bluuebunny/crossref_metadata_2025_split huggingface dataset:
FIB-4
Authors: Vallet-Pichard Anaïs , Mallet Vincent , Nalpas Bertrand , Verkarre Virginie , Nalpas Antoine , Dhalluin-Venier Valérie , Fontaine Hélène , Pol Stanislas 
Published: June 2007

Abstract

To optimize the management of patients with chronic hepatitis C virus (HCV) infection, noninvasive tests to determine the degree of hepatic fibrosis have been developed. The aims of this study were (1) to validate a simple, inexpensive, noninvasive test called FIB-4, which combines standard biochemical values (platelets, ALT, AST) and age, in a series of 847 liver biopsies performed in HCV-monoinfected patients; and (2) to compare the results of 780 FIB-4 and FibroTests performed the same day in a series of 592 HCV-infected patients. The FIB-4 index enabled the correct identification of patients with severe fibrosis (F3-F4) and cirrhosis with an area under the receiver operating characteristic curve of 0.85 (95% CI 0.82-0.89) and 0.91 (95% CI 0.86-0.93), respectively. An FIB-4 index <1.45 had a negative predictive value of 94.7% to exclude severe fibrosis with a sensitivity of 74.3%. An FIB-4 index higher than 3.25 had a positive predictive value to confirm the existence of a significant fibrosis (F3-F4) of 82.1% with a specificity of 98.2%. Using these ranges, 72.8% of the 847 liver biopsies were correctly classified. The FIB-4 index was strongly correlated to the FibroTest results for a score <1.45 or >3.25 (κ = 0.561,

P

< 0.01). A FIB-4 value <1.45 or >3.25 (64.6% of the cases) was concordant with FibroTest results in 92.1% and 76%, respectively.

Conclusion:

For values outside 1.45-3.25, the FIB-4 index is a simple, accurate, and inexpensive method for assessing liver fibrosis and proved to be concordant with FibroTest results. (HEPATOLOGY 2007.)
Hepatitis C virus protein expression causes calcium-mediated mitochondrial bioenergetic dysfunction and nitro-oxidative stress
Authors: Piccoli Claudia , Scrima Rosella , Quarato Giovanni , D'Aprile Annamaria , Ripoli Maria , Lecce Lucia , Boffoli Domenico , Moradpour Darius , Capitanio Nazzareno 
Published: June 2007

Abstract

Hepatitis C virus (HCV) infection induces a state of oxidative stress that is more pronounced than that in many other inflammatory diseases. In this study we used well-characterized cell lines inducibly expressing the entire HCV open-reading frame to investigate the impact of viral protein expression on cell bioenergetics. It was shown that HCV protein expression has a profound effect on cell oxidative metabolism, with specific inhibition of complex I activity, depression of mitochondrial membrane potential and oxidative phosphorylation coupling efficiency, increased production of reactive oxygen and nitrogen species, as well as loss of the Pasteur effect. Importantly, all these effects were causally related to mitochondrial calcium overload, as inhibition of mitochondrial calcium uptake completely reversed the observed bioenergetic alterations.

Conclusion

: Expression of HCV proteins causes deregulation of mitochondrial calcium homeostasis. This event occurs upstream of further mitochondrial dysfunction, leading to alterations in the bioenergetic balance and nitro-oxidative stress. These observations provide new insights into the pathogenesis of hepatitis C and may offer new opportunities for therapeutic intervention. (HEPATOLOGY 2007.)
Use of mixed bivariate distributions for deriving inter‐station correlation coefficients of rain rate
Authors: Ha Eunho , Yoo Chulsang 
Published: June 2007

AbstractEven though rain rate is notorious for its spatial and temporal intermittency, its effect on the second‐order statistics of rain rate, especially the inter‐station correlation coefficients, has not been intensively evaluated before. This study has derived and compared the inter‐station correlation coefficient of rain rate for three cases of data: (1) only the positive measurements at both locations; (2) the positive measurements at either one or both locations; (3) all the measurements including zero measurement at both locations. For these three cases, the inter‐station correlation coefficients are analytically derived by applying the mixed bivariate log‐normal distribution. As an application example, the model parameters are estimated using the rain rate data collected at the Geum River basin, Korea, and the resulting inter‐station correlation coefficients are evaluated and compared with those estimated by applying the Gaussian distribution. We could find that highly biased inter‐station correlation coefficients are unavoidable when simply estimating them under the assumption of Gaussian distribution, or even when using the log‐transformed rain rate data. Copyright © 2007 John Wiley & Sons, Ltd.
Hybrid nanofibrous membranes of PLGA/chitosan fabricated via an electrospinning array
Authors: Duan Bin , Wu Lili , Yuan Xiaoyan , Hu Zhen , Li Xiulan , Zhang Yang , Yao Kangde , Wang Min 
Published: June 2007

AbstractHybrid nanofibrous membranes of poly(lactic‐co‐glycolic acid) (PLGA) and chitosan with different chitosan amounts (32.3, 62.7, and 86.5%) were fabricated via a specially designed electrospinning setup consisting of two sets of separate syringe pumps and power supplies. After soaking in chloroform overnight to dissolve PLGA, the amount of chitosan in the hybrid membranes was determined. The structure, mechanical properties, water uptake, and cytocompatibilities of the nanofibrous membranes were investigated by scanning electron microscopy, tensile testing, incubation in phosphate buffer solution, and human embryo skin fibroblasts culturing. Results showed that the chitosan amount in PLGA/chitosan membranes could be well controlled by adjusting the number of syringe for electrospinning of PLGA or chitosan, respectively. Because of the introduction of chitosan, which is a naturally hydrophilic polymer, the hybrid PLGA/chitosan membranes after chitosan crosslinking exhibited good mechanical and water absorption properties. The cytocompatibility of hybrid PLGA/chitosan membranes was better than that of the electrospun PLGA membrane. The electrospun hybrid nanofibrous membranes of PLGA and chitosan appear to be promising for skin tissue engineering. The concept of using an electrospinning array to form multicomponent nanofibrous membranes will lead to the creation of novel scaffolds for tissue engineering applications. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res, 2007
Biocompatibility and antibacterial activity of plasma sprayed titania coating grafting collagen and gentamicin
Authors: Li Baoe , Liu Xuanyong , Cao Cong , Ding Chuanxian 
Published: June 2007

AbstractIn this article, the plasma sprayed titania coatings were treated by grafting pure and gentamicin loaded collagen to improve the biocompatibility and antibacterial activity. The biocompatibility of the titania coating grafting collagen was evaluated by in vitro cell culturing test. The release rate of gentamicin from collagen was measured in tris‐HCl buffer using UV spectrophotometer, and the antibacterial activity of the titania coating with gentamicin against Staphylococcus aureus was examined using the zone of inhibition test. The results showed that collagen was successfully grafted on the surface of titania coatings treated by sulfuric acid. The in vitro cell culturing test revealed that collagen significantly improved the cell adhesion and proliferation on the surface of titania coatings. The gentamicin loaded in collagen matrix could retain a sustained release in tris‐HCl for 30 days, which was efficient to protect against the postoperative infection caused by S. aureus. The results indicated that the plasma sprayed titania coating grafting collagen and gentamicin would have the antibacterial activity together with the biocompatibility, which might be beneficial for the long term stability and surgical success rate of implants. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res, 2007
Preparation and characterization of nano‐hydroxyapatite/chitosan/konjac glucomannan composite
Authors: Zhou Gang , Li Yubao , Zhang Li , Zuo Yi , Jansen John A. 
Published: June 2007

AbstractNano‐hydroxyapatite (n‐HA)/chitosan (CS)/konjac glucomannan (KGM) composite was prepared by coprecipitation method and investigated by thermal gravitivity/differentiate thermal analysis, Fourier transform infrared spectroscopy, X‐ray diffraction, inductively coupled plasma emission spectroscopy, scanning electron microscopy, and energy dispersive X‐ray analyzer. The analyses showed that the three phases of n‐HA, CS, and KGM combined closely to each other. Further, in vitro tests were conducted to investigate the degradation and bioactivity of the composite. During immersion in simulated body fluid (SBF), pores appeared and a new substance containing Ca and P formed on the surface of the composite. Also, the concentration of Ca and P in SBF changed and weight loss of the composite was observed during time. The composite revealed a high degradation in SBF. Evidently, the new composite has a potential to be used as a carrier of implantable drug delivery system. The biodegradation rate and route could be different from CS and KGM, which will provide an opportunity to control the degradation rate or drug releasing rate by simply adjusting the ratio of CS and KGM. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res, 2007
Epigenetic and genetic mechanisms contribute to telomerase inhibition by EGCG
Authors: Berletch Joel B. , Liu Canhui , Love William K. , Andrews Lucy G. , Katiyar Santosh K. , Tollefsbol Trygve O. 
Published: June 2007

AbstractThe ends of human chromosomes are protected from the degradation associated with cell division by 15–20 kb long segments of hexameric repeats of 5′‐TTAGGG‐3′ termed telomeres. In normal cells telomeres lose up to 300 bp of DNA per cell division that ultimately leads to senescence; however, most cancer cells bypass this lifespan restriction through the expression of telomerase. hTERT, the catalytic subunit essential for the proper function of telomerase, has been shown to be expressed in approximately 90% of all cancers. In this study we investigated the hTERT inhibiting effects of (−)‐epigallocatechin‐3‐gallate (EGCG), the major polyphenol found in green tea catechins, in MCF‐7 breast cancers cells and HL60 promyelocytic leukemia cells. Exposure to EGCG reduced cellular proliferation and induced apoptosis in both MCF‐7 and HL60 cells in vitro, although hTERT mRNA expression was decreased only in MCF‐7 cells when treated with EGCG. Furthermore, down‐regulation of hTERT gene expression in MCF‐7 cells appeared to be largely due to epigenetic alterations. Treatment of MCF‐7 cells with EGCG resulted in a time‐dependent decrease in hTERT promoter methylation and ablated histone H3 Lys9 acetylation. In conjunction with demethylation, further analysis showed an increase in hTERT repressor E2F‐1 binding at the promoter. From these findings, we propose that EGCG is effective in causing cell death in both MCF‐7 and HL60 cancer cell lines and may work through different pathways involving both anti‐oxidant effects and epigenetic modulation. J. Cell. Biochem. 103: 509–519, 2008. © 2007 Wiley‐Liss, Inc.
PKD, PKD2, and p38 MAPK mediate Hsp27 serine‐82 phosphorylation induced by neurotensin in pancreatic cancer PANC‐1 cells
Authors: Yuan Jingzhen , Rozengurt Enrique 
Published: June 2007

AbstractIt is widely recognized that Hsp27 is a downstream substrate of the p38 MAPK cascade whereas the role of PKD family members in mediating receptor‐stimulated Hsp27 Ser‐82 phosphorylation has not been evaluated. Here, we show that neurotensin induced a rapid and striking increase in Hsp27 Ser‐82 phosphorylation in PANC‐1 cells, which was closely correlated with stimulation of activation loop phosphorylation of PKDs and p38 MAPK Thr180/Tyr182 phosphorylation. Treatment of PANC‐1 cells with either the selective PKC inhibitor GF‐I or the p38 MAPK inhibitor SB202190 partially reduced neurotensin‐induced Hsp27 Ser‐82 phosphorylation. However, treatment of the cells with a combination of GF‐I and SB202190 virtually abolished neurotensin‐induced Hsp27 Ser‐82 phosphorylation. Overexpression of PKD in stably transfected PANC‐1 cells increased the magnitude and prolonged the duration of Hsp27 Ser‐82 phosphorylation in response to neurotensin. Either PKD or PKD2 gene silencing utilizing siRNAs targeting distinct PKD or PKD2 sequences reduced neurotensin‐stimulated Hsp27 Ser‐82 phosphorylation, but cotransfection of siRNAs targeting both, PKD and PKD2, markedly decreased neurotensin‐induced Hsp27 Ser‐82 phosphorylation. Knockdown of PKD and PKD2 abolished Hsp27 phosphorylation in cells treated with SB202190. Thus, neurotensin induces Hsp27 Ser‐82 phosphorylation through p38 MAPK‐ and PKC/PKD‐dependent pathways in PANC‐1 cells. Our results demonstrate, for the first time, that neurotensin induces a striking increase in Hsp27 phosphorylation on Ser‐82 in PANC‐1 cells through convergent p38 MAPK, PKD, and PKD2 signaling. J. Cell. Biochem. 103: 648–662, 2008. © 2007 Wiley‐Liss, Inc.
Analytical excited state forces for the time‐dependent density‐functional tight‐binding method
Authors: Heringer D. , Niehaus T. A. , Wanko M. , Frauenheim TH. 
Published: June 2007

AbstractAn analytical formulation for the geometrical derivatives of excitation energies within the time‐dependent density‐functional tight‐binding (TD‐DFTB) method is presented. The derivation is based on the auxiliary functional approach proposed in [Furche and Ahlrichs, J Chem Phys 2002, 117, 7433]. To validate the quality of the potential energy surfaces provided by the method, adiabatic excitation energies, excited state geometries, and harmonic vibrational frequencies were calculated for a test set of molecules in excited states of different symmetry and multiplicity. According to the results, the TD‐DFTB scheme surpasses the performance of configuration interaction singles and the random phase approximation but has a lower quality than ab initio time‐dependent density‐functional theory. As a consequence of the special form of the approximations made in TD‐DFTB, the scaling exponent of the method can be reduced to three, similar to the ground state. The low scaling prefactor and the satisfactory accuracy of the method makes TD‐DFTB especially suitable for molecular dynamics simulations of dozens of atoms as well as for the computation of luminescence spectra of systems containing hundreds of atoms. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Hartree–Fock exchange fitting basis sets for H to Rn †
Authors: Weigend Florian 
Published: June 2007

AbstractFor elements H to Rn (except Lanthanides), a series of auxiliary basis sets fitting exchange and also Coulomb potentials in Hartree–Fock treatments (RI‐JK‐HF) is presented. A large set of small molecules representing nearly each element in all its common oxidation states was used to assess the quality of these auxiliary bases. For orbital basis sets of triple zeta valence and quadruple zeta valence quality, errors in total energies arising from the RI‐JK approximation are below ∼1 meV per atom in molecular compounds. Accuracy of RI‐JK‐approximated HF wave functions is sufficient for being used for post‐HF treatments like Møller–Plesset perturbation theory, MP2. Compared to nonapproximated treatments, RI‐JK‐HF leads to large computational savings for quadruple zeta valence orbital bases and, in case of small to midsize systems, to significant savings for triple zeta valence bases. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Searching for globally optimal functional forms for interatomic potentials using genetic programming with parallel tempering
Authors: Slepoy A. , Peters M. D. , Thompson A. P. 
Published: June 2007

AbstractMolecular dynamics and other molecular simulation methods rely on a potential energy function, based only on the relative coordinates of the atomic nuclei. Such a function, called a force field, approximately represents the electronic structure interactions of a condensed matter system. Developing such approximate functions and fitting their parameters remains an arduous, time‐consuming process, relying on expert physical intuition. To address this problem, a functional programming methodology was developed that may enable automated discovery of entirely new force‐field functional forms, while simultaneously fitting parameter values. The method uses a combination of genetic programming, Metropolis Monte Carlo importance sampling and parallel tempering, to efficiently search a large space of candidate functional forms and parameters.The methodology was tested using a nontrivial problem with a well‐defined globally optimal solution: a small set of atomic configurations was generated and the energy of each configuration was calculated using the Lennard‐Jones pair potential. Starting with a population of random functions, our fully automated, massively parallel implementation of the method reproducibly discovered the original Lennard‐Jones pair potential by searching for several hours on 100 processors, sampling only a minuscule portion of the total search space. This result indicates that, with further improvement, the method may be suitable for unsupervised development of more accurate force fields with completely new functional forms. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review
Authors: Christen Markus , van Gunsteren Wilfred F. 
Published: June 2007

AbstractMethods to search for low‐energy conformations, to generate a Boltzmann‐weighted ensemble of configurations, or to generate classical‐dynamical trajectories for molecular systems in the condensed liquid phase are briefly reviewed with an eye to application to biomolecular systems. After having chosen the degrees of freedom and method to generate molecular configurations, the efficiency of the search or sampling can be enhanced in various ways: (i) efficient calculation of the energy function and forces, (ii) application of a plethora of search enhancement techniques, (iii) use of a biasing potential energy term, and (iv) guiding the sampling using a reaction or transition pathway. The overview of the available methods should help the reader to choose the combination that is most suitable for the biomolecular system, degrees of freedom, interaction function, and molecular or thermodynamic properties of interest. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Efficiency of numerical basis sets for predicting the binding energies of hydrogen bonded complexes: Evidence of small basis set superposition error compared to Gaussian basis sets
Authors: Inada Yasuji , Orita Hideo 
Published: June 2007

AbstractBinding energies of selected hydrogen bonded complexes have been calculated within the framework of density functional theory (DFT) method to discuss the efficiency of numerical basis sets implemented in the DFT code DMol3 in comparison with Gaussian basis sets. The corrections of basis set superposition error (BSSE) are evaluated by means of counterpoise method. Two kinds of different numerical basis sets in size are examined; the size of the one is comparable to Gaussian double zeta plus polarization function basis set (DNP), and that of the other is comparable to triple zeta plus double polarization functions basis set (TNDP). We have confirmed that the magnitudes of BSSE in these numerical basis sets are comparative to or smaller than those in Gaussian basis sets whose sizes are much larger than the corresponding numerical basis sets; the BSSE corrections in DNP are less than those in the Gaussian 6‐311+G(3df,2pd) basis set, and those in TNDP are comparable to those in the substantially large scale Gaussian basis set aug‐cc‐pVTZ. The differences in counterpoise corrected binding energies between calculated using DNP and calculated using aug‐cc‐pVTZ are less than 9 kJ/mol for all of the complexes studied in the present work. The present results have shown that the cost effectiveness in the numerical basis sets in DMol3 is superior to that in Gaussian basis sets in terms of accuracy per computational cost. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Extensive theoretical study on the low‐lying electronic states of silicon monofluoride cation including spin‐orbit coupling
Authors: Liu Kun , Bian Wensheng 
Published: June 2007

AbstractAb initio calculations on the low‐lying electronic states of SiF+ are performed using the internally contracted multireference configuration interaction method with the Davidson correction and entirely uncontracted aug‐cc‐pV5Z basis set. The effects of spin‐orbit coupling are accounted for by the state interaction approach with the full Breit–Pauli Hamiltonian. The entire 23 Ω states generated from the 12 valence Λ–S states, which correlate with the first dissociation channel are studied for the first time. Good agreement is found between the calculated results and the available experimental data. The spin‐orbit coupling effects on the potential energy curves and spectroscopic properties are studied. Various curve crossings are revealed, which could lead to the predissociation of the a3Π, A1Π, and (2)3Σ+ states and the predissociation pathways are analyzed based upon the calculated spin‐orbit matrix elements. The calculated ionization potentials of the ground‐state SiF to a few states of SiF+ are in good agreement with the available experimental measurements. Moreover, the transition dipole moments of the dipole‐allowed transitions and the transition properties for the A3Π0+–X1Σ and B3Π1–X1Σ transitions are predicted, including the Franck–Condon factors and the radiative lifetimes. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Efficient bond function basis set for π‐π interaction energies
Authors: Ding Yun , Mei Ye , Zhang John Z. H. , Tao Fu‐Ming 
Published: June 2007

AbstractSystematic study has been carried out to investigate the accuracy of mid‐bond functions in describing π‐π interactions in benzene dimer. Potential energy curves are calculated for the sandwich, T‐shaped, and parallel‐displaced configurations of benzene dimer by adding bond functions in MP2 (second‐order Møller–Plesset perturbation theory) calculations with a wide range of split‐valence and augmented, correlation‐consistent basis sizes. At MP2 level, the largest basis set used with a bond function (denoted aug‐cc‐pVDZf‐6s6p4d2f) differs by only ∼0.1 kcal/mol relative to the result obtained from the standard aug‐cc‐pVQZ basis calculation (without the bond function). The calculated potential energy curves from the bond function basis aug‐cc‐pVDZf‐6s6p4d2f and the larger standard basis aug‐cc‐pVTZ are in excellent agreement with each other for all three configurations. The number of bond function basis aug‐cc‐pVDZf‐6s6p4d2f is 526 compared to 828 of aug‐cc‐pVTZ and 1512 of aug‐cc‐pVQZ. Current study shows that bond functions can be effectively employed to give accurate description of π‐π interactions with the addition of only a minimal number of bond functions. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008