bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biocompatibility evaluation of surface‐treated AISI 316L austenitic stainless steel in human cell cultures
Authors: Martinesi M. , Bruni S. , Stio M. , Treves C. , Bacci T. , Borgioli F. 
Published: September 2006

AbstractThe effects of AISI 316L austenitic stainless steel, tested in untreated state or subjected to glow‐discharge nitriding (at 10 or 20 hPa) and nitriding + post‐oxidizing treatments, on human umbilical vein endothelial cells (HUVEC) and on peripheral blood mononuclear cells (PBMC) were evaluated. All the treated samples showed a better corrosion resistance in PBS and higher surface hardness in comparison with the untreated alloy. In HUVEC put in contact for 72 h with the sample types, proliferation and apoptosis decreased and increased, respectively, in the presence of the nitrided + post‐oxidized samples, while only slight differences in cytokine (TNF‐α, IL‐6, and TGF‐β1) release were registered. Intercellular adhesion molecule‐1 (ICAM‐1) increased in HUVEC incubated with all the treated samples, while vascular cell adhesion molecule‐1 (VCAM‐1) and E‐selectin increased in the presence of all the sample types. PBMC incubated for 48 h with the samples showed a decrease in proliferation and an increase in apoptosis in the presence of the untreated samples and the nitrided + post‐oxidized ones. All the sample types induced a remarkable increase in TNF‐α and IL‐6 release in PBMC culture medium, while only the untreated sample and the nitrided at 10 hPa induced an increase in ICAM‐1 expression. In HUVEC cocultured with PBMC, previously put in contact with the treated AISI 316L samples, increased levels of ICAM‐1 were detected. In HUVEC coincubated with the culture medium of PBMC, previously put in contact with the samples under study, a noteworthy increase in ICAM‐1, VCAM‐1, and E‐selectin levels was always registered, with the exception of VCAM‐1, which was not affected by the untreated sample. In conclusion, even if the treated samples do not show a marked increase in biocompatibility in comparison with the untreated alloy, their higher corrosion resistance may suggest a better performance as the contact with physiological environment becomes longer. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res, 2007
18β‐glycyrrhetinic acid promotes src interaction with connexin43 in rat cardiomyocytes
Authors: Chung Tun‐Hui , Wang Seu‐Mei , Chang Yun‐Chieh , Chen Yuh‐Lien , Wu Jiahn‐Chun 
Published: September 2006

AbstractThe mechanism by which 18β‐glycyrrhetinic acid regulates gap junction intercellular communication (GJIC) remains poorly understood. In this study, treatment of cultured rat neonatal cardiomyocytes with 18β‐glycyrrhetinic acid resulted in dose‐dependent inhibition of GJIC as assessed by fluorescent dye transfer analysis. 18β‐Glycyrrhetinic acid induced time‐dependent serine/threonine dephosphorylation and redistribution of connexin43 (Cx43) in cardiomyocytes and the induced Cx43 dephosphorylation was prevented by the protein phosphatase inhibitor, calyculin A. However, functional analyses showed that the inhibitory effect of 18β‐glycyrrhetinic acid on dye spreading among cardiomyocytes was not blocked by calyculin A, but was blocked by the Src‐selective tyrosine kinase inhibitor, PP2. 18β‐Glycyrrhetinic acid also induced an increase in the levels of phosphorylated Src, and this effect was prevented by PP2. Immunoprecipitation using anti‐Cx43 and anti‐p‐Src antibodies showed that 18β‐glycyrrhetinic acid increased the association between p‐Src and Cx43 and induced tyrosine phosphorylation of Cx43. We conclude that the inhibitory effect of 18β‐glycyrrhetinic acid on GJIC in cardiomyocytes involves Src‐mediated tyrosine phosphorylation of Cx43. J. Cell. Biochem. 100: 653–664, 2007. © 2006 Wiley‐Liss, Inc.
Acetyl‐coenzyme A carboxylases: Versatile targets for drug discovery
Authors: Tong Liang , Harwood H. James 
Published: September 2006

AbstractAcetyl‐coenzyme A carboxylases (ACCs) have crucial roles in fatty acid metabolism in humans and most other living organisms. They are attractive targets for drug discovery against a variety of human diseases, including diabetes, obesity, cancer, and microbial infections. In addition, ACCs from grasses are the targets of herbicides that have been in commercial use for more than 20 years. Significant progresses in both basic research and in drug discovery have been made over the past few years in the studies on these enzymes. At the basic research level, the crystal structures of the biotin carboxylase (BC) and the carboxyltransferase (CT) components of ACC have been determined, and the molecular basis for ACC inhibition by small molecules are beginning to be understood. At the drug discovery level, a large number of nanomolar inhibitors of mammalian ACCs have been reported and the extent of their therapeutic potential is being aggressively explored. This review summarizes these new progresses and also offers some prospects in terms of the future directions for the studies on these important enzymes. J. Cell. Biochem. 99: 1476–1488, 2006. © 2006 Wiley‐Liss, Inc.
Large‐scale plant protein subcellular location prediction
Authors: Chou Kuo‐Chen , Shen Hong‐Bin 
Published: September 2006

AbstractCurrent plant genome sequencing projects have called for development of novel and powerful high throughput tools for timely annotating the subcellular location of uncharacterized plant proteins. In view of this, an ensemble classifier, Plant‐PLoc, formed by fusing many basic individual classifiers, has been developed for large‐scale subcellular location prediction for plant proteins. Each of the basic classifiers was engineered by the K‐Nearest Neighbor (KNN) rule. Plant‐PLoc discriminates plant proteins among the following 11 subcellular locations: (1) cell wall, (2) chloroplast, (3) cytoplasm, (4) endoplasmic reticulum, (5) extracell, (6) mitochondrion, (7) nucleus, (8) peroxisome, (9) plasma membrane, (10) plastid, and (11) vacuole. As a demonstration, predictions were performed on a stringent benchmark dataset in which none of the proteins included has ≥25% sequence identity to any other in a same subcellular location to avoid the homology bias. The overall success rate thus obtained was 32–51% higher than the rates obtained by the previous methods on the same benchmark dataset. The essence of Plant‐PLoc in enhancing the prediction quality and its significance in biological applications are discussed. Plant‐PLoc is accessible to public as a free web‐server at http://202.120.37.186/bioinf/plant. Furthermore, for public convenience, results predicted by Plant‐PLoc have been provided in a downloadable file at the same website for all plant protein entries in the Swiss‐Prot database that do not have subcellular location annotations, or are annotated as being uncertain. The large‐scale results will be updated twice a year to include new entries of plant proteins and reflect the continuous development of Plant‐PLoc. J. Cell. Biochem. 100: 665–678, 2007. © 2006 Wiley‐Liss, Inc.
Numerical characterization of DNA sequences based on the k‐step Markov chain transition probability
Authors: Dai Qi , Liu Xiao‐Qing , Wang Tian‐Ming 
Published: September 2006

AbstractA DNA sequence can be regarded as a discrete‐time Markov chain. Based on k‐step transition probabilities, we construct a series of 4 × 4 k‐step transition matrices to characterize the DNA primary sequences. According to the properties of Markov chains, we obtain distributions of A, T, C and G, and analyze the changes among them from yesterday to tomorrow. We can calculate the probabilities of nucleotide triples of DNA primary sequences. Finally, we introduce a correlation of this kind of transition matrices and consider it as an invariant to analyze the similarities/dissimilarities of DNA sequences. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006
Transition metal–boron complexes BnM: From bowls (n = 8–14) to tires (n = 14)
Authors: Li Si‐Dian , Miao Chang‐Qing , Guo Jin‐Chang , Ren Guang‐Ming 
Published: September 2006

AbstractTransition metal–boron complexes BnM have been predicted at density functional theory level to be molecular bowls (n = 8–14) hosting a transition metal atom (M) inside or molecular tires (n = 14) centered with a transition metal atom. Small Bn clusters prove to be effective inorganic ligands to all the VB–VIIIB transition metal elements in the periodic table. Density functional evidences obtained in this work strongly suggest that bowl‐shaped fullerene analogues of Bn units exist in small BnM complexes and the bowl‐to‐tire structural transition occur to the first‐row transition metal complexes BnM (M = Mn, Fe, Co) at n = 14, a size obviously smaller than n = 20 where the 2D‐3D structural transition occurs to bare Bn. The half‐sandwich‐type B12Cr (C3v), full sandwich‐type (B12)2Cr (D3d), bowl‐shaped B14Fe (C2), and tire‐shaped B14Fe (D7d) and B14Fe− (C7v) are the most interesting prototypes to be targeted in future experiments. These BnM complexes may serve as building blocks to form extended boron‐rich BnMm tubes or cages (m ≥ 2) or as structural units to be placed inside carbon nanotubes with suitable diameters. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006
An iterative knowledge‐based scoring function to predict protein–ligand interactions: I. Derivation of interaction potentials
Authors: Huang Sheng‐You , Zou Xiaoqin 
Published: September 2006

AbstractUsing a novel iterative method, we have developed a knowledge‐based scoring function (ITScore) to predict protein–ligand interactions. The pair potentials for ITScore were derived from a training set of 786 protein–ligand complex structures in the Protein Data Bank. Twenty‐six atom types were used based on the atom type category of the SYBYL software. The iterative method circumvents the long‐standing reference state problem in the derivation of knowledge‐based scoring functions. The basic idea is to improve pair potentials by iteration until they correctly discriminate experimentally determined binding modes from decoy ligand poses for the ligand‐protein complexes in the training set. The iterative method is efficient and normally converges within 20 iterative steps. The scoring function based on the derived potentials was tested on a diverse set of 140 protein–ligand complexes for affinity prediction, yielding a high correlation coefficient of 0.74. Because ITScore uses SYBYL‐defined atom types, this scoring function is easy to use for molecular files prepared by SYBYL or converted by software such as BABEL. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006
Importance of individual side chains for the stability of a protein fold: Computational alanine scanning of the insulin monomer
Authors: Zoete Vincent , Meuwly Markus 
Published: September 2006

AbstractA new computational approach is proposed to probe the importance of residue side chains for the stability of a protein fold. Computational mutations to estimate protein stability (CMEPS) is based on the notion that the binding free energy corresponding to the complexation of a given side chain, considered as a “pseudo‐ligand” of the wild type protein, reflects the importance of this side chain to the thermodynamic stability of the protein. The contribution of a particular side chain to the folding energy is estimated according to the molecular mechanics‐generalized born surface area MM‐GBSA approach, using a single molecular dynamics simulation trajectory of the wild type protein. CMEPS is a first principles method which does not contain any adjustable parameter that could be fitted to experimental data. The approach is first validated for Barnase and the B1 domain of protein L, for which a correlation coefficient R = 0.73, between experimental and CMEPS calculated ΔΔG values, is found and then applied to the insulin monomer. In the present application, CMEPS replaces each amino acid by an alanine residue. Therefore, most mutations lead to cavities in the protein. From this the change in stability can be correlated with increased cavity volume. For insulin, this correlation is very similar compared with data previously analyzed for T4 lysozyme from an experiment for buried apolar side chains. There, the increased cavity volume has been related to the hydrophobic effect. However, since CMEPS uses the energetics in terms of electrostatic and van der Waals interactions (and not the hydrophobic effect which is difficult to relate to physical interactions), it is possible to study the effect of mutations of polar and solvent accessible side chains. According to CMEPS, residues Leu A16, Tyr A19, Leu B11, Leu B15, and Arg B22 are most important for the stability of the monomeric insulin fold. This is in agreement with experimental data. As a consequence, mutation of these residues may lead to misfolded and inactive insulin analogues. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006
On the mechanism of ion formation from the aqueous solutions irradiated with 3 µm IR laser pulses under atmospheric pressure
Authors: Laiko Victor V. , Taranenko Nelli I. , Doroshenko Vladimir M. 
Published: September 2006

AbstractThe mechanism of atmospheric pressure (AP) laser ionization of water and water/glycerol liquid samples at a 3‐µm wavelength is studied experimentally. For the ion desorption, an in‐house built Yb : YAG‐pumped optical parametric oscillator (OPO) infrared (IR) laser has been coupled with AP MALDI ion source interfaced to an ion trap mass spectrometer (MS). It has been shown that water is primarily responsible for ion generation in water/glycerol samples, while glycerol increases the solution viscosity and decreases the water evaporation rate and sample losses. In contrast to AP UV‐MALDI, the electric field in the case of AP IR‐MALDI does not assist in ion production. It was found that the absence of the electrical field provides the optimum ionization condition both for water and water/glycerol liquid samples at the 3‐µm laser irradiation. A two‐stage ion formation mechanism, which includes the initial emission of microdroplets and release of molecular ions at the second stage, can explain the experimentally observed ion signal dependencies upon the voltage applied between MS inlet and the MALDI sample plate. Postionization using additional corona discharge APCI increases the observed signal by approximately 50%, which indicates that some portion of the analyte is desorbed in the form of neutral molecules. Copyright © 2006 John Wiley & Sons, Ltd.
Neuroprotective effect of N‐acetylcysteine on neuronal apoptosis induced by a synthetic gingerdione compound: Involvement of ERK and p38 phosphorylation
Authors: Lin Chia‐Ho , Kuo Sheng‐Chu , Huang Li‐Jiau , Gean Po‐Wu 
Published: September 2006

AbstractBesides being used as a spice, ginger has been applied in oriental medicine to ameliorate symptoms such as inflammatory, rheumatic disorders, and gastrointestinal discomforts. The effects of ginger on neuronal cells, however, have not been explored. We investigate the effect of 1‐(3,4‐dimethoxyphenyl)‐3,5‐dodecenedione (I6), a derivative of gingerdione, on cultured cortical neurons. After a 5‐day maturation period in vitro, cortical neurons were treated with I6 for 24 hr and cell viability was assessed using MTT assay. I6 induced neuronal death in a concentration‐dependent manner. Hoechst 33342, propidium iodide (PI), and TUNEL staining confirmed that the reduced cell viability by I6 was due to apoptosis. Pre‐treatment of cell with N‐acetylcysteine (NAC) prevented cell death in a concentration‐dependent manner. N‐acetylcysteine increased phosphorylated levels of p42 and p44 extracellular signal‐regulated kinases (ERKs). In parallel, farnesyltransferase and MEK inhibitors blocked ERK phosphorylation and neuroprotective effect of NAC. Unexpectedly, NAC also increased phosphorylated level of p38 mitogen‐activated protein kinase (MAPK) and p38 specific inhibitors dose‐dependently attenuated the effect of NAC. Farnesyltransferase and MEK inhibitors completely abolished NAC‐induced p38 phosphorylation whereas p38 inhibitor did not influence NAC‐induced ERK phosphorylation. These results show that NAC serially activates ERKs and p38 MAPK, and ERKs and p38 work together to mediate the neuroprotective effect of NAC. © 2006 Wiley‐Liss, Inc.
Inhibition of EphA7 up‐regulation after spinal cord injury reduces apoptosis and promotes locomotor recovery
Authors: Figueroa Johnny D. , Benton Richard L. , Velazquez Ixane , Torrado Aranza I. , Ortiz Cristina M. , Hernandez Carmen M. , Diaz Juan J. , Magnuson David S. , Whittemore Scott R. , Miranda Jorge D. 
Published: September 2006

AbstractFunctional impairment after spinal cord injury (SCI) is partially attributed to neuronal cell death, with further degeneration caused by the accompanying apoptosis of myelin‐forming oligodendrocytes. The Eph receptor protein tyrosine kinase family and its cognate ligands, the ephrins, have been identified to be involved in axonal outgrowth, synapse formation, and target recognition, mainly mediated by repulsive activity. Recent reports suggest that ephrin/Eph signaling might also play a role as a physiological trigger for apoptosis during embryonic development. Here, we investigated the expression profile of EphA7, after SCI, by using a combination of quantitative real‐time PCR (QRT‐PCR) and immunohistochemical techniques. QRT‐PCR analysis showed an increase in the expression of full‐length EphA7 at 7 days postinjury (DPI). Receptor immunoreactivity was shown mostly in astrocytes of the white matter at the injury epicenter. In control animals, EphA7 expression was observed predominantly in motor neurons of the ventral gray matter, although some immunoreactivity was seen in white matter. Furthermore, blocking the expression of EphA7 after SCI using antisense oligonucleotides resulted in significant acceleration of hindlimb locomotor recovery at 1 week. This was a transient effect; by 2 weeks postinjury, treated animals were not different from controls. Antisense treatment also produced a return of nerve conduction, with shorter latencies than in control treated animals after transcranial magnetic stimulation. We identified EphA7 receptors as putative regulators of apoptosis in the acute phase after SCI. These results suggest a functional role for EphA7 receptors in the early stages of SCI pathophysiology. © 2006 Wiley‐Liss, Inc.
pH is an intracellular effector controlling differentiation of oligodendrocyte precursors in culture via activation of the ERK1/2 pathway
Authors: Bernard Frédéric , Vanhoutte Peter , Bennasroune Amar , Labourdette Gérard , Perraut Martine , Aunis Dominique , Gaillard Stéphane 
Published: September 2006

AbstractWe reported previously that onset of oligodendrocyte precursor cell (OPC) differentiation is accompanied by an increase in intracellular pH (pHi). We show that OPC differentiation is dependent primarily on a permissive pHi value. The highest differentiation levels were observed for pHi values around 7.15 and inhibition of differentiation was observed at slightly more acidic or alkaline values. Clamping the pHi of OPCs at 7.15 caused a transient activation of ERK1/2 that was not observed at more acidic or alkaline values. Furthermore, inhibition of ERK activation with the UO126 compound totally prevented OPC differentiation in response to pHi shift. These results indicate that pHi, acting through the ERK1/2 pathway, is a key determinant for oligodendrocyte differentiation. We also show that this pHi pathway is involved in the process of retinoic acid‐induced OPC differentiation. © 2006 Wiley‐Liss, Inc.
Morphine upregulates functional expression of neurokinin‐1 receptor in neurons
Authors: Wan Qi , Douglas Steven D. , Wang Xu , Kolson Dennis L. , O'Donnell Lauren A. , Ho Wen‐Zhe 
Published: September 2006

AbstractNeuronkinin‐1 receptor (NK‐1R), the neuropeptide substance P (SP) preferring receptor, is highly expressed in areas of the central nervous system (CNS) that are especially implicated in depression, anxiety, and stress. Repeated exposure to opioids may sensitize neuronal systems involved in stress response. We examined the effects of morphine, the principal metabolite of heroin, on the functional expression of NK‐1R in the cortical neurons. NK‐1R and mu‐opioid receptor (MOR) are co‐expressed in the cortical neurons. Morphine enhanced NK‐1R expression in the cortical neurons at both the mRNA and protein levels. The upregulated NK‐1R by morphine had functional activity, because morphine‐treated cortical neurons had greater SP‐induced Ca2+ mobilization than untreated neurons. Blocking opioid receptors on the cortical neurons by naltrexone or CTAP (a μ‐opioid receptor antagonist) abolished the morphine action. Investigation of the mechanism(s) responsible for the morphine action showed that morphine activated NK‐1R promoter and induced the phosphorylation of p38 MAPK protein in the cortical neurons. These in vitro data provide a plausible cellular mechanism for opioid‐mediated neurological disorders. © 2006 Wiley‐Liss, Inc.
Termination Kinetics of tert‐Butyl Methacrylate and of n‐Butyl Methacrylate Free‐Radical Bulk Homopolymerizations
Authors: Buback Michael , Junkers Tanja 
Published: September 2006

AbstractSummary: Termination kinetics in tert‐butyl methacrylate (tert‐BMA) and n‐butyl methacrylate (n‐BMA) bulk homopolymerizations has been studied via the single pulse‐pulsed laser polymerization‐near infrared (SP‐PLP‐NIR) method between 40 and 80 °C at pressures from 500 to 2 250 bar. Toward increasing monomer conversion, the chain‐length averaged termination rate coefficient, 〈kt〉, for both monomers exhibits the methacrylate‐specific sequence of an initial plateau region, assigned to control by segmental diffusion, followed by a steep decrease of 〈kt〉 at intermediate conversion, which is assigned to translational diffusion control, and a weaker decrease of 〈kt〉, associated with reaction‐diffusion control, at still higher degrees of monomer conversion. Despite this similarity, the two isomeric monomers clearly differ in absolute size of 〈kt〉 and in the monomer concentration ranges where the transitions between the different types of diffusion control occur. The differences are assigned to effects of chain mobility which is hindered to a larger extent in tert‐BMA than in n‐BMA. As a consequence, the 〈kt〉 behavior of tert‐BMA at 80 °C is close to the one of n‐BMA at 40 °C. Investigations into the chain‐length dependence of kt, in particular into kt(i,i), the rate coefficient for termination of two radicals of identical size, support the evidence on the different types of diffusion control that operate as a function of monomer conversion. In the initial conversion range, the power‐law exponent which characterizes the chain‐length dependence of larger (entangled) radicals, is found for both monomers to be close to the theoretical value of α = 0.16.Dependence of log(〈kt〉/kp) on monomer conversion, X, for n‐BMA and tert‐BMA bulk homopolymerizations at 2 000 bar and 70 °C. Circles and triangles represent independent data sets obtained from separate experiments.magnified imageDependence of log(〈kt〉/kp) on monomer conversion, X, for n‐BMA and tert‐BMA bulk homopolymerizations at 2 000 bar and 70 °C. Circles and triangles represent independent data sets obtained from separate experiments.