bluuebunny/crossref_metadata_2025_split huggingface dataset:
Semistrong edge coloring of graphs
Authors: Gyárfás András , Hubenko Alice 
Published: February 2005

AbstractWeakening the notion of a strong (induced) matching of graphs, in this paper, we introduce the notion of a semistrong matching. A matching M of a graph G is called semistrong if each edge of M has a vertex, which is of degree one in the induced subgraph G[M]. We strengthen earlier results by showing that for the subset graphs and for the Kneser graphs the sizes of the maxima of the strong and semistrong matchings are equal and so are the strong and semistrong chromatic indices. Similar properties are conjectured for the n‐dimensional cube. © 2005 Wiley Periodicals, Inc. J Graph Theory 49: 39–47, 2005
Thin‐layer chromatography/electrospray ionization triple‐quadrupole linear ion trap mass spectrometry system: analysis of rhodamine dyes separated on reversed‐phase C8 plates
Authors: Ford Michael J. , Kertesz Vilmos , Van Berkel Gary J. 
Published: February 2005

AbstractThe direct analysis of separated rhodamine dyes on reversed‐phase C8 thin‐layer chromatography plates using a surface sampling/electrospray emitter probe coupled with a triple‐quadrupole linear ion trap mass spectrometer is presented. This report represents continuing work to advance the performance metrics and utility of this basic surface sampling electrospray mass spectrometry system for the analysis of thin‐layer chromatography plates. Experimental results examining the role of sampling probe spray end configuration on liquid aspiration rate and gas‐phase ion signal generated are discussed. The detection figures‐of‐merit afforded by full‐scan, automated product ion and selected reaction monitoring modes of operation were examined. The effect of different eluting solvents on mass spectrum signal levels with the reversed‐phase C8 plate was investigated. The combined effect of eluting solvent flow‐rate and development lane surface scan rate on preservation of chromatographic resolution was also studied. Analysis of chromatographically separated red pen ink extracts from eight different pens using selected reaction monitoring demonstrated the potential of this surface sampling electrospray mass spectrometry system for targeted compound analysis with real samples. Copyright © 2005 John Wiley & Sons, Ltd.
Aberrations in the progesterone receptor gene and the risk of recurrent endometrial carcinoma
Authors: Pijnenborg JMA , Romano A , Dam‐de Veen GC , Dunselman GAJ , Fischer D‐C , Groothuis PG , Kieback DG 
Published: February 2005

AbstractA case–control study was performed in order to determine whether expression of the progesterone receptor (PR) and/or aberrations of the PR gene contribute to the development of recurrent endometrial carcinoma. Primary tumours from 44 patients with recurrence of stage I endometrial carcinoma (patients) within 3 years after initial treatment were compared with tumours from 44 matched patients who were free of recurrence for a minimum of 3 years (controls). Paraffin wax‐embedded primary tumours (n = 88) and recurrent tumours (n = 32) were analysed immunohistochemically for PR expression. A staining index (SI = 0–9) based on the staining intensity and the number of stained cells was calculated. DNA extracted from paraffin wax‐embedded tissues was subjected to PCR–restriction fragment length polymorphism analysis (PCR–RFLP) for determination of the PROGINS DNA sequence alterations and the +331G/A‐promoter polymorphism. Low PR expression (SI < 1.0) was observed in 7% of primary tumours derived from controls, 25% of primary tumours from patients with recurrence, and 38% of recurrent tumours. The expression of PR was significantly lower in primary tumours from patients with recurrence (SI = 4.0 ± 0.5) than in the tumours in the control group (SI = 5.6 ± 0.5) (T‐test for paired analysis, p < 0.05). The PROGINS and +331G/A‐promoter polymorphism were not related to age at diagnosis, tumour grade or myometrial invasion. The +331G/A‐promoter polymorphism was present in 14% of primary tumours from patients without recurrence, compared with 17% of patients with recurrence. The PROGINS polymorphism was observed in 16% of primary tumours from patients without, and in 34% of patients with, recurrence (OR 2.6; 95% CI: 0.9–7.6). Most interestingly, patients who carried the PROGINS variant and in whom a PR‐expressing tumour was diagnosed were at significantly enhanced risk of relapse (OR 4.7; 95% CI: 1.3–17.1). In conclusion, low PR expression tended to be associated with recurrent disease, and PR expression in tumours from patients carrying the PROGINS allele was predictive of the risk of recurrence. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Aberrant expression of transforming growth factor β‐1 (TGFβ‐1) per se does not discriminate fibrotic from non‐fibrotic chronic myeloproliferative disorders
Authors: Bock Oliver , Loch Gero , Schade Ulrika , von Wasielewski Reinhard , Schlué Jerome , Kreipe Hans 
Published: February 2005

AbstractTransforming growth factor β‐1 (TGFβ‐1) is a potent inducer of fibrosis and has been shown to be essential for the development of bone marrow fibrosis in an animal model of idiopathic myelofibrosis (IMF). IMF belongs to the Philadelphia chromosome negative chronic myeloproliferative disorders (Ph− CMPD). Megakaryocytes and platelets have been suggested as the major cellular source of TGFβ‐1 in IMF. The osteoclastogenesis inhibitory factor osteoprotegerin (OPG) seems to be regulated by TGFβ‐1 and substantial involvement of OPG expression in the process of osteosclerosis in IMF has recently been suggested. In order to determine TGFβ‐1 expression in IMF and other Ph− CMPD, total bone marrow cells as well as laser‐microdissected megakaryocytes were quantitatively analysed by real‐time RT‐PCR. OPG mRNA expression in fibrotic IMF was correlated with TGFβ‐1 mRNA expression in a case‐specific manner. Both OPG and TGFβ‐1 were detected immunohistochemically in order to delineate cellular origin. When total bone marrow cells were investigated, TGFβ‐1 mRNA expression was increased in some but not all cases of IMF (n = 21), with highest values in fibrotic cases. Unexpectedly, increased values were also observed in essential thrombocythaemia (ET, n = 11) when compared to non‐neoplastic haematopoiesis (n = 38). Megakaryocytes isolated by laser microdissection displayed elevated TGFβ‐1 mRNA levels in most of the CMPD samples with no significant differences discernible between fibrotic IMF, polycythaemia vera (PV) and ET. TGFβ‐1 protein was predominantly expressed by the myeloid lineage in Ph− CMPD and non‐neoplastic haematopoiesis, which, however, displayed lower expression. IMF cases with advanced fibrosis concomitantly overexpressed TGFβ‐1 and OPG. Immunohistochemically, OPG expression was found in different stromal cells and a subfraction of megakaryocytes. In conclusion, enhanced TGFβ‐1 expression occurs in megakaryocytes as well as myeloid cells in Ph− CMPD. TGFβ‐1 may be necessary, but is not sufficient, to induce bone marrow fibrosis in IMF because non‐fibrotic Ph− CMPD entities share this feature with IMF and cannot be discriminated from each other on the basis of TGFβ‐1 expression. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Block balance in hydrogenated polybutadiene‐b‐polymethylmethacrylate diblock copolymer for efficient interfacial activity in low‐density polyethylene/polymethylmethacrylate blend: Phase morphology development
Authors: Harrats C. , Jérôme R. 
Published: February 2005

AbstractThe objective of the present study was to determine the best molecular balance between the two hydrogenated polybutadiene (HPB) and polymethylmethacrylate (PMMA) blocks that promotes an HPB‐b‐PMMA diblock copolymer with efficient compatibilization activity in a low‐density polyethylene (LDPE)/PMMA immiscible blend. The model blend selected, LDPE/PMMA, is “more immiscible” than the LDPE/polystyrene pair largely reported in open literature. The blends having a composition of 80LDPE/20PMMA exhibit a droplet‐in‐matrix phase morphology whereas in 20LDPE/80PMMA a co‐continuous phase morphology was developed. In the droplet‐in‐matrix phase morphology, the emulsifying efficiency of the copolymer was evaluated based on the maximum reduction of the PMMA droplet size it is able to promote. Whereas, in the co‐continuous phase morphology, the copolymer was evaluated based on its ability to stabilize the maximum phase co‐continuity. The sequences of the best emulsifying copolymer revealed are not symmetrical. An HPB‐b‐PMMA where the ratio of molar mass of the blocks, $\overline{M_{\rm n}}$ HPB/$\overline{M_{\rm n}}$ PMMA, is within 1.8–1.95 exhibits a much better interfacial activity in LDPE/PMMA blends than a copolymer of much lower ratio (longer PMMA block). This is ascribed to the much higher interactions (cohesive energy density) encountered in PMMA (PMMA of the copolymer and PMMA phase of the blend) compared with the LDPE side (HPB of the copolymer and LDPE phase of the blend). © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 837–848, 2005
Volume transition and internal structures of small poly(N‐isopropylacrylamide) microgels
Authors: Arleth Lise , Xia Xiaohu , Hjelm Rex P. , Wu Jianzhong , Hu Zhibing 
Published: February 2005

AbstractMonodispersed poly(N‐isopropylacrylamide) (PNIPAM) nanoparticles, with hydrodynamic radius less than 50 nm at room temperature, have been synthesized in the presence of a large amount of emulsifiers. These microgel particles undergo a swollen–collapsed volume transition in an aqueous solution when the temperature is raised to around 34 °C. The volume transition and structure changes of the microgel particles as a function of temperature are probed using laser light scattering and small angle neutron scattering (SANS) with the objective of determining the small particle internal structure and particle–particle interactions. Apart from random fluctuations in the crosslinker density below the transition temperature, we find that, within the resolution of the experiments, these particles have a uniform radial crosslinker density on either side of the transition temperature. This result is in contrast to previous reports on the heterogeneous structures of larger PNIPAM microgel particles, but in good agreement with recent reports based on computer simulations of smaller microgels. The particle interactions change across the transition temperature. At temperatures below the transition, the interactions are described by a repulsive interaction far larger than that expected for a hard sphere contact potential. Above the volume transition temperature, the potential is best described by a small, attractive interaction. Comparison of the osmotic second virial coefficient from static laser light scattering at low concentrations with similar values determined from SANS at 250‐time greater concentration suggests a strong concentration dependence of the interaction potential. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 849–860, 2005
Functional analysis of CYP2D6.31 variant: Homology modeling suggests possible disruption of redox partner interaction by Arg440His substitution
Authors: Allorge Delphine , Bréant Didier , Harlow Jacky , Chowdry Joey , Lo‐Guidice Jean‐Marc , Chevalier Dany , Cauffiez Christelle , Lhermitte Michel , Blaney Frank E. , Tucker Geoffrey T. , Broly Franck , Ellis S. Wynne 
Published: February 2005

AbstractCytochrome P450 2D6 (CYP2D6) is an important human drug‐metabolizing enzyme that exhibits a marked genetic polymorphism. Numerous CYP2D6 alleles have been characterized at a functional level, although the consequences for expression and/or catalytic activity of a substantial number of rare variants remain to be investigated. One such allele, CYP2D6*31, is characterized by mutations encoding three amino acid substitutions: Arg296Cys, Arg440His and Ser486Thr. The identification of this allele in an individual with an apparent in vivo poor metabolizer phenotype prompted us to analyze the functional consequence of these substitutions on enzyme activity using yeast as a heterologous expression system. We demonstrated that the Arg440His substitution, alone or in combination with Arg296Cys and/or Ser486Thr, altered the respective kinetic parameters [Km (μM) and kcat (min−1)] of debrisoquine 4‐hydroxylation (wild‐type, 25; 0.92; variants, 43–68; 0.05–0.11) and dextromethorphan O‐demethylation (wild‐type, 1; 4.72; variants, 12–23; 0.64‐1.43), such that their specificity constants (kcat/Km) were decreased by more than 95% compared to those observed with the wild‐type enzyme. The rates of oxidation of rac‐metoprolol at single substrate concentrations of 40 and 400 μM were also markedly decreased by approximately 90% with each CYP2D6 variant containing the Arg440His substitution. These in vitro data confirm that the CYP2D6*31 allele encodes an enzyme with a severely impaired but residual catalytic activity and, furthermore, that the Arg440His exchange alone is the inactivating mutation. A homology model of CYP2D6 based on the crystal structure of rabbit CYP2C5 locates Arg440 on the proximal surface of the protein. Docking the structure of the FMN domain of human cytochrome P450 reductase to the CYP2D6 model suggests that Arg440 is a key member of a cluster of basic amino acid residues important for reductase binding. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Solution structure of a tobacco lipid transfer protein exhibiting new biophysical and biological features
Authors: Da Silva Pedro , Landon Céline , Industri Benoit , Marais Antoine , Marion Didier , Ponchet Michel , Vovelle Françoise 
Published: February 2005

AbstractPlant lipid transfer proteins are small soluble extracellular proteins that are able to bind and transfer a variety of lipidsin vitro. Recently, it has been proposed that lipid transfer proteins may play a key role in plant defence mechanisms, especially during the induction of systemic acquired resistance. However, very little is known about the proteins expressed in developing plants and tissues, since almost all the biophysical and structural data available to date on lipid transfer proteins originate from proteins present in storage tissues of monocot cereal seeds. In this paper, we report the structural and functional characteristics of a lipid transfer protein (named LTP1_1) constitutively expressed in young aerial organs ofNicotiana tabacum(common tobacco). The unlabelled and uniformly labelled proteins were produced in the yeastPichia pastoris, and we determined the three‐dimensional (3D) structure of LTP1_1 using nuclear magnetic resonance (NMR) spectroscopy and molecular modeling techniques. The global fold of LTP1_1 is very close to the previously published structures of LTP1 extracted from cereal seeds, including an internal cavity. However, the chemical shift variations of several NMR signals upon lipid binding show that tobacco LTP1_1 is able to bind only one LysoMyristoylPhosphatidylCholine (LMPC), while wheat and maize LTPs can bind either one or two. Titration experiments using intrinsic tyrosine fluorescence confirm this result not only with LMPC but also with two fatty acids. These differences can be explained by the presence in tobacco LTP1_1 of a hydrophobic cluster closing the second possible access to the protein cavity. This result suggests that LTP1 lipid binding properties could be modulated by subtle changes in a conserved global structure. The biological significance of this finding is discussed in the light of the signalling properties of the tobacco LTP1_1–jasmonate complex described elsewhere.1Proteins 2005. © 2005 Wiley‐Liss, Inc.
Evolution and similarity evaluation of protein structures in contact map space
Authors: Gupta Nitin , Mangal Nitin , Biswas Somenath 
Published: February 2005

AbstractPrediction of fold from amino acid sequence of a protein has been an active area of research in the past few years, but the limited accuracy of existing techniques emphasizes the need to develop newer approaches to tackle this task. In this study, we use contact map prediction as an intermediate step in fold prediction from sequence. Contact map is a reduced graph‐theoretic representation of proteins that models the local and global inter‐residue contacts in the structure. We start with a population of random contact maps for the protein sequence and “evolve” the population to a “high‐feasibility” configuration using a genetic algorithm. A neural network is employed to assess the feasibility of contact maps based on their 4 physically relevant properties. We also introduce 5 parameters, based on algebraic graph theory and physical considerations, that can be used to judge the structural similarity between proteins through contact maps. To predict the fold of a given amino acid sequence, we predict a contact map that will sufficiently approximate the structure of the corresponding protein. Then we assess the similarity of this contact map with the representative contact map of each fold; the fold that corresponds to the closest match is our predicted fold for the input sequence. We have found that our feasibility measure is able to differentiate between feasible and infeasible contact maps. Further, this novel approach is able to predict the folds from sequences significantly better than a random predictor. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Solution structure of two insect‐specific spider toxins and their pharmacological interaction with the insect voltage‐gated Na+ channel
Authors: Ferrat G. , Bosmans F. , Tytgat J. , Pimentel C. , Chagot B. , Gilles N. , Nakajima T. , Darbon H. , Corzo G. 
Published: February 2005

Abstractδ‐PaluIT1 and δ‐paluIT2 are toxins purified from the venom of the spider Paracoelotes luctuosus. Similar in sequence to μ‐agatoxins from Agelenopsis aperta, their pharmacological target is the voltage‐gated insect sodium channel, of which they alter the inactivation properties in a way similar to α‐scorpion toxins, but they bind on site 4 in a way similar to β‐scorpion toxins. We determined the solution structure of the two toxins by use of two‐dimensional nuclear magnetic resonance (NMR) techniques followed by distance geometry and molecular dynamics. The structures of δ‐paluIT1 and δ‐paluIT2 belong to the inhibitory cystine knot structural family, i.e. a compact disulfide‐bonded core from which four loops emerge. δ‐PaluIT1 and δ‐paluIT2 contain respectively two‐ and three‐stranded anti‐parallel β‐sheets as unique secondary structure. We compare the structure and the electrostatic anisotropy of those peptides to other sodium and calcium channel toxins, analyze the topological juxtaposition of key functional residues, and conclude that the recognition of insect voltage‐gated sodium channels by these toxins involves the β‐sheet, in addition to loops I and IV. Besides the position of culprit residues on the molecular surface, difference in dipolar moment orientation is another determinant of receptor binding and biological activity differences. We also demonstrate by electrophysiological experiments on the cloned insect voltage‐gated sodium channel, para, heterologuously co‐expressed with the tipE subunit in Xenopus laevis oocytes, that δ‐paluIT1 and δ‐paluIT2 procure an increase of Na+ current. δ‐PaluIT1‐OH seems to have less effect when the same concentrations are used. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Hydrophobic tendency of polar group hydration as a major force in type I antifreeze protein recognition
Authors: Yang Cheng , Sharp Kim A. 
Published: February 2005

AbstractThe random network model of water quantitatively describes the different hydration heat capacities of polar and apolar solutes in terms of distortions of the water–water hydrogen bonding angle in the first hydration shell (Gallagher and Sharp, JACS 2003;125:9853). The distribution of this angle in pure water is bimodal, with a low‐angle population and high‐angle population. Polar solutes increase the high‐angle population while apolar solutes increase the low‐angle population. The ratio of the two populations quantifies the hydrophobicity of the solute and provides a sensitive measure of water structural distortions. This method of analysis is applied to study hydration of type I thermal hysteresis protein (THP) from winter flounder and three quadruple mutants of four threonine residues at positions 2, 13, 24, and 35. Wild‐type and two mutants (VVVV and AAAA) have antifreeze (thermal hysteresis) activity, while the other mutant (SSSS) has no activity. The analysis reveals significant differences in the hydration structure of the ice‐binding site. For the SSSS mutant, polar groups have a typical polar‐like hydration, that is, more high‐angle H‐bonds than bulk water. For the wild‐type and active mutants, polar groups have unusual, very apolar‐like hydration, that is, more low‐angle H‐bonds than bulk water. This pattern of hydration was seen previously in the structurally distinct type III THPs (Yang & Sharp Biophys Chem 2004;109:137), suggesting for the first time a general mechanism for different THP classes. The specific shape, residue size, and clustering of both polar and apoler groups are essential for an active ice binding surface. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Determination of the mobility ratio in InSb at the temperature of the conductivity type conversion
Authors: Somogyi K. 
Published: February 2005

AbstractThe temperature dependence of magneto‐transport in bulk p‐type InSb was investigated, and a special approach was applied for the precise determination of the temperature dependence. Such measurements also allow the determination of the mobility ratio (b) which is known to be large in InSb. Although this type of investigation is standard, in this work an improved method of carrying out temperature‐dependent Hall measurements is reported and improved calculations for the determination of large b values in InSb are presented. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Second and third harmonic generations in random composites of spheroidal particles
Authors: Liu Bo , Gao Lei 
Published: February 2005

AbstractWith the aid of the spectral representation and decoupling approximation, we investigate the effective optical susceptibilities for second harmonic generation (SHG) and third harmonic generation (THG) of nonlinear composites media, in which the nonlinear spheroidal particles are embedded in a linear host medium. We emphasize the effect of the granular shape on SHG and THG susceptibilities in two types of microstructures corresponding to those described by the generalized Maxwell–Garnett Theory (MGT) and Effective Medium Approximation (EMA). Numerical results show that large enhancement of SHG and THG can be achieved by the adjustment of the depolarization factor (or the granular shape). (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Luminescence and defects creation in Ce3+‐doped YAlO3 and Lu0.3Y0.7AlO3 crystals
Authors: Blazek K. , Krasnikov A. , Nejezchleb K. , Nikl M. , Savikhina T. , Zazubovich S. 
Published: February 2005

AbstractLuminescence, energy transfer and defects creation processes were studied for the Ce3+‐doped YAlO3 and LuxY1–xAlO3 (x = 0.3) crystals in the temperature range 4.2–300 K under selective photoexcitation in the energy range 3.5–11.5 eV. For the first time, defects creation spectra were measured and analyzed. Influence of the charge and ionic radii of co‐doping ions on the luminescence and defects creation efficiency was considered. The origin of the defects created and possible mechanisms of their formation were discussed. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)