bluuebunny/crossref_metadata_2025 huggingface dataset:
Time‐Dependent Problems with the Boundary Integral Equation Method
Authors: Costabel Martin
Published: January 2005

Time‐dependent problems that are modeled by initial‐boundary value problems for parabolic or hyperbolic partial differential equations can be treated with the boundary integral equation method. The ideal situation is when the right‐hand side in the partial differential equation and the initial conditions vanish, the data are given only on the boundary of the domain, the equation has constant coefficients, and the domain does not depend on time. In this situation, the transformation of the problem to a boundary integral equation follows the same well‐known lines as for the case of stationary or time‐harmonic problems modeled by elliptic boundary value problems. The same main advantages of the reduction to the boundary prevail: Reduction of the dimension by one, and reduction of an unbounded exterior domain to a bounded boundary.

There are, however, specific difficulties due to the additional time dimension; apart from the practical problems of increased complexity related to the higher dimension, there can appear new stability problems. In the stationary case, one often has unconditional stability for reasonable approximation methods, and this stability is closely related to variational formulations based on the ellipticity of the underlying boundary value problem. In the time‐dependent case, instabilities have been observed in practice, but due to the absence of ellipticity, the stability analysis is more difficult and fewer theoretical results are available.

In this article, the mathematical principles governing the construction of boundary integral equation methods for time‐dependent problems are presented. We describe some of the main algorithms that are used in practice and have been analyzed in the mathematical literature.
Buckling
Authors: Riks Eduard
Published: January 2005

Although the first known solution of a buckling problem was given by the outstanding Swiss ‘natural philosopher’ Leonhard Euler (1744), buckling theory as an engineering subject is an outgrowth of a development that was established during the last century. The overview of the present knowledge regarding the computational analysis of buckling problems is here given in the context of the theory's most important historical developments.
Computational Structural Dynamics
Authors: Hulbert Gregory M.
Published: January 2005

This chapter presents an overview and a state‐of‐the art compilation of time integration methods for solving problems of dynamics, with a particular focus on developments that have occurred during the past 25 years. Various classifications of time integration algorithms are provided that assist the reader in understanding the many different types of numerical methods available for solving time‐dependent problems. Time integration algorithms for linear structural dynamics are reviewed thoroughly, from classical Newmark‐type schemes, to recent developments in time finite element‐based approaches. The distinction between linear and nonlinear dynamics is articulated and numerical methods developed for direct application towards solving nonlinear dynamics probems are presented. The chapter concludes with guidelines towards selecting an appropriate time integration method, along with guidelines towards choosing appropriate time step sizes.
Homogenization Methods and Multiscale Modeling
Authors: Zohdi Tarek I.
Published: January 2005

The relatively recent increase in computational power available for mathematical modeling and simulation raises the possibility that modern numerical methods can play a significant role in the analysis of materials possessing heterogeneous microstructure. Ideally, in an attempt to reduce laboratory expense, one would like to make predictions of a new material's behavior by numerical simulations, with the primary goal being to accelerate the trial and error laboratory development of novel high performance materials. This fact, among others, has motivated the work that will be presented in this monograph.
Damage, Material Instabilities, and Failure
Authors: de Borst René
Published: January 2005

This chapter begins with an overview of damage mechanics. Isotropic and anisotropic models are described, as well as the coupling to plasticity, including the algorithmic treatment. Next, the implications of strain softening, which starts at a certain level of damage accumulation, are discussed as regards important notions such as material stability and ellipticity. The consequences of loss of ellipticity in terms of grid sensitivity of computations are illustrated for static and for dynamic instabilities. Next, the important role of cohesive‐zone models is highlighted, both in its original (discrete) format, a derived smeared format and as an embedded discontinuum description. To avoid loss of ellipticity, the introduction of higher‐order continua is necessary. Various higher‐order continua incorporating damage or coupled damage‐plasticity models are discussed, including aspects of numerical implementation. Finally, the numerical implementation of cohesive‐zone models in a discrete format is considered, where attention is given to conventional interface elements as well as to approaches that exploit the partition‐of‐unity property of finite element shape functions.
Computational Modelling of Damage and Failures in Composite Laminates
Authors: Reddy J. N. , Robbins D. H.
Published: January 2005

This chapter provides an overview of issues that are important in finite element modeling of progressive damage and failure in fiber‐reinforced composite laminates. Topics discussed include the multiscale nature of composite laminate problems, equivalent single layer and layerwise laminate theories and models, macroscopic failure theories, computational homogenization and localization, and the application of continuum damage mechanics to composite laminate problems, with emphasis on methods that are practical for large scale analysis of composite structural components.
Identification of Material Parameters for Constitutive Equations
Authors: Mahnken R.
Published: January 2005

This contribution addresses various topics on parameter identification for constitutive equations on the basis of experimental data. Starting from basic characteristics of inverse problems illustrated by simple examples, four different identification methods are introduced. Then particular aspects of the least squares approach are outlined, such as optimization, local minima, sensitivity analysis, consequences of instabilities, and stochastic methods. Uniform small strain problems and nonuniform large strain problems are considered, where for the latter finite element results are incorporated into the optimization process. The examples are concerned with a perturbation technique in order to detect possible instabilities, a stochastic analysis in order to examine the uncertainty of parameter estimates, and a necking problem observed with an optical method in order to take into account nonuniform large strains during the experiment.
Fluid‐Structure Interaction Problems
Authors: Ohayon Roger
Published: January 2005

Several so‐called reduced order formulations are reviewed in the case of linear vibration analysis of bounded fluid‐structure systems for low modal density situations. Compressibility effects in the fluid for interior structural‐acoustic problems, and free‐surface gravity effects, as well as for hydroelastic‐sloshing interaction problems in the case of incompressible liquids, are examined. Reduced order models leading to symmetric matrix systems are then described using static well‐posed behavior of the irrotational fluid. In this respect, the fluid‐structure boundary value local equations, expressed in terms of fluid scalar field variables for the fluid (and displacement variables for the structure), are regularized for zero‐frequency limit.
Computability and Adaptivity inCFD
Authors: Hoffman J. , Johnson C.
Published: January 2005

We present an approach to Computational Fluid Dynamics CFD based on adaptive stabilized Galerkin finite element methods with duality based a posteriori error control for chosen output quantities of interest. We address the basic question of computability in CFD: For a given flow, what quantity is computable to what tolerance to what cost? We focus on incompressible Newtonian flow with medium to large Reynolds numbers involving both laminar and turbulent flow features. Our basic tool is a representation formula for the error in the quantity of interest in terms of a space–time integral of the residual of a computed solution multiplied by weights related to derivatives of the solution of an associated linear dual problem with data connected to the output. We use the error representation formula to derive an a posteriori error estimate combining residuals with computed dual weights, which is used for mesh adaptivity in space–time with the objective of satisfying a given error tolerance with minimal computational effort. We show in concrete examples that outputs, such as mean values in time of drag and lift of turbulent flow around a bluff body are computable on a PC with a tolerance of a few percent using a few hundred thousand mesh points in space. We refer to our methodology asAdaptive DNS/LES, where automatically by adaptivity certain features of the flow are resolved in a Direct Numerical Simulation DNS, while certain other small‐scale turbulent features are left unresolved in a Large Eddy Simulation LES. The stabilization of the Galerkin method giving a weighted least square control of the residual acts as the subgrid model in the LES. The a posteriori error estimate takes into account both the error from discretization and the error from the subgrid model.
Dynamic Multilevel Methods and Turbulence
Authors: Dubois T. , Jauberteau F. , Temam R. M.
Published: January 2005

In this article, we describe numerical multilevel methods applied to the Navier–Stokes equations (homogeneous isotropic turbulence and channel flow problem), to the shallow water equations (geophysical problems), and to the renormalization of small eddies. The first difficulties with multilevel methods is to separate the scales. In this work, various cases are considered: the case of spectral methods, the case of finite difference methods, and the case of finite element methods. Then the numerical treatment is adapted to the size of the computed scales. The aim is to obtain new schemes, with better modeling properties and improved numerical stability. The spectral case is studied in detail, and results of numerical simulations are reported in this case.

Multilevel numerical methods are indispensable for the approximation of phenomena involving a large number of scales, such as turbulence. Although the methods described in this article are generally limited to two levels, they can, as explained in the text, be extended to a more important number of levels, thus extending significantly their performances.
Turbulence Direct Numerical Simulation and Large‐Eddy Simulation
Authors: Sagaut Pierre
Published: January 2005

This article deals with direct numerical simulation and large‐eddy simulation of turbulent flows, which are two techniques for the unsteady three‐dimensional simulation of turbulent motion. For the sake of clarity and brevity, the present framework is restricted to Newtonian, single‐phase, single‐specie fluids. Both compressible and incompressible cases are considered. Numerical requirements for these two approaches are discussed, including grid resolution and control of numerical errors. The specific problem of compressible flows with shocks is detailed. The problem of the definition of the filtering procedure and subgrid models for the large‐eddy simulation approach is presented, and the main theoretical and practical solutions are given. The difficult question of the definition of boundary conditions is also considered, with emphasis on turbulent inflow conditions and wall stress models. The last section is devoted to the presentation of the evolution of the application of these two techniques.
Aerodynamics
Authors: Jameson Antony
Published: January 2005

Computational methods are now pervasive in the science of aerodynamics. Because previously existing numerical methods proved inadequate for fluid flow simulations, the emergence of computational fluid dynamics (CFD) as a distinct discipline has sparked the development of an entirely new class of algorithms and a supporting body of theory, which are the main theme of this article. After a review of mathematical models of fluid flow, methods for solving the transonic potential flow equation (of mixed type) are examined. The central part of the article discusses the formulation and implementation of shock‐capturing schemes for the Euler and Navier–Stokes equations. The article next discusses the merits of the contrasting approaches of finite difference, finite volume, and finite element methods for the treatment of flows in complex geometric domains, together with the treatment of boundary conditions. A detailed presentation of explicit and implicit time‐stepping schemes for both steady and unsteady flows precedes a discussion of preconditioning and multigrid procedures for accelerating the convergence of steady state calculations. Dual time‐stepping schemes are recommended for the simulation of unsteady flow. In order to realize the potential benefits of CFD, it is essential to move beyond simulation to aerodynamic (and ultimately multidisciplinary) optimization. The article concludes with a discussion of aerodynamic shape optimization via control theory.
Combustion
Authors: Poinsot T. J. , Veynante D. P.
Published: January 2005

This chapter describes the basic phenomena controlling reacting flows and the corresponding computational methodologies. Combustion regimes (premixed or diffusion flames, laminar or turbulent cases, stable or unstable behavior) are first defined before introducing the basic terminology required to understand numerical techniques for reacting flows. The governing equations for combustion are more complex than those used in classical aerodynamics, and their specificities are discussed before describing numerical methods for laminar flames. Finally, the various methods used for turbulent flames are discussed, focusing on recent techniques such as Direct Numerical Simulations and Large Eddy Simulations.
Direct adaptive active noise control algorithms in case of uncertain secondary path dynamics
Authors: Kohno Toshikazu , Sano Akira
Published: January 2005

Almost all adaptive feedforward control algorithms for active noise control require an identified model of the secondary path dynamics from the control loudspeaker to the error and reference microphones. This paper is concerned with new direct adaptive algorithms which will be applicable when the secondary path dynamics are unknown or uncertainly changeable. In the first approach, the control algorithm consists of a robust adaptive feedforward control algorithm and robust feedback control scheme permitting bounded uncertainty in the nominal secondary path model. The second one is a fully direct adaptive feedforward control algorithm which does not require explicit identification of the secondary path dynamics even when all of the path dynamics are uncertain. Simulation and experimental results validate the effectiveness of the proposed algorithms. Copyright © 2005 John Wiley & Sons, Ltd.
Compartmental modelling of the uptake kinetics of the anti‐cancer agent topotecan in human breast cancer cells
Authors: Evans Neil D. , Errington Rachel J. , Chapman Michael J. , Smith Paul J. , Chappell Michael J. , Godfrey Keith R.
Published: January 2005

A compartmental model for the in vitro uptake kinetics of the anti‐cancer agent topotecan is proposed. This model provides a description of the activity of the drug, and subsequent delivery of active form to the nuclear DNA target. The unknown model parameters are estimated from two‐photon laser‐scanning microscopy data, which provide concentrations of topotecan (active plus inactive forms) in the extracellular region containing live human breast tumour cells (MCF‐7 cell line), the cytoplasm and the nucleus. This determines an output structure for which the model is uniquely identifiable, that is, the unknown parameters are uniquely determined from noise‐free, continuous and perfect data. The model allows in silico predictions of the dose dependence of target binding. Copyright © 2005 John Wiley & Sons, Ltd.
CHARGE syndrome from birth to adulthood: An individual reported on from 0 to 33 years
Authors: Searle Lisa C. , Graham John M. , Prasad Chitra , Blake Kim D.
Published: January 2005

CHARGE syndrome was independently reported by Hall [(1979): J Pediatr 95:395–398] and Hittner et al. [(1979): J Pediatr Ophthalmol Strabismus 16:122–128] and was initially considered to be a non‐random association between distinct multiple congenital anomalies. It is now considered to be a recognizable syndrome with well‐characterized diagnostic criteria and a genetic pathogenesis. We report on a 33‐year‐old adult male with CHARGE syndrome, with emphasis on the unique medical, behavioral, and psychological issues faced in adulthood. Characteristic facial and ear abnormalities were obvious in early childhood, and bilateral retinal colobomata, left choanal atresia, right congenital hip dislocation, and hypogonadism were diagnosed during the first year. Walking was delayed due to vestibular problems, speech was impaired due to moderately severe hearing loss, and use of sign communication was limited. Choanal atresia was surgically corrected in infancy, and atrial septal defect, ventricular septal defect, and patent ductus arteriosus were surgically corrected in childhood. Undescended testes were removed in adolescence, and gallstones were removed in early adulthood. Puberty was delayed until hormone replacement therapy began at 15 years. Behavioral disturbances and anxiety persisted throughout childhood, adolescence, and into adulthood, often resulting from communication challenges. At 33 years of age, he lives independently in a supervised group home, receives regular eye check‐ups and is being monitored for severely reduced bone density. © 2005 Wiley‐Liss, Inc.
Familial cognitive deficits in schizophrenia
Authors: Hoff Anne L. , Svetina Christine , Maurizio Andrea M. , Crow Timothy J. , Spokes Kate , DeLisi Lynn E.
Published: January 2005

Susceptibility to schizophrenia is considered familial, but the mechanism for transmission has not been found. Since widespread cognitive deficits have been found in patients with schizophrenia, several of these have been proposed as candidate familial endophenotypes that may or may not be predictive of who develops the illness. The current study examines these candidates in individuals from 32 families with at least 2 members having the diagnosis of chronic schizophrenia and normal comparison subjects using an extensive neuropsychological battery. Consistent with previous literature, family members with schizophrenia were significantly impaired on all measures compared with controls. Well relatives demonstrated significantly worse performance on a measure of verbal learning, delayed visual recall, perceptual‐motor, and pure motor speed. Expressive and receptive language, but not other functions, were highly correlated within both concordant for schizophrenia and discordant sibling pairs, suggesting that they are familial vulnerability endophenotypes, but not predictive of whom becomes ill. On the other hand, some measures of perceptual‐motor, pure motor speed, and frontal/executive functioning were significantly correlated in concordant, but not discordant pairs. These latter correlations suggest that some cognitive measures may be genetically related to the illness. © 2004 Wiley‐Liss, Inc.
Insecticidal potency of certain organosilicon compounds
Authors: Saxena P N , Saxena A K
Published: January 2005

A small series of organosilicon compounds were screened for efficacy against the housefly Musca domestica. The activity of organosilicon compounds is attributed to the silicon atom, the presence of halogens and the alkyl groups.
Compounds of arsenic, antimony, and tin in mollusc shells
Authors: Cullen William R , Dodd Mathew , Nwata Basil U , Reimer Deborah A , Reimer Kenneth J
Published: January 2005

Inorganic arsenic(III) and arsenic(V), methyl‐arsenicals, antimony(III), and antimony(V), and butyltin derivatives are present in the shells of molluscs found in the coastal waters of British Columbia.
Triphenylstibine oxide–phosphorus(V) sulfide as a novel condensation catalyst system: application to the synthesis of dipeptides
Authors: Nomura Ryoki , Yamada Yasuhiro , Matsuda Haruo
Published: January 2005

Triphenylstibine oxide (Ph3SbO) and phosphorus(V) sulfide (P4S10) synergistically catalyzed the aminolysis of N‐protected amino‐acids with amino‐acid esters in benzene. Ph3SbO accelerated both the initial conversion of carboxylic moieties into the corresponding thiocarboxylic moieties by P4S10 and the subsequent aminolysis of the resulting thiocarboxylic acids. Thus, dipeptides such as Z–A–A′–OEt (where Z = PhCH2OC(O)– and A,A′ = Ala,Gly; Gly,Gly; Leu,Gly; Phe,Gly; Phe,Leu;Ser,Gly; Val,Gly, respectively) were conveniently prepared even at 35°C.
Dimethylheptyl [3‐(N‐hetaryl)propyl]silanes: Synthesis, antimicrobial and antiblastic activity
Authors: Sturkovich R , Goldberg Yu , Verovsky V , Augustane I , Prodanchuk N , Deineka S , Lukevics E
Published: January 2005

The alkylation of monoazoles, diazoles, triazoles and tetrazoles with dimethylheptyl(3‐iodopropyl)silane using liquid/liquid phase‐transfer catalysis affords the corresponding [3‐(N‐azolyl)propyl]silanes in high yield, by which means the nonsymmetric ambident heterocycles 1,2,4‐triazole and tetrazole undergo alkylation regiospecifically in position 1 and 2, respectively. Dimethylheptyl[3‐(N‐imidazolyl)propyl]silane demonstrated high fungistatic activity with respect to S. cerevisiae and T.rubrum in combination with high cytotoxicity.
Persistence of fungitoxicity of two triorganotin(IV) compounds in soil
Authors: Kuthubutheen A J , Wickneswari R , Kumar Das V G
Published: January 2005

The persistence of triphenyltin chloride‐triphenylphosphine oxide (Ph3SnCl·Ph3PO) and diphenylbutyltin bromide (Ph2BuSnBr) in unsterilized sandy loam soil maintained in the dark at 60% of its water‐holding capacity and at 27±2°C was studied over a period of 29 days. The percentage recovery of the compounds upon extraction with acetone immediately after application to soil was 60% for Ph3SnCl·Ph3PO and 9.8% for Ph2BuSnBr. The half‐lives of the compounds were 15 days for Ph3SnCl·Ph3PO and 14.2 days for Ph2BuSnBr. After 29 days following application of the compounds in soil < 8.3 μg g−1 of Ph3SnCl·Ph3PO and < 5.1 μg g−1 of Ph2BuSnBr remained in soil compared with the starting concentration of 50 μg of each compound per gram soil. The two triorganotin compounds were evidently easily degraded and the compounds may be applied every 2–3 weeks in the field at a rate of at least 0.005–0.01 kg ha−1.
A kinetic model for the growth of znte by metal organic chemical vapour deposition
Authors: Dumont Hervé , Qu'hen Bruno , Bourée Jean Eric , Gorochov Ouri , Marbeuf Alain
Published: January 2005

A kinetic model for the metal organic chemical vapour deposition (MOCVD) growth of ZnTe is presented, taking into account the competitive adsorption of organometallic precursors. By assuming that diethylzinc (DEZn) and diethyltellurium (DETe) or di‐isopropyltellurium (DIpTe) are adsorbed onto the surface by two sites, the model yields the growth rate as a function of the gas‐phase concentrations of the constitutents and is corroborated by experimental results obtained by the MOCVD growth (at 400°C with DETe or 350°C with DIpTe), which shows asymmetric behaviour: for a given DETe or DIpTe pressure (10−4 atm), the growth rate as a function of DEZn partial pressure passes through a maximum, whereas, at the same constant DEZn pressure, the growth rate increases monotonically when the DETe or DIpTe partial pressure increases
Some further observations on polymethylsilane as a precursor for silicon carbide
Authors: Mu Ying , Harrod John F. , Laine Richard M.
Published: January 2005

Poly(methylsilanes) produced by sodium coupling of methyldichlorosilane (2:1 molar ratio) contain residual chlorine which can be removed by reduction with LiAlH4 at low temperature. Following this reduction, the polymers contain catalytically active centers (presumed to be silyl anions) which, in THF solution, further polymerize and crosslink the polymer at room temperature, while in toluene solution they are inactive. The reduced polymethylsilane gives high yields (ca 75%) of ceramic product on pyrolysis, but the composition is rich in silicon, compared with pure silicon carbide (SiC). Addition of catalytic amounts of dimethylzirconocene (DMZ) to this polymer gives a product which pyrolyzes to a product with stoichiometry close to that of SiC. It is concluded that the DMZ has an important influence in promoting Si–C bond formation, relative to Si–Si bond formation, during the pyrolysis.
Dibutyltin‐3‐hydroxyflavone titrates a dissociable component (cofactor) of mitochondrial ATP synthase: An energy‐transfer component linked to the ubiquinone pool
Authors: Griffiths David E.
Published: January 2005

Dibutyltin‐3‐hydroxyflavone, Bu2Sn(of), is a new fluorescence probe inhibitor of F1F0‐ATPase and oxidative phosphorylation which inhibits by titration of an unidentified component of F0. Its site of action is closely related to that of the trialkyltins and of venturicidin. This F0 component is part of a pool of this component which is present in the heart mitochondrial inner membrane at levels of 5–7 nmol (mg protein)−1 [18 ± 3 Bu2Sn(of) sites per mol F1F0‐ATPase]. However, ATPase activity in submitochondrial particles is near maximally inhibited by titration of approx. three Bu2Sn(of) sites per mol F1F0‐ATPase.

Over 60% (60–80%) of the Bu2Sn(of) interaction sites can be lost during the purification of F1F0‐ATPase from submitochondrial particles. The number of Bu2Sn(of) interaction sites in various F1F0‐ATPase preparations is variable. The high numbers of Bu2Sn(of) sites per mol F1F0‐ATPase for heart mitochondria (18–21) and submitochondrial particles (15–19.5) decline in ATP synthase (11–15) to the low values obtained in Complex V (7–10.5) and the minimal values observed in highly purified F1F0−ATPase (3.5–5.6), thus indicating a variable dissociable component or cofactor of ATP synthase.

The Bu2Sn(of) interaction site, a component of ATP synthase, is responsive to the redox status of the respiratory chain and the interaction with Bu2Sn(of) is with the reduced form of this component. Fluorescence titration studies show that this component is in redox equilibrium with the ubiquinone pool of the respiratory chain. It is proposed that this redox component serves as an inhibitor titratable cofactor pool which cycles through an F0 interaction site (or sites) via a system which serves as an energy‐transfer link between the respiratory chain and ATP synthase.
o‐Cyclohexadiamine complexes of some diorganotin, mono‐organtotin and stannic carboxylates: Synthesis and spectral properties
Authors: Bonire Josiah J. , Crowe Alan J. , Smith Peter J.
Published: January 2005

o‐Cyclohexadiamine (the base component of tetraplatin) adducts of Ph2Sn(OCOCH3)2, nBu2Sn(OCOH3)2, (PhCH2)2Sn(OCOCH3)2, PhSn(OCOCF3)3, BuSn(OCOCH3)3 and Sn(OCOCH3)4 have been synthesized and characterized by elemental analysis and spectroscopy. The compounds appear to be the first such adducts in their class.
Substituent effects on titanocenium catalysts
Authors: Kucht Andreas , Kucht Homa , Song Wei , Rausch Marvin D. , Chien James C. W.
Published: January 2005

Titanocene dichloride (1) and its bis(trifluoromethyl) (2) and bis(N,N‐dimethylamino) (3) derivatives have been compared as catalysts for ethylene and propylene polymerizations using both methylaluminoxane (MAO) and triphenylcarbenium tetrakis(pentafluorophenyl)borate (4)/triisobutylaluminum (TIBA) as cocatalysts. The differences between the activities of the three ‘free’ titanocenium ions and the Mw of the polyolefins produced by them may be attributable to the relative stabilities of the intermediate olefin–titanocenium π‐complexes. Interaction of either the neutral MAO or its anion with the titanocenium species may be responsible for the significantly lower catalytic efficiencies when the precursors were activated by MAO than by the 4/TIBA system.
Short‐term bioconcentration and distribution of methylmercury, tributyltin and corresponding inorganic species in the starfish leptasterias polaris
Authors: Rouleau Claude , Pelletier Émilien , Tjälve Hans
Published: January 2005

Starfish, Leptasterias polaris, were exposed between 30 min and 48 h to seawater containing 0.25 nmol dm−3 of radiolabelled methylmercury (Me203HgCI), tributyltin [(C4H9)3113SnCI], and inorganic 203HgCI2 and 113SnCI4, with the objectives of comparing the uptake and distribution kinetics of these metal species in organs and tissues of treated organisms. Some starfish exposed to metals for 48 h were allowed to depurate for 24 h in clean seawater. Whole‐body autoradiography was used to locate radiotracers very precisely within starfish tissues. The total amount of methylmercury (MeHg) accumulated in the whole animal after 48 h reached 0.53 nmol compared with 0.09 nmol for inorganic mercury, while tributyltin (TBT) reached 0.72 nmol compared with 0.017 nmol for inorganic tin. No significant reduction of body burdens occurred during the depuration period. The first‐order rate constant characterizing the uptake of metals by whole animals, k1, ranged from 0.102 h−1 for MeHg to 3.6 × 10−3h−1 for inorganic mercury(II) and to 8.4 × 10−4 h−1 for inorganic tin(IV). The first‐order rate constant characterizing the translocation of metals from seawater‐exposed tissues toward internal organs, k3, was available for inorganic Hg and Sn and had values similar to k1. Concentration ratios between external tissues and internal organs after a 48 h exposure were 11.5 and 25.4 for MeHg and TBT, respectively, and 2.1 and 6.1 for inorganic mercury and tin. Furthermore, autoradiograms showed that MeHg and TBT were accumulated only on the external surface of the body wall and podia. This finding indicates a much slower translocation process for organometallic species than inorganic species, a process which seems to be related to the binding mode of MeHg and TBT to the organic matrix of external tissues of starfish.
The reactivity of Samarium(II) in a Bis(indenyl) coordination environment
Authors: Evans William J. , Gummersheimer Tammy S. , Ziller Joseph W.
Published: January 2005

The reactivity of the organosamarium(II) indenyl complex (C9H7)2Sm(THF)x, 1, has been compared with that of (C5Me5)2Sm(THF)2, 2, and (C5Me5)2Sm, 3, by examination of characteristic organosamarium(II) reactions which form trivalent oxide, iodide, cyclo‐octatetraenyl and azobenzene complexes. Complex 1 reacts with excess N2O to form [(C9H7)2Sm(THF)]2(μ‐O), 4, and (C9H7)3Sm(THF), 5, as the major products. Two equivalents of 1 react with one equivalent of 1,2‐di‐iodoethane in THF to give (C9H7)SmI2(THF)2, 6, as well as 5. Complex 1 reacts with 1,3,5,7‐cyclo‐octatetraene in a 2:1 ratio in THF to form 5 and (C9H7)Sm(C8H8)(THF)x, 7, which has been fully characterized as the 2,2′‐bipyridine adduct (C9H7)Sm(C8H8)(C10H8N2), 7a. The reaction of 1 with azobenzene in a 2:1 ratio forms [(C9H7)Sm(N2Ph2)(THF)]x, 8, and 5. Complexes 4–6 and 7a have been definitively identified by X‐ray crystallography.

Complex 4 crystallizes from THF in space group P1― [C; No. 2] with unit cell parameters at 163 K of a = 8.072(2) Å, b = 9.502(2) Å, c = 12.250(3) Å, α = 101.42(2)°, β = 90.71(2)°, γ = 102.50(2)°, V = 897.7(4) Å3 and Z = 1 for Dcalcd = 1.704 Mgm−3. Least‐squares refinement of the model based on 3924 reflections (|F0|)>3.0 σ (|F0|)) converged to a final RF=2.4%. The geometry around each Sm atom is a distorted tetrahedron and the Sm–O–Sm angle is 180°.

Complex 5 crystallizes from THF/hexanes at −35°C in space group P63 [C; No. 173] with unit cell parameters at 163 K of a = 11.7370(14) Å, c = 10.1994(12) Å, V = 1216.8(3) Å3 and Z = 2 for Dcalcd = 1.550 Mg m−3. Least‐squares refinement of the model based on 976 reflections (|F0|> 3.0σ (|F0|) converged to a final RF = 2.3%. The three ring centroids and the THF oxygen atom define a distorted tetrahedron around samarium with a (ring centroid)–Sm–(ring centroid) angle of 116.0°.

Complex 6 crystallizes from THF/hexanes as the trisolvate (C9H7)SmI2(THF)3, 6a, in space group P21/n [C; No. 14] with unit cell parameters at 163 K of a = 8.3969(12) Å, b = 17.165(5) Å, c = 33.592(7) Å, β = 96.468(15)°, V = 4811(2) Å3 and Z = 8 for Dcalcd = 2.031 Mg m−3. Least‐squares refinement of the model based on 5664 reflections (|F0|> 2.0 σ (|F0|)) converged to a final RF = 3.3%. The six ligands around Sm in 6a describe a distorted octahedron. The iodide ligands are trans to each other with a 153.8(1)° I–Sm–I angle.

Adduct 7a crystallizes from hot THF/toluene in space group P1 [C; No. 2] with a unit cell parameters at 163 K of a = 7.886(7) Å, b = 16.72(2) Å, c = 17.48(2) Å, α = 62.96(7)°, β = 85.17(7)°, γ = 85.23(9)°, V = 2042(3) Å3 and Z = 4. The cyclooctateraenyl and indenyl ligands generate a bent metallocene structure for 7a which contains a chelating bipyridyl group in the plane bisecting the two rings.
Lanthanum isopropoxide catalyzed addition of activated nucleophiles to imines
Authors: Yamamoto Yoshinori , Fukui Hiroyuki , Honda Yoshihiro
Published: January 2005

The addition of certain activated nucleophiles to activated imines is catalyzed by lanthanum isopropoxide. As activated nucleophiles, methylmalononitrile and methyl 2‐cyanopropanoate can be utilized. Imines having an electronwithdrawing group either at the carbon or at the nitrogen atom of the C=N double bond can be used; for example N‐toluenesulfonylimines, N‐(4‐methoxycarbonylphenyl)imines and α‐imino esters.
Lanthanide silanolates: Development of new procedures for the modification of silicones with rare‐earth metals
Authors: Voskoboynikov Alexander Z. , Beletskaya Irina P.
Published: January 2005

The reactions of Lnl33 (Ln = La, Ce, Er, Yb) with sodium silanolate (NaOSiMe3) in THF at room temperature yield lanthanide silanolates Ln(OSiMe3)3 which seem to be oligomers with μ‐OSiMe3 ligands. Reaction of Cel3 with potassium siliconate, KO[Me1.96Ph0.04SiO]20.75K, yields a netted polymer [Me61.59Ph1.29Si31.44O39.02Ce]x. An analogous procedure which involves reaction of Lnl3 (Ln = Ln, Er) with KO[Me1.96Ph0.04SiO]50.00 K, and following treatment with NaOSiMe3, results in the formation of solublé product (Me3SiO)2LnO[Me1.96Ph0.04SiO]50.00 Ln(OSiMe3)2.
Maintaining rapid growth in moderate‐density Escherichia coli fermentations
Authors: Zawada James , Swartz James
Published: January 2005

A novel feeding strategy that prolongs rapid growth rates for Escherichia coli fermentations to moderately high cell density is presented. High‐density fermentations are a common and successful means of producing biological products. However, acetate accumulation can be a substantial problem in these procedures. To avoid this problem, many feeding strategies and host modifications have been developed, but all result in relatively low growth rates. If a faster growth rate could be maintained, the growth phase of the process would be shortened, leading to increased productivity. It is also possible that the subsequent specific production rate could be enhanced by growing the early culture at a faster rate. We have developed a procedure to enable rapid growth to a cell density of 20 g/L and have used cell‐free protein synthesis to evaluate the relative potential of the resulting cells for producing recombinant proteins. The method uses glucose pulses and the duration of the dissolved oxygen response to calculate the appropriate glucose feed rate based on the glucose demand of the culture. Amino acids and vitamins were supplied in the medium to increase the growth rate. We were able to sustain a growth rate of 0.8/h up to 20 g/L dry cell weight without significant acetate accumulation. Analysis of amino acid consumption indicates that cell composition is an accurate predictor of amino acid demand for most amino acids. Cell‐free protein synthesis was used to compare the protein production potential of the high‐density cultures with that of cells grown in complex medium and harvested at low cell density and maximum growth rate. Protein production for the extract from the controlled, high‐density fermentations was 950 mg/L compared with 860 mg/L for the low‐density control. Therefore, the new control procedure has promising potential for developing rapid and productive industrial fermentations. ©2004 Wiley Periodicals, Inc.
Navigating public microarray databases
Authors: Penkett Christopher J. , Bähler Jürg
Published: January 2005

With the ever‐escalating amount of data being produced by genome‐wide microarray studies, it is of increasing importance that these data are captured in public databases so that researchers can use this information to complement and enhance their own studies. Many groups have set up databases of expression data, ranging from large repositories, which are designed to comprehensively capture all published data, through to more specialized databases. The public repositories, such as ArrayExpress at the European Bioinformatics Institute contain complete datasets in raw format in addition to processed data, whilst the specialist databases tend to provide downstream analysis of normalized data from more focused studies and data sources. Here we provide a guide to the use of these public microarray resources. Copyright © 2004 John Wiley & Sons, Ltd.
Ontologies for the description of mouse phenotypes
Authors: Gkoutos G. V. , Green E. C. J. , Mallon A.‐M. , Blake A. , Greenaway S. , Hancock J. M. , Davidson D.
Published: January 2005

Ontologies are becoming increasingly important for the efficient storage, retrieval and mining of biological data. The description of phenotypes using ontologies is a particularly complex problem. We outline a schema that can be used to describe phenotypes by combining orthologous axiomatic ontologies. We also describe tools for storing, browsing and searching such complex ontologies. Central to this approach is that assays (protocols for measuring phenotypic characters) describe what has been measured as well as how this was done, allowing assays to link individual organisms to ontologies describing phenotypes. We have evaluated this approach by automatically annotating data on 600 000 mutant mice phenotypes using the SHIRPA protocol. We believe this approach will enable the flexible, extensible and detailed description of phenotypes from any organism. Copyright © 2004 John Wiley & Sons, Ltd.
Screening for prostate carcinoma
Authors: D'Amico Anthony V.
Published: January 2005

To date, the use of prostate‐specific antigen (PSA) screening in the U.S. has translated into lower PSA failure rates and, perhaps, to lower rates of disease‐specific mortality in men with prostate carcinoma. However, this later point remains a hypothesis and will be proven right or wrong in short order based on upcoming results from randomized screening studies.

See also pages 943–51.
Single base pair change in the long‐range Sonic hedgehog limb‐specific enhancer is a genetic basis for preaxial polydactyly
Authors: Maas Sarah A. , Fallon John F.
Published: January 2005

In most instances of preaxial polydactyly (PPD), Sonic Hedgehog (Shh), an essential limb patterning signal, is ectopically expressed in an anterior region of the developing limb in addition to the normal posterior domain. It is thought that this anterior Shh expression leads directly to the development of the extra digits. Recent reports have identified a conserved limb‐specific Shh enhancer ∼1 megabase upstream of the Shh transcription initiation site, and individual base pair changes within this region are associated with PPD. We report here that a single base pair change within this enhancer is sufficient to drive β‐galactosidase expression in both anterior and posterior limb domains, similar to Shh expression in animal PPD models, whereas a wild‐type construct is expressed only in the posterior limb, similar to Shh expression in normal embryos. These findings provide the first direct evidence that a single base pair change within the limb‐specific Shh enhancer acts as a genetic basis for PPD. Developmental Dynamics 232:345–348, 2005. © 2005 Wiley‐Liss, Inc.
New simple tests for age‐at‐onset anticipation: Application to panic disorder
Authors: Tsai W.Y. , Heiman Gary A. , Hodge Susan E.
Published: January 2005

Recently, testing for anticipation has received renewed interest. It is well known that standard statistical methods are inappropriate for this purpose due to problems of sampling bias. Few statistical tests have been proposed for comparing mean age of onset in affected parents with mean age of onset in affected children. All of them are difficult to compute and lack software to perform the tests. In this report, we formulate the problem in terms of symmetry tests. We propose a simple generalized paired t‐test and a Wilcoxon signed rank test to adjust for the bias caused by the right truncation of both the parent's and child's ages at onset. We also extend the generalized paired t‐test to a random effects model that enables analysis of correlated data from nuclear families, and could be further extended to larger family structures. We illustrate the approaches with an example of panic disorder. Genet. Epidemiol. © 2005 Wiley‐Liss, Inc.
Conformational analysis of proteins: Algorithms and data structures for array processing
Authors: Pottle C. , Pottle M. S. , Tuttle R. W. , Kinch R. J. , Scheraga H. A.
Published: January 2005

Current efforts to determine the nature of the interactions that influence protein folding involve, among other things, minimization of an appropriate empirical conformational energy function (ECEPP, Emprical Conformational Energy Program for Peptides) to obtain the native structure. Because of the prohibitive cost of such a massive computational project, either on a conventional large‐scale machine at a self‐supporting installation or on a dedicated minicomputer, an alternative computer hardware system has been developed to aid in the conformational analysis of proteins. It consists of a Floating Point Systems AP‐120B array processor and a Prime 350 minicomputer host. A version of ECEPP has been adapted to run on the AP‐120B. The data structures and algorithms chosen for this version reflect the highly unusual parallel architecture of this machine. Benchmark comparisons with BPTI (Bovine Pancreatic Trypsin Inhibitor), a protein of 58 residues and a known structure, have been carried out on this system as well as on an IBM 370/168. They show a significant advantage in speed for the AP‐120B/Prime 350 system as well as a substantially lower cost. An energy minimization of BPTI with 154 variable dihedral angles is reported, an effort heretofore prohibited by the computer costs involved.
Hartree Fock instabilities of sulfur‐nitrogen ring systems: S2N2
Authors: Laidlaw W. G. , Bénard M.
Published: January 2005

The Hartree‐Fock instablities of S2N2 are reported and compared with those of S3N and S4N. These unsaturated sulfur nitrogen planar rings are π electron rich and although the symmetry adapted HF solutions are singlet stable at the experimental bond lengths they become unstable with only a very modest increase in bond length. The broken symmetry solutions for S2N3, S3N, and S4N are of planar C2v type with one of the nitrogens stripped of its π electrons, producing a π hole.
The photolysis of 3,3‐dimethylbutan‐2‐one (methyl t‐butyl ketone) and the decomposition of the acetyl radical
Authors: Frey H. M. , Vinall I. C.
Published: January 2005

The photolysis of 3,3‐dimethylbutan‐2‐one (MTBK) has been studied in the gas phase at 408 and 326 K, mainly with light of 313 nm wavelength. At the higher temperature, the major products were methane, ethane, isobutane, isobutene, neopentane, tetramethylbutane, and carbon monoxide. At 326 K, in addition to these products, appreciable quantities of acetaldehyde, acetone, and biacetyl were detected. Quantum yields were determined using acetone and pentan‐3‐one as actinometers. A conventional mechanism is able to explain most of the experimental data. At 326 K, the results may be interpreted to yield a value for the rate constant for decomposition of the acetyl radical. Some theoretical calculations are reported on the acetyl radical decomposition and some earlier experimental work on this radical reevaluated.
Liquid‐phase hydrogen abstraction from chlorinated ethanes by chlorine atoms
Authors: Martens G. J. , Franklin J. A. , Godfroid M. , Delvaux M. , Verbeyst J.
Published: January 2005

The hydrogen abstraction from the chlorinated ethanes by chlorine atoms has been investigated in the liquid phase. Rate constants relative to that for hydrogen abstraction from chloroform have been measured between 267° and 333°K using a competition technique. The results are compared with gas‐phase data.
Deactivation of vibrationally excited hydrogen fluoride (v=2 and v=1) by atomic fluorine
Authors: Blauer Jay A. , Solomon Wayne C.
Published: January 2005

Measurements have been made which provide information concerning the rate of energy transfer between vibrationally excited HF and atomic fluorine. It was found that HF (v = 1) deactivates about seven times slower than was determined in previous experiments. The deactivation rate constant for HF (v = 2) is about six times larger than for HF (v = 1).
Constant time interval method for analysis of reaction rate data
Authors: Shank Norman E.
Published: January 2005

In the study of chemical kinetics, many integrated reaction rate equations have the form In [f(A) + a] = bt + c, where a, b, and c are constants and f(A) is some function of the concentration of a reactant (or product) which can be calculated from the data. The left‐hand side of this equation cannot be graphed versus time if the constant a is unknown. However, it is shown that f(A2) varies linearly with f(A1) if A2 is the concentration of reactant measured at a constant time interval later than A1. The constants a and b can be determined from the linear graph. A number of specific examples are considered.
Explosion of acetylene–chlorine mixture at room temperatures initiated by small additions of oxygen: Kinetic study and mechanism
Authors: Shtern V. Ya. , Revsin A. F. , Sokolova E. I.
Published: January 2005

Oxygen added in amounts of 0.01‐0.1% was found to cause the explosion of an acetylene–chlorine mixture at temperatures as low as −78°C. Explosion occurrence and nature depend on the mode of mixing the reactants, the effect of oxygen being associated with concentration limits. The dependence of explosion‐inducing oxygen amounts on temperature, pressure, concentrations of reactants, reactor surface type and area, additions of inert gases, and reaction products were investigated. The effect of light on the C2H2 + Cl2 + O2 was studied. The composition of gaseous products resulting from acetylene–chlorine mixture explosion in the presence of minute amounts of oxygen, from a slow reaction inhibited and noninhibited by oxygen, and also from explosion at 400°C in the absence of oxygen, was determined. The results obtained point to the fact that any acetylene–chlorine mixture flash caused by small amounts of oxygen is a branched chain reaction involving activated particles, chain branching presumably being associated with the decomposition of radical CHCl=CHOO* → CH + HCl + CO2.
Thermal decomposition of 1,1,2,2‐tetramethylcyclopropane in a single‐pulse shock tube
Authors: Tsang Wing
Published: January 2005

1,1,2,2‐Tetramethylcyclopropane (TTMC) has been decomposed in a single‐pulse shock tube. The main reaction process is magnified image Side reactions are unimportant. From comparative rate experiments (with cyclohexene decomposition as standard) the rate expression for these reactions are

These numbers are consistent with a «best» value for cyclohexene decomposition of