou Hirotaka , Kunimasa Kazuhiro , Ayuzawa Rie , Fujimori Yoshihiro , Ohashi Norio , Kaji Kazuhiko , Ohta Toshiro 
Published: July 2008

AbstractWe recently reported that hypoxia could induce the breakdown of capillary‐like tubes formed by human umbilical vein endothelial cells (HUVECs) and that this breakdown was regulated by p38 and not by a caspase cascade, although the exact molecular mechanisms remain unknown. The aim of this study was to identify proteins that regulated hypoxia‐induced tube breakdown through p38‐regulated and caspase‐independent mechanisms. The involvement of adhesion proteins, integrins, VE‐cadherin, PECAM‐1, and occludin was first investigated. Although some of these proteins decreased after hypoxia, none of them met the conditions of being quantitatively restored by p38 inhibition but not by caspase inhibition. We then conducted 2‐D DIGE coupled with MALDI‐TOF/TOF‐MS to identify altered protein expression. The differential proteomic analysis of tube‐forming HUVECs treated with normoxia or hypoxia and treated with hypoxia in the presence or absence of SB203580, a specific p38 inhibitor, revealed the involvement of heat shock proteins in this tube breakdown. We also confirmed that the amount of HSP27 and HSP70 changed in a p38‐regulated and caspase‐independent manner during hypoxia. Knocking down HSP27 expression using RNAi further augmented hypoxia‐induced tube breakdown. Taken together, it was shown that p38‐regulated and caspase‐independent reduction of HSP27 plays an important role in hypoxia‐induced tube breakdown.
Inhaled anesthetics elicit region‐specific changes in protein expression in mammalian brain
Authors: Pan Jonathan Z. , Xi Jin , Eckenhoff Maryellen F. , Eckenhoff Roderic G. 
Published: July 2008

AbstractInhaled anesthetics bind specifically to many proteins in the mammalian brain. Within the subgroup of proteins whose activity is substantially modulated by anesthetic binding, it is reasonable to expect anesthetic‐induced alterations in host expression level. Thus, in an attempt to define the group of functional targets for these commonly used drugs, we examined changes in protein expression after anesthetic exposure in both intact rodent brains and in neuronal cell culture. Differential in‐gel electrophoresis was used to minimize variance, in order to detect small changes. Quantitative analysis shows that 5 h exposures to 1 minimum alveolar concentration (1 MAC) halothane caused changes in the expression of ∼2% of detectable proteins, but only at 2–24 h after awakening, and only in the cortex. An equipotent concentration of isoflurane altered the expression of only ∼1% of detectable proteins, and only in the hippocampus. Primary cortical neurons were exposed to three‐fold higher concentrations of anesthetics with no evidence of cytotoxicity. Small changes in protein expression were elicited by both drugs. Despite the fact that anesthetics produce profound changes in neurobiology and behavior, we found only minor changes in brain protein expression. A pronounced degree of regional selectivity was noted, indicating an under appreciated degree of specificity for these promiscuous drugs.
Free‐flow electrophoresis for top‐down proteomics by Fourier transform ion cyclotron resonance mass spectrometry
Authors: Ouvry‐Patat Séverine A. , Torres Matthew P. , Quek Hung‐Hiang , Gelfand Craig A. , O'Mullan Patrick , Nissum Mikkel , Schroeder Gottfried K. , Han Jun , Elliott Monica , Dryhurst Deanna , Ausio Juan , Wolfenden Richard , Borchers Christoph H. 
Published: July 2008

AbstractHigh‐efficiency prefractionation of complex protein mixtures is critical for top‐down proteomics, i.e., the analysis of intact proteins by MS. Free‐flow electrophoresis (FFE) can be used for IEF to separate proteins within a pH gradient according to their pIs. In an FFE system, this separation is performed entirely in the liquid phase, without the need for particulate chromatographic media, gels, or membranes. Herein, we demonstrated the compatibility of IEF‐FFE with ESI‐Fourier transform ICR MS (ESI‐FTICR‐MS) for top‐down experiments. We demonstrated that IEF‐FFE of intact proteins were highly reproducible between FFE instruments, between laboratories, and between analyses. Applying native (0.2% hydroxypropylmethyl cellulose) IEF‐FFE to an enzyme resulted in no decrease in enzyme activity; applying either native or denaturing (8 M urea) IEF‐FFE to a four‐protein mixture with different pIs resulted in isolation of each protein into separate fractions in a 96‐well plate. After desalting, each protein was sequenced by top‐down MS/MS. As an application of this technique, chicken erythrocyte histone H2A‐IV and its major modified forms were enriched by IEF‐FFE. Top‐down analysis revealed Lys‐5 to be a major acetylation site, in addition to N‐terminal acetylation.
Proteomic identification of a PSF/p54nrb heterodimer as RNF43 oncoprotein‐interacting proteins
Authors: Miyamoto Kentaro , Sakurai Hidetaka , Sugiura Takeyuki 
Published: July 2008

AbstractRNF43 is an oncogenic RING finger protein overexpressed in colorectal cancer. To dissect its biological functions, we explored RNF43‐interacting proteins by pull‐down assay and MS. We identified a heterodimer, p54nrb and PSF, as RNF43's binding partners and confirmed their physical interaction in vivo by the co‐immunoprecipitation experiment. Immunofluorescence analysis revealed that co‐expression of PSF relocates RNF43 from the nuclear periphery to the nucleoplasm. Thus, proteomic identification of RNF43‐associated proteins sheds light on its dynamic interaction network in nuclear events.
A whole‐genome bioinformatics approach to selection of antigens for systematic antibody generation
Authors: Berglund Lisa , Björling Erik , Jonasson Kalle , Rockberg Johan , Fagerberg Linn , Al‐Khalili Szigyarto Cristina , Sivertsson Åsa , Uhlén Mathias 
Published: July 2008

AbstractHere, we present an antigen selection strategy based on a whole‐genome bioinformatics approach, which is facilitated by an interactive visualization tool displaying protein features from both public resources and in‐house generated data. The web‐based bioinformatics platform has been designed for selection of multiple, non‐overlapping recombinant protein epitope signature tags by display of predicted information relevant for antigens, including domain‐ and epitope sized sequence similarities to other proteins, transmembrane regions and signal peptides. The visualization tool also displays shared and exclusive protein regions for genes with multiple splice variants. A genome‐wide analysis demonstrates that antigens for approximately 80% of the human protein‐coding genes can be selected with this strategy.
Surface segregation of highly branched polymer additives in linear hosts
Authors: Qian Zhenyu , Minnikanti Venkatachala S. , Archer Lynden A. 
Published: July 2008

AbstractEntropy‐driven segregation of various branched and hyperbranched polymeric additives in chemically similar linear polymer hosts is studied using self‐consistent (SCF) mean‐field lattice simulations. The simulations account for the effect of molecular architecture on local configurational entropy in the blends, but ignores the effect of architecture on local density and blend compressibility. Star, dendrimer, and comb‐like additives are all found to be enriched at the surface of chemically identical linear host polymers. The magnitude of their surface excess increases with increased number of chain ends and decreases with increased segmental crowding near the branch point. Provided the number of arms and molecular weight of the branched additives are maintained constant, we find that the simplest branched architecture, the symmetric star, exhibits the strongest preference for the surface of binary polymer blends. We show that a single variable, here termed the “entropic driving force density,” controls the relative surface affinities of branched additives possessing a wide range of architectures. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1788–1801, 2008
An acrylic acid modified polypropylene as a compatibilizing agent for the intercalation/exfoliation of an organically modified montmorillonite in polypropylene
Authors: Chinellato A. C. , Vidotti S. E. , Hu G.‐H. , Pessan L. A. 
Published: July 2008

AbstractThis work dealt with the effect of using an acrylic acid modified polypropylene (PP‐g‐AA) as a compatibilizing agent for the intercalation/exfoliation of an organically modified montmorillonite (o‐MMT) in a polypropylene matrix (PP). Two PP‐g‐AA containing the same AA content (6 wt %) and having different molar masses were used. The o‐MMT content was 0, 1, or 5 wt % of total mass and the PP‐g‐AA/o‐MMT mass ratio was 0/1, 1/1, 2/1, or 5/1. Results of wide angle X‐ray scattering (WAXS) and transmission electronic microscopy (TEM) showed that without the PP‐g‐AA, the o‐MMT was dispersed in the PP/o‐MMT in a micrometer scale, similar to a conventional microcomposite. With the PP‐g‐AA, the o‐MMT was much better dispersed and its interlayers were intercalated and partly exfoliated by the polymer chains. Compared with the neat PP, some PP/PP‐g‐AA/o‐MMT systems exhibited higher G′ values and a yield stress at low frequencies, indicating that the PP‐g‐AA promoted the intercalation/exfoliation of the o‐MMT. The compatibilizing efficiency of those two PP‐g‐AA was very similar. Generally speaking, the higher the PP‐g‐AA/o‐MMT mass ratio, the better the state of dispersion and the degree of intercalation/exfoliation. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1811–1819, 2008
Delayed Effects of Cold Atmospheric Plasma on Vascular Cells
Authors: Stoffels Eva , Roks Anton J. M. , Deelman Leo E. 
Published: July 2008

AbstractWe investigated the long‐term behaviour of vascular cells (endothelial and smooth muscle) after exposure to a cold atmospheric plasma source. The cells were treated through a gas‐permeable membrane, in order to simulate intravenous treatment with a gas plasma‐filled catheter. Such indirect treatment resulted in (dose‐dependent) apoptosis and necrosis in smooth muscle cells; these effects were visible 6–10 h after exposure. We ascribed cell damage to poisoning by active nitrogen species. A not yet resolved phenomenon of total (irreversible) cell inactivation without necrosis was observed in endothelial cells. Conditions for non‐inflammatory plasma treatment (no cell necrosis) can be realized. Furthermore, the current experiments have brought new insights in the mechanism of cell detachment, which was observed in many previous studies.magnified image
Finite temperature behaviour of O'KKLT model
Authors: Anguelova L. , Calo V. 
Published: July 2008

AbstractWe summarize our work on the O'Raifeartaigh uplifted KKLT model at finite temperature. We study the system for parameter values for which the zero temperature potential for the volume modulus has a dS minimum. The temperature‐dependent part of the effective potential has a runaway behaviour for one exponent in the superpotential, whereas it can have local minima at finite field vevs for two exponents in the superpotential. However, it turns out that, despite the presence of those minima, the zero temperature dS vacuum is not destabilized by thermal corrections within the whole range of validity of our approximations.
Backreacting flavors in the Klebanov‐Witten model via D7‐branes
Authors: Benini F. 
Published: July 2008

AbstractWe discuss the addition of backreacting D7‐branes to (fractional) D3‐brane solutions in IIB supergravity which is dual to the addition of a large number of fields in the fundamental representation to known field theories in the Veneziano limit. We specialize to D7/D3‐branes on the conifold (flavored Klebanov‐Witten theory); we then generalize to massive flavors and to the case of fractional D3‐branes and D7‐branes with gauge flux (flavored Klebanov‐Tseytlin theory). This talk is mainly based on [16, 18].
(D)‐instanton effects in magnetized brane worlds
Authors: Billó M. 
Published: July 2008

AbstractWe consider systems of magnetized D9 branes on orbifolds supporting 𝒩 = 1 gauge theories. In such realizations, the matter multiplets arise from “twisted” strings connecting different stacks of branes. The introduction of Euclidean 5‐branes wrapped on the six‐dimensional compact space leads to instanton effects. We examine the interplay between the annuli diagrams with an E5 boundary and the holomorphicity properties of the effective low‐energy supergravity action which describes the system, including its instanton corrections. This talk is mostly based on [1].
E7(7) invariant measures of entanglement
Authors: Borsten L. 
Published: July 2008

AbstractA study, centred on the Freudenthal triple system, of the E7(7) invariant tripartite entanglement of seven qubits and its relationship to black hole entropy in N = 8 supergravity. Based on work done in collaboration with D. Dahanayake, M. J. Duff and H. Ebrahim.
String dual of 𝒩 = 1 super Yang‐Mills on the cylinder
Authors: Canoura F. 
Published: July 2008

AbstractWe study the stringy description of 𝒩 = 1 supersymmetric SU(N) gauge theory on ℝ1,2 × S1. Our description is based on the known Maldacena‐Núñez solution, properly modified to account for the compact dimension. The most interesting of its properties is that extra BPS M‐branes are present, which generate a non‐perturbative superpotential that we explicitly compute.
Instantons and Donaldson–Thomas invariants
Authors: Cirafici M. , Sinkovics A. , Szabo R.J. 
Published: July 2008

AbstractWe review some recent progress in understanding the relation between a six dimensional topological Yang–Mills theory and the enumerative geometry of Calabi–Yau threefolds. The gauge theory localizes on generalized instanton solutions and is conjecturally equivalent to Donaldson–Thomas theory. We evaluate the partition function of the U(N) theory in its Coulomb branch on flat space by employing equivariant localization techniques on its noncommutative deformation. Geometrically this corresponds to a higher dimensional generalization of the ADHM formalism. This formalism can be extended to a generic toric Calabi–Yau.
Unquenched flavors in the Klebanov‐Strassler theory
Authors: Cremonesi S. 
Published: July 2008

AbstractWe present an analytic solution of type IIB supergravity plus D7‐branes, describing the addition of any number of flavors to the Klebanov‐Strassler background. The dual field theory and its self‐similar RG flow, described by a cascade of Seiberg dualities also in the presence of flavors, are discussed. The solution indicates that the dual gauge theory enjoys a duality wall in the UV. We stress the correspondence between Seiberg duality on the field theory side, and large gauge transformations on the RR and NSNS potentials on the gravity side. This contribution is mostly based on [1].
Notes on quantum evolution across singularities
Authors: Evnin O. 
Published: July 2008

AbstractIn a number of model contexts, evolution across space‐time singularities (reminiscent of the cosmological singularities) involves time‐dependent quantum Hamiltonians developing a singularity as a function of time. In this contribution to the proceedings of the 3rd RTN workshop in Valencia, I review some recent investigations of the general properties of such systems.
The minimally immersed 4D supermembrane
Authors: Garcıa del Moral M.P. , Pena J.M. , Restuccia A. 
Published: July 2008

AbstractIn this note we summarize some of the properties found in [1], and its relation with [2]. We comment on the construction of the action of the 11D supermembrane with nontrivial central charges minimally immersed on a 7D toroidal manifold is obtained (MIM2).The transverse coordinates to the supermembrane are maps to a 4D Minkowski space‐time. The action is invariant under additional symmetries in comparison to the supermembrane on a 11D Minkowski target space. The hamiltonian in the LCG is invariant under conformal transformations on the Riemann surface base manifold. The spectrum of the regularized hamiltonian is discrete with finite multiplicity. Its resolvent is compact. Susy is spontaneously broken, due to the topological central charge condition, to four supersymmetries in 4D, the vacuum belongs to an N = 1 supermultiplet. When assuming the target‐space to be an isotropic 7‐tori, the potential does not contain any flat direction, it is stable on the moduli space of parameters. Moreover due to the discrete symmetries of the hamiltonian, there are only 7 possible minimal holomorphic immersions of the MIM2 on the 7‐torus. When these symmetries are identified on the target space, it corresponds to compactify the MIM2 on a orbifold with G2 structure. Once the singularities are resolved it leads to the compactification of the MIM2 on a G2 manifold as shown in [2].
Q‐branes in type IIB supergravity
Authors: Bergshoeff E.A. , Hartong J. , Sorokin D. 
Published: July 2008

AbstractThe notion of Q7‐branes and Q‐instantons is introduced. These are one‐half BPS solutions of the type IIB supergravity theory characterized by a set of three parameters p,q,r such that r^2>4pq. The numbers p,q,r parameterize the electric and magnetic couplings of, respectively, the Q7‐branes and Q‐instantons to a triplet of 8‐forms. The (p,q) 7‐branes and instantons including the D7‐brane and the D‐instanton have r2 = 4pq. Seven‐brane solutions containing Q7‐branes are discussed and the Q‐instanton on‐shell action is computed. The Q7‐branes are either novel bound states of a (p,q) 7‐brane and a (p′,q′) 7‐brane with (p,q) ≠ (p′,q′) or they form an independent new object in the theory.
Higher‐spin dynamics and Chern‐Simons theories
Authors: Engquist J. , Hohm O. 
Published: July 2008

AbstractWe review the construction of consistent higher‐spin theories based on Chern‐Simons actions. To this end we first introduce the required higher‐spin algebras and discuss curvature and torsion tensors in an unconstrained way. Finally we perform a perturbative analysis of the Chern‐Simons theory in D = 5 for a non‐maximally symmetric AdS4 background and obtain the required four‐dimensional Frønsdal equations in the compensator formulation.
Warped generalized geometry compactifications, effective theories and non‐perturbative effects
Authors: Koerber P. , Martucci L. 
Published: July 2008

AbstractSummarizing the results of [1], we discuss the four‐dimensional effective approach to type II N = 1 supersymmetric flux compactifications with general SU(3) × SU(3)‐structure. In particular, we study the effect of a non‐trivial warp factor, which we argue leads naturally to a supergravity formulation invariant under local complexified Weyl transformations. We show that the full ten‐dimensional supersymmetry equations can be obtained as F‐flatness and D‐flatness conditions from the superpotential and Kähler potential. We then consider non‐perturbative corrections to these supersymmetry conditions, following from adding instanton or gaugino condensation effects to the superpotential. As examples, we show how smeared instantons allow to understand the ten‐dimensional geometry of KKLT‐like AdS vacua and we give an explanation for the superpotential for “mobile” D3‐branes in terms of a non‐perturbatively induced generalized complex structure.