bluuebunny/crossref_metadata_2025 huggingface dataset:
Application of chain of events analysis to process safety management
Authors: Triplett Timothy L. , Zhou Yifeng , Mannan M. Sam
Published: June 2004

Process industries rely on process control and safety instrumented systems (SIS) to minimize the potential and consequence of hazardous incidents. As the computer‐based systems become more complex, there is the potential for inaccuracies and errors in program logic to introduce new causes of process deviations (abnormal situations) to the process plant. Finding these errors requires extensive review of the software utilizing traditional document tools. The novel chain‐of‐events analysis provides an effective aid in this process by extracting the linkage information from the system and creating an interaction table from which displays and reports may be generated to illustrate the influencing relationships among process control and SIS entities (points and their parameters). This method is also useful for routine maintenance and operation of a facility. It also provides assistance in analyzing alarms for abnormal situation management. © 2004 American Institute of Chemical Engineers Process Saf Prog 23: 132–135, 2004
Laser‐assisted conductance of molecular wires: Two‐photon contributions
Authors: Urdaneta I. , Keller A. , Atabek O. , Mujica V.
Published: June 2004

We extend to second order in the field intensity a previously obtained first‐order expression for the conductance of a tight‐binding molecular wire, bridging two electrodes, illuminated by a weak laser. The higher‐order term brings in corrections due to two‐photon processes that, for low intensities and strong molecule–electrode contacts, are several orders of magnitude smaller than the first‐order leading terms. For other ranges of parameters, the second‐order correction may be significant mostly due to processes involving the absorption or emission of two photons. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Alternative techniques in open‐shell SCF theory
Authors: Glushkov V. N.
Published: June 2004

An alternative to the Roothaan's open‐shell method that does not involve off‐diagonal Lagrangian multipliers has been proposed. The orthogonality of the closed‐ and open‐shell orbitals is discussed. Two possible schemes of designing the restricted open‐shell Hartree–Fock (HF) wave functions are discussed: In the first scheme the self‐consistent field (SCF) functions are linear combination of Slater determinants with coefficients fixed by symmetry whereas the second one uses the unrestricted HF formalism to build a single open‐shell Slater determinant from which a well‐defined open‐shell Møller–Plesset‐like perturbation theory can be performed. It has been shown that the Euler SCF equations based on the proposed technique lead to an optimum set of orbitals satisfying the correct variational conditions. A structure and correspondence of the proposed equations to those of the conventional approach are discussed. Practical calculations carried out at SCF and perturbation theory levels demonstrate some features of the proposed technique. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Macroconfigurations in molecular electronic structure theory
Authors: Khait Yuriy G. , Song Jie , Hoffmann Mark R.
Published: June 2004

Based on the well‐known idea of dividing a molecular orbital set into groups, and imposing restrictions on allowed group occupancies, a more general formalism, which we refer to as the macroconfiguration approach, is developed. The approach is shown to be useful in four complementary contexts: First, as with previous uses of orbital groupings, physical considerations can actively be taken into account in constructing configuration spaces; second, the approach is demonstrated to enable the screening of a vast number of noninteracting electron configuration pairs in a computationally efficient manner; third, all advantages of the Table–configuration interaction (CI) technique can be used effectively for evaluating Hamiltonian matrix elements between interacting configurations; finally, the macroconfiguration technique provides an efficient way of regenerating excited configurations as needed in a calculation. These characteristics indicate that the suggested approach is promising for improving the computational efficiency of methods describing electron dynamic correlation and, in particular, for CI calculations involving highly (e.g., triply and quadruply) excited configurations and for methods of effective Hamiltonian theory. The advantages of the suggested technique are illustrated by the results of calculations on the ground and excited states of the difluorodioxirane (CF2O2) molecule at the second‐order generalized Van Vleck perturbation theory (GVVPT2) level. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Fast and accurate evaluation of three‐center, two‐electron Coulomb, hybrid, and three‐center nuclear attraction integrals over Slater‐type orbitals using the SD transformation
Authors: Berlu Lilian , Safouhi Hassan , Hoggan Philip
Published: June 2004

In this work, Slater‐type atomic orbitals (STOs) are expanded over B functions to exploit the compact Fourier transform of these functions. The analytic representations of three‐center nuclear attraction integrals and multicenter bielectronic integrals over B functions involve semiinfinite highly oscillatory integrals, which can be transformed into infinite series. These integrals must be evaluated precisely and quickly. This work describes an efficient method for the evaluation of these integrals based on the nonlinear SD transformation, recently developed by Safouhi. The SD method was applied to multicenter integrals over B functions, and it is shown that this method is highly efficient compared with alternatives previously used. The SD approach should lead to a definitive suite of ab initio Slater software. The convergence properties were analyzed and they showed that the approximations obtained using the SD approach converge to the exact values of the semiinfinite integrals without any constraint. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
First‐principles analysis for the optical absorption spectra of metal ions in solids
Authors: Ishii Takugo , Ogasawara Kazuyoshi , Adachi Hirohiko , Burmester Philipp , Huber Günter
Published: June 2004

The authors developed a general first‐principles method for the direct calculation of multiplet structures. The method is a configuration interaction (CI) method combined with a general cluster method based on density functional theory. The present version of the method is based on a fully relativistic framework in which four‐component wave functions are handled. The calculations run independently of the semiempirical crystal field and ligand field theories, which have been the only the methods to analyze the absorption spectra involving the multiplet structures of transition metal and rare‐earth ion centers. One application of the present method is the analyses of the absorption spectra of solid‐state laser crystals. In this article, the authors focus on the multiplet structures originating from the f–f transition of Eu3+ ion in solids. In Eu3+‐doped Y2O3, the overall electronic structure is shown in agreement with the experimentally known absorption spectrum. A comparison of the multiplet structures between Eu3+ and Sm2+ ions is also shown. Although they have the same 4f6 electron configuration, the electronic structures showed different energy positions, and the tendency well agreed with that observed in experimentally known absorption spectra. In the one‐electron molecular orbital energies, the energies of Sm 4f levels were higher than those of Eu 4f levels. The difference is considered to originate from the difference in electron–nucleus attractive potential. The molecular orbitals of Eu 4f levels showed obvious mixing with O 2p orbitals, but those of Sm 4f levels did not. The calculated multiplet energies of Sm2+ were systematically smaller than those of Eu3+. The smaller multiplet energies originated from the smaller values of two‐electron integrals, indicating the relatively larger distribution of Sm 4f orbitals than those of Eu. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Exact analytic total energy functional for Hooke's atom generated by local‐scaling transformations
Authors: Ludeña Eduardo V. , Gómez Daniel , Karasiev Valentin , Nieto Pedro
Published: June 2004

An analytic closed form for the total energy density functional for Hooke's atom—an artificial two‐electron system with harmonic electron–nuclear and Coulombic electron–electron interaction terms—has been constructed by means of local‐scaling transformations. This is the first time that an exact density functional is obtained for a quantum mechanical many‐electron system containing electron correlation. The density‐dependent functional advanced in the present work is strictly variational: It yields the exact value of the total energy of Hooke's atom at the exact density and upper bounds for all other densities. Although the functional is not “universal” it contains the density‐dependent term ρ5/3 in the kinetic energy expression and an infinite sum of universal terms of the type ρ(l+4)/3, for l = 0, 1, … ∞, in the electron–electron energy. In all cases, these density‐dependent terms are multiplied by their corresponding enhancement factors F5/3(r) and {F(r)} that contain system‐specific information. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Effect of rotations on the generation of coherent internal molecular motion
Authors: Hervé Stephen , Le Quéré Frédéric , Marquardt Roberto
Published: June 2004

We discuss the quantum dynamics of the excitation of a diatomic molecule in the presence of external force fields and the general role of orientation on the manipulation of molecular structure. We review the dynamics of the HF molecule in the presence of a static electric field during and after coherent infrared radiation. The time‐dependent dynamics is induced by infrared multiphoton excitation and the time evolution of the rovibrational wave packet is calculated in configuration space. The coherent motion of rotational wave packets obtained from orientation in a static field is compared with the motion of rotational coherent states. Values are given for static field strengths needed to orient molecules such that their internal dynamics can be described by simplified, purely vibrational models. The results are discussed in comparison with the orientation of adsorbed molecules on metal surfaces. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Quantum‐phase dynamics of molecular systems interacting with a two‐mode squeezed vacuum field: Detuning effects
Authors: Nakano M. , Yamaguchi K.
Published: June 2004

We 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

As 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

Atomic 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

We 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

The 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

Abamectin, 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

A 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

Quantitative 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

Gas‐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

An 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

Aldehydes 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

McNemar'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

We 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

The 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

One 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

Traditionally, 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

We 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.
A critical period requiring Rho proteins for cell cycle progression uncovered by reversible protein transduction in endothelial cells
Authors: Hirano Katsuya , Hirano Mayumi , Nishimura Junji , Kanaide Hideo
Published: June 2004

The time‐specific requirement of Rho proteins for the S phase progression of vascular endothelial cells was determined by reversibly introducing inhibitor proteins with a cell‐penetrating peptide. We found evidence of the reversibility of protein transduction. The removal of extracellular protein caused the transduced protein to decay in a manner sensitive to low temperatures. The time required for a 50% decay correlated with the protein size. The time‐specific transduction of the inhibitor proteins uncovered a critical period requiring Rho proteins in the G1–S transition phase. Reversible protein transduction may thus be a powerful tool to investigate the time‐specific role of signaling proteins.
The Enhancement of Stereoselectivity of a Pd-Catalyzed Three-Component Cascade Reaction Using Parallel Synthesis and Multivariate Analysis
Authors: Ross Kate , Grigg Ron
Published: June 2004

Automated parallel synthesis with multivariate analysis was employed in the optimization of a Pd-catalyzed three-component cascade reaction of 7-buta-2,3-dienyl-1,3-dimethyl-3,7-dihydropurine-2,6-dione with iodobenzene and morpholine (see Scheme 1 ). Initially a range of reaction factors were analyzed using experimental design to optimize for selectivity, conversion, and impurity levels. Solvents and bases were screened separately as the substantial number of discrete variables involved is unsuited to the fractional factorial design used. Instead, a solvent principal component analysis (PCA) model was used in selection of solvents for screening, so gaining maximum variation in solvent properties. Similarly, tertiary amines were chosen by pKa for screening as bases alongside inorganic salts. This investigation yielded twofold results, not only in enhancement of the reaction selectivity, but since significantly dierent findings were obtained on changing the solvent, the importance of the sequence of experimentation is also emphasized.
SOS—A Sample Ordering System for Delivering “Assay-Ready” Compound Plates for Drug Screening
Authors: Brideau C. , Hunter J. , Maher J. , Adam S. , Fortin L. J. , Ferentinos J.
Published: June 2004

Many bottlenecks in drug discovery have been addressed with the advent of new assay and instrument technologies. However, storing and processing chemical compounds for screening remains a challenge for many drug discovery laboratories. Although automated storage and retrieval systems are commercially available for medium to large collections of chemical samples, these samples are usually stored at a central site and are not readily accessible to satellite research labs.

Drug discovery relies on the rapid testing of new chemical compounds in relevant biological assays. Therefore, newly synthesized compounds must be readily available in various formats to biologists performing screening assays. Until recently, our compounds were distributed in screw cap vials to assayists who would then manually transfer and dilute each sample in an “assay-ready” compound plate for screening. The vials would then be managed by the individuals in an ad hoc manner.

To relieve the assayist from searching for compounds and preparing their own assay-ready compound plates, a newly customized compound storage system with an ordering software application was implemented at our research facility that eliminates these bottlenecks. The system stores and retrieves compounds in 1 mL-mini-tubes or microtiter plates, facilitates compound searching by identifier or structure, orders compounds at varying concentrations in specified wells on 96- or 384-well plates, requests the addition of controls (vehicle or reference compounds), etc. The orders are automatically processed and delivered to the assayist the following day for screening. An overview of our system will demonstrate that we minimize compound waste and ensure compound integrity and availability. (JALA 2004;9:123-7)
Automated Genomic and Proteomic Applications on the Biomek® NX Laboratory Automation Workstation
Authors: Pajak Laura , Zhang Ruth , Pittman Chad , Roby Keith , Boyer Scott
Published: June 2004

This technical paper describes the utilization of a new automated liquid handler from Beckman Coulter, Inc., the Biomek® NX Laboratory Automation Workstation, for genomic and proteomic applications. For genomic applications, methodology for plasmid DNA purification using Promega Wizard® SV 96 reagents was developed for the Biomek NX. A single plate of bacterial pellets can be processed to purified plasmid DNA without user interaction after initial setup. DNA quantity and quality were assessed by spectrophotometric analysis, restriction digestion, PCR (The PCR process is covered by patents owned by Roche Molecular Systems, Inc., and F. Homan La Roche, Ltd.), and capillary sequencing. Additionally, the plasmid preparation method was used to purify plasmid DNA from bacterial clones isolated in a bacterial two-hybrid screening procedure. In this case, the system quickly and efficiently prepared clones for rapid identification of target sequences. For proteomic applications, His-tag proteins were purified from bacterial cultures in a 96-well plate format. Following purification, a Bradford assay was used to determine the quantitative yields of the His-tag protein products in each of the aliquots from the purified samples. The AD 340 Automated Labware Positioner (ALP), an integrated absorbance reader, was used for absorbance measurements in the Bradford assay. Given the placement of this ALP on the deck of the Biomek NX, the entire process of protein purification and quantitation was performed in a complete walk-away automated format. Results obtained when purifying proteins, from both uninduced and induced bacterial cultures, on the worksurface of the Biomek NX will be described. (JALA 2004;9:177-84)
A Novel System for Automated RNA Isolation: Increasing Throughput without Increasing Footprint
Authors: Laffitte Bryan , Murray David , Smith Ginger , Liacos Jim , Siu Amy , Finlay Cathy , Bruner Jimmy
Published: June 2004

The High Throughput Biology (HTB) department at GlaxoSmithKline is developing in vitro models to better predict the efficacy of compounds in the clinic. The development and progression of disease is often associated with characteristic changes in gene expression. These “transcriptional profiles” (mRNA gene expression patterns associated with a given disease) can be used as biomarkers to monitor disease states. Therefore, we are utilizing transcriptional profiling as a way to understand diseases and the effects of pharmaceuticals on those diseases. Transcriptional profiling has numerous advantages over other techniques including highly sensitive and highly quantitative assays, simple assay development, and accessibility of nearly the entire genome to transcriptional readouts. Our transcriptional profiling strategy involves isolation of total RNA from samples followed by real-time quantitative PCR assays (Taqman® assays). (JALA 2004;9:146-9)
Toxicological and Pharmacological Evaluation of New Drug Candidates by in Vitro Robotic High-Throughput Cell Assays
Authors: Thurow Kerstin , Entzian Kristin , Eberlein Gert
Published: June 2004

A high-throughput cell-based fluorescence screening assay was used to determine the cytotoxic activity of various cytostatic reference agents, unknown compounds of natural sources and pharmaceutic standard excipients in different cell lines such as HEK-293 and DLD-1 cells. In this paper we exemplarily show results for a selection of compounds and excipients. The cytostatic agent piposulfan has a much higher cytotoxic activity in DLD-1 cells (EC50=0.001 mg/mL) than in HEK-293 cells (EC50=0.3 mg/mL) in contrast to busulfan and vinblastine where the EC50 values are close together in both cell lines.

From 113 tested compounds from natural sources the cytotoxic activity of 75 compounds showed no difference in both cell lines, 34 of them had a higher activity in HEK-293 cells than in DLD-1 cells and 4 compounds showed less cytotoxic activity in HEK-293 cells than in DLD-1 cells. We demonstrate the rather potent cytotoxic action of Cremophor EL; this finding is in accordance with previously published observations. The presented results demonstrate that the used assay system is reliable, enables the ranking of the cytotoxic potential of compounds of various chemical classes, and allows the determination of cell type-specific cytotoxicity. (JALA 2004;9:159-62)
Automated Process of Q-PCR/Gene Expression
Authors: Cherry James M. , Stewart Claudia , Frankenberger Casey , Martin Kelly , Tudor Gabriela , Owens Garrison , Bhat Narayan K. , Munroe David J.
Published: June 2004

PCR-based fluorescent detection assays for the relative and quantitative measurement of gene expression, such as Taq Man™, LUX™, and SYBR Green™, are currently in wide spread use due to their general applicability, low cost, reproducibility, accuracy, and ease of use. One current limitation of quantitative PCR (Q-PCR) is the lack of a fully integrated and high-throughput method for general genomic and diagnostic applications. Here we report a reliable and high-throughput system for the automated extraction of RNA, first-strand cDNA synthesis, quality control measures, consecutive real-time PCR amplification, and primary data analysis. As described, this procedure utilizes commonly available reagents and pre-packaged “kits” for RNA extraction, first strand cDNA synthesis, Q-PCR, liquid handling, and capillary electrophoresis that are generally applicable to a wide variety of robotic platforms. (JALA 2004;9:128-34)
Automated Real-Time Hit Picking, Retesting, and Reflux Testing
Authors: Edwards Todd C. , LaSalle Stephanie , Luong Steve , Andresen Fred , Quarles Jason , Wilson David , Ito Ralph , Endress Greg
Published: June 2004

Advances in automation have enabled screening methods, such as enzymatic assays and ELISAs, to be performed in a high-throughput fashion. Instruments can perform each of the steps more rapidly and with fewer errors than humans, however, in many cases, humans still perform the key steps of integrating the instruments and Laboratory Information Management Systems (LIMS). Typically, the screening process involves multiple steps for sample testing, manual data entry and design of protocols to handle the positive samples, and final processing of positives. Fully integrated systems such as Protedyne's BioCube™ System combine liquid handling, LIMS, plate washing, and plate reading in a device that is controlled via a single user interface. As an example, we present the results of automating plate reading and retesting of positive samples in a model protocol based on ELISA testing. By performing an automated initial screening of results, our system enables positive samples to be retested at higher stringency or sent to a technician for corroboration of results. The screening process then becomes a single protocol that starts with a sample set and results in a data set of tested and retested/reflux tested positives as well as re-arrayed plates of positive samples that are ready for additional downstream processing. (JALA 2004;9:135-9)
High-Throughput Sample Preparation for Gene Expression Profiling and in Vitro Target Validation
Authors: Fang Xingwang , Willis Roy C. , Hoang Quoc , Kelnar Kevin , Xu Weiwei
Published: June 2004

The demand for high-throughput RNA isolation has been dramatically increasing with wide applications of RNAi, expression profiling, and molecular diagnosis. A comparison of various RNA isolation methods that have been adapted to high-throughput platforms, focusing on consistently high yield and quality of isolated RNA, reduction of cross-contamination, and simplicity and robustness of the protocol is presented. The streamlining of RNA isolation with RNA quantification by qRT-PCR and amplification for microarray analysis is also discussed. In general, a microspheric bead-based approach results in more consistent RNA recovery than glass fiber filter-based RNA isolation method, and RNA can be eluted in a smaller volume. This is because beads can be fully re-suspended in solution to enable more thorough mixing, washing, and elution, whereas the glass fiber matrix is fixed in a filter plate. (JALA 2004;9:140-5)
Quantitative Small Molecule Bioanalysis Using Chip-Based NanoESI-MS/MS
Authors: Zhang Lei , Laycock John D. , Miller Krys J.
Published: June 2004

A fully automated chip-based nanoelectrospray (nanoESI) system, NanoMate® 100 (Advion Bio-Sciences, Inc., Ithaca, NY), was evaluated for its application on quantitative bioanalysis of small molecules in support of exploratory pharmacokinetic (PK) studies. The NanoMate® 100 was compared with the conventional autosampler coupled with liquid chromatography-electrospray (LC-ESI) interface. An API® 3000 triple quadrupole mass spectrometer (Applied Biosystems, Inc., Foster City, CA) was used for the evaluation. The results show that the NanoMate® 100 performs comparably to LC-ESI in terms of standard curve fitting, low limit of quantitation (LLOQ), dynamic range, accuracy, and precision. Parallel analyses of exploratory PK study samples show high correlation ( R2 = 0.971) between the NanoMate® 100 and the LC-ESI. The NanoMate® 100 exhibits advantages in carryover, sample consumption, sample cycle time, and the ability to be full automated. Despite these advantages, the necessarily rigorous sample preparation process limits the application of the NanoMate® 100 for quantitative analysis in areas such as exploratory PK studies, which often involve multiple compounds in one study and require rapid turnaround. However, the NanoMate® 100 has great potential in qualitative work (e.g., metabolite identification) as well as in high-throughput quantitative analysis of compound in the development stage (i.e., a single analyte with a well-established sample extraction method). (JALA 2004;9:109-16)