bluuebunny/crossref_metadata_2025 huggingface dataset:
An algebraic multigrid method for finite element discretizations with edge elements
Authors: Reitzinger S. , Schöberl J.
Published: August 2002

This paper presents an algebraic multigrid method for the efficient solution of the linear system arising from a finite element discretization of variational problems in H0(curl,Ω). The finite element spaces are generated by Nédélec's edge elements.

A coarsening technique is presented, which allows the construction of suitable coarse finite element spaces, corresponding transfer operators and appropriate smoothers. The prolongation operator is designed such that coarse grid kernel functions of the curl‐operator are mapped to fine grid kernel functions. Furthermore, coarse grid kernel functions are ‘discrete’ gradients. The smoothers proposed by Hiptmair and Arnold, Falk and Winther are directly used in the algebraic framework.

Numerical studies are presented for 3D problems to show the high efficiency of the proposed technique. Copyright © 2002 John Wiley & Sons, Ltd.
Preconditioning of the second‐kind boundary integral equations for 3D eddy current problems
Authors: Schmidlin G. , Fischer U. , Andjelič Z. , Schwab C.
Published: August 2002

Starting from the time‐harmonic Maxwell equations at low‐frequency eddy current approximation the H–ϕ formulation is presented. An equivalent system of boundary integral equations of the second kind on the conductor surface (resp. the conductor/dielectric) is derived. Discretizing these equations with a boundary element method (BEM) yields a block linear equation system

\[
\left[\begin{array}{cc} A_{1} & B_{1} \\ \tfrac{\mu}{\mu_{0}}\tilde{B}_{2} & A_{2}\end{array}
\right] \left( \begin{array}{c}
j \\ \sigma \end{array}
\right)=\left(\begin{array}{c}
b_{1} \\ b_{2}\end{array}
\right) \]
with a fully populated stiffness matrix. This system is non‐symmetric and, for large μ/μ0 (of interest in practice) ill‐conditioned. Iterative solvers like GMRES converge very slowly, in general. We propose a new preconditioner which depends on μ. We present numerical results with a serial and parallel version of this preconditioner also on large industrial eddy current problems with compex geometry. The performance of preconditioned GMRES is found to be practically independent of μ/μ0. Copyright © 2001 John Wiley & Sons, Ltd.
Molecular dynamics and multiscale homogenization analysis of seepage/diffusion problem in bentonite clay
Authors: Ichikawa Y. , Kawamura K. , Fujii N. , Nattavut Theramast
Published: August 2002

A scheme combining a molecular behaviour and macro‐continuum phenomenon is presented for bentonite clay, which is a key component of a barrier system for disposal and containment of hazardous wastes. On designing a disposal facility we use a macro‐phenomenological model. However the existing model is not sufficiently effective. Bentonite is a microinhomogeneous material. Properties of the saturated bentonite are characterized by montmorillonite and water, called montmorillonite hydrate. Since the crystalline structure of montmorillonite determines the fundamental properties of the montmorillonite hydrate, we analyse its molecular behaviour by applying a molecular dynamics simulation to enquire into the physicochemical properties of the montmorillonite hydrate such as diffusivity of chemical species. For extending the microscopic characteristics of constituent materials to a macroscopic diffusion behaviour of the microinhomogeneous material we apply a multiscale homogenization analysis, especially in order to treat micro‐level of adsorption behaviour. Copyright © 2002 John Wiley & Sons, Ltd.
A general and efficient formulation of fractures and boundary conditions in the finite element method
Authors: Juanes Ruben , Samper Javier , Molinero Jorge
Published: August 2002

The need to assess quantitatively the safety of waste repositories in deep geological media has fostered the development of efficient numerical models of groundwater flow and contaminant transport in fractured media. These models usually account for water flow through fracture zones embedded in a 3D rock matrix continuum. The first formulation of fractures in groundwater flow finite element models was proposed by Kiraly, and later revisited and generalized by Perrochet. From a mathematical viewpoint, fractures can be considered as m‐dimensional manifolds in an n‐dimensional Euclidean space (m⩽n). The key step of this formulation lies in an expression relating the hypersurface element dSm to the infinitesimal local co‐ordinates dξi(i=1,…,m). Here we present a novel proof for this relation using a different approach to that of Perrochet, and explore the efficiency and accuracy of the formulation. It is shown that the aforementioned relation leads to a general and compact formulation which is not only applicable to elements of any dimension (e.g. 1D, 2D and 3D elements in a 3D domain), but also overcomes the cumbersome and case‐specific calculations of traditional approaches. This formulation has been implemented in a versatile finite element program for modelling groundwater flow, solute transport and heat transport in porous and fractured media. The efficiency and accuracy of the proposed formulation has been analysed using a synthetic case dealing with flow and solute transport through a 2D fractured rock block. The proposed formulation, in which fractures are discretized by means of 1D elements is more efficient and accurate than the traditional finite element formulation of discretizing fractures by means of 2D elements. The capability of the proposed formulation to cope with complex systems is illustrated with a case study of groundwater flow induced by the construction of the access tunnel to an underground research laboratory in Äspö (Sweden). The numerical model is able to reproduce the observed records of water levels in boreholes and flow rates into the tunnel. Although the proposed formulation has been implemented and tested within the framework of groundwater flow and solute transport in fractured porous media, it should be of interest for other boundary value problems. Copyright © 2002 John Wiley & Sons, Ltd.
An unconditionally stable and O(τ2 + h4) order L∞ convergent difference scheme for linear parabolic equations with variable coefficients
Authors: Sun Zhi‐Zhong
Published: August 2002

M. K. Jain, R. K. Jain, and R. K. Mohanty presented a finite difference scheme of O(τ2 + τh2 + h4) for solving the one‐dimensional quasilinear parabolic partial differential equation, uxx = f(x, t, u, ut, ux), with Dirichlet boundary conditions. The method, when applied to a linear constant coefficient case, was shown to be unconditionally stable by the Von Neumann method. In this article, we prove that the method, when applied to a linear variable coefficient case, is unconditionally stable and convergent with the convergence order O(τ2 + h4) in the L∞‐norm. In addition, we obtain an asymptotic expansion of the difference solution, with which we obtain an O(τ4 + τ2h4 + h6) order accuracy approximation after extrapolation. And last, we point out that the analysis method in this article is efficacious for complex equations. © 2001 John Wiley & Sons, Inc. Numer Methods Partial Differential Eq 17:619–631, 2001
Evidence of surgery in Ancient India: trepanation at Burzahom (Kashmir) over 4000 years ago
Authors: Sankhyan Anek R. , Weber George H.J.
Published: August 2002

The article describes a neolithic skeleton with multiple‐trepanated skull found in Kashmir, the archaeological circumstances of the find, the dating, the background, the skeletal evidence, the details of the trepanation and possible affiliations of the Indus civilization. It speculates briefly about possible medical grounds for the surgery. Copyright © 2001 John Wiley & Sons, Ltd.
Medicaid matters: children's health and medicaid eligibility expansions
Authors: Lykens Kristine A. , Jargowsky Paul A.
Published: August 2002

In the late 1980s, a series of federal laws were enacted which expanded Medicaid eligibility to more of the
nation's children. States had a great amount of discretion in how fast and how far these expansions were
implemented. As a result, there was great variation among the states in defining who was eligible for the
program. This variation provides a rare opportunity to disentangle the effect of Medicaid from a child's
socioeconomic status. Using data from the National Health Interview Survey, we address whether the Medicaid
expansions improved the health and functional status of children. Econometric models were developed using
fixed‐effects regressions, and were estimated separately for white, black, and Hispanic children. White
children experienced statistically significant reductions in acute health conditions and functional limitations.
Black and Hispanic children showed some evidence of improved health conditions and functional status, but this
evidence is inconclusive in the study sample. This may be due to differences in their access to appropriate
health services or to the smaller sample size of minorities in each geographic area. The findings are also
relevant to the implementation of the Children' Health Insurance Program (CHIP), the latest
federal effort to expand access to health care to poor and near poor children. In many states, CHIP is being
implemented in whole or in part through further Medicaid expansions. © 2002 by the Association for Policy
Analysis and Management.
Yielding behaviour of thermoplastic/elastomer blends cured by gamma irradiation
Authors: Shaltout N A , Abou Zeid M M , Abdel‐Aziz M M , El Miligy A A
Published: August 2002

Mechanical blends of thermoplastic medium density polyethylene (MDPE) and elastomeric ethylene propylene diene monomer (EPDM) have been prepared with a fixed composition of 60/40 wt%. They have been used either in their gum form or loaded with two different reinforcing fillers, high abrasion furnace (HAF) carbon black or precipitated SiO2 (Hi Sil) of concentration 25–100 phr (parts per hundred parts of resin) with respect to the blend. Curing was achieved by gamma irradiation. Yielding properties (yield stress, yield strain and cold drawing) have been followed as a function of irradiation dose for different blend compositions. Yield stress values increased with irradiation dose and with the content of the reinforcing filler, but yield strain and cold drawing values decreased with irradiation dose and also with the filler content. The data obtained reveal that Hi Sil is more effective as a reinforcing filler, and the prepared blends are suitable for load‐bearing applications.

© 2001 Society of Chemical Industry
A comparison of white rice husk ash and silica as fillers in ethylene–propylene–diene terpolymer vulcanizates
Authors: Siriwardena S , Ismail H , Ishiaku U S
Published: August 2002

White rice husk ash (WRHA) and silica filled ethylene–propylene–diene terpolymer (EPDM) vulcanizates were prepared using a laboratory size two‐roll mill. Curing characteristics and physical properties of vulcanizates were studied with respect to the filler loading and filler type. Filler loading was varied from 0–50 parts per hundred resin (phr) at 10 phr intervals. Curing was carried out using a semi‐efficient vulcanization system in a Monsanto rheometer. Enhancement of the curing rate was observed with increasing WRHA loading, whereas the opposite trend was observed for silica‐filled vulcanizates. It was also indicated by the maximum torque and Mooney viscosity results that WRHA offers processing advantages over silica. Compared to the silica‐filled vulcanizates, the effect of filler loading on the physical properties of WRHA‐filled vulcanizates was not significant. According to these observations, WRHA could be used as a diluent filler for EPDM rubber, while silica can be used as a reinforcing filler.

© 2001 Society of Chemical Industry
ILGAR‐ZnO Window Extension Layer: an adequate substitution of the conventional CBD‐CdS buffer in Cu(In,Ga) (S,Se)2‐based solar cells with superior device performance
Authors: Bär M. , Muffler H.‐J. , Fischer Ch.‐H. , Zweigart S. , Karg F. , Lux‐Steiner M. C.
Published: August 2002

A novel Window Extension Layer (WEL) concept for chalcopyrite‐based thin‐film solar cell devices has been developed. The optimization of its deposition is presented. WEL means the replacement of the conventional buffer layer by a layer consisting of the same material as the window, i.e., a part of the window is directly deposited onto the absorber by a soft process, such as ILGAR (Ion Layer Gas Reaction). This sequential cyclic technique has been applied to Cu(In,Ga)(S,Se)2absorber substrates. The ILGAR procedure was optimized with respect to the efficiency of the resulting Mo/Cu(In,Ga)(S,Se)2/WEL/ZnO solar cells. The devices were characterized by J–V (under AM 1.5 and without illumination) as well as by quantum efficiency measurements. Devices with ZnO WEL yield total area (0.5 cm2) efficiencies of 14.6% (best cell) without any anti‐reflecting coating. The efficiencies are superior to those of the corresponding devices with CBD (Chemical Bath Deposition)‐CdS buffer (14.1%, best cell). Thus, in contrast to other ZnO buffers, ILGAR‐ZnO achieves record efficiencies exceeding those of CBD‐CdS buffered reference cells. Copyright © 2001 John Wiley & Sons, Ltd.
Implicit theories, goal orientations, and perceived competence: Impact on students' achievement behavior
Authors: Leondari Angeliki , Gialamas Vasilios
Published: August 2002

The present study was designed to explore relations between implicit theories of intelligence, goal orientations, perceived competence, and school achievement. It was assumed that implicit theories of intelligence orient individuals toward particular goals, which in turn influence achievement behavior. Perceived competence was hypothesized to moderate the relationship between implicit theories, goal orientations and actual achievement. Subjects were 451 elementary and junior high school students. The results of Pearson product moment correlations and Path analysis show theoretically important intercorrelations that replicated previous research. Implicit theories were not related to academic achievement. Goal orientations had an indirect effect on achievement, which was mediated through perceived competence. Educational implications of these findings are discussed. © 2002 Wiley Periodicals, Inc.
A cross‐cultural comparison of student social attributions
Authors: Armbrister Robin C. , McCallum R. Steve , Lee Hee Do
Published: August 2002

One hundred sixty American and 397 Korean fourth‐ and fifth‐graders were administered the Student Social Attribution Scale (SSAS), designed to assess students' explanations for social successes and failures. A Korean version of the SSAS was developed for the study. The American and Korean instruments' internal consistency reliability were determined (rs ranged from .56 to .86 for the Korean instrument and .62 to .88 for the American instrument). The means from both the American and Korean SSAS versions on the 8 scales and global scores (e.g., internal, external) were compared. Based on the literature, Korean children should have had higher scores for effort attributions in failure situations than the American children and Americans should have shown higher scores for ability attributions in successful situations. In fact, Korean children did show significantly higher ( p < .005) Failure Effort scores and American children showed significantly higher ( p < .005) Success Ability scores. Findings indicate that Korean children are potentially more willing to accept responsibility for social failure than American students. © 2002 John Wiley & Sons, Inc.
Effects of psycholinguistic instruction on spelling performance
Authors: Arra Christopher T. , Aaron P.G.
Published: August 2002

Two studies were conducted in which phonology‐based instructional strategies designed for improving spelling skills of elementary school children were compared against instruction strategies that relied only on visual exposure of words. The first study involved a total of 93 children. Of these, 46 were instructed by drawing their attention to the psycholinguistic nature of their spelling errors. The remaining 47 children in the comparison group were shown the correct version of all the words. In study II 15 children were placed in a treatment group and were taught phoneme awareness, and 15 children were placed in a comparison group and were exposed to printed words only. In both studies, posttests showed that children taught through psycholinguistic and phoneme awareness methods significantly outperformed the visual training groups. Further, these gains were retained after a period of 2 weeks. © 2001 John Wiley & Sons, Inc.
Synthesis and characterization of polyisocyanides derived from alanine and glycine dipeptides
Authors: Cornelissen Jeroen J. L. M. , Graswinckel W. Sander , Adams P. J. H. M. , Nachtegaal Gerda H. , Kentgens Arno P. M. , Sommerdijk Nico A. J. M. , Nolte Roeland J. M.
Published: August 2002

The synthesis and characterization of polymers derived from isocyanopeptides are described. Optically pure dipeptides based on alanine and glycine were equipped with an isocyano function and subsequently polymerized with a Ni(II) catalyst. Infrared and NMR spectroscopy indicated that the side chains of the polymers were connected by well‐defined arrays of intramolecular hydrogen bonds. The weight‐average molecular weights of the polymers were determined by atomic force microscopy to be 200–400 kg/mol (polydispersity index = 1.4–1.7). © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 4255–4264, 2001
Poly(ethylene terephthalate) copolymers containing 5‐tert‐butyl isophthalic units
Authors: Kint Darwin P. R. , de Ilarduya Antxon Martínez , Muñoz‐Guerra Sebastián
Published: August 2002

Poly(ethylene terephthalate‐co‐5‐tert‐butyl isophthalate) copolymers, abbreviated as PETtBI, with compositions ranging between 95/5 and 25/75, as well as the two parent homopolymers, PET and PEtBI, were prepared from comonomer mixtures by a two‐step melt‐polycondensation. Polymer intrinsic viscosities varied from 0.4 to 0.7 dL g−1 with weight‐average molecular weights ranging between 31,000 and 80,000. The copolymers were found to have a random microstructure with a composition according to that used in the corresponding feed. The melting temperature and crystallinity of PETtBI decreased with the content in 5‐tert‐butyl isophthalic units, whereas the glass‐transition temperature increased from 82 °C for PET up to 99 °C for PEtBI. Copolymerization slightly improved the thermal stability of PET. Preliminary X‐ray diffraction studies revealed that PETtBI adopt the same crystal structure as PET with the alkylated isophthalic units probably excluded from the crystal lattice. The homopolymer PEtBI appeared to be a highly crystalline polymer taking up a crystal structure clearly different from that of PET and PETtBI copolymers. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 1994–2004, 2001
Microemulsion polymerization of styrene stabilized by sodium dodecyl sulfate and short‐chain alcohols
Authors: Chern Chorng‐Shyan , Wu Long‐Jiang
Published: August 2002

Styrene microemulsion polymerizations with different short‐chain alcohols [n‐CiH2i+1OH (CiOH), where i = 4, 5, or 6] as the cosurfactant were investigated. Sodium dodecyl sulfate and sodium persulfate (SPS) were used as the surfactant and initiator, respectively. The desorption of free radicals out of latex particles played an important role in the polymerization kinetics. An Arrhenius expression for the radical desorption rate coefficient was obtained from the polymerizations at temperatures of 50–70 °C. The polymerization kinetics were not very sensitive to the alkyl chain length of alcohols compared with the temperature effect. The maximal polymerization rate in decreasing order was C6OH > C4OH > C5OH. This was related to the differences in the water solubility of CiOH and the structure of the oil–water interface. The feasibility of using a water‐insoluble dye to study the particle nucleation mechanisms was also evaluated. The parameters chosen for the study of the particle nucleation mechanisms include the cosurfactant type (CiOH), the SPS concentration, and the initiator type (oil‐soluble 2,2′‐azobisisobutyronitrile versus water‐soluble SPS). © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 3199–3210, 2001
Resilience, reflection, and residual stress in ovarian cancer survivorship: A gynecologic oncology group study
Authors: Wenzel Lari B. , Donnelly James P. , Fowler Jeffery M. , Habbal Rana , Taylor Thomas H. , Aziz Noreen , Cella David
Published: August 2002

Ovarian cancer is a life‐threatening diagnosis which poses multiple challenges. The purpose of this study is to describe the quality of life (QOL) concerns and survivorship sequelae of long‐term (>5 yr) early‐stage ovarian cancer survivors accrued through the clinical cooperative Gynecologic Oncology Group. Forty‐nine ovarian cancer survivors with a mean age at diagnosis of 55.9 yr (range 30–76) completed a telephone interview assessing QOL, psychosocial status, sexual functioning and late‐effects of treatment. Results indicate that this disease‐free early‐stage sample enjoys a good QOL, with physical, emotional, and social well‐being comparable to other survivors and same‐aged noncancer cohorts. However, 20% of survivors indicated the presence of long‐term treatment side effects, with a subset reporting problems related to abdominal and gynecologic symptoms, and neurotoxicity. Spiritual well‐being was significantly positively associated with personal growth and mental health, and negatively associated with a declining health status. Lingering psychological survivorship sequelae included fear of follow‐up diagnostic tests and fear of recurrence. Forty‐three percent of respondents expressed that they would likely participate in a counseling program today to discuss psychosocial issues raised by having had ovarian cancer, and 56% stated that they would have attended a support program during the initial treatment if it had been offered. This information provides some insight into the complex survivorship relationships between quality of life, long‐term physical and sexual sequelae, and factors of resilience and growth which appear to promote a sense of well‐being as a result of the cancer experience. Copyright © 2002 John Wiley & Sons, Ltd.
Are peak flow and symptom measures good predictors of asthma hospitalizations and unscheduled visits?†
Authors: Mortimer Kathleen M. , Redline Susan , Kattan Meyer , Wright Elizabeth C. , Kercsmar Carolyn M.
Published: August 2002

Epidemiologic studies of pediatric respiratory health often include objective measures such as peak expiratory flow (PEF), and subjective measures such as symptom reports. These measures, however, are poorly correlated with each other, and there is little evidence that PEF is useful in predicting important health outcomes. Within a cohort of 791 inner‐city children with asthma, we examined correlations between a series of five peak flow measures and five symptom scores obtained from 2‐week diaries.

The strongest correlations were found between “total peak flow lability” defined as: [(diary maximum − diary minimum)/diary mean] and “% of days with chest tightness” (r = 0.31). Logistic models evaluated peak flow and symptoms as predictors of an important health outcome: hospitalization or emergency department or unscheduled clinic visit for asthma within 30 days of starting the diary. Each of the peak flow and symptom measures was significantly related to utilization. However, the predictive power of each measure was low (range of area under ROC curve, 0.54–0.67). Models including only peak flow or symptoms had greater prediction than models with risk factors such as atopy, asthma persistence, and age. The prediction from a model with the risk factors and symptoms was not improved by adding a peak flow measure to the model (increase in area under ROC, 0.67–0.68). Stratified analyses suggest that prediction was similar in the fall vs. winter, spring, and summer months. Greater prediction of health outcomes was found among more persistent asthmatics and children who were nonatopic.

These findings suggest that in a research setting, peak flow monitoring in children did not add prediction beyond that obtained from symptom reports. Pediatr Pulmonol. 2001; 31:190–197. Published 2001 Wiley‐Liss, Inc.
Survival following Burkholderia cepacia sepsis in a patient with cystic fibrosis treated with corticosteroids
Authors: Kazachkov Mikhail , Lager Joanne , LiPuma John , Barker Pierre M.
Published: August 2002

We describe an 11‐year‐old girl with cystic fibrosis (CF) who presented with respiratory failure and Burkholderia cepacia bacteremia (cepacia syndrome). She survived her illness after aggressive treatment with parenteral antibiotics and corticosteroids. We speculate that treatment with corticosteroids may decrease the influx of proinflammatory cytokines and neutrophil‐induced inflammation, with resulting improvement in the outcome of cepacia syndrome in CF patients. Pediatr Pulmonol. 2001; 32:338–340. © 2001 Wiley‐Liss, Inc.
Clusterin expression is significantly enhanced in prostate cancer cells following androgen withdrawal therapy
Authors: July Laura V. , Akbari Majid , Zellweger Tobias , Jones Edward C. , Goldenberg S. Larry , Gleave Martin E.
Published: August 2002

BACKGROUND

Progression of prostate cancer to androgen independence (AI) results in part from the upregulation of anti‐apoptotic genes following androgen withdrawal, and androgen‐independent disease remains the primary obstacle to improved survival. Testosterone‐repressed prostate message‐2 (TRPM‐2) encodes the anti‐apoptotic protein clusterin, which is upregulated in response to cellular compromise as observed in normal and malignant tissues undergoing apoptosis. Systemic administration of antisense clusterin oligonucleotides in prostate cancer xenograft models delays progression to AI and enhances chemosensitivity. The objective of this study was to define changes in clusterin expression following neoadjuvant hormone therapy (NHT) in prostate cancer patients.

MATERIALS AND METHODS

Archival radical prostatectomy (RP) specimens were obtained for 128 patients who received either no NHT or treatment for 2–8 weeks, 3 months, or 8 months. Paired needle biopsy specimens were acquired for 30 patients and all tissues were subjected to clusterin immunohistochemistry. Western blot analysis was performed on frozen tissue from 5 untreated and 5 treated patients.

RESULTS

Clusterin expression in malignant prostatic tissue was significantly greater in patients who underwent preoperative NHT (P ≪ 0.001). Needle biopsies obtained prior to NHT consistently demonstrated lower staining intensity than corresponding RP specimens (P ≪ 0.001). Western blot analysis confirmed clusterin levels increased 17‐fold beginning within 4 weeks after androgen withdrawal.

CONCLUSIONS

Upregulation of clusterin levels following androgen ablation therapy may represent an adaptive cell survival response following apoptotic signals like androgen withdrawal. These findings support clusterin as a valid therapeutic target in strategies employing novel multimodality therapy for advanced prostate cancer. Prostate 50: 179–188, 2002. © 2002 Wiley‐Liss, Inc.
Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation
Authors: Bürgi Roland , Kollman Peter A. , van Gunsteren Wilfred F.
Published: August 2002

For the structure and function of proteins, the pH of the solution is one of the determining parameters. Current molecular dynamics (MD) simulations account for the solution pH only in a limited way by keeping each titratable site in a chosen protonation state. We present an algorithm that generates trajectories at a Boltzmann distributed ensemble of protonation states by a combination of MD and Monte Carlo (MC) simulation. The algorithm is useful for pH‐dependent structural studies and to investigate in detail the titration behavior of proteins. The method is tested on the acidic residues of the protein hen egg white lysozyme. It is shown that small structural changes may have a big effect on the pKA values of titratable residues. Proteins 2002;47:469–480. © 2002 Wiley‐Liss, Inc.
Contributions to the binding free energy of ligands to avidin and streptavidin
Authors: Lazaridis Themis , Masunov Artëm , Gandolfo Francois
Published: August 2002

The free energy of binding of a ligand to a macromolecule is here formally decomposed into the (effective) energy of interaction, reorganization energy of the ligand and the macromolecule, conformational entropy change of the ligand and the macromolecule, and translational and rotational entropy loss of the ligand. Molecular dynamics simulations with implicit solvation are used to evaluate these contributions in the binding of biotin, biotin analogs, and two peptides to avidin and streptavidin. We find that the largest contribution opposing binding is the protein reorganization energy, which is calculated to be from 10 to 30 kcal/mol for the ligands considered here. The ligand reorganization energy is also significant for flexible ligands. The translational/rotational entropy is 4.5–6 kcal/mol at 1 M standard state and room temperature. The calculated binding free energies are in the correct range, but the large statistical uncertainty in the protein reorganization energy precludes precise predictions. For some complexes, the simulations show multiple binding modes, different from the one observed in the crystal structure. This finding is probably due to deficiencies in the force field but may also reflect considerable ligand flexibility. Proteins 2002;47:194–208. © 2002 Wiley‐Liss, Inc.
Geometry and physics of proteins
Authors: Banavar Jayanth R. , Maritan Amos , Micheletti Cristian , Trovato Antonio
Published: August 2002

A conceptual framework for understanding the protein folding problem has remained elusive in spite of many significant advances. We show that geometrical constraints imposed by chain connectivity, compactness, and the avoidance of steric clashes can be encompassed in a natural way using a three‐body potential and lead to a selection in structure space, independent of chemical details. Strikingly, secondary motifs such as hairpins, sheets, and helices, which are the building blocks of protein folds, emerge as the chosen structures for segments of the protein backbone based just on elementary geometrical considerations. Proteins 2002;47:315–322. © 2002 Wiley‐Liss, Inc.
Prediction of protein interaction sites from sequence profile and residue neighbor list
Authors: Zhou Huan‐Xiang , Shan Yibing
Published: August 2002

Protein–protein interaction sites are predicted from a neural network with sequence profiles of neighboring residues and solvent exposure as input. The network was trained on 615 pairs of nonhomologous complex‐forming proteins. Tested on a different set of 129 pairs of nonhomologous complex‐forming proteins, 70% of the 11,004 predicted interface residues are actually located in the interfaces. These 7732 correctly predicted residues account for 65% of the 11,805 residues making up the 129 interfaces. The main strength of the network predictor lies in the fact that neighbor lists and solvent exposure are relatively insensitive to structural changes accompanying complex formation. As such, it performs equally well with bound or unbound structures of the proteins. For a set of 35 test proteins, when the input was calculated from the bound and unbound structures, the correct fractions of the predicted interface residues were 69 and 70%, respectively. Proteins 2001;44:336–343. © 2001 Wiley‐Liss, Inc.
Examination of possible structural constraints of MHC‐binding peptides by assessment of their native structure within their source proteins
Authors: Schueler‐Furman Ora , Altuvia Yael , Margalit Hanah
Published: August 2002

Antigenic peptides bind to major histocompatibility complex (MHC) molecules as a prerequisite for their presentation to T cells. In this study, we investigate possible structural preferences of MHC‐binding peptides by examining the conformation space defined by the structures of these peptides within their native source proteins. Comparison of the conformation space of the native structures of MHC‐binding nonamers and a corresponding conformation space defined by a random set of nonamers showed no significant difference. This suggests that the environment of the MHC binding groove has evolved to bind peptides with essentially any “structural background.” A slight tendency for an extended β‐conformation at positions 8 and 9 was observed for the set of native structures. We suggest that such a preference may facilitate the binding of the C‐terminal anchor position of processed peptides into the corresponding specificity pocket. MHC‐binding peptides represent examples of short subsequences that are present in two different structural environments: within their native protein and within the MHC binding groove. Comparison of the native and of the bound structure of the peptides showed that peptides up to 14 residues long may adopt different conformations within different protein environments. This has direct implications for structure prediction algorithms. Proteins 2001;45:47–54. © 2001 Wiley‐Liss, Inc.
Quantification of plasma and egg 4,4′‐dinitrocarbanilide (DNC) residues for the efficient development of a nicarbazin‐based contraceptive for pest waterfowl
Authors: Johnston John J , Britton Walter M , MacDonald Alexander , Primus Thomas M , Goodal Margaret J , Yoder Christi A , Miller Lowell A , Fagerstone Kathleen A
Published: August 2002

Urbanization and associated landscaping has increased the abundance of year‐round habitat for waterfowl, resulting in vegetation damage, loss of recreational activities, air transportation mishaps and health hazards. As part of a research program to develop socially acceptable techniques for management of pest bird populations, we are evaluating nicarbazin as a contraceptive in pest and surrogate avian species. As reproductive studies with Canada Geese (Branta canadensis) are tedious due to the difficulty of conducting controlled field studies and/or breeding geese in captivity, we evaluated the effects of oral nicarbazin administration on the production and hatchability of chicken eggs. Blood plasma and egg DNC concentrations were correlated to contraceptive efficacy. Subsequent studies are being conducted with geese to determine the diet nicarbazin concentration required to produce the desired blood and plasma DNC concentrations. This approach permits the expeditious evaluation of formulations and dosing regimes by simply monitoring blood DNC concentrations in target species.

Published in 2001 by John Wiley & Sons, Ltd.
Synthesis and solution characterization of a porphyrin‐CCK8 conjugate
Authors: De Luca Stefania , Tesauro Diego , Di Lello Paola , Fattorusso Roberto , Saviano Michele , Pedone Carlo , Morelli Giancarlo
Published: August 2002

In this paper we report the synthesis and a detailed NMR solution characterization of a new CCK8 analogue and its indium(III) complex, PK‐CCK8 and In‐PK‐CCK8. The new compounds contain a porphyrin moiety covalently bound through an amide bond to the side chain of a Lys residue introduced at the N‐terminus of CCK8. A molecular dynamics simulation, based on the NMR structure of the complex between CCK8 and the N‐terminal extracellular arm of the CCKA receptor, is also reported. Both the NMR study and the molecular dynamics simulation indicate that the porphyrin–peptide conjugate might be able to bind to the CCKA receptor model. The results of the molecular dynamics calculations show that the conformational features of the CCK8/CCKA receptor model complex and of the PK‐CCK8/CCKA receptor‐model complex are similar. This evidence supports the view that the introduction of the porphyrin‐Lys moiety does not influence the mode of ligand binding to the CCKA receptor model. The NMR structure of PK‐CCK8 in DMSO consists of a well defined pseudo‐helical N‐terminal region, while the C‐terminal region is flexible. Moreover, the absence of NOE contacts between the porphyrin and the peptide indicates that the macrocyclic ring is directed away from the peptide region involved in the binding with the receptor. Copyright © 2001 European Peptide Society and John Wiley & Sons, Ltd.
Effect of Aloe vera leaves on blood glucose level in type I and type II diabetic rat models
Authors: Okyar Alper , Can Ayşe , Akev Nuriye , Baktir Gül , Sütlüpinar Nurhayat
Published: August 2002

Aloe vera (L.) Burm. fil. (= A. barbadensis Miller) (Liliaceae) is native to North Africa and also cultivated in Turkey. Aloes have long been used all over the world for their various medicinal properties. In the past 15 years, there have been controversial reports on the hypoglycaemic activity of Aloe species, probably due to differences in the parts of the plant used or to the model of diabetes chosen. In this study, separate experiments on three main groups of rats, namely, non‐diabetic (ND), type I (IDDM) and type II (NIDDM) diabetic rats were carried out. A. vera leaf pulp and gel extracts were ineffective on lowering the blood sugar level of ND rats. A. vera leaf pulp extract showed hypoglycaemic activity on IDDM and NIDDM rats, the effectiveness being enhanced for type II diabetes in comparison with glibenclamide. On the contrary, A. vera leaf gel extract showed hyperglycaemic activity on NIDDM rats. It may therefore be concluded that the pulps of Aloe vera leaves devoid of the gel could be useful in the treatment of non‐insulin dependent diabetes mellitus Copyright © 2001 John Wiley & Sons, Ltd.
Evaluation of Ophthacare® eye drops—a herbal formulation in the management of various ophthalmic disorders
Authors: Biswas N. R. , Gupta S. K. , Das G. K. , Kumar N. , Mongre P. K. , Haldar D. , Beri S.
Published: August 2002

An open prospective multicentre clinical trial was conducted in patients suffering from various ophthalmic disorders namely, conjunctivitis, conjunctival xerosis (dry eye), acute dacryocystitis, degenerative conditions (pterygium or pinguecula) and postoperative cataract patients with a herbal eye drop preparation (Ophthacare®) containing basic principles of different herbs which have been conventionally used in the Ayurvedic system of medicine since time immemorial. These include Carum copticum, Terminalia belirica, Emblica officinalis, Curcuma longa, Ocimum sanctum, Cinnamomum camphora, Rosa damascena and meldespumapum. These herbs reportedly possess antiinfective and antiinflammatory properties. The present study was undertaken to elucidate the role of this herbal product in a variety of eye ailments. Side effects, if any, were noted during the study. An improvement was observed with the treatment of the herbal eye drop treatment in most cases.

There were no side effects observed during the course of the study and the eye drop was well tolerated by the patients. The herbal eye drop Ophthacare® has a useful role in a variety of infective, inflammatory and degenerative ophthalmic disorders. Copyright © 2001 John Wiley & Sons, Ltd.
Rice Bran Oil and γ‐Oryzanol in the Treatment of Hyperlipoproteinaemias and Other Conditions
Authors: Cicero A. F. G. , Gaddi A.
Published: August 2002

Diet is the first (and sometimes the only) therapeutic approach to hyperlipoproteinaemias. Rice bran oil and its main components (unsaturated fatty acids, triterpene alcohols, phytosterols, tocotrienols, α‐tocopherol) have demonstrated an ability to improve the plasma lipid pattern of rodents, rabbits, non‐human primates and humans, reducing total plasma cholesterol and triglyceride concentration and increasing the high density lipoprotein cholesterol level. Other potential properties of rice bran oil and γ‐oryzanol, studied both in vitro and in animal models, include modulation of pituitary secretion, inhibition of gastric acid secretion, antioxidant action and inhibition of platelet aggregation. This paper reviews the available data on the pharmacology and toxicology of rice bran oil and its main components with particular attention to those studies relating to plasma lipid altering effects. Copyright © 2001 John Wiley & Sons, Ltd.
Antiinflammatory activity from aerial parts of Baccharis Medullosa, Baccharis rufescens and Laennecia sophiifolia in mice
Authors: Cifuente Diego A. , Simirgiotis Mario J. , Favier L. Silvina , Rotelli Alejandra E. , Pelzer Lilian E.
Published: August 2002

The antiinflammatory activities of ten organic extracts from the aerial parts of Baccharis medullosa DC., Baccharis rufescens S. and Laennecia sophiifolia (Kunth) G. L. Nesom were investigated in mice subjected to carrageenan induced paw oedema. Intraperitoneally administered organic extracts given at doses equivalent to 80 mg/kg of material inhibited the acute phases of inflammation in this model. Our results indicate that the most effective extracts were: n‐hexane (I) from B. medullosa, acetone (V) and chloroform (VII) from L. sophiifolia, and acetone (VIII) and chloroform (X) from B. rufescens. All exerted the strongest effect at 5 h after injection of the phlogistic agent. Copyright © 2001 John Wiley & Sons, Ltd.
Ab initio study of electronic spectra of merocyanine 540 and its photoproducts
Authors: Mach P. , Urban J. , Leszczynski J.
Published: August 2002

Molecular structures of three derivatives of merocyanine 540 (MC 540) were studied using the density functional method in conjunction with the 6‐31G*, 6‐31G**, and 6‐311G** basis sets. The excited states were calculated using the configuration interaction method involving singly excited configurations (CIS). The predicted transition energies and oscillator strength agree well with the experimental UV adsorption spectra of the studied systems. The existence of two stable conformers of merocyanine explain the experimentally observed dependence of the UV spectra upon the change of concentration of added salts. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Hamiltonian factorization on the quantum phase space
Authors: Morales‐Guzmán J. D. , Morales J. , Peña J. J.
Published: August 2002

Using a special phase space representation, we propose a factorization of the Hamiltonian in this representation in spite of its more complex structure. Also, based on the link existing between the intertwining technique and SUSY we find the phase space supercharges and the supersymmetric partner Hamiltonian. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Theoretical study of the Rydberg spectra of chemically relevant isovalent radicals
Authors: Martín I. , Velasco A. M. , Lavín C.
Published: August 2002

In the present work we have studied the Rydberg spectroscopic behavior of the CH3 and SiH3 isovalent radicals. The molecular‐adapted quantum defect orbital (MQDO) method has been employed in our calculations, which have been extended to the radicals' isolated central atoms, C and Si. The similarities observed between the intensities of analogous transitions in the atoms and the corresponding radicals have not only served the purpose of assessing the quality of our calculations but also offer some potential practical usefulness. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Molecular view of charge exchange in ion–C60 collisions
Authors: Ruiz L. F. , Hervieux P. A. , Hanssen J. , Politis M. F. , Martín F.
Published: August 2002

We present a theoretical study of charge transfer in H++C60 and He2++C60 collisions using an extension of the molecular time‐dependent method of ion–atom collisions. Energy‐correlation diagrams have been evaluated for the corresponding (C60–H)+ and (C60–He)2+ quasi‐molecules. Single and double charge‐transfer cross sections in C60+He2+ collisions are reported for the first time. The results show that double charge‐transfer cross sections are only one order of magnitude smaller than single charge‐transfer cross sections. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
In search of new resonance structures in dissociative photoionization of H2
Authors: Fernández J. , Martín F.
Published: August 2002

We present a theoretical study of dissociative photoionization of H2 via the 1Πu symmetry in the photon energy range 30–43 eV. Our results explain the various peaks observed in the experiments below 40 eV and illustrate, in particular, the important role of the 2Πu(2pπu) ionization threshold. At higher photon energies, they suggest the existence of new resonance structures that may be associated with doubly excited states of H2 lying above the third and fourth ionization thresholds (the Q3 and Q4 resonance series). From the calculated resonance parameters, we conclude that the dominant mechanism at high photon energies should involve the Q4 (and probably higher) doubly excited states of H2. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2002
Frequency map analysis and scars in molecular vibrations
Authors: Losada J. C. , Benito R. M. , Arranz F. J. , Borondo F.
Published: August 2002

In a previous paper [ J Chem Phys 1998, 108, 63], an analysis of the phase space structure of the isomerizing molecular system LiNC/LiCN was presented, with the conclusion that the chaotic region was extremely influenced by the dynamics associated to a 1:8 resonance between the stretching LiCN and the bending modes. This result was inferred based on a very restricted calculation. In this work we generalize our previous study in order to assess the generality of our former conclusion. The quantum implications of this finding are also addressed. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Comparison of gas chromatography and liquid chromatography mass spectrometric measurements for high accuracy analysis of cholesterol in human serum by isotope dilution mass spectrometry
Authors: Wolff Briche Céline S. J. , Carter David , Webb Kenneth S.
Published: August 2002

Cholesterol measurements are of vital clinical importance and reliable reference materials are essential for method validation. Gas chromatography with mass spectrometry (GC/MS) is usually used for the high accuracy analysis of cholesterol by isotope dilution. A certified reference material for cholesterol content in human serum was analysed by isotope dilution utilising GC/MS and liquid chromatography mass spectrometry (LC/MS). The use of LC/MS avoided the need for a derivatisation step. Both LC/MS and GC/MS produced results on the measurement of cholesterol that agreed within 0.5% of the certified value. Moreover, the precision obtained for ratio measurement using both techniques are comparable and lead to relative expanded standard uncertainties (with a coverage factor of 2) varying between 0.2 and 0.5%. Copyright © 2002 John Wiley & Sons, Ltd.
Treatment of Perchlorate‐Contaminated Groundwater Using Highly Selective, Regenerable Ion‐Exchange Technology: A Pilot‐Scale Demonstration
Authors: Gu Baohua , Ku Yee‐Kyoung , Brown Gilbert M.
Published: August 2002

Treatment of perchlorate‐contaminated groundwater using highly selective, regenerable ion‐exchange
technology has been recently demonstrated at Edwards Air Force Base, California. At an influent concentration of
about 450 μg/l ClO4−, the bifunctional anion‐exchange resin bed treated
approximately 40,000 empty bed volumes of groundwater before a significant breakthrough of
ClO4− occurred. The presence of relatively high concentrations of chloride and sulfate
in site groundwater did not appear to affect the ability of the bifunctional resin to remove
ClO4−. The spent resin bed was successfully regenerated using the
FeCl3−HCl regeneration technique recently developed at the Oak Ridge National
Laboratory, and nearly 100 percent of sorbed ClO4− was displaced or recovered after
elution with as little as about two bed volumes of the regenerant solution. In addition, a new methodology was
developed to completely destroy ClO4− in the FeCl3−HCl
solution so that the disposal of perchlorate‐containing hazardous wastes could be eliminated. It is
therefore anticipated that these treatment and regeneration technologies may offer an efficient and
cost‐effective means to remove ClO4− from contaminated groundwater with
significantly reduced generation of waste requiring disposal. © 2002 Wiley Periodicals, Inc.