bluuebunny/crossref_metadata_2025_split huggingface dataset:
Support vector machines for the classification and prediction of β‐turn types
Authors: Cai Yu‐Dong , Liu Xiao‐Jun , Xu Xue‐biao , Chou Kuo‐Chen 
Published: September 2002

AbstractThe support vector machines (SVMs) method is proposed because it can reflect the sequence‐coupling effect for a tetrapeptide in not only a β‐turn or non‐β‐turn, but also in different types of β‐turn. The results of the model for 6022 tetrapeptides indicate that the rates of self‐consistency for β‐turn types I, I′, II, II′, VI and VIII and non‐β‐turns are 99.92%, 96.8%, 98.02%, 97.75%, 100%, 97.19% and 100%, respectively. Using these training data, the rate of correct prediction by the SVMs for a given protein: rubredoxin (54 residues, 51 tetrapeptides) which includes 12 β‐turn type I tetrapeptides, 1 β‐turn type II tetrapeptide and 38 non‐β‐turns reached 82.4%. The high quality of prediction of the SVMs implies that the formation of different β‐turn types or non‐β‐turns is considerably correlated with the sequence of a tetrapeptide. The SVMs can save CPU time and avoid the overfitting problem compared with the neural network method. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd.
Estimation of dispersion effects from robust design experiments with censored response data
Authors: Chowdhury Abdul H. , Fard Nasser S. 
Published: September 2002

AbstractA method is presented for estimating dispersion effects (DE) from robust design experiments (RDE) with control and noise factors involving censored response data. This method is developed to discern the significance of DE from RDE and the method aims at analyzing a multi‐level/multi‐factor experiment. This method imputes censored data by a regression based imputation technique, assuming that the distribution of lifetime before and after censoring is identical. This method also models the residuals to identify important DE, assuming that the distribution of the observed random variables of the model is the same with or without censored response data. Finally, the method is demonstrated through a numerical example. Copyright © 2001 John Wiley & Sons, Ltd.
Confidence intervals and sample size determination for Cpm
Authors: Zimmer LS , Hubele NF , Zimmer WJ 
Published: September 2002

AbstractThe capability index, Cpm, sometimes called the Taguchi index, has the desirable characteristic of being sensitive to both dispersion and deviation of the process average from the engineering target. As a result, the proposed estimators of Cpm have a sampling distribution that is dependent on the non‐central chi‐square distribution. Hence, constructing confidence intervals, performing hypothesis testing or estimating sample size requirements necessitates manipulation of a rather complex functional expression, typically beyond the capabilities of practitioners who need readily available tools. Here, a simple graphical procedure is proposed and illustrated for obtaining exact confidence intervals for Cpm. The graphical procedure allows the user to simply enter the graph with an estimate of the index and a value of the non‐centrality parameter for a given sample size to arrive at end‐points of 90%, 95% or 99% one‐sided or two‐sided confidence intervals. Detailed tables are also provided to assist the user for a wider range of sample values and sample sizes. In addition, a procedure is also presented for determining the minimum sample size required for attaining a pre‐specified level of accuracy of the Cpm. Extensive tables are provided for the user with a simple example illustrating the facility of the technique. Copyright © 2001 John Wiley & Sons, Ltd.
The use of not logic in fault tree analysis
Authors: Andrews J. D. 
Published: September 2002

AbstractRisk and safety assessments carried out on potentially hazardous industrial systems commonly employ fault tree analysis to predict the probability or frequency of system failure. Causes of the system failure mode are developed in an inverted tree structure where the events are linked using logic gates. The type of logic is usually restricted to AND and OR gates which makes the fault tree structure coherent. The use, directly or indirectly, of the NOT logic gate is generally discouraged as this can result in a non‐coherent structure. Non‐coherent structures mean that components' working states contribute to the failure of the system. The qualitative and quantitative analysis of such fault trees can present additional difficulties when compared to the coherent versions. This paper examines some of the difficulties that can occur, and what potential benefits can be derived from the incorporation of NOT logic. It is shown that the binary decision diagram (BDD) method can overcome some of the difficulties in the analysis of non‐coherent fault trees. Copyright © 2001 John Wiley & Sons, Ltd.
Eliciting engineering knowledge about reliability during design‐lessons learnt from implementation
Authors: Hodge R. , Evans M. , Marshall J. , Quigley J. , Walls L. 
Published: September 2002

AbstractIn electronic design the use of engineering knowledge and experience is considered important in understanding and estimating the reliability performance of complex systems. There are numerous methods proposed for eliciting this knowledge in order to ensure that the data collected are valid and reliable. In this paper we describe our experiences in implementing an elicitation process that aims to extract engineering knowledge about the impact of design changes on a new aerospace product that is a variant of an existing product. The elicitation procedures used will be outlined and the ways in which we evaluated their usefulness will be described. This research generated many useful insights from the engineers and facilitators involved in the elicitation exercise. This paper shares their perspectives on the gains and losses associated with the exercise and makes recommendations for enhancing future procedures based on the lessons learnt. Copyright © 2001 John Wiley & Sons, Ltd.
Loss of isocyanic acid from the internal oxadiazole ring of protonated molecules of some 2,5‐diaryl‐1,3,4‐oxadiazoles
Authors: Frański Rafał , Schroeder Grzegorz , Rybachenko Volodymir , Szwajka Oles P. 
Published: September 2002

AbstractThe fragmentation pattern of some protonated 2,5‐diaryl‐1,3,4‐oxadiazoles is discussed. An unusual decomposition consisting of elimination of the isocyanic acid molecule from the internal oxadiazole ring was found. This fragmentation pathway was deduced on the basis of B/E linked scan mass spectra of metastable ions with liquid secondary ion mass spectrometry as the ionization method and also of low‐energy CID mass spectra where electrospray was used as the ionization technique. High resolution measurements were also performed. Copyright © 2002 John Wiley & Sons, Ltd.
Automated system for simultaneous analysis of δ13C, δ18O and CO2 concentrations in small air samples
Authors: Ribas‐Carbo Miquel , Still Chris , Berry Joe 
Published: September 2002

AbstractIn this paper we present an automated system for simultaneous measurement of CO2 concentration, δ13C and δ18O from small (<1 mL) air samples in a short period of time (≈1 hour). This system combines continuous‐flow isotope ratio mass spectrometry (CF‐IRMS) and gas chromatography (GC) with an inlet system similar to conventional dual‐inlet methods permitting several measurement cycles of standard and sample air. Analogous to the dual‐inlet method, the precision of this system increases with the number of replicate cycles measured. The standard error of the mean for a measurement with this system is 0.7 ppm for the CO2 concentration and 0.05‰ for the δ13C and δ18O with four replicate cycles and 0.4 ppm and 0.03‰ respectively with nine replicate cycles. The mean offset of our measurements from NOAA/CMDL analyzed air samples was 0.08 ppm for the CO2 concentration, 0.01‰ for δ13C and 0.00‰ for δ18O. A specific list of the parts and operation of the system is detailed as well as some of the applications for micrometeorological and ecophysiological applications. Copyright © 2002 John Wiley & Sons, Ltd.
Combined quantum chemical and RRKM modeling of the main fragmentation pathways of protonated GGG. II. Formation of b2, y1, and y2 ions
Authors: Paizs Béla , Suhai Sándor 
Published: September 2002

AbstractQuantum chemical and RRKM calculations were performed on protonated GGG in order to determine the atomic details of the main fragmentation pathways leading to formation of b2,y1, and y2 ions. Formation of y1 ions on the ‘diketopiperazine’ pathway is initiated from relatively high‐energy C‐terminal amide nitrogen protonated species for which the N‐terminal amide bond is in the cis isomerization state. The reaction goes through a transition structure which is only slightly less favored than the reactive configuration itself. RRKM calculations indicate that this reaction is extremely fast as soon as the fragmenting species have more internal energy than the reaction threshold. The calculated energetics suggests that y1 ions are formed on the ‘diketopiperazine’ pathway with a non‐negligible (6–10 kcal/mol) reverse activation barrier. Investigation of species occurring during the formation of b2 ions having an oxazolone structure indicates that y1 ions can be formed also from intermediates previously thought to result in only b2 ions. As the first step of the ‘bx‐yz’ pathway proposed here the extra proton must reach the nitrogen of the C‐terminal amide bond. Attack of the N‐terminal amide oxygen on the carbon center of the C‐terminal amide bond results in formation of the oxazolone ring while the detaching G leaves the precursor ion. Under low‐energy collision conditions the complex of protonated 2‐aminomethyl‐5‐oxazolone and G can rearrange to form a proton‐bonded dimer of these species. In such circumstances the extra proton is shared by the two monomers and dissociation of the dimer will be determined by the thermochemistry involved. Based on the ‘bx‐yz’ pathway one can easily explain the linear relationship between the logarithm of the y1/b2 ion abundance ratio and the proton affinity of the C‐terminal amino acid substituent for the series of H‐Gly‐Gly‐Xxx‐OH tripeptides where Xxx was varied (Morgan DG, Bursey MM. Org. Mass. Spectrom. 1994; 29: 354). The calculated energetics indicates that both y1 and b2 ions are formed with no reverse activation barrier on the ‘bx‐yz’ pathway. Copyright © 2002 John Wiley & Sons, Ltd.
Cluster ions derived from sodium and potassium tetrafluoroborate and their collision induced dissociation in an ion trap mass spectrometer
Authors: Van Stipdonk M. J. , Ince M. P. , Perera B. A. , Martin J. A. 
Published: September 2002

AbstractElectrospray ionization was used to produce distributions of gas‐phase cluster ions from solutions of sodium and potassium tetrafluoroborate. The majority of the cluster species followed the trend (MBF4)nM+, where M = Na and K. The values of n, for both salts, ranged from 1–15. Collision induced dissociation (MS/MS and MSn) in an ion trap mass spectrometer was used to determine the dissociation pathways for the cluster ions. The (NaBF4)nNa+ cluster ions fragmented via two pathways: (a) the loss of one or multiple neutral BF3 molecules and (b) the loss of one or more NaBF4 units. Of the two, the product ions corresponding to the loss of BF3 units were more prominent. Unlike the Na salt, the (KBF4)nK+ cluster ions decomposed primarily by the loss of one or multiple KBF4 units. Similar differences in dissociation behavior were observed when the heated transfer capillary, normally used to desolvate ions, was used to investigate cluster ion stability to thermal degradation and dissociation. The dissociation profiles (decrease in ion abundance with increasing activation amplitude) for several (NaF)nNa+ and (KF)nK+ cluster ions were measured and compared to probe the influence of the relative stability of the alkali fluorides (NaF and KF) on the dissociation behavior exhibited by the tetrafluoroborate cluster distributions. We found that the (NaF)nNa+ cluster ions required higher activation amplitudes to induce fragmentation than the corresponding (KF)nK+ species, indicative of stronger ionic bonding and higher gas‐phase stability for the former. This in turn indicates that the reaction pathway involving only the loss of one or multiple units of BF3, favored for the (NaBF4)nNa+ cluster series, but not for the analogous (KBF4)nK+ series, may be due to the high gas‐phase stability of NaF, and relatively lower stability of KF, towards dissociation. Copyright © 2002 John Wiley & Sons, Ltd.
New algorithms for processing and peak detection in liquid chromatography/mass spectrometry data
Authors: Hastings Curtis A. , Norton Scott M. , Roy Sushmita 
Published: September 2002

AbstractTwo new algorithms for automated processing of liquid chromatography/mass spectrometry (LC/MS) data are presented. These algorithms were developed from an analysis of the noise and artifact distribution in such data. The noise distribution was analyzed by preparing histograms of the signal intensity in LC/MS data. These histograms are well fit by a sum of two normal distributions in the log scale. One new algorithm, median filtering, provides increased performance compared to averaging adjacent scans in removing noise that is not normally distributed in the linear scale. Another new algorithm, vectorized peak detection, provides increased robustness with respect to variation in the noise and artifact distribution compared to methods based on determining an intensity threshold for the entire dataset. Vectorized peak detection also permits the incorporation of existing algorithms for peak detection in ion chromatograms and/or mass spectra. The application of these methods to LC/MS spectra of complex biological samples is described. Copyright © 2002 John Wiley & Sons, Ltd.
Improved peptide detection with matrix‐assisted laser desorption/ionization mass spectrometry by trimethylation of amino groups
Authors: Stewart N. A. , Pham V. T. , Choma C. T. , Kaplan H. 
Published: September 2002

AbstractTrimethyl α‐amino derivatives of peptides (penta to deca) with a permanent positive charge on their α‐amino groups were prepared by in vacuo reaction with iodomethane and subjected to matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS). Compared to the unmodified peptide, the signal intensity of the trimethyl α‐amino derivative in MALDI‐MS is increased by at least an order of magnitude. Similarly, an octapeptide with a trimethylated ϵ‐amino group derived from the solitary lysine residue of the B‐chain of insulin also shows the same relative increase in signal intensity. Another advantage of the in vacuo methylation procedure is that trimethylation of a peptide amino group can be carried out readily with a combination of isotopes 13CH3I and 12CH3I or CD3I and CH3I, yielding a doublet signal either 3 or 9 units apart, respectively. The presence or absence of such a doublet signal can be used as a criterion to discriminate between peptide and non‐peptide signals in the mass spectrum. Copyright © 2002 John Wiley & Sons, Ltd.
High‐throughput liquid chromatography ultraviolet/mass spectrometric analysis of combinatorial libraries using an eight‐channel multiplexed electrospray time‐of‐flight mass spectrometer
Authors: Fang Liling , Cournoyer Jason , Demee Michael , Zhao Jiang , Tokushige Duayne , Yan Bing 
Published: September 2002

AbstractWe report a high‐throughput liquid chromatography/mass spectrometry (LC/MS) protocol for analyzing large combinatorial libraries using an eight‐channel parallel LC/UV/MS (MUX‐LCT) system. System configuration, linear response range in UV absorbance, LC column selection, and flow rate were optimized for 24 h/7 day unattended operations. Combinatorial libraries were analyzed on this system at a rate of 3200 compounds per day for a 3.5 min cycle time per injection. This parallel system is compared with a single‐channel system in terms of performance and operation. Copyright © 2002 John Wiley & Sons, Ltd.
Taylor dispersion monitored by electrospray mass spectrometry: a novel approach for studying diffusion in solution
Authors: Clark Sonya M. , Leaist Derek G. , Konermann Lars 
Published: September 2002

AbstractThis work describes a novel approach for monitoring analyte diffusion in solution that is based on electrospray ionization mass spectrometry (ESI‐MS). A mass spectrometer at the end of a laminar flow tube is used to measure the Taylor dispersion of an initially sharp boundary between two solutions of different analyte concentration. This boundary is dispersed by the laminar flow profile in the tube. However, this effect is diminished by analyte diffusion that continuously changes the radial position, and hence the flow velocity of individual analyte molecules. The steepness of the resulting dispersion profile therefore increases with increasing diffusion coefficient of the analyte. A theoretical framework is developed to adapt the equations governing the dispersion process to the case of mass spectrometric detection. This novel technique is applied to determine the diffusion coefficients of choline and cytochrome c. The measured diffusion coefficients, (11.9 ± 1.0) × 10−10 m2 s−1 and (1.35 ± 0.08) × 10−10 m2 s−1, respectively, are in agreement with the results of control experiments where the Taylor dispersion of these two analytes was monitored optically. Due to the inherent selectivity and sensitivity of ESI‐MS, it appears that the approach described in this work could become a valuable alternative to existing methods for studying diffusion processes, especially for experiments on multicomponent systems. Copyright © 2002 John Wiley & Sons, Ltd.
Influence of the 6th and 10th spatial harmonics on the peak shape of a quadrupole mass filter with round rods
Authors: Douglas D. J. , Konenkov N. V. 
Published: September 2002

AbstractThe influence of the ratio of the rod radius, r, to field radius, r0, on the peak shape for a linear quadrupole mass filter constructed with round rods has been investigated. The expansion of the potential in multipoles, $\phi _N,\Phi (x, y) = \sum_{N = 0}^{\infty} A_N \phi_N/r_{0}^{N}$, has been considered, and the peak shape and resolution have been determined by numerical calculation of ion trajectories in quadrupoles with different ratios, r/r0. Geometries that make the dodecapole term (A6) zero (r/r0 = 1.14511) do not give the best performance because the contribution of the 20‐pole term, A10, must be considered. The optimum ratio is r/r0 ≈ 1.13. With this ratio the dodecapole term (A6) is ca. 1 × 10−3, but its effects are partially compensated by the A10 term which has similar magnitude, but opposite sign. Copyright © 2002 John Wiley & Sons, Ltd.
Characterisation of adducts of the lipid peroxidation product 4‐hydroxy‐2‐nonenal and amyloid β‐peptides by liquid chromatography/electrospray ionisation mass spectrometry
Authors: Magni F. , Galbusera C. , Tremolada L. , Ferrarese C. , Kienle M. Galli 
Published: September 2002

AbstractAlzheimer's disease is characterised by brain neuritic plaques composed of a 39–44 amino acid peptide (Aβ). Lipid peroxidation is an early event induced by these amyloid β‐peptides, leading to the formation of 4‐hydroxy‐2‐nonenal (HNE), which is one of the major end products of this process. HNE has been reported to form adducts via a stable covalent binding to proteins through a Michael addition to amino acid residues with a nucleophilic side chain. The present study reports an investigation of the conditions for formation of Aβ‐HNE (Aβ 1–28 and Aβ 1–42) adducts, and their characterisation by liquid chromatography/electrospray ionisation mass spectrometry (LC/ESI‐MS). The results suggest that one or more HNE moieties are localised in the 6–16 region of these adducts, while Asp‐1, Lys‐16 and Lys‐28 are not modified under the described reaction conditions. Copyright © 2002 John Wiley & Sons, Ltd.
The application of molecular phylogenetics to the analysis of viral genome diversity and evolution
Authors: McCormack Grace P. , Clewley Jonathan P. 
Published: September 2002

AbstractDNA sequencing and molecular phylogenetics are increasingly being used in virology laboratories to study the transmission of viruses. By reconstructing the evolutionary history of viral genomes the behaviour of viral populations can be modelled, and the future of epidemics may be forecast. The manner in which such viral DNA sequences are analysed is the focus of this review. Many researchers resort to the often‐quoted ‘black box’ approach because phylogenetics theory can be daunting, and phylogenetics software packages can appear to be difficult to use. However, because phylogenetic analyses are often used in important and sensitive arenas, for example to provide evidence indicating transmission between persons, it is vital that appropriate care is taken to estimate reliably true relationships. In this review, we discuss how a molecular phylogenetics study should be approached, give an overview of the methods and programs for analysing DNA sequence data, and point readers to appropriate texts for further details. The aim of this review, therefore, is to provide researchers with an easy to understand guide to molecular phylogenetics, with special reference to viral genomes. Copyright © 2002 John Wiley & Sons, Ltd.
Protein–protein interactions as targets for antiviral chemotherapy
Authors: Loregian Arianna , Marsden Howard S. , Palù Giorgio 
Published: September 2002

AbstractMost cellular and viral processes depend on the coordinated formation of protein–protein interactions. With a better understanding of the molecular biology and biochemistry of human viruses it has become possible to screen for and detect inhibitors with activity against specific viral functions and to develop new approaches for the treatment of viral infections. A novel strategy to inhibit viral replication is based on the disruption of viral protein–protein complexes by peptides that mimic either face of the interaction between subunits. Peptides and peptide mimetics capable of dissociating protein–protein interactions have such exquisite specificity that they hold great promise as the next generation of therapeutic agents. This review is focused on recent developments using peptides and small molecules to inhibit protein–protein interactions between cellular and/or viral proteins with comments on the practicalities of transforming chemical leads into derivatives with the characteristics desired of medicinal compounds. Copyright © 2002 John Wiley & Sons, Ltd.
Three‐dimensional nonlinearH∞guidance law
Authors: Yang Ciann‐Dong , Chen Hsin‐Yuan 
Published: September 2002

AbstractThis paper proposes a novel three‐dimensional missile guidance law design based on nonlinearH∞control. The complete nonlinear kinematics of pursuit–evasion motion is considered in the three‐dimensional spherical co‐ordinates system; neither linearization nor small angle assumption is made here. The nonlinearH∞guidance law is expressed in a simple form by solving the associated Hamilton–Jacobi partial differential inequality analytically. Unlike adaptive guidance laws, the implement of the proposed robustH∞guidance law does not require the information of target acceleration, while ensuring acceptable interceptive performance for arbitrary target with finite acceleration. The resulting pursuit–evasion trajectories for both theH∞‐guided missile and the worst‐case target are determined in closed form, and the performance robustness against variations in target acceleration, in engagement condition, and in control loop gain, is verified by numerical simulations. Copyright © 2001 John Wiley & Sons, Ltd.