bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unusual cerium(III) chloride‐promoted reactions of alkenyl grignard reagents or alkenyl‐lithiums with 1,3‐diphenyl‐2‐propanone: Formation and trapping of diorganometallic species
Authors: Imamoto Tsuneo , Hatajima Toshihiko , Ogata Koreharu , Nishiura Masayoshi 
Published: January 2005

AbstractTreatment of vinylmagnesium chloride with anhydrous cerium(III) chloride in tetrahydrofuran at −20°C, followed by reaction with 1,3‐diphenyl‐2‐propanone, afforded (Z)‐2,7‐dibenzyl 1,8‐diphenyl‐4‐octene‐2,7‐diol and (Z)‐2,7‐dibenzyl‐1,8‐diphenyl‐4,6‐octadien‐2‐ol in 19% and 9% yield, respectively. Isopropenyl‐magnesium bromide underwent trimerization on treatment with cerium chloride at 20°C, and the subsequent reaction with the same ketone provided (Z,Z)‐2,9‐dibenzyl‐4,5,7‐trimethyl‐1,10‐diphenyl‐4,6‐decadiene‐2, 9‐diol in 22% yield. Under similar conditions, the reaction of 2‐methyl‐1‐propenylmagnesium bromide provided (Z)‐2,6‐dibenzyl‐4‐methyl‐1,7‐diphenyl‐3,5‐heptadien‐2‐ol in 7% yield. Vinyl‐lithium and isopropenyl‐lithium were also subjected to dimerization by the action of cerium chloride, and the generated diorganometallic species were trapped by 1,3‐diphenyl‐2‐propanone.
Yb/TMSBr promoted homocoupling reactions of aliphatic ketones, α,β‐unsaturated ketones and aliphatic imines
Authors: Taniguchi Yuki , Kuno Tatsuhiro , Nakahashi Manabu , Takaki Ken , Fujiwara Yuzo 
Published: January 2005

AbstractA powerful reducing reagent, ytterbium dibromide (YbBr2), was synthesized by a new method using ytterbium metal and trimethylsilyl bromide (TMSBr) in tetrahydrofuran‐hexamethylphosphoramide (THF–HMPA). YbBr2, thus formed in situ, causes coupling reactions of aliphatic ketones, α,β‐unsaturated ketones and aliphatic aldimines to give bis‐silylated 1,2‐diols, 1,6‐diketones and 1,2‐diamines, respectively, in good yields. In the case of aliphatic ketimines, the corresponding reduced and silylated amines are obtained. In this solvent system, the trialkylsilyl moiety of trialkylsilyl bromide is converted to trialkylsilanes quantitatively. These results show that the Yb/TMSBr reagent generates YbBr2 in situ and the YbBr2 thus formed acts as a single‐electron reductant for these coupling reactions.
Development and application of a model for chitosan hydrolysis by a family 18 chitinase
Authors: Sikorski Pawel , Stokke Bjørn T. , Sørbotten Audun , Vårum Kjell M. , Horn Svein J. , Eijsink Vincent G. H. 
Published: January 2005

AbstractHydrolysis of partially deacetylated chitosans by ChitinaseB (ChiB) from Serratia marcescens results in mixtures of oligosaccharides typically between 2 and 20 sugar residues. The amounts of different oligomer fractions depend on the degree of acetylation of the starting chitosans. We have used experimentally determined distributions of hydrolysis products to develop a model for chitosan hydrolysis by ChiB. Important elements of the model include interaction parameters for acetylated/deacetylated units in each of the six subsites in the active cleft and degree of processivity (multiple attack). The hydrolysis reaction is described as a chemical reaction with an activation barrier that depends on the substrate sequence presented to the enzyme subsites. Using a Monte Carlo approach, the interaction parameters were refined by minimizing the difference between observed and predicted amounts of hydrolysis products obtained upon degradation of chitosan with a degree of acetylation of 65%. The final model can accurately predict complex patterns of oligosaccharides produced in the hydrolysis of chitosans with various degrees of acetylation, as well as patterns observed during reactions with chito‐oligosaccharides. The behavior of a ChiB mutant with a mutation in subsite +2 (Gly188Asp), which reduces the affinity for an acetylated sugar, could be predicted correctly by introducing one single change in the model parameters (the interaction energy for an acetylated unit in the +2 subsite). The proposed model may be used to explore degradation products for different enzyme–substrates combinations and to optimize conditions for preparation of specific oligosaccharides. In addition, the model provides insight into subsite interaction parameters and the degree of processivity, which complements previous experimental studies on the mode of action of ChiB. © 2005 Wiley Periodicals, Inc. Biopolymers 77: 273–285, 2005
The effect of temperature on DNA structural transitions under the action of Cu2+ and Ca2+ ions in aqueous solutions
Authors: Hackl Elene V. , Blagoi Yurij P. 
Published: January 2005

AbstractThe work examines the structural transitions of DNA under the action of Cu2+ and Ca2+ ions in aqueous solution at temperatures of 29 and 45°C by ir spectroscopy. Upon binding to the divalent ions studied, DNA transits into the compact state both at 29 and 45°C. In the compact state DNA remains in B‐form limits. The compaction process is of high positive cooperativity. As temperature increases the divalent metal ion concentration required to induce DNA compaction decreases in the case of Cu2+‐induced compaction and increases in the case of Ca2+‐induced compaction. It is suggested that the mechanism of the temperature effect on DNA compaction in the presence of Cu2+ ions possessing higher affinity for DNA bases differs from that of the temperature influence on Ca2+‐induced DNA compaction. In the case of copper ions the determining factor is the increase of binding constants of the Cu2+ ions interacting with the denatured parts formed on DNA while in the case of calcium ions it is the decreased screening action of counterions upon the increase of their hydration with temperature. The efficiency of divalent metal ions studied in inducing DNA compaction depends on hydration of counterions. DNA compaction occurs in a narrow interval of Cu2+ concentrations. As the Cu2+ ion concentration increases, DNA compaction is replaced with Cu2+‐induced DNA aggregation. At elevated temperatures Cu2+‐induced DNA compaction could acquire a phase transition character. © 2005 Wiley Periodicals, Inc. Biopolymers 77: 315–324, 2005
Workshop—predicting the structure of biological molecules
Authors: Counsell Damian 
Published: January 2005

AbstractThis April, in Cambridge (UK), principal investigators from the Mathematical Biology Group of the Medical Research Council's National Institute of Medical Research organized a workshop in structural bioinformatics at the Centre for Mathematical Sciences. Bioinformatics researchers of several nationalities from labs around the country presented and discussed their computational work in biomolecular structure prediction and analysis, and in protein evolution. The meeting was intensive and lively and gave attendees an overview of the healthy state of protein bioinformatics in the UK. Copyright © 2004 John Wiley & Sons, Ltd.
The molecule role ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature
Authors: Yamamoto Satoko , Asanuma Takao , Takagi Toshihisa , Fukuda Ken Ichiro 
Published: January 2005

AbstractIn general, it is not easy to specify a single sequence identity for each molecule name that appears in a pathway in the scientific literature. A molecule name may stand for concepts of various granularities, from concrete objects such as H‐Ras and ERK1 to abstract concepts or categories such as Ras and MAPK. Typically, the relations among molecule names derive a hierarchical structure; without a proper way to handle this knowledge, it becomes ever more difficult to develop a reliable pathway database. This paper describes an ontology that is designed to annotate molecules in the scientific literature on signal transduction pathways. Copyright © 2004 John Wiley & Sons, Ltd.
Obol: integrating language and meaning in bio‐ontologies
Authors: Mungall Christopher J. 
Published: January 2005

AbstractOntologies are intended to capture and formalize a domain of knowledge. The ontologies comprising the Open Biological Ontologies (OBO) project, which includes the Gene Ontology (GO), are formalizations of various domains of biological knowledge. Ontologies within OBO typically lack computable definitions that serve to differentiate a term from other similar terms. The computer is unable to determine the meaning of a term, which presents problems for tools such as automated reasoners. Reasoners can be of enormous benefit in managing a complex ontology. OBO term names frequently implicitly encode the kind of definitions that can be used by computational tools, such as automated reasoners. The definitions encoded in the names are not easily amenable to computation, because the names are ostensibly natural language phrases designed for human users. These names are highly regular in their grammar, and can thus be treated as valid sentences in some formal or computable language. With a description of the rules underlying this formal language, term names can be parsed to derive computable definitions, which can then be reasoned over. This paper describes the effort to elucidate that language, called Obol, and the attempts to reason over the resulting definitions. The current implementation finds unique non‐trivial definitions for around half of the terms in the GO, and has been used to find 223 missing relationships, which have since been added to the ontology. Obol has utility as an ontology maintenance tool, and as a means of generating computable definitions for a whole ontology.The software is available under an open‐source license from: http://www.fruitfly.org/∼cjm/obol. Supplementary material for this article can be found at: http://www.interscience.wiley.com/jpages/1531‐6912/suppmat. Copyright © 2004 John Wiley & Sons, Ltd.
Ontology for genome comparison and genomic rearrangements
Authors: Flanagan Keith , Stevens Robert , Pocock Matthew , Lee Pete , Wipat Anil 
Published: January 2005

AbstractWe present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation. Copyright © 2004 John Wiley & Sons, Ltd.
Characterization of multilocus linkage disequilibrium
Authors: Rinaldo Alessandro , Bacanu Silviu‐Alin , Devlin B. , Sonpar Vibhor , Wasserman Larry , Roeder Kathryn 
Published: January 2005

AbstractLinkage disequilibrium (LD) in the human genome, often measured as pairwise correlation between adjacent markers, shows substantial spatial heterogeneity. Congruent with these results, studies have found that certain regions of the genome have far less haplotype diversity than expected if the alleles at multiple markers were independent, while other sets of adjacent markers behave almost independently. Regions with limited haplotype diversity have been described as “blocked” or “haplotype blocks.” In this article, we propose a new method that aims to distinguish between blocked and unblocked regions in the genome. Like some other approaches, the method analyses haplotype diversity. Unlike other methods, it allows for adjacent, distinct blocks and also multiple, independent single nucleotide polymorphisms (SNPs) separating blocks. Based on an approximate likelihood model and a parsimony criterion to penalize for model complexity, the method partitions a genomic region into blocks relatively quickly, and simulations suggest that its partitions are accurate. We also propose a new, efficient method to select SNPs for association analysis, namely tag SNPs. These methods compare favorably to similar blocking and tagging methods using simulations. Genet. Epidemiol. © 2005 Wiley‐Liss, Inc.
Involvement of glial cell line‐derived neurotrophic factor in activation processes of rodent macrophages
Authors: Hashimoto Manabu , Nitta Atsumi , Fukumitsu Hidefumi , Nomoto Hiroshi , Shen Liya , Furukawa Shoei 
Published: January 2005

AbstractThe physiological roles of glial cell line‐derived neurotrophic factor (GDNF) expressed in the microglia/macrophages of the injured spinal cord have not yet been clarified. mRNA expression of chemokines, including monocyte chemoattractant protein (MCP)‐1, was evoked within 1 hr after transection of the spinal cord, and GDNF mRNA expression was similarly up‐regulated. Immunohistochemical analysis showed that GDNF was coexpressed with MCP‐1 in the CD11b‐positive cells. Therefore, we examined further the effects of GDNF on cultured rat peritoneal macrophages. GDNF enhanced the phagocytic activity of the macrophages via GFRα‐1, glycosylphosphatidylinositol‐anchored specific binding site of GDNF, in a c‐Ret‐independent manner. The influence of autocrine and/or paracrine GDNF synthesis was evaluated by performing activation experiments using macrophages cultured from heterozygous (+/−) GDNF gene‐deficient mice or wild‐type (+/+) mice. There were no morphological differences dependent on genetic types or stimulators. However, the GDNF mRNA level, but not the MCP‐1 or GFRα‐1 mRNA level, was substantially lower in the mutant macrophages than in the +/+ cells irrespective of stimulation with MCP‐1 or lipopolysaccharide (LPS). The phagocytic activity enhanced by MCP‐1 or LPS was significantly lower in the mutant cells (+/−) than in the +/+ ones, demonstrating the involvement of endogenous GDNF in the activation processes of macrophages in vitro and suggesting that not only neuroprotective function but also activation of macrophages is effected by the GDNF produced after a spinal cord injury. © 2005 Wiley‐Liss, Inc.
Schwann cell‐autonomous role of neuropilin‐2
Authors: Ara J. , Bannerman P. , Shaheen F. , Pleasure D.E. 
Published: January 2005

AbstractNeuropilins and group A plexins are components of receptor complexes for class 3 semaphorins, gradients of which help to guide migration of neural progenitor cells and axonal growth cones during development. We demonstrated previously that neuropilins and class 3 semaphorins are induced in sciatic nerve by crush or transection. We now report that in cultured rat Schwann cells, expression of mRNA encoding neuropilin‐2 (NRP2) and plexin‐A3 (PlexA3), proteins involved in semaphorin‐3F (Sema3F) signal transduction, is diminished markedly by forskolin, an adenylate cyclase activator that, like axonal contact, induces Schwann cell synthesis of myelin lipids and proteins. Interestingly, Schwann cell expression of mRNA encoding NRP1, which participates in Sema3A signaling, is not downregulated by forskolin. Antibodies that recognize ectodomains of NRP2 but not control antibodies prevented cultured Schwann cells from aligning in parallel and forming columns. These results are consistent with the view that in nerves undergoing Wallerian degeneration, Schwann cell NRP2 facilitates assembly of Schwann cells into the tubular aggregates (bands of Büngner) that guide regenerating axons. © 2005 Wiley‐Liss, Inc.
Mercury compounds disrupt neuronal glutamate transport in cultured mouse cerebellar granule cells
Authors: Fonfría Elena , Vilaró M. Teresa , Babot Zoila , Rodríguez‐Farré Eduard , Suñol Cristina 
Published: January 2005

AbstractCerebellar granule cells are targeted selectively by mercury compounds in vivo. Despite the affinity of mercury for thiol groups present in all cells, the molecular determinant(s) of selective cerebellar degeneration remain to be elucidated fully. We studied the effect of mercury compounds on neuronal glutamate transport in primary cultures of mouse cerebellar granule cells. Immunoblots probed with an antibody against the excitatory amino acid transporter (EAAT) neuronal glutamate transporter, EAAT3, revealed the presence of a specific band in control and mercury‐treated cultures. Micromolar concentrations of both methylmercury and mercuric chloride increased the release of endogenous glutamate, inhibited glutamate uptake, reduced mitochondrial activity, and decreased ATP levels. All these effects were completely prevented by the nonpermeant reducing agent Tris‐(2‐carboxyethyl)phosphine (TCEP). Reduction of mitochondrial activity by mercuric chloride, but not by methylmercury, was inhibited significantly by 4,4′‐diisothiocyanato‐stilbene‐2,2′‐disulfonic acid (DIDS) and by reduced extracellular Cl− ion concentration. In addition, DIDS and low extracellular Cl− completely inhibited the release of glutamate induced by mercuric chloride, and produced a partial although significant reduction of that induced by methylmercury. We suggest that a direct inhibition of glutamate uptake triggers an imbalance in cell homeostasis, leading to neuronal failure and Cl−‐regulated cellular glutamate efflux. Our results demonstrate that neuronal glutamate transport is a novel target to be taken into account when assessing mercury‐induced neurotoxicity. © 2005 Wiley‐Liss, Inc.
The reactions of atomic hydrogen and active nitrogen with hydrogen azide
Authors: Le Bras G. , Combourieu J. 
Published: January 2005

AbstractDetection of atoms by mass spectrometry has been used to study the reactions of hydrogen azide, HN3, with H atoms and active nitrogen, in a fast flow reactor at pressures of about 1 torr. Stoichiometry and products of the H + HN3 reaction have been determined and the rate constant of the initial step, assumed to be H + HN3 → NH2 + N2, was found to be 2.54 × 10−11 exp (−4600/RT) cm3 molecule−1 s−1, in the temperature range of 300–460K. The formation of NH3 and H2 products has been discussed from the different secondary steps which may occur in the mechanism. For the reaction of active nitrogen with HN3, evidence has been found for the participation of excited nitrogen molecules produced by a microwave discharge through molecular nitrogen. The influence of excited nitrogen molecules has been reduced by lowering the gas flow velocity. It was then possible to study the N + HN3 reaction for which the rate constant of the initial step was found to be 4.9 × 10−15 cm3 molecule−1 s−1 at room temperature. Finally, the occurrence of these elementary reactions has been discussed in the mechanism of the decomposition flame of HN3.
Are HO radicals produced in the reaction of O(3P) with 1‐C4H8?
Authors: Luria Menachem , Simonaitis R. , Heicklen Julian 
Published: January 2005

AbstractThe reaction of O(3P) with 1‐C4H8 was examined in the presence of CO which scavenges HO radicals to produce CO2. From the CO2 quantum yield, an upper limit to the efficiency of HO production in the reaction of O(3P) with 1‐C4H8 was found to be 0.02 at both 298° and 473°K.
Methyl‐radical association studied by time‐resolved mass spectroscopy
Authors: Truby Frank K. , Rice James K. 
Published: January 2005

AbstractTime‐resolved mass spectroscopy has been utilized to study the kinetics of methylradical association. The rate coefficient for the association process was determined by following the time dependence of ethane formation after flash photolysis of CH3I in the presence of N2. The net rate coefficient for the process 2CH3 (+M) → C2H6(+M) has a high‐pressure limit of (4.0 ± 0.3) × 10−11 cm3 molecule−1 sec−1 at 313°K. This rate coefficient has found to be insensitive to the third‐body number densities for pressures ranging from 13 Torr down to below 0.5 Torr, indicating that the lifetime for dissociation of the intermediate C2H6* species is greater than 2 × 10−7 sec at 313°K for a gas pressure of 0.5 Torr.
Vibrational energy transfer in near resonance due to dipole–dipole interactions
Authors: Lev‐on Miriam , Palke William E. , Millikan Roger C. 
Published: January 2005

AbstractThe contribution of long‐range forces to the observed rates of V → V energy transfer processes has been studied. The theoretical model uses the first order perturbation approximation to generate a probability function, with the dipole–dipole perturbing potential as given by Margenau: Vif = [(1/6)1/2μ1 · μ2]R−3. The probability function derived is shown to be a strong function of the energy mismatch between the IR bands of the colliding molecules. The calculation emphasizes the importance of rotational state population effects, the most important J states being those which minimize the energy mismatch. A complete analysis of energy transfer between CO(v) and COS(000) where v = 1,2, ⃛ 13 is presented. The calculation reveals the importance of combination bands in the energy transfer mechanism of polyatomics. The temperature dependence for near‐resonant processes is also studied and the importance of the V → R energy transfer leads to the classification of ω0 (band‐center energy mismatch) into three categories small, medium, and large, according to the temperature dependence that the corresponding processes exhibit. The predictions of the theoretical model are compared to experimental data for the same system.
Electronically excited oxygen atoms, O(21D2). A time‐resolved study of the collisional quenching by the gases H2, D2, CH4, NO, NO2, N2O, and C3O2 using atomic absorption spectroscopy in the vacuum ultraviolet
Authors: Heidner R. F. , Husain D. 
Published: January 2005

AbstractTime‐resolved atomic absorption spectroscopy in the vacuum ultraviolet has been employed to monitor electronically excited oxygen atoms, O(21D2), following their genera‐tion by the flash photolysis of ozone in the Hartley band region. We report the first values for the absolute second‐order rate constants describing the removal of the excited atom on collision with the molecules H2, D2, CH4, NO, NO2, N2O, and C3O2. Where possible, these data are considered within the context of restrictions arising from spin and orbital symmetry and are further discussed in tems of previously reported relative rate data derived from indirect measurements. Consideration is given to the importance of these rate con‐stants in discussing processes taking place in the earth's atmosphere and in systems giving rise to chemical laser action.
A flash photolysis–resonance fluorescence kinetics study of the reactions of ground‐state sulfur atoms. V. Rate parameters for the reaction of S(3P)with cis‐2‐butene and tetramethylethylene
Authors: Davis D. D. , Klemm R. B. 
Published: January 2005

AbstractRate parameters for the reaction of ground‐state atomic sulfur, S(3P), with the olefins cis‐2‐butene and tetramethylethylene have been determined over a temperature range of ∽280°K. A major finding of this study was that the rate constants for both reactions showed negative temperature dependencies. When k is expressed in the form of an Arrhenius equation, this necessarily leads to negative activation energies: k1 = (4.68 ± 0.70) × 10−12 exp (+0.23 ± 0.09 kcal/mole)/RT (219°‐500°K) k2 = (4.68 ± 1.70) × 10−12 exp (+1.29 ± 0.23 kcal/mole)/RT (252°‐500°K) Units are cm3 molec−1s−1. When a threshold energy of 0.0 kcal/mole is assumed for reaction (2), the temperature dependence of the preexponential term has a value of T−2. Making the usual simplifying assumptions, neither collision theory nor transition state theory leads to a preexponential factor with a strong enough negative temperature dependence. A comparison of these results with those derived from studies of the reactions of atomic oxygen, O(3P), with the same olefins shows that in both studies simple bimolecular processes were being examined. Also discussed are the possible experimental and theoretical ramifications of these new results.