bluuebunny/crossref_metadata_2025 huggingface dataset:
Planar inverted‐F antenna with a hollow shorting cylinder for mobile phone with an embedded camera
Authors: Chien Shao‐Lun , Hsiao Fu‐Ren , Lin Yeh‐Chian , Wong Kin‐Lu
Published: April 2004

A novel planar inverted‐F antenna (PIFA) with a large hollow shorting cylinder suitable for integration with an embedded digital camera for a mobile phone is proposed. A design example of the proposed PIFA for application in a UMTS (1920–2170 MHz) mobile phone is demonstrated. The antenna design and experimental results are presented and discussed. © 2004 Wiley Periodicals, Inc. Microwave Opt Technol Lett 41: 418–419, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20157
Cross‐coupled hairpin filter design using high‐permittivity substrates
Authors: Hsu Cheng‐Shing , Huang Cheng‐Liang
Published: April 2004

A four‐pole elliptic‐function bandpass filter is designed using a compact miniaturized microstrip hairpin resonator. This miniaturized hairpin resonator is realized by using a stepped‐impedance structure with parallel coupled lines. In addition, the bandpass filter is implemented using a high‐permittivity ceramic substrate. These factors result in the reduction of the filter's size. The full‐wave simulator IE3D is used to design the hairpin resonator, and to calculate the coupling coefficient of the basic coupling strictures. The responses of the fabricated filters using Al2O3 (εr = 9.7, Q × f = 350,000 GHz) and MgNb2O6 (εr = 20, Q × f = 110,000 GHz) ceramic substrates are designed at a center frequency of 2 GHz. The compact size and the performance of this class of filters are demonstrated. © 2004 Wiley Periodicals, Inc. Microwave Opt Technol Lett 41: 419–423, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20158
A study of waveguides filled with anisotropic metamaterials
Authors: Xu Yansheng
Published: April 2004

In this paper, a rectangular waveguide and a nonraditive dielectric (NRD) waveguide, filled with anisotropic negative permittivity and permeability, are studied in detail. A general condition of the existence of TE and TM modes in these waveguides is derived. The unique characteristics of these waveguides are explored. Both fully‐ and partially‐filled cases of rectangular waveguides are examined. Characteristics of NRD waveguides with anisotropic metamaterial cores are studied. © 2004 Wiley Periodicals, Inc. Microwave Opt Technol Lett 41: 426–431, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20160
Formation of nano‐dots of phenylazomethine dendrimers with Rhodamine 6G on mica
Authors: Satoh Norifusa , Watanabe Takeshi , Iketaki Yoshinori , Omatsu Takashige , Fujii Masaaki , Yamamoto Kimihisa
Published: April 2004

The phenylazomethine dendrimer (DPA) is associated with Rhodamine 6G in chloroform, which results in the chemical shift attributed to the aromatic protons of phenylazomethine being moved upfield in the 1H‐NMR spectrum by increasing the Rhodamine 6G. The shift is saturated at the ratio of 1 : 1. On the basis of the NMR analysis, the association constant K of phenylazomethine with Rhodamine 6G was determined to be 1.4 × 104 (l/mol) in CDCl3 at 20°C. The association is also confirmed by UV‐vis spectroscopy, in which the absorption around 450 and 527 nm changes during the addition of Rhodamine 6G. The fluorescence intensity of the 1 : 1 complex of Rhodamine 6G and DPA G4 is stronger than that of the solution dissolved only in Rhodamine 6G at greater than 1 mM though it is generally known that the intermolecular interaction quenches the dye fluorescence in a concentrated solution. The association of DPA G4 with Rhodamine 6G suppresses the quenching at higher concentrations. Homogenous nano‐dots were observed on mica by casting the DPA G4 complex with Rhodamine 6G, in which the height and average area were 1.5–3 nm and 1.6 × 103 nm2 (the standard deviation σ = 3.7 nm2), respectively. Copyright © 2004 John Wiley & Sons, Ltd.
Catalytic behavior of wool‐osmium tetroxide complex for asymmetric dihydroxylation of olefins
Authors: Miao Ju‐Hong , Yang Ji‐Huo , Chen Li‐Yi , Tu Bu‐Xin , Huang Mei‐Yu , Jiang Ying‐Yan
Published: April 2004

A new chiral polymer‐metal complex, wool‐osmium tetroxide (wool‐OsO4) complex was prepared by a very simple method. This complex was found to be able to catalyze the asymmetric dihydroxylation of allylamine to (R)‐(+)‐3‐amino‐1, 2‐propanediol and allyl chloride to (S)‐(+)‐3‐chloro‐1,2‐propanediol. The optical yields amounted to 83.7 and 57.2%, and the product yields were 80.2 and 68.5% respectively. The experimental results showed that OsO4 content in the complex, reaction time, allylamine/OsO4 molar ratio and solvent all have an effect on the product and optical yields. Additionally, wool‐OsO4 complex catalyst could be reused without any remarkable change in optical catalytic activity. Copyright © 2004 John Wiley & Sons, Ltd.
Aromatic character of annelated dimethyldihydropyrenes
Authors: Aihara Jun‐ichi , Ishida Toshimasa
Published: April 2004

Mitchell and co‐workers recently estimated the order of aromaticity for dimethyldihydropyrene (DDP) nuclei in annelated derivatives using nucleus‐independent chemical shifts (NICS). We found that two graph‐theoretically defined energetic quantities, percentage topological resonance energy (% TRE) and bond resonance energy (BRE), can be used to predict readily the relative aromaticities of these hydrocarbons and their DDP nuclei, respectively. Since these quantities are not dependent on the areas of individual rings, they are better suited for estimating the degree of aromaticity. Copyright © 2004 John Wiley & Sons, Ltd.
Kinetics and mechanisms of the gas‐phase elimination of 2‐substituted primary, secondary and tertiary hydroxy groups in nitroalkanes
Authors: Domínguez Rosa María , Herize Armando , Rotinov Alexandra , Alvarez‐Aular Alvaro , Visbal Gonzalo , Chuchani Gabriel
Published: April 2004

The kinetics of the gas‐phase elimination of several 2‐substituted primary, secondary and tertiary hydroxy groups in nitroalkanes were determined in a static reaction system over the temperature range 220–400°C and pressure range of 29–235 Torr. The reactions, in seasoned vessels, are homogeneous and unimolecular and obey a first‐order rate law. The presence of secondary and tertiary hydroxy substituent at the 2‐position of the nitro group in nitroalkanes leads to a retro‐aldol type of decomposition. The mechanism may be rationalized in terms of a six‐membered cyclic transition state to give the corresponding aldehyde or ketone and the nitroalkane, respectively. However, some of the primary 2‐hydroxy groups in nitroalkanes undergo a dehydration process with very limited isomerization to the corresponding alkyl nitrate. The mechanism of dehydration is believed to proceed through a six‐membered rather than the already reported four‐membered cyclic transition state to give the nitroalkene and water. In the case of the primary hydroxy substituent in 2‐methyl‐2‐nitro‐1‐pentanol, the products of elimination are HNO2 gas and 3‐hydroxy‐2‐methyl‐1‐propene. This reaction is rationalized in terms of a four‐membered cyclic transition state type of mechanism. The kinetic and thermodynamic parameters of the hydroxynitroalkane substrates are presented and discussed. Copyright © 2004 John Wiley & Sons, Ltd.
Ground‐ and excited‐state reactivity of some ketenylcarbenes
Authors: Dogaru D. , Pietri N. , Aycard J. P. , Hillebrand M.
Published: April 2004

The reactivity of ketenylcarbenes has been widely discussed on experimental and theoretical grounds in connection with the photochemical decomposition in cryogenic matrices of some substituted cyclobutenediones and maleic anhydrides. It was found that, although the presence of these intermediates was postulated in the decomposition mechanisms, only monofluoroketenylcarbene was experimentally evidenced and characterized by its IR spectrum. In all other cases, the experimental data revealed the formation of the corresponding cyclopropenones and, under continuing irradiation, of the alkynes. Theoretical calculations also point to their high reactivity towards the ring closure reaction. In order to gain an insight into the main factors determining the ketenylcarbene reactivity, ab initio calculations on both the ground (HF/6–31G* and MP2/6–31G*) and the first excited state (HF/6–31G*) were performed. The results indicate that the ring closure reaction is mainly determined by the electrostatic interaction between the carbene center and the Cα atom of the ketenyl group. The role of the in‐plane interaction between the molecular orbital localized on the carbene center and the first two vacant orbitals is also discussed. The excited‐state optimized geometries allow for the characterization of the excited‐state reactivity. Copyright © 2004 John Wiley & Sons, Ltd.
Correlation and prediction of critical micelle concentration using polar surface area and LFER methods
Authors: Saunders Robert A. , Platts James A.
Published: April 2004

Models of critical micelle concentration (CMC) using two separate methods, the linear free energy relationship of Abraham and a modified polar surface area approach, are reported. Individual models are developed for anionic, non‐ionic and structurally diverse molecules, the last including many commercially important drugs such as analgesics, anaesthetics and antibiotics. Statistical analysis demonstrates the predictive accuracy of both methods, with R2 values around 0.90 throughout. A further model for the simultaneous calculation of CMC for anionic and non‐ionic surfactants was developed, giving reasonable correlations of observed vs calculated CMC. Both methods show similar patterns in regression coefficients; the most significant factor affecting a molecule's CMC is its size, with larger surfactants giving lower CMC. Strong H‐bond acidic surfactants form micelles at lower concentrations, and increasing the H‐bond basicity of a surfactant acts to raise the CMC. Copyright © 2004 John Wiley & Sons, Ltd.
Electrochemical and theoretical study of a family of fully conjugated dendritic oligomers
Authors: Osorio Gabriela , Frontana Carlos , Guadarrama Patricia , Frontana‐Uribe Bernardo A.
Published: April 2004

Novel dendritic oligomers of β,β‐dibromo‐4‐ethynylstyrene and formyl‐4‐ethynylstyrene were electrochemically and theoretically studied in order to gain a better insight into their redox behavior. Correlations between calculated ionization and experimental oxidation potentials (anodic peak potentials) were established. The best correlation was obtained when two important effects are considered in the theoretical calculations, probing their strong influence: (a) structural re‐accommodation in the formed radical cation and (b) solvation effects. The effect of dendritic terminal groups (dibromovinyl and formyl groups) was also analyzed. A different redox behavior was observed for these two terminal groups, presumably due to a difference in their oxidation mechanisms. A global chemical transformation for the oxidation of dibromovinyl‐terminated oligomers was proposed, providing a satisfactory explanation of the electrochemical behavior within this family of compounds (presence of adsorptive phenomena). Taking these results into account, it is possible to explain how the cation‐radical species formed in these conjugated dendritic oligomers behave when cyclic voltammetry technique is applied. Copyright © 2004 John Wiley & Sons, Ltd.
Copolymers of phenylacetylene and para‐nitrophenylacetylene with nonlinear optical properties: Further insight on the conformational structure
Authors: Sone Takeyuki , D'Amato Rosaria , Mawatari Yasuteru , Tabata Masayoshi , Furlani Anita , Russo Maria Vittoria
Published: April 2004

Copolymers of phenylacetylene (PA) and para‐nitrophenylacetylene (pNPA), named poly(PA‐co‐pNPA), were obtained in different PA/pNPA ratios and different reaction conditions with Rh(I) catalysts. The structure of the copolymers was investigated with IR, laser Raman, 1H NMR, electron spin resonance (ESR), and diffuse reflective ultraviolet–visible (DRUV) light spectroscopies. The pristine polymers had a cis–transoidal structure as the predominant conformation with some trans sequences. Detailed ESR studies supported by computer simulation and conformation analysis have suggested that the trans sequences were due to pNPA sequences and that the cis‐CC bond sequences of pNPA were associated with a stabilized cis radical formed by four to five of pNPA monomers. This particular stabilization was probably the reason for the higher reactivity of pNPA as compared with PA. These cis sequences were preferentially cleaved to generate π radicals. The compression and, to a minor extent, thermal treatment of poly(PA‐co‐pNPA) samples induced a cis‐to‐trans isomerization, leading to a trans–transoidal form with a planar zigzag structure and with a conjugation length up to n = 24 repeat units, determined by DRUV and Raman experiments. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 2365–2376, 2004
Synthesis and characterization of a multiarm star polymer
Authors: Xiaoying Sun , Xiaohui Yang , Yunhang Liu , Xinling Wang
Published: April 2004

A multiarm star polymer was synthesized through the grafting of oligo polyglycol with urethane chain end units onto the core of hyperbranched polyglycerol (HPG), which was obtained through the cationic ring‐opening polymerization of glycidol. Samples were characterized with 13C NMR, liquid chromatography/mass spectrometry, vapor pressure osmometry, and Raman spectroscopy. The degree of branching of HPG was 0.54, and the number of arms grafting onto HPG was 4. The urethane of the arms mainly reacted with the terminal hydroxy groups of HPG. The differences between the spin–spin relaxation times indicated that the terminal segments of the star were more flexible than those of the core. Grafting polyglycol polyurethane (soft segments of polyurethane is polyglycol) onto HPG improved its dimensional stability. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 2356–2364, 2004
Homologous series of alkylsilylphenyl‐substituted poly (p‐phenylenevinylene)s for light‐emitting diodes
Authors: Jin Sung‐Ho , Koo Dae‐Sung , Seo Hwang‐Un , Kim Young‐Inn , Gal Yeong‐Soon , Park Dong‐Kyu
Published: April 2004

Substituent‐induced electroluminescence polymers—poly[2‐(2‐dimethyldodecylsilylphenyl)‐1,4‐phenylenevinylene] [(o‐R3Si)PhPPV], poly[2‐(3‐dimethyldodecylsilylphenyl)‐1,4‐phenylenevinylene] [(m‐R3Si)PhPPV], and poly[2‐(4‐dimethyldodecylsilylphenyl)‐1,4‐phenylenevinylene] [(p‐R3Si)PhPPV]—were synthesized according to the Gilch polymerization method. The band gap and spectroscopic data were tuned by the dimethyldodecylsilyl substituent being changed from the ortho position to the para position in the phenyl side group along the polymer backbone. The weight‐average molecular weights and polydispersities were 8.0–96 × 104 and 3.0–3.4, respectively. The maximum photoluminescence wavelengths for (o‐R3Si)PhPPV, (m‐R3Si)PhPPV, and (p‐R3Si)PhPPV appeared around 500–530 nm in the green emission region. Double‐layer light‐emitting diodes with an indium tin oxide/poly(3,4‐ethylenedioxythiophene)/polymer/Al configuration were fabricated with these polymers. The turn‐on voltages and the maximum brightness of (o‐R3Si)PhPPV, (m‐R3Si)PhPPV, and (p‐R3Si)PhPPV were 6.5–8.7 V and 1986–5895 cd/m2, respectively. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 2347–2355, 2004
Role of protein in the primary step of the photoreaction of yellow protein
Authors: Yamada Atsushi , Ishikura Takakazu , Yamato Takahisa
Published: April 2004

We show the unexpectedly important role of the protein environment in the primary step of the photoreaction of the yellow protein after light illumination. The driving force of the trans‐to‐cis isomerization reaction was analyzed by a computational method. The force was separated into two different components: the term due to the protein‐chromophore interaction and the intrinsic term of the chromophore itself. As a result, we found that the contribution from the interaction term was much greater than that coming from the intrinsic term. This accounts for the efficiency of the isomerization reaction in the protein environment in contrast to that in solution environments. We then analyzed the relaxation process of the chromophore on the excited‐state energy surface and compared the process in the protein environment and that in a vacuum. Based on this analysis, we found that the bond‐selectivity of the isomerization reaction also comes from the interaction between the chromophore and the protein environment. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Sequence and structure of epoxide hydrolases: A systematic analysis
Authors: Barth Sandra , Fischer Markus , Schmid Rolf D. , Pleiss Jürgen
Published: April 2004

Epoxide hydrolases (EC 3.3.2.3) are ubiquitous enzymes that catalyze the hydrolysis of epoxides to the corresponding vicinal diols. More than 100 epoxide hydrolases (EH) have been identified or predicted, and 3 structures are available. Although they catalyze the same chemical reaction, sequence similarity is low. To identify conserved regions, all EHs were aligned. Phylogenetic analysis identified 12 homologous families, which were grouped into 2 major superfamilies: the microsomal EH superfamily, which includes the homologous families of Mammalian, Insect, Fungal, and Bacterial EHs, and the cytosolic EH superfamily, which includes Mammalian, Plant, and Bacterial EHs. Bacterial EHs show a high sequence diversity. Based on structure comparison of three known structures from Agrobacterium radiobacter AD1 (cytosolic EH), Aspergillus niger (microsomal EH), Mus musculus (cytosolic EH), and multisequence alignment and phylogenetic analysis of 95 EHs, the modular architecture of this enzyme family was analyzed. Although core and cap domain are highly conserved, the structural differences between the EHs are restricted to only two loops: the NC‐loop connecting the core and the cap and the cap‐loop, which is inserted into the cap domain. EHs were assigned to either of three clusters based on loop length. By using this classification, core and cap region of all EHs, NC‐loops and cap‐loops of 78% and 89% of all EHs, respectively, could be modeled. Representative models are available from the Lipase Engineering Database, http://www.led.uni‐stuttgart.de. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
An unusual triosephosphate isomerase from the early divergent eukaryote Giardia lamblia
Authors: López‐Velázquez Gabriel , Molina‐Ortiz Dora , Cabrera Nallely , Hernández‐Alcántara Gloria , Peon‐Peralta Jorge , Yépez‐Mulia Lilian , Pérez‐Montfort Ruy , Reyes‐Vivas Horacio
Published: April 2004

Recombinant triosephosphate isomerase from the parasite Giardia lamblia (GlTIM) was characterized and immunolocalized. The enzyme is distributed uniformly throughout the cytoplasm. Size exclusion chromatography of the purified enzyme showed two peaks with molecular weights of 108 and 55 kDa. Under reducing conditions, only the 55‐kDa protein was detected. In denaturing gel electrophoresis without dithiothreitol, the enzyme showed two bands with molecular weights of 28 and 50 kDa; with dithiotretitol, only the 28‐kDa protein was observed. These data indicate that GlTIM may exist as a tetramer or a dimer and that, in the former, the two dimers are covalently linked by disulfide bonds. The kinetics of the dimer were similar to those of other TIMs. The tetramer exhibited half of the kcat of the dimer without changes in the Km. Studies on the thermal stability and the apparent association constants between monomers showed that the tetramer was slightly more stable than the dimer. This finding suggests the oligomerization is not related to enzyme thermostability as in Thermotoga maritima. Instead, it could be that oligomerization is related to the regulation of catalytic activity in different states of the life cycle of this mesophilic parasite. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Superfamily active site templates
Authors: Meng Elaine C. , Polacco Benjamin J. , Babbitt Patricia C.
Published: April 2004

We show that three‐dimensional signatures consisting of only a few functionally important residues can be diagnostic of membership in superfamilies of enzymes. Using the enolase superfamily as a model system, we demonstrate that such a signature, or template, can identify superfamily members in structural databases with high sensitivity and specificity. This is remarkable because superfamilies can be highly diverse, with members catalyzing many different overall reactions; the unifying principle can be a conserved partial reaction or chemical capability. Our definition of a superfamily thus hinges on the disposition of residues involved in a conserved function, rather than on fold similarity alone. A clear advantage of basing structure searches on such active site templates rather than on fold similarity is the specificity with which superfamilies with distinct functional characteristics can be identified within a large set of proteins with the same fold, such as the (β/α)8 barrels. Preliminary results are presented for an additional group of enzymes with a different fold, the haloacid dehalogenase superfamily, suggesting that this approach may be generally useful for assigning reading frames of unknown function to specific superfamilies and thereby allowing inference of some of their functional properties. Proteins 2004;9999:000–000. © 2004 Wiley‐Liss, Inc.
Relationships between amino acid sequence and backbone torsion angle preferences
Authors: Keskin O. , Yuret D. , Gursoy A. , Turkay M. , Erman B.
Published: April 2004

Statistical averages and correlations for backbone torsion angles of chymotrypsin inhibitor 2 are calculated by using the Rotational Isomeric States model of chain statistics. Statistical weights of torsional states of ϕψ pairs, needed for the statistics of the full chain, are obtained in two different ways: 1) by using knowledge‐based pairwise dependent ϕψ energy maps from Protein Data Bank (PDB) and 2) by collecting torsion angle data from a large number of random coil configurations of an all‐atom protein model with volume exclusion. Results obtained by using PDB data show strong correlations between adjacent torsion angle pairs belonging to both the same and different residues. These correlations favor the choice of the native‐state torsion angles, and they are strongly context dependent, determined by the specific amino acid sequence of the protein. Excluded volume or steric clashes, only, do not introduce context‐dependent ϕψ correlations into the chain that would affect the choice of native‐state torsional angles. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Exploring structural features of the interaction between the scorpion toxinCnErg1 and ERG K+ channels
Authors: Frénal Karine , Xu Chen‐Qi , Wolff Nicolas , Wecker Karine , Gurrola Georgina B. , Zhu Shun‐Yi , Chi Cheng‐Wu , Possani Lourival D. , Tytgat Jan , Delepierre Muriel
Published: April 2004

The γ‐KTx–type scorpion toxins specific for K+ channels were found to interact with ERG channels on the turret region, while α‐KTx3.2 Agitoxin‐2 binds to the pore region of the Shaker K+ channel, and α‐KTx5.3 BmP05 binds to the intermediate region of the small‐conductance calcium‐activated K‐channel (SKCa). In order to explore the critical residues for γ‐KTx binding, we determined the NMR structure of native γ‐KTx1.1 (CnErg1), a 42 amino acid residues scorpion toxin isolated from the venom of the Mexican scorpion Centruroïdes noxius Hoffmann, and we used computational evolutionary trace (ET) analysis to predict possible structural and functional features of interacting surfaces. The 1H‐NMR three‐dimensional solution structure of native ergtoxin (CnErg1) was solved using a total of 452 distance constraints, 13 3JNH‐Hα and 10 hydrogen bonds. The structure is characterized by 2 segments of α‐helices and a triple‐stranded antiparallel β‐sheet stabilized by 4 disulfide bridges. The ET and structural analysis provided indication of the presence of two important amino acid residue clusters, one hydrophobic and the other hydrophilic, that should be involved in the surface contact between the toxin and the channel. Some features of the proposed interacting surface are discussed. Proteins 2004. © 2004 Wiley‐Liss, Inc.
YbdK is a carboxylate‐amine ligase with a γ‐glutamyl:Cysteine ligase activity: Crystal structure and enzymatic assays
Authors: Lehmann Christopher , Doseeva Victoria , Pullalarevu Sadhana , Krajewski Wojciech , Howard Andrew , Herzberg Osnat
Published: April 2004

The Escherichia coli open reading frame YbdK encodes a member of a large bacterial protein family of unknown biological function. The sequences within this family are remotely related to the sequence of γ‐glutamate‐cysteine ligase (γ‐GCS), an enzyme in the glutathione biosynthetic pathway. A gene encoding γ‐GCS in E. coli is already known. The 2.15 Å resolution crystal structure of YbdK reveals an overall fold similar to that of glutamine synthetase (GS), a nitrogen metabolism enzyme that ligates glutamate and ammonia to yield glutamine. GS and γ‐GCS perform related chemical reactions and require ATP and Mg2+ for their activity. The Mg2+‐dependent binding of ATP to YbdK was confirmed by fluorescence spectroscopy employing 2′(or 3′)‐O‐(trinitrophenyl)adenosine 5′‐triphosphate, and yielding a dissociation constant of 3 ± 0.5 μM. The structure of YbdK contains a crevice that corresponds to the binding sites of ATP, Mg2+ and glutamate in GS. Many of the GS residues that coordinate the metal ions and interact with glutamic acid and the phosphoryl and ribosyl groups of ATP are also present in YbdK. GS amino acids that have been associated with ammonia binding have no obvious counterparts in YbdK, consistent with a substrate specificity that is different from that of GS. Ligase activity between glutamic acid and each of the twenty amino acid residues was tested on high performance liquid chromatography (HPLC) by following the hydrolysis of ATP to ADP. Catalysis was observed only with cysteine. A pyruvate kinase/lactic acid dehydrogenase coupled assay was used to rule out GS activity and to determine that YbdK exhibits γ‐GCS activity. The catalytic rate was found to be approximately 500‐fold slower than that reported for authentic γ‐GCS. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Calculating proton uptake/release and binding free energy taking into account ionization and conformation changes induced by protein–inhibitor association: Application to plasmepsin, cathepsin D and endothiapepsin–pepstatin complexes
Authors: Alexov Emil
Published: April 2004

The protein‐inhibitor binding energies of enzymes are often pH dependent, and binding induces either proton uptake or proton release. The proton uptake/release and the binding energy for three complexes with available experimental data were numerically studied: pepstatin–cathepsin D, pepstatin–plasmepsin II and pepstatin–endothiapepsin. Very good agreement with the experimental data was achieved when conformational changes were taken into account. The role of the desolvation energy and the conformational changes was revealed by modeling the complex, the separated molecules in the complex conformation and the free molecules. It was shown that the conformational changes induced by the complex formation are as important for the proton transfer as the loss of solvation energy caused by the burial of interface residues. The residues responsible for the proton transfer were identified and their contribution to the proton uptake/release calculated. These residues were found to be scattered along the whole protein rather than being localized only at the active site. In the case of cathepsin D, these residues were found to be highly conserved among the cathepsin D sequences of other species. It was shown that conformation and ionization changes induced by the complex formation are critical for the correct calculation of the binding energy. Taking into account the electrostatics and the van der Waals (vdW) energies within the Boltzmann distribution of energies and allowing ionization and conformation changes to occur makes the calculated binding energy more realistic and closer to the experimental value. The interplay between electrostatic and vdW forces makes the pH dependence of the binding energy smoother, because the vdW force acts in reaction to the changes of the electrostatic energy. It was found that a small fraction of the ionizable groups remain uncharged in both the free and complexed molecules. The sequence and structural position of these groups aligns well within the three proteases, suggesting that these may have specific role. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Towards a structural classification of phosphate binding sites in protein–nucleotide complexes: An automated all‐against‐all structural comparison using geometric matching
Authors: Brakoulias Andreas , Jackson Richard M.
Published: April 2004

A method is described for the rapid comparison of protein binding sites using geometric matching to detect similar three‐dimensional structure. The geometric matching detects common atomic features through identification of the maximum common sub‐graph or clique. These features are not necessarily evident from sequence or from global structural similarity giving additional insight into molecular recognition not evident from current sequence or structural classification schemes. Here we use the method to produce an all‐against‐all comparison of phosphate binding sites in a number of different nucleotide phosphate‐binding proteins. The similarity search is combined with clustering of similar sites to allow a preliminary structural classification. Clustering by site similarity produces a classification of binding sites for the 476 representative local environments producing ten main clusters representing half of the representative environments. The similarities make sense in terms of both structural and functional classification schemes. The ten main clusters represent a very limited number of unique structural binding motifs for phosphate. These are the structural P‐loop, di‐nucleotide binding motif [FAD/NAD(P)‐binding and Rossman‐like fold] and FAD‐binding motif. Similar classification schemes for nucleotide binding proteins have also been arrived at independently by others using different methods. Proteins 2004. © 2004 Wiley‐Liss, Inc.
β‐Hairpin folding and stability: molecular dynamics simulations of designed peptides in aqueous solution
Authors: Santiveri Clara M. , Jiménez M. Ángeles , Rico Manuel , van Gunsteren Wilfred F. , Daura Xavier
Published: April 2004

The structural properties of a 10‐residue and a 15‐residue peptide in aqueous solution were investigated by molecular dynamics simulation. The two designed peptides, SYINSDGTWT and SESYINSDGTWTVTE, had been studied previously by NMR at 278 K and the resulting model structures were classified as 3:5 β‐hairpins with a type I + G1 β‐bulge turn. In simulations at 278 K, starting from the NMR model structure, the 3:5 β‐hairpin conformers proved to be stable over the time period evaluated (30 ns). Starting from an extended conformation, simulations of the decapeptide at 278 K, 323 K and 353 K were also performed to study folding. Over the relatively short time scales explored (30 ns at 278 K and 323 K, 56 ns at 353 K), folding to the 3:5 β‐hairpin could only be observed at 353 K. At this temperature, the collapse to β‐hairpin‐like conformations is very fast. The conformational space accessible to the peptide is entirely dominated by loop structures with different degrees of β‐hairpin character. The transitions between different types of ordered loops and β‐hairpins occur through two unstructured loop conformations stabilized by a single side‐chain interaction between Tyr2 and Trp9, which facilitates the changes of the hydrogen‐bond register. In agreement with previous experimental results, β‐hairpin formation is initially driven by the bending propensity of the turn segment. Nevertheless, the fine organization of the turn region appears to be a late event in the folding process. Copyright © 2004 European Peptide Society and John Wiley & Sons, Ltd.
Tissue distribution of antihypertensive dipeptide, Val‐Tyr, after its single oral administration to spontaneously hypertensive rats
Authors: Matsui Toshiro , Imamura Miho , Oka Hiromi , Osajima Katsuhiro , Kimoto Ko‐Ichi , Kawasaki Terukazu , Matsumoto Kiyoshi
Published: April 2004

The distribution of an antihypertensive dipeptide, Val‐Tyr (VY), in the tissues of spontaneously hypertensive rats (SHR) was investigated in this study. A single oral administration of VY (10 mg/kg) to 18‐week‐old SHR resulted in a prolonged reduction of systolic blood pressure (SBP) up to 9 h (SBP0h198.0 ± 3.6 mmHg; SBP9h 154.6 ± 3.5 mmHg). As a result of VY determination, a roughly 10‐fold higher increment of plasma VY level was observed at 1 h than that at 0 h, whereas thereafter the level declined rapidly. In tissues, VY was widely accumulated in the kidney, lung, heart, mesenteric artery and abdominal aorta with the area under the curve over 9 h of more than 40 pmol h/g tissue; of these a higher VY level was observed in the kidney and lung. In addition, a mean resident time (MRT) for each tissue (>5 h except for liver) revealed that VY preferably accumulated in the tissues rather than in the plasma (MRT 3.8 h). Significant reductions of tissue angiotensin I‐converting enzyme activity and angiotensin II level were found in the abdominal aorta as well as in the kidney, suggesting that these organs could be a target site associated with the antihypertensive action of VY. Copyright © 2004 European Peptide Society and John Wiley & Sons, Ltd.
Interval Charting Schemes for Joint Monitoring of Process Mean and Variance
Authors: Gan F. F. , Ting K. W. , Chang T. C.
Published: April 2004

Shewhart mean and variance schemes continue to enjoy great popularity among process engineers because they are easy to understand and are the most sensitive in detecting large process shifts. For some processes, for example the screen printing process in memory modules assembly, there is a possibility of the process mean and variance shifting at the same time due to special causes. Thus, instead of studying the joint behavior by looking at the mean and variance information on two separate charts, it is practical and usually more meaningful to look at the combined mean and variance information on an interval charting scheme. The interval scheme is found to have a similar run length performance to the Shewhart mean and variance schemes and only a single chart needs to be managed. A simple design procedure for the interval scheme that matches the corresponding Shewhart scheme is provided for easy implementation. Also, the interval and Shewhart schemes are compared based on real manufacturing data sets. Copyright © 2004 John Wiley & Sons, Ltd.
JaRec: a portable record/replay environment for multi‐threaded Java applications
Authors: Georges A. , Christiaens M. , Ronsse M. , De Bosschere K.
Published: April 2004

This paper describes JaRec, a portable record/replay system for Java. It correctly replays multi‐threaded, data‐race free Java applications, by recording the order of synchronization operations, and by executing them in the same order during replay. The record/replay infrastructure is developed in Java, and does not require a modification of the Java Virtual Machine (JVM) if it provides the JVM Profiler Interface (JVMPI). If the JVM does not support JVMPI, which is used for intercepting the loaded classes, only a minor modification to the JVM is required in order to run the system. On ystems with limited memory resources, JaRec can be executed in a distributed fashion. This also makes it suitable to aid debugging of multi‐threaded applications on embedded systems. Copyright © 2004 John Wiley & Sons, Ltd.
A Web‐based distributed system for hurricane occurrence projection
Authors: Chen Shu‐Ching , Gulati Sneh , Hamid Shahid , Huang Xin , Luo Lin , Morisseau‐Leroy Nirva , Powell Mark D. , Zhan Chengjun , Zhang Chengcui
Published: April 2004

As an environmental phenomenon, hurricanes cause significant property damage and loss of life in coastal areas almost every year. Research concerning hurricanes and their aftermath is gaining more and more attention nowadays. This paper presents our work in designing and building a Web‐based distributed software system that can be used for the statistical analysis and projection of hurricane occurrences. Firstly, our system is a large‐scale system and can handle the huge amount of hurricane data and intensive computations in hurricane data analysis and projection. Secondly, it is a distributed system, which allows multiple users at different locations to access the system simultaneously and to share and exchange the data and data model. Thirdly, our system is a database‐centered system where the Oracle database is employed to store and manage the large amount of hurricane data, the hurricane model and the projection results. Finally, a three‐tier architecture has been adopted to make our system robust and resistant to the potential change in the lifetime of the system. This paper focuses on the three‐tier system architecture, describing the design and implementation of the components at each layer. Copyright © 2004 John Wiley & Sons, Ltd.
Tracing system‐level communication in distributed systems
Authors: Mann Zoltán Ádám , Kondorosi Károly
Published: April 2004

Traditional tracing mechanisms, usually developed for use in a single‐computer environment, are bound to a specific programming language. Today's highly distributed and heterogeneous computing environments require new tracing methodologies. This paper addresses the problem by reviewing ways in which the middleware might—and should—support tracing. In particular, CORBA (Common Object Request Broker Architecture) meta‐objects that can be applied for tracing are studied. One meta‐object, namely the interceptor concept, is presented in more depth, followed by a detailed description of an interceptor‐based tracing architecture for CORBA applications. Implementation details and evaluation experience are given. Copyright © 2004 John Wiley & Sons, Ltd.
A softerware monitor for shared‐memory multiprocessor computers
Authors: Liu Xian , Xu Feilong
Published: April 2004

ANIX is a multiprocessor operating system to be used in the backbone Asynchronous Transfer Mode (ATM) switches. In ANIX, memory contention by processes running on different CPUs is managed with a protocol called WWWH (when to sleep, who to sleep, where to sleep, and how to sleep). Tools are needed to test, debug, and tune the system running WWWH. This paper describes the experience and practice in design of SHMON, a performance tool that monitors the dynamic behavior of the running system. Copyright © 2004 John Wiley & Sons, Ltd.
Brain vesicular acetylcholine transporter in human users of drugs of abuse
Authors: Siegal Deborah , Erickson Jeffrey , Varoqui H́el̀ene , Ang Lee , Kalasinsky Kathryn S. , Peretti Frank J. , Aiken Sally S. , Wickham Dennis J. , Kish Stephen J.
Published: April 2004

Limited animal data suggest that the dopaminergic neurotoxin methamphetamine is not toxic to brain (striatal) cholinergic neurons. However, we previously reported that activity of choline acetyltransferase (ChAT), the cholinergic marker synthetic enzyme, can be very low in brain of some human high‐dose methamphetamine users. We measured, by quantitative immunoblotting, concentrations of a second cholinergic marker, the vesicular acetylcholine transporter (VAChT), considered to be a “stable” marker of cholinergic neurons, in autopsied brain (caudate, hippocampus) of chronic users of methamphetamine and, for comparison, in brain of users of cocaine, heroin, and matched controls. Western blot analyses showed normal levels of VAChT immunoreactivity in hippocampus of all drug user groups, whereas in the dopamine‐rich caudate VAChT levels were selectively elevated (+48%) in the methamphetamine group, including the three high‐dose methamphetamine users who had severely reduced ChAT activity. To the extent that cholinergic neuron integrity can be inferred from VAChT concentration, our data suggest that methamphetamine does not cause loss of striatal cholinergic neurons, but might damage/downregulate brain ChAT in some high‐dose users. However, the finding of increased VAChT levels suggests that brain VAChT concentration might be subject to up‐ and downregulation as part of a compensatory process to maintain homeostasis of neuronal cholinergic activity. This possibility should be taken into account when utilizing VAChT as a neuroimaging outcome marker for cholinergic neuron number in human studies. Synapse 52:223–232, 2004. Published 2004 Wiley‐Liss, Inc.
Management options for the Blackwater herring, a local spring-spawning stock in the Thames Estuary
Authors: Roel Beatriz A. , O'Brien Carl M. , Basson Marinelle
Published: April 2004

Herring caught in the Thames Estuary sustain a small local commercial fishery (peak catch of 606 t during the 1972–1973 fishing season). Loss of local consumers' interest in the herring product has resulted in a gradual decline in catches and fishing effort for the stock. The stock is assessed using an age-structured model that relies on the information provided by a scientific trawl survey, and management advice is provided before the fishing season starts in October. Given its current low economic value, managers have requested evaluation of options for multi-annual Total Allowable Catches (TACs) in an attempt to reduce the frequency (and costs) of assessment and associated management advice. A tentative relationship between sea surface temperature and recruitment is used to predict the impact of increasing sea temperatures on future recruitment in the context of global warming. Hypotheses of auto-correlation and of an environmental effect on recruitment, together with trends in weight-at-age and the overestimation of spawning-stock biomass, form the basis for sensitivity tests of the management options considered. Implementation of a 3-year fixed TAC with 40% constraint in TAC variability and a slight reduction in target F would seem appropriate for the stock, given that it is within safe biological limits and compares well in terms of yield and risk with the current approach of annual TAC revision.
FRS2 family docking proteins with overlapping roles in activation of MAP kinase have distinct spatial‐temporal patterns of expression of their transcripts
Authors: Gotoh Noriko , Laks Shaked , Nakashima Misako , Lax Irit , Schlessinger Joseph
Published: April 2004

FRS2α and FRS2β, two members of the FRS2 family of docking proteins, become tyrosine phosphorylated in response to fibroblast growth factor (FGF) or nerve growth factor (NGF) stimulation. Tyrosine phosphorylated FRS2α serves as a platform for the recruitment of multiple signaling proteins for activation of the Ras‐mitogen‐activated protein (MAP) kinase signaling cascade. We report that Frs2α and Frs2β have distinct spatio‐temporal expression patterns in mouse embryos. We further show that FRS2β can compensate for the loss of FRS2α for activation of MAP kinase when expressed in fibroblasts from Frs2α
−/− mouse embryos. We propose that the FRS2 family proteins have distinct roles in vivo through activation of common signaling proteins including MAP kinase.
Integrative ecological restoration and the involvement of local communities in the Tehuacán-Cuicatlán Valley, Mexico
Authors: DHILLION SHIVCHARN S. , AGUILAR-STØEN MARIEL , CAMARGO-RICALDE SARA LUCIA
Published: April 2004

Restoration ecology is a science focusing on using ecological principles to improve ecosystems degraded usually through habitat destruction (Bradshaw & Chadwik 1980, Handel et al. 1994). Successful ecological restoration depends on negotiation and understanding of different stakeholders, including the daily users of the resources, government institutions that will regulate resource use and the research community working in the area.
Accelerating deforestation in Brazilian Amazonia: towards answering open questions
Authors: FEARNSIDE PHILIP M. , BARBOSA REINALDO IMBROZIO
Published: April 2004

The annual rate of deforestation in Brazilian Amazonia jumped by an estimated 40% between 2001 and 2002. This increase is in addition to a 15% upward revision by the Brazilian government of the estimated rate for 2001. Examination of the data underlying these estimates and comparisons with other measurements indicates that important questions remain unanswered, especially in the state of Mato Grosso, where assessment of the effectiveness of a deforestation licensing and control programme is critical to future efforts to contain forest destruction. The increase in deforestation rate in Mato Grosso in 2002 (23%) was less than half the increase in the remainder of Brazilian Amazonia (55%), indicating that the state government's deforestation control programme may have had some effect.
Effects of artificial water points on the Oshana ecosystem in Namibia
Authors: NANGULA S. , OBA G.
Published: April 2004

In the semi-arid rangelands of the Oshana ecosystem in Northern Namibia, there are general concerns that artificial water points for domestic use contribute to the processes that lead to desertification. The processes begin in piospheres of artificial water points. Among the processes suggested to correlate with radial distance and age of water points are loss of perennial grass species, an increase in annuals, and general loss of herbaceous species richness, herbaceous biomass and grass cover, as well as an increase in forb cover and in bare ground and litter cover. Radial distance and age of artificial water points impacts were compared using these indicators with benchmarks in saline grassland and mopane landscape at the end of the wet season. Radial distance influenced herbaceous species richness, grass cover and bare ground, while the variability of the perennial:annual grass ratio, herbaceous biomass, forb and litter cover were attributed to differences between landscape types. Age of water points influenced only herbaceous species richness, while forb cover was associated more with water points than benchmarks. Forb cover was sporadic in relation to age of water points. In the Oshana ecosystem, therefore, radial-grazing distance could not be used to explain changes in the perennial:annual grass ratio. Many of the changes were explained by differences between landscape types. The mopane landscape was more vulnerable to degradation induced by artificial water points than the grassland landscape. The implication is that, in the future, greater care should be taken to space water points in the mopane landscape.
Household production and forest clearing: the role of farming in the development of the Amazon
Authors: CAVIGLIA-HARRIS JILL L.
Published: April 2004

Global tropical deforestation continues to be a critical environmental issue and nowhere in the world is the issue more pronounced than in Brazil. This paper examines the land-use choices of small-scale farmers in Ouro Preto do Oeste, Rondônia, Brazil and investigates how agricultural production impacts deforestation levels. The data used to explore these issues consist of a panel collected from 152 households in 1996 and 2000. Overall, the empirical models indicate that access to credit, wealth, lot size, product markets, and off-farm labor opportunities, largely influence deforestation and production decisions. Among other things, the results suggest that more sustainable production methods are unlikely to be adopted by a majority of households under current conditions because the production of milk has rapidly advanced due to its moderate labor requirements and existing market infrastructure. Households with greater levels of wealth have focused on milk while those with access to credit have focused on crops. Since the production of crops is largely influenced by access to credit, similar incentives may be proposed to support more sustainable production activities to help reduce deforestation.