bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repair of DNA lesions associated with triplex‐forming oligonucleotides
Authors: Chin Joanna Y. , Glazer Peter M. 
Published: December 2008

AbstractTriplex‐forming oligonucleotides (TFOs) are gene targeting tools that can bind in the major groove of duplex DNA in a sequence‐specific manner. When bound to DNA, TFOs can inhibit gene expression, can position DNA‐reactive agents to specific locations in the genome, or can induce targeted mutagenesis and recombination. There is evidence that third strand binding, alone or with an associated cross‐link, is recognized and metabolized by DNA repair factors, particularly the nucleotide excision repair pathway. This review examines the evidence for DNA repair of triplex‐associated lesions. © 2008 Wiley‐Liss, Inc.
From delocalized lipophilic cations to hypoxia: Blocking tumor cell mitochondrial function leads to therapeutic gain with glycolytic inhibitors
Authors: Kurtoglu Metin , Lampidis Theodore J. 
Published: December 2008

AbstractAn unexpected similarity between cancer and cardiac muscle cells in their sensitivity to anthracyclines and delocalized lipophilic cations (DLC) prompted a series of studies in which it was shown that the positive charge of these compounds is central to their selective accumulation and toxicity in these two distinct cell types. An initial finding to explain this phenomenon was that cancer and cardiac muscle cells exhibit high negative plasma membrane potentials resulting in increased uptake of these agents. However, thep‐glycoprotein efflux pump was shown to be another factor underlying differential accumulation of these compounds, since it recognizes positively charged drugs and thereby actively reduces their intracellular concentrations. The delocalized positive charge and lipophilicity of DLCs leads to their retention and inhibition of ATP synthesis in mitochondria. Years later it was realized that cancer cells in the hypoxic portions of solid tumors were similar to those treated with DLCs in relying mainly on anaerobic metabolism for survival and could thus be targeted with a glycolytic inhibitor, 2‐deoxy‐D‐glucose (2‐DG). This hypothesis has lead to a Phase I clinical trial in which 2‐DG is used to selectively kill the hypoxic tumor cell population which are resistant to standard chemotherapy or radiation.
Vitamin E analogues as mitochondria‐targeting compounds: From the bench to the bedside?
Authors: Zhao Yan , Neuzil Jiri , Wu Kun 
Published: December 2008

AbstractDespite considerable effort focusing on designing and finding efficient anti‐cancer drugs over the last decade, little progress has been achieved, in particular in case of highly recalcitrant malignancies. Also, since there is a trend suggesting that deaths from cancers may be more frequent than from cardiovascular diseases, it is important to look for novel efficient and selective therapeutic approaches to gradually start winning the battle with cancer. Redox‐silent vitamin E analogues, epitomised by α‐tocopheryl succinate, give some hope in the quest for drugs with such properties. Thus far, these agents have been successfully tested in experimental animals with different types of cancer, showing high efficacy against malignancies including HER2‐positive breast carcinomas or malignant mesotheliomas. Further research will provide additional, necessary data to launch clinical trials, possibly in near future, translating into development of innovative anti‐cancer drugs acting by targeting mitochondria selectively in cancer cells.
Resveratrol analog‐3,5,4′‐trimethoxy‐trans‐stilbene inhibits invasion of human lung adenocarcinoma cells by suppressing the MAPK pathway and decreasing matrix metalloproteinase‐2 expression
Authors: Yang Ya‐Ting , Weng Chia‐Jui , Ho Chi‐Tang , Yen Gow‐Chin 
Published: December 2008

AbstractResveratrol (3,5,4′‐trihydroxystilbene) is a natural polyphenol that presents various physiological activities. It has been reported that the methylated derivatives of resveratrol show better potential antifungal and antiproliferative activities than resveratrol. In the present study, we investigated the inhibitory effect of 3,5,4′‐trimethoxy‐trans‐stilbene (MR‐3), a methylated derivative of resveratrol, on the invasion of A549 cells (a human lung adenocarcinoma cell line). We found that treatment with MR‐3 at the concentration of 5 μM resulted in antiadhesive, antimigratory, and antiinvasive activities on A549 cells through the suppression of matrix metalloproteinase (MMP)‐2 protein expression and transcriptional levels in a time‐dependent manner. The suppression of MMP‐2 expression by MR‐3 led to an inhibition of A549 cell invasion by inactivating phosphorylation of SAPK/c‐Jun N‐terminal kinase (JNK) and p38 MAPK signaling pathways. A time‐dependent inhibition of protein levels for p65, c‐Jun, and c‐Fos in the nucleus by MR‐3 treatment was also observed. In conclusion, our data demonstrate that the antiinvasive effects of MR‐3 on A549 cells are likely mediated through the inhibition of phosphorylation of JNK and p38, as well as a reduction in the protein levels of nuclear factor‐kappa B (NF‐κB) and activator protein‐1 (AP‐1) in the nucleus, ultimately leading to downregulation of MMP‐2 expression.
Vertical dynamic response of a rigid foundation embedded in a poroelastic soil layer
Authors: Cai Y. Q. , Hu X. Q. , Xu C. J. , Hong Z. S. 
Published: December 2008

AbstractA simplified analytical method is presented for the vertical dynamic analysis of a rigid, massive, cylindrical foundation embedded in a poroelastic soil layer. The foundation is subjected to a time‐harmonic vertical loading and is perfectly bonded to the surrounding soil in the vertical direction. The soil underlying the foundation base is represented by a single‐layered poroelastic soil based on rigid bedrock while the soil at the side of the foundation is modeled as an independent poroelastic layer composed of a series of infinitesimally thin layers. The behavior of the soil is governed by Biot's poroelastodynamic theory and its governing equations are solved by the use of Hankel integral transform. The contact surface between the foundation base and the soil is smooth and fully permeable. The dynamic interaction problem is solved following standard numerical procedures. The accuracy of the present solution is verified by comparisons with the well‐known solutions obtained from other approaches for both the elastodynamic interaction problem and poroelastodynamic interaction problem. Numerical results for the vertical dynamic impedance and response factor of the foundation are presented to demonstrate the influence of nondimensional frequency of excitation, soil layer thickness, poroelastic material parameters, depth ratio and mass ratio on the dynamic response of a rigid foundation embedded in a poroelastic soil layer. Copyright © 2008 John Wiley & Sons, Ltd.
Symmetries and solutions of reaction‐diffusion‐convection equations with power diffusivities
Authors: Cherniha Roman , Pliukhin Oleksii 
Published: December 2008

AbstractNew Q‐conditional symmetries for two classes of reaction‐diffusion‐convection equations with power diffusivities are derived. The symmetries obtained for constructing exact solutions of the relevant nonlinear equations are successfully applied. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Modeling dissipative effects in anisotropic materials by means of evolving generalized structural tensors
Authors: Ehret Alexander E. , Itskov Mikhail 
Published: December 2008

AbstractIn this work, an anisotropic dissipative model is proposed as an extension of a recently presented polyconvex anisotropic strain‐energy function for fiber‐reinforced materials. This thermodynamically consistent model is able to describe different softening phenomena and includes residual deformations. The so‐called preconditioning behavior of a soft biological tissue sample is considered as a numerical example. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Numerical approximation of the Smagorinsky model by a two‐level method
Authors: Borggaard Jeff , Iliescu Traian , Lee Hyesuk , Roop John Paul , Son Hyunjin 
Published: December 2008

AbstractA two‐level method for discretizing the Smagorinsky model for the numerical simulation of turbulent flows is proposed. In the two‐level algorithm, the solution to the fully nonlinear coarse mesh problem is utilized in a single‐step linear fine mesh problem. When modeling parameters are chosen appropriately, the error in the two‐level algorithm is comparable to the error in solving the fully nonlinear problem on the fine mesh. We provide an a priori error estimate for the two‐level method, which yields appropriate scalings between the coarse and fine mesh‐sizes (H and h, respectively), and the radius of the spatial filter used in the Smagorinsky model (δ). In addition, we provide an algorithm in which a coarse mesh correction is performed to further enhance the accuracy. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Bugs, errors, and unexpected results in computer algebra packages
Authors: Krämer Walter 
Published: December 2008

AbstractThe following is a citation from the description and aims of the Dagstuhl Seminar on Algebraic and Numerical Algorithms and Computer‐assisted Proofs:In contrast, most algorithms in computer algebra are ‘never failing’, that is they are proved to provide a solution for any input, and the maximum computing time for this is estimated a priori.The focus of this contribution is the reliability of the computer algebra system Maple. We will show that ‘never failing’ algorithms may be the theory but concerning actual implementations such a statement seems not to be drawn from life. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Path integrals as analysis on path space by time slicing approximation
Authors: Kumano‐go Naoto , Fujiwara Daisuke 
Published: December 2008

AbstractThis is a survey of our papers [3, 4]. We give a fairly general class of functionals on a path space so that Feynman path integral has a mathematically rigorous meaning. More precisely, for any functional belonging to our class, the time slicing approximation of Feynman path integral converges uniformly on compact subsets of the configuration space. Our class of functionals is closed under addition, multiplication, translation, real linear transformation and functional differentiation. The invariance under translation and orthogonal transformation, the interchange of the order with Riemann‐Stieltjes integrals and some limits, the semiclassical approximation, the integration by parts and the Taylor expansion formula with respect to functional differentiation, and the fundamental theorem of calculus hold in Feynman path integral. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Critical phenomena in evolving networks: Ferromagnetic phase transition in evolving network of stochastic cellular automata
Authors: Makowiec Danuta 
Published: December 2008

AbstractIt is shown by MC simulations that ferromagnetic system modeled by cellular automata with synchronously rewired interconnections changes critically when preference in rewiring is added – the system becomes resistant against stochastic noise. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The LANS‐alpha turbulence model in primitive‐equation ocean modeling
Authors: Petersen Mark R. , Hecht Matthew W. , Holm Darryl D. , Wingate Beth A. 
Published: December 2008

AbstractThe Lagrangian‐Averaged Navier‐Stokes alpha (LANS‐α) and Leray turbulence parameterizations are demonstrated in a primitive‐equation ocean model using an idealized channel domain. For LANS‐α, turbulence statistics such as kinetic energy, eddy kinetic energy, and temperature profiles resemble doubled‐resolution statistics with the standard model. In a North Atlantic domain with realistic topography, the Leray model increases eddy activity. The LANS‐α and Leray models show great promise to improve heat transport and temperature distributions in global ocean‐climate simulations, as these processes depend on better resolution of eddies near the grid‐scale. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A functional iteration for the quantum drift–diffusion model: existence analysis and numerical approximation
Authors: Falco Carlo de , Jerome Joseph W. , Sacco Riccardo 
Published: December 2008

AbstractThis communication describes a functional iteration technique, denoted Generalized Gummel Map (GGM), for the solution of the Quantum Drift–Diffusion (QDD) model. The assumptions needed to establish existence of a fixed point for the GGM are described and their plausibility is assessed via physical arguments supported by one–dimensional numerical experiments. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Tensor product methods for stochastic problems
Authors: Zander Elmar , Matthies H. G. 
Published: December 2008

AbstractIn the solution of stochastic partial differential equations (SPDEs) the generally already large dimension N of the algebraic system resulting from the spatial part of the problem is blown up by the huge number of degrees of freedom P coming from the stochastic part. The number of degrees of freedom of the full system will be NP, which poses severe demands on memory and processor time. We present a method how to approximate the system by a data‐sparse tensor product (based on the Karhunen‐Loève decomposition with M terms), which uses only memory in the order of M (N + P), and how to keep this representation also inside the iterative solvers. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Continuous workspace analysis for parallel cable‐driven Stewart‐Gough platforms
Authors: Bruckmann Tobias , Mikelsons Lars , Schramm Dieter , Hiller Manfred 
Published: December 2008

AbstractParallel cable‐driven Stewart‐Gough platforms consist of a end‐effector which is connected to the machine frame by motor driven cables. Since cables can transmit only tension forces, at leastm=n+ 1 cables are needed to tense a system havingndegrees‐of‐freedom. This results in a kinematical redundancy and leads to a (m–n)‐dimensional solution space for the cable force distribution. For this reason, performing a workspace analysis requires advanced methods and is time consuming. However, reliable and robust algorithms are demanded to calculate the workspace for a given parameter set (winch positions and platform anchor points). Discrete methods are widely used to analyze the workspace. Singularities as well as cable collisions inside the workspace of a cable‐driven Stewart‐Gough platform are possible [1]. Therefore discrete methods may deliver wrong results due to the fact that intermediate points on the discrete calculation grids are neglected. In this paper, another approach is presented. The use of intervals avoids the problems described above and leads to reliable results. In the following the basic ideas of this continuous workspace analysis are shown. For practical application, e.g. in robotics, even more important is the parameter synthesis, i.d. the process of designing a robot for a predefined workspace. However, the workspace geometries are very complex and not intuitive in general. Here, the analysis methods are also extended for synthesis. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Shape derivatives without taking the shape derivative
Authors: Ito K. , Kunisch K. , Peichl G. 
Published: December 2008

AbstractA general framework for calculating shape derivatives for optimization problems with partial differential equations as constraints is presented. Exploiting the structure of the cost functional the proposed technique allows to obtain the shape derivative of the cost without the necessity to involve the shape derivative of the state variable. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The characteristic Chern type classes and integrability of multidimensional differential systems on Riemannian manifolds
Authors: Prykarpatsky Anatoliy K. , Bogolubov Nikolai N. 
Published: December 2008

AbstractThe differential‐geometric properties of generalized de Rham‐Hodge complexes naturally related with integrable multidimensional differential systems of M. Gromov type are analyzed. The geometric structure of Chern type characteristic classes are studied, special differential invariants of the Chern type are constructed. The integrability of multi‐dimensional nonlinear differential systems on Riemannian manifolds is discussed. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Influence oflow Mach numbers on thenumerical dissipation of Godunov‐typeschemes: a comparison between Roeand HLLscheme
Authors: Rieper Felix 
Published: December 2008

AbstractUpwind schemes for the Euler equations face three kinds of problems in the low Mach number regime: The stiffness due to the presence of fast acoustic and slow entropy and shear waves can be overcome – at least for steady problems – by preconditioning the physical equations, see for example [1, 2]. Secondly, the 𝒪(M2)‐pressure variations get lost in the O(1)‐global pressure due to finite precision arithmetics. This cancellation problem was dealt with in [3]. The third problem originates in the numerical viscosity of the upwind schemes and is – in the author's view of the matter – not fully understood to date. Asymptotic analyses of the upwind schemes such as [4] suggest that the pressure field will completely degenerate, producing variations of the wrong order of magnitude. Our numerical andanalytical results give a more precise picture of the problem and are – at least in parts – contradicting the established view. We will prove in this paper that complete Riemann solvers such as Roe's behave completely different to incomplete Riemann solvers such as HLL in the low Mach number regime. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Modeling laboratory data from clinical trials
Authors: Rosenkranz Gerd 
Published: December 2008

AbstractLaboratory data from clinical trials are considered precursors of potential organ dysfunctions. The routine analysis of these data focusses on the occurrence of extremely high or low values relative to normal ranges, the change of these incidences compared to baseline, or the worst values from each individual patient. However, only rarely is an attempt made to model the dynamics of the measurements over time. In this paper we propose to model laboratory measurements by stochastic processes, specifically by Ornstein‐Uhlenbeck processes. The aim is to estimate parameters of these processes in order to characterize a potential effect of drugs or other medical treatments. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Aspects of sensitivity analysis using the level‐set method in structural optimization
Authors: Rotthaus Monika , Barthold Franz‐Joseph 
Published: December 2008

AbstractThe level‐set method is very common for modelling structural optimization problems, e.g. multi‐material structures. Essentially two different approaches are known. The first method describes the shape by an implicit function formulation. The weak form is expressed as a Heaviside function of this implicit function and the optimization problem is solved by an iterative procedure. This method is applied to topology optimization by e.g. Belytschko et al. [1]. The second approach is based on the combination of the shape derivative and the level‐set method for front propagation, which has been devised by Osher and Sethian [2]. Allaire et. al. [3] use the shape derivative for the minimization problem to compute the advection velocity in the Hamilton‐Jacobi equation. The Hamilton‐Jacobi equation can be solved numerically by an explicit first order upwind scheme on a Cartesian grid. We propose a new numerical method for shape optimization of multi‐material structures. This approach is based on the level‐set method combined with the variational sensitivity analysis, see Barthold [4]. The aim of the present contribution is to point out the essential aspects of this combination and to compare it with the two methods mentioned above. Furthermore the sensitivity of multi‐material structures in terms of various design parameters is discussed. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
An atomic interaction‐based continuum model for computational multiscale contact mechanics
Authors: Sauer Roger A. , Li Shaofan 
Published: December 2008

AbstractA computational multiscale contact mechanics model is presented which describes the interaction between deformable solids based on the interaction of individual atoms or molecules. The contact model is formulated in the framework of large deformation continuum mechanics and combines the approaches of molecular modelling [1] and continuum contact mechanics [2]. In the following a brief overview of the contact model is given. Further details can be found in [3], [4] and [5]. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Geometrically nonlinear finite‐shell elements with magnetostrictive layers
Authors: Lentzen Sven , Schmidt Rüdiger 
Published: December 2008

AbstractIn this paper a geometrically nonlinear composite shell element with integrated magnetostrictive layers is presented. Three translational and two rotational nodal degrees of freedom are used for the first‐order transverse shear approximation. The finite element is used in order to investigate shape and stability control problems of structures with magnetostrictive actuator layers in the range of large deformations. The numerical approximations to this static problem are obtained using the total Lagrangian formulation for the moderate rotation shell theory. The aforementioned finite element is used to numerically investigate the actuation behaviour of the integrated magnetostrictive layers. Since the magnetic field is prescribed, the coupled magnetoelastic problem turns into a decoupled problem. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Cahn‐Hilliard inpainting and the Willmore functional
Authors: Burger Martin , Chu Shun‐Yin , Markowich Peter , Schönlieb Carola‐Bibiane 
Published: December 2008

AbstractThe Cahn‐Hilliard equation has its origin in material sciences and serves as a model for phase separation and phase coarsening in binary alloys. A new approach in the class of fourth order inpainting algorithms is inpainting of binary images using the Cahn‐Hilliard equation. Like solutions of the Cahn‐Hilliard equation converging to two main values during the phase separation process, the grayvalues inside the missing part of the image are oriented towards the binary states black and white. We present stability/instability results for solutions of the Cahn‐Hilliard equation and their connection to the Willmore functional. In particular we will consider the Willmore functional as a quantity to find the optimal scale of the inpainting result. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Exact local nonreflecting boundary conditions for time‐dependent multiple scattering
Authors: Grote Marcus J. , Sim Imbo 
Published: December 2008

AbstractIn [2, 3] a nonreflecting boundary condition(NBC) for time‐dependent multiple scattering was derived, which is local in time but nonlocal in space. Here, based on a high‐order local nonreflecting boundary condition (NBC) for single scattering [4], we seek a local NBC for time‐dependent multiple scattering, which is completely local both in space and time. To do so, we first develop a high order representation formula for a purely outgoing wave field, given its values and those of certain auxiliary functions needed for the artificial boundary condition. By combining that representation formula with a decomposition of the total scattered field into purely outgoing contributions, we obtain the first exact, completely local, NBC for time‐dependent multiple scattering. The accuracy and stability of this local NBC is evaluated by coupling it to standard finite element and finite difference methods. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)