bluuebunny/crossref_metadata_2025 huggingface dataset:
Theory of NMR Parameters: From Ramsey to Relativity (1953—1983)
Authors: Pyykkoe Pekka
Published: March 2005

For Abstract see ChemInform Abstract in Full Text.
Supramolecular Optical Chemosensors for Organic Analytes
Authors: Bell Thomas W. , Hext Nicholas M.
Published: March 2005

For Abstract see ChemInform Abstract in Full Text.
Semiempirical Methods for the Calculation of NMR Chemical Shifts
Authors: Heine Thomas , Seifert Gotthard
Published: March 2005

For Abstract see ChemInform Abstract in Full Text.
Electron‐Correlated Methods for the Calculation of NMR Chemical Shifts
Authors: Gauss Juergen , Stanton John F.
Published: March 2005

For Abstract see ChemInform Abstract in Full Text.
Love‐wave‐type/Rayleigh‐wave‐type SAW resonators with thick Al‐grating structure
Authors: Isobe Atsushi , Hikita Mitsutaka , Asai Kengo
Published: March 2005

A Love‐wave SAW propagating on a thick Al grating on a LiNbO3piezoelectric substrate exhibits a resonant characteristic with an extremely small capacitance ratio γ(=3.0) while it elastically couples with Rayleigh waves in a complex manner. In the application to a resonator, the Rayleigh wave becomes spurious and must be suppressed sufficiently. With a view to development of a broadband SAW resonator for a VCO, the propagation/reflection characteristics of this Love‐wave/Rayleigh‐wave configuration are analyzed. The following results are found by simulation and experiments. (1) Both the Love wave and Rayleigh wave have extremely wide reflection bandwidths. (2) Two types of spurious Rayleigh wave appear in the resonant characteristics. (3) The stopband of the Rayleigh wave is superior in reflection characteristic to the Love wave. It is also demonstrated experimentally that a broadband SAW‐VCO can be realized if the VCO oscillation frequency is chosen within the Rayleigh wave stopband after the Al film thickness is optimized. © 2005 Wiley Periodicals, Inc. Electron Comm Jpn Pt 2, 88(4): 1–8, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecjb.20157
The rat orthologue to the inhibitory receptor gp49B is expressed by neutrophils and monocytes, but not by NK cells or mast cells
Authors: Bryceson Yenan T. , Torgersen Knut Martin , Inngjerdingen Marit , Berg Siri F. , Hoelsbrekken Sigurd E. , Fossum Sigbjørn , Dissen Erik
Published: March 2005

Mouse gp49B is a member of the leukocyte immunoglobulin‐like receptor family. It is constitutively expressed by mast cells and certain myeloid cells, and expression can be induced on natural killer (NK) cells and T cells. We have cloned several rat cDNA, 78% identical to mouse gp49B at the amino acid level, that represent the rat orthologue to mouse gp49B. A mouse monoclonal antibody (WEN29) against rat gp49B was generated. By flow cytometry and Northern blot analysis, gp49B was found to be expressed by neutrophils and monocytes, but not NK cells (primary or IL‐2‐activated), T cells (resting or concanavalin A‐stimulated) or peritoneal mast cells. Following pervanadate treatment, the tyrosine phosphatase SHP‐1 was co‐immunoprecipitated with gp49B in the macrophage cell line R2. In glutathione S‐transferase pull‐down experiments, the cytoplasmic tail of rat gp49B associated with the SH2 domains of both SHP‐1 and SHP‐2, dependent on intact and phosphorylated immunoreceptor tyrosine‐based inhibition motifs (ITIM). Compared to mouse, the cytoplasmic domain of rat gp49B contains a third ITIM‐like sequence (YLYASV) that was phosphorylated by several Src family tyrosine kinases, enhanced the phosphorylation of other ITIM, and bound to the SH2 domains of SHP‐2, suggesting a role in the recruitment of downstream phosphatases.
A polyclonal anti‐vaccine CD4 T cell response detected with HLA‐DP4 multimers in a melanoma patient vaccinated with MAGE‐3.DP4‐peptide‐pulsed dendritic cells
Authors: Zhang Yi , Renkvist Nicolina , Sun Zhaojun , Schuler‐Thurner Beatrice , Glaichenhaus Nicolas , Schuler Gerold , Boon Thierry , van der Bruggen Pierre , Colau Didier
Published: March 2005

During the last few years, HLA class I tetramers have been successfully used to demonstrate anti‐vaccine CD8 CTL proliferation in cancer patients vaccinated with tumor antigens. Frequencies of CTL as low as 10–6 among CD8 cells were observed even in patients showing tumor regression. Little is known about the role of tumor‐antigen‐specific CD4 T cells in the context of these anti‐vaccine responses. Therefore, we developed a very sensitive approach using fluorescent class‐II–peptide multimers to detect antigen‐specific CD4 T cells in vaccinated cancer patients. We produced HLA‐DP4 multimers loaded with the MAGE‐3243–258 peptide and used them to stain ex vivo PBL from melanoma patients injected with dendritic cells pulsed with several class I and class II tumor antigenic peptides, including the MAGE‐3243–258 peptide. The multimer+ CD4 T cells were sorted and amplified in clonal conditions; specificity was assessed by their ability to secrete IFN‐γ upon contact with the MAGE‐3 antigen. We detected frequencies of about 1×10–6 anti‐MAGE‐3.DP4 cells among CD4 cells. A detailed analysis of one patient showed an anti‐MAGE‐3.DP4 CD4 T cell amplification of at least 3000‐fold upon immunization. TCR analysis of the clones from this patient demonstrated a polyclonal response against the MAGE‐3 peptide.
Chiral capillary electrophoresis‐mass spectrometry of amino acids in foods
Authors: Simó Carolina , Rizzi Andreas , Barbas Coral , Cifuentes Alejandro
Published: March 2005

In this work, the development of a new chiral capillary electrophoresis‐mass spectrometry (CE‐MS) method to separate D‐ and L‐amino acids is shown. On‐line coupling between CE and MS is established through an electrospray‐coaxial sheath flow interface. Enantiomer separation is achieved by using a cheap, nonvolatile, chiral selector as β‐cyclodextrin in the background electrolyte (BGE) together with a physically coated capillary that is aimed to prevent contamination of the electrospray. The capillary coating is simple and easy to obtain as it only requires flushing of the capillary with a polymer aqueous solution for 3 min. Optimization of CE parameters (pH of BGE, type and concentration of chiral selector, and capillary inner diameter) and electrospray‐MS parameters (nature and flow rate of the sheath liquid, nebulizer pressure) is carried out. Two different derivatization protocols of amino acids using dansyl chloride (DNS) and fluorescein isothiocyanate (FITC) are compared in terms of MS sensitivity and chiral resolution. Under optimum CE‐MS conditions it is observed that the MS sensitivity obtained for FITC‐ and DNS‐amino acids is similar (with limit of detection (LOD) in the µM range, corresponding to amounts injected in the fmol range) while chiral resolution is better for FITC‐amino acids. The optimized method is demonstrated to provide the simultaneous analysis of 15 selected amino acids (i.e., FITC‐D/L‐Asp, ‐Glu, ‐Ser, ‐Asn, ‐Ala, ‐Pro, ‐Arg, and FITC‐γ‐aminobutyric acid (GABA) in a single chiral CE‐MS run, corresponding to the main amino acids that can be found in orange. Moreover, as a result of the high resolution achieved, it is possible to detect down to 2% of D‐Asp in the presence of 98% of L‐Asp. The good possibilities of chiral CE‐MS in food analysis are corroborated through the detection of the main amino acids in a commercial orange juice (i.e., FITC‐L‐Asp, ‐Glu, ‐Ser, ‐Asn, ‐Pro, ‐Arg, and the nonchiral FITC‐GABA) as well as the determination of the fraudulent addition of synthetic amino acids (containing D‐ and L‐forms) to a fresh orange juice.
Analysis of melamine resins by capillary zone electrophoresis with electrospray ionization‐mass spectrometric detection
Authors: Cook Helmy A. , Klampfl Christian W. , Buchberger Wolfgang
Published: March 2005

A method for the determination of the major components of (methoxymethyl)melamine resins, with quantitative analysis of unreacted melamine by capillary zone electrophoresis (CZE) using electrospray ionization‐mass spectrometry (ESI‐MS) is presented. Using a low background electrolyte (BGE) pH, components are separated according to their charge/ionic radius ratio with a distinctly different separation selectivity compared to the HPLC methods commonly employed in melamine‐resin analysis. The use of a time‐of‐flight mass spectrometer (TOF‐MS) was concluded to be necessary, as the complex samples studied required maximum sensitivity and resolution, which is clearly superior for TOF‐MS detectors over their quadrupole counterparts. A standard curve of free melamine was determined with an R2 = 0.999 over a concentration range of an order of magnitude. This method offers the unique separation selectivity of CZE as well as a quicker analysis time, especially for dimers compared to the HPLC methods used to date.
Capillary electrophoresis and matrix‐assisted laser desorption/ionization‐time of flight‐mass spectrometry for analysis of the novel erythropoiesis‐stimulating protein (NESP)
Authors: Sanz‐Nebot Victoria , Benavente Fernando , Giménez Estela , Barbosa José
Published: March 2005

NESP (novel erythropoiesis‐stimulating protein) is a recently approved hyperglycosylated analogue of human erythropoietin (EPO) with a long‐lasting effect. In this work, the capillary electrophoresis (CE) methodology proposed by the European Pharmacopoeia for the separation of EPO glycoforms has been modified for the separation of NESP glycoforms. Optimization of pH of the separation electrolyte has been fundamental in order to achieve baseline resolution of seven peaks corresponding to NESP glycoforms. Intact NESP has also been characterized by matrix‐assisted laser desorption/ionization‐time of flight‐mass spectrometry (MALDI‐TOF‐MS). An accurate approximation to an average molecular mass of the NESP molecule has been obtained, taking into account the strong influence of laser intensity upon the MALDI‐TOF mass spectra found.
Speciation of arsenic compounds in fish and oyster tissues by capillary electrophoresis‐inductively coupled plasma‐mass spectrometry
Authors: Yeh Ching‐Fen , Jiang Shiuh‐Jen
Published: March 2005

A capillary electrophoresis‐inductively coupled plasma‐mass spectrometric (CE‐ICP‐MS) method for the speciation of six arsenic compounds, namely arsenite [As(III)], arsenate [As(V)], monomethylarsonic acid, dimethylarsinic acid, arsenobetaine and arsenocholine is described. The separation has been achieved on a 70 cm length×75 µm ID fused‐silica capillary. The electrophoretic buffer used was 15 mM Tris (pH 9.0) containing 15 mM sodium dodecyl sulfate (SDS), while the applied voltage was set at +22 kV. The arsenic species in biological tissues were extracted into 80% v/v methanol‐water mixture, put in a closed centrifuge tube and kept in a water bath, using microwaves at 80°C for 3 min. The extraction efficiencies of individual arsenic species added to the sample at 0.5 µg As/g level were between 96% and 107%, except for As(III), for which it was 89% and 77% for oyster and fish samples, respectively. The detection limits of the species studied were in the range 0.3–0.5 ng As/mL. The procedure has been applied for the speciation analysis of two reference materials, namely dogfish muscle tissue (NRCC DORM‐2) and oyster tissue (NIST SRM 1566a), and two real‐world samples.
Protein profiling by capillary isoelectric focusing, reversed‐phase liquid chromatography, and mass spectrometry
Authors: Zhou Feng , Johnston Murray V.
Published: March 2005

An automated system for intact protein analysis is described that combines capillary isoelectric focusing (CIEF), reversed‐phase liquid chromatography (RPLC), and electrospray ionization‐mass spectrometry (ESI‐MS). Performance is demonstrated with a complex yeast enzyme concentrate. CIEF is performed with a microdialysis membrane‐based cathodic cell that permits pI fractions to be sampled and stored for subsequent LC‐MS analysis. A total of 50 µg protein is loaded onto the capillary. Ten fractions are stored which span the pI range 3–10. Each fraction is subsequently cleaned on a reversed‐phase trap column and then characterized by LC‐MS. MaxEnt1 is used to deconvolute the raw mass spectra to obtain the molecular weight (MW) of intact proteins/peptides in the sample. A two‐dimensional display of pI vs. MW is illustrated for the 500 most prevalent species as identified by MaxEnt1.
An interface Newton–Krylov solver for fluid–structure interaction
Authors: Michler C. , van Brummelen E. H. , de Borst R.
Published: March 2005

The numerical solution of fluid–structure interactions with the customary subiteration method incurs numerous deficiencies. We propose a novel solution method based on the conjugation of subiteration with a Newton–Krylov method, and demonstrate its superiority and beneficial characteristics. Copyright © 2004 John Wiley & Sons, Ltd.
Combinatorial gene therapy for bone regeneration: Cooperative interactions between adenovirus vectors expressing bone morphogenetic proteins 2, 4, and 7
Authors: Zhao Ming , Zhao Zhuoran , Koh Jeong‐Tae , Jin Taocong , Franceschi Renny T.
Published: March 2005

Bone morphogenetic proteins (BMPs) have demonstrated effectiveness as bone regeneration agents whether delivered as recombinant proteins or via gene therapy. Current gene therapy approaches use vectors expressing single BMPs. In contrast, multiple BMPs are coordinately expressed during bone development and fracture healing. Furthermore, BMPs likely exist in vivo as heterodimeric molecules having enhanced biological activity. In the present study, we test the hypothesis that gene therapy‐based bone regeneration can be enhanced by expressing combinations of BMPs. For in vitro studies, mesenchymal cell lines were transduced with individual adenoviruses containing BMP2, 4, or 7 cDNA under control of a CMV promoter (AdBMP2, 4, 7) or virus combinations. Significantly, combined transduction with AdBMP2 plus AdBMP7 or AdBMP4 plus AdBMP7 resulted in a synergistic stimulation of osteoblast differentiation. This synergy is best explained by formation of BMP2/7 and 4/7 heterodimers. To test in vivo biological activity, fibroblasts were transduced with specific virus combinations and implanted into C57BL6 mice. Consistent with in vitro results, strong synergy was observed using combined AdBMP2/BMP7 treatment, which induced twofold to threefold more bone than would be predicted based on the activity of individual AdBMPs. These studies show that dramatic enhancement of osteogenesis can be achieved using gene therapy to express specific combinations of interacting regenerative molecules. © 2005 Wiley‐Liss, Inc.
Transfection efficiency and uptake process of polyplexes in human lung endothelial cells: a comparative study in non‐polarized and polarized cells
Authors: Mennesson Eric , Erbacher Patrick , Piller Véronique , Kieda Claudine , Midoux Patrick , Pichon Chantal
Published: March 2005

Background

Following systemic administration, polyplexes must cross the endothelium barrier to deliver genes to the target cells underneath. To design an efficient gene delivery system into lung epithelium, we evaluated capture and transfection efficiencies of DNA complexed with either Jet‐PEI™ (PEI‐polyplexes) or histidylated polylysine (His‐polyplexes) in human lung microvascular endothelial cells (HLMEC) and tracheal epithelial cells.

Methods

After optimizing growth conditions to obtain a tight HLMEC monolayer, we characterized uptake of polyplexes by flow cytometry and evaluated their transfection efficiency. Polyplexes were formulated as small particles. YOYO‐labelled plasmid fluorescence intensity and luciferase activity were used as readouts for uptake and gene expression, respectively.

Results

PEI‐polyplexes were more efficiently taken up than His‐polyplexes by both non‐polarized (2‐fold) and polarized HLMEC (10‐fold). They were mainly internalized by a clathrin‐dependent pathway whatever the cell state. In non‐polarized cells, His‐polyplexes entered also mainly via a clathrin‐dependent pathway but with an involvement of cholesterol. The cell polarization decreased this way and a clathrin‐independent pathway became predominant. PEI‐polyplexes transfected more efficiently HLMEC than His‐polyplexes (107 vs. 105 relative light units (RLU)/mg of proteins) with a more pronounced difference in polarized cells. In contrast, no negative effect of the cell polarization was observed with tracheal epithelial cells in which both polyplexes had comparable efficiency.

Conclusions

We show that the efficiency of polyplex uptake by HLMEC and their internalization mechanism are polymer‐dependent. By contrast with His‐polyplexes, the HLMEC polarization has little influence on the uptake process and on the transfection efficiency of PEI‐polyplexes. Copyright © 2005 John Wiley & Sons, Ltd.
Plane waves with negative phase velocity in isotropic chiral mediums
Authors: Mackay Tom G.
Published: March 2005

The propagation of plane waves in an isotropic chiral medium (ICM) is investigated. Simple conditions are derived—in terms of the constitutive parameters of the ICM—for the phase velocity to be directed opposite to the direction of power flow. It is demonstrated that phase velocity and power flow may be oppositely directed, provided that the magneto‐electric coupling is sufficiently strong. © 2005 Wiley Periodicals, Inc. Microwave Opt Technol Lett 45: 120–121, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20742
A case study to improve the impedance bandwidth of a planar monopole
Authors: Qiu Jianming , Du Zhengwei , Lu Jianhua , Gong Ke
Published: March 2005

This paper presents a new technique to improve the impedance bandwidth of a rectangular planar monopole. The method involves beveling one part while keeping the other edges near the ground plane, which is connected to the antenna‐feeding port. The measured impedance bandwidth of the monopole can reach a ratio of 14:1 for a voltage standing wave ratio (VSWR) equal to 2:1. The measured radiation patterns of the antenna retain the typical monopole characteristics throughout the bandwidth. © 2005 Wiley Periodicals, Inc. Microwave Opt Technol Lett 45: 124–126, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20744
One‐turn stub‐loaded loop patch antenna on a small ground plane
Authors: Thaysen J. , Jakobsen K. B.
Published: March 2005

A small 1.1‐cm3 one‐turn loop patch antenna located 2.5 mm above an 18 × 25 mm ground plane separated by a dielectric substrate with relative permittivity of 9.8 is presented. By varying the length of a thin quarter‐wavelength matching line, it is possible to change the resonant frequency. An RLC circuit model is used to determine the minimum quality factor Q. It is shown that the proposed loop yields a bandwidth performance close to the theoretical limit. The antenna has a 14.5% bandwidth at the resonant frequency of 2.04 GHz. © 2005 Wiley Periodicals, Inc. Microwave Opt Technol Lett 45: 126–128, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20745
Compact printed ultra‐wideband slot antenna with a band‐notched operation
Authors: Su Saou‐Wen , Wong Kin‐Lu , Chang Fa‐Shian
Published: March 2005

A compact printed ultra‐wideband (UWB, 3.1–10.6 GHz) circular‐slot antenna with a notched frequency band at 5 GHz is presented. The antenna is a uniplanar structure and occupies a compact area of 25 × 26 mm2 only (the side length is less than 27% of the lower edge frequency at 3.1 GHz). The antenna has a U‐slotted circular stub embedded inside the circular slot. By choosing the length of the U‐slot cut in the circular stub to be about a half‐wavelength of the desired notched frequency, band‐notched UWB operation is obtained. © 2005 Wiley Periodicals, Inc. Microwave Opt Technol Lett 45: 128–130, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20746
A hybrid fast converging series expansion for the 2D Green's function of a multilayered medium
Authors: Rogier Hendrik
Published: March 2005

A new formalism combining modal expansions based on perfectly matched layers (PMLs) and on Floquet modes is proposed to derive a fast‐converging series expansion for the 2D Green's function of layered media. The PML‐based modal expansion is obtained by terminating the waveguide, formed by the layered medium, with PMLs. The convergence of this series is improved by adding an expansion of Floquet modes corresponding to an auxiliary periodic problem. The period of this auxiliary problem acts as a parameter, the convergence rate of both series allowing to be controlled. The formalism is applied to a dielectric‐slab waveguide to illustrate the improved convergence and the efficiency of the new approach. © 2005 Wiley Periodicals, Inc. Microwave Opt Technol Lett 45: 130–134, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20747
Rectangular dielectric resonator antenna on a conductor‐backed co‐planar waveguide
Authors: Suma M. N. , Menon Sreedevi K. , Bijumon P. V. , Sebastian M. T. , Mohanan P.
Published: March 2005

In this paper, we present an effective excitation of a rectangular dielectric resonator antenna (DRA) with a conductor‐backed co‐planar waveguide (CB‐CPW). The radiation and resonance characteristics are found to vary, depending on the orientation of the DR on the coplanar feed line. The effect of finite and infinite ground planes of CB‐CPW on the radiation characteristics of the rectangular DRA is studied. The orientation and position of the DR are optimized for maximum gain and bandwidth. The optimized antenna geometry offers ∼10.46 dBi gain and 7.5% bandwidth with low cross‐polar radiation characteristics. © 2005 Wiley Periodicals, Inc. Microwave Opt Technol Lett 45: 154–156, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20754
Analysis and testing of a novel OADM based on FBG and Mach‐ Zehnder interferometer
Authors: Huang Yonglin , Dong Xingfa , Li Jie , Dong Xiaoyi
Published: March 2005

A novel optical add‐drop multiplexer (OADM) based on the Mach–Zehnder interferometer (MZI) and the fiber Bragg grating (FBG) is proposed for the first time to the authors' knowledge. In the structure, the Mach–Zehnder interferometer acts as an optical switch. The principle of the OADM is analyzed in this paper. The OADM can add/drop one of the multi‐input channels or pass the channel directly by adjusting the difference of the two arms of the interferometer. The channel isolation is more than 20 dB. © 2005 Wiley Periodicals, Inc. Microwave Opt Technol Lett 45: 156–158, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20755
RF equivalent‐circuit model of interconnect bends based onS‐parameter measurements
Authors: Shi Xiaomeng , Ma Jianguo , Ong Beng Hwee , Yeo Kiat Seng , Do Manh Anh , Li Erping
Published: March 2005

A modified model for RF interconnect bends on lossy substrate in CMOS technology is presented. The model parameters are extracted directly from the on‐wafer S‐parameter measurements. The accuracy is verified up to 20 GHz by the measurements of the test structures. © 2005 Wiley Periodicals, Inc. Microwave Opt Technol Lett 45: 170–173, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20760
Comparisons of brain metabolites observed by HRMAS 1H NMR of intact tissue and solution 1H NMR of tissue extracts in SIV‐infected macaques
Authors: Ratai Eva M. , Pilkenton Sarah , Lentz Margaret R. , Greco Jane B. , Fuller Robert A. , Kim John P. , He Julian , Cheng L. Ling , González R. Gilberto
Published: March 2005

The objective of this study was to compare ex vivo proton high‐resolution magic angle spinning magnetic resonance spectra of intact tissue with those spectra obtained by solution 1H NMR of brain extracts of the same sample. Sixteen brain tissue samples from simian immunodeficiency virus‐infected rhesus macaques from both frontal cortex and putamen were evaluated by comparing brain metabolite quantities of N‐acetylaspartate (NAA), choline‐containing compounds (Cho), myo‐inositol (MI), creatine (Cr), lactate (Lac), glutamate (Glu) and acetate (Ace). The ratios of the individual NMR peak areas of all metabolites relative to the creatine peak area were calculated. Linear regression analysis revealed significant correlations between measurements using the two methods. The strength of the correlations varied depending on the metabolite studied. We found highly significant correlations for NAA/Cr (r2 = 0.77; p < 0.0001), NAA + Ace/Cr (r2 = 0.73; p < 0.0001) and MI/Cr (r2 = 0.75; p < 0.0001). We observed somewhat less strong correlations for Glu/Cr (r2 = 0.54; p < 0.002) and Lac/Cr (r2 = 0.54; p < 0.002). There was a substantially weaker correlation for Cho/Cr (r2 = 0.32; p = 0.02). When plotting the metabolite ratios obtained by 1H HRMAS NMR of the intact tissue sample on the ordinate vs 1H NMR of the tissue extract on the abscissa, most metabolites exhibited a slope close to unity, and a positive intercept probably due to macromolecular contributions to the MAS spectra. The slope for Cho/Cr was substantially less than unity. Generally, samples from the frontal cortex showed a better correlation between intact and extracted tissue samples than putamen. This is most prominent in the cases of NAA/Cr and Cho/Cr. We conclude that both methods provide substantially the same information for most major brain metabolites, with the exception of the Cho resonance. Copyright © 2005 John Wiley & Sons, Ltd.
Fast time‐domain simulation for large‐order linear time‐invariant state space systems
Authors: Cheong Sou Kin , de Weck Olivier L.
Published: March 2005

Time‐domain simulation is essential for both analysis and design of complex systems. Unfortunately, high model fidelity leads to large system size and bandwidths, often causing excessive computation and memory saturation. In response we develop an efficient scheme for large‐order linear time‐invariant systems. First, the A matrix is block diagonalized. Then, subsystems of manageable dimensions and bandwidth are formed, allowing multiple sampling rates. Each subsystem is then discretized using a O(ns) scheme, where ns is the number of states. Subsequently, a sparse matrix O(ns) discrete‐time system solver is employed to compute the history of the state and output. Finally, the response of the original system is obtained by superposition. In practical engineering applications, closing feedback loops and cascading filters can hinder the efficient use of the simulation scheme. Solutions to these problems are addressed in the paper. The simulation scheme, implemented as a MATLAB function fastlsim, is benchmarked against the standard LTI system simulator lsim and is shown to be superior for medium to large systems. The algorithm scales close to O(n) for a set of benchmarked systems. Simulation of a high‐fidelity model of (ns ≈ 2200) the Space Interferometry Mission spacecraft illustrates real world application of the method. Copyright © 2005 John Wiley & Sons, Ltd.
Influence functions and goal‐oriented error estimation for finite element analysis of shell structures
Authors: Grätsch Thomas , Bathe Klaus‐Jürgen
Published: March 2005

In this paper, we first present a consistent procedure to establish influence functions for the finite element analysis of shell structures, where the influence function can be for any linear quantity of engineering interest. We then design some goal‐oriented error measures that take into account the cancellation effect of errors over the domain to overcome the issue of over‐estimation. These error measures include the error due to the approximation in the geometry of the shell structure. In the calculation of the influence functions we also consider the asymptotic behaviour of shells as the thickness approaches zero. Although our procedures are general and can be applied to any shell formulation, we focus on MITC finite element shell discretizations. In our numerical results, influence functions are shown for some shell test problems, and the proposed goal‐oriented error estimation procedure shows good effectivity indices. Copyright © 2005 John Wiley & Sons, Ltd.
The development of an algorithm for the mass spectral interpretation of phosphoproteins
Authors: Zhao Yupeng , Lin Yen‐Han
Published: March 2005

Extended from the peptide mapping method (Fenyo, D., Curr. Opin. Biotechnol. 2000, 11, 391–395) the proposed algorithm takes the mass information of a precursor ion to reconstruct all possible phosphorylated peptide sequences. The mass spectra of product ions from the corresponding precursor ion is then used and compared to the reconstructed sequences to deduce the most probable phosphoprotein. The proposed algorithm also predicts all possible combinations of phosphopeptides, which may serve as a clue for designing proper phosphorylation experiments to validate the existence of these peptides and the corresponding proteins.
Differential protein expression in human gliomas and molecular insights
Authors: Chumbalkar Vaibhav C. , Subhashini Chanumolu , Dhople Vishnu M. , Sundaram Curam S. , Jagannadham Medicharla V. , Kumar Kafnam N. , Srinivas Pasumarti N. B. S. , Mythili Ravinutala , Rao Mulla K. , Kulkarni Mahesh J. , Hegde Sridevi , Hegde Alangar S. , Samual Cini , Santosh Vani , Singh Lalji , Sirdeshmukh Ravi
Published: March 2005

Gliomas are the most common of the primary intracranial tumors with astrocytomas constituting about 40%. Using clinically and histologically assessed astrocytomas, we have studied their protein profiles using a two‐dimensional gel electrophoresis‐mass spectrometry approach and identified differentially expressed proteins which may be useful molecular indicators to understand these tumors. Examination of the protein profiles of 27 astrocytoma samples of different grades revealed 72 distinct, differentially expressed proteins belonging to various functional groups such as cytoskeleton and intermediate filament proteins, heat shock proteins (HSPs), enzymes and regulatory proteins. Based on the consistency of their differential expression, 29 distinct proteins could be short‐listed and may have a role in the pathology of astrocytomas. Some were found to be differentially expressed in both Grade III and IV astrocytomas while others were associated with a particular grade. A notable observation was underexpression of Prohibitin, a potential tumor suppressor protein, Rho‐GDP dissociation inhibitor, Rho‐GDI, a regulator of Rho GTPases and HSPs as well as destabilization of glial fibrillary acidic protein, GFAP, major protein of the glial filaments, in Grade III malignant tumors. We attempt to explain glioma malignancy and progression in terms of their combined role.
Tryptic transpeptidation products observed in proteome analysis by liquid chromatography‐tandem mass spectrometry
Authors: Schaefer Heike , Chamrad Daniel C. , Marcus Katrin , Reidegeld Kai A. , Blüggel Martin , Meyer Helmut E.
Published: March 2005

Commonly, prior to mass spectrometry based analysis of proteins or protein mixtures, the proteins are subjected to specific enzymatic proteolysis. For this purpose trypsin is most frequently used. However, the process of proteolysis is not unflawed. For example, some side activities of trypsin are known and have already been described in the literature (e.g., chymotryptic activity). Here, we describe the occurrence of transpeptidated peptides during standard proteome analysis using two‐dimensional polyacrylamide gel electrophoresis followed by mass spectrometric protein identification. Different types of transpeptidated peptides have been detected. The most frequently observed transpeptidation reaction is N‐terminal addition of arginine or lysine to peptides. Furthermore, addition of two amino acids to the N‐terminus of a peptide has also been detected. Another transpeptidation that we observed, is combination of two peptides, which were originally located in different regions of the analyzed protein. Currently, the full amount of peptides generated by transpeptidation is not clear. However, it should be recognized that protein information is presently lost as these effects are not detectable with available database search software.
Defect structures and three‐body potential of the mean force for nanoparticles in a nematic host
Authors: Guzmán O. , Abbott N. L. , de Pablo J. J.
Published: March 2005

We have investigated the defect structures and potential of mean force (PMF) of three colloidal spheres immersed in a nematic liquid crystal (for linear and equilateral‐triangular configurations), using a coarse‐grained theory for the tensor order parameter. At large separations, each sphere is surrounded by an equatorial Saturn ring defect; at short separations, the theory predicts a drastic reorganization of the disclination lines: additional disclination rings are observed in planes perpendicular to the original ones. For both types of configurations, the PMF is attractive and always greater than a pairwise sum of binary PMFs. Comparing the PMFs of linear and equilateral‐triangular configurations, we have found the triangular configuration to be more stable than the linear configuration. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 1033‐1040, 2005
The role of QSARs and fate models in chemical hazard and risk assessment
Authors: Mackay Don , Hubbarde Jennifer , Webster Eva
Published: March 2005

A structure is suggested and discussed for the assessment of hazard and risk of chemicals of commerce, starting from a knowledge of molecular structure and proceeding to estimation of chemical properties, environmental fate and presence in organisms. Two metrics of risk are described, the external risk ratio which is based on concentrations external to the organism and the internal risk ratio based on concentrations internal to the organism. Where possible, the latter is preferred. Aspects of this multi‐stage strategy are discussed in more detail including the need for more experimental data in support of QSARs, the need for consistency in QSARs describing related properties and the complementary roles of fate models and QSARs. Whereas most screening‐level regulatory assessments of large numbers of chemicals focus on hazard, it is argued that the public concern is primarily with risk. Since risk assessment depends on the availability of data on rates of emission and such data are often very uncertain, this stage is often delayed and may only be done for relatively few substances. This is unfortunate because many hazardous substances are used under conditions such that there is minimal risk of exposure and effects. It is suggested that risk assessment can be facilitated by “backtracking” from an arbitrarily assumed risk ratio to calculate a hypothetical “critical” emission rate which would support that ratio. This rate can then be compared with likely emission to give an indication of proximity to levels of concern and thus the sustainability of present chemical emission practices.
Modeling Discrimination between Antibacterial and Non‐Antibacterial Activity based on 3D Molecular Descriptors
Authors: Aptula Aynur O. , Kühne Ralph , Ebert Ralf‐Uwe , Cronin Mark T. D. , Netzeva Tatiana I. , Schüürmann Gerrit
Published: March 2005

For a data set of 661 organic chemicals including many drug‐like compounds, discrimination between antibacterial and non‐antibacterial activity was modeled using hydrophobicity in terms of the logarithmic octanol/water partition coefficient (log Kow) and AM1‐level molecular descriptors encoding geometric, electrostatic, nucleophilic and electrophilic characteristics of the compounds. Linear discriminant analysis (LDA) and binary logistic regression (BLR) achieved an overall classification rate of around 90%, using two to three variables selected from log Kow, charged‐weighted negative surface area (PNSA‐3), positive surface area of heavy atoms (PPSA‐1Z), and maximum donor delocalizability (DEmax). Model validation was performed using complementary subsets for training and prediction as well as by training the total set with 50% of the activity data allocated wrongly in several arbitrarily selected ways. The discussion includes a comparative analysis of force‐field and AM1 geometries as well as of the 3D variation of AM1‐level molecular descriptors. Surprisingly, 3D geometry variations have only little impact on the discriminatory performance of the models.
Comparative Study of Activities between Verbascoside and Rutin by Docking Method
Authors: Gao Kun , Fan Bo Tao , El Fassi Nadia , Zakrzewska Krystyna , Jia Zhongjian , Zheng Rongliang , Panaye Annick , Couesnon T. , Doucet Jean‐Pierre
Published: March 2005

Verbascoside and rutin possess anti‐cancer properties and are capable of repairing DNA damaged by oxygen radicals, acting as powerful antioxidants. Based on kinetic measurements and experiments on tumor cells, docking studies of the two ligand molecules with the receptor telomeric DNA fragments have been carried out. The docking calculations performed using JUMNA software showed that the both molecules can be docked into the minor groove of telomeric DNA and form complexes with suitable geometry for electron transfer between guanine radical and ligands. The reaction mechanism via the electron transfer process is further confirmed through energy calculations for transition states using MOPAC 93 program. Complexes can be formed without major distortion of DNA structure and are further stabilized by the interaction of DNA with the saccharide side‐groups. By comparing their energies, the difference of activities of the two compounds can be explained.
Time‐Modulated Combinatorially Developed Optical Sensors for Determination of Non‐Volatile Analytes in Complex Samples
Authors: Potyrailo Radislav A. , Lemmon John P.
Published: March 2005

We have demonstrated rapid determination of non‐volatile analytes in multiple complex liquid‐phase samples such as those created in combinatorial chemistry and other experiments. The method utilizes analyte‐enhanced fluorescence of a combinatorially selected pair of a solvatochromic reagent bound to a solid support matrix. Our method involves an evaporation step that removes volatile sample components that otherwise interfere with analyte quantification. By applying this time‐modulated analysis of optical signature of a support‐bound solvatochromic reagent after the contact with a liquid sample and interference removal, our method improves selectivity of chemical determinations of liquid samples. The porous nature of the solid support and its packing geometry along with the optical illumination strategy of the sensor permitted volume‐independent analyte determinations over the 30–40‐μL sample volume, typical for the robotic delivery systems. Using our detection method and bisphenol A (BPA) as a model analyte, we were able to provide rapid selective determinations of BPA over 880 ppm‐25 wt.‐% concentration range without interferences from phenol, acetone, acetonitrile, and water.
Asymmetric Catalytic Ketone Hydrogenation: Relating Substrate Structure and Product Enantiomeric Excess Using QSPR
Authors: van der Linden Johannes B. , Ras Erik‐Jan , Hooijschuur Simone M. , Klaus Guido M. , Luchters Niels T. , Dani Paulo , Verspui Göran , Smith Alan A. , Damen Eric W. P. , McKay Ben , Hoogenraad Marcel
Published: March 2005

Partial Least Squares (PLS) was used to develop Quantitative Structure–Property Relationships (QSPRs) to analyze substrate structures in asymmetric ketone hydrogenation reactions with Noyori's catalyst. For a set of benzophenone substrates, PLS models were obtained which could correlate the substrate structure to the product enantiomeric excess (e.e.). The structural conformation used for calculating some of the descriptors was found to be important for obtaining satisfying model properties. Acceptable R2 and Q2 values could be obtained despite the small training data set of only 13 benzophenones. The model was subsequently used for the systematic estimation of product e.e. values for a series of other benzophenone substrates. Reaction results for two benzophenones show that the model can correctly indicate a low, medium or high expected e.e. value.
Current Status of Combinatorial and High‐Throughput Methods for Discovering New Materials and Catalysts
Authors: Woo Seong Ihl , Kim Ki Woong , Cho Hyun Yong , Oh Kwang Seok , Jeon Min Ku , Tarte Naresh Hiralal , Kim Tai Suk , Mahmood Asif
Published: March 2005

Combinatorial technology has been evaluated as the revolutionary approach to overcome the limitation of conventional research and to advance research in the development of novel materials and catalysts. For the past decade, because of the advance in library synthetic method and characterization tools, combinatorial and high‐throughput methodology surprisingly matured and nowadays has been extended to discovering novel olefin polymerization catalysts. However, despite such an advance, the characterization methodology did not keep pace with the increase in library density and limited the application of combinatorial technology. Therefore, in combinatorial technologies, the development of novel characterization methods is urgent and very important. In this review, we introduce several characterization tools and synthetic apparatus that are currently applied to discovering inorganic materials and catalysts using combinatorial technology, and consider how to overcome these limitations.
Design of Discovery Libraries for Solids Based on QSAR Models
Authors: Farrusseng D. , Klanner C. , Baumes L. , Lengliz M. , Mirodatos C. , Schüth F.
Published: March 2005

A method is described which is used to construct a descriptor vector of solid catalysts in the oxidation of propene. Different methods are described which allow one to construct a correlation between characteristics of the catalysts and their performance in propene oxidation. Successful descriptor vectors are generated which predict catalytic performance substantially better than statistically expected. These descriptor vectors do not contain explicit information on the elemental composition of the catalysts any more, but only parameters that are either derived from the elemental composition, such as the enthalpy of oxide formation, or are related to the synthetic method. The general concept can probably be extended to the development of descriptors for solids to be used in other applications as well.
Mass spectral analysis of synthones of nerve agents for verification of the Chemical Weapons Convention
Authors: Gupta Arvind K. , Shakya Purushottam D. , Pardasani Deepak , Palit Meehir , Dubey Devendra K.
Published: March 2005

This communication describes the synthesis and gas chromatography/mass spectrometric (GC/MS) analysis of N,N‐dialkylphosphoramidic dihalides and alkylphosphonic difluorides, which are synthones of nerve agents. The study was undertaken with a view to developing a spectral database of these compounds for verification purposes of the Chemical Weapons Convention (CWC). The modified synthetic approach reported here has advantages over traditional syntheses in terms of time and yield. GC/MS analysis of these synthones yielded electron ionization (EI) mass spectra and, based on these spectra, generalized fragmentation routes are proposed that rationalize most of the characteristic ions. Copyright © 2005 John Wiley & Sons, Ltd.
Electrospray ionization mass spectrometric study of purine base‐cisplatin complexes
Authors: Frańska Magdalena , Frański Rafał , Schroeder Grzegorz , Springer Andreas , Beck Sebastian , Linscheid Michael
Published: March 2005

By mixing cisplatin (cis‐diamminedichloroplatinum(II)) with purine base the following ions have been obtained under electrospray ionization conditions: [A+Pt(NH3)2Cl]+, [A+PtNH3Cl]+, [G+Pt(NH3)2Cl]+ and [G+PtNH3Cl]+. Their collision‐induced dissociation led to the loss of NH3 and HCl and formation of the protonated base. The last process is strongly favoured for adenine over guanine. It confirms that, analogously as for DNA, formation of the guanine‐cisplatin complex is favoured over that of the adenine complex and, as a consequence, it suggests that the mass spectrometric study of nucleic base complexes with platinum may provide some information on the interactions of DNA with other platinum drugs. The loss of NH3 accompanied by that of CO from the guanine ring has experimentally confirmed the presence of a strong hydrogen bond between the NH3 molecule and the OC6 moiety of guanine found by theoretical calculations. Copyright © 2005 John Wiley & Sons, Ltd.
Natural and post‐European settlement variability in water quality of the lower Snowy River floodplain, eastern Victoria, Australia
Authors: MacGregor Angus J. , Gell Peter A. , Wallbrink Peter J. , Hancock Gary
Published: March 2005

Millennial to decadal resolution palaeoenvironmental records from the terminal floodplain lakes of the lower Snowy River in eastern Victoria have been obtained to determine the water quality history of the lower Snowy River floodplain and more specifically, the ecological impact of the inter‐basin diversion of water from one of Australia's hallmark river systems. Lake Curlip, as evidenced through variations in the fossil‐diatom flora, has evolved through the Holocene from a saline (17–22 g salt/l) open system (c. 7000 years BP) as sea levels reached their maxima, to a brackish (5–10 g/l), and then a fresh (as low as 0.4 g/l), possibly acidic system prior to European settlement (c. 300 years BP). The upper post‐European sediments reveal a complex, highly variable, anthropogenically induced shift to a brackish and nutrient‐tolerant diatom flora, with recent diatom‐inferred salinities in the order of 20 g/l. Explained as a combination of land clearance, drainage practices, and more recently, the regulation of the Snowy River, recent changes are as pronounced as any experienced through the Holocene, but have occurred at a rate faster than any brought on by past climatic or geomorphic change. By quantifying the limnological changes before and after regulation this study informs on the relative benefits that may accrue from allocating environmental flows to the Snowy River. Copyright © 2005 John Wiley & Sons, Ltd.
Effects of dam‐induced flow regime change on downstream river morphology and vegetation cover in the Hwang River, Korea
Authors: Choi Sung‐UK , Yoon Byungman , Woo Hyoseop
Published: March 2005

The Hapchon Dam, located in the headwaters of the Hwang River, Korea, was completed in 1988. Due to low storage levels, the spillway has not been operated over the past decade. Thus, a new ecosystem has become established in the river downstream of the dam. This is not a common phenomenon in Korean rivers. This study investigates the effect of flow regime change on the river morphology and vegetation cover in a reach downstream of the dam following its construction. Geomorphological effects shown by pre‐ and post‐construction surveys of the channel include channel incision over a stream length of approximately 25 km immediately downstream of the dam. Analysis of pre‐ and post‐construction aerial photography reveals significant encroachment of riparian vegetation onto previously active bar surfaces. Copyright © 2005 John Wiley & Sons, Ltd.