bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum‐phase dynamics of molecular systems interacting with a two‐mode squeezed vacuum field: Detuning effects
Authors: Nakano M. , Yamaguchi K. 
Published: June 2004

AbstractWe investigated several three‐state molecular models interacting with an on/off‐resonant two‐mode squeezed vacuum field (TSV) to clarify the detuning effects on the dynamic behaviors of on/off‐diagonal molecular density matrices. For comparison, we perform a parallel study in which the initial field is an on/off‐resonant two‐mode coherent field. In the case of satisfying both a large one‐photon detuning and a two‐photon resonance conditions, the magnitude of off‐diagonal density matrix (|ρ13|) between the second excited and the ground states for (TSV) exhibits distinct increase and decrease behaviors similar to the case of a two‐mode coherent field in contrast to the case of one‐ and two‐photon resonances, in which a random oscillation of |ρ13| with a relatively high averaged value is observed. The change in the contribution of one‐ and two‐photon processes due to the detuning of external fields and the differences in the quantum statistics of the initial quantum fields are found to cause such attractive variations in dynamics of the coherency between molecular electronic states as well as their populations. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Ground state of the beryllium atom: Reinvestigation based on a proper independent particle model
Authors: Barbosa André Gustavo Horta , Nascimento Marco Antonio Chaer 
Published: June 2004

AbstractAs pointed out a long time ago by Hylleraas, Eckhart, Coulson, Shull, and Löwdin, the Hartree–Fock model does not provide the lower‐energy wave function expressed as a single orbital product. Valence bond‐like wave functions, with one configuration of optimized nonorthogonal singly occupied orbitals, provide the best possible independent particle model (IPM) wave function. In this article, we present IPM calculations, beyond the Hartree–Fock model, at the generalized valence bond and generalized multistructural (GMS) levels for the ground state of the beryllium atom. The electronic structure of the beryllium atom can be viewed as resonance hybrid of three configurations. A simple prescription to transform a CASSCF(2,4) to a GMS‐3S wave function yielding a fully optimized and uniquely defined IPM is presented. With these wave functions, using a variety of basis sets it is shown that, contrary to what is usually assumed in the literature, the valence electronic correlation energy in the beryllium atom is small and the stabilization brought about by including the 1s22p2 configuration is neither due to nondynamic nor dynamic correlation effects. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Momentum space properties for the atoms helium to neon from energy‐optimized explicitly correlated wave functions
Authors: Gálvez F. J. , Buendía E. , Sarsa A. 
Published: June 2004

AbstractAtomic momentum space properties have been calculated starting from explicitly correlated wave functions. The one‐body momentum distribution and some of their radial moments and related properties for the atoms helium to neon are reported. The wave functions include a generalized Jastrow factor and in some cases a multideterminant expansion to take care of the nondynamic correlation effects such as the 2s‐2p near degeneracy. Both the variational trial wave functions and the momentum space properties have been calculated using the variational Monte Carlo method. The optimization of the free parameters of the trial wave functions is done by using a recently developed energy‐optimization technique. Most of the previous variational Monte Carlo applications to quantum chemistry rely on variance‐optimized wave functions. A comparison of momentum space properties calculated with energy‐optimized wave functions with those obtained by means of variance‐optimized wave functions shows a better performance of the former. Despite the simple parameterization of the wave functions used here, they present a good agreement with the results obtained from extensive configuration interaction wave functions. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Calculations of photodissociation in intense laser fields: Validity of the adiabatic elimination of the continuum
Authors: Sukharev M. E. , Charron E. , Suzor‐Weiner A. , Fedorov M. V. 
Published: June 2004

AbstractWe investigate the range of applicability of the approximations of adiabatic and semiadiabatic elimination of the continuum in the numerical simulation of strong field photodissociation processes. By comparing exact and approximate calculations of the fragmentation of the H molecular ion when excited by a short and intense laser pulse, we show that these approximations do not hold when a few excited vibrational states are transiently populated. This failure mainly arises from the fast variation of the phases of the excited‐state time‐dependent amplitudes. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Protein effects on the O2 binding to the active site of the methane monooxygenase: ONIOM studies
Authors: Hoffmann Marcin , Khavrutskii Ilja V. , Musaev Djamaladdin G. , Morokuma Keiji 
Published: June 2004

AbstractThe protein effects on the initial step of O2 binding to the diiron active site in the Methane Monooxygenase (MMO) were studied at the ONIOM(QM:MM) level with and without electronic embedding. The significant part of the hydroxylase component of MMO, every aminoacid residue at least one atom of which is within 11 Å radius from either of the iron‐centers of the active site, was included into the calculations. The computed “real” system contained almost 1200 atoms and we treated it at, ONIOM low level, Amber molecular mechanics force field. Position of every atom of each amino acid residue within 7‐Å radius from either of the iron atoms as well as all hydrogen atoms was optimized. The “model” system, treated at the B3LYP/lan12dz level (ONIOM high level) encompassed 44 atoms including: (i) two iron atoms, (ii) functional groups forming first coordination sphere, such as two water molecules, two imodazoles, two bridging (between the Fe atoms) and two terminal carboxylates, as well as (iii) the dioxygen molecule. The comparison of the obtained results in vacuo and in protein, both with and without electronic embedding, clearly indicates that the protein profoundly affects initial binding of dioxygen molecule to the diiron center of the MMOHred. It was shown that at the early stages methane monooxygenase protein environment plays a crucial role as it effectively facilitates the activation of the dioxygen molecule. Furthermore, the obtained results demonstrated the usefulness of the ONIOM approach in studying such large systems including a dozen of hundreds atoms. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Determination of abamectin in soil samples using high‐performance liquid chromatography with tandem mass spectrometry
Authors: Brewer Bobby N. , Armbrust Kevin L. , Mead Keith T. , Holmes William E. 
Published: June 2004

AbstractAbamectin, which is comprised of a mixture of avermectins B1a and B1b, is a natural pesticide used as an anti‐parasitic agent in livestock, ornamental, and agricultural crops, which can potentially be transported to aquatic systems. These compounds are highly toxic to both aquatic vertebrates and invertebrates at low concentrations in water. This investigation developed high‐performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS) techniques to support automated extraction by an accelerated solvent extraction (ASE®) system and chromatographic techniques to measure residues of avermectins in complex soil samples. HPLC along with atmospheric pressure chemical ionization (APCI) MS/MS was used for separation and determination of avermectin isomers in soil samples. Average method recovery for abamectin by UV was 91%, while detection by MS/MS resulted in a 68% recovery for abamectin. Individual method recoveries by MS/MS were 53.6% for avermectin B1a and 36.8% for avermectin B1b. The use of tandem technology eliminated matrix interferences and resulted in an approximately eight‐fold increase in sensitivity. Copyright © 2004 John Wiley & Sons, Ltd.
Quantification of mephenytoin and its metabolites 4′‐hydroxymephenytoin and nirvanol in human urine using a simple sample processing method
Authors: Klaassen Tobias , Kasel Dirk , Harlfinger Stefanie , Fuhr Uwe 
Published: June 2004

AbstractA reliable and easy to use liquid chromatography/tandem mass spectrometry (LC/MS/MS) method without the use of sample extraction was developed for the simultaneous quantification of urinary concentrations of mephenytoin, a standard phenotyping substrate for the cytochrome P450 enzyme CYP2C19, and its phase I metabolites 4′‐hydroxymephenytoin and nirvanol.Fifty μL of urine were diluted with a buffered β‐glucuronidase solution and incubated at 37°C for 6 h followed by addition of methanol, containing the internal standard 4′‐methoxymephenytoin. The chromatographic separation was achieved using a 100 × 3 mm, 5 μ Thermo Electron Aquasil C18 column with a gradient flow, increasing the organic fraction (acetonitrile/methanol 50:50) of the mobile phase from 10 to 90%. Quantification by triple‐stage mass spectrometry (TSQ Quantum, Thermo Electron) was accomplished by negative electrospray ionization in the selected reaction monitoring mode. Linearity was observed for all substances in the concentration range 15–10 000 ng/mL. The lower limit of quantification (LLOQ) was 20 ng/mL for 4′‐hydroxymephenytoin and 30 ng/mL for nirvanol and mephenytoin, respectively. Intra‐ and inter‐day inaccuracy did not exceed 9.5% for all substances from LLOQ to 10 000 ng/mL. Intra‐ and inter‐day precision were in the range of 0.8–10.5%. The method was validated according to international ICH and FDA guidelines and successfully applied for phenotyping of Caucasian male volunteers who received an oral dose of 50 mg mephenytoin. Copyright © 2004 John Wiley & Sons, Ltd.
Quantitation of drug metabolites in the absence of pure metabolite standards by high‐performance liquid chromatography coupled with a chemiluminescence nitrogen detector and mass spectrometer
Authors: Deng Yuzhong , Wu Jing‐Tao , Zhang Hongwei , Olah Timothy V. 
Published: June 2004

AbstractQuantitative information on drug metabolites with pharmacological or toxicological activities is of great interest during the drug discovery and development process. Because the analyte response with mass spectrometry can change significantly due to small variations in chemical structure, pure standards are required to construct standard curves for quantitation. However, for most programs at the discovery stage, pure metabolite standards are not available. In this work, an evaluation was conducted using a chemiluminescent nitrogen detector (CLND) as a calibrator to obtain the response factor ratio on a mass spectrometer generated from a metabolite and its parent compound in biological fluids. Using the response factor ratio obtained from the CLND, the metabolite could be quantified with the liquid chromatography/tandem mass spectrometry (LC/MS/MS) response obtained from the parent drug's standard curve. For this evaluation, oxazepam and temazepam were chosen as a ‘drug/metabolite’ pair. Temazepam was treated as the methylated metabolite of oxazepam. A spiked dog urine sample with a known concentration of oxazepam and unknown concentration of temazepam was injected onto the HPLC system and detected by both the CLND and MS/MS. Taking advantage of the equimolar response feature of the CLND, a response factor ratio between temazepam and oxazepam on the mass spectrometer was obtained by comparing the peak areas generated on the CLND and the mass spectrometer. From this ratio, temazepam was quantified using the oxazepam standard curve. The difference between the concentration of temazepam obtained from the reconstructed standard curve and the concentration obtained directly from a real temazepam standard curve was within 13% except the least concentrated standard (31%). This methodology has been successfully applied to measure quantities of the metabolite of a proprietary compound in a dog pharmacokinetic (PK) study. Copyright © 2004 John Wiley & Sons, Ltd.
A computational and experimental study of cation affinity (Na+) of nucleobases and modified nucleobases by electrospray ionization ion trap mass spectrometry
Authors: Rochut S. , Pepe C. , Paumard J.‐P. , Tabet J.‐C. 
Published: June 2004

AbstractGas‐phase Na+ affinities of modified or unmodified nucleobases were determined theoretically at the density functional theory level, with the B3P86 functional and the 6–31 + G* basis set, and experimentally using electrospray ionization ion trap mass spectrometry (ESI‐ITMS) and the kinetic method. For the calculations, the sodium cation affinities (SCA) were obtained from energies of the most stable complexes of the free nucleobases. Experimentally and theoretically relative scales of cation affinities were determined using eight modified and unmodified nucleobases and a very good agreement was obtained. Copyright © 2004 John Wiley & Sons, Ltd.
Determination of amphetamine in rat brain by in vivo microdialysis and ion‐pairing liquid chromatography with electrospray tandem mass spectrometry
Authors: Fuh Ming‐Ren , Haung Chiuan‐Hung , Wu Ti‐Yu , Lin Shiang‐Ling , Pan Wynn H. T. 
Published: June 2004

AbstractAn ion‐pairing liquid chromatography/electrospray tandem mass spectrometry (LC/ES‐MS/MS) method with in vivo microdialysis for the determination of amphetamine in rat brain has been developed. A microdialysis probe was surgically implanted into the striatum of the rat and artificial cerebrospinal fluid (aCSF) was used as the perfusion medium. Samples were collected and then analyzed off‐line by LC/ES‐MS/MS. A reversed‐phase C18 column was employed for LC separation and MS/MS was utilized for detection. Trifluoroacetic acid (TFA) was added to the mobile phase (acetonitrile/water) as an ion‐pairing reagent. Detection was by ES‐MS/MS directly, and no post‐column addition of organic modifier was needed. Dual linear ranges were determined from 0.1–0.5 μg/mL and 0.005–0.1 μg/mL, respectively. The detection limit, based on a signal‐to‐noise ratio of 3, was 0.001 μg/mL (5 nM). Good precision and accuracy were obtained. The applicability of this newly developed method was demonstrated by continuous monitoring of amphetamine concentrations in rat brain. Amphetamine reached a maximum concentration of 0.086 ± 0.017 μg/mL over 20–40 min after a single 3.0 mg/kg intraperitoneal administration. Copyright © 2004 John Wiley & Sons, Ltd.
A simple, rapid and sensitive method for determination of aldehydes in human blood by gas chromatography/mass spectrometry and solid‐phase microextraction with on‐fiber derivatization
Authors: Deng Chunhui , Zhang Xiangmin 
Published: June 2004

AbstractAldehydes are considered potential markers for enhanced oxidative stress and have been proposed as a diagnostic measure of cancer status. Duo to their volatility and activity, it is very difficult to accurately measure aldehydes in human blood. In the present work, gas chromatography/mass spectrometry (GC/MS) and solid‐phase microextraction (SPME) with on‐fiber derivatization was developed for determination of aldehydes in human blood. O‐(2,3,4,5,6‐Pentafluorobenzyl)hydroxylamine hydrochloride (PFBHA) in aqueous solution was first adsorbed by a SPME fiber, and then the aldehydes in blood samples were headspace extracted by the SPME fiber and rapidly derivatized with PFBHA on the SPME fiber. Finally, the oximes formed were desorbed and detected by GC/MS in electron ionization (EI) mode. Validation of the present method was carried out, and the method was applied to quantitative analysis of the aldehydes in lung cancer blood. The results demonstrated that GC/MS and SPME with on‐fiber derivatization is a simple, rapid, sensitive and solvent‐free method for the determination of aldehydes in human blood. Copyright © 2004 John Wiley & Sons, Ltd.
Sample size and power for McNemar's test with clustered data
Authors: Gönen Mithat 
Published: June 2004

AbstractMcNemar's test is used to compare the distribution of two paired binary random variables. When the data are clustered adjustment is needed to ensure that it is still a valid test. This article presents two approximations for calculating the power and sample size for the adjusted McNemar's test for clustered data, working with a particular adjustment. A simulation study is conducted to demonstrate the accuracy of these approximations. The method is also applied to the design of a study involving positron emission tomography in detecting metastatic colorectal cancer and sensitivity of sample size computations to the design parameters are explored in this context. Copyright © 2004 John Wiley & Sons, Ltd.
A latent normal distribution model for analysing ordinal responses with applications in meta‐analysis
Authors: Poon Wai‐Yin 
Published: June 2004

AbstractWe consider the comparison of two treatments (or a treatment and a control/placebo) with responses that are classified into ordinal categories. By operating on the assumption that the responses are manifestations of some underlying continuous variables and that the definitions of the categories for the treatment group and the placebo group are the same in the same clinical test centre, we develop a model to examine the possible treatment effects. These treatment effects can be identified as location effect or dispersion effect. The method can be generalized to analyse clinical test results coming from different centres, where each centre may have its own standard in classifying responses. The method is technically undemanding and can be implemented in a very simple and straightforward way by using easily accessible software that can be downloaded at no cost. Real data sets are analysed for illustration. Copyright © 2004 John Wiley & Sons, Ltd.
Analysis of longitudinal studies with death and drop‐out: a case study
Authors: Dufouil Carole , Brayne Carol , Clayton David 
Published: June 2004

AbstractThe analysis of longitudinal data has recently been an active area of biostatistical research. Two main approaches to analysis have emerged, the first concentrating on modelling evolution of marginal distributions of the main response variable of interest and the other on subject‐specific trajectories. In epidemiology the analysis is usually complicated by missing data and by death of study participants. Motivated by a study of cognitive decline in the elderly, this paper argues that these two types of incomplete follow‐up may need to be treated differently in the analysis, and proposes an extension to the marginal modelling approach. The problem of informative drop‐out is also discussed. The methods are implemented in the ‘Stata’ statistical package. Copyright © 2004 John Wiley & Sons, Ltd.
Quantile regression via vector generalized additive models
Authors: Yee Thomas W. 
Published: June 2004

AbstractOne of the most popular methods for quantile regression is the LMS method of Cole and Green. The method naturally falls within a penalized likelihood framework, and consequently allows for considerable flexible because all three parameters may be modelled by cubic smoothing splines. The model is also very understandable: for a given value of the covariate, the LMS method applies a Box–Cox transformation to the response in order to transform it to standard normality; to obtain the quantiles, an inverse Box–Cox transformation is applied to the quantiles of the standard normal distribution. The purposes of this article are three‐fold. Firstly, LMS quantile regression is presented within the framework of the class of vector generalized additive models. This confers a number of advantages such as a unifying theory and estimation process. Secondly, a new LMS method based on the Yeo–Johnson transformation is proposed, which has the advantage that the response is not restricted to be positive. Lastly, this paper describes a software implementation of three LMS quantile regression methods in the S language. This includes the LMS–Yeo–Johnson method, which is estimated efficiently by a new numerical integration scheme. The LMS–Yeo–Johnson method is illustrated by way of a large cross‐sectional data set from a New Zealand working population. Copyright © 2004 John Wiley & Sons, Ltd.
Advantages to transforming the receiver operating characteristic (ROC) curve into likelihood ratio co‐ordinates
Authors: Johnson Nils P. 
Published: June 2004

AbstractTraditionally, the receiver operating characteristic (ROC) curve for a diagnostic test plots true positives (sensitivity) against false positives (one minus specificity). However, this representation brings with it several drawbacks. A transformation to positive and negative likelihood ratio co‐ordinates, scaled by base‐ten logarithms, offers several advantages. First we motivate the use of positive and negative likelihood ratios, emphasizing their relationship to modification of the odds ratio. Then we highlight properties of likelihood ratios using the traditional ROC axes. Finally, we demonstrate ROC curves and their properties after conversion to likelihood ratio co‐ordinates. These graphs do not waste space for tests lacking diagnostic power, and offer a simple visual assessment of a test's impact on the odds ratio. Copyright © 2004 John Wiley & Sons, Ltd.
Analysis of foraging movements of Atlantic bluefin tuna (Thunnus thynnus): individuals switch between two modes of search behaviour
Authors: Newlands Nathaniel K. , Lutcavage Molly E. , Pitcher Tony J. 
Published: June 2004

AbstractWe investigate the application of quantitative techniques for distinguishing adaptive search behaviour in Atlantic bluefin tuna (Thunnus thynnus). The analysis demonstrates the application of a novel spectral analysis technique for resolving and measuring periodicity in animal behaviour patterns. Two different search strategies are identified that include regulation of turning (klinokinesis) and speed (orthokinesis). Our results provide evidence that bluefin tuna attempt to optimize their searching efficiency through adjustments in the duration and timing of switching between these two searching strategies. Repetitive, diurnal deep dives were also found to coincide with switching of search behaviour. Additional tracking experiments with larger sample sizes are needed to better identify how individuals switch between the two search strategies and how such decisions may collectively improve the searching and foraging efficiency of their schools (synchrokinesis, social taxis) in response to changes in the size or composition of prey aggregations.