bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Identification and Characterization of Fusogenic Domains in Herpes Virus Glycoprotein B Molecules
Authors: Galdiero Stefania , Vitiello Mariateresa , D'Isanto Marina , Falanga Annarita , Cantisani Marco , Browne Helena , Pedone Carlo , Galdiero Massimiliano 
Published: February 2008

AbstractThe molecular mechanism of entry of herpes viruses requires a multicomponent fusion system. Virus entry and cell–cell fusion of Herpes simplex virus (HSV) requires four glycoproteins: gD, gB and gH/gL. The role of gB remained elusive until recently, when the crystal structure of HSV‐1 gB became available. Glycoprotein B homologues represent the most highly conserved group of herpes virus glycoproteins; however, despite the high degree of sequence and structural conservation, differences in post‐translational processing are observed for different members of this virus family. Whereas gB of HSV is not proteolytically processed after oligomerization, most other gB homologues are cleaved by a cellular protease into subunits that remain linked through disulfide bonds. Proteolytic cleavage is common for activation of many other viral fusion proteins, so it remains difficult to envisage a common role for different herpes virus gB structures in the fusion mechanism. We selected bovine herpes virus type 1 (BoHV‐1) and herpes simplex virus type 1 (HSV‐1) as representative viruses expressing cleaved and uncleaved gBs, and have screened their amino acid sequences for regions of highly interfacial hydrophobicity. Synthetic peptides corresponding to such regions were tested for their ability to induce the fusion of large unilamellar vesicles and to inhibit herpes virus infection. These results underline that several regions of the gB protein are involved in the mechanism of membrane interaction.
Spectroscopic studies of oligomers containing 2,5‐trans furanoid sugar amino acids
Authors: Edwards Alison A. , Alexander Bruce D. , Fleet George W. J. , Tranter George E. 
Published: February 2008

AbstractSugar amino acids and their oligomers, known as carbopeptoids, are commonly studied as foldamers. However, study of their conformational preference is often challenging when the adopted conformations are extended and/or disordered. This study is the first to explore the disordered nature of such carbopeptoids by utilizing a family of 2,5‐trans carbopeptoids. An array of spectroscopic techniques has been used to investigate the conformational preference of these carbopeptoids. However, using this data alone it has not been possible to assign conformational preference as an ordered extended conformation or as a disordered family of closely related conformations. Computational methods need to be employed to achieve reliable interpretation of the spectroscopic data. Chirality, 2008. © 2008 Wiley‐Liss, Inc.
Dendritic crystal growth, differential circular scattering, and the origin of biomolecular homochirality
Authors: Kahr Bart , Freudenthal John H. 
Published: February 2008

AbstractPhthalic acid rapidly crystallizing in thin aqueous films is deposited radially and rhythmically as dendritic banded spherulites that have heterochiral meso‐textures in hemi‐circles. The chiral fields differentially scatter left and right circularly polarized light. A scenario for chiral amplification and the origin of biomolecular homochirality is thus proposed that combines the influences of crystals and light. Chirality, 2008. © 2008 Wiley‐Liss, Inc.
SyGMa: Combining Expert Knowledge and Empirical Scoring in the Prediction of Metabolites
Authors: Ridder Lars , Wagener Markus 
Published: February 2008

AbstractPredictions of potential metabolites based on chemical structure are becoming increasingly important in drug discovery to guide medicinal chemistry efforts that address metabolic issues and to support experimental metabolite screening and identification. Herein we present a novel rule‐based method, SyGMa (Systematic Generation of potential Metabolites), to predict the potential metabolites of a given parent structure. A set of reaction rules covering a broad range of phase 1 and phase 2 metabolism has been derived from metabolic reactions reported in the Metabolite Database to occur in humans. An empirical probability score is assigned to each rule representing the fraction of correctly predicted metabolites in the training database. This score is used to refine the rules and to rank predicted metabolites. The current rule set of SyGMa covers approximately 70 % of biotransformation reactions observed in humans. Evaluation of the rule‐based predictions demonstrated a significant enrichment of true metabolites in the top of the ranking list: while in total, 68 % of all observed metabolites in an independent test set were reproduced by SyGMa, a large part, 30 % of the observed metabolites, were identified among the top three predictions. From a subset of cytochrome P450 specific metabolites, 84 % were reproduced overall, with 66 % in the top three predicted phase 1 metabolites. A similarity analysis of the reactions present in the database was performed to obtain an overview of the metabolic reactions predicted by SyGMa and to support ongoing efforts to extend the rules. Specific examples demonstrate the use of SyGMa in experimental metabolite identification and the application of SyGMa to suggest chemical modifications that improve the metabolic stability of compounds.
Design optimization of switched reluctance machines for starter/generator of hybrid electric vehicle by genetic algorithm
Authors: Faiz Jawad , Moayed‐zadeh K. 
Published: February 2008

AbstractA switched reluctance machine for starter/generator of a hybrid electric vehicle is designed to optimize two objective functions: (1) high starting torque over low speed and (2) high efficiency over high speed. For static modeling of flux‐linkage, a quick analytical model is used and its accuracy is verified by comparison with the finite element results. In addition, a suitable technique is adopted to estimate the losses. Comparison of the optimal design between a conventional technique and genetic algorithm shows that the genetic algorithm enables to optimize the proposed objective functions over whole range of the speed. Copyright © 2008 John Wiley & Sons, Ltd.
Investigation of suppressing PD white noise by compound information of complex wavelet transform
Authors: Tang Ju , Xu Zhongrong , Sun Caixin 
Published: February 2008

AbstractAccording to the distinct properties between the complex wavelet coefficients of partial discharge (PD) signals and white noises, this paper presents the specific compound information (CI) of WTRInseries for complex wavelet transform (CWT), which are utilized to suppress white noises. Through the simulation case, the influence of n‐index value on denoising effect is discussed and the optimal CI of corresponding to different PD waveforms is analyzed by the simulation investigation. The parameters of variable tendency parameter (VTP), normalized correlation coefficient (NCC), and signal‐to‐noise ratio (SNR) are defined to synthetically evaluate the denoising effect. The db4 complex wavelet is constructed to suppress the white noise in ultra high frequency (UHF) PD detection system. The results indicate that the denoising effect of the CI for CWT is better than the simple information (SI) for CWT and the CI of WTRInseries have the optimal denoising effect to suppress white noise for UHF PD signals. Copyright © 2008 John Wiley & Sons, Ltd.
Decentralized decision on operating reserve considering insurance and penalty policies
Authors: Chan C. Y. , Shi L. B. , Ni Y. X. 
Published: February 2008

AbstractIn power markets, operating reserve procurement is usually centrally handled according to certain reliability rules and aiming at minimizing the total procurement cost. In this approach, there are no customer choices, no incentives for the independent system operator (ISO) to minimize the social cost or for reserve suppliers to commit promised reserve capacity. It may lead to inefficiency. In this paper, we propose a decentralized approach for operating reserve procurement. In the approach, gencos try to maximize their own expected profits and consumers try to minimize their own expected cost with certain market information announced by the ISO. Insurance theory is applied to the approach. With the insurance policy, consumers are able to transfer their financial risk of loss of supply to the ISO. The claim defined in the insurance policy induces incentive for the ISO to manage the reserve capacity in an efficient manner. A penalty system is introduced as well. Under the penalty system, a genco is required to pay a high penalty if it does not commit the reserve capacity provision, which enforces the liability of gencos to provide operating reserve. A detailed math model and a solution procedure are presented. It is shown that with a properly defined reserve market rule, the decentralized approach can yield same optimal solution as its centralized counterpart aiming at maximizing social welfare in reserve markets. Numerical test results illustrate the effectiveness of the suggested approach. Copyright © 2008 John Wiley & Sons, Ltd.
The role of Poynting's vector in polyphase power calculations
Authors: Faria J. A. Brandão 
Published: February 2008

AbstractThis paper is a tutorial contribution to the clarification of the role played by Poynting's vector (PV) in power calculations. In polyphase power systems, the standard computation of the instantaneous power is usually performed by using a summation of voltage–current products. We show analytically how such a result can be deduced directly from Maxwell's equations together with the evaluation of the PV flux. A simple application example is provided to illustrate the issue under discussion. Copyright © 2008 John Wiley & Sons, Ltd.
Optimal Control of Rigid‐Link Manipulators by Indirect Methods
Authors: Callies Rainer , Rentrop Peter 
Published: February 2008

AbstractThe present paper is a survey and research paper on the treatment of optimal control problems of rigid‐link manipulators by indirect methods. Maximum Principle based approaches provide an excellent tool to calculate optimal reference trajectories for multi‐link manipulators with high accuracy. Their major drawback was the need to explicitly formulate the complicated system of adjoint differential equations and to apply the full apparatus of optimal control theory. This is necessary in order to convert the optimal control problem into a piecewise defined, nonlinear multi‐point boundary value problem. An accurate and efficient access to first‐ and higher‐order derivatives is crucial. The approach described in this paper allows it to generate all the derivative information recursively and simultaneously with the recursive formulation of the equations of motion. Nonlinear state and control constraints are treated without any simplifications by transforming them into sequences of systems of linear equations. By these means, the modeling of the complete optimal control problem and the accompanying boundary value problem is automated to a great extent. The fast numerical solution is by the advanced multiple shooting methodJANUS. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Lie Theory for Quantum Control
Authors: Dirr G. , Helmke U. 
Published: February 2008

AbstractOne of the main theoretical challenges in quantum computing is the design of explicit schemes that enable one to effectively factorize a given final unitary operator into a product of basic unitary operators. As this is equivalent to a constructive controllability task on a Lie group of special unitary operators, one faces interesting classes of bilinear optimal control problems for which efficient numerical solution algorithms are sought for. In this paper we give a review on recent Lie‐theoretical developments in finite‐dimensional quantum control that play a key role for solving such factorization problems on a compact Lie group. After a brief introduction to basic terms and concepts from quantum mechanics, we address the fundamental control theoretic issues for bilinear control systems and survey standard techniques fromLie theory relevant for quantum control. Questions of controllability, accessibility and time optimal control of spin systems are in the center of our interest. Some remarks on computational aspects are included as well. The idea is to enable the potential reader to understand the problems in clear mathematical terms, to assess the current state of the art and get an overview on recent developments in quantum control‐an emerging interdisciplinary field between physics, control and computation. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Daily precipitation observations over Emilia‐Romagna: mean values and extremes
Authors: Pavan V. , Tomozeiu R. , Cacciamani C. , Di Lorenzo M. 
Published: February 2008

AbstractDaily precipitation data from a dense observational network covering Emilia‐Romagna, a region of Northern Italy, are described and analysed. Data are available for all stations for the period 1951–2004 and for a selected group of stations located over the Reno hydrological basin for the period 1925–2004. Indices describing seasonal values of mean precipitation and frequency of extreme events are computed starting from daily data and are used to describe the temporal and spatial variability of precipitation over the region.Data referring to the period 1951–2004 are used to describe trends of relevant precipitation indices over the same period in all seasons, and the relation between the variability of these indices and major Euro‐Atlantic large‐scale circulation indices over winter.Data referring to the period 1925–2004 are used to analyse the decadal and long‐term variability over the Reno Basin and its relation with the winter daily discharge of the river. This analysis allows identifying the presence of a clear decadal periodicity in river discharge, strongly related with the decadal variability in both total precipitation and frequency of intense events. Copyright © 2008 Royal Meteorological Society
Organizational networks of collaboration for community‐based living
Authors: Poole Dennis L. 
Published: February 2008

AbstractThis exploratory study of the Texas Community Awareness and Relocation Services (CARS) Project examines organizational networks of collaboration for community‐based living. A high degree of collaboration in these networks is needed to help nursing facility residents negotiate the complex process of moving to community‐based settings. Social network analysis reveals considerable variations in local organizational networks of collaboration among lead nonprofit providers before and after implementation of the CARS Project in five test sites. These variations probably affected their collaborative capacity of each site and, ultimately, the project's outcomes.
Two Fast Marching Methods for Hamilton–Jacobi Equations
Authors: Cristiani Emiliano , Falcone Maurizio 
Published: February 2008

AbstractWe introduce and analyze two new Fast Marching (FM) methods based on a semi‐Lagrangian (SL) approximation (see [2] for a more complete presentation). The Characteristics driven Fast Marching method accepts more than one node at every iteration using a dynamic condition which leads to a faster convergence. The Buffered Fast Marching method allows to deal with convex and non–convex Hamilton–Jacobi equations including anisotropic front propagation and differential games. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A Haptotaxis Model with Age and Spatial Structure and Nonlinear Age‐Boundary Conditions
Authors: Walker Christoph 
Published: February 2008

AbstractGlobal existence and uniqueness of solutions is shown for a system of nonlinear pde's modeling tumor invasion into tissue. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Sparse direct factorizations through unassembled hyper‐matrices
Authors: Bientinesi Paolo , Eijkhout Victor , Kurtz Jason , van de Geijn Robert 
Published: February 2008

AbstractWe set out to efficiently compute the solution of a sequence of linear systems Aixi = bi, where the matrix Ai is tightly related to matrix Ai –1. In the setting of an hp ‐adaptive Finite Element Method, the sequence of matrices Ai results from successive local refinements of the problem domain. At any step i > 1, a factorization already exists and it is the updated linear system relative to the refined mesh for which a factorization must be computed in the least amount of time. This observation holds the promise of a tremendous reduction in the cost of an individual refinement step. We argue that traditional matrix storage schemes, whether dense or sparse, are a bottleneck, limiting the potential efficiency of the solvers. We propose a new hierarchical data structure, the Unassembled Hyper‐Matrix (UHM), which allows the matrix to be stored as a tree of unassembled element matrices, hierarchically ordered to mirror the refinement history of the physical domain. The factorization of such an UHM proceeds in terms of element matrices, only assembling nodes when they need to be eliminated. Efficiency comes in terms of both performance and space requirements. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Image analysis using p ‐Laplacian and geometrical PDEs
Authors: Kuijper A. 
Published: February 2008

AbstractMinimizing the integral ∫Ω1/p |∇L |p d Ω for an image L under suitable boundary conditions gives PDEs that are well‐known for p = 1, 2, namely Total Variation evolution and Laplacian diffusion (also known as Gaussian scale space and heat equation), respectively. Without fixing p, one obtains a framework related to the p ‐Laplace equation. The partial differential equation describing the evolution can be simplified using gauge coordinates (directional derivatives), yielding an expression in the two second order gauge derivatives and the norm of the gradient. Ignoring the latter, one obtains a series of PDEs that form a weighted average of the second order derivatives, with Mean Curvature Motion as a specific case. Both methods have the Gaussian scale space in common. Using singularity theory, one can use properties of the heat equation (namely. the role of scale) in the full L (x, t) space and obtain a framework for topological image segmentation. In order to be able to extend image analysis aspects of Gaussian scale space in future work, relations between these methods are investigated, and general numerical schemes are developed. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Acoustics of gas‐saturated foams: Modelling comparisons
Authors: Steeb Holger 
Published: February 2008

AbstractWe show results obtained by Biot's equations and a simple Theory of Porous Media‐based hybrid model describing acoustical waves in a gas‐saturated high‐porous foam. The resulting dispersion relations for the longitudinal mode and phase velocities vs. porosity show the extraordinary effect of waves in gas‐saturated porous media. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Resonance in viscous film flow over topography
Authors: Heining Christian , Wierschem Andreas , Bontozoglou Vasilis , Aksel Nuri , Uecker Hannes 
Published: February 2008

AbstractWe study viscous gravity‐driven films flowing over periodically undulated substrates. Linear analysis describes resonance in steady flow along small bottom corrugations for films of arbitrary thickness. Depending on the dimensionless film thickness we find different regimes for the resonance, which is associated with the interaction of the undulated film with capillarygravity waves traveling against the flow. Nonlinear resonance produces higher harmonics and bistable resonance. The higher harmonics are due to higher harmonics resonance and due to the nonlinear coupling to lower harmonics. For the bistable resonance we derive a minimum model showing that the bistability corresponds essentially to that of the driven Duffing oscillator. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Surfactant‐driven instability in two‐fluid pipe and channel flows
Authors: Blyth M.G. , Luo H. , Pozrikidis C. 
Published: February 2008

AbstractRecent work on the stability of two‐layer channel flow, with either smooth or corrugated walls, and core‐annular flow is discussed with the emphasis on the potentially destabilising effect of an insoluble surfactant. Linearised normal mode analyses are conducted to identify unstable parametric conditions, and these are followed up by computer simulations which confirm the linear results and, furthermore, reveal a rich array of dynamical behaviour in the nonlinear regime. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Retrieving knowledge from auditing log‐files for computer and network forensics and accountability
Authors: Takahashi Daisuke , Xiao Yang 
Published: February 2008

AbstractThis paper analyzes and simulates the complexity of searching a particular database called a computer or network auditing log database. In order to observe behaviors of users in a computer or a computer network, system authorities in a particular domain first keep logs of all the actions conducted by the users. In general, we can grasp the users' actions by analyzing their actions in a computer system, or messages in a computer network, especially analyzing headers of packets in a particular network protocol. From this bunch of data (database), we can retrieve particular knowledge according to some requirements for computer and network forensics and accountability. For example, in a computer or network system, if at some point the fact that the content of a secret file is leaking has been already known, to figure out the reasons of the leaking, we can search partial or entire log‐files to find out direct or indirect accesses to the file; since a user who accessed the secret before may send messages containing the secret to other users (the secret is leaking due to indirect accesses) via packets in a computer network, or via pipe/FIFO/Message‐Queue in a computer system, finding the reasons of the leaking is not a trivial task. In this paper, we analyze and simulate the complexity of retrieving knowledge from the computer and network auditing log database for forensics and accountability. Copyright © 2008 John Wiley & Sons, Ltd.
An efficient data structure for network anomaly detection
Authors: Fan Jieyan , Wu Dapeng , Lu Kejie , Nucci Antonio 
Published: February 2008

AbstractDespite the rapid advance in networking technologies, detection of network anomalies at high‐speed switches/routers is still far from maturity. To push the frontier, two major technologies need to be addressed. The first one is efficient feature‐extraction algorithms/hardware that can match a line rate in the order of Gb/second; the second one is fast and effective anomaly detection schemes. In this paper, we focus on design of efficient data structure and algorithms for feature extraction. Specifically, we propose a novel data structure that extracts the so‐called two‐directional (2D) matching features, which are shown to be effective indicators of network anomalies. Our key idea is to use a Bloom filter array (BFA) to trade‐off a small amount of accuracy in feature extraction, for much less space and time complexity, so that our data structure can catch up with a line rate in the order of Gb/second. Different from the existing work, our data structure has the following properties: (1) it dynamic Bloom filter, (2) combination of a it sliding window with Bloom filter, and (3) using an insertion–removal pair to enhance Bloom filter with a removal operation. Our analysis and simulation demonstrate that the proposed data structure has a better space/time trade‐off than conventional algorithms. For example, for a fixed time complexity, the conventional algorithm (i.e., hash table [1—8]) requires a memory of 1.01 Gbits while our data structure requires a memory of only 62.9 Mbits, at the cost of losing 1% accuracy in feature extraction. Copyright © 2008 John Wiley & Sons, Ltd.