bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the quality of the hardness kernel and the Fukui function to evaluate the global hardness
Authors: Torrent‐Sucarrat Miquel , Salvador Pedro , Geerlings Paul , Solà Miquel 
Published: December 2006

AbstractAn approximated hardness kernel, which includes the second derivative with respect to the density of the kinetic energy, the electron–electron coulomb repulsion, and the exchange density functionals, has been tested for the calculation of the global hardness. The results obtained for a series of 40 cations and neutral systems and 16 anions represent in most cases an improvement of the results obtained using the HOMO‐LUMO gap approach and indicate the viability of this approach to evaluate global hardness. In addition, the relevance of the Fukui function approximation and the role of the three components of the hardness kernel in the evaluation of the global hardness have been analyzed. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 574–583, 2007
A theoretical study of fullerene–ferrocene hybrids
Authors: Kang Hong Seok 
Published: December 2006

AbstractUsing density functional theory within the generalized gradient approximation, I analyzed the electronic structure of a C60–ferrocene hybrid [= C FeCp] around HOMO in comparison with that of ferrocene, where C and Cp denote C60(CH3)5 and a cyclopentadienyl ring. HOMO–LUMO gap is significantly smaller than that of ferrocene because of the intervention of π(C) states below LUMO. In addition, geometrical and electronic structures of N@C FeCp are also investigated. I find that there are two isomers with the energy difference of 0.13 eV. In one of the two, the encased nitrogen atom is located at the center of the fullerene cage. The Fe atom is η5‐coordinated to both Cp and R*, where R* is a five‐membered ring of C cage. On the other hand, the atom is coordinated to R* with η4‐hapticity, and the nitrogen atom is bonded to a carbon atom of the R* ring in the other isomer. Upon the isomerization between the two isomers, there occurs a partial transfer of spin density between the nitrogen and Fe atoms as well as the creation and breaking of a CN bond. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 594–600, 2007
Comparison of basis set effects and the performance of ab initio and DFT methods for probing equilibrium fluctuations
Authors: Walker Ross C. , Mercer Ian P. , Gould Ian R. , Klug David R. 
Published: December 2006

AbstractThe electronic absorption and emission spectra of large molecules reflect the extent and timescale of electron‐vibration coupling and therefore the extent and timescale of relaxation/reorganization in response to a perturbation. In this paper, we present a comparison of the calculated absorption and emission spectra of NADH in liver alcohol dehydrogenase (LADH), using quantum mechanical/molecular mechanical methods, in which we vary the QM component. Specifically, we have looked at the influence of basis set (STO‐3G, 3‐21G*, 6‐31G*, CC‐pVDZ, and 6‐311G**), as well as the influence of applying the DFT TD‐B3LYP and ab initio TD‐HF and CIS methods to the calculation of absorption/emission spectra and the reorganization energy (Stokes shift). The ab initio TD‐HF and CIS methods reproduce the experimentally determined Stokes shift and spectral profiles to a high level of agreement, while the TD‐B3LYP method significantly underestimates the Stokes shift, by 45%. We comment on the origin of this problem and suggest that ab initio methods may be naturally more suited to predicting molecular behavior away from equilibrium geometries. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 478–490, 2007
Elucidating the mechanism for the reduction of nitrite by copper nitrite reductase—A contribution from quantum chemical studies
Authors: De Marothy S. A. , Blomberg M. R. A. , Siegbahn P. E. M. 
Published: December 2006

AbstractDensity functional methods have been applied to investigate the properties of the active site of copper‐containing nitrite reductases and possible reaction mechanisms for the enzyme catalysis. The results for a model of the active site indicate that a hydroxyl intermediate is not formed during the catalytic cycle, but rather a state with a protonated nitrite bound to the reduced copper. Electron affinity calculations indicate that reduction of the T2 copper site does not occur immediately after nitrite binding. Proton affinity calculations are indicative of substantial pKa differences between different states of the T2 site. The calculations further suggest that the reaction does not proceed until uptake of a second proton from the bulk solution. They also indicate that Asp‐92 may play both a key role as a proton donor to the substrate, and a structural role in promoting catalysis. In the D92N mutant another base, presumably a nearby histidine (His‐249) may take the role as the proton donor. On the basis of these model calculations and available experimental evidence, an ordered reaction mechanism for the reduction of nitrite is suggested. An investigation of the binding modes of the nitric oxide product and the nitrite substrate to the model site has also been made, indicating that nitric oxide prefers to bind in an end‐on fashion to the reduced T2 site. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 528–539, 2007
Similarity of RNA secondary structures
Authors: Li Chun , Wang Ai‐hua , Xing Lili 
Published: December 2006

AbstractIn this article, we propose a relatively similar measure to compare RNA secondary structures. We first transform an RNA secondary structure into a special sequence representation. Then, on the basis of symbolic sequence complexity, we obtain the relative distance of RNA secondary structures. The examination of similarities/dissimilarities of a set of RNA secondary structures at the 3′‐terminus of different viruses illustrates the utility of the approach. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 508–512, 2007
Free energy profiles for monomer capture in Grubbs‐ and SHOP‐type olefin polymerization catalysts: A constraint ab initio molecular dynamics study
Authors: Yang Sheng‐Yong , Xiang MIng‐Li , Chen Li‐Juan , Xie Guo‐Bin , Shi Bing , Wei Yu‐Quan , Ziegler Tom 
Published: December 2006

AbstractDensity functional theory together with Car‐Parrinello ab initio molecular dynamics simulation has been used to investigate the free energy profiles (FEP) of monomer capture in Grubbs‐ and SHOP‐type olefin polymerization catalysts. The FEPs along the reaction coordinates at 300 K were determined directly by a point wise thermodynamic integration technique. Comparison between potential energy profile (PEP) and the FEP has been made. The results show that, for both catalysts, the PEP for the monomer ethylene uptake by the metal center is a typical Morse curve without energy barrier. However, a small barrier (1.8 kcal/mol for Grubbs catalyst and 2.4 kcal/mol for SHOP catalyst) exists on the FEP. The π complexation energy on the FES at 300 K is higher by 10–12 kcal/mol over that on the PES. The differences between FES and PES are due to entropy contribution. Slow growth simulations on the ethylene capture process show that the ethylene attacks the metal center by an asynchronous mode. This indicates that the forming of the π‐bonding between the metal and ethylene is initiated by electrophilic attack of the metal to one of the ethylene carbons. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 513–518, 2007
P2Y2 receptors induced cell surface redistribution of αv integrin is required for activation of ERK 1/2 in U937 cells
Authors: Chorna Nataliya E. , Chevres Migdalia , Santos‐Berrios Cynthia , Orellano Elsie A. , Erb Laurie , González Fernando A. 
Published: December 2006

AbstractNucleotides released from cells due to stress, injury or inflammation, induce mitogenic effects in monocytes via activation of P2Y2 nucleotide receptors (P2Y2Rs). Here we show that P2Y2 nucleotide receptors in U937 monocytic cells regulate the activation of extracellular signal‐regulated kinases 1 and 2 (ERK 1/2) by inducing the clustering of αv integrins. The activation of phosphatidylinositol 3‐kinase by P2Y2R ligands was required for αv clustering, suggesting a means whereby two different classes of receptors communicate to induce mitogenic responses in monocytic cells. P2Y2R‐induced αv clustering was also associated with a flattened phenotype of the U937 cells, consistent with the role of the P2Y2R in regulating early events in cell migration. J. Cell. Physiol. 211: 410–422, 2007. © 2006 Wiley‐Liss, Inc.
Downregulation of catalase by reactive oxygen species via PI 3 kinase/Akt signaling in mesangial cells
Authors: Venkatesan Balachandar , Mahimainathan Lenin , Das Falguni , Ghosh‐Choudhury Nandini , Ghosh Choudhury Goutam 
Published: December 2006

AbstractReactive oxygen species (ROS) contribute to many glomerular diseases by targeting mesangial cells. ROS have been shown to regulate expression of many antioxidant enzymes including catalase. The mechanism by which the expression of catalase protein is regulated by ROS is not precisely known. Here we report that increased intracellular ROS level by hydrogen peroxide (H2O2) reduced the expression of catalase. H2O2 increased phosphorylation of Akt kinase in a dose‐dependent and sustained manner with a concomitant increase in the phosphorylation of FoxO1 transcription factor. Further analysis revealed that H2O2 promoted rapid activation of phosphatidylinositol (PI) 3 kinase. The PI 3 kinase inhibitor Ly294002 and expression of tumor suppressor protein PTEN inhibited Akt kinase activity, resulting in the attenuation of FoxO1 phosphorylation and preventing the downregulating effect of H2O2 on catalase protein level. Dominant negative Akt attenuated the inhibitory effect of H2O2 on expression of catalase. Constitutively active FoxO1 increased the expression of catalase. However, dominant negative FoxO1 inhibited catalase protein level. Catalase transcription was reduced by H2O2 treatment. Furthermore, expression of dominant negative Akt and constitutively active FoxO1 increased catalase transcription, respectively. These results demonstrate that ROS downregulate the expression of catalase in mesangial cells by PI 3 kinase/Akt signaling via FoxO1 as a target. J. Cell. Physiol. 211: 457–467, 2007. © 2006 Wiley‐Liss, Inc.
Activation of Prn‐p gene and stable transfection of Prn‐p cDNA in leukemia MEL and neuroblastoma N2a cells increased production of PrPC but not prevented DNA fragmentation initiated by serum deprivation
Authors: Gougoumas Dimitrios D. , Vizirianakis Ioannis S. , Triviai Ioanna N. , Tsiftsoglou Asterios S. 
Published: December 2006

AbstractPrion protein (PrPC) via its isoform PrPSC is involved in the pathogenesis of transmissible spongiform encephalopathies (TSEs). We observed that murine erythroleukemia (MEL) cells arrested in phase G1 undergo transcriptional activation of Prn‐p gene. Here, we explored the potential role of activation of Prn‐p gene and cytosolic accumulation of PrPC in growth arrest, differentiation, and apoptotic DNA fragmentation by stably transfecting MEL and N2a cells with Prn‐p cDNA. Stably transfected MEL cells (clones # 6, 12, 20, 38, and 42) were assessed for growth and differentiation, while clones N2a13 and N2a8 of N2a cells for growth and apoptosis by flow cytometry using Annexin V and propidium iodide (PI). Our results indicate that (a) Induction of terminal differentiation of stably transfected MEL cells led to growth arrest, activation of Prn‐p gene, concomitant expression of transfected Prn‐p cDNA, suppression of bax gene, cytosolic accumulation of PrPC, and DNA fragmentation. The latter was also induced in non‐differentiated MEL cells growing under serum‐free conditions; (b) similarly, serum deprivation promoted growth arrest, apoptosis/necrosis associated with DNA fragmentation in parental N2a and N2a13 cells that produced relative high level of PrPC and not PrPSC. These data indicate that activation of Prn‐p gene and expression of transfected Prn‐p cDNA in cells of both hematopoietic and neuronal origin occurred concomitantly, and led to cytosolic accumulation of PrPC and DNA damage induced by serum deprivation. PrPC production failed to protect DNA fragmentation induced by serum deprivation. The question how does PrPC contribute to growth arrest and DNA fragmentation is discussed. J. Cell. Physiol. 211: 551–559, 2007. © 2006 Wiley‐Liss, Inc.
Reduced aggression in mice lacking GABA transporter subtype 1
Authors: Liu Guo‐Xiang , Liu Shuai , Cai Guo‐Qiang , Sheng Zhe‐Jing , Cai You‐Qing , Jiang Jie , Sun Xia , Ma Sun‐Kai , Wang Long , Wang Zhu‐Gang , Fei Jian 
Published: December 2006

AbstractDysregulation of the brain GABAergic system has been implicated in the pathophysiology of violence and aggression. As a key regulator of central GABAergic activity, dysfunction of the GABA transporter subtype 1 (GAT1) represents a potential mechanism mediating pathologic aggression. We provide evidence that GAT1−/− mice and GAT1+/− mice exhibit lower aggressive behavior both in home cage resident–intruder test and neutral arena resident–intruder test, compared to wild‐type mice (GAT1+/+). The pharmacologic effects of the GAT1 inhibitor, tiagabine and the GABAA receptor antagonist, bicuculline have been assessed in GAT1+/+ mice: tiagabine inhibits attacks but bicuculline induces attacks. Compared to GAT1+/− and +/+ mice, the GAT1−/− mice displayed a normal circadian pattern of home cage activity, but more activity overall. Meanwhile, reduced testosterone concentration was found in GAT1−/− mice compared to GAT1+/+ mice but not in GAT1+/+ mice treated with tiagabine, suggesting that testosterone is not directly involved in GAT1 mediated aggressive behavior regulation. These results showed that GAT1 is an important target involved in the regulation of aggressive behavior in mice, and long‐term dysfunction of GAT1 may also result in the alteration of testosterone secretion. © 2006 Wiley‐Liss, Inc.
Diurnal variations in summer season precipitation in India
Authors: Sen Roy Shouraseni , Balling Robert C. 
Published: December 2006

AbstractIn the present study, we have analyzed the spatial patterns in the diurnal cycle of precipitation over the Indian subcontinent. We assembled hourly precipitation data for 78 stations spread across the Indian subcontinent for the period 1980 to 2000. On the basis of the results of the first harmonic, we found the presence of a distinct diurnal cycle over most of the Indian subcontinent for frequency, total, and intensity of precipitation events. The standardized amplitudes, indicative of the strength of diurnal cycle over a region, are strongest in peninsular India, with greater than 80% explained variance. The diurnal spatial patterns are broadly a result of the interaction of local orography and convectional processes. The time of maximum precipitation along the west coast is predominantly concentrated a few hours after midnight to predawn hours. The interiors of the subcontinent generally experience late afternoon to early evening showers, which may be attributed to local convective processes. The time of maximum for total amount of precipitation are mostly about half an hour to 1 h before the time of maximum for the frequency. The overall patterns of diurnal cycle were also found to be robust against interannual variations, in the form of ENSO and La Niña years. Copyright © 2006 Royal Meteorological Society
Raman and ab initio study of the conformational isomerism in the 1‐ethyl‐3‐methyl‐imidazolium bis(trifluoromethanesulfonyl)imide ionic liquid
Authors: Lassègues J. C. , Grondin J. , Holomb R. , Johansson P. 
Published: December 2006

AbstractThe calculated and experimental Raman spectra of the (EMI+)TFSI− ionic liquid, where EMI+ is the 1‐ethyl‐3‐methylimidazolium cation and TFSI− the bis(trifluoromethanesulfonyl)imide anion, have been investigated for a better understanding of the EMI+ and TFSI− conformational isomerism as a function of temperature. Characteristic Raman lines of the planar (p) and non‐planar (np) EMI+ conformers are identified using the reference (EMI+)Br− salt. The anion conformer of C2 symmetry is confirmed to be more stable than the cis (C1) one by 4.5 ± 0.2 kJ mol−1. At room temperature, the population of trans (C2) anions and np cations is 75 ± 2% and 87 ± 4%, respectively. Fast cooling quenches a metastable glassy phase composed of mainly C2 anion conformers and p cation conformers, whereas slow cooling gives a crystalline phase composed of C1 anion conformers and of np cation conformers. Copyright © 2006 John Wiley & Sons, Ltd.
High‐resolution stimulated Raman spectroscopy and analysis of the ν1 stretching band of GeD4
Authors: Boudon V. , Radhouani D. , Loëte M. , Martínez R. Z. , Bermejo D. 
Published: December 2006

AbstractThe high‐resolution stimulated Raman spectrum of the ν1 band of GeD4 with natural isotopic abundance germanium has been recorded. It has been analyzed as part of the ν1/ν3 stretching dyad. The ν1 and ν3 band centers have been deduced for all the isotopologues. Copyright © 2006 John Wiley & Sons, Ltd.
Growth arrest‐specific gene 6 and Axl signaling enhances gastric cancer cell survival via Akt pathway
Authors: Sawabu Tateo , Seno Hiroshi , Kawashima Tomoko , Fukuda Akihisa , Uenoyama Yoshito , Kawada Mayumi , Kanda Naoki , Sekikawa Akira , Fukui Hirokazu , Yanagita Motoko , Yoshibayashi Hiroshi , Satoh Seiji , Sakai Yoshiharu , Nakano Toru , Chiba Tsutomu 
Published: December 2006

AbstractActivation of tyrosine kinases is an important factor during cancer development. Axl, one of the receptor tyrosine kinases, binds to the specific ligand growth arrest‐specific gene 6 (Gas6), which encodes a vitamin K‐dependent γ‐carboxyglutamyl protein. Although many receptor tyrosine kinases and their ligands are involved in gastric carcinogenesis, whether Gas6‐Axl signaling is involved in gastric carcinogenesis has not been elucidated. The aim of this study was to investigate the expression of Gas6 and Axl in gastric cancer and also their roles during gastric carcinogenesis. mRNA and protein of Gas6 and Axl were highly expressed in a substantial proportion of human gastric cancer tissue and cell lines, and Gas6 expression was significantly associated with lymph node metastasis. With recombinant Gas6 and a decoy‐receptor of Axl in vitro, we demonstrated that Gas6‐Axl signaling pathway enhanced cellular survival and invasion and suppressed apoptosis via Akt pathway. Our results suggests that Gas6‐Axl signaling plays a role during gastric carcinogenesis, and that targeting Gas6‐Axl signaling could be a novel therapeutic for gastric cancer. © 2006 Wiley‐Liss, Inc.
Elevated urokinase‐specific surface receptor expression is maintained through its interaction with urokinase plasminogen activator
Authors: Mahanivong Chitladda , Yu Jianqiang , Huang Shuang 
Published: December 2006

AbstractUrokinase plasminogen activator (uPA) and its receptor (uPAR) are overexpressed in various neoplasms, and play a key role in tumor progression and metastasis. In this study, we examined uPA and uPAR expression in a variety of human breast cancer cell lines and found that lines with elevated uPA expression also exhibited high uPAR expression, suggesting the possibility that uPA and uPAR are regulated in concert. To test this possibility, we introduced antisense uPA RNA and antisense uPAR RNA in MDA‐MB‐231 and BT‐549 lines that express high levels of uPA and uPAR. Antisense uPA RNA not only downregulated uPA expression, but also greatly reduced uPAR expression in both lines. However, antisense uPAR RNA‐reduced uPAR expression with no apparent inhibitory effect on the levels of uPA. These results indicate that expression of uPAR requires uPA but not vice versa. With a panel of uPA and uPAR monoclonal antibodies (mAbs), we observed that the mAbs disrupting uPA and uPAR interaction, rather than mAb inhibiting uPA protease activity, reduced uPAR expression. Moreover, adding soluble single chain uPA (scuPA) to MDA‐MB‐231 or BT‐549 cells expressing antisense uPA mRNA‐restored uPAR expression. These findings suggest that uPA dictates uPAR expression and that uPA binding to uPAR transmits signals for uPAR expression. Finally, we provided evidence that Fyn, a Src family kinase, is involved in uPA‐induced uPAR expression. © 2006 Wiley‐Liss, Inc.
Connexin 32 potentiates vinblastine‐induced cytotoxicity in renal cell carcinoma cells
Authors: Sato Hiromi , Senba Hironobu , Virgona Nantiga , Fukumoto Keiko , Ishida Tatsuya , Hagiwara Hiromi , Negishi Etsuko , Ueno Koichi , Yamasaki Hiroshi , Yano Tomohiro 
Published: December 2006

AbstractWe have reported that connexin (Cx) 32 gene, a member of gap junction protein family, acts as a tumor suppressor gene in human renal cell carcinoma (RCC). Of solid tumors, RCC is one of the most chemoresistant cancers, and there is no effective cancer chemotherapy against RCC at present. In this study, we examined if the combination of Cx32‐dependent tumor‐suppressive effect and vinblastine (VBL), a chemotherapeutic agent which has been utilized for clinical RCC treatment, could be effective in enhancing the sensitivity of RCC to VBL treatment. Cx32 expression in a human metastatic RCC cell (Caki‐1 cell) significantly enhanced in vitro and in vivo VBL‐induced cytotoxicity on the cell. Cx32 expression in the RCC cells potentiated VBL‐induced apoptosis compared to the Cx32‐negative RCC cells in vitro as well as in vivo. The enhancing apoptosis in the RCC cells by Cx32 mainly depended on the decrease of P‐glycoprotein (P‐gp), a multidrug resistance gene‐1 (MDR‐1) product responsible for reduction of VBL accumulation into the cells. We also observed that silencing of Cx32 by short interfering RNA (siRNA) treatment elevated the level of P‐gp in Caki‐1 cells and that inhibition of P‐gp function enhanced VBL‐induced apoptosis in the RCC cells. These results suggest that Cx32 is effective to enhance VBL‐induced cytotoxicity in Caki‐1 cells via the reduction of P‐gp. Overall, it seems that the combination of Cx32‐dependent tumor‐suppressive effect and VBL is promising as a new cancer therapy against RCC. © 2006 Wiley‐Liss, Inc.
Role of IKK and oscillatory NFκB kinetics in MMP‐9 gene expression and chemoresistance to 5‐fluorouracil in RKO colorectal cancer cells
Authors: Fukuyama Ryuichi , Ng Kwok Peng , Cicek Muzaffer , Kelleher Clare , Niculaita Roxana , Casey Graham , Sizemore Nywana 
Published: December 2006

AbstractNuclear factor kappa B (NFκB) is a central participant in the metastasis and chemoresistance of colorectal cancer (CRC). However, it is not fully understood to what extent NFκB contributes to induction of the metastasis‐associated matrix metalloprotease‐9 (MMP‐9) gene and sensitivity to the commonly used chemotherapeutic 5‐fluorouracil (5‐Fu) in CRC. Using the RKO human CRC cell line and two NFκB signaling deficient RKO mutants, we investigated NFκB's role in the induction of MMP‐9 and 5‐Fu sensitivity in RKO CRC cells. NFκB plays a predominant role in MMP‐9 gene induction in RKO cells, as evidenced by the failure of tumor necrosis factor alpha (TNFα) to induce MMP‐9 in either of the NFκB signaling mutants. RKO cells exhibit a robust, oscillatory NFκB activity in response to TNFα not seen in either of the NFκB mutant cell lines, which instead demonstrate diminished, nonoscillatory NFκB activation. Analysis of TNFα‐induced phosphorylation and MMP‐9 promoter recruitment of the p65 NFκB subunit revealed a significant reduction in p65 phosphorylation as well as reduced and altered recruitment of p65 to the MMP‐9 gene promoter in the mutants compared to the parental RKO cell line. 5‐Fu only activated NFκB in the parental RKO cells through induction of IκB‐kinase (IKK) activity and increased sensitivity to 5‐Fu is observed in both NFκB mutant lines. Our results suggest that TNFα‐dependent induction of MMP‐9 gene expression is tightly regulated by oscillatory/cumulative activation of NFκB and that 5‐Fu stimulates NFκB and RKO CRC cell survival through induction of IKK activity. © 2006 Wiley‐Liss, Inc.