bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of proteome and transcriptome of tumor necrosis factor α stimulated vascular smooth muscle cells with or without alpha lipoic acid
Authors: Jang Won Gu , Kim Hye Soon , Park Keun‐Gyu , Park Yong Bok , Yoon Kun‐Ho , Han Seong‐Wook , Hur Seung‐Ho , Park Kyong Soo , Lee In‐Kyu 
Published: September 2004

AbstractVascular smooth muscle cells (VSMCs) play an important role in the development and progression of atherosclerosis. Tumor necrosis factor α (TNFα), a cytokine secreted by VSMCs and macrophages in atherosclerotic lesions, regulates a variety of cellular functions of inflammatory cells and VSMCs by promoting cell growth and motility, which are critical for the initiation and progression of vascularlesions. Alpha lipoic acid (ALA), a well known antioxidant, acts as a pyruvate dehydrogenase cofactor in mitochondrial metabolism. Recently, we reported that ALA has many beneficial effects on vascular cells in atherosclerosis. The aim of the current study was to examine VSMCs, treated for 24 hours with TNFα (10 ng/mL) in the presence or absence of ALA (2 mM), for differential protein and genes expression using two‐dimensional gel electrophoresis (2‐DE) and DNA microarray analysis, respectively. Using 2‐DE, we identified proteins whose expression changed by at least 2.5‐fold after TNFα stimulation. Proteins up‐regulated by TNFα that were subsequently down‐regulated in the presence of ALA were identified by matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry as plasminogen activator inhibitor‐2, fetal liver LKB‐interacting protein, osteoblast‐specific factor 2, glucosidase II, cyclin‐dependent kinase 3, endoplasmin precursor and glutathione synthetase. TNFα down‐regulated proteins that were up‐regulated in the presence of ALA were keratin 19, eukaryotic translation elongation factor and Rho GDP dissociation inhibitor α. Gene expression analysis using DNA microarray tools confirmed the up‐regulation or down‐regulation of some, but not all, of the proteins observed in ALA challenged, TNFα‐treated cells. This data should provide valuable information about the underlying mechanisms of atherosclerosis.
Antigens secreted fromMycobacterium tuberculosis: Identification by proteomics approach and test for diagnostic marker
Authors: Bahk Young Yil , Kim Suk Am , Kim Ji‐Soo , Euh Hyung‐Jin , Bai Gil‐Han , Cho Sang‐Nae , Kim Yu Sam 
Published: September 2004

AbstractTuberculosis caused by mycobacteria, mainlyMycobacterium tuberculosis, is a major infectious disease of the respiratory system. An early diagnosis followed by chemotherapy is the major control strategy. In an effort to identify the antigens suitable for immunodiagnosis and vaccines, the proteins secreted in a culture medium from theM. tuberculosisK‐strain, which is the most prevalent among the clinical isolates in Korea and belongs to the Beijing family, were analyzed by two‐dimensional polyacrylamide gel electrophoresis (2‐D PAGE) and compared with those from theM. tuberculosisH37Rv and CDC1551 strains. Eight proteins, Rv0652, Rv1636, Rv2818c, Rv3369, Rv3865, Rv0566c, MT3304, and Rv3160, were identified by matrix‐assisted laser desorption/ionization‐time of flight‐mass spectrometry (MALDI‐TOF‐MS) or liquid chromatography‐electrospray ionization‐mass spectrometry (LC‐ESI‐MS) and found to be relatively abundant in the culture medium from theM. tuberculosisK‐strain but less so from the CDC1551 or H37Rv strains. In addition, Rv3874 (CFP‐10), Rv‐0560c and Rv3648c, which were expressed increasingly in the K and CDC1551 strains, were also identified using the same proteomics technology. All proteins were prepared by molecular cloning, expression inEscherichia colifollowed by affinity purification. Among them, three proteins, rRv3369, rRv0566c, and rRv3874, were selected by prescreening and examined for their potential as serodiagnostic antigens using an enzyme‐linked immunosorbent assay. When 100 sera from tuberculosis patients and 100 sera from the healthy controls were analyzed, rRV3369, rRv3874, and rRv0566c showed a sensitivity of 60%, 74%, and 43%, and a specificity of 96%, 97%, and 84%, respectively. These results suggest that the rRv3369 and rRv3874 proteins, which were expressed more abundantly in the more recently obtained clinical isolates ofM. tuberculosisthan in the laboratory‐adapted H37Rv strain, are promising for use in the serodiagnosis of tuberculosis.
Reactions of dimethoxycarbene with carbon–sulfur double bonds
Authors: Dawid Malgorzata , Reid Darren L. , Warkentin John , Mloston Grzegorz 
Published: September 2004

AbstractUnlike electrophilic carbenes, which react at sulfur to produce thiocarbonyl ylide intermediates, dimethoxycarbene (DMC), generated by thermolysis of an oxadiazoline at 110°C in benzene in a sealed tube, reacts at carbon, possibly to generate a zwitterionic intermediate, or at both carbon and sulfur in a concerted process that generates a thiirane. In case of the strained 2,2,4,4‐tetramethylcyclobutane‐1,3‐dithione (2), an assumed zwitterion undergoes ring expansion. In analogous reactions, unstrained thiones afford thiiranes, possibly by ring closure of the postulated intermediates or by concerted addition. Desulfurization of thiiranes, which occurs spontaneously in some instances, results in the formation of ketene acetals, many of which hydrolyze during workup. O‐Alkyl thioesters and xanthates react to afford products via insertion of the DMC into C—O or C—S bonds, respectively. Copyright © 2004 John Wiley & Sons, Ltd.
The search for efficient intramolecular proton transfer from carbon: the kinetically silent intramolecular general base‐catalysed elimination reaction of O‐phenyl 8‐dimethylamino‐1‐naphthaldoximes
Authors: Asaad Nabil , Davies John E. , Hodgson David R. W. , Kirby Anthony J. , Vliet Liisa van , Ottavi Laura 
Published: September 2004

AbstractThe ready elimination of phenol/phenoxide from the O‐phenyl oxime 10E derived from 8‐dimethylamino‐1‐naphthaldehyde, necessarily involving proton transfer from carbon, is catalysed by the neighbouring NMe2 group at pH > 9. However, reaction is faster, rather than slower, at lower pH. It is shown that the step involving proton transfer is not cleanly rate determining at any pH: the preferred route involves syn/anti isomerization to form the more reactive Z‐isomer. The rate constant for the anti elimination cannot be extracted from the available data, so no reliable estimate of effective molarity (EM) is possible. Copyright © 2004 John Wiley & Sons, Ltd.
Dynamics and reactivity of chiral ion–dipole pairs
Authors: Speranza Maurizio 
Published: September 2004

AbstractModeling ionic reactions in a dynamic environment, such as in a solvent cage, requires the generation of tailor‐made ionic adducts involved in the process and the investigation of the intrinsic structural and electronic factors governing their behavior in the unsolvated state. A compendium of the most recent studies on the gas‐phase dynamics and reactivity of chiral ion–dipole pairs involved in classical organic reactions is reported, together with a presentation of the experimental and theoretical methodologies adopted. Copyright © 2004 John Wiley & Sons, Ltd.
Synthesis and characterization of new polystyrenes containing tributyltin moieties linked to the aromatic ring through a methylenic spacer
Authors: Angiolini Luigi , Caretti Daniele , Mazzocchetti Laura , Salatelli Elisabetta , Willem Rudolph , Biesemans Monique 
Published: September 2004

AbstractNovel polymeric derivatives bearing tributyltin carboxylate moieties in the side chain were synthesized. The coordination at tin in solution and in the solid state was investigated by both Sn‐NMR and FT‐IR: the metal atom appears completely tetracoordinated in chloroform solution, while in the solid state all polymeric products exhibit both tetra‐ and pentacoordination at tin, the latter increasing with the amount of tin containing units. No evidence of tin leaching by hydrolysis of the organometallic ester was observed for these materials. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5372–5383, 2004
Structure and mechanical behavior of nylon‐6 fibers filled with organic and mineral nanoparticles. I. Microstructure of spun and drawn fibers
Authors: Ibanes C. , David L. , De Boissieu M. , Séguéla R. , Epicier T. , Robert G. 
Published: September 2004

AbstractThe crystalline structure and fibrillar texture of nylon‐6 fibers filled with nanosized particles were investigated using wide‐angle and small‐angle X‐ray scattering. As‐spun fibers filled with organic nanoparticles consisting of aromatic polyamide‐like hyperbranched molecules with amine‐terminating groups exhibited strong modification of both the molecular orientation and the crystalline structure compared with that of unfilled spun fibers. Montmorillonite‐filled fibers mainly exhibited orientation improvement. The differences are discussed in terms of the rheological and nucleating effects during spinning. Drawing at 140 °C involves structural changes that resulted in the three kinds of fibers having a similar crystalline form and molecular orientation. In parallel, after significant strain‐induced changes, the microfibrillar texture of the various fibers displayed subtle differences at the ultimate stage of drawing. The changes in the fibril long period and fibril radius as a function of draw ratio are discussed in terms of the two sequential deformation processes of microfibril stretching and microfibril slipping. The occurrence of interfibrillar strain‐induced cavitation is discussed in relation to the nature of the interactions between the filler and the nylon‐6 matrix. And, finally, the mechanical properties are discussed in relation to the filler–matrix interaction. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3876–3892, 2004
Determining the effects of vapor sorption in polymers with the quartz crystal microbalance/heat conduction calorimeter
Authors: Smith Allan L. , Mulligan Rose B. , Shirazi Hamid M. 
Published: September 2004

AbstractThe quartz crystal microbalance/heat conduction calorimeter (QCM/HCC) is a versatile instrument coupling both gravimetric and calorimetric techniques. The QCM/HCC is used to probe vapor sorption in thin films. Three parameters are measured simultaneously as a thin film undergoes vapor sorption, namely: mass changes in the film (±10 ng), corresponding thermal effects upon vapor sorption (±100 nW), and motional resistance (±0.5Ω) changes within the film. A range of film thicknesses (0.75 to 8.5 μm) of the polymer, Tecoflex™ are cast on QCMs and the interaction of each film with ethanol and water is determined. From the direct calorimetric measurements, sorption enthalpies (ΔsorptionH kJ/mol) are determined for the film–vapor interactions. Sorption isotherms are then analyzed for each film. The isotherms shown here generally display a linear Henry's Law dissolution relationship between the vapor pressure and the amount of vapor sorbed into the film. Motional resistance data provides a window to view viscoelastic effects of the polymer films upon vapor sorption. Motional resistance data are compared for ethanol sorption in a relatively thin (0.75 μm) and thicker (8.5 μm) Tecoflex™ film. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3893–3906, 2004
Prediction of Carbonic Anhydrase Activation by Tri‐/Tetrasubstituted‐pyridinium‐azole Compounds: A Computational Approach using Novel Topochemical Descriptor
Authors: Bajaj Sanjay , Sambi S. S. , Madan A. K. 
Published: September 2004

AbstractA novel highly discriminating adjacency‐cum‐distance based topochemical descriptor, termed as Superadjacency topochemical index, has been derived and its discriminating power investigated with regard to activation of Carbonic anhydrase (CA) isozyme‐I by tri‐/tetrasubstituted‐pyridinium‐azole compounds. The new index is not only sensitive to the presence of heteroatoms but also overcomes the problem of degeneracy of many topological descriptors. The discriminating power of Superadjacency topochemical index was found to be far superior when compared with that of distance based Wiener‘s index and adjacency based Molecular connectivity index. The values of Wiener‘s index, path‐one Molecular connectivity index and Superadjacency topochemical index of each of the 42 substituted‐pyridinium‐azole compounds comprising the dataset were computed. Resultant data was analyzed and suitable models developed after identification of the active ranges. Subsequently, a biological activity was assigned to each of the compounds involved in the dataset using these models, which was then compared with the reported activation constants for Carbonic Anhydrase isozyme‐I. Excellent correlations were observed between the activation constants of CA isozyme‐I and all the topological/topochemical descriptors. The overall accuracy of prediction was about 91% for models based upon both Molecular connectivity index as well as Wiener‘s index, and 96% for model based upon Superadjacency topochemical index. Surprisingly, the accuracy of prediction in the active range was found to be 100% in all the models. Thus the proposed index offers a vast potential for structure‐activity/structure‐property studies.
Ensembles in classical statistical mechanics and their unification via nonlinear field theory
Authors: Zakharov A. Yu 
Published: September 2004

AbstractThe connection between accessible volume of phase space for microcanonical ensemble and canonical partition function of complex temperature is established. Functional‐integral representation for both canonical and microcanonical ensembles in classical statistical mechanics is obtained. Random external field manifestation as interatomic potentials renormalization is derived. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Electronic excited states and stabilities of fullerenes: Isomers of C78 and Mg@C72
Authors: Slanina Zdenĕk , Uhlík Filip , Adamowicz Ludwik , Kobayashi Kaoru , Nagase Shigeru 
Published: September 2004

AbstractThere is one factor in relative stabilities of isomeric fullerenes that has rarely been studied so far—the contribution of excited electronic states. The contribution is clearly quantified by the electronic partition function, supposing the related excitation energies can be evaluated. As temperatures in fullerene synthesis are high, the term should be taken into account. In this article the problem is studied on two isomeric systems. One is the set of five isolated pentagon rule isomers of C78, relatively well known from experiments. The other is a model set of four isomers of Mg@C72 (not isolated yet). The electronic excitation energies are computed by the limited configuration interaction (CI) method. In the case of the C78 isomeric set, the ZINDO semiempirical method is used. Isomers of Mg@C72 are evaluated by means of the single‐excitation CI or CI‐singles (CIS) in the standard LanL2MB and LanL2DZ basis sets—CIS/LanL2MB and CIS/LanL2DZ. It is found that the electronic partition function can cause significant changes in the computed equilibrium relative concentrations of isomers at high temperatures. Metallofullerenes are more likely candidates for such enhanced effects. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Interatomic potential for the X1Σ state of Be2, revisited
Authors: Røeggen I. , Veseth L. 
Published: September 2004

AbstractAn extended geminal model has been applied to determine the interatomic potential for the X1Σ state of Be2. By adopting a (23s, 10p, 8d, 6f, 3g, 2h) uncontracted Gaussian‐type basis, the following spectroscopic parameters are obtained: Re = 4.633 a.u. (4.63 a.u.), De = 945 ± 15 cm (790 ± 30 cm), G(1)–G(0) = 221.7 cm−1 (223.8 ± 2 cm−1), G(2)–G(1) = 175.0 cm−1 (169 ± 3 cm−1), G(3)–G(2) = 123.1 cm−1 (122 ± 3 cm−1), and G(4)–G(3) = 80.8 cm−1 (79 ± 3 cm−1), experimental values in parentheses. The calculated binding energy is substantially higher than the accepted experimental value. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Critical angle and energy of DCS surface for e‐argon scattering
Authors: Paikeday Joseph M. , Ashley Brad T. 
Published: September 2004

AbstractThe differential scattering cross‐section (DCS) for electrons scattered elastically by Argon atoms is studied using a model potential. In the current study the long‐range polarization potential is represented by an energy‐dependent function in the form: Vp(E,r) = αd/[r + ξ(a,b,E)]4, and the short‐range part is constructed from the nonrelativistic Hartree–Fock wavefunction of the target atom in the form Vs(r) = (2Z/r)ΣnCnexp{−nCor}. Accurate phase shifts have been computed for angular momentum in the range 0 < ℓ < 13 from the Schrodinger equation and for 13 < ℓ < 1000 using the Born approximation. The computed DCS obtained using the approximate effective interaction potential for electrons scattered by the target atoms in their ground state is compared with available published results. In the current study the parameters contained in the energy‐dependent polarization potential are determined by the minimization of the DCS with respect to angle θ and the incident energy of E. The critical values of angle and energy (θc, Ec) are found to be (117.8°, 120.8 eV), (64.6°, 43.0 eV), and (141.2°, 40.7 eV). The resulting DCS in the angular range 2° < θ < 178° is found to be an improvement over earlier results and in better agreement with the available experimental data in the intermediate energy range. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Short‐range exchange‐correlation energy of a uniform electron gas with modified electron–electron interaction
Authors: Toulouse Julien , Savin Andreas , Flad Heinz‐Jürgen 
Published: September 2004

AbstractWe calculate the short‐range exchange‐correlation energy of the uniform electron gas with two modified electron–electron interactions. While the short‐range exchange functionals are calculated analytically, coupled‐cluster and Fermi‐hypernetted‐chain calculations are carried out for the correlation energy and the results are fitted to an analytical parametrization. These data enable us to construct the local density approximation corresponding to these modified interactions. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Reactions of ·OH with thymine studied using density functional theory
Authors: Ji Yanju , Xia Yueyuan , Zhao Mingwen , Li Feng , Huang Boda 
Published: September 2004

AbstractWe studied three possible reactions of a free ·OH radical with thymine by using density functional theory calculations. The results indicate that there is no energy barrier in the reactions of a free ·OH radical adding to the C6 position of thymine, while the reactions of a free ·OH radical adding to the C5 position of thymine and the reaction of an ·OH abstracting a hydrogen from the C5 methyl group should overcome the energy barriers of ∼0.70 kcal/mol and ∼1.88 kcal/mol, respectively. The C6‐hydroxylated radical formed is energetically more favorable than the C5‐hydroxylated radical. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Structural analysis of permethylated oligosaccharides using electrospray ionization quadrupole time‐of‐flight tandem mass spectrometry and deutero‐reduction
Authors: Morelle Willy , Faid Valegh , Michalski Jean‐Claude 
Published: September 2004

AbstractDeutero‐reduced permethylated oligosaccharides were analyzed by electrospray ionization mass spectrometry (ESI‐MS) and tandem mass spectrometry (MS/MS) using a hybrid quadrupole orthogonal acceleration time‐of‐flight mass spectrometer, fitted with a nanoflow ESI source. Under these ionization conditions such derivatives preferentially form sodiated molecular species in addition to protonated molecular species. Under collision‐induced dissociation, protonated and sodiated molecular species yield simple and predictable fragment mass spectra. A systematic study was conducted on a series of deutero‐reduced permethylated glycans to allow rationalization of the fragmentation processes. MS/MS spectra were characterized by fragments resulting from the cleavage of glycosidic bonds. These fragments originating from both the reducing and the non‐reducing ends of the glycan yield information on sequence and branching. Furthermore, the substituent 3‐linked to a HexNAc unit was readily eliminated. Special attention was devoted to a systematic study of fucosylated glycans. The fucosylated deutero‐reduced permethylated glycans were submitted to an acidic hydrolysis, releasing specifically the fucosyl residues. The nascent free hydroxyl groups were subsequently CD3‐labelled in order to determine the positions initially bearing the fucosyl residues along the oligosaccharide backbone. This methodology was finally applied to characterize a glycan pool enzymatically released from glycoproteins. The present data show that structural elucidation can be achieved at the 50 fmol level. Copyright © 2004 John Wiley & Sons, Ltd.
Automated interpretation of mass spectra of complex mixtures by matching of isotope peak distributions
Authors: Fernández‐de‐Cossio Jorge , Gonzalez Luis Javier , Satomi Yoshinori , Betancourt Lazaro , Ramos Yassel , Huerta Vivian , Besada Vladimir , Padron Gabriel , Minamino Naoto , Takao Toshifumi 
Published: September 2004

AbstractMass spectrometry is now firmly established as a powerful technique for the identification and characterization of proteins when used in conjunction with sequence databases. Various approaches involving stable‐isotope labeling have been developed for quantitative comparisons between paired samples in proteomic expression analysis by mass spectrometry. However, interpretation of such mass spectra is far from being fully automated, mainly due to the difficulty of analyzing complex patterns resulting from the overlap of multiple peaks arising from the assortment of natural isotopes. In order to facilitate the interpretation of a complex mass spectrum of such a mixture, such as an MS spectrum of a stable‐isotope‐enriched ion species, we report on the development of a software application, ‘Matching’ (web accessible), that enables the automatic matching of theoretical isotope envelopes to multiple ion peaks in a raw spectrum. It is particularly useful for resolving the relative abundances of narrow‐split paired peaks caused by enrichment with a stable isotope, such as 18O, 13C, 2H, or 15N. Copyright © 2004 John Wiley & Sons, Ltd.
Nanospray ‘taxation’ and how to avoid it
Authors: Chernushevich I. V. , Bahr U. , Karas M. 
Published: September 2004

AbstractIn mass spectrometric analysis with nanospray ionization, some analytes were found to appear in spectra with a delay of tens of minutes, while a few others could not be detected at all. The effect was found to be related to cation‐exchange chromatography with negative charge on the glass surface, and with the most affected peptide or protein ions having strong localization of positive charge in blocks of two or more adjacent basic amino acid residues (e.g. melittin). The ‘affinity’ to the glass surface was studied with a peptide mixture and bovine serum albumin (BSA) tryptic digest solutions at sub‐micromolar concentration. About 20% fewer tryptic peptides could be identified from spectra recorded with a glass nanospray capillary compared to those acquired with either conventional 1 μL/min electrospray or a quartz nanospray capillary. Protein identification studies are not likely to be seriously affected by this loss, but other protein applications, such as investigations of mutations or post‐translational modifications, may suffer due to reduced sequence coverage. Ways to avoid losses of useful ions are discussed. Copyright © 2004 John Wiley & Sons, Ltd.