bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of fluoxetine and norfluoxetine in rat plasma by HPLC with pre‐column derivatization and fluorescence detection
Authors: Guo Xingjie , Fukushima Takeshi , Li Famei , Imai Kazuhiro 
Published: February 2003

AbstractBoth fluoxetine (FLX) and its N‐demethylated metabolite, norfluoxetine (NFLX), have been reported to be potent serotonin‐reuptake inhibitors. A sensitive and reliable method that allows simultaneous quantification of their plasma levels would be valuable and was developed in this work. The procedure included extraction of FLX and NFLX from plasma, fluorescence derivatization with 4‐(N‐chloroformylmethyl‐N‐methyl) amino‐7‐nitro‐2,1,3‐benzoxadiazole (NBD‐COCl), separation of the derivatives on an octadecylsilica column with acetonitrile–water (55:45,v/v) as mobile phase and fluorescence detection with emission at 537 nm and excitation at 478 nm. The calibration curves were linear for FLX and NFLX concentration over the range of 10–1000 nM (r = 0.9992 and r = 0.9997) and the limits of quantitation were 10 nM in 100 µL of plasma. Precision of intra‐ and inter‐day RSD of less than 12% and accuracy of intra‐ and inter‐day RE within −6.0–13% were achieved. The method described was applied to analysis of the plasma samples from rats treated with FLX hydrochloride and to the pharmacokinetic study. Copyright © 2002 John Wiley & Sons, Ltd.
Re‐Based Heterogeneous Catalysts for Olefin Metathesis Prepared by Surface Organometallic Chemistry: Reactivity and Selectivity
Authors: Chabanas Mathieu , Copéret Christophe , Basset Jean‐Marie 
Published: February 2003

AbstractHerein we describe the catalytic activity of 1, a well‐defined Re alkylidene complex supported silica, in the reaction of olefin metathesis. This system is highly active for terminal and internal olefins with initial rates up to 0.7 mol per mol Re per s. It also catalyses the self‐metathesis of methyl oleate (MO) without the need of co‐catalysts. The turnover numbers can reach up to 900 for MO, which is unprecedented for a heterogeneous Re‐based catalyst. Moreover the use of silica as a support can bring major advantages, such as the possibility to use branched olefins like isobutene, which are usually incompatible with alumina‐based supports; therefore, the formation of isoamylene from the cross‐metathesis of propene and isobutene can be performed. All these results are in sharp contrast to what has been found for other silica‐ or alumina‐supported rhenium oxide systems, which are either completely inactive (silica system) or typically need co‐catalysts when functionalised olefins are used. Finally the initiation step corresponds to a cross‐metathesis reaction to give a 3:1 mixture of 3,3‐dimethylbutene and trans‐4,4‐dimethylpent‐2‐ene, and make this catalyst the first generation of well‐defined Re‐based heterogeneous catalysts.
Metal Nanowire Arrays by Electrodeposition
Authors: Walter Erich C. , Zach Michael P. , Favier Frédéric , Murray Benjamin J. , Inazu Koji , Hemminger John C. , Penner Reginald M. 
Published: February 2003

AbstractWe describe two related methods for preparing arrays of nanowires composed of molybdenum, copper, nickel, gold, and palladium. Nanowires were obtained by selectively electrodepositing either a metal oxide or a metal at the step edges present on the basal plane of highly oriented pyrolytic graphite (HOPG) electrodes. If a metal oxide was electrodeposited, then nanowires of the parent metal were obtained by reduction at elevated temperature in hydrogen. The resulting nanowires were organized in parallel arrays of 100–1000 wires. These nanowires were long (some >500 μm), polycrystalline, and approximately hemicylindrical in cross‐section. The nanowire arrays prepared by electrodeposition were also “portable”: After embedding the nanowires in a polymer or cyanoacrylate film, arrays of nanowires could be lifted off the graphite surface thereby facilitating the incorporation of metal nanowire arrays into devices such as sensors.
Dynamics of Full Fusion During Vesicular Exocytotic Events: Release of Adrenaline by Chromaffin Cells
Authors: Amatore Christian , Arbault Stéphane , Bonifas Imelda , Bouret Yann , Erard Marie , Guille Manon 
Published: February 2003

AbstractVesicular exocytosis is important in the communication between cells in complex organisms. It controls the release of specific chemical or biochemical messengers stored in the emitting cell, which elicit a response upon detection by the target cells. Secretion of a messenger molecule (a neurotransmitter) was measured electrochemically, which allowed the quantification of cellular events and the validation of current physicochemical models. This model led us to formulate predictions about the occurrence and kinetics of vesicular exocytotic events based on the physicochemical meaning of its key parameters. These predictions were tested successfully through a series of experiments on chromaffin cells, involving changes of osmotic conditions, presence of trivalent ions and cholesterol‐induced structuring of the cell plasmic membrane.
Regular Irregularity in the Transfer of Anionic Surfactant across the Liquid/Liquid Interface
Authors: Kakiuchi Takashi , Nishi Naoya , Kasahara Takuya , Chiba Minako 
Published: February 2003

AbstractIrregular current spikes and other anomalies seen in voltammetry of the transfer of anionic surfactants, alkyl sulfonates, and alkyl sulfates across the 1,2‐dichloroethane/water (DCE/W) interface are reproducible. The anomalies have a certain regularity that is predicted by a recently proposed concept, the electrochemical instability. Irregular current spikes follow after the augmentation of the current induced when the phase‐boundary potential is brought close to the mid‐point potential of the transferring surfactant ions. Potential‐step chronoamperometry clearly demonstrates the presence of the instability window, that is, the potential region where the interface becomes unstable only in the limited range of the phase‐boundary potential.
An Olefin Metathesis/Double Bond Isomerization Sequence Catalyzed by an In Situ Generated Ruthenium Hydride Species
Authors: Schmidt Bernd 
Published: February 2003

AbstractThe direct conversion of allyl ethers to cyclic enol ethers using an olefin metathesis/double bond migration sequence is described. Ruthenium carbene complexes were activated to catalyze the double bond migration step by addition of hydride sources, such as NaH or NaBH4. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)
Imprinted Polymer – Modified Hanging Mercury Drop Electrode for Differential Pulse Adsorptive Stripping Voltammetric Analysis of a Diquat Herbicide
Authors: Prasad Bhim Bali , Arora Bhavana 
Published: February 2003

AbstractAn imprinted polymer modified hanging mercury drop electrode (HMDE) in Model 303A system in conjunction with a PAR Model 264A Polarographic Analyzer/Stripping Voltammeter has been used for the selective analysis of a diquat herbicide viz., 5,6‐dihydropyrazino[1,2,3,4‐[lmn]‐1,10‐phenanthrolinium dichlorides in differential pulse cathodic stripping voltammetry mode. Complex aqueous samples (drinking water and agricultural soil suspension), spiked with a diquat herbicide, were directly analyzed by the adsorptive accumulation of the analyte over the working electrode (accumulation potential −0.8 V (vs. Ag/AgCl), accumulation time 120 s, pH 7.0, supporting electrolyte 0.1 M KCl, scan rate 10 mV s−1, pulse amplitude 25 mV). The limit of detection for diquat herbicide was found to be 0.34 nmol L−1 (0.1 ppb, RSD 2%, S/N=2).
Voltammetric Behavior of MoS$\rm{ {_{4}^{2-}}}$ and SbS$\rm{ {_{4}^{3-}}}$ as Possible Components of “Dissolved Sulfide” in Oxic Natural Waters
Authors: Ciglenečki Irena , Helz George R. 
Published: February 2003

AbstractNanomolar concentrations of dissolved sulfide have been observed in O2‐ bearing natural waters. The sulfide consists of oxidation‐resistant, unknown chemical components that might include metal‐sulfide complexes, elemental sulfur in various forms or organic sulfur compounds. Here we show that thioanions are also plausible components. Tetrathiomolybdate and tetrathioantimonate ions deposit respectively 3 and 4 equivalents of HgS at mercury electrodes. In cathodic stripping voltammetry, a common method to quantify nanomolar sulfide in nature, MoS$\rm{ {_{4}^{2-}}}$ and SbS$\rm{ {_{4}^{3-}}}$ would therefore contribute to “total dissolved sulfide.” Limited evidence suggests that thioanions may be powerful complexing agents that would be capable of affecting trace metal speciation and bioavailability in natural waters.
Modelling nonlinear dynamics of shape‐memory‐alloys with approximate models of coupled thermoelasticity
Authors: Melnik R.V.N. , Roberts A.J. 
Published: February 2003

AbstractWe present a general methodology for constructing approximate models describing shape memory alloys dynamics. We base our discussion on a general three‐dimensional model and the Falk‐Konopka representation for the free energy function. By considering a one‐dimensional counterpart of that model, we show that with little computational efforts we can reproduce successfully phase transition phenomena with our numerical scheme. The same scheme is applied in our code for the general case. Then, we describe a systematic approach to modelling SMA materials, and demonstrate that approach in deriving a centre‐manifold‐based low‐dimensional model from the general three‐dimensional model, preserving all main features of the dynamics. Computer algebra technique allows us to derive such models efficiently and with arbitrary degree of accuracy.
Discovering well-ordered folding patterns in nucleotide sequences
Authors: Le Shu-Yun , Chen Jih-H. , Konings Danielle , Maizel Jacob V. 
Published: February 2003

Abstract
Motivation: Growing evidence demonstrates that local well-ordered structures are closely correlated with cis-acting elements in the post-transcriptional regulation of gene expression. The prediction of a well-ordered folding sequence (WFS) in genomic sequences is very helpful in the determination of local RNA elements with structure-dependent functions in mRNAs.
Results: In this study, the quality of local WFS is assessed by the energy difference (Ediff) between the free energies of the global minimal structure folded in the segment and its corresponding optimal restrained structure (ORS). The ORS is an optimal structure under the condition in which none of the base-pairs in the global minimal structure is allowed to form. Those WFSs in HIV-1 mRNA, various ferritin mRNAs and genomic sequences containing let-7 RNA gene were searched by a novel method, ed_scan. Our results indicate that the detected WFSs are coincident with known Rev response element in HIV-1 mRNA, iron-responsive elements in ferritin mRNAs and small let-7 RNAs in Caenorhabditis elegans, Caenorhabditis briggsae and Drosophila melanogaster genomic sequences. Statistical significance of the WFS is addressed by a quantitative measure Zscre that is a z-score of Ediff and extensive random simulations. We suggest that WFSs with high statistical significance have structural roles involving their sequence information.
Availability: The source code of ed_scan is available via anonymous ftp as ftp://ftp.ncifcrf.gov/pub/users/shuyun/scan/ed_scan.tar.
Contact: shuyun@orleans.ncifcrf.gov
* To whom correspondence should be addressed.
FORRepeats: detects repeats on entire chromosomes and between genomes
Authors: Lefebvre A. , Lecroq T. , Dauchel H. , Alexandre J. 
Published: February 2003

Abstract
Motivation: As more and more whole genomes are available, there is a need for new methods to compare large sequences and transfer biological knowledge from annotated genomes to related new ones. BLAST is not suitable to compare multimegabase DNA sequences. MegaBLAST is designed to compare closely related large sequences. Some tools to detect repeats in large sequences have already been developed such as MUMmer or REPuter. They also have time or space restrictions. Moreover, in terms of applications, REPuter only computes repeats and MUMmer works better with related genomes.
Results: We present a heuristic method, named FORRepeats, which is based on a novel data structure called factor oracle. In the first step it detects exact repeats in large sequences. Then, in the second step, it computes approximate repeats and performs pairwise comparison. We compared its computational characteristics with BLAST and REPuter. Results demonstrate that it is fast and space economical. We show FORRepeats ability to perform intra-genomic comparison and to detect repeated DNA sequences in the complete genome of the model plant Arabidopsis thaliana.
Availability: see contact
Contact: arnaud.lefebvre@univ-rouen.fr
* To whom correspondence should be addressed.
‘Hybrid Protein Model’ for optimally defining 3D protein structure fragments
Authors: de Brevern A.G. , Hazout S. 
Published: February 2003

Abstract
Motivation: Our aim is to develop a process that automatically defines a repertory of contiguous 3D protein structure fragments and can be used in homology modeling. We present here improvements to the method we introduced previously: the ‘hybrid protein model’ (de Brevern and Hazout, Theor. Chem. Acc., 106, 36–47, (2001)) The hybrid protein learns a non-redundant databank encoded in a structural alphabet composed of 16 Protein Blocks (PBs; de Brevern et al., Proteins, 41, 271–287, (2000)). Every local fold is learned by looking for the most similar pattern present in the hybrid protein and modifying it slightly. Finally each position corresponds to a cluster of similar 3D local folds.
Results: In this paper, we describe improvements to our method for building an optimal hybrid protein: (i) ‘baby training,’ which is defined as the introduction of large structure fragments and the progressive reduction in the size of training fragments; and (ii) the deletion of the redundant parts of the hybrid protein. This repertory of contiguous 3D protein structure fragments should be a useful tool for molecular modeling
Contact: debrevern@urbb.jussieu.fr
* To whom correspondence should be addressed.
SimiTri—visualizing similarity relationships for groups of
sequences
Authors: Parkinson John , Blaxter Mark 
Published: February 2003

Abstract
Global sequence comparisons between large datasets, such as those arising from genome projects, can be problematic to display and analyze. We have developed SimiTri, a Java/Perl-based application, which allows simultaneous display and analysis of relative similarity relationships of the dataset of interest to three different databases. We illustrate its utility in identifying Caenorhabditis elegans genes that have distinct patterns of phylogenetic affinity suggestive of horizontal gene transfer. SimiTri is freely downloadable from http://www.nematodes.org/SimiTri/ and the source code is freely available from the authors.
Contact: john.parkinson@ed.ac.uk
* To whom correspondence should be addressed.
KnowledgeEditor: a new tool for interactive modeling and analyzing
biological pathways based on microarray data
Authors: Toyoda Tetsuro , Konagaya Akihiko 
Published: February 2003

Abstract
Summary: KnowledgeEditor is a graphical workbench for biological experts to model biomolecular network graphs. The modeled network data are represented by SRML, and can be published via the internet with the help of plug-in module ‘GSCope’. KnowledgeEditor helps us to model and analyze biological pathways based on microarray data. It is possible to analyze the drawn networks by simulating up–down regulatory cascade in molecular interactions.
Availability: KnowledgeEditor is available at http://gscope.gsc.riken.go.jp/
Contact: bioinfo@gsc.riken.go.jp
* To whom correspondence should be addressed.
PCMA: fast and accurate multiple sequence alignment based on profile consistency
Authors: Pei Jimin , Sadreyev Ruslan , Grishin Nick V. 
Published: February 2003

Abstract
Summary: PCMA (profile consistency multiple sequence alignment) is a progressive multiple sequence alignment program that combines two different alignment strategies. Highly similar sequences are aligned in a fast way as in ClustalW, forming pre-aligned groups. The T-Coffee strategy is applied to align the relatively divergent groups based on profile–profile comparison and consistency. The scoring function for local alignments of pre-aligned groups is based on a novel profile–profile comparison method that is a generalization of the PSI-BLAST approach to profile–sequence comparison. PCMA balances speed and accuracy in a flexible way and is suitable for aligning large numbers of sequences.
Availability: PCMA is freely available for non-commercial use. Pre-compiled versions for several platforms can be downloaded from ftp://iole.swmed.edu/pub/PCMA/
Contact: jpei@mednet.swmed.edugrishin@chop.swmed.edu
* To whom correspondence should be addressed.
cMap: the comparative genetic map viewer
Authors: Fang Z. , Polacco M. , Chen S. , Schroeder S. , Hancock D. , Sanchez H. , Coe E. 
Published: February 2003

Abstract
Summary: cMap, a www comparative genetic map graphical utility, has a search capability and provides comparison of two genetic maps within or between species with dynamic links to data resources and text lists of the shared loci, running in a relational database environment. Currently, maps from three species (maize ‘Zea mays L.’, rice‘ Oryza sativa L.’, and sorghum ‘Sorghum bicolor L.’), representing over 13 800 distinct loci, are available for comparison at http://www.agron.missouri.edu/cMapDB/cMap.html
Availability: cMap source code is available without cost on request for non-commercial use.
Contact: fangz@missouri.edu
* To whom correspondence should be addressed.
† Current address: Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611, USA
Human Papillomavirus Type 31 E5 Protein Supports Cell Cycle Progression and Activates Late Viral Functions upon Epithelial Differentiation
Authors: Fehrmann Frauke , Klumpp David J. , Laimins Laimonis A. 
Published: February 2003

ABSTRACT
The function of the E5 protein of human papillomaviruses (HPV) is not well characterized, and controversies exist about its role in the viral life cycle. To determine the function of E5 within the life cycle of HPV type 31 (HPV31) we first constructed HPV31 mutant genomes that contained an altered AUG initiation codon or stop codons in E5. Cell lines were established which harbored transfected wild-type or E5 mutant HPV31 genomes. These cell lines all maintained episomal copies of HPV31 and revealed similar phenotypes with respect to growth rate, early gene expression, and viral copy number in undifferentiated monolayer cultures. Following epithelial differentiation, genome amplification and differentiation-dependent late gene expression were observed in mutant cell lines, but at a rate significantly reduced from that observed in cells containing the wild-type genomes. Organotypic raft cultures indicated that E5 does not effect the expression of differentiation markers but does reduce expression of late viral proteins. Western analysis and immunofluorescence staining for cyclins during epithelial differentiation revealed a decreased expression of cyclin A and B in E5 mutant cells compared to HPV wild-type cells. Using a replating assay, a significant reduction in colony-forming ability was detected in the absence of E5 expression when cells containing wild-type or E5 mutant HPV genomes were allowed to proliferate following 24 h in suspension-induced differentiation. This suggests that HPV E5 modifies the differentiation-induced cell cycle exit and supports the ability of HPV31-positive keratinocytes to retain proliferative competence. In these studies, E5 was found to have little effect on the levels of the epidermal growth factor receptor (EGFR) or on its phosphorylation status. This indicates that EGFR is not a target of E5 action. Our results propose a role for high risk HPV E5 in modulation of late viral functions through activation of proliferative capacity in differentiated cells. We suspect that the primary target of E5 is a membrane protein or receptor that then acts to alter the levels or activities of cell cycle regulators.
Neutralization of Human Immunodeficiency Virus Type 1 by sCD4-17b, a Single-Chain Chimeric Protein, Based on Sequential Interaction of gp120 with CD4 and Coreceptor
Authors: Dey Barna , Del Castillo Christie S. , Berger Edward A. 
Published: February 2003

ABSTRACT
We designed a novel single-chain chimeric protein, designated sCD4-17b, for neutralization of human immunodeficiency virus type 1 (HIV-1). The recombinant protein contains domains 1 and 2 of soluble CD4 (sCD4), connected via a flexible polypeptide linker to a single-chain variable region construct of 17b, a human monoclonal antibody that targets a conserved CD4-induced epitope on gp120 overlapping the coreceptor binding region. We hypothesized that the sCD4 moiety would bind gp120 and expose the 17b epitope; the 17b moiety would then bind, thereby blocking coreceptor interaction and neutralizing infection. The sCD4-17b protein, expressed by a recombinant vaccinia virus, potently neutralized a prototypic R5 clade B primary isolate, with a 50% inhibitory concentration of 3.2 nM (0.16 μg/ml) and >95% neutralization at 32 nM (1.6 μg/ml). The individual components (sCD4 and 17b, singly or in combination) had minimal effects at these concentrations, demonstrating that the activity of sCD4-17b reflected the ability of a single chimeric molecule to bind gp120 simultaneously via two independent moieties. sCD4-17b was highly potent compared to the previously characterized broadly cross-reactive neutralizing monoclonal antibodies IgGb12, 2G12, and 2F5. Multiple primary isolates were neutralized, including two previously described as antibody resistant. Neutralization occurred for both R5 and X4 strains and was not restricted to clade B. However, several primary isolates were insensitive over the concentration range tested, despite the known presence of binding sites for both CD4 and 17b. sCD4-17b has potential utility for passive immunization against HIV-1 in several contexts, including maternal transmission, postexposure prophylaxis, and sexual transmission (topical microbicide).
Mutation of Host
dnaJ
Homolog Inhibits Brome Mosaic Virus Negative-Strand RNA Synthesis
Authors: Tomita Yuriko , Mizuno Tomomitsu , Díez Juana , Naito Satoshi , Ahlquist Paul , Ishikawa Masayuki 
Published: February 2003

ABSTRACT

The replication of positive-strand RNA viruses involves not only viral proteins but also multiple cellular proteins and intracellular membranes. In both plant cells and the yeast
Saccharomyces cerevisiae
, brome mosaic virus (BMV), a member of the alphavirus-like superfamily, replicates its RNA in endoplasmic reticulum (ER)-associated complexes containing viral 1a and 2a proteins. Prior to negative-strand RNA synthesis, 1a localizes to ER membranes and recruits both positive-strand BMV RNA templates and the polymerase-like 2a protein to ER membranes. Here, we show that BMV RNA replication in
S. cerevisiae
is markedly inhibited by a mutation in the host
YDJ1
gene, which encodes a chaperone Ydj1p related to
Escherichia coli
DnaJ. In the
ydj1
mutant, negative-strand RNA accumulation was inhibited even though 1a protein associated with membranes and the positive-strand RNA3 replication template and 2a protein were recruited to membranes as in wild-type cells. In addition, we found that in
ydj1
mutant cells but not wild-type cells, a fraction of 2a protein accumulated in a membrane-free but insoluble, rapidly sedimenting form. These and other results show that Ydj1p is involved in forming BMV replication complexes active in negative-strand RNA synthesis and suggest that a chaperone system involving Ydj1p participates in 2a protein folding or assembly into the active replication complex.