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  • Articles: DFG German National Licenses  (11,796)
  • Engineering General  (9,884)
  • Biochemistry
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  • Articles: DFG German National Licenses  (11,796)
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Years
  • 1
    ISSN: 1432-0878
    Keywords: Key words Molecular biology ; Cell biology ; Bioassay ; Analytical chemistry ; Biochemistry ; Diagnosis ; Therapy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  Significant amounts of endogenous biotin were detected by avidin-peroxidase in fixed rat kidney, liver, and brain. The staining was indistinguishable from the true signals of immunoreactivity and could not be consistently blocked by pretreatment with avidin. The finding that certain neurons in the hippocampus contain more biotin than neurons in other areas of the brain suggests that biotin might have novel functions in the brain other than its well-known role as cofactor of carboxylases. Critical examination of published immunohistochemical localization studies on rat kidney strongly suggests that many false-positive results have been considered as true signals. Interference of endogenous biotin in any study using avidin-biotin technology must be considered if biological tissues are involved. The published data obtained by this method should therefore be reevaluated. Furthermore, appropriate controls, blockers and caution in interpreting results must be exercised, not only in immunohistochemistry but also in any applications of avidin-biotin technology.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1437-1596
    Keywords: Key words Diabetes mellitus ; Biochemistry ; Fructosamine ; Postmortem ; Vitreous humor
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine , Law
    Notes: Abstract In clinical practice, biochemical markers, particularly serum glucose levels are used to diagnose diabetes mellitus. However, at autopsy this marker is of no value due to the substantial and capricious fluctuations in glucose levels after death. The aim of this study was to evaluate the usefulness of the postmortem determination of fructosamine in vitreous humor for confirming the presence of antemortem hyperglycemia. This was a study of 92 cadavers with a mean age of 60.05 years (SD 17.73) and a mean postmortem interval of 17.02 h (SD 9.76, range 2–58 h). Cases were assigned to two diagnostic groups according to the antemortem diagnosis of diabetes mellitus based on the patients’ medical records. In vitreous humor statistically significant differences were found in glucose and fructosamine concentrations between the two diagnostic groups, the highest values being obtained in the group of subjects with a previous diagnosis of diabetes mellitus.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    International journal of legal medicine 111 (1998), S. 173-176 
    ISSN: 1437-1596
    Keywords: Key words Myocardial ischaemia ; Biochemistry ; Troponin ; Postmortem ; Pericardial fluid
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine , Law
    Notes: Abstract In clinical practice several biochemical markers are used for the diagnosis of myocardial infarction. Because of its extremely high specificity for myocardial damage, cardiac troponin I (cTn I) is frequently used. The aim of this study was to evaluate the diagnostic efficacy of postmortem cTn I determinations in pericardial fluid and serum and to compare these results with other biochemical markers and with structural findings used to diagnose acute myocardial ischaemia. We studied 89 cadavers with a mean age of 51.38 ± 2.04 (SD 19.27 years). Cases were allocated to 1 of 4 diagnostic groups depending on the probable intensity of myocardial damage and cause of death. In pericardial fluid we obtained statistically significant differences for the four biochemical parameters, while in serum myosin heavy chains and myoglobin showed statistically significant differences. The highest levels of biochemical markers in pericardial fluid were observed in subjects who had died from definite myocardial infarction.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
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    Springer
    Journal of comparative physiology 178 (1996), S. 329-336 
    ISSN: 1432-1351
    Keywords: Grasshopper ; Sexual behavior ; Spermatophore ; Accessory gland secretion ; Surgical ablations ; Biochemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract In the female grasshopper Gomphocerus rufus mating elicits ‘secondary defense’ which makes remating impossible. The behavioral change is caused by the liquid white secretions, proteins of less than 90 kD, which are produced by the white tubuli of the male's accessory glands. Experimental injection of the white secretions directly into the spermathecal duct of receptive virgins provokes ‘secondary defense’ instantly whereas sperm transfer had no such effect. ‘Secondary defense’ is also released by eggs entering the oviducts and excerting pressure against the oviductal walls on their way to oviposition.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
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    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 9 (1996), S. 258-258 
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
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    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 9 (1996), S. 52-52 
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 7
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    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 9 (1996), S. 53-53 
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 8
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    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 9 (1996) 
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
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    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 9 (1996) 
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 9 (1996) 
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 11
    Electronic Resource
    Electronic Resource
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 9 (1996) 
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 12
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    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 9 (1996), S. 752-752 
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 13
    Electronic Resource
    Electronic Resource
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 9 (1996) 
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 14
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    New York, NY [u.a.] : Wiley-Blackwell
    Numerical Linear Algebra with Applications 3 (1996), S. 1-20 
    ISSN: 1070-5325
    Keywords: preconditioning saddle-point problems ; eigenvalue estimation ; mixed finite element method ; minimum residual method ; second-order elliptic problems ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We consider saddle-point problems that typically arise from the mixed finite element discretization of second-order elliptic problems. By proper equivalent algebraic operations the considered saddle-point problem is transformed to another saddle-point problem. The resulting problem can then be efficiently preconditioned by a block-diagonal matrix or by a factored block-matrix (the blocks correspond to the velocity and pressure, respectively). Both preconditioners have a block on the main diagonal that corresponds to the bilinear form(δ is a positive parameter) and a second block that is equal to a constant times the identity operator. We derive uniform bounds for the negative and positive eigenvalues of the preconditioned operator. Then any known preconditioner for the above bilinear form can be applied. We also show some numerical experiments that illustrate the convergence properties of the proposed technique.
    Additional Material: 2 Tab.
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  • 15
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    New York, NY [u.a.] : Wiley-Blackwell
    Numerical Linear Algebra with Applications 3 (1996) 
    ISSN: 1070-5325
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Type of Medium: Electronic Resource
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  • 16
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    New York, NY [u.a.] : Wiley-Blackwell
    Numerical Linear Algebra with Applications 3 (1996), S. 275-300 
    ISSN: 1070-5325
    Keywords: sparse QR factorization ; multifrontal method ; parallelism ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We describe the design and implementation of a parallel QR decomposition algorithm for a large sparse matrix A. The algorithm is based on the multifrontal approach and makes use of Householder transformations. The tasks are distributed among processors according to an assembly tree which is built from the symbolic factorization of the matrix ATA.We first address uniprocessor issues and then discuss the multiprocessor implementation of the method. We consider the parallelization of both the factorization phase and the solve phase. We use relaxation of the sparsity structure of both the original matrix and the frontal matrices to improve the performance. We show that, in this case, the use of Level 3 BLAS can lead to very significant gains in performance. We use the eight processor Alliant˜FX/80 at CERFACS to illustrate our discussion.
    Additional Material: 12 Ill.
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  • 17
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    New York, NY [u.a.] : Wiley-Blackwell
    Numerical Linear Algebra with Applications 3 (1996), S. 113-124 
    ISSN: 1070-5325
    Keywords: iterative methods ; linear systems ; multisplittings ; overlap ; parallel algorithms ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: Parallel two-stage multisplitting methods with overlap for the solution of linear systems of algebraic equations are studied. It is shown that, under certain hypotheses, the method with overlap is asymptotically faster than that without overlap. Experiments illustrating this phenomenon are presented.
    Additional Material: 2 Ill.
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  • 18
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    New York, NY [u.a.] : Wiley-Blackwell
    Numerical Linear Algebra with Applications 3 (1996), S. 91-111 
    ISSN: 1070-5325
    Keywords: boundary integral operators ; domain decomposition ; interface operators ; fast elliptic problem solvers ; parallel algorithms ; preconditioning ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In this paper a method for fast computations with the inverse to weakly singular, hypersingular and double layer potential boundary integral operators associated with the Laplacian on Lipschitz domains is proposed and analyzed. It is based on the representation formulae suggested for above-mentioned boundary operations in terms of the Poincare-Steklov interface mappings generated by the special decompositions of the interior and exterior domains. Computations with the discrete counterparts of these formulae can be efficiently performed by iterative substructuring algorithms provided some asymptotically optimal techniques for treatment of interface operators on subdomain boundaries. For both two- and three-dimensional cases the computation cost and memory needs are of the order O(N logp N) and O(N log2 N), respectively, with 1 ≤ p ≤ 3, where N is the number of degrees of freedom on the boundary under consideration (some kinds of polygons and polyhedra). The proposed algorithms are well suited for serial and parallel computations.
    Additional Material: 2 Ill.
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  • 19
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Numerical Linear Algebra with Applications 3 (1996), S. 173-177 
    ISSN: 1070-5325
    Keywords: diagonally dominant matrix ; determinant ; norm ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: A property of strictly diagonally dominant matrices and a generalization of a Varga's bound for ∥ A-1∥∞ to the case ∥ A-1B∥∞ are given and the two-sided bounds for the determinants of strictly diagonally dominant matrices are derived
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  • 20
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    New York, NY [u.a.] : Wiley-Blackwell
    Numerical Linear Algebra with Applications 3 (1996), S. 513-524 
    ISSN: 1070-5325
    Keywords: regularization ; I-norm ; discontinuous solutions ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In certain inverse problems it is useful to be able to compute solutions which are, in some sense, as simple as possible. For example,k one may wish to compute solutions which are piecewise constant and with as few discontinuities as possible. Such solutions are suited to describe models, e.g., geological layers, where the coarse structure is more important than the fine structure. A natural generalization of piecewise constant functions is piecewise polynomial solutions. In this paper we present a new algorithm which is capable of computing solutions that are piecewise polynomials, without having to specify a priori the positions of the break points between the polynomial pieces.
    Additional Material: 5 Ill.
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  • 21
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    New York, NY [u.a.] : Wiley-Blackwell
    Numerical Linear Algebra with Applications 3 (1996), S. 491-512 
    ISSN: 1070-5325
    Keywords: unsymmetric ; Krylov subspace ; IOM(q) ; FOM ; truncated ; basis vector ; orthonormality ; convergence ; restarted ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The incomplete orthogonalization method (IOM(q)), a truncated version of the full orthogonalization method (FOM) proposed by Saad, has been used for solving large unsymmetric linear systems. However, no convergence analysis has been given. In this paper, IOM(q) is analysed in detail from a theoretical point of view. A number of important results are derived showing how the departure of the matrix A from symmetric affects the basis vectors generated by IOM(q), and some relationships between the residuals for IOM(q) and FOM are established. The results show that IOM(q) behaves much like FOM once the basis vectors generated by it are well conditioned. However, it is proved that IOM(q) may generate an ill-conditioned basis for a general unsymmetric matrix such that IOM(q) may fail to converge or at least cannot behave like FOM. Owing to the mathematical equivalence between IOM(q) and the truncated ORTHORES(q) developed by Young and Jea, insights are given into the convergence of the latter. A possible strategy is proposed for choosing the parameter q involved in IOM(q). Numerical experiments are reported to show convergence behaviour of IOM(q) and of its restarted version.
    Additional Material: 6 Tab.
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  • 22
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    New York, NY [u.a.] : Wiley-Blackwell
    Numerical Linear Algebra with Applications 3 (1996), S. 413-426 
    ISSN: 1070-5325
    Keywords: iterative methods ; linear systems ; singular matrices ; block methods ; multisplitting ; two-stage ; non-stationary ; Markov chains ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The use of block two-stage methods for the iterative solution of consistent singular linear systems is studied. In these methods, suitable for parallel computations, different blocks, i.e., smaller linear systems, can be solved concurrently by different processors. Each of these smaller systems are solved by an (inner) iterative method. Hypotheses are provided for the convergence of non-stationary methods, i.e., when the number of inner iterations may vary from block to block and from one outer iteration to another. It is shown that the iteration matrix corresponding to one step of the block method is convergent, i.e., that its powers converge to a limit matrix. A theorem on the convergence of the infinite product of matrices with the same eigenspace corresponding to the eigenvalue 1 is proved, and later used as a tool in the convergence analysis of the block method. The methods studied can be used to solve any consistent singular system, including discretizations of certain differential equations. They can also be used to find stationary probability distribution of Markov chains. This last application is considered in detail.
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  • 23
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    Numerical Linear Algebra with Applications 3 (1996), S. 349-350 
    ISSN: 1070-5325
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: No Abstract
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  • 24
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    New York, NY [u.a.] : Wiley-Blackwell
    Numerical Linear Algebra with Applications 3 (1996), S. 427-453 
    ISSN: 1070-5325
    Keywords: mixed method ; nonconforming method ; multilevel preconditioner ; condition number ; second order elliptic problem ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: A new approach for constructing algebraic multilevel preconditioners for mixed finite element methods for second order elliptic problems with tensor coefficients on general geometry is proposed. The linear system arising from the mixed methods is first algebraically condensed to a symmetric, positive definite system for Lagrange multipliers, which corresponds to a linear system generated by standard nonconforming finite element methods. Algebraic multilevel preconditioners for this system are then constructed based on a triangulation of the domain into tetrahedral substructures. Explicit estimates of condition numbers and simple computational schemes are established for the constructed preconditioners. Finally, numerical results for the mixed finite element methods are presented to illustrate the present theory.
    Additional Material: 4 Ill.
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  • 25
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    New York, NY [u.a.] : Wiley-Blackwell
    Numerical Linear Algebra with Applications 3 (1996), S. 455-457 
    ISSN: 1070-5325
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
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  • 26
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    New York, NY [u.a.] : Wiley-Blackwell
    Numerical Linear Algebra with Applications 3 (1996), S. 473-489 
    ISSN: 1070-5325
    Keywords: conjugate gradients ; biconjugate gradients ; conjugate directions ; non-symmetric linear systems ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In this paper three basic conjugate direction methods for solving non-symmetric linear systems are described and compared. All three have entirely different basic structures and, consequently, completely different characteristics. The motivation for this work is the comparative assessment of the methods in order to decide which of the three is the most suitable for further development.
    Additional Material: 8 Ill.
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  • 27
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    New York, NY [u.a.] : Wiley-Blackwell
    Numerical Linear Algebra with Applications 3 (1996) 
    ISSN: 1070-5325
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
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  • 28
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    New York, NY [u.a.] : Wiley-Blackwell
    Numerical Linear Algebra with Applications 3 (1996), S. 543-545 
    ISSN: 1070-5325
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
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  • 29
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    New York, NY [u.a.] : Wiley-Blackwell
    Numerical Linear Algebra with Applications 3 (1996), S. 21-44 
    ISSN: 1070-5325
    Keywords: first-order PDEs ; iterative methods ; preconditioners ; Toeplitz ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: Preconditioners to nonsymmetric, nondiagonally dominant systems of equations are constructed and examined numerically. The preconditioners are based on a Toeplitz approach with a certain symmetry that we define. The inversion of the preconditioners is defined through a Fast Modified Sine Transform. As a model problem we study the systems of equations arising from a implicit time-discretization with a large time-step of a scalar hyperbolic PDE.
    Additional Material: 17 Ill.
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  • 30
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    New York, NY [u.a.] : Wiley-Blackwell
    Numerical Linear Algebra with Applications 3 (1996), S. 45-64 
    ISSN: 1070-5325
    Keywords: Toeplitz least squares problems ; circulant preconditioned conjugate gradient method ; deconvolution ; image restoration ; atmospheric imaging ; medical imaging ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In this paper, we propose a method to generalize Strang's circulant preconditioner for arbitrary n-by-n matrices An. The th column of our circulant preconditioner Sn is equal to the th column of the given matrix An. Thus if An is a square Toeplitz matrix, then Sn is just the Strang circulant preconditioner. When Sn is not Hermitian, our circulant preconditioner can be defined as . This construction is similar to the forward-backward projection method used in constructing preconditioners for tomographic inversion problems in medical imaging. We show that if the matrix An has decaying coefficients away from the main diagonal, then is a good preconditioner for An. Comparisons of our preconditioner with other circulant-based preconditioners are carried out for some 1-D Toeplitz least squares problems: min ∥ b - Ax∥2. Preliminary numerical results show that our preconditioner performs quite well, in comparison to other circulant preconditioners. Promising test results are also reported for a 2-D deconvolution problem arising in ground-based atmospheric imaging.
    Additional Material: 5 Ill.
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  • 31
    ISSN: 1075-2617
    Keywords: FMDV ; structure ; NMR spectrocopy ; NEO constraints ; RGD (Arg-Gly-Asp) ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solution structure of a 20 amino acid long peptide corresponding to the region 141-160 of the envelope protein Vp1 from foot-and-mouth disease virus (FMDV) serotype A, variant A, has been determined by a combination of NMR experiments and computer calculations. The peptide contains both the immunodominant epitope as well as the sequence (RGD) used by the virus to bind the cell receptor in the initial stages of infection. These two sites have been shown to partially overlap.One hundred and thirty-five NMR distance constraints were used to obtain a set of 11 structures by distance geometry, minimization and molecular dynamics simulations. These structures were divided into two homogeneous families based upon backbone superimposition. The first and most populated family was characterized by a backbone RMS of 1.5±0.4 Å, the second by a backbone RMS of 0.8±0.2 Å. The two families had similar structural features and differed mainly in the backbone angles of G149. In the larger of the two families these angles favoured the formation of a loop comprising residues 147 to 152 and stabilized by a H-bond between the NH of D147 and the CO of A152. In the second family, where this bond was absent, the peptide adopted in this region the shape of an irregular helix. The C-terminal half of the peptide (152-159) was similar in both families and largely helical. Similar structural features were also found within the VRGDS sequence (144-148) which was assigned to a β-turn type IV. The features of the two families of structures were found to be different from those of the recently published X-ray structure of the antigenic loop of a chemically modified form of FMDV. Proposals accounting for these differences are provided which take into account the dual activity of the 141-160 sequence (i.e. antibody binding and cell invasion through receptor binding).
    Additional Material: 11 Ill.
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  • 32
    ISSN: 1075-2617
    Keywords: FMDV ; NMR spectrocopy ; RGD (Arg-Gly-Asp) ; NEO constraints ; structure-activity correlation ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solution structure of a peptide corresponding to the VP1 region 141-160 of foot-and-mouth disease virus (FMDV) serotype A variant USA has been studied by NMR and computer calculations and compared with the results from a study on a highly homologous peptide deriving from serotype A, variant A. The two peptides differ in their serological behaviour and contain the immunodominant epitope of the virus which partly overlaps with its receptor binding region. Distance constraints, derived both from 2D and 3D homonuclear NMR and 2D-heteronuclear NMR experiments, were combined with DG calculations to yield 50 structures. After refinement through EM and restrained molecular dynamics simulations the selected structures shared several general features. In particular the 151-158 region was a helix in all cases while a large loop similar to that found in peptide A but comprising less residues and stabilized by an H-bond between the side chains of D147 and S150 was found in the majority of structures. A further loop, common to all structures, was identified around the RGD sequence (145-147). This was different from that found in the corresponding region of peptide A as were the conformations of the individual residues within the RGDX sequence.The different structural features shown by the two peptides were rationalized in terms of the S148 (peptide A) to F148 (peptide USA) mutation. The second mutation, that at position 153 (L in A, P in USA) did not appear to affect the structure of the peptide significantly although the different dimensions of the loop in the central region and the type of H-bond stabilizing it could be potentially ascribed to this second mutation.All criteria used pointed to different structural features for the two peptides consistent with their serological behaviour.
    Additional Material: 11 Ill.
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  • 33
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Peptide Science 2 (1996), S. 125-133 
    ISSN: 1075-2617
    Keywords: SPPS ; labelled peptides ; cellular localization ; amphipathic peptide ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report the solid-phase synthesis by the Fmoc strategy of a peptide containing a cysteamide group at its C-terminus. This peptide was subject to further modifications including the linkage of fluorophores, namely lucifer yellow and coumarin respectively, at the C- and/or N-terminals. After incubation with living cultured cells these two probes were localized and it is concluded that the post-synthesis modifications can strongly modify the localization of the peptide.
    Additional Material: 5 Ill.
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  • 34
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Peptide Science 2 (1996) 
    ISSN: 1075-2617
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 35
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    Journal of Peptide Science 2 (1996), S. 106-116 
    ISSN: 1075-2617
    Keywords: all parallel helix assemblies ; helix transition ; 310-/Α-HELICES ; two conformers ; water associated with non-polar helices ; X-ray crystallography ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The role of end groups in determining stereochemistry and packing in hydrophobic helical peptides has been investigated using an α-aminosobutyric acid (Aib) containing model nonapeptide sequence. In contrast to the Boc-analogue, Ac-(Aib-Val-Ala-Leu)2-Aib-OMe crystallizes with two independent molecules in a triclinic cell. The cell parameters are: space group P1, a=10.100(2)Å, b=15.194(4) Å, c=19.948(5) Å, α=63.12(2)°, β=88.03(2)°, γ=88.61(2)°, Z=2, R=7.96% for 5140 data where |Fo|〉3σ(F). The two independent molecules alternate in infinite columns formed by head-to-tail hydrogen bonding. The helices in the two independent molecules are quite similar to each other but one molecule is rotated ≍123° about its helix axis with respect to the other. All the helical columns pack parallel to each other in the crystal. Replacement of the bulky Boc group does not lead to any major changes in conformation. Packing characteristics are also similar to those observed for similar helical peptides.
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  • 36
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Peptide Science 2 (1996), S. 117-124 
    ISSN: 1075-2617
    Keywords: peptides ; neuropeptide ; antimicrobial agent ; skin secretion ; frogs ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The granular dorsal glands of the giant tree frog Litoria infrafrenata contain five peptides including caerulein (a known neuropeptide), and four new peptides named frenatins 1 (MH+ = 1140 Da), 2 (1423), 3 (2180) and 4 (2493). The amino acid sequences of the frenatins are detailed: their structures do not correspond to those of peptides isolated from other amphibians or animals. Frenatin 3, Gly-Leu-Met-Ser-Val-Leu-Gly-His-Ala-Val-Gly-Asn-Val-Leu-Gly- Gly-Leu-Phe-Lys-Pro-Lys-Ser-(OH), has wide spectrum antimicrobial properties.
    Additional Material: 6 Ill.
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  • 37
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    Journal of Peptide Science 2 (1996), S. 141-156 
    ISSN: 1075-2617
    Keywords: gramacidin A ; channel forming peptides ; Peptide conformational analysis ; cicular dichroism ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relation between the various spatial structures of the gramicidin A channels and their ionic conductance has been studied. For this aim, various conformations of the peptide were pre-formed in liposomal bilayer and after subsequent fusion of liposomes with planar lipid bilayer the measured channel conductance was correlated with gramicidin structures established in liposomes. To form the single-stranded π6.3π 6.3 helix the peptide and lipid were co-dissolved in TFE prior to liposome preparation. THF and other solvents were used to form parallel (↑ ↑ π π) and antiparallel (↑ ↓ π π) double helices. Conformation of gramicidin in liposomes made by various phosphatidylcholines was monitored by CD spectroscopy, and computer analysis of the spectra obtained was performed. After fusion of gramicidin containing liposomes with planar bilayer membranes from asolectin, the histograms of single-channel conductance were obtained. The histograms had one or three distinct peaks depending on the liposome preparation. Assignment of the structure of the channel to conductance levels was made by correlation of CD data with conductance histograms. The channel-forming analogue, des(Trp-Leu)2-gramicidin A, has been studied by the same protocol. The channel conductances of gramicidin A and the shortened analogue increase in the following order: ↑ ↓ π π 2 ↑ ↑ π π 〈 π 6.3π6.3. Single-channels formed by double helices have higher dispersity of conductance than the π6.3π6.3 helical channel. Lifetimes of the double helical and the π6.3π6.3 helical channels are very close to each other. The data obtained were compared with theoretically predicted properties of double helices [1].
    Additional Material: 15 Ill.
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  • 38
    ISSN: 1075-2617
    Keywords: HIV ; peptide library ; immune response ; cytokines ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The hypervariable domain of the HIV gp120, the V3 loop domain, represents a target for neutralizing antibodies and for HIV vaccine strategies. In this study, we have investigated in murine species the potential cross-reactivity of immune responses elicited by immunization either with individual V3 peptides, derived from distinct HIV sequences (BRU, RF, SF2, MN and ELI sequences), or with a V3 combinatorial peptide library.We observed that individual V3 peptides are immunogenic but elicit a specific B- and T-cell immune response that is mainly restricted to the sequence of the immunizing peptide. In particular, T-cell responses that depend on T-cell receptor recognition of peptides bound to the molecules encoded by the major histocompatibility complex were significantly influenced by small differences in the peptide amino acid sequence. The combinatorial V3 peptide library, previously described as B- and T-cell immunogens, induced a more broadly reactive immune response, specially when T-cell cytokine secretion was used as a readout for restimulation of T-cells with individual V3 peptides.These data suggest that amino acid variations in the sequence of an antigenic peptide could lead to the induction of different transducing signals in the primed T-cell population and to the activation of T-cells with distinct cytokine secretion properties. These observations may have implications in the understanding of antigenic variability and in the design of vaccine strategies.
    Additional Material: 6 Ill.
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  • 39
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Peptide Science 2 (1996), S. 157-164 
    ISSN: 1075-2617
    Keywords: sideropore ; peusdobactin ; peusdomycin ; solution-phase peptide synthesis ; unusual amino acids ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Pseudobactin is a structurally complex and physiologically important siderophore (microbial iron chelator) from Pseudomonas putida- fluorescens. Various fragments of the unusual peptide component of pseudobactin listed below were prepared by solution-phase peptide synthesis.L-Lys· D-threo-β-OH Asp· L-Ala· D-allo-Thr· L-AlaL-Lys· D-threo-βOH Asp· L-Ala· D-allo-ThrD-threo-β-OH Asp· L-Ala· D- allo-Thr· L-Ala· D-N-OH-cycloOrnD-threo-β-OH-Asp· L-Ala· D-allo-Thr· L-AlaL-Ala· D-allo-Thr· L- Ala· D-N-OH-cycloOrnA class of related peptides named pseudomycins have shown promising antifungal activity. To examine if these peptide fragments above would elicit similar activity, the fragments were tested and found to have no antifungal activity in limited bioassays.
    Additional Material: 3 Ill.
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  • 40
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Peptide Science 2 (1996) 
    ISSN: 1075-2617
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 41
    ISSN: 1075-2617
    Keywords: Nformylmethionyl peptides ; human neutrophils ; chemotaxis ; superoxide anion generation ; lysozyme release ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The formylpeptides formyl-methionyl-Nmethylleucyl- phenylaline methyl ester [for-Met-(NMe)Leu-Phe-OMe] 1, formyl-methionyl-2-aminotetralin-2-carboxyl-phenylalanine methyl ester [for-Met Act-Phe-OMe] 2, formyl-methionyl-1,2,3,4-terahydroisoquinoline-3-carboxl- phenylalanine methyl ester [for-Met-Tic-Phe-OMe] 3 and formyl- methionyl-2-aminoxy-4-methylvaleryl-phenylalanine methyl ester [for-Met-OLeu-Phe-OMe] 4 were synthesized in order to investigate the role of the amide bond at position 2 on biological activities on human neutrophils. Only analogue 2, which keeps the NH group at position 2, was found to retain activity though sterically encumbered.
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  • 42
    ISSN: 1075-2617
    Keywords: NPY ; conformational analysis (CD, NMR) ; molecular dynamics ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Neuropeptide Y (NPY), a peptide amide comprising 36 residue has been shown to act as a potent vasoconstrictor. In order to shed light on the structural requirements for the biological activities with respect to the different prerequisites for affinity to the NPY receptor subtypes Y1 and Y2, in the present study the syntheses and conformational analyses of two C-terminal segments, NPY(18-36) and NPY(13-36), are described.The results obtained by CD measurements, two-dimensional NMR spectros copy and a conformational refinement of the NMR-derived structure by molecular mechanics simulations support the findings of previously published structure -activity relationship studies for biologically active and selective compounds. In particular, the α-helical conformation as well as an appropriate exposure of the side chains of the critical C-terminal dipeptide within NPY(18-36) are in agreement with the prerequisites proposed for Y2 receptor binding of that segment.
    Additional Material: 11 Ill.
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  • 43
    ISSN: 1075-2617
    Keywords: antimicrobial peptides ; hydrophobic residue ; ion-channels ; pores ; α-helix ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The design of cecropin-melittin hybrid analogues is of interest due to the similarities in the structure of the antimicrobial peptides cecropin and melittin but differences in their lytic properties. We suspected that a hydrophobic residue in position 2 of milittin (Ile8 in the hybrid) plays an important role in the activity of the 15-residue hybrid, KWKLFKKIGAVLKVL-NH2, [CA(1-7)M(2-9)NH2] and have now examined its role in the analogue toward five test bacteria. Deletion of Ile8 reduced activity, and it was not restored by lengthening to 15 residues by addition of another threonine at the C-terminus. Replacement of Ile8 by a hydrophobic leucine maintained good activity and Ala8 was equally active for four organisms, although less active against Staphylococcus aureus. Replacement by the hydrophilic Ser8 strongly reduced potency against all five organisms. Deletion of Leu15 decreased activity, but addition of Thr16 maintained good activity. The presence of hydrophobic residues appears to have a significant effect on the process of antibacterial activity. These peptide analogues showed voltage-dependent conductance changes and are capable of forming ion-pores in planar lipid bilayers. The antibacterial action of the peptides is thought to be first an ionic interaction with the anionic phosphate groups of the membrane followed by interaction with the hydrocarbon core of the membrane and subsequent reorientation into amphipathic α-helical peptides that form pores (ion-channels), which span the membrane. The analogue also showed an increase in α-helicity with an increase in hexafluoro 2-propanol concentration.
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  • 44
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    Journal of Peptide Science 2 (1996), S. 233-239 
    ISSN: 1075-2617
    Keywords: NMR ; chemical shift estimation ; restrained refinement ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: For flexible peptides, nuclear Overhauser Effects (NOE) experiments do not provide enough information to ensure a correct definition of their solution structure. The use of distance constraints, derived from the knowledge of proton chemical shifts, is developed to restrict the number of possible conformations. In the case of flexible molecules, randomization appears as an important factor of the correct estimation of the chemical shifts from the 3D structure. The refinement of the solution structure of the highly flexible AVP-like parallel dimer is described to illustrate this process.
    Additional Material: 2 Ill.
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  • 45
    ISSN: 1075-2617
    Keywords: mucin glycopeptides ; tumour associated antigen ; cancer ; MHC Class II binding ; glycopeptide synthesis ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A series of peptides and glycopeptides derived by amino acid and glycosyl amino acid scans through the self peptide from CBA/J mouse haemoglobin Hb (67-76), VITAFNEGLK, was synthesized by multiple column peptide synthesis (MCPS). Investigation of glycopeptide binding to the mouse major histocompatibility class II molecule Ek showed that glycans in position 72 did not interfere with the binding to Ek. Immunization experiments revealed that glycopeptides with the glycan in position 72 were immunogenic. Therefore a series of N-linked and O-linked glycopeptides with the glycan attached in the position 72 either to serine, threonine or asparagine was synthesized by MCPS. The glycan structure was furthermore varied with respect to monosacc haride component, size of oligosaccharide, anomer configuration and stereoche mistry of essential hydroxyl groups in order to investigate the specificity of the interaction with the T-cell receptor. Easy synthesis of ready to use Ser and Thr building blocks corresponding to mucin core 1, the Tn-antigen and its β-anomer were developed using trichloroacetimidates as glycosyl donors and reduction with in situ acetylation of the azide containing glycosylation products. Synthesis of an α-linked GlcNAc-Thr building block was achieved by glycosylation of Fmoc-Thr-OPfp with 2-azido-2-deoxy-3,4,6-tri-O-acetyl-D- glycopyranosyl trichloroacetimidate as a glycosyl donor. Other building blocks were obtained by previously described procedures.
    Additional Material: 6 Ill.
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  • 46
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    Journal of Peptide Science 2 (1996), S. 195-211 
    ISSN: 1075-2617
    Keywords: peptide absorption ; dipeptide carrier ; brush border membrane ; M-cell, Caco-2 cell ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Today there is considerable interest in oral peptide delivery. However, oral administration of peptides is limited by a low bioavailability and a high variability in plasma levels. A review is given of the literature describing the major barriers in peptide absorption, the basic mechanisms of intestinal peptide transport, the experimental models and the pharmaceutical approaches currently used in the investigation of peptide and protein absorption processes.
    Additional Material: 4 Ill.
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  • 47
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    Journal of Peptide Science 2 (1996), S. 252-260 
    ISSN: 1075-2617
    Keywords: melittin immunogenicity ; antigen recognition ; membrane involvement ; haptenic position ; late IgG responses ; cellular dynamics ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Melittin peptides carrying 2,4-dinitro-6-carboxyphenyl (Dncp) haptenic groups regularly evoked anti-hapten IgG responses in mice or guinea pigs when the hapten was C-terminally attached. Single haptens on the N-terminal helix in several positions gave poor or no responses in the early stages but adequate titres after prolonged immunization. Peptides with Dncp at the C-terminus as an invariant feature and a second Dncp in various positions along the peptide chain did not fail to produce adequate responses. The hampering effect is not due to a defect at the T-cell level but involves the recognition step on the B-cell. It is implied that the haptenic interaction with the paratope of the recognizing immunoglob ulin on the B-cell involves the cell membrane in an important way. It is also suggested that late antibody responses should not be overlooked during the development of proteinaceous immunogens for vaccination.
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  • 48
    ISSN: 1075-2617
    Keywords: substance P ; agonist ; conformational constraint ; backbone cyclization ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Novel backbone-to-side chain and backbone-to-backbone cyclic analogues of substance P (SP) were prepared by solid-phase synthesis and screened for biological activity. An analogue containing a thioether- lactam ring between positions 9 and 11 showed an EC50 value of 20nM toward the neurokinin 1 (NK-1) and was inactive toward the NK-2 and NK-3 receptors. On the other hand, in a multiple backbone cyclic peptide library of similar analogues, in which the sulphur was excluded from the ring, very low activity was detected. The activity was re-evaluated and was found to be even lower (EC50=0.11 mM) than the previously published data. These results indicate that the thioether moiety has a crucial role in receptor activation. The results also show tolerance of the NK-1 receptor, but not NK-2 or NK-3, to cyclization of the C-terminal portion of the SP6-11 hexapeptide.
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  • 49
    ISSN: 1075-2617
    Keywords: opioid peptides ; selectivity ; antagonism ; conformation ; NMR ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The sequence of deltorphin I, a δ-selective opioid agonist, has been systematically modified by inserting conformationally constrained Cα,α disubstituted apolar residues in the third position. As expected, substitution of Phe with Ac6c, Ac5c and Ac3c yields analogues with decreasing but sizeable affinity. Surprisingly, substitution with Aib yields an analogue with almost the same binding affinity of the parent compound but with a greatly increased selectivity. This is the first case of a potent and very selective opioid peptide containing a single aromatic residue in the message domain, that is, only Tyr1. Here we report a detailed conformational analysis of [Aib3]deltorphin I and [Ac6c3]deltorphin I in DMSO at room temperature and in a DMSO/water cryomixture at low temperature, based on NMR spectroscopy and energy calculations. The peptides are highly structured in both solvents, as indicated by the exceptional finding of a nearly zero temperature coefficient of Val5 NH resonance. NMR data cannot be explained on the basis of a single structure but it was possible to interpret all NMR data on the basis of a few structural families. The conformational averaging was analysed by means of an original computer program that yields qualitative and quantitative composition of the mixture. Comparison of the preferred solution conformations with two rigid δ-selective agonists shows that the shapes of [Aib3]deltorphin I and [Ac6c3]deltorphin I are consistent with those of rigid agonists and that the message domain of opioid peptides can be defined only in conformational terms.
    Additional Material: 7 Ill.
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  • 50
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    Journal of Peptide Science 2 (1996), S. 318-324 
    ISSN: 1075-2617
    Keywords: p53 protein ; peptide immunomodulators ; TP5 analogues ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Taking into account the sequence homology existing between thymopoietin II and the DNA-binding domain of p53 protein, a series of octapeptides was synthesized, related to the wild p53 type protein as well as to its mutated forms, appearing in some human tumours. The wild type octapeptide has immunostimulative activity with regard to the humoral immune response, but is inactive in the cellular immune response. The mutated peptides of p53 differ in their immunomodulatory activity from the wild type octapeptide. The Ser5 analogue of the wild type peptide is a strong stimulant of the humoral immune response and enhances TNF-α production, while at the same time suppressing the cellular immune response. The data suggest that the mutations of p53, which favour tumour development and growth, may also change the immune activity of respective p53 fragments.
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  • 51
    ISSN: 1075-2617
    Keywords: conformational constraints ; CD spectroscopy ; fluorescence quenching ; synthetic peptides ; tyrosine phosphorylation ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We synthesized by classical solution methods three conformational constrained analogues of EDNEYTA, a heptapeptide sequence that represents the common major autophosphorylation site of the protein tyrosine kinases (PTKs) of the Src family. The correlation between the different structural properties induced by the modifications of the native sequence and the propensity of the peptides to act as PTK substrates was examined. The kinetic data obtained indicate that the introduction of the tyrosine-analogue constraints Tic(OH) and MeTyr, which block the ring flexibility, completely prevents the phosphorylation catalysed by the kinases Lyn and Fgr. On the other hand PTKIIB/p38syk can phosphorylate the two derivatives albeit with an efficiency lower than that found with the native sequence. A third derivative contained side chain to side chain cyclization. This analogue, in which the freedom of the phenolic moiety is not altered, can be phosphorylated by all the PTKs tested with kinetic constants comparable to the parent peptide.
    Additional Material: 11 Ill.
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  • 52
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    Journal of Peptide Science 2 (1996) 
    ISSN: 1075-2617
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 53
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    Journal of Peptide Science 2 (1996), S. 351-356 
    ISSN: 1075-2617
    Keywords: DPDPE ; enkephalins ; NMR structure analysis ; molecular dynamics simulations ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solution conformation of [D-Pen2,D-Pen5] enkephalin (DPDPE), a highly potent δ-selective opioid agonist, was examined by means of NMR, molecular mechanics and molecular dynamics methods. The structural information in the solvent water was obtained employing one- and two-dimensional methods of 1H and 13C-NMR spectroscopy. Based on the distance geometry technique using the ROE data as input, 400 conformers were obtained and considered in the structure analysis. Alternatively, about 2000 conformers were stochastically generated and related to the NMR data after energy minimization. The structure analysis provides one conformer in agreement with all NMR data, which belongs to the lowest energy conformation group. This structure may serve as a reference conformer for DPDPE analogues synthesized with the aim of activity increase.
    Additional Material: 1 Ill.
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  • 54
    ISSN: 1075-2617
    Keywords: Biosynthesis ; deuterium ; nitrogen 15 ; positive ion FAB mass spectrometry ; ion channel-forming peptide ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A simple procedure for the preparation of the specifically labelled peptide antibiotic zervamicins IC, IIA and IIB has been developed. The zervamicin molecules are labelled with stable isotopes by culturing the Emericellopsis salmosynnemata on a well-defined synthetic medium containing the highly isotopically enriched amino acid. To obtain the peptide with the specifically and highly enriched amino acid residue, precautions have been taken to prevent any de novo biosynthesis of the particular amino acid from unlabelled precursors. The enrichment of the labelled peptide is determined by mass spectrometric analysis. Following this method we have incorporated [2′,4′, 5′,6′,7′-2H5]-L-Trp-1, [1′-15N]-L-Trp-1 and [2′, 3′,4′,5′,6′-2H5]-L- Phl-16 into zervamicins IC, IIA and IIB on the preparative scale and without scrambling of the label. Thus, using the procedures described, isotopically labelled zervamicins can be prepared, allowing them to be studied by solid- state NMR.
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  • 55
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    Journal of Peptide Science 2 (1996), S. 364-370 
    ISSN: 1075-2617
    Keywords: conformation ; glutamine ; folding ; simulation ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational preferences of the methylenic sequence in the side chain of the glutamine residue were investigated by ab initio and semi-empirical quantum mechanical calculations and examination of both the Brookhaven Protein Databank and Cambridge Structural Data Base. The results were analysed on the basis of our previous findings about the folding of methylene groups in aliphatic segments. Both energy calculations and the crystallographic structure of small peptides indicate that methylene units of the glutamine residue tend to fold in a gauche conformation. In contrast, such groups usually adopt an all-trans conformation in proteins due basically to the entropic and solvent contributions. These results have been demonstrated by computing the entropic correction to the free energy and evaluating the solvent effects through SCRF calculations
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  • 56
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    Journal of Peptide Science 2 (1996) 
    ISSN: 1075-2617
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 57
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    Journal of Peptide Science 2 (1996), S. 381-391 
    ISSN: 1075-2617
    Keywords: conformational analysis ; crystal structure ; folded structures ; pseudopeptides ; reduced peptides ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Reduced dipeptides with the general formula RCO-Xaa- rXbb-N+HR′R′′ (rXbb, reduced analogue of residue Xbb: NH-Cα HR1 -Cr H2) are shown to adopt a folded conformation in solution and in the solid state. The protonated reduced amide bond is an active proton donor capable of interacting with a peptide carbonyl to give a strong hydrogen bond topologically equivalent to the i+2 or i+3⇒ i interaction. The resulting conformation is similar to the γ- or β-turn structure found in peptides and proteins.
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  • 58
    ISSN: 1075-2617
    Keywords: β-turns ; folded conformation ; dehydro-residue ; X-ray diffraction ; consecutive dehydro-residue ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: To obtain general rules of peptide design using α,β-dehydro-residues, a sequence with two consecutive ΔPhe-residues, Boc-L-Val-ΔPhe-ΔPhe- L-Ala-OCH3, was synthesized by azlactone method in solution phase. The peptide was crystallized from its solution in an acetone/water mixture (70:30) in space group P61 with a=b=14.912(3)  Å, c= 25.548(5)  Å, V=4912.0(6)  Å3. The structure was determined by direct methods and refined by a full matrix least-squares procedure to an R value of 0.079 for 2891 observed [I≥3σ(I)] reflections. The backbone torsion angles φ1=-54(1)°, ψ1= 129(1)°, ω1=-177(1)°, φ2 =57(1)°, ψ2=15(1)°, ω2 =-170(1)°, φ3=80(1)°, ψ3 =7(2)°, ω3=-177(1)°, φ4 =-108(1)° and ψT4=-34 (1)° suggest that the peptide adopts a folded conformation with two overlapping β-turns of types II and III′. These turns are stabilized by two intramolecular hydrogen bonds between the CO of the Boc group and the NH of ΔPhe3 and the CO of Val1 and the NH of Ala4. The torsion angles of ΔPhe2 and ΔPhe3 side chains are similar and indicate that the two ΔPhe residues are essentially planar. The folded molecules form head-to- tail intermolecular hydrogen bonds giving rise to continuous helical columns which run parallel to the c-axis. This structure established the formation of two β-turns of types II and III′ respectively for sequences containing two consecutive ΔPhe residues at (i+2) and (i+3) positions with a branched β-carbon residue at one end of the tetrapeptide.
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  • 59
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    Numerical Linear Algebra with Applications 3 (1996), S. 65-80 
    ISSN: 1070-5325
    Keywords: boundary value problem ; boundary element method ; preconditioning ; iterative method ; fast Fourier transform ; parallel algorithm ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The parallel version of precondition iterative techniques is developed for matrices arising from the panel boundary element method for three-dimensional simple connected domains with Dirichlet boundary conditions. Results were obtained on an nCube-2 parallel computer showing that preconditioned iterative methods are very well suited also in three-dimensional cases for implementation on an MIMD computer and that they are much more efficient than usual direct solution techniques.
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    Numerical Linear Algebra with Applications 3 (1996), S. 91-93 
    ISSN: 1070-5325
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
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    Numerical Linear Algebra with Applications 3 (1996) 
    ISSN: 1070-5325
    Keywords: Engineering ; Engineering General
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    Numerical Linear Algebra with Applications 3 (1996), S. 345-348 
    ISSN: 1070-5325
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
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    Numerical Linear Algebra with Applications 3 (1996), S. 391-411 
    ISSN: 1070-5325
    Keywords: finite difference discretization ; fast adaptive composite grid method ; convergence rate ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The fast adaptive composite grid (FAC) method is an iterative method for solving discrete boundary value problems on composite grids. McCormick introduced the method in [8] and considered the convergence behaviour for discrete problems resulting from finite volume element discretization on composite grids. In this paper we consider discrete problems resulting from finite difference discretization on composite grids. We distinguish between two obvious discretization approaches at the grid points on the interfaces between fine and coarse subgrids. The FAC method for solving such discrete problems is described. In the FAC method several intergrid transfer operators appear. We study how the convergence behaviour depends on these intergrid transfer operators. Based on theoretical insights, (quasi-)optimal intergrid transfer operators are derived. Numerical results illustrate the fast convergence of the FAC method using these intergrid transfer operators.
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    Numerical Linear Algebra with Applications 3 (1996) 
    ISSN: 1070-5325
    Keywords: Engineering ; Engineering General
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    Topics: Mathematics
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    Numerical Linear Algebra with Applications 3 (1996), S. 459-471 
    ISSN: 1070-5325
    Keywords: alternating projection method ; Dykstra's algorithm ; patterned matrix ; constrained least-squares ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We apply Dykstra's alternating projection algorithm to the constrained least-squares matrix problem that arises naturally in statistics and mathematical economics. In particular, we are concerned with the problem of finding the closest symmetric positive definite bounded and patterned matrix, in the Frobenius norm, to a given matrix. In this work, we state the problem as the minimization of a convex function over the intersection of a finite collection of closed and convex sets in the vector space of square matrices.We present iterative schemes that exploit the geometry of the problem, and for which we establish convergence to the unique solution. Finally, we present preliminary numberical results to illustrate the performance of the proposed iterative methods.
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    Numerical Linear Algebra with Applications 3 (1996), S. 125-145 
    ISSN: 1070-5325
    Keywords: orthogonalization ; QR factorization ; polar decomposition ; subspace tracking ; error analysis ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We consider the problem of computing Uk = QkUk-1(where U0 is given) in finite precision (εM = machine precision) where U0 and theQi are known to be unitary. The problem is that Ûk, the computed product may not be unitary, so one applies an O(n2) orthogonalizing step after each multiplication to(a) prevent Ûk from drifing too far from the set of untary matrices(b) prevent Ûk from drifting too far from Uk the true product.Our main results are1. Scaling the rows to have unit length after each multiplication (the cheaptest of the algorithms considered) is usually as good as any other method with respect to either of the criteria (a) or (b).2. A new orthogonalization algorithm that guarantees the distance of Ûk (k = 1, 2, …) to the set of unitary matrices is bounded by n3.5εM for any choice of Qi.
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    Numerical Linear Algebra with Applications 3 (1996) 
    ISSN: 1070-5325
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
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    Numerical Linear Algebra with Applications 3 (1996), S. 147-159 
    ISSN: 1070-5325
    Keywords: elasticity ; finite-element ; multilevel ; a posteriori error estimation ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The constant γ in the strengthened Cauchy-Buniakowski-Schwarz (C.B.S.) inequality plays a crucial role in the convergence rate of multilevel iterative methods as well as in the efficiency of a posteriori error estimators, that is in the framework of finite element approximations of SPD problems.We consider the approximation of the 2D elasticity problem by the Courant element. Concerning multilevel convergence rate, that is the γ corresponding to nested general triangular meshes of size h and 2h, we have proved that γ2≤ 3/4$ uniformly on the mesh and the Poisson ratio. Concerning error estimator, that is the γ corresponding to quadratic and linear approximations on the same mesh, numerical computations have shown that the exact γ for a reference element deteriorates that is goes to one, when the Poisson ratio tends to 1/2
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    Numerical Linear Algebra with Applications 3 (1996), S. 161-172 
    ISSN: 1070-5325
    Keywords: smoothing property ; multigrid method ; semi-iterative smoother ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In this paper we present an extension of Reusken's Lemma about the smoothing property of a multigrid method for solving non-symmetric linear systems of equations. One of the consequences of this extended lemma is the verification of the smoothing property for all damping factors οε(0, 1). Additionally, a semi-iterative smoother is constructed which gives, in some sense, optimal smoothing rate estimates.
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    Numerical Linear Algebra with Applications 3 (1996), S. 179-183 
    ISSN: 1070-5325
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
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    Numerical Linear Algebra with Applications 3 (1996), S. 185-203 
    ISSN: 1070-5325
    Keywords: orthotropic partial differential equation ; preconditioned conjugate gradient method ; parallel algorithm ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: Finite element meshes and node-numberings suitable for parallel solution with equally loaded processors are presented for linear orthotropic elliptic partial differential equations. These problems are of great importance, for instance in the oil and airfoil industries. The linear systems of equations are solved by the conjugate gradient method preconditioned by modified incomplete factorization, MIC. The basic method presented, is based on fronts of uncoupled nodes and unlike earlier methods it has the advantage of no requirement of a specific orientation of the mesh. This method is however, in general, restricted to small degree of anisotropy in the differential equation. Another method, which does not suffer from this limitation, uses rotation of the differential equation and spectral equivalence. The rotation is made in such a way that in the new co-ordinate system, the basic method is applicable. The spectral equivalence property is used for estimation of the condition number of the preconditioned system. Both methods are suitable for implementation on parallel computers. The computer architecture could be single instruction multiple data (SIMD) as well as multiple instruction multiple data (MIMD) with shared or distributed memory. Implementation of the basic method on a shared memory parallel computer shows a significant improvement by use of the MIC method compared with the diagonal scaling preconditioning method.
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    Numerical Linear Algebra with Applications 3 (1996), S. 221-237 
    ISSN: 1070-5325
    Keywords: sparse matrix ; iterative methods ; preconditioning ; graph partitioning ; domain decomposition ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: Domain decomposition methods for finite element problems using a partition based on the underlying finite element mesh have been extensively studied. In this paper, we discuss algebraic extensions of the class of overlapping domain decomposition algorithms for general sparse matrices. The subproblems are created with an overlapping partition of the graph corresponding to the sparsity structure of the matrix. These algebraic domain decomposition methods are especially useful for unstructured mesh problems. We also discuss some difficulties encountered in the algebraic extension, particularly the issues related to the coarse solver.
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    Numerical Linear Algebra with Applications 3 (1996), S. 205-220 
    ISSN: 1070-5325
    Keywords: elliptic equations ; multilevel methods ; finite element ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: New uniform estimates for multigrid algorithms are established for certain non-symmetric indefinite problems. In particular, we are concerned with the simple additive algorithm and multigrid (V(1,0)-cycle) algorithms given in [5]. We prove, without full elliptic regularity assumption, that these algorithms have uniform reduction per iteration, independent of the finest mesh size and number of refinement levels, provided that the coarsest mesh size is sufficiently small.
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    Numerical Linear Algebra with Applications 3 (1996) 
    ISSN: 1070-5325
    Keywords: Engineering ; Engineering General
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    Topics: Mathematics
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    Numerical Linear Algebra with Applications 3 (1996), S. 239-249 
    ISSN: 1070-5325
    Keywords: non-linear equations ; global convergence ; Lagrangians ; non-linear programming ; Lagrangian globalization ; detour potentials ; homotopy methods ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The Lagrangian globalization (LG) method for non-linear equation-solving proposed in [10] is developed through theoretical analysis, the formulation of a particular LG algorithm, and a numerical illustration. New merit functions (termed detour potentials) for non-linear equation-solving, which broaden the LG concept, are also defined.
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    Numerical Linear Algebra with Applications 3 (1996), S. 251-254 
    ISSN: 1070-5325
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
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    Numerical Linear Algebra with Applications 3 (1996), S. 255-274 
    ISSN: 1070-5325
    Keywords: conjugate gradient method ; preconditioning ; two-level method ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The presented paper contains a suggestion and an analysis of a two-level preconditioner appropriate for unstructured meshes. The convergence analysis is done for H1-equivalent forms in the two-dimensional case; ways for generalization are discussed, too. The efficiency is demonstrated by numerical experiments.
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    Numerical Linear Algebra with Applications 3 (1996), S. 329-343 
    ISSN: 1070-5325
    Keywords: iterative methods ; GMRES ; Krylov methods ; incomplete orthogonalization ; quasi-minimization ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: We describe a Krylov subspace technique, based on incomplete orthogonalization of the Krylov vectors, which can be considered as a truncated version of GMRES. Unlike GMRES(m), the restarted version of GMRES, the new method does not require restarting. Like GMRES, it does not break down. Numerical experiments show that DQGMRES(k) often performs as well as the restarted GMRES using a subspace of dimension m=2k. In addition, the algorithm is flexible to variable preconditioning, i.e., it can accommodate variations in the preconditioner at every step. In particular, this feature allows the use of any iterative solver as a right-preconditioner for DQGMRES(k). This inner-outer iterative combination often results in a robust approach for solving indefinite non-Hermitian linear systems.
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    Numerical Linear Algebra with Applications 3 (1996), S. 81-90 
    ISSN: 1070-5325
    Keywords: linear systems ; regularization ; divided differences ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: A regularization procedure for linear systems of the type fi(zj)xi = g(zj), (j = 1, 2, …, n) is presented, which is particularly useful in the case when z1, z2, …, zn are close to each other. The associated numerical algorithm was tested on several examples for which analytic solutions do exist and was found to yield highly accurate results.
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    Numerical Linear Algebra with Applications 3 (1996), S. 301-327 
    ISSN: 1070-5325
    Keywords: information ; latent semantic indexing ; low-rank ; orthogonal ; matrices ; metrieval ; singular value decomposition ; sparse ; ULV and URV decompositions ; updating ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: Current methods to index and retrieve documents from databases usually depend on a lexical match between query terms and keywords extracted from documents in a database. These methods can produce incomplete or irrelevant results due to the use of synonyms and polysemus words. The association of terms with documents (or implicit semantic structure) can be derived using large sparse {\it term-by-document} matrices. In fact, both terms and documents can be matched with user queries using representations in k-space (where 100 ≤ k ≤ 200) derived from k of the largest approximate singular vectors of these term-by-document matrices. This completely automated approach called latent semantic indexing or LSI, uses subspaces spanned by the approximate singular vectors to encode important associative relationships between terms and documents in k-space. Using LSI, two or more documents may be closeto each other in k-space (and hence meaning) yet share no common terms. The focus of this work is to demonstrate the computational advantages of exploiting low-rank orthogonal decompositions such as the ULV (or URV) as opposed to the truncated singular value decomposition (SVD) for the construction of initial and updated rank-k subspaces arising from LSI applications.
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    Numerical Linear Algebra with Applications 3 (1996), S. 369-390 
    ISSN: 1070-5325
    Keywords: multigrid ; incomplete Gaussian elimination ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: In this paper we introduce and analyse a new Schur complement approximation based on incomplete Gaussian elimination. The approximate Schur complement is used to develop a multigrid method. This multigrid method has an algorithmic structure that is very similar to the algorithmic structure of classical multigrid methods. The resulting method is almost purely algebraic and has interesting properties with respect to variation in problem parameters.
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    Numerical Linear Algebra with Applications 3 (1996), S. 351-367 
    ISSN: 1070-5325
    Keywords: multilevel preconditioning ; Krylov subspace methods ; GMRES, nonsymmetric elliptic problems ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics
    Notes: The subject of this paper is to study the performance of multilevel preconditioning for nonsymmetric elliptic boundary value problems. In particular, a minimal residual method with respect to an appropriately scaled norm, measuring the size of the residual projections on all levels, is studied. This norm, induced by the multilevel splitting, is also the basis for a proper stopping criterion. Our analysis shows that the convergence rate of this minimal residual method using the multilevel preconditioner by Bramble, pasciak and Xu is bounded independently of the mesh-size. However, the convergence rate deteriorates with increasing size of the skew-symmetric part. Our numerical results show that by incorporating this into a multilevel cycle starting on the coarsest level, one can save fine-level-iterations and, therefore, computational work.
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    Journal of Peptide Science 2 (1996), S. 245-251 
    ISSN: 1075-2617
    Keywords: enkephalin ; neurotensin ; opioid receptor affinity ; multivalent ligand ; liposome ; fluorescence microscopy ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A multivalent ligand system was constructed by coimmobilization of two kinds of peptide ligands, enkephalin and neurotensin derivatives having a dioctadecyl group, on dimyristoylphosphatidylcholine (DMPC) liposomes. The enkephalin derivatives are Tyr-D-Ala-Gly-Trp-Leu- (Sar-Sar-Pro)n-[N(C18H37)2] (Enk3nD, n=0, 1, 2), where a dioctadecyl group was connected to the C-terminal side of enkephalin directly or through a hydrophilic and flexible spacer chain of different lengths. The neurotensin derivatives are Ac-Glu[N(C18H37)2]-(Sar-Sar-Pro)n-Arg-Arg-Pro-Tyr-Ile-Leu-OH (D3nNT, n=0, 1, 2, 3). The derivatives were spontaneously immobilized on DMPC liposomes by overnight incubation. The receptor affinity of the enkephalin derivatives became significantly higher upon immobilization on liposomes. The highest affinity was obtained for the δ receptor by Enk6D immobilized on DMPC liposomes. This affinity is higher than that of enkephalinamide. Neurotensin derivatives coimmobilized with large amounts of Enk3D on DMPC liposomes show higher affinity than the neurotensin derivatives immobilized alone. The effect of Enk3D on the receptor affinity of the coimmobilized neurotensin derivative disappeared by the addition of [Ala2, MePhe4, Gly-ol5]enkephalin (DAGO). Therefore, the receptor affinity of a peptide hormone is altered by immobilization on DMPC liposomes and by coimmobilization with other peptide hormones. It was confirmed by fluorescent microscopy that the multivalent ligand system binds to receptors without release of the bound ligands from DMPC liposomes.
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    Journal of Peptide Science 2 (1996) 
    ISSN: 1075-2617
    Keywords: Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Journal of Peptide Science 2 (1996), S. 271-275 
    ISSN: 1075-2617
    Keywords: peptide synthesis ; cysteine ; racemization ; enantiomeric resolution ; capillary electrophoresis ; gas chromatography ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new method has been developed for the rapid determination of D-cysteine contents in synthetic peptides. It is based on the reduction of cystine residues, when present, with tris- alkylphosphines, selective derivatization of the cysteine residues with 4-vinylpyridine, followed by acid hydrolysis of the (4-pyridylethyl)cysteine -peptides. Baseline enantiomeric resolution of theD,L-S-β-(4-pyridylethyl)cysteine, and thus quantification ofD- enantiomer contents at levels ≤1%, is easily achieved by capillary zone electrophoresis exploiting the host-guest complexation principle with crown ethers or by gas chromatography on chiral glass capillary columns upon conventional derivatization of the hydrolysate. The acid-stability of the (4-pyridylethyl)cysteine derivative prevents racemization via thiazoline intermediates and allows for standardization of the acid hydrolysis-dependent racemization.
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    Journal of Peptide Science 2 (1996), S. 240-244 
    ISSN: 1075-2617
    Keywords: solid-phase synthesis ; peptide synthesis ; multiple synthesis ; inclusion volume synthesis ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solid-phase synthesis of peptides was carried out using only the volume of the solvent included in the swollen solid-phase resin beads [inclusion volume synthesis]. This approach enables (i) the use of higher concentrations of activated amino acids, resulting in increased coupling rates, (ii) drastically decreased consumption of solvents, and (iii) the construction of multiple peptide synthesizers having virtually no reaction vessels.
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    Journal of Peptide Science 2 (1996), S. 309-317 
    ISSN: 1075-2617
    Keywords: solid-phase synthesis ; calcium channel blocker ; spider toxins ; side reaction ; peptide folding ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ω-Agatoxin IVA, isolated from the venom of funnel web spider Agelenopsis aperta, blocks potently and selectively P-type calcium channels. This toxin, composed of 48 amino acids and containing 8 cysteine residues, was synthesized by the solid-phase procedure. The Cys residues were protected by acetamidomethyl (Acm) groups which were removed by mercuric acetate. During treatment with mercuric acetate, a by-product was detected, involving modification of tryptophan residues by the Acm groups. This side reaction can be completely prevented by addition of an excess of tryptophan in the reaction medium during Acm deprotection.The resulting peptide was submitted to an oxidative refolding, in different conditions, in order to determine the most favourable protocol. After formation of the four disulphide bonds, the toxin was purified by successive preparative HPLC, on two different supports, and fully characterized by analytical HPLC, capillary electrophoresis, amino acid analysis, mass spectrometry and Edman degradation. It was found to block the P-type calcium channel with a similar biological potency as described for the natural product.
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    Journal of Peptide Science 2 (1996), S. 279-289 
    ISSN: 1075-2617
    Keywords: peptide synthesis ; frozen aqueous solution ; protease ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: During the past decade proteases have been widely used as catalysts in peptide synthesis. Unfortunately, they are not ideal ligases. Enzymatic peptide synthesis in frozen aqueous systems has been developed as an approach towards the suppression of competitive reactions. This paper summarizes reports concerning the behaviour of non-enzymatic as well as of enzyme-catalysed reactions when the reaction mixture is frozen. The advantages of freezing the reaction mixture in serine and cysteine protease-catalysed peptide synthesis, the influence of modified reaction conditions and the possible reasons for the yield-increasing effect of freezing are discussed.
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    Communications in Numerical Methods in Engineering 12 (1996), S. 43-50 
    ISSN: 1069-8299
    Keywords: view factor ; radiation ; parallel computation ; heat transfer ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: Two implementations for parallel computation of radiation heat transfer view factors are formulated and tested for a model problem. Using a sufficiently large number of processors and a suitable communications paradigm, the solution time for the problem considered here scales linearly with the number of surface elements in the parallel implementation rather than the quadratic scaling obtained using a serial approach. For larger problems, significantly shorter solution times are obtained using the massively parallel Connection Machine 5 than those obtained on a single processor of the Cray C-90, a traditional vector supercomputer. Parallel performance was degraded for implementations using too few processors or data layouts leading to inefficient processor communication.
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    Communications in Numerical Methods in Engineering 12 (1996), S. 51-62 
    ISSN: 1069-8299
    Keywords: boundary element method ; hypersingular integrals ; singular integration ; elasticity ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: An algorithm based on the Taylor series expansion is extended to deal with the problem of near-hypersingular integrals occurring in a 3D electrostatic BEM formulation. The integral is evaluated by subtracting out the leading terms in the near-hypersingular part of the integrand and adding it back. The accuracy of the proposed method is demonstrated for a curved element. It is shown that accurate values can be obtained with low orders of Gaussian quadrature.
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    Communications in Numerical Methods in Engineering 12 (1996) 
    ISSN: 1069-8299
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
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    Communications in Numerical Methods in Engineering 12 (1996), S. 147-148 
    ISSN: 1069-8299
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Type of Medium: Electronic Resource
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  • 93
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    Electronic Resource
    Chichester : Wiley-Blackwell
    Communications in Numerical Methods in Engineering 12 (1996), S. 149-150 
    ISSN: 1069-8299
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Type of Medium: Electronic Resource
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  • 94
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    Electronic Resource
    Chichester : Wiley-Blackwell
    Communications in Numerical Methods in Engineering 12 (1996), S. 63-73 
    ISSN: 1069-8299
    Keywords: asymptotic solution ; natural frequencies ; membrane vibrations ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: In the paper an asymptotic formula has been developed to correct the discretization error for the finite element predicted natural frequencies of membrane transverse vibration problems. The general idea behind deriving this asymptotic formula is that, when the finite element size approaches zero, a discretized finite element system approaches a continuous system and the predicted natural frequencies of the system from the finite element analysis therefore approach the exact solutions of the system. Without losing generality, several different finite element mesh patterns have been considered and the same asymptotic formula for correcting the finite element predicted natural frequency has been obtained for all the different mesh patterns because of the uniqueness of the exact solution to the natural frequency of a real structure. The usefulness, effectiveness and efficiency of the present asymptotic formula have been assessed by a simple but critical problem, for which the exact solution is available for comparison. In order to investigate the applicability of the asymptotic formula to practical engineering problems, two challenging membrane vibration problems of irregular shapes, an L-shape and a tapered shape with a circular hole in the centre, have also been analysed. The related numerical results have demonstrated that the asymptotic formula provides a very useful post-processing error corrector for the finite element predicted natural frequencies of membrane transverse vibration problems, even though the problem domains are of irregular shape. The greatest advantage in using the present asymptotic formula is that it yields a solution of higher accuracy, by simply using the formula to correct the rough solution obtained from a much coarser finite element mesh with fewer degrees of freedom, without any further finite element calculation.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 95
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    Electronic Resource
    Chichester : Wiley-Blackwell
    Communications in Numerical Methods in Engineering 12 (1996), S. 77-83 
    ISSN: 1069-8299
    Keywords: eigenvalue extraction ; conjugate gradient method ; finite element method ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: A new conjugate gradient algorithm is presented for extracting eigenvalues from large systems of equations encountered in finite element analysis. The new algorithm involves applying the conjugate gradient method (CGM) to a static problem to generate an equivalent tridiagonal matrix used for eigenvalue computation. The eigenvalues of the tridiagonal matrix are then extracted using a QR factorization. The similarity of the new CGM with the Lanczos method is discussed regarding the need for matrix inversion and reorthogonalization. Several examples using the new method are presented to illustrate its performance.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 96
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    Communications in Numerical Methods in Engineering 12 (1996), S. 185-196 
    ISSN: 1069-8299
    Keywords: homogenization ; boundary conditions ; periodicity ; finite element ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: The numerical solution of homogenization equations by the finite element (FE) method is explained briefly. The issue of extracting boundary conditions from the periodicity assumption is addressed and a direct method utilizing symmetry is presented. Using this method, the computation of the elements of the constitutive matrix of a composite material is reduced to a very conventional boundary value problem with known forces and boundary conditions which can be carried out with any FE code. Two examples are presented.
    Additional Material: 15 Ill.
    Type of Medium: Electronic Resource
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  • 97
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    Communications in Numerical Methods in Engineering 12 (1996) 
    ISSN: 1069-8299
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Type of Medium: Electronic Resource
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  • 98
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    Electronic Resource
    Chichester : Wiley-Blackwell
    Communications in Numerical Methods in Engineering 12 (1996), S. 229-234 
    ISSN: 1069-8299
    Keywords: higher-order beam element ; best-fit stress prediction ; a priori error analysis ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: It is known that finite elements try to capture stresses within each discretized local region in a ‘best-fit’ sense. In the paper we examine the performance of a beam element based on a higher-order shear deformation theory and show that the best-fit paradigm accounts for the manner in which through-the-thickness displacement and stresses are modelled. An a priori prediction derived from the paradigm is confirmed by a carefully chosen numerical experiment. This provides a measure of the quality of approximation as well as another ‘falsification’ of the best-fit paradigm.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 99
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    Electronic Resource
    Chichester : Wiley-Blackwell
    Communications in Numerical Methods in Engineering 12 (1996), S. 223-228 
    ISSN: 1069-8299
    Keywords: Discretization ; heat conduction ; simulation ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: A different approach to discretization is described with which complicated three-dimensional heat transfer problems can be solved with a finite volume approach on a general curvilinear grid. It represents an improvement on the existing methods in that it can easily be expanded to three-dimensional problems. A concise explanation of the transformation process is given, together with a discussion of the discretization procedure. The method is evaluated by solving two simple test problems and comparing the results with those of existing methods and the analytical solution. In conclusion it is found that this method yields equally or more accurate results than the existing methods, with the additional advantage of being easily expandable to three-dimensional problems.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 100
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    Communications in Numerical Methods in Engineering 12 (1996), S. 243-248 
    ISSN: 1069-8299
    Keywords: finite elements ; automatic generation ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: Finite element generation methods, such as Delaunay, allow the meshing of shapes from a set of nodes. These nodes must previously exist. The authors present a simple, fast and reliable method to generate them in an unstructured way in N-dimensional space. Its main characteristic is to easily allow variation of the node density by introducing a density function, either analytical or discretized. This function can also be anisotropic. Some nodes can have a pre-fixed position. Inner lines and holes can also be specified in the domain to be meshed. Generated nodes are to be connected according to triangles in 2D and tetrahedrals in 3D.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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