bluuebunny/crossref_metadata_2025_split huggingface dataset:
NMR structural studies of the Ste11 SAM domain in the dodecyl phosphocholine micelle
Authors: Bhunia Anirban , Domadia Prerna N. , Mohanram Harini , Bhattacharjya Surajit 
Published: July 2008

AbstractThe sterile α‐motif (SAM), a relatively small (∼70 amino acids) interaction domain, is found in a variety of proteins involved in cell signaling, transcription regulation, and scaffolding. The Ste11 protein kinase from the mitogen activated protein kinase (MAPK) signaling cascades of the budding yeast is regulated by a SAM domain located at the N‐terminus of full‐length protein. In solution, the Ste11 SAM domain exists as a well‐folded dimeric structure that is involved in interaction with the cognate SAM domain from an adaptor protein Ste50. In this work, we show that the Ste11 SAM domain has an intrinsic affinity towards the lipid membranes. The solution conformation of the Ste11 SAM determined in perdeuterated DPC micelle, using NMR spectroscopy, is defined by five helices of different lengths connected by a number of loops. In the micelle bound state, the non‐polar and aromatic residues of the Ste11 SAM lack a native‐like packing and are presumably engaged in interactions with the micelle. Using two different paramagnetic doxyl‐lipids; we have mapped out localization of Ste11 SAM residues at the micelle surface. Most of the residues appear to localize at the interfacial region of the micelle. However, a number of non‐polar residues from the central region of the domain are found to be located inside the core of the micelle including residues from the helix 4 and a loop between helix 2 and helix 3. Isothermal titration calorimetry studies demonstrate that a facile insertion of the Ste11 SAM into the DPC micelle is primarily driven by a large change in enthalpy, −50 kcal/mol with an apparent equilibrium association constant (Ka) of 7.86 × 106 M−1. Interestingly, an interfacial mutant L60R of the Ste11 SAM lacking the dimeric structure does not show detectable interactions with the lipid micelle. The micelle‐bound structure of the Ste11 SAM domain described in this work may have potential implications in the regulation of MAPK signaling whereby positioning of the Ste11 protein in close proximity to the membrane may facilitate efficient phosphorylation of the Ste11 kinase by the membrane attached upstream Ste20/pak kinase. Proteins 2009. © 2008 Wiley‐Liss, Inc.
A complementary La/SSB epitope anchored to Sequential Oligopeptide Carrier regulates the anti‐La/SSB response in immunized animals
Authors: Voitharou Chryssa , Krikorian Dimitrios , Sakarellos Constantinos , Sakarellos‐Daitsiotis Maria , Panou‐Pomonis Eugenia 
Published: July 2008

AbstractComplementary peptide epitopes, derived from complementary RNA sequences, have been used for suppressing the autoimmune response in experimental autoimmune diseases as myasthenia gravis, allergic neuritis and allergic encephalomyelitis. Aiming at contributing to the development of a tool that could regulate the autoantibody production against La/SSB, which is the main target of autoantibodies in Sjogren's syndrome (SS) and systemic lupus erythematosus (SLE), the complementary epitope, cpep349–364, of the minor T/major B cell epitope of La/SSB, pep349–364, was utilized for the induction of neutralizing anti‐cpep349–364 antibodies in rabbit immunizations. Complementary peptides were coupled to an artificial carrier, developed in our laboratory, in order to enhance the complementary potency of cpep349–364 and its counterpart. This carrier, named Sequential Oligopeptide Carrier, SOCn, formed by the repeating tripeptide Lys‐Aib‐Gly, adopts helical conformation, which allows the anchored peptide epitopes to preserve their initial reactivity such as molecular recognition, antigenicity/immunogenicity. Our study provides proof of evidence of specific interactions between idiotypic (Id)/anti‐idiotypic (anti‐Id) antibodies generated in immunized animals by the sense epitope (conjugate I) of La/SSB and its complementary counterpart (conjugate II). It was also demonstrated that the Id/anti‐Id association is specifically disrupted by adding either the sense epitope (conjugate I) or its complementary counterpart (conjugate II). A mutual neutralization of Id/anti‐Id antibodies was observed in vivo, which implies that generation of anti‐Id antibodies by immunization with the complementary La/SSB epitope could scavenge the anti‐La/SSB response. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
Preface: phys. stat. sol. (c) 5/9
Authors: Arakawa Yasuhiko , Hirayama Yoshiro , Sogawa Tetsuomi 
Published: July 2008

AbstractThe present issue of physica status solidi (c) contains the papers presented at the 34th International Symposium on Compound Semiconductors (ISCS‐2007). The symposium was held in Kyoto, Japan, 15–18 October 2007. This conference was one of the annual series, which rotates between America, Europe and Asia. The last three conferences were held in Vancouver, Canada (2006), Rust, Germany (2005) and Seoul, Korea (2004).The symposium, whose history goes back to 1966 under the name “International Symposium on GaAs and Related Compounds” has a long standing tradition in science, technology, and applications of compound semiconductors. In this conference, 11 subcommittees (Growth and Nanostructure Formation; Transport Devices; Photonic Devices; Physics; Spintronics; Characterization, Nanoprobe and Nanomechanics; GaN and Related Semiconductors; Oxide Semiconductors; SiGe and Related Semiconductors; Carbon Related Materials; Organic Semiconductors and Other Soft Materials) cover the entire spectrum of III–V compound semiconductors as well as II–VI, SiGe, oxide semiconductors and carbon related materials.The symposium was attended by 550 registered participants from more than 25 countries all over the world. During the course of the symposium, 4 plenary talks, 27 invited papers, 7 late news papers as well as 295 contributed papers were given as oral or poster presentation. ISCS‐2007 highlighted emerging wide‐band gap and oxide semiconductor materials and devices as well as high‐speed electronics, next‐generation photonics and physics studies based on the traditional compound semiconductors.The symposium is also the venue for the attribution of three prestigious scientific awards, the Welker Award, the Quantum Device Award and the Young Scientist Award.The Proceedings contain many papers presented at the conference. The chapters are organized in a way that related papers are grouped by the subjects of the subcommittees.We would like to thank all the participants of ISCS‐2007 for contributing to the success of the symposium and acknowledge the diligent work of the committee members and referees of the manuscripts. We also thank Prof. Shizuo Fujita, Kyoto University, for the excellent local organization. Kyoto, the ancient capital of Japan with more than one thousand years of history, is full of beautiful temples, shrines, and gardens, giving us an ideal location to combine a scientific conference with motivating entertainment. Finally, we extend our thanks to Ms. Kaori Yoshida for her excellent secretary job for these proceedings.The 35th International Symposium on Compound Semiconductors, organized by Prof. Günter Weimann and Prof. Oliver Ambacher will be held at Euro‐Park, Rust near Freiburg, Germany, 21–24 September 2008.May 2008
Do transient gravity waves in a shear flow break?
Authors: Pulido M. , Rodas C. 
Published: July 2008

AbstractThe propagation of transient gravity waves in a shear flow towards their critical levels is examined using a ray tracing approximation and a higher‐degree (quasi‐optic) approximation. Because of its transient forcing, the amplitude of transient waves decays to zero in the neighbourhood of the critical region so that it is not clear whether transient gravity waves will reach the convective instability threshold or not. The analysis shows that the horizontal perturbation decays asymptotically as the inverse of the square root of time, while the vertical wavenumber depends linearly on time, thus transient gravity waves attain convective instability for long times. The theoretical results are compared with numerical simulations. The ray path approximation is not able to reproduce the maximum amplitude, but the quasi‐optic approximation gives a reasonable agreement at short and long times. There are three breaking regimes for transient gravity waves. For wave packets with a narrow frequency spectrum (quasi‐steady waves) and large enough initial wave amplitude, the wave breaking is similar to the abrupt monochromatic wave overturning. On the other hand, highly transient wave packets will dissipate near the critical region for very long times with small wave amplitudes and high vertical wavenumber. The third regime is a transition between the two extremes; in this case both wave amplitude and vertical wavenumber are important to produce the convective threshold. The dependencies of the convective instability height (a quantity that may be useful for gravity wave parametrizations) on the Richardson number and the frequency spectral width are obtained. Copyright © 2008 Royal Meteorological Society
Selecting explanatory variables with the modified version of the Bayesian information criterion
Authors: Bogdan Małgorzata , Ghosh Jayanta K. , Żak‐Szatkowska Małgorzata 
Published: July 2008

AbstractWe consider the situation in which a large database needs to be analyzed to identify a few important predictors of a given quantitative response variable. There is a lot of evidence that in this case classical model selection criteria, such as the Akaike information criterion or the Bayesian information criterion (BIC), have a strong tendency to overestimate the number of regressors. In our earlier papers, we developed the modified version of BIC (mBIC), which enables the incorporation of prior knowledge on a number of regressors and prevents overestimation. In this article, we review earlier results on mBIC and discuss the relationship of this criterion to the well‐known Bonferroni correction for multiple testing and the Bayes oracle, which minimizes the expected costs of inference. We use computer simulations and a real data analysis to illustrate the performance of the original mBIC and its rank version, which is designed to deal with data that contain some outlying observations. Copyright © 2008 John Wiley & Sons, Ltd.
Conclusive evidence on the insensitivity of additive rules to the combinational details of exchange and correlation functional in hybrid DFT methods
Authors: Firouzi Rohoullah , Zahedi Mansour 
Published: July 2008

AbstractThis account is a quest to evaluate the sensitivity of additive rules among total electronic energies of some triple molecular sets to the employed computational level. To achieve the goal, seven randomly generated hybrid functionals have been constructed and employed for calculation on a test set of 29 molecules containing second and third row elements. The computational results based on these nonoptimized DFT methods in conjunction with those of standard B3LYP method clearly demonstrates that in contrast to atomization or isomerization energies, additive rules among total electronic energies are insensitive to reliability or precision of computational method. This insensitivity to details of exchange‐correlation functional indicates that additive rules can be generally well considered using simple computational methods. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Convergence of the generalized simulated annealing method with independent parameters for the acceptance probability, visitation distribution, and temperature functions
Authors: de Andrade M. D. , Mundim K. C. , Malbouisson L. A. C. 
Published: July 2008

AbstractIn their original form, the Generalized Simulated Annealing (GSA), proposed by Tsallis and Stariolo, was defined with two independent parameters, qa and qv, used in the definition of the acceptance probability, visitation distribution, and temperature functions. In the posterior applications of this algorithm, however, another independent parameter has been introduced, replacing qv in the definition of the temperature function, becoming more efficient and allowing a convergence with a small number of cycles. Nevertheless, there is no convergence proof of the GSA algorithm to the absolute minimum in this case. In this work it is presented a convergence proof of the GSA method to the absolute minimum, with three independent parameters, qa, qv, and qT, to define the acceptance probability, visitation distribution, and temperature functions, using a modified form of the distribution function, ′g, in the formulation of the algorithm. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Electrostatic properties of small molecules by means of atomic multipoles from the quantum theory of atoms in molecules
Authors: Rodrigues Eduardo F. F. , de Sá Eduardo L. , Haiduke Roberto L. A. 
Published: July 2008

AbstractAtomic multipoles from the Quantum Theory of Atoms in Molecules (QTAIM), up to quadrupoles, and CHELPG charges are employed in the description of electrostatic properties of some small linear molecules: H2, HF, HCl, HBr, HCN, HNC, and CO. A proton is placed on the molecular axis in distances within the range 3–8 Å from the terminal atoms. The polarization of molecular electronic densities induced by the proton is readily included by the calculation of atomic multipoles in each proton‐molecule arrangement. Electrostatic potentials at the proton position as given by QTAIM multipoles are always in better agreement with the reference results, calculated directly at the B3LYP/6‐311G(3d,3p) level, than those predicted with CHELPG charges, particularly for cases in which QTAIM multipoles showed that the contribution of atomic charges to these potentials is not clearly predominant over other contributions as in H2, HCl, HBr, HNC, and CO. The lone pair at the carbon atoms in CO and HNC, as described by QTAIM atomic dipoles, is indispensable in studies of electrostatic properties of these molecules. Moreover, QTAIM multipoles are also able to describe properly the large polarizations induced by the proton along the proton‐molecule distances studied. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
New perspectives on the fundamental theorem of density functional theory
Authors: Pan Xiao‐Yin , Sahni Viraht 
Published: July 2008

AbstractThe fundamental theorem of time‐independent/time‐dependent density functional theory due to Hohenberg–Kohn (HK)/Runge–Gross (RG) proves the bijectivity between the density ρ(r)/ρ(rt) and the Hamiltonian /(t) to within a constant C/function C(t), and wave function Ψ/Ψ (t). The theorems are each proved for scalar external potential energy operators. By a unitary or equivalently a gauge transformation that preserves the density, we generalize the realm of validity of each theorem to Hamiltonians, which additionally include the momentum operator and a curl‐free vector potential energy operator defined in terms of a gauge function α (R)/α (Rt). The original HK/RG theorems then each constitute a special case of this generalization. Thereby, a fourfold hierarchy of such theorems is established. As a consequence of the generalization, the wave function Ψ/Ψ (t) is shown to be a functional of both the density ρ(r)/ρ(rt), which is a gauge‐invariant property, and a gauge function α(R)/α(Rt). The functional dependence on the gauge function ensures that as required by quantum mechanics, the wave function written as a functional is gauge variant. The hierarchy and the dependence of the wave function functional on the gauge function thus enhance the significance of the phase factor in density functional theory in a manner similar to that of quantum mechanics. Various additional perspectives on the theorem are arrived at. These understandings also address past critiques of time‐dependent theory. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
New approaches to the treatment of human herpesvirus 8‐associated disease
Authors: Casper Corey 
Published: July 2008

AbstractHuman herpesvirus 8 (HHV‐8, also known as Kaposi sarcoma‐associated herpesvirus or KSHV) is the etiologic agent of Kaposi sarcoma (KS) and primary effusion lymphoma (PEL), as well as many cases of Castleman disease. Despite significant advances in understanding the biology and natural history of these diseases, current treatment options have important limitations, and strategies to prevent their development in high‐risk individuals are lacking. This article reviews the scope of HHV‐8‐associated disease, as well as the efficacy of current treatment options. Finally, novel approaches to treatment and prevention are described, including antiviral agents, targeted molecular therapy and a combination of these modalities. Copyright © 2008 John Wiley & Sons, Ltd.
The enigma of yellow fever in East Africa
Authors: Ellis Brett R. , Barrett Alan D. T. 
Published: July 2008

AbstractDespite a safe and effective vaccine, there are approximately 200 000 cases, including 30 000 deaths, due to yellow fever virus (YFV) each year, of which 90% are in Africa. The natural history of YFV has been well described, especially in West Africa, but in East Africa yellow fever (YF) remains characterised by unpredictable focal periodicity and a precarious potential for large epidemics. Recent outbreaks of YF in Kenya (1992–1993) and Sudan (2003 and 2005) are important because each of these outbreaks have involved the re‐emergence of a YFV genotype (East Africa) that remained undetected for nearly 40 years and was previously unconfirmed in a clinically apparent outbreak. In addition, unlike West Africa and South America, YF has yet to emerge in urban areas of East Africa and be vectored by Aedes (Stegomyia) aegypti. This is a significant public health concern in a region where the majority of the population remains unvaccinated. This review describes historical findings, highlights a number of disease indicators, and provides clarification regarding the natural history, recent emergence and future risk of YF in East Africa. Copyright © 2008 John Wiley & Sons, Ltd.
Personalized satellite‐based audio and multimedia services for vehicular terminals
Authors: Berioli Matteo , Scalise Sandro , Klinkenberg Frank , Midthassel Rolv , Loeillet Christophe 
Published: July 2008

AbstractThis paper presents the personalized satellite radio, a novel satellite‐based radio concept, capable of providing radio services to vehicular terminals. This paper describes the technical solution proposed, which overcomes the classical streaming approach used for traditional radio. The main concept behind it is that individual audio and multimedia files are broadcast to the mobile users instead of transmitting a number of continuous streams. The received files are stored in a large cache located in the receiver of each mobile terminal and are sequentially played to generate a service similar to traditional radio/entertainment programmes. The resulting file‐based radio approach makes, in particular, use of higher‐layer coding at the transport layer and smart techniques to build up an audible programme with no interruptions and full audio quality based on the available files. This paper also presents the results of extensive trials that were conducted with a system prototype developed in the framework of an European Space Agency funded project. Copyright © 2008 John Wiley & Sons, Ltd.
Bayesian Markov switching models for the early detection of influenza epidemics
Authors: Martínez‐Beneito Miguel A. , Conesa David , López‐Quílez Antonio , López‐Maside Aurora 
Published: July 2008

AbstractThe early detection of outbreaks of diseases is one of the most challenging objectives of epidemiological surveillance systems. In this paper, a Markov switching model is introduced to determine the epidemic and non‐epidemic periods from influenza surveillance data: the process of differenced incidence rates is modelled either with a first‐order autoregressive process or with a Gaussian white‐noise process depending on whether the system is in an epidemic or in a non‐epidemic phase. The transition between phases of the disease is modelled as a Markovian process. Bayesian inference is carried out on the former model to detect influenza epidemics at the very moment of their onset. Moreover, the proposal provides the probability of being in an epidemic state at any given moment. In order to validate the methodology, a comparison of its performance with other alternatives has been made using influenza illness data obtained from the Sanitary Sentinel Network of the Comunitat Valenciana, one of the 17 autonomous regions in Spain. Copyright © 2008 John Wiley & Sons, Ltd.
Analysis of familial aggregation studies with complex ascertainment schemes
Authors: Matthews Abigail G. , Finkelstein Dianne M. , Betensky Rebecca A. 
Published: July 2008

AbstractFamilial aggregation studies are a common first step in the identification of genetic determinants of disease. If aggregation is found, more refined genetic studies may be undertaken. Complex ascertainment schemes are frequently employed to ensure that the sample contains a sufficient number of families with multiple affected members, as required to detect aggregation. For example, an eligibility criterion for a family might be that both the mother and daughter have disease. Adjustments must be made for ascertainment to avoid bias. We propose adjusting for complex ascertainment schemes through a joint model for the outcomes of disease and ascertainment. This approach improves upon previous simplifying assumptions regarding the ascertainment process. Copyright © 2008 John Wiley & Sons, Ltd.
Variance identification and efficiency analysis in randomized experiments under the matched‐pair design
Authors: Imai Kosuke 
Published: July 2008

AbstractIn his 1923 landmark article, Neyman introduced randomization‐based inference to estimate average treatment effects from experiments under the completely randomized design. Under this framework, Neyman considered the statistical estimation of the sample average treatment effect and derived the variance of the standard estimator using the treatment assignment mechanism as the sole basis of inference. In this paper, I extend Neyman's analysis to randomized experiments under the matched‐pair design where experimental units are paired based on their pre‐treatment characteristics and the randomization of treatment is subsequently conducted within each matched pair. I study the variance identification for the standard estimator of average treatment effects and analyze the relative efficiency of the matched‐pair design over the completely randomized design. I also show how to empirically evaluate the relative efficiency of the two designs using experimental data obtained under the matched‐pair design. My randomization‐based analysis differs from previous studies in that it avoids modeling and other assumptions as much as possible. Finally, the analytical results are illustrated with numerical and empirical examples. Copyright © 2008 John Wiley & Sons, Ltd.