bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the impact of sets of scientific papers: The Garfield (impact) factor
Authors: Vinkler Peter 
Published: February 2004

AbstractThe Garfield (Impact) Factor (GF) is one of the most frequently used scientometric indicators. In the present article it is shown that the main factors determining the value of the mean GF representing a set of journals are the number of articles published recently (articles referencing) related to those published in a previous time period (articles to be referenced) and the mean number of references in journal papers referring to the time period selected. It has been proved further that GF corresponds to the mean chance for citedness of journal papers. A new indicator, Specific Impact Contribution (SIC), is introduced, which characterizes the contribution of a subset of articles or a journal to the total impact of the respective articles or journals. The SIC index relates the share of a journal in citations divided by that in publications within a set of papers or journals appropriately selected. It is shown, however, that the normalized GFs of journals and the normalized SIC indicators are identical measures within any set of journals selected. It may be stated therefore that Garfield Factors of journals (calculated correctly) are appropriate scientometric measures for characterizing the relative international eminence of journals within a set of journals appropriately selected. It is demonstrated further that SIC indicators (and so GF indexes) correspond to the (number of citations per paper) indicators generally used, within the same set of papers.
A survey of nucleotide cyclases in Actinobacteria: unique domain organization and expansion of the class III cyclase family in Mycobacterium tuberculosis
Authors: Shenoy Avinash R. , Sivakumar K. , Krupa A. , Srinivasan N. , Visweswariah Sandhya S. 
Published: February 2004

AbstractCyclic nucleotides are well‐known second messengers involved in the regulation of important metabolic pathways or virulence factors. There are six different classes of nucleotide cyclases that can accomplish the task of generating cAMP, and four of these are restricted to the prokaryotes. The role of cAMP has been implicated in the virulence and regulation of secondary metabolites in the phylum Actinobacteria, which contains important pathogens, such as Mycobacterium tuberculosis, M. leprae, M. bovis and Corynebacterium, and industrial organisms from the genus Streptomyces. We have analysed the actinobacterial genome sequences found in current databases for the presence of different classes of nucleotide cyclases, and find that only class III cyclases are present in these organisms. Importantly, prominent members such as M. tuberculosis and M. leprae have 17 and 4 class III cyclases, respectively, encoded in their genomes, some of which display interesting domain fusions seen for the first time. In addition, a pseudogene corresponding to a cyclase from M. avium has been identified as the only cyclase pseudogene in M. tuberculosis and M. bovis. The Corynebacterium and Streptomyces genomes encode only a single adenylyl cyclase each, both of which have corresponding orthologues in M. tuberculosis. A clustering of the cyclase domains in Actinobacteria reveals the presence of typical eukaryote‐like, fungi‐like and other bacteria‐like class III cyclase sequences within this phylum, suggesting that these proteins may have significant roles to play in this important group of organisms. Copyright © 2004 John Wiley & Sons, Ltd.
Identification and analysis of novel tandem repeats in the cell surface proteins of archaeal and bacterial genomes using computational tools
Authors: Adindla S. , Inampudi K. K. , Guruprasad K. , Guruprasad L. 
Published: February 2004

AbstractWe have identified four novel repeats and two domains in cell surface proteins encoded by the Methanosarcina acetivorans genome and in some archaeal and bacterial genomes. The repeats correspond to a certain number of amino acid residues present in tandem in a protein sequence and each repeat is characterized by conserved sequence motifs. These correspond to: (a) a 42 amino acid (aa) residue RIVW repeat; (b) a 45 aa residue LGxL repeat; (c) a 42 aa residue LVIVD repeat; and (d) a 54 aa residue LGFP repeat. The domains correspond to a certain number of aa residues in a protein sequence that do not comprise internal repeats. These correspond to: (a) a 200 aa residue DNRLRE domain; and (b) a 70 aa residue PEGA domain. We discuss the occurrence of these repeats and domains in the different proteins and genomes analysed in this work. Copyright © 2004 John Wiley & Sons, Ltd.
UTOPIA—user‐friendly tools for operating informatics applications
Authors: Pettifer S. R. , Sinnott J. R. , Attwood T. K. 
Published: February 2004

AbstractBioinformaticians routinely analyse vast amounts of information held both in large remote databases and in flat data files hosted on local machines. The contemporary toolkit available for this purpose consists of an ad hoc collection of data manipulation tools, scripting languages and visualization systems; these must often be combined in complex and bespoke ways, the result frequently being an unwieldy artefact capable of one specific task, which cannot easily be exploited or extended by other practitioners. Owing to the sizes of current databases and the scale of the analyses necessary, routine bioinformatics tasks are often automated, but many still require the unique experience and intuition of human researchers: this requires tools that support real‐time interaction with complex datasets. Many existing tools have poor user interfaces and limited real‐time performance when applied to realistically large datasets; much of the user's cognitive capacity is therefore focused on controlling the tool rather than on performing the research. The UTOPIA project is addressing some of these issues by building reusable software components that can be combined to make useful applications in the field of bioinformatics. Expertise in the fields of human computer interaction, high‐performance rendering, and distributed systems is being guided by bioinformaticians and end‐user biologists to create a toolkit that is both architecturally sound from a computing point of view, and directly addresses end‐user and application‐developer requirements. Copyright © 2004 John Wiley & Sons, Ltd.
The evolution of protein interaction networks in regulatory proteins
Authors: Amoutzias Gregory D. , Robertson David L. , Bornberg‐Bauer Erich 
Published: February 2004

AbstractInteractions between proteins are essential for intracellular communication. They form complex networks which have become an important source for functional analysis of proteins. Combining phylogenies with network analysis, we investigate the evolutionary history of interaction networks from the bHLH, NR and bZIP transcription‐factor families. The bHLH and NR networks show a hub‐like structure with varying γ values. Mutation and gene duplication play an important role in adding and removing interactions. We conclude that in several of the protein families that we have studied, networks have primarily arisen by the development of heterodimerizing transcription factors, from an ancestral gene which interacts with any of the newly emerging proteins but also homodimerizes. Copyright © 2004 John Wiley & Sons, Ltd.
Signal analysis on strings for immune‐type pattern recognition
Authors: Atreas Nikolaos D. , Karanikas Costas , Polychronidou Persefoni 
Published: February 2004

AbstractWe use wavelet‐type discrete transforms for signal analysis on strings of finite length. We apply these transforms for edge and hidden Markov process detection. We also present new approaches for string matching and for measures of the diversity of chaotic strings. Copyright © 2004 John Wiley & Sons, Ltd.
Individual‐based modelling of bacterial ecologies and evolution
Authors: Vlachos C. , Gregory R. , Paton R. C. , Saunders J. R. , Wu Q. H. 
Published: February 2004

AbstractThis paper presents two approaches to the individual‐based modelling of bacterial ecologies and evolution using computational tools. The first approach is a fine‐grained model that is based on networks of interactivity between computational objects representing genes and proteins. The second approach is a coarser‐grained, agent‐based model, which is designed to explore the evolvability of adaptive behavioural strategies in artificial bacteria represented by learning classifier systems. The structure and implementation of these computational models is discussed, and some results from simulation experiments are presented. Finally, the potential applications of the proposed models to the solution of real‐world computational problems, and their use in improving our understanding of the mechanisms of evolution, are briefly outlined. Copyright © 2004 John Wiley & Sons, Ltd.
ArraySolver: an algorithm for colour‐coded graphical display and Wilcoxon signed‐rank statistics for comparing microarray gene expression data
Authors: Khan Haseeb Ahmad 
Published: February 2004

AbstractThe massive surge in the production of microarray data poses a great challenge for proper analysis and interpretation. In recent years numerous computational tools have been developed to extract meaningful interpretation of microarray gene expression data. However, a convenient tool for two‐groups comparison of microarray data is still lacking and users have to rely on commercial statistical packages that might be costly and require special skills, in addition to extra time and effort for transferring data from one platform to other. Various statistical methods, including the t‐test, analysis of variance, Pearson test and Mann–Whitney U test, have been reported for comparing microarray data, whereas the utilization of the Wilcoxon signed‐rank test, which is an appropriate test for two‐groups comparison of gene expression data, has largely been neglected in microarray studies. The aim of this investigation was to build an integrated tool, ArraySolver, for colour‐coded graphical display and comparison of gene expression data using the Wilcoxon signed‐rank test. The results of software validation showed similar outputs with ArraySolver and SPSS for large datasets. Whereas the former program appeared to be more accurate for 25 or fewer pairs (n ≤ 25), suggesting its potential application in analysing molecular signatures that usually contain small numbers of genes. The main advantages of ArraySolver are easy data selection, convenient report format, accurate statistics and the familiar Excel platform. Copyright © 2004 John Wiley & Sons, Ltd.
ProbSeq—a fragmentation model for interpretation of electrospray tandem mass spectrometry data
Authors: Skilling John , Denny Richard , Richardson Keith , Young Phillip , McKenna Thérèse , Campuzano Iain , Ritchie Mark 
Published: February 2004

AbstractWe describe a probabilistic peptide fragmentation model for use in protein databank searching and de novo sequencing of electrospray tandem mass spectrometry data. A probabilistic framework for tuning of the model using a range of well‐characterized samples are introduced. We present preliminary results of our tuning efforts. Copyright © 2004 John Wiley & Sons, Ltd.
Enabling proteomics: the need for an extendable ‘workbench’ for user‐configurable solutions
Authors: Beynon Robert J. 
Published: February 2004

AbstractProteomics has the capability to generate overwhelming quantities of data in relatively short timescales, and it is not uncommon to see experimenters investing substantially more time in data analysis than in data gathering. Although several sophisticated tools for data reduction and analysis are available, they lack the flexibility to cope with increasingly innovative experimental strategies and new database resources that encode both qualitative and quantitative data. I will outline a specification of a flexible proteomics tool that could address many current bottlenecks and deficiencies. Copyright © 2004 John Wiley & Sons, Ltd.
Synthetic Applications in Radical/Radical Cationic Cascade Reactions
Authors: Rinderhagen Heiko , Mattay Jochen 
Published: February 2004

AbstractOxidative photoinduced electron transfer (PET) reactions have been performed with various cyclic cyclopropyl(vinyl) silyl ethers bearing an olefinic or acetylenic side chain. The reactions result in bi‐ to tetracyclic ring systems via a fragmentation–radical/radical cationic addition reaction pathway with well defined ring juncture. The mode of cyclisation (endo/exo) can be partially controlled by addition of nucleophiles due to the suppression of radical cationic reaction pathways. Quantum chemical calculation of the cyclisation transition states underline the experimentally found selectivities. Additional mechanistic studies concerning the saturation step reveal that the final radical is saturated mostly by the solvent and traces of water in the solvent.
Nanostructured Pure γ‐Fe2O3 via Forced Precipitation in an Organic Solvent
Authors: Khaleel Abbas A. 
Published: February 2004

AbstractPure maghemite, γ‐Fe2O3, was prepared as ultra fine particles in the nanometer‐sized range via the forced precipitation method in an organic solvent. The precipitation of iron(III) ions, from iron(III) chloride in 2‐propanol led selectively to highly dispersed particles of ferrihydrite, which upon treatment with temperatures higher than 200 °C under dynamic vacuum resulted in high‐surface‐area particles of γ‐Fe2O3. Precipitation in water also led to ferrihydrite, but the final product, after heating at 300 °C, contained a mixture of γ‐Fe2O3 and α‐Fe2O3 (hematite). The precipitation from iron(III) nitrate in water resulted in goethite which was converted to hematite upon heating. On the other hand, the final product in 2‐propanol was a mixture of maghemite and hematite. The products were characterized by FTIR, TGA, XRD, and gas sorption analysis. Nitrogen gas adsorption studies for the pure γ‐Fe2O3 samples revealed mesoporous particles with high surface areas in the range of 70–120 m2 g−1 after heat treatment at 300 °C. The γ‐Fe2O3 particles retained their γ‐phase as well as their mesoporous structure at relatively high temperatures, as high as 400 °C.
Ring Currents as Probes of the Aromaticity of Inorganic Monocycles : P5−, As5−, S2N2, S3N3−, S4N3+, S4N42+, S5N5+, S42+ and Se42+
Authors: De Proft Frank , Fowler Patrick W. , Havenith Remco W. A. , Schleyer Paul von Ragué , Van Lier Gregory , Geerlings Paul 
Published: February 2004

AbstractCurrent‐density maps were calculated by the ipsocentric CTOCD‐DZ/6‐311G** (CTOCD‐DZ=continuous transformation of origin of current density‐diamagnetic zero) approach for three sets of inorganic monocycles: S42+, Se42+, S2N2, P5− and As5− with 6 π electrons; S3N3−, S4N3+ and S4N42+ with 10 π electrons; and S5N5+ with 14 π electrons. Ipsocentric orbital analysis was used to partition the currents into contributions from small groups of active electrons and to interpret the contributions in terms of symmetry‐ and energy‐based selection rules. All nine systems were found to support diatropic π currents, reinforced by σ circulations in P5−, As5−, S3N3−, S4N3+, S4N42+ and S5N5+, but opposed by them in S42+, Se42+ and S2N2. The opposition of π and σ effects in the four‐membered rings is compatible with height profiles of calculated NICS (nucleus‐independent chemical shifts).
Perturbation of the NH2 pKa Value of Adenine in Platinum(II) Complexes: Distinct Stereochemical Internucleobase Effects
Authors: Garijo Añorbe Marta , Lüth Marc Sven , Roitzsch Michael , Morell Cerdà Marta , Lax Patrick , Kampf Gunnar , Sigel Helmut , Lippert Bernhard 
Published: February 2004

AbstractThe degree of acidification of the exocyclic N6 amino group of the model nucleobase 9‐methyladenine (9MeA) in relation to the number and site(s) of PtII binding has been studied in detail. It is found that twofold PtII binding to N1 and N7 lowers the pKa value from 16.7 in the free base to 12–8. The lowest pKa values are observed when the resulting N6H− amide group is intramolecularly stabilized by an H‐bond donor such as the N6H2 group of a suitably positioned second 9MeA ligand. Deprotonation of the N6 amino group facilitates Pt migration from N1 to N6, and subsequent reprotonation of the N1 position yields a twofold N7,N6‐metalated form of the rare imino tautomer of 9MeA, which has a pKa value of 5.03. These findings demonstrate a principle that is of potential relevance to the topic of “shifted pKa” values of adenine nucleobases, which is believed to be important with regard to acid–base catalysis of RNAs at physiological pH values. The principle states that a nucleobase pKa value can be sufficiently lowered to reach near‐neutral values and that the pKa value of the protonated base does not necessarily have to be increased to accomplish this effect.
Supramolecular Self‐Assembly of Conjugated Diblock Copolymers
Authors: Wang Hengbin , You Wei , Jiang Ping , Yu Luping , Wang H. Hau 
Published: February 2004

AbstractThis paper describes the synthesis and characterization of a novel series of copolymers with different lengths of oligo(phenylene vinylene) (OPV) as the rod block, and poly(propylene oxide) as the coil block. Detailed characterization by means of transmission electron microscopy (TEM), atomic force microscopy (AFM), and small‐angle neutron scattering (SANS) revealed the strong tendency of these copolymers to self‐assemble into cylindrical micelles in solution and as‐casted films on a nanometer scale. These micelles have a cylindrical OPV core surrounded by a poly(propylene glycol) (PPG) corona and readily align with each other to form parallel packed structures when mica is used as the substrate. A packing model has been proposed for these cylindrical micelles.
Three‐Phase Microemulsion/Sol–Gel System for Aqueous Catalysis with Hydrophobic Chemicals
Authors: Abu‐Reziq Raed , Blum Jochanan , Avnir David 
Published: February 2004

AbstractA facile three‐phase transport process is described that allows to carry out catalytic reactions in water, whereby all components are hydrophobic. According to this process a hydrophobic substrate is microemulsified in water and subjected to an organometallic catalyst, which is entrapped within a partially hydrophobized sol–gel matrix. The surfactant molecules, which carry the hydrophobic substrate, adsorb/desorb reversibly on the surface of the sol–gel matrix breaking the micellar structure, spilling their substrate load into the porous medium that contains the catalyst. A catalytic reaction then takes place within the ceramic material to form the desired products that are extracted by the desorbing surfactant, carrying the emulsified product back into the solution. The method is general and versatile and has been demonstrated with the catalytic hydrogenations of alkenes, alkynes, aromatic CC bonds, and nitro and cyano groups.
Kinetics and Mechanisms for the Reactions of Phenyl Radical with Ketene and its Deuterated Isotopomer: An Experimental and Theoretical Study
Authors: Choi Y. M. , Lin M. C. 
Published: February 2004

AbstractKinetics and mechanism for the reaction of phenyl radical (C6H5) with ketene (H2CβCαO) were studied by the cavity ring‐down spectrometric (CRDS) technique and hybrid DFT and ab initio molecular orbital calculations. The C6H5 transition at 504.8 nm was used to detect the consumption of the phenyl radical in the reaction. The absolute overall rate constants measured, including those for the reaction with CD2CO, can be expressed by the Arrhenius equation k=(5.9±1.8)×1011 exp[−(1160±100)/T] cm3 mol−1 s−1 over a temperature range of 301–474 K. The absence of a kinetic isotope effect suggests that direct hydrogen abstraction forming benzene and ketenyl radical is kinetically less favorable, in good agreement with the results of quantum chemical calculations at the G2MS//B3LYP6‐31G(d) level of theory for all accessible product channels, including the above abstraction and additions to the Cα, Cβ, and O sites. For application to combustion, the rate constants were extrapolated over the temperature range of 298–2500 K under atmospheric pressure by using the predicted transition‐state parameters and the adjusted entrance reaction barriers Eα=Eβ=1.2 kcal mol−1; they can be represented by the following expression in units of cm3 mol−1 s−1: kα=6.2×1019 T−2.3 exp[−7590/T] and kβ=3.2×104 T2.4 exp[−246/T].
Two‐ and Three‐Dimensional Molecular Organization of Schiff‐Base Derivatives
Authors: Mu Zhong‐Cheng , Kong Jian‐Fei , Wang Yue , Ye Ling , Yang Guang‐Di , Zhang Xi 
Published: February 2004

AbstractWe have designed and synthesized a series of Schiff base derivatives, and studied their structural features in two‐dimensional (2D) and three‐dimensional (3D) states by combining scanning tunneling microscopy (STM) and X‐ray diffraction experiments. The Schiff‐base derivatives with short alkyl chains crystallize easily, which allows a detailed structural analysis by X‐ray diffraction. Due to the strong adsorbate–substrate interactions, those bases with long alkyl chains easily form 2D assemblies on highly oriented pyrolytic graphite (HOPG). The STM images indicate also that the introduction of two methoxy groups into the molecule can change the structure of these 2D assemblies as a result of the increased steric hindrances, for example: the Schiff‐base derivative, bearing both methoxy groups and C16H33 tails, forms 2D Moiré patterns, and an alignment of pairing Schiff‐base molecules may be easily resolved. Conversely, the Schiff base derivative, bearing solely C16H33 tails, forms 2D non‐Moiré patterns. It is demonstrated that the 3D structural features result from the compromise of intermolecular interactions of different molecular moieties. However, there is one more factor, which also governs the 2D structure: the adsorbate‐substrate interaction. The 3D crystal structure may thus help to understand many factors involved in the formation of 2D structures, and would be helpful for designing new molecular assemblies with tailoring functions.
Functional Microdomains of Glycolipids with Partially Fluorinated Membrane Anchors: Impact on Cell Adhesion
Authors: Gege Christian , Schneider Matthias F. , Schumacher Gabriele , Limozin Laurent , Rothe Ulrich , Bendas Gerd , Tanaka Motomu , Schmidt Richard R. 
Published: February 2004

AbstractFunctional microdomains of glycolipids were designed by mixing neoglycolipids with partially fluorinated alkyl (F‐alkyl) chains and matrix lipids with alkyl chains. Fluorescence images of the mixed lipid monolayers at the air–water interface demonstrated that it is possible to control both size and distribution of the microdomains by means of the strong demixing of alkyl and F‐alkyl membrane anchors, while the carbohydrate head groups seemed to play a rather minor role. These microdomains in monolayers could be transferred onto hydrophobized substrates and subjected to experiments in a dynamic flow chamber. The results obtained here clearly indicated that the dynamic adhesion of Chinese hamster ovarial cells expressing E‐selectin (CHO‐E cells) on a lipid monolayer containing microdomains of sialyl LewisX (sLeX) can be both enhanced and reduced by controlled demixing of ligands and matrices. Moreover, the same clusters of sLeX could also be formed in giant lipid vesicles, which can be used as a model cell that locally expresses biospecific functions.