bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative proteomes and in vivo secretomes of progressive and regressive UV‐induced fibrosarcoma tumor cells: Mimicking tumor microenvironment using a dermis‐based cell‐trapped system linked to tissue chamber
Authors: Shi Yang , Elmets Craig A. , Smith Jeffery W. , Liu Yu‐Tsueng , Chen Yun‐Ru , Huang Cheng‐Po , Zhu Wenhong , Ananthaswamy Honnavara N. , Gallo Richard L. , Huang Chun‐Ming 
Published: November 2007

AbstractThe alterations of tumor proteome and/or in vivo secretome created by host‐tumor cell interaction may be crucial factors for tumors to undergo progression or regression in a host system. Two UV‐induced fibrosarcoma tumor cell lines (UV‐2237 progressive cells and UV‐2240 regressive cells) were used as models to address this issue. Hundreds of proteins including in vivo secretome have been identified and quantified via an isotope‐coded protein label (ICPL) in conjunction with high‐throughput NanoLC‐LTQ MS analysis. A newly designed technology using a dermis‐based cell‐trapped system was employed to encapsulate and grow 3‐D tumor cells. A tissue chamber inserted with a tumor cell‐trapped dermis was implanted into mice to mimic the tumor microenvironment. The in vivo secretome created by host‐tumor interaction was characterized from samples collected from tissue chamber fluids via ICPL labeling mass spectrometric analysis. Twenty‐five proteins including 14‐3‐3 proteins, heat shock proteins, profilin‐1, and a fragment of complement C3 with differential expression in proteomes of UV‐2237 and UV‐2240 cells were revealed. Three secreted proteins including myeloperoxidase, alpha‐2‐macroglobulin, and a vitamin D‐binding protein have different abundances in the in vivo secretome in response to UV‐2237 and UV‐2240 cells. Differential tumor proteomes and in vivo secretome were thus accentuated as potential therapeutic targets to control tumor growth.
Proteolytic cleavage of the Chlamydia pneumoniae major outer membrane protein in the absence of Pmp10
Authors: Juul Nicolai , Timmerman Evy , Gevaert Kris , Christiansen Gunna , Birkelund Svend 
Published: November 2007

AbstractThe genome of the obligate intracellular bacteria Chlamydia pneumoniae contains 21 genes encoding polymorphic membrane proteins (Pmp). While no function has yet been attributed to the Pmps, they may be involved in an antigenic variation of the Chlamydia surface. It has previously been demonstrated that Pmp10 is differentially expressed in the C. pneumoniae CWL029 isolate. To evaluate whether the absence of Pmp10 in the outer membrane causes further changes to the C. pneumoniae protein profile, we subcloned the CWL029 isolate and selected a clone with minimal Pmp10 expression. Subsequently, we compared the proteome of the CWL029 isolate with the proteome of the subcloned strain and identified a specific cleavage of the C‐terminal part of the major outer membrane protein (MOMP), which occurred only in the absence of Pmp10. In contrast, when Pmp10 was expressed we predominantly observed full‐length MOMP. No other proteins appeared to be regulated according to the presence or absence of Pmp10. These results suggest a close association between MOMP and Pmp10, where Pmp10 may protect the C‐terminal part of MOMP from proteolytic cleavage.
Proteome and phosphoproteome analysis of chromatin associated proteins in rice (Oryza sativa)
Authors: Tan Feng , Li Guosheng , Chitteti Brahmananda Reddy , Peng Zhaohua 
Published: November 2007

AbstractThe eukaryotic chromatin/chromosome stores genomic information, controls genetic material distribution, and plays an essential role in the establishment and maintenance of spatial and temporal gene expression profile. Despite over a century of research, the protein composition and higher level structure of chromatin still remain obscure, particularly in plants. In this report, we have developed a protocol for chromatin purification from rice suspension cells and examined proteins copurified with chromatin using both 2‐DE gel and shotgun approaches. Nine hundred seventy‐two distinct protein spots have been resolved on 2‐DE gels and 509 proteins have been identified by MALDI‐MS/MS following gel excision, which correspond to 269 unique proteins. When the chromatin copurified proteins are examined using shotgun method, a large number of histone variants in addition to the four common core histones have been identified. Other proteins identified include nucleosome assembly proteins, high mobility group proteins, histone modification proteins, transcription factors, and a large number of hypothetical and function unknown proteins. Furthermore, putative phosphoproteins copurified with chromatin have been examined using Pro‐Q Diamond phosphoprotein stain and followed by MALDI‐MS/MS. Our studies have provided valued new insight into chromatin composition in plants.
Protein partners in the life history of activated fibroblast growth factor receptors
Authors: Vecchione Anna , Cooper Helen J. , Trim Kimberley J. , Akbarzadeh Shiva , Heath John K. , Wheldon Lee M. 
Published: November 2007

AbstractFibroblast growth factor receptors (FGFRs) are a family of four transmembrane (TM) receptor tyrosine kinases (RTKs) which bind to a large family of fibroblast growth factor (FGF) ligands with varying affinity and specificity. FGFR signaling regulates many physiological and pathological processes in development and tissue homeostasis. Understanding FGFR signaling processes requires the identification of partner proteins which regulate receptor function and biological outputs. In this study, we employ an epitope‐tagged, covalently dimerized, and constitutively activated form of FGFR1 to identify potential protein partners by MS. By this approach, we sample candidate FGFR effectors throughout the life history of the receptor. Functional classification of the partners identified revealed specific subclasses involved in protein biosynthesis and folding; structural and regulatory components of the cytoskeleton; known signaling effectors and small GTPases implicated in endocytosis and vesicular trafficking. The kinase dependency of the interaction was determined for a subset of previously unrecognized partners by coimmunoprecipitation, Western blotting, and immunocytochemistry. From this group, the small GTPase Rab5 was selected for functional interrogation. We show that short hairpin (sh) RNA‐mediated depletion of Rab5 attenuates the activation of the extracellular‐regulated kinase (ERK) 1/2 pathway by FGFR signaling. The strategic approach adopted in this study has revealed bona fide novel effectors of the FGFR signaling pathway.
Self‐ and cross‐associations in two‐component mixed polymer gels
Authors: Mao Ching‐Feng 
Published: November 2007

AbstractThe gel properties of two‐component mixed polymer gels are investigated using a cascade model, which assumes that the gel network is formed via the self‐association of one of the two components and the cross‐association of the two components. The effects of the model parameters, such as the equilibrium constants and the functionalities for cross‐associations and self‐associations, on the composition dependence of the modulus and gel point curves are examined to elucidate the contribution of self‐associations to the gel network. The results show that the characteristics of self‐associations become pronounced when the equilibrium constant or the functionality for self‐associations is comparable to that for cross‐associations. The model is applied to analyze the critical gelling concentration data for xanthan/locust bean gum mixed gels, which shows significant self‐associations at high xanthan compositions. The resulting model curves agree well with the experimental data at all temperatures. The analysis of the temperature dependence of the best‐fit equilibrium constant yields values of enthalpy change that are consistent with previous findings. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 80–91, 2008
Plastic deformation behavior of β phase isotactic polypropylene in plane‐strain compression at elevated temperatures
Authors: Lezak E. , Bartczak Z. 
Published: November 2007

AbstractIsotactic polypropylene (iPP) rich in β crystal modification was deformed by plane‐strain compression at T = 55–100 °C. The evolution of phase structure, morphology, and orientation were studied by DSC, X‐Ray, and SEM. The most important deformation mechanisms found were interlamellar slip operating in the amorphous layers, resulting in numerous fine deformation bands and the crystallographic slip systems, including the (110)[001]β chain slip and (110)[$1{\bar {1}}0$]β transverse slip. Shear within deformation bands leads to β→α solid state phase transformation in contrast to β→smectic transformation observed at room temperature. Newly formed α crystallites deform with an advancing strain by crystallographic slip mechanism, primarily the (010)[001]α chain slip. As a result of deformation and phase transformation within deformation bands β lamellae are locally destroyed and fragmented into smaller crystals. Deformation to high strains, above e = 1, brings further heavy fragmentation of lamellae, followed by fast rotation of crystallites with chain axis towards the direction of flow FD. This process, together with still active crystallographic slip, leads to the final texture with molecular axis of both crystalline β and α phase oriented along FD. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 92–108, 2008
The design of duct venting of gas explosions
Authors: Benedetto Almerinda Di , Russo Paola , Salzano Ernesto 
Published: November 2007

AbstractVenting systems are useful for the mitigation of accidental explosions. Vent ducts should be used if equipment is located indoors, as NFPA 68 (2007) suggests, for discharging combustion products to safe location. However, the presence of a duct is likely to increase the severity of the explosion with respect to simply vented vessels.Up to now, no reliable correlations are available for the sizing of ducted vented systems. The only correlation available was developed by Bartknecht in 1993 for gas explosion, also acknowledged by NFPA 68.In this study, we propose an engineering correlation based on semi‐empirical engineering methodologies, which is able to quantify the relations between geometric properties and the peak pressure occurring in the combustion chamber in the presence of a duct fitted on the vent panel. To this aim, we have regressed all the available experimental data on gas explosion in ducted‐vented vessels. © 2007 American Institute of Chemical Engineers Process Saf Prog, 2008
Monte Carlo simulations of ferroelectric properties based on a microscopic model for PVDF
Authors: Kühn M. , Kliem H. 
Published: November 2007

AbstractFerroelectricity can be found in the organic vinylidene fluoride polymer (PVDF) which consists of the polar – [CH2–CF2]n– units. This material shows both orientational and electronic polarisation. Thus, the ferroelectric PVDF can be modelled by an interacting system which consists of permanent dipoles and field‐induced point dipoles. The orthorhombic dipole system is placed between two coplanar electrodes. All electrostatic dipole–dipole interactions are considered and the electrodes are taken into account using the method of image dipoles. Based on thermally activated pro‐ cesses, the permanent dipoles fluctuate in double well potentials according to the Boltzmann statistics. The numerical calculations are based on deterministic local field computations and on weighted probabilistic dynamic Monte Carlo steps. In this paper, we focus on the simulation of typical ferroelectric properties like hysteresis effects, the ferroelectric‐paraelectric phase transition at the Curie‐temperature, and the switching curves from the negative remanent polarisation to positive values. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Luminescence spectroscopy of Eu‐implanted zincblende GaN
Authors: Roqan I. S. , O'Donnell K. P. , Trager‐Cowan C. , Hourahine B. , Martin R. W. , Lorenz K. , Alves E. , As D. J. , Panfilova M. , Watson I. M. 
Published: November 2007

AbstractCathodoluminescence (CL) and Photoluminescence (PL) of Eu‐implanted zincblende‐GaN (ZB‐GaN:Eu) and wurtzite‐GaN (W‐GaN:Eu) are compared in order to investigate the optical activation of GaN by Eu. The Eu3+ emission spectrum depends critically on the crystal structure of the GaN host; implantation and post‐annealing at 800 °C partially converts implantation‐damaged ZB‐GaN:Eu to W‐GaN:Eu. Selective excitation of PL at wavelengths below the ZB‐GaN band edge reveals a new sharp emission line at 627 nm, together with a number of satellites, which we ascribe to ZB‐GaN:Eu. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Matrix‐assisted laser desorption/ionization mass spectrometry using a visible laser
Authors: Chen Lee Chuin , Asakawa Daiki , Hori Hirokazu , Hiraoka Kenzo 
Published: November 2007

AbstractVisible matrix‐assisted laser desorption/ionization (VIS‐MALDI) was performed using 2‐amino‐3‐nitrophenol as matrix. The matrix is of near‐neutral pH, and has an optical absorption band in the near‐UV and visible region. A frequency‐doubled Nd:YAG laser operated at 532 nm wavelength was used for matrix excitation and comparisons were made with a frequency‐tripled Nd:YAG laser (355 nm). Visible and ultraviolet (UV)‐MALDI produce similar mass spectra for peptides, polymers, and small proteins with comparable sensitivities. Due to the smaller optical absorption coefficient of the matrix at 532 nm wavelength, the optical penetration depth is larger, and the sample consumption per laser shot in VIS‐MALDI is higher than that of UV‐MALDI. Nevertheless, VIS‐MALDI using 2‐amino‐3‐nitrophenol as matrix may offer a complementary technique to the conventional UV‐MALDI method in applications where deeper laser penetration is required. Copyright © 2007 John Wiley & Sons, Ltd.
A field‐derived oxygen isotope fractionation equation for Salvelinus species
Authors: Storm‐Suke Andrea , Dempson J. Brian , Reist James D. , Power Michael 
Published: November 2007

AbstractField‐collected otolith samples of young‐of the‐year Arctic charr (Salvelinus alpinus) and brook charr (Salvelinus fontinalis) and monitored water temperatures were used to estimate a δ18O fractionation equation for the genus Salvelinus. When compared to literature reported equations, the developed fractionation equation had a statistically similar slope but dissimilar intercept. Statistical similarities among fractionation equation slope estimates suggest a common otolith δ18O incorporation response among fish species that may be interpreted as widespread equilibrium otolith δ18O deposition. Statistical dissimilarities among intercept estimates question broad applicability of any single fractionation equation to all fish species and were interpreted here to have biological meaning as a result of known differences in standard metabolic rates among species. Attempts to statistically cross‐validate fractionation equations by prediction of water temperatures used in other fractionation studies indicated significant biases in the range of −7.9 to 6.7°C that preclude the broad use of any single fractionation equation for accurate thermal reconstructions. Differences in equation intercepts and the prevalence of predictive biases do not support the conclusion of previous studies concerning the wide applicability and/or general accuracy of fractionation equations and suggest fractionation equations are best developed at the species‐ or taxon‐specific (e.g., genus) level. Copyright © 2007 John Wiley & Sons, Ltd.
Application of fast gas chromatography/mass spectrometry for the rapid screening of synthetic anabolic steroids and other drugs in anti‐doping analysis
Authors: Mazzarino Monica , Orengia Manuela , Botrè Francesco 
Published: November 2007

AbstractThis paper describes a fast gas chromatographic/mass spectrometric (GC/MS) screening method for the detection, in urine, of 36 xenobiotics (30 synthetic anabolic steroids, four narcotics, one diuretic and one stimulant) excreted free or as glucuro‐conjugates in urine and detectable as trimethylsilyl (TMS) derivatives. These drugs (and/or their urinary metabolites) can be simultaneously extracted by a single liquid/liquid separation step, at alkaline pH, after enzymatic hydrolysis with beta‐glucuronidase and then assayed as TMS derivatives by GC/MS using electron ionisation (EI) and single ion monitoring (SIM) acquisition mode. The total time needed for the GC run is less than 8 min. Good reproducibility of the retention times (CV% <1) and the relative abundances of the diagnostic fragment ions (CV% <10) was observed for all target analytes. The sensitivity of the method is sufficient to match the requirements of the World Anti‐Doping Agency (WADA) for the accredited laboratories, with limits of detection (LODs) that are lower than the corresponding WADA minimum required performance limits (MRPLs) for all target compounds. Copyright © 2007 John Wiley & Sons, Ltd.
Localized identification of shear building with embedded foundation in frequency domain
Authors: Sholeh K. , Vafaie A. , Kaveh A. 
Published: November 2007

AbstractFor studying the behavior of structure in an earthquake, it is advisable to model the structure as a multi‐degrees of freedom system, consisting of numerous single‐degree of freedom substructures and pay attention to soil–structure interaction. System identification is divided into two categories: namely time domain method and frequency domain approach. In this paper, a localized substructure identification of shear building considering the soil–structure interaction is presented using a frequency domain approach. In order to deal with noise‐corrupted data, a spectral smoothing technique with Parzen's window reduction method is adapted. It is shown that better convergence and accuracy can be achieved by the present technique. As a result, it is shown that by taking into account the soil–structure interaction more realistic results can be obtained. Copyright © 2007 John Wiley & Sons, Ltd.
The wind‐induced response characteristics of atypical tall buildings
Authors: You Ki‐Pyo , Kim Young‐Moon 
Published: November 2007

AbstractA tall building reacts sensitively to winds because the wind force increases according to the height and shape of the building. Various shapes of tall buildings and their aerodynamic characteristics have been studied extensively. For structural design and occupant comfort, the dynamic displacement of a tall building must be maintained within the criteria for acceptable levels of wind‐induced motion. An aerodynamically appropriate building shape needs to be selected at the design stage of a tall building. In this study, wind‐induced vibration responses were investigated, according to the criteria for maximum acceptable displacement and acceleration. Copyright © 2007 John Wiley & Sons, Ltd.
Helminth parasites of the endangered Iberian lynx (Lynx pardinus) and sympatric carnivores
Authors: Millán Javier , Casanova Joan Carles 
Published: November 2007

AbstractFive critically endangered Iberian lynxes (Lynx pardinus) and 35 other sympatric carnivores (19 feral catsFelis catus, 12 Egyptian mongoosesHerpestes ichneumon, and 4 common genetsGenetta genetta) were analysed for helminths in Sierra Morena and Doñana area (southern Spain).Ancylostoma tubaeforme, which was believed to be harmful for lynx cubs according to a previous study, was present in the only lynx and in 53% of cats analysed in Doñana (80% in adult cats). Other species shared in both areas wereToxocara cati(1 lynx, 31% of cats),Joyeuxiella pasqualei(1 lynx, 21% of cats) andMesocestoidessp. (2 lynxes, 5% of cats). Only one mongoose was parasitized, harbouring larvae of two acantocephalan species not previously reported in the Iberian peninsula (Centrorhynchus(Sphaerirostris)lanceaandCentrorhynchus(Longirostris)undulatus). Feral cats may be a reservoir for hookworms and other helminths affecting the Iberian lynx. In contrast, mongooses and genets may not play a role in the epidemiology of these species.
Suppression of inflammatory and immune responses by the A2Aadenosine receptor: an introduction
Authors: Palmer T M , Trevethick M A 
Published: November 2007

The purine nucleoside adenosine has been described as a ‘retaliatory metabolite’ by virtue of its ability to function in an autocrine manner to modify the activity of a range of cell types following its extracellular accumulation during cell stress or injury. These effects are largely protective and are triggered by the binding of adenosine to any of four G‐protein‐coupled adenosine receptors. Most of the anti‐inflammatory effects of adenosine have been assigned to the adenosine A2Areceptor subtype, which is expressed in many immune and inflammatory cells. In this brief article, we will outline the growing evidence to support the hypothesis that the development of agonists selective for the A2Areceptor is an effective strategy for suppressing the exaggerated inflammatory responses associated with many diseases by virtue of the receptor's ability to inhibit multiple pro‐inflammatory signalling cascades.British Journal of Pharmacology(2008)153, S27–S34; doi:10.1038/sj.bjp.0707524; published online 19 November 2007
Intracellular machinery for the transport of AMPA receptors
Authors: Esteban J A 
Published: November 2007

AMPA‐type glutamate receptors are one of the most dynamic components of excitatory synapses. Their regulated addition and removal from synapses leads to long‐lasting forms of synaptic plasticity, known as long‐term potentiation (LTP) and long‐term depression (LTD). In addition, AMPA receptors reach their synaptic targets after a complicated journey involving multiple transport steps through different membrane compartments. This review summarizes our current knowledge of the trafficking pathways of AMPARs and their relation to synaptic function and plasticity.British Journal of Pharmacology(2008)153, S35–S43; doi:10.1038/sj.bjp.0707525; published online 19 November 2007