bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sigmoidal cosine series on the interval
Authors: Yun Beong In 
Published: February 2009

AbstractWe construct a set of functions, say, composed of a cosine function and a sigmoidal transformation γr of order r > 0. The present functions are orthonormal with respect to a proper weight function on the interval [−1, 1]. It is proven that if a function f is continuous and piecewise smooth on [−1, 1] then its series expansion based on converges uniformly to f so long as the order of the sigmoidal transformation employed is 0 < r ≤ 1. Owing to the variational feature of according to the value of r, one can expect improvement of the traditional Fourier series approximation for a function on a finite interval. Several numerical examples show the efficiency of the present series expansion in comparison with the Fourier series expansion.
A closed-form analytical solution for the valuation of convertible bonds with constant dividend yield
Authors: Zhu Song-Ping 
Published: February 2009

AbstractIn this paper, a closed-form analytical solution for pricing convertible bonds on a single underlying asset with constant dividend yield is presented. A closed-form analytical formula has apparently never been found for American-style convertible bonds (CBs) of finite maturity time although there have been quite a few approximate solutions and numerical approaches proposed. The solution presented here is written in the form of a Taylor's series expansion, which contains infinitely many terms, and thus is completely analytical and in a closed form. Although it is only for the simplest CBs without call or put features, it is nevertheless the first closed-form solution that can be utilised to discuss convertibility analytically. The solution is based on the homotopy analysis method, with which the optimal converting price has been elegantly and temporarily removed in the solution process of each order, and consequently, the solution of a linear problem can be analytically worked out at each order, resulting in a completely analytical solution for the optimal converting price and the CBs' price.
Robustness with respect to small delays for exponential stability of abstract differential equations in Banach spaces
Authors: Guo Faming , Tang Bin , Huang Falun 
Published: February 2009

AbstractThis paper is concerned with robustness with respect to small delays for the exponential stability of abstract differential equations in Banach spaces. Some necessary and sufficient conditions are given in terms of the uniformly square integrability of the fundamental operator family and the uniform boundedness of its resolvent on the imaginary axis.
A note on the small-time development of the solution to a coupled, nonlinear, singular reaction-diffusion system
Authors: Leach J. A. 
Published: February 2009

AbstractIn this paper, we consider a coupled, nonlinear, singular (in the sense that the reaction terms in the equations are not Lipschitz continuous) reaction-diffusion system, which arises from a model of fractional order chemical autocatalysis and decay, with positive initial data. In particular, we consider the cases when the initial data for the the dimensionless concentration of the autocatalyst, β, is of (a) O(x−λ) or (b) O(e−σ x) at large x (dimensionless distance), where σ > 0 and λ are constants. While initially the dimensionless concentration of the reactant, α, is identically unity, we establish, by developing the small-t (dimensionless time) asymptotic structure of the solution, that the support of β(x, t) becomes finite in infinitesimal time in both cases (a) and (b) above. The asymptotic form for the location of the edge of the support of β as t → 0 is given in both cases.
The Wiener-Hopf integral equation for fractional Riesz-Bessel motion
Authors: Anh V. V. , Grecksch W. , Angulo J. M. , Ruiz-Medina M. D. 
Published: February 2009

AbstractThis paper gives an approximate solution to the Wiener-Hopf integral equation for filtering fractional Riesz-Bessel motion. This is obtained by showing that the corresponding covariance operator of the integral equation is a continuous isomorphism between appropriate fractional Sobolev spaces. The proof relies on properties of the Riesz and Bessel potentials and the theory of fractional Sobolev spaces.
Sinc approximation of Cauchy-type integrals over arcs
Authors: Stenger Frank 
Published: February 2009

AbstractIn 1984, Elliott and Stenger wrote a joint paper on the approximation of Hilbert transforms over analytic arcs. In the present paper we sharpen the previously obtained results of Elliott and Stenger, and we also obtain formulas for approximating Cauchy integrals over analytic arcs.
A quadrature method for constant-coefficient Cauchy singular integral equations on an interval
Authors: Jeon Youngmok 
Published: February 2009

AbstractWe consider a mesh grading quadrature method for real constant-coefficient Cauchy singular integral equations of index 0. The quadrature method is based on the trapezoidal rule. A complete stability and convergence analysis is given by the use of the noncompact perturbation analysis as in Jeon [10] and Elschner and Stephan [7]. The order of convergence can be arbitrarily high if the order of mesh grading is high enough. We also provide an efficient way of evaluating asymptotics of the solution at the end points. Experimentally, we observe that the method also works well for Cauchy singular integral equations with variable coefficients.
Bilateral estimates of the critical Mach number for some classes of carrying wing profiles
Authors: Avkhadiev F. G. , Elizarov A. M. 
Published: February 2009

AbstractA problem of estimation of the critical Mach number for a class of carrying wing profiles with a fixed theoretical angle of attack is considered. The Chaplygin gas model is used to calculate the velocity field of the flow. The original problem is reduced to a special minimax problem. A solution is constructed for an extended class of flows including multivalent ones, hence M* is estimated from above. For a fixed interval [0, β0], β0 ≅ 3π/8, an estimate of M* is given from below.
Observer-based robust H∞, control for uncertain time-delay systems
Authors: Guan Xinping , Liu Yichang , Chen Cailian , Shi Peng 
Published: February 2009

AbstractIn this paper, we present a method for the construction of a robust observer-based H∞ controller for an uncertain time-delay system. Cases of both single and multiple delays are considered. The parameter uncertainties are time-varying and norm-bounded. Observer and controller are designed to be such that the uncertain system is stable and a disturbance attenuation is guaranteed, regardless of the uncertainties. It has been shown that the above problem can be solved in terms of two linear matrix inequalities (LMIs). Finally, an illustrative example is given to show the effectiveness of the proposed techniques.
Control of singularly perturbed Markov chains: A numerical study
Authors: Yang H. , Yin G. , Yin K. , Zhang Q. 
Published: February 2009

AbstractThis work is devoted to numerical studies of nearly optimal controls of systems driven by singularly perturbed Markov chains. Our approach is based on the ideas of hierarchical controls applicable to many large-scale systems. A discrete-time linear quadratic control problem is examined. Its corresponding limit system is derived. The associated asymptotic properties and near optimality are demonstrated by numerical examples. Numerical experiments for a continuous-time hybrid linear quadratic regulator with Gaussian disturbances and a discrete-time Markov decision process are also presented. The numerical results have not only supported our theoretical findings but also provided insights for further applications.
Minimal approximate Hessians for continuously Gâteaux differentiable functions
Authors: Li Hongxu , Huang Falun 
Published: February 2009

AbstractIn this paper, we investigate minimal (weak) approximate Hessians, and completely answer the open questions raised by V. Jeyakumar and X. Q. Yang. As applications, we first give a generalised Taylor's expansion in terms of a minimal weak approximate Hessian. Then we characterise the convexity of a continuously Gâteaux differentiable function. Finally some necessary and sufficient optimality conditions are presented.
The pressure field in the gas-lubricated step slider bearing
Authors: Penesis I. , Shepherd J. J. , Connell H. J. 
Published: February 2009

AbstractSingular perturbation methods are applied to an analysis of the operation of an isothermal gas step slider bearing of narrow geometry and operating at moderate bearing numbers. Approximate expressions are obtained for the pressure field in the lubricating gap, as well as the load-carrying capacity of the bearing; and the influence of the nature of the bearing step on those quantities is investigated. Comparisons are made with results obtained using a standard numerical package.
A solution method for combined semi-infinite and semi-definite programming
Authors: Li S. J. , Yang X. Q. , Teo K. L. , Wu S. Y. 
Published: February 2009

AbstractIn this paper, we develop a discretisation algorithm with an adaptive scheme for solving a class of combined semi-infinite and semi-definite programming problems. We show that any sequence of points generated by the algorithm contains a convergent subsequence; and furthermore, each accumulation point is a local optimal solution of the combined semi-infinite and semi-definite programming problem. To illustrate the effectiveness of the algorithm, two specific classes of problems are solved. They are relaxations of quadratically constrained semi-infinite quadratic programming problems and semi-infinite eigenvalue problems.
Phase-retardation effects at radio frequencies in flat-plate conductors
Authors: Bulte D. P. , Forbes L. K. , Crozier S. 
Published: February 2009

AbstractA system of new integral equations is presented. They are derived from Maxwell's equations and describe radio-frequency (RF) current densities on a two-dimensional flat plate. The equations are generalisations of Pocklington's integral equation showing phase-retardation in two dimensions. These singular equations are solved, numerically, for the case of one-dimensional geometry. The solutions are shown to display effects which correspond to damped resonance when the wavelength of the current matches aspects of the geometry of the conductor.
Flow ratio design of primal and dual network models of distribution
Authors: Mohr G. A. 
Published: February 2009

AbstractThe finite element method can be used to provide network models of distribution problems. In the present work ‘flow ratio design’ is applied to such models to obtain approximate minima and maxima for both the primal and dual FEM models. The resulting primal MIN and dual MAX solutions are equal to or close to the exact solutions but, intriguingly, the primal MAX and dual MIN solutions are approximately equal to an intermediate saddle point solution.
The structure of solutions for equations related to the motions of plane curves
Authors: Guo Jong-Shenq , Lo Chu-Pin , Tsai Je-Chiang 
Published: February 2009

AbstractWe study the structure of solutions of an initial value problem arising in the study of steadily rotating spiral waves in the kinematic theory of excitable media. In particular, we prove that under certain conditions there is a unique global positive monotone increasing solution.
Pontryagin's maximum principle for optimal control of a non-well-posed parabolic differential equation involving a state constraint
Authors: Lee Mi Jin , Park Jong Yeoul 
Published: February 2009

AbstractIn this paper, we study Pontryagin's maximum principle for some optimal control problems governed by a non-well-posed parabolic differential equation. A new penalty functional is applied to derive Pontryagin's maximum principle and an application for this system is given.
Substitution rates in α‐helical transmembrane proteins
Authors: Stevens Timothy J. , Arkin Isaiah T. 
Published: February 2009

AbstractIt has been shown previously that some membrane proteins have a conserved core of amino acid residues. This idea not only serves to orient helices during model building exercises but may also provide insight into the structural role of residues mediating helix–helix interactions. Using experimentally determined high‐resolution structures of α‐helical transmembrane proteins we show that, of the residues within the hydrophobic transmembrane spans, the residues at lipid and subunit interfaces are more evolutionarily variable than those within the lipid‐inaccessible core of a polypeptide's transmembrane domain. This supports the idea that helix–helix interactions within the same polypeptide chain and those at the interface between different polypeptide chains may arise in distinct ways. To show this, we use a new method to estimate the substitution rate of an amino acid residue given an alignment and phylogenetic tree of closely related proteins. This method gives better sensitivity in the otherwise‐conserved transmembrane domains than a conventional similarity analysis and is relatively insensitive to the sequences used.
Structure determination of human and murine β‐defensins reveals structural conservation in the absence of significant sequence similarity
Authors: Bauer Finn , Schweimer Kristian , Klüver Enno , Conejo‐Garcia Jose‐Ramon , Forssmann Wolf‐Georg , Rösch Paul , Adermann Knut , Sticht Heinrich 
Published: February 2009

AbstractDefensins are cationic and cysteine‐rich peptides that play a crucial role in the host defense against microorganisms of many organisms by their capability to permeabilize bacterial membranes. The low sequence similarity among the members of the large mammalian β‐defensin family suggests that their antimicrobial activity is largely independent of their primary structure. To investigate to what extent these defensins share a similar fold, the structures of the two human β‐defensins, hBD‐1 and hBD‐2, as well as those of two novel murine defensins, termed mBD‐7 and mBD‐8, were determined by nuclear magnetic resonance spectroscopy. All four defensins investigated share a striking similarity on the level of secondary and tertiary structure including the lack of a distinct hydrophobic core, suggesting that the fold is mainly stabilized by the presence of three disulfide bonds. In addition to the overall shape of the molecules, the ratio of solvent‐exposed polar and hydrophobic side chains is also very similar among the four defensins investigated. It is significant that β‐defensins do not exhibit a common pattern of charged and hydrophobic residues on the protein surface and that the β‐defensin‐specific fold appears to accommodate a wide range of different amino acids at most sequence positions. In addition to the implications for the mode of biological defensin actions, these findings are of particular interest because β‐defensins have been suggested as lead compounds for the development of novel peptide antibiotics for the therapy of infectious diseases.
Structure and function of the N‐linked glycans of HBP/CAP37/azurocidin: Crystal structure determination and biological characterization of nonglycosylated HBP
Authors: Iversen L. F. , Kastrup J. S. , Bjørn S. E. , Wiberg F. C. , Larsen I. K. , Flodgaard H. J. , Rasmussen P. B. 
Published: February 2009

AbstractThe three N‐glycosylation sites of human heparin binding protein (HBP) have been mutated to produce a nonglycosylated HBP (ng‐HBP) mutant. ng‐HBP has been crystallized and tested for biological activity. Complete X‐ray data have been collected to 2.1 Å resolution, and the structure has been fully refined to an R‐factor of 18.4% (Rfree 27.7%). The ng‐HBP structure reveals that neither the secondary nor tertiary structure have changed due to the removal of the glycosylation, as compared to the previously determined glycosylated HBP structure. Although the primary events in N‐linked glycosylation occurs concomitant with polypeptide synthesis and therefore possesses the ability to influence early events in protein folding, we see no evidence of glycosylation influencing the structure of the protein. The root‐mean‐square deviation between the superimposed structures was 0.24 Å (on Cα atoms), and only minor local structural differences are observed. Also, the overall stability of the protein seems to be unaffected by glycosylation, as judged by the B‐factors derived from the two X‐ray structures. The flexibility of a glycan site may be determined by the local polypeptide sequence and structure rather than the glycan itself. The biological in vitro activity assay data show that ng‐HBP, contrary to glycosylated HBP, mediates only a very limited stimulation of the lipopolysaccharide induced cytokine release from human monocytes. In animal models of fecal peritonitis, glycosylated HBP treatment rescues mice from and an otherwise lethal injury. It appears that ng‐HBP have significant effect on survival, and it can be concluded that ng‐HBP can stimulate the host defence machinery albeit to a lesser extent than glycosylated HBP.
N5‐(L‐1‐carboxyethyl)‐L‐ornithine synthase: Physical and spectral characterization of the enzyme and its unusual low pKa fluorescent tyrosine residues
Authors: Sackett Dan L. , Ruvinov Sergei B. , Thompson John 
Published: February 2009

AbstractN5‐(L‐1‐carboxyethyl)‐L‐ornithine synthase [E.C. 1.5.1.24] (CEOS) from Lactococcus lactis has been cloned, expressed, and purified from Escherichia coli in quantities sufficient for characterization by biophysical methods. The NADPH‐dependent enzyme is a homotetramer (Mr ≡ 140,000) and in the native state is stabilized by noncovalent interactions between the monomers. The far‐ultraviolet circular dichroism spectrum shows that the folding pattern of the enzyme is typical of the α,β family of proteins. CEOS contains one tryptophan (Trp) and 19 tyrosines (Tyr) per monomer, and the fluorescence spectrum of the protein shows emission from both Trp and Tyr residues. Relative to N‐acetyltyrosinamide, the Tyr quantum yield of the native enzyme is about 0.5. All 19 Tyr residues are titratable and, of these, two exhibit the uncommonly low pKa of ∼8.5, 11 have pKa ∼10.75, and the remaining six titrate with pKa ∼11.3. The two residues with pKa ∼8.5 contribute approximately 40% of the total tyrosine emission, implying a relative quantum yield >1, probably indicating Tyr‐Tyr energy transfer. In the presence of NADPH, Tyr fluorescence is reduced by 40%, and Trp fluorescence is quenched completely. The latter result suggests that the single Trp residue is either at the active site, or in proximity to the sequence GSGNVA, that constitutes the βαβ fold of the nucleotide‐binding domain. Chymotrypsin specifically cleaves native CEOS after Phe255. Although inactivated by this single‐site cleavage of the subunit, the enzyme retains the capacity to bind NADPH and tetramer stability is maintained. Possible roles in catalysis for the chymotrypsin sensitive loop and for the low pKa Tyr residues are discussed.
A molecular dynamics study of the 41‐56 β‐hairpin from B1 domain of protein G
Authors: Roccatano Danilo , Amadei Andrea , Nola Alfredo Di , Berendsen Herman J. C. 
Published: February 2009

AbstractThe structural and dynamical behavior of the 41‐56 β‐hairpin from the protein G B1 domain (GB1) has been studied at different temperatures using molecular dynamics (MD) simulations in an aqueous environment. The purpose of these simulations is to establish the stability of this hairpin in view of its possible role as a nucleation site for protein folding. The conformation of the peptide in the crystallographic structure of the protein GB1 (native conformation) was lost in all simulations. The new equilibrium conformations are stable for several nanoseconds at 300 K (>10 ns), 350 K (>6.5 ns), and even at 450 K (up to 2.5 ns). The new structures have very similar hairpin‐like conformations with properties in agreement with available experimental nuclear Overhauser effect (NOE) data. The stability of the structure in the hydrophobic core region during the simulations is consistent with the experimental data and provides further evidence for the role played by hydrophobic interactions in hairpin structures. Essential dynamics analysis shows that the dynamics of the peptide at different temperatures spans basically the same essential subspace. The main equilibrium motions in this subspace involve large fluctuations of the residues in the turn and ends regions. Of the six interchain hydrogen bonds, the inner four remain stable during the simulations. The space spanned by the first two eigenvectors, as sampled at 450 K, includes almost all of the 47 different hairpin structures found in the database. Finally, analysis of the hydration of the 300 K average conformations shows that the hydration sites observed in the native conformation are still well hydrated in the equilibrium MD ensemble.
Cooperative effects of potassium, magnesium, and magnesium‐ADP on the release of Escherichia coli dihydrofolate reductase from the chaperonin GroEL
Authors: Clark A. Clay , Karon Brad S. , Frieden Carl 
Published: February 2009

AbstractPrevious investigation has shown that at 22 °C and in the presence of the chaperonin GroEL, the slowest step in the refolding of Escherichia coli dihydrofolate reductase (EcDHFR) reflects release of a late folding intermediate from the cavity of GroEL (Clark AC, Frieden C, 1997, J Mol Biol 268:512‐525). In this paper, we investigate the effects of potassium, magnesium, and MgADP on the release of the EcDHFR late folding intermediate from GroEL. The data demonstrate that GroEL consists of at least two conformational states, with apparent rate constants for EcDHFR release that differ by four‐ to fivefold. In the absence of potassium, magnesium, and ADP, ∼80‐90% of GroEL resides in the form with the faster rate of release. Magnesium and potassium both shift the distribution of GroEL forms toward the form with the slower release rate, though cooperativity for the magnesium‐induced transition is observed only in the presence of potassium. MgADP at low concentrations (0‐50 μM) shifts the distribution of GroEL forms toward the form with the faster release rate, and this effect is also potassium dependent. Nearly identical results were obtained with a GroEL mutant that forms only a single ring, demonstrating that these effects occur within a single toroid of GroEL. In the presence of saturating magnesium, potassium, and MgADP, the apparent rate constant for the release of EcDHFR from wild‐type GroEL at 22 °C reaches a limiting value of 0.014 s−1. For the single ring mutant of GroEL, the rate of EcDHFR release under the same conditions reaches a limiting value of 0.024 s−1, suggesting that inter‐ring negative cooperativity exists for MgADP‐induced substrate release. The data suggest that MgADP preferentially binds to one conformation of GroEL, that with the faster apparent rate constant for EcDHFR release, and induces a conformational change leading to more rapid release of substrate protein.
Protein histidine phosphorylation: Increased stability of thiophosphohistidine
Authors: Lasker Michael , Bui Cuong D. , Besant Paul G. , Sugawara Kiyoshi , Thai Philip , Medzihradszky Gergely , Turck Christoph W. 
Published: February 2009

AbstractPosttranslational phosphorylation of proteins is an important event in many cellular processes. Whereas phosphoesters of serine, threonine and tyrosine have been extensively studied, only limited information is available for other amino acids modified by a phosphate group. The formation of phosphohistidine residues in proteins has been discovered in prokaryotic organisms as well as in eukaryotic cells. The ability to biochemically analyze phosphohistidine residues in proteins, however, is severely hampered by its extreme lability under acidic conditions. In our studies we have found that by replacing the phosphate linked to the histidine residue with a thiophosphate, a phosphohistidine derivative with increased stability is formed. This allows the analysis of phosphohistidine‐containing proteins by established biochemical techniques and will greatly aid in the investigation of the role of this posttranslational modification in cellular processes.