bluuebunny/crossref_metadata_2025 huggingface dataset:
CLN3, the protein associated with batten disease: Structure, function and localization
Authors: Phillips Seasson N. , Benedict Jared W. , Weimer Jill M. , Pearce David A.
Published: January 2005

Batten disease, an inherited neurodegenerative storage disease affecting children, results from the autosomal recessive inheritance of mutations in Cln3. The function of the CLN3 protein remains unknown. A key to understanding the pathology of this devastating disease will be to elucidate the function of CLN3 at the cellular level. CLN3 has proven difficult to study as it is predicted to be a membrane protein expressed at relatively low levels. This article is a critical review of various approaches used in examining the structure, trafficking, and localization of CLN3. We conclude that CLN3 is likely resident in the lysosomal/endosomal membrane. Different groups have postulated conflicting orientations for CLN3 within this membrane. In addition, CLN3 undergoes several posttranslational modifications and is trafficked through the endoplasmic reticulum and Golgi. Recent evidence also suggests that CLN3 traffics via the plasma membrane. Although the function of this protein remains elusive, it is apparent that genetic alterations in Cln3 may have a direct affect on lysosomal function. © 2005 Wiley‐Liss, Inc.
Bose-Einstein condensates in fast rotation
Authors: Stock S , Battelier B , Bretin V , Hadzibabic Z , Dalibard J
Published: January 2005

In this short review we present our recent results concerning the rotation of atomic Bose-Einstein condensates confined in quadratic or quartic potentials, and give an overview of the field. We first describe the procedure used to set an atomic gas in rotation and briefly discuss the physics of condensates containing a single vortex line. We then address the regime of fast rotation in harmonic traps, where the rotation frequency is close to the trapping frequency. In this limit the Landau Level formalism is well suited to describe the system. The problem of the condensation temperature of a fast rotating gas is discussed, as well as the equilibrium shape of the cloud and the structure of the vortex lattice. Finally we review results obtained with a quadratic + quartic potential, which allows to study a regime where the rotation frequency is equal to or larger than the harmonic trapping frequency.
Optimization of Bragg reflectors in AlGaAs/GaAs VCSELs
Authors: Passaro V M N , Magno F , De Leonardis F
Published: January 2005

In this paper a detailed investigation of the
distributed Bragg reflectors in GaAs-based vertical cavity surface
emitting lasers is presented. The influence of layer doping
concentration, number of periods, oxide aperture and
AlxGa1-xAs alloy composition on output emission power
and threshold current has been found. Both oxidized and non
oxidized structures have been considered. A number of
interpolation curves are extracted and presented for design and
fabrication purposes. Although the results are presented for
GaAs-based structures, the theoretical approach is very general.
Diamond-shaped-core hollow photonic-crystal fiber
Authors: Konorov S O , Mel'nikov L A , Ivanov A A , Alfimov M V , Shcherbakov A V , Zheltikov A M
Published: January 2005

We report fabrication and characterization of hollow
photonic-crystal fibers (PCFs) with a diamond-shaped core and a
Kagome-lattice cladding. Air-guides modes strongly confined to the
hollow core of the fiber are shown to exist within the ranges of
wavelengths from 450 to 560 nm and from 470 to 630 nm for two
hollow diamond-shaped-core PCFs with slightly different geometry
parameters. Polarization-maintaining air-mode guidance of 100-fs
second-harmonic pulses of 625-nm Cr:forsterite laser radiation is
demonstrated.
Chain‐End and Chain‐Internal Crosslinking in “Latent Reactive” Silicon Elastomers
Authors: Matloka Piotr P. , Sworen John C. , Zuluaga Fabio , Wagener Kenneth B.
Published: January 2005

Summary: Latent reactivity has been employed to create processable elastomers constructed of carbosilane and either carbosiloxane or polyether segments. Two types of latent modes have been introduced: “chain‐internal” and “chain‐end” sites through the use of labile silicon methoxy and trifunctional olefinic functionalities. These latent reactive sites remain inert during formation of the linear copolymer; subsequent exposure to moisture triggers hydrolysis of the methoxy group and formation of a chemically crosslinked thermoset. These “chain‐end” sites limit the formation of dangling chains improving the overall mechanical properties of the material. The thermoset's mechanical response can be potentially varied from plastic to elastic behavior, depending on the ratio of hard and soft monomers employed. The concentration of “chain‐internal” and “chain‐end” crosslink sites enhances strength; modification to the run length and structure of the soft phase enhances elasticity, generating samples having moduli of 6 MPa, tensile strengths of 0.6 MPa and elongations of 400%.

“Latent reactive” silicon elastomer.

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“Latent reactive” silicon elastomer.
Morphology and Phase Characteristics of High‐Density Polyethylene Probed by NMR Spin Diffusion and Second Moment Analysis
Authors: Lili Zhang , Chen Qun , Hansen Eddy W.
Published: January 2005

Summary: A dipolar filter pulse sequence combined with cross‐polarization‐MAS is applied to characterize the phase distribution, morphology, and spin diffusion within a high‐density polyethylene sample. A new method to obtain quantitative 13C NMR by combining cross‐polarization‐MAS and spin diffusion NMR is presented. The derived crystallinity is consistent with the corresponding crystallinity obtained by 1H NMR.

Illustration of the pulse sequence(s) applied in the present work.

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Illustration of the pulse sequence(s) applied in the present work.
Poly(vinyl acetate)/Silver Nanocomposite Microspheres Prepared by Suspension Polymerization at Low Temperature
Authors: Yeum Jeong Hyun , Sun Qunhui , Deng Yulin
Published: January 2005

Summary: High molecular weight (HMW) poly(vinyl acetate)/silver nanocomposite microspheres (PVAc/Ag), which are promising precursors of embolic materials with radiopacity, were prepared via a suspension polymerization approach in the presence of silver nanoparticles. It was found that a high yield and high molecular weight PVAc/Ag could be concurrently obtained even using a low‐temperature initiator 2,2′‐azobis(2,4‐dimethylvaleronitrile) (≈30 °C). In the case of presence of silver nanoparticles, the rate of polymerization was slightly slower than that without Ag. The suspension polymerization approach introduced could produce PVAc/Ag composite with conversion and viscosity‐average molecular weight ($\overline M _{\rm v}$) up to 95% and 1 300 000, respectively, in spite of the low polymerization temperature (≈30 °C), in sharp contrast with an only ≈30% conversion of VAc under bulk polymerization. Morphology studies revealed that except normal suspension microspheres with a smooth surface, a golf ball‐like appearance of the microspheres was observed, due to the migration and aggregating of the hydrophilic Ag nanoparticles at the sublayer beneath the microsphere's surface.

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The impact of water on photopolymerization kinetics of methacrylate/vinyl ether hybrid systems
Authors: Lin Yan , Stansbury Jeffrey W.
Published: January 2005

Real‐time FT‐near infrared (NIR) spectroscopy was used to monitor individual monomer photopolymerization kinetics within the hybrid methacrylate/vinyl ether system composed of 2‐hydroxyethyl methacrylate and tri(ethylene glycol) methyl vinyl ether. Photoinitiation conditions have been manipulated to provide staged polymer formation of the selected hybrid systems. Significant differences were observed in the effect of water on hybrid systems with different polymerization sequence. The radical/cationic dual initiator system drastically decreased the effect of water on the vinyl ether polymerization. Even with significant water present, both the methacrylate and vinyl ether monomers can be effectively polymerized under certain initiation conditions. Copyright © 2005 John Wiley & Sons, Ltd.
Synthesis and characterization of bismaleimide‐polyetherimide‐silica hybrid by sol‐gel process
Authors: Li Shanjun , Tian Junxiang , Gan Wenjun , Zhao Lin , Li Liang , Wang Jinchen
Published: January 2005

A ternary hybrid of bismaleimide‐polyetherimide‐silica (BMI‐PEI‐SiO2) was synthesized by sol‐gel reaction and characterized by scanning electron microscopy (SEM), energy dispersive X‐ray analysis (EDX), thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC).

The results indicated that silica could be introduced into the blend of thermoplastic‐thermosetting system by sol‐gel reaction and dispersed uniformly as nanoparticles. The phase separation of BMI‐PEI was not affected apparently by the presence of silica. The coupling agent 3‐aminopropyl (triethoxy)silane was chosen to enhance the interaction between the polymer‐matrix and silica. Thermal properties and mechanical properties of the hybrids both were improved with increasing silica content. Copyright © 2005 John Wiley & Sons, Ltd.
Effect of filler and void content on mechanical properties of pultruded composite materials under shear loading
Authors: Park Jin Y. , Zureick Abdul‐Hamid
Published: January 2005

This paper presents the results of an analytical investigation aimed at examining the mechanical behavior of fiber‐reinforced polymer matrix materials containing nonhomogeneous constituents such as fine clay fillers under shear loading. Analytical formulae that account for the presence of inhomogeneities in the matrix materials were developed for estimating the extensional and in‐plane shear moduli and Poisson's ratio. The analytical results were compared with the properties obtained from experiments. For the experiments, the pultruded composites containing clay fillers and voids as well as glass fiber and vinylester resin were selected, analyzed, and tested under shear loading. The effects of presence of constituents on the mechanical properties of matrix materials were also investigated based on the obtained volume fraction of their constituents. POLYM. COMPOS., 26:181–192, 2005. © 2005 Society of Plastics Engineers
Determination of dynamic delamination toughness of a graphite‐fiber/epoxy composite using Hopkinson pressure bar
Authors: Wu Xiang‐Fa , Dzenis Yuris A.
Published: January 2005

Modified dynamic three‐point‐bending and compact shearing test configurations based on Hopkinson pressure bar (HPB) and crack detection gage (CDG) (Vishay Intertechnology, Inc) were used for the determination of the dynamic mode I and mode II delamination‐initiation toughness of a unidirectional graphite‐fiber/epoxy composite made of P7051S‐20Q‐1000 prepregs (Toray Composites America). The transient loading history was recorded precisely by the HPB installed with a high‐resolution digital oscilloscope, and the crack initiation and delay time were captured using the CDG. By means of dynamic finite‐element analysis (FEA) of the impact processes with the loading history and crack initiation time as input, the critical dynamic stress intensity factors (DSIFs) (KIDC/KIIDC) were extracted from numerical results of the crack opening displacements (CODs). Results show that under the present transient loadings, the KIDCvalue is about 80–90% of the static one, while the KIIDCvalue is nearly unchanged. Dynamic failure mechanisms of the composite specimens were evaluated by fractography using a scanning electron microscope (SEM). POLYM. COMPOS., 26:165–180, 2005. © 2005 Society of Plastics Engineers
Evaluation of starch‐PE multilayers: Processing and properties
Authors: Dole Patrice , Avérous Luc , Joly Catherine , Valle Guy Della , Bliard Christophe
Published: January 2005

Adhesion tests performed on various plasticized starch‐polyethylene multi‐layer systems led to the selection of a suitable combination of polymers compatible with the starch‐based layer. The compatibility of starch and polyethylene was better achieved through maleic anhydride functionalized polyethylene (PEg) than chemically modifying starch. The PEg method proved efficient provided that the water content, and the plasticizer nature and contents of the starch layer were carefully chosen. Computed shear viscosity allowed us to select a suitable botanical origin of starch such that the interfacial instabilities of the coextrusion process were minimized. The use of a multilayer structure (PE/PEg/starch/PEg/PE) improved gas barrier properties at high relative humidity. The higher quantity of water sorbed by thermoplastic starch (as compared to EVOH) coupled with starch's specific water sorption isotherm lengthened the water equilibration time in the hydrophilic inner layer significantly. As a result the gas barrier properties of the starch based multiplayer systems were enhanced as compared to existing commercial multiplayer systems (PE/PEg/EVOH/PEg/PE). This specific “water‐buffering property” of the starch inner layer should prove useful in packaging applications of perishables with extended shelf life in environments of varying relative humidity. Polym. Eng. Sci. 45:217–224, 2005. © 2005 Society of Plastics Engineers.
Synthesis and characterization of polyamides containing octadecanedioic acid: Nylon‐2,18, nylon‐3,18, nylon‐4,18, nylon‐6,18, nylon‐8,18, nylon‐9,18, and nylon‐12,18
Authors: Bennett Carl , Mathias Lon J.
Published: January 2005

High‐aliphatic‐content linear nylons were produced with an 18‐carbon diacid with diamines containing both odd and even methylene segments. The resulting polymers were characterized with viscosimetric, thermal, and spectroscopic techniques. Solid‐state 15N NMR was used to determine the nylon crystalline form present. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 936–945, 2005
Synthesis and copolymerization of fluorinated monomers bearing a reactive lateral group. XX. Copolymerization of vinylidene fluoride with 4‐bromo‐1,1,2‐trifluorobut‐1‐ene
Authors: Guiot J. , Néouze M.‐A. , Sauguet L. , Améduri B. , Boutevin B.
Published: January 2005

The radical copolymerization of vinylidene fluoride (VDF) with 4‐bromo‐1,1,2‐trifluorobut‐1‐ene (C4Br) was examined. This bromofluorinated alkene was synthesized in three steps, which started with the addition of bromine to chlorotrifluoroethylene. In contrast to the ethylenation of 1,1‐difluoro‐1,2‐dibromochlorethane, which failed, that of 2‐chloro‐1,1,2‐trifluoro‐1,2‐dibromoethane was optimized and led to 2‐chloro‐1,1,2‐trifluoro‐1,4‐dibromobutane. The kinetics of the copolymerization of VDF with this brominated monomer initiated by t‐butyl peroxypivalate led to an assessment of the reactivity ratios, rVDF = 0.96 ± 0.67 and rC4Br = 0.09 ± 0.63, at 50 °C. The suspension copolymerization was also carried out, and the chemical modifications of the resulting bromo‐containing poly(vinylidene fluoride)s were attempted and consisted mainly of elimination or nucleophilic substitution of the bromine. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 917–935, 2005
Ybiv from Escherichia coli K12 is a HAD phosphatase
Authors: Roberts Anne , Lee Seok‐Yong , McCullagh Emma , Silversmith Ruth E. , Wemmer David E.
Published: January 2005

The protein YbiV from Escherichia coli K12 MG1655 is a hypothetical protein with sequence homology to the haloacid dehalogenase (HAD) superfamily of proteins. Although numerous members of this family have been identified, the functions of few are known. Using the crystal structure, sequence analysis, and biochemical assays, we have characterized YbiV as a HAD phosphatase. The crystal structure of YbiV reveals a two‐domain protein, one with the characteristic HAD hydrolase fold, the other an inserted α/β fold. In an effort to understand the mechanism, we also solved and report the structures of YbiV in complex with beryllofluoride (BeF3−) and aluminum trifluoride (AlF3), which have been shown to mimic the phosphorylated intermediate and transition state for hydrolysis, respectively, in analogy to other HAD phosphatases. Analysis of the structures reveals the substrate‐binding cavity, which is hydrophilic in nature. Both structure and sequence homology indicate YbiV may be a sugar phosphatase, which is supported by biochemical assays that measured the release of free phosphate on a number of sugar‐like substrates. We also investigated available genomic and functional data in an effort to determine the physiological substrate. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Properties of polyproline II, a secondary structure element implicated in protein–protein interactions
Authors: Cubellis M. V. , Caillez F. , Blundell T. L. , Lovell S. C.
Published: January 2005

The polyproline II (PPII) conformation of protein backbone is an important secondary structure type. It is unusual in that, due to steric constraints, its main‐chain hydrogen‐bond donors and acceptors cannot easily be satisfied. It is unable to make local hydrogen bonds, in a manner similar to that of α‐helices, and it cannot easily satisfy the hydrogen‐bonding potential of neighboring residues in polyproline conformation in a manner analogous to β‐strands. Here we describe an analysis of polyproline conformations using the HOMSTRAD database of structurally aligned proteins. This allows us not only to determine amino acid propensities from a much larger database than previously but also to investigate conservation of amino acids in polyproline conformations, and the conservation of the conformation itself. Although proline is common in polyproline helices, helices without proline represent 46% of the total. No other amino acid appears to be greatly preferred; glycine and aromatic amino acids have low propensities for PPII. Accordingly, the hydrogen‐bonding potential of PPII main‐chain is mainly satisfied by water molecules and by other parts of the main‐chain. Side‐chain to main‐chain interactions are mostly nonlocal. Interestingly, the increased number of nonsatisfied H‐bond donors and acceptors (as compared with α‐helices and β‐strands) makes PPII conformers well suited to take part in protein–protein interactions. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Understanding the energetics of helical peptide orientation in membranes
Authors: Sengupta Durba , Meinhold Lars , Langosch Dieter , Ullmann G. Matthias , Smith Jeremy C.
Published: January 2005

Understanding the energetic factors determining the positioning and orientation of single‐helical peptides in membranes is of fundamental interest in structural biology. Here, a simple 5‐slab continuum dielectric model for the membrane is examined that distinguishes between the solvent, headgroup, and core regions. An analytical solution for the electrostatic solvation of a single dipole and an all‐atom model of N‐methylacetamide are used to demonstrate the effect of the dielectric boundaries in the system on peptide dipole orientation. The dipole orientation energy is shown to dominate the electrostatic solvation energy of a polyalanine helix in the membrane. With an additional surface‐area‐dependent term to account for the cavity formation in the aqueous region, the continuum electrostatics description is used to examine several helical peptides, the atoms of which are explicitly represented with a molecular mechanics force field. The experimentally determined tilt angles of a number of peptides of alternating alanine and leucine residues, and of glycophorin and melittin, are accurately reproduced by the model. The factors determining the tilt angles and their fluctuations are analyzed. The tilt angles of the simpler peptides are found to increase approximately linearly with peptide length; this effect is also rationalized. The analysis and model presented here provide a step toward the prediction of helical membrane protein structure. Proteins 2005. © 2005 Wiley‐Liss, Inc.
The Protein Coil Library: A structural database of nonhelix, nonstrand fragments derived from the PDB
Authors: Fitzkee Nicholas C. , Fleming Patrick J. , Rose George D.
Published: January 2005

Approximately half the structure of folded proteins is either α‐helix or β‐strand. We have developed a convenient repository of all remaining structure after these two regular secondary structure elements are removed. The Protein Coil Library (http://roselab.jhu.edu/coil/) allows rapid and comprehensive access to non‐α‐helix and non‐β‐strand fragments contained in the Protein Data Bank (PDB). The library contains both sequence and structure information together with calculated torsion angles for both the backbone and side chains. Several search options are implemented, including a query function that uses output from popular PDB‐culling servers directly. Additionally, several popular searches are stored and updated for immediate access. The library is a useful tool for exploring conformational propensities, turn motifs, and a recent model of the unfolded state. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Involvement of a sodium channel mutation in pyrethroid resistance in Cydia pomonella L, and development of a diagnostic test
Authors: Brun‐Barale Alexandra , Bouvier Jean‐Charles , Pauron David , Bergé Jean‐Baptiste , Sauphanor Benoit
Published: January 2005

Populations of the codling moth, Cydia pomonella L (Lepidoptera, Tortricidae) have developed resistance to several classes of insecticide such as benzoylureas, juvenile hormone analogues, ecdysone agonists and pyrethroids, but the corresponding resistance mechanisms have not been extensively studied. Knockdown resistance (kdr) to pyrethroid insecticides has been associated with point mutations in the para sodium channel gene in a great variety of insect pest species. We have studied two susceptible strains (S and Sv) and two resistant strains (Rt and Rv) of C pomonella that exhibited 4‐ and 80‐fold resistance ratios to deltamethrin, respectively. The region of the voltage‐dependent sodium channel gene which includes the position where kdr and super‐kdr mutations have been found in Musca domestica L was amplified. The kdr mutation, a leucine‐to‐phenylalanine replacement at position 1014, was found only in the Rv strain. In contrast, the super‐kdr mutation, a methionine‐to‐threonine replacement at position 918, was not detected in any C pomonella strain. These data allowed us to develop a PCR‐based diagnostic test (PASA) to monitor the frequency of the kdr mutation in natural populations of C pomonella in order to define appropriate insecticide treatments in orchards. Copyright © 2005 Society of Chemical Industry
Jahn–Teller effect and electron correlation in alkali doped fullerides
Authors: Chibotaru L. F.
Published: January 2005

The interplay between Jahn–Teller effect and electron correlation in alkali doped fullerides is reviewed for compounds from both sides of Mott–Hubbard transition. In Mott–Hubbard fullerides the nature of low‐lying excitations strongly depends on the symmetry of the compounds, corresponding either to spin (Heisenberg) type for low symmetry compounds (K3(NH3)C60) or to spin‐vibronic superexchange for cubic compounds (Li3(NH3)6C60). In the band fullerides (A3C60, A4C60, A = K, Rb) the Jahn–Teller effect leads to a splitting of the cubic band structure in three or two unequally populated subbands (orbital disproportionation), which gives rise to a number of features in the spectroscopy of these compounds. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Spin‐polarized transport through carbon nanotubes
Authors: Krompiewski S.
Published: January 2005

Carbon nanotubes (CNT) belong to the most promising new materials which can in the near future revolutionize the conventional electronics. When sandwiched between ferromagnetic electrodes, the CNT behaves like a spacer in conventional spin‐valves, leading quite often to a considerable giant magneto‐resistance effect (GMR). This paper is devoted to reviewing some topics related to electron correlations in CNT. The main attention however is directed to the following effects essential for electron transport through nanotubes: (i) nanotube/electrode coupling and (ii) inter‐tube interactions. It is shown that these effects may account for some recent experimental reports on GMR, including those on negative (inverse) GMR. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The physics of quantum impurities – a bridge from micro/nano to macro systems
Authors: Pruschke Th.
Published: January 2005

We will give a comprehensive introduction into the concept of quantum impurities and survey on where and why quantum impurity problems arise in modern solid‐state physics. The physical properties of these systems and their applications will be discussed for a selected set of examples. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Onset of metallic ferromagnetism in a doped spin–orbital chain
Authors: Daghofer Maria , Oleś Andrzej M. , von der Linden Wolfgang
Published: January 2005

Starting from a spin–orbital model for doped manganites, we investigate a competition between ferromagnetic and antiferromagnetic order in a one‐dimensional model at finite temperature. The magnetic and orbital order at half filling support each other and depend on a small antiferromagnetic superexchange between t2g spins and on an alternating Jahn–Teller potential. The crossover to a metallic ferromagnetic phase found at finite doping is partly suppressed by the Jahn–Teller potential which may localize eg electrons. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Large‐scale quantum effects in biological systems
Authors: Mesquita Marcus V. , Vasconcellos Áurea R. , Luzzi Roberto , Mascarenhas Sergio
Published: January 2005

Particular aspects of large‐scale quantum effects in biological systems, such as biopolymers and also microtubules in the cytoskeleton of neurons which can have relevance in brain functioning, are discussed. The microscopic (quantum mechanical) and macroscopic (quantum statistical mechanical) aspects, and the emergence of complex behavior, are described. This phenomena consists of the large‐scale coherent process of Fröhlich–Bose–Einstein condensation in open and sufficiently far‐from‐equilibrium biopolymers. Associated with this phenomenon is the presence of Schrödinger–Davydov solitons, which propagate, undistorted and undamped, when embedded in the Fröhlich–Bose–Einstein condensate, thus allowing for the transmission of signals at long distances, involving a question relevant to bioenergetics. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
A theoretical study of vibrational properties of neutral and cationic B12 clusters
Authors: Lau Kah Chun , Deshpande Mrinalini , Pandey Ravindra
Published: January 2005

Calculations based on density functional theory predict the ground state of B12 and B to be a convex planar configuration with C1 symmetry. A small ionization‐induced structural change in B12 is also predicted. It is suggested that multicentered bonds together with delocalized charge density are dominant factors in stabilizing the planar configuration over 3D configuration for B12 and B. The calculated vibrational frequencies lie in the range of 200–1328 cm−1 in which the high‐frequency modes are associated with asymmetric stretching of the boron atoms located at the cluster surface. The infrared spectra of both neutral and cationic B12 show similar infrared active modes in the high‐frequency region, but different modes in the low‐frequency region due to dissimilar atomic charges in the cationic B12. The combined effect of charge delocalization and reduced dimensionality is reflected in the calculated static dipole polarizability of these clusters. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Electrospray ionization tandem mass spectrometry of model peptides reveals diagnostic fragment ions for protein ubiquitination
Authors: Esteban Warren Maria R. , Parker Carol E. , Mocanu Viorel , Klapper David , Borchers Christoph H.
Published: January 2005

In this work, synthetic peptides were used to determine the fragmentation behavior of ubiquitinated peptides and to find ions diagnostic for peptide ubiquitination. The ubiquitin‐calmodulin peptide1 was chosen as the model peptide for naturally occurring ubiquitinated proteins cleaved with endoproteinase gluC. In addition, the fragmentation behavior of model ubiquitinated peptides produced by tryptic digestion was also of great interest since the standard protocols for proteomics‐based protein identification use trypsin as the protease. Attachment of ubiquitin to a target protein results in a branched structure, but only ions from the ubiquitin side chain (and the lysine to which it is attached) can be used as diagnostic ions, since fragment ions that contain other amino acids from the parent protein will vary in mass. Characteristic b‐type fragment ions from the gluC cleavage of the ubiquitin side chain (designated as b ions) were found which involve only the ubiquitin tail (b2, b3, b4, b5 and b6 ions at m/z 189.06, 302.12, 439.18, 552.30 and 651.30, respectively). Maximum production of these ions occurred at a collision energy of 45 eV in a Q‐TOF instrument. Although a non‐ubiquitinated peptide may produce isobaric fragment ions, it is unlikely that it can produce these ions in combination. With liquid chromatography/tandem mass spectrometry (LC/MS/MS) experiments, ubiquitinated peptides can readily be determined by surveying the reconstructed or extracted ion chromatograms of the diagnostic fragment ions for common peaks. Characteristic ions resulting from tryptic cleavage of the side chain were found in cleavage products with a missed cleavage, resulting in a LRGG‐ tag instead of a GG‐ tag. For the LRGG‐tagged peptide, diagnostic MS/MS fragment ions (at m/z 270.17 and 384.21) from the ubiquitin tail (b2 and b4, respectively) were found, along with an internal fragment ion (LRGGK‐28) at m/z 484.30. These ions should prove useful in precursor‐ion scanning experiments for identifying peptides modified by attachment of ubiquitin, and for locating the site of ubiquitin attachment. Copyright © 2005 John Wiley & Sons, Ltd.
Differential adduction of proteins vs. deoxynucleosides by methyl methanesulfonate and 1‐methyl‐1‐nitrosourea in vitro
Authors: Zhang Fagen , Bartels Michael J. , Pottenger Lynn H. , Gollapudi B. Bhaskar
Published: January 2005

The reactions of two model mutagenic and carcinogenic alkylating agents, N‐methyl‐N‐nitrosourea (MNU) and methyl methanesulfonate (MMS), with proteins and deoxynucleosides in vitro, were investigated. The protein work used an approach involving trypsin digestion and high‐performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC/ESI‐MS/MS). This technique permitted identification of the specific location of protein adduction by both MNU and MMS with commercial apomyoglobin and human hemoglobin, under physiological conditions. MNU treatment resulted in predominantly carbamoylation adducts on the proteins, but in contrast only methylated protein adducts were found following treatment with MMS. Further analyses, using TurboSequest®, and the Scoring Algorithm for Spectral Analysis (SALSA), revealed that MNU carbamoylation was specific for modification of either the N‐terminal valine or the free amino group in lysine residues of apomyglobin and human hemoglobin. However, MMS methylation modified the N‐terminal valine and histidine residues of the proteins. Despite their clear differences in protein modifications, MNU and MMS formed qualitatively the same methylated deoxynucleoside adduct profiles with all four deoxynucleosides in vitro under physiological conditions. In light of their different biological potencies, where MMS is considered a ‘super clastogen’ while MNU is a ‘super mutagen’, these differences in reaction products with proteins vs. deoxynucleosides may indicate that these two model alkylating agents work via different mechanisms to produce their mutagenic and carcinogenic effects. Copyright © 2005 John Wiley & Sons, Ltd.
Benzene‐assisted atmospheric‐pressure chemical ionization: a new liquid chromatography/mass spectrometry approach to the analysis of selected hydrophobic compounds
Authors: Perazzolli Chiara , Mancini Ines , Guella Graziano
Published: January 2005

Charge‐exchange reactions involving benzene have been successfully exploited to increase the sensitivity of atmospheric‐pressure chemical ionization mass spectrometry (APCI‐MS) towards hydrophobic compounds of significant environmental relevance which are not detectable with the ordinary APCI techniques. Among them, good sensitivity have been found for (a) highly chlorinated biphenyl derivatives such as dichlorodiphenyltrichloroethane (DDT), dichlorodiphenyldichloroethane (DDD) and dichlorodiphenyldichloroethene (DDE); (b) cyclopentadienes such as Aldrin and its epoxy derivatives Dieldrin and Endrin; and (c) dibenzofurans and dibenzo‐para‐dioxins such as 2,3,7,8‐tetrachlorodibenzofuran (2,3,7,8‐TCDF) and 2,3,7,8‐tetrachloro‐dibenzo‐para‐dioxin (2,3,7,8‐TCDD). The reactant benzene molecules were introduced into the source either through the nebulizer gas or by direct post‐column addition of neat liquid, whereas the targeted compounds were analyzed using a high‐performance liquid chromatography (HPLC) RP‐18 column using methanol/water solutions as mobile phase. By using benzene as post‐column reagent, positive ion mode detection was proven to be significantly enhanced as compared with APCI measurements carried out without benzene assistance. Copyright © 2005 John Wiley & Sons, Ltd.
Implications of enzymatic, acidic and thermal hydrolysis of DNA on the occurrence of cross‐linked melphalan DNA adducts
Authors: Van den Driessche Bart , Lemière Filip , Witters Erwin , Van Dongen Walter , Esmans Eddy L.
Published: January 2005

Calf thymus DNA was treated with melphalan, a nitrogen mustard, and the formation of melphalan cross‐linked DNA adducts was investigated. These cross‐linked adducts could not be detected either in the enzymatically or in the thermally generated DNA hydrolysates. However, a search for DNA cross‐linked adducts in the hydrolysates obtained under acidic conditions revealed the presence of different types of cross‐links, mainly containing an adenine moiety. These results are very important because they show that the detection of cross‐links is dependent on the hydrolytic procedure used and that these cross‐linked adducts are formed under totally different reaction conditions from those in in vivo situations. This can explain the very low abundance or even the absence of cross‐linked adducts in nitrogen mustard treated animals. The generally accepted theory that the anti‐cancer activity of bifunctional mustards such as melphalan is due to cross‐linking of DNA strands remains therefore from our point of view questionable. Copyright © 2005 John Wiley & Sons, Ltd.
Tandem mass spectra of transition‐metal ion adducts of glycosyl dithioacetals; distinction among stereoisomers
Authors: Madhusudanan K. P. , Kumar Brijesh , Tiwari Pallavi , Madhusudan Soni Kamlesh , Misra A. K.
Published: January 2005

Electrospray ionization mass spectra of some glycosyl dithioacetals recorded in the presence of transition‐metal chlorides, XCl2 (where X = Co, Mn and Zn), give abundant adduct ions such as [M+XCl]+ and [2MH+X]+ and minor ions such as [MH+X]+ and [2M+XCl]+. The tandem mass spectra of these adducts show characteristic elimination of neutral molecules such as H2O, HCl, EtSH, CH2O, C2H4O2/C2H4O. [M+XCl]+ ions fragment readily and the fragmentation appears to be stereochemically controlled as the relative abundances of the fragments are different for three stereoisomers. The added metal is lost as neutral molecules in the form of XCl(OH) and XCl(SEt). This is a predominant pathway in the ZnCl+ adducts. [2M+XCl]+ ions fragment preferentially by elimination of HCl, indicating strong metal interactions in the resulting dimeric [2MH+X]+ ion. As there are several electron‐rich centers in the molecule, the dimeric complex [2MH+X]+ can have several structures and the observed fragmentations may reflect the sum of those of all these structures. The dimeric complexes fragment by elimination of neutral molecules leaving the dimeric interactions intact. The extent of fragmentation varies for the stereoisomers, leading to stereochemical differentiation. Copyright © 2005 John Wiley & Sons, Ltd.
Isotope analysis of hydrocarbons: trapping, recovering and archiving hydrocarbons and halocarbons separated from ambient air
Authors: Pupek M. , Assonov S. S. , Mühle J. , Rhee T. S. , Oram D. , Koeppel C. , Slemr F. , Brenninkmeijer C. A. M.
Published: January 2005

It is argued that isotope analysis of atmospheric non‐methane hydrocarbons (NMHCs) and, in particular, the analysis of the deuterium/hydrogen (D/H) ratio is valuable because the dominant self‐cleansing property of the troposphere is based on the OH radical which removes, e.g., CH4 and other alkanes by H‐atom abstraction, which induces large kinetic isotope effects. The major obstacle in applying D/H isotope analysis to atmospheric NMHCs is not only the low abundance of D itself but, in particular, the low concentrations of NMHCs in the parts per trillion range. We show how a selection of NMHCs can be quantitatively separated from 300 L air samples together with CO2 as carrier gas matrix, by using high efficiency cryogenic traps. After diluting the extracted NMHC mixtures with hydrocarbon free air, and determining the mixing ratios, good agreement with original whole air sample analysis exists for alkanes and several halocarbons. For unsaturated hydrocarbons and some other halocarbons the extraction and recovery yield under the given conditions fell considerably, as a function of boiling point. Furthermore, the mixture of NMHCs in the CO2 matrix is proven to remain unchanged over several years when conveniently stored in glass ampoules. The ‘extracts’ or ‘concentrates’ of condensables extracted from larger air samples will enable the D/H isotope analysis of ultra trace gases in the atmosphere. Copyright © 2005 John Wiley & Sons, Ltd.
Multidimensional statistical analysis applied to electron ionization mass spectra to determine steroid stereochemistry
Authors: Le Bizec Bruno , Antignac Jean‐Philippe , Bertrand Dominique , Qannari El Mostafa , Andre François
Published: January 2005

The differentiation of stereoisomers on the basis of their mass spectra only is usually a difficult challenge even when an informative ionization technique such as electron ionization is used; this is particularly the case for steroids. In this study, multivariate statistical techniques have been applied to the mass spectra of derivatized 5ξ‐androstane‐3ξ,17ξ‐diols (ξ = α,β) in order to investigate the possibility of discrimination among the different isomers. After collection of the data from the mass spectra (20 replicates for each of the 8 isomers), each ion was considered as a statistical variable and each mass spectrum as an observation. The more discriminative variables (42 out of the 160 initial ones) were selected using the analysis of variance technique (ANOVA). Thereafter, a linear discriminant analysis (LDA) allowed us to set up a predictive model for stereochemistry determination. The two‐dimensional graphical display of the 160 observations on the basis of the canonical variables derived from LDA made it possible to separate the eight isomers. The discrimination of 5α and 5β isomers as well as 3α and 3β was unambiguous, whereas, the discrimination of 17α and 17β epimers was less obvious. The robustness of the model was checked with 40 mass spectra recorded over a 6‐month period on different quadrupole mass spectrometers and under different signal acquisition conditions. The percentage of correct assignment of these ‘unknown’ stereoisomers was 92%; only three 17α and 17β epimers were not correctly plotted in the expected zone. Nevertheless, the performance score was better than those observed with traditional mass spectral libraries. Furthermore, this statistical approach allowed us to identify the main fragment ions involved in the discrimination between isomers: m/z 256 and 421 for isomers 5a‐5b; m/z 241 and 331 for isomers 5α3α‐5α3β; m/z 143 and 162 for isomers 5β3α‐5β3β; and m/z 255 for epimers 17α‐17β. Copyright © 2005 John Wiley & Sons, Ltd.
Determination of the ionophoric coccidiostats narasin, monensin, lasalocid and salinomycin in eggs by liquid chromatography/tandem mass spectrometry
Authors: Mortier Leen , Daeseleire Els , Peteghem Carlos Van
Published: January 2005

A sensitive and selective liquid chromatographic tandem mass spectrometric method (LC/MS/MS) for the simultaneous detection of the ionophoric coccidiostats narasin, monensin, lasalocid and salinomycin in whole eggs has been developed. A very simple sample preparation consisting of an extraction with an organic solvent was carried out. Sample extracts were injected into the LC/MS/MS system on a C18 column and an isocratic elution was performed. Nigericin was used as internal standard. The precursor ions produced by electrospray positive ionisation were selected for collisional dissociation with argon into product ions. Validation of the methods was performed based on Commission Decision 2002/657/EC.1 CCα was found to be 1 μg/kg for all four compounds. Monitoring of Belgian egg samples in 2004 revealed that residues of salinomycin, lasalocid and monensin could be found. Copyright © 2005 John Wiley & Sons, Ltd.
Early prediction of wheat quality: analysis during grain development using mass spectrometry and multivariate data analysis
Authors: Ghirardo Andrea , Sørensen Helle Aagaard , Petersen Marianne , Jacobsen Susanne , Søndergaard Ib
Published: January 2005

Matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry and multivariate data analysis have been used for the determination of wheat quality at different stages of grain development. Wheat varieties with one of two different end‐use qualities (i.e. suitable or not suitable for bread‐making purposes) were investigated. The samples were collected from grains from 15 until 45 days post‐anthesis (dpa). Gluten proteins from wheat grains were extracted and subsequently analysed by mass spectrometry. Discrimination partial least‐squares regression and soft independent modelling of class analogy were used to determine the quality of new and unknown wheat samples. With these methods, we were able to predict correctly the end‐use qualities at every stage investigated. This new fast technique, based on the rapidity of mass spectrometry combined with the objectivity of multivariate data analysis, offers a method that can replace the traditional rather time‐consuming ones such as gel electrophoresis. This study focused on the determination of wheat quality at 15 dpa, when the grain is due for harvest 1 month later. Copyright © 2005 John Wiley & Sons, Ltd.
Primary stenting for traumatic coronary artery dissection resulting from blunt chest Trauma—A Case Report
Authors: Shukkur Abdul Mohammed , Ridha Mustafa , George Susan
Published: January 2005

Traumatic coronary artery dissection is an extremely uncommon cause of myocardial infarction. We report a case of spontaneous coronary artery dissection in an 18-year-old previously healthy male caused by myocardial contusion. He was admitted to the hospital with a history of chest trauma and fracture of the radius and ulna bilaterally resulting from a motorcycle accident. The electrocardiograms, elevated creatine kinase, and cardiac troponins revealed acute anterior myocardial infarction. The transthoracic echocardiogram showed significant segmental wall motion abnormalities and moderate left ventricular systolic dysfunction. The coronary angiogram showed a traumatic dissection involving the proximal left anterior descending coronary artery. He underwent a dobutamine echocardiography “viability study” that revealed significant viable myocardium involving 50% of the left anterior descending coronary artery territory. He was treated by primary stent implantation (Cypher and regular stents) with an excellent result.
NATURAL RESOURCES MANAGEMENT RESEARCH IN THE CGIAR: THE ROLE OF THE TECHNICAL ADVISORY COMMITTEE
Authors: HARWOOD R. R. , KASSAM A. H. , GREGERSEN H. M. , FERERES E.
Published: January 2005

Judicious management of our natural resources is a major pillar of sustainable agriculture, broadly defined. It is, therefore, unfortunate that, until now, research in natural resources management (NRM) has not received sufficient support, or the recognition that other agricultural research topics have had. The Consultative Group on International Agricultural Research (CGIAR) recognized, early on, the complementarities and synergies between NRM research and other themes, notably genetic improvement, and its research Centres have pursued some vigorous programmes for many years. The Technical Advisory Committee (TAC) to the CGIAR was supportive of such programmes from the start and provided advice to the CGIAR System on NRM research strategies. Highlights of such advice over the last 20 years are discussed, including the ecoregional approach, the 1996 study of Priorities and Strategies for Soil and Water Research, and the CGIAR Vision and Strategy of 2000. Recent developments at the Centres leading to the promotion of integrated approaches to NRM (INRM) are described, and a set of priority areas in INRM research for future CGIAR activities is presented.
MECHANIZATION OF POTATO GRADING ON SMALL-SCALE FARMS: A CASE STUDY FROM PERU
Authors: BUTLER G. P. , BERNET T. , MANRIQUE K.
Published: January 2005

Potatoes are an important cash crop for small-scale producers worldwide. The move away from subsistence to commercialized farming, combined with the rapid growth in demand for processed agricultural products in developing countries, implies that small-scale farmers and researchers alike must begin to respond to these market changes and consider post-harvest treatment as a critical aspect of the potato farming system. This paper presents and assesses a low cost potato-grading machine that was designed explicitly to enable small-scale potato growers to sort tubers by size for supply to commercial processors. The results of ten experiments reveal that the machine achieves an accuracy of sort similar to commercially available graders. The machine, which uses parallel conical rollers, has the capacity to grade different tuber shapes and to adjust sorting classes, making it suitable for locations with high potato diversity. Its relatively low cost suggests that an improved and adapted version of this machine might enhance market integration of small-scale potato producers not only in Peru, but in other developing countries as well.
FROM THE EDITOR
Authors: Tucker Judith
Published: January 2005

Although this issue of the journal goes out with my name on the masthead as editor, all the pre-production editing was in the expert hands of my predecessor, Juan R. I. Cole, and his able assistant, Alissa Surges. I want to take this opportunity to thank them for their years of service to the journal and to the profession. Juan Cole guided the journal for five years with a remarkable blend of energy, vision, and attention to detail. We all profited from the breadth of his scholarly background and research interests, which bridge many of the geographical, disciplinary, and cultural divides of Middle East studies. During his tenure as the editor, the journal flourished and fulfilled its mission as a journal of record for our field. Juan Cole also left his particular stamp of engagement with current theoretical questions coupled with high-quality empirical research, as exemplified in the special issue he co-edited in May 2002 on nationalism and the colonial legacy. Thanks to his management skills, and those of Alissa Surges, the journal also moved into the electronic world of the 21st century under his watch. I am very grateful for the time and effort they put into developing the databases, office procedures, and filing systems that streamlined the editorial process. I am inheriting a healthy and thriving operation because of their skills and commitment.