bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractA 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

AbstractA 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

AbstractThe 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

AbstractTime‐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

AbstractIn 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

AbstractExtended 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

AbstractGliomas 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

AbstractCommonly, 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

AbstractWe 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

AbstractA 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

AbstractFor 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

AbstractVerbascoside 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

AbstractWe 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

AbstractPartial 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

AbstractCombinatorial 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

AbstractA 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

AbstractThis 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

AbstractBy 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.