bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developmental capacity of porcine nuclear transfer embryos correlate with levels of chromatin‐remodeling transcripts in donor cells
Authors: Magnani Luca , Lee Kiho , Fodor William L. , Machaty Zoltan , Cabot Ryan A. 
Published: February 2008

AbstractSomatic cell nuclear transfer (SCNT) still retains important limitations. Impaired epigenetic reprogramming is considered responsible for altered gene expression and developmental failure in SCNT‐derived embryos. After nuclear transfer the donor cell nucleus undergoes extensive changes in gene expression that involve epigenetic modifications and chromatin remodeling. We hypothesized that SNF2‐type ATP‐dependent chromatin factors contribute to epigenetic reprogramming and the relative amount of these factors in the donor cell affects developmental potential of the reconstructed embryos. In order to test this hypothesis, we assessed the relative amount of SNF2‐type ATPases (Brahma, Brg1, SNF2H, SNF2L, CHD3, and CHD5) in three different donor cells as well as in porcine metaphase II oocytes. We performed SCNT with fetal fibroblast cells, olfactory bulb (OB) progenitor cells, and porcine skin originating sphere stem cells (PSOS). We found that OB‐NT embryos and PSOS‐NT embryos resulted in a higher morulae/blastocysts ratio as compared to fibroblast‐NT embryos (23.53%, 16.98%, and 11.63%, respectively; P < 0.05). Fibroblast cells contained a significantly higher amount of SNF2L and CHD3 transcripts while Brg1 and SNF2H were the most expressed transcripts in all the cell lines analyzed. Metaphase II oocyte expression profile appeared to be unique compared to the cell lines analyzed. This work supports our hypothesis that an array of chromatin‐remodeling proteins on donor cells may influence the chromatin structure, effect epigenetic reprogramming, and developmental potential. Mol. Reprod. Dev. 75: 766–776, 2008. © 2008 Wiley‐Liss, Inc.
A simple mesh deformation technique for fluid–structure interaction based on a submesh approach
Authors: Lefrançois E. 
Published: February 2008

AbstractThis paper describes an improvement in techniques currently used for mesh deformations in fluid–structure calculations in which large body motions are encountered. The proposed approach moving submesh approach (MSA) is based on the assumption of a pseudo‐material deformation applied on a triangular coarse mesh to significantly reduce the CPU time. The computation mesh is then updated using an interpolation technique similar to the finite element method. This method may be applied on structured as well as on unstructured meshes. An extension to complex boundaries undergoing large rigid‐body motions is proposed combining the MSA and an encapsulation box. The influence of the coarse mesh on the quality mesh is discussed. Copyright © 2008 John Wiley & Sons, Ltd.
Comparison of DIGE and post‐stained gel electrophoresis with both traditional and SameSpots analysis for quantitative proteomics
Authors: Karp Natasha A. , Feret Renata , Rubtsov Denis V. , Lilley Kathryn S. 
Published: February 2008

Abstract2‐DE is an important tool in quantitative proteomics. Here, we compare the deep purple (DP) system with DIGE using both a traditional and the SameSpots approach to gel analysis. Missing values in the traditional approach were found to be a significant issue for both systems. SameSpots attempts to address the missing value problem. SameSpots was found to increase the proportion of low volume data for DP but not for DIGE. For all the analysis methods applied in this study, the assumptions of parametric tests were met. Analysis of the same images gave significantly lower noise with SameSpots (over traditional) for DP, but no difference for DIGE. We propose that SameSpots gave lower noise with DP due to the stabilisation of the spot area by the common spot outline, but this was not seen with DIGE due to the co‐detection process which stabilises the area selected. For studies where measurement of small abundance changes is required, a cost–benefit analysis highlights that DIGE was significantly cheaper regardless of the analysis methods. For studies analysing large changes, DP with SameSpots could be an effective alternative to DIGE but this will be dependent on the biological noise of the system under investigation.
Cartilage proteomics: Challenges, solutions and recent advances
Authors: Wilson Richard , Bateman John F. 
Published: February 2008

AbstractThe mammalian skeleton is largely composed of cartilage and bone. The major functions of cartilage are first to provide a transient template for development of the axial and appendicular skeleton and secondly to provide permanent articulating joint surfaces. The unique cartilage extracellular matrix (ECM) is essential for the load‐bearing and viscoelastic properties of cartilage tissues. Maintained by the chondrocytes, the ECM contains a myriad of proteins and proteoglycans organized into precise networks. Many cartilage disorders result from genetic disruption of cartilage ECM components, their interactions and/or degradation. Although technically challenging, the proteomic analysis of cartilage in development and disease is now emerging as a clinically important research area. In this article, we will review progress in the proteomic characterization of cartilage‐related samples.
Proteomics and naturally occurring animal diseases: Opportunities for animal and human medicine
Authors: Doherty Mary K. , Beynon Robert J. , Whitfield Phillip D. 
Published: February 2008

AbstractThe exquisite sensitivity and selectivity of contemporary protein analysis means that proteomics is increasingly at the forefront of biomedical investigation. The molecular basis of diseases states can now be revealed at the protein level, complementing transcript and genomics data. Moreover, protein biomarkers are increasingly accessible to the scrutiny of the protein chemist. The focus of these studies has been on human systems but diseases that occur naturally in nonhuman mammalian species may provide additional perspectives on the pathophysiology of human disorders. As a result, veterinary research aimed at promoting animal health may lead to concomitant improvements in the characterisation, clinical management and treatment of human diseases. This review will focus on the use of proteomic approaches to study naturally occurring disease states in animals and discuss ways by which these investigations may advance the health of both animals and humans.
Electronic structure and linear optical properties of the double perovskite La2NaRuO6
Authors: Ahmed A. S. , Chen H. , Yuan H. K. 
Published: February 2008

AbstractFirst‐principle calculations with the full‐potential linearized augmented plane‐wave (FP‐LAPW) method have been performed to investigate electronic and linear optical properties of the La2NaRuO6 double perovskite. Within the general gradient approximation (GGA), the spin‐polarized calculations predict La2NaRuO6 to be an insulator with antiferromagnetic interactions between the Ru atoms. A gap separation of about 0.64 eV has been shown in the band‐structure feature between the majority and minority spin components. The total spin magnetic moment is about 3.06μB, that mainly comes from Ru atom. The calculated structural parameters and spin moment are consistent with experimental values. The optical constants and energy‐loss spectrum are calculated within the electric‐dipole approximation and the main features shown by the optical function curves can be ascertained on the base of the analysis of the band structure. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Investigation of relaxation stresses in amorphous Pd52Ni32P16
Authors: Melnick A. B. , Djafarov E. J. 
Published: February 2008

AbstractIt is suggested to measure relaxation stresses in amorphous alloys on the basis of diffraction data. Using this procedure, we analysed the elimination of local stresses on low‐temperature annealing of amorphous Pd52Ni32P16. As a result, a three‐dimensional pattern of a stress distribution in raw alloy was obtained, the main feature of which was nanoscale heterogeneities. We found that the value of relaxation energy for Pd52Ni32P16 is 1.49 kJ/mol. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Fe in III–V and II–VI semiconductors
Authors: Malguth Enno , Hoffmann Axel , Phillips Matthew R. 
Published: February 2008

AbstractMany theoretical and experimental studies deal with the realization of room‐temperature ferromagnetism in dilute magnetic semiconductors (DMS). However, a detailed quantitative understanding of the electronic properties of transition metal doped semiconductors has often been neglected. This article points out which issues concerning electronic states and charge transfers need to be considered using Fe as an example. Methods to address these issues are outlined, and a wealth of data on the electronic properties of Fe doped III–V and II–VI compound semiconductors that have been obtained over a few decades is reviewed thoroughly. The review is complemented by new results on the effective‐mass‐like state consisting of a hole bound to Fe2+ forming a shallow acceptor state.The positions of established Fe3+/2+ and Fe2+/1+ charge transfer levels are summarized and predictions on the positions of further charge transfer levels are made based on the internal reference rule. The Fe3+/4+ level has not been identified unambiguously in any of the studied materials. Detailed term schemes of the observed charge states in tetrahedral and trigonal crystal field symmetry are presented including hyperfine structure, isotope effects and Jahn–Teller effect. Particularly, the radiative transitions Fe3+(4T1 → 6A1) and Fe2+(5E → 5T2) are analyzed in great detail.An effective‐mass‐like state [Fe2+, h] consisting of a hole bound to Fe2+ is of great significance for a potential realization of spin‐coupling in a DMS. New insights on this shallow acceptor state could be obtained by means of stress dependent and temperature dependent absorption experiments in the mK range. The binding energy and effective Bohr radius were determined for GaN, GaP, InP and GaAs and a weak exchange interaction between the hole and the Fe2+ center was detected.With regard to the Fe3+ ground state, 6A1, in GaP and InP, the hyperfine structure level Γ8 was found to be above the Γ8 level.All results are discussed with respect to a potential realization of a ferromagnetic spin‐coupling in DMSs. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Doping asymmetry in wide‐bandgap semiconductors: Origins and solutions
Authors: Yan Yanfa , Wei Su‐Huai 
Published: February 2008

AbstractWide‐bandgap (WBG) semiconductors are essential materials for making short‐wavelength and transparent optoelectronic devices. However, a serious obstacle to realizing WBG semiconductor‐based devices is their common doping asymmetry problem, i.e., a WBG semiconductor can be doped easily either p‐type or n‐type, but not both. This paper reviews the possible origins for doping asymmetry problems and updates our recent progress in searching for approaches to overcome the doping bottleneck in WBG semiconductors. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Calculating scattering matrices by wave function matching
Authors: Zwierzycki M. , Khomyakov P. A. , Starikov A. A. , Xia K. , Talanana M. , Xu P. X. , Karpan V. M. , Marushchenko I. , Turek I. , Bauer G. E. W. , Brocks G. , Kelly P. J. 
Published: February 2008

AbstractThe conductance of nanoscale structures can be conveniently related to their scattering properties expressed in terms of transmission and reflection coefficients. Wave function matching (WFM) is a transparent technique for calculating transmission and reflection matrices for any Hamiltonian that can be represented in tight‐binding form. A first‐principles Kohn–Sham Hamiltonian represented on a localized orbital basis or on a real space grid has such a form. WFM is based upon direct matching of the scattering‐region wave function to the Bloch modes of ideal leads used to probe the scattering region. The purpose of this paper is to give a pedagogical introduction to WFM and present some illustrative examples of its use in practice. We briefly discuss WFM for calculating the conductance of atomic wires, using a real space grid implementation. A tight‐binding muffin‐tin orbital implementation very suitable for studying spin‐dependent transport in layered magnetic materials is illustrated by looking at spin‐dependent transmission through ideal and disordered interfaces. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Coarse‐grained modelling of polypyrrole morphologies
Authors: Rühle Victor , Kirkpatrick James , Kremer Kurt , Andrienko Denis 
Published: February 2008

AbstractA multiscale model to simulate large scale morphologies and study charge transport in polypyrrole is developed. First, ab‐initio methods are used to derive an atomistic force field. Coarse graining of this atomistic model is then performed. At a final stage, the analysis of simulated morphologies allows to split polymer chains into conjugated segments, which can further be used to simulate both inter‐ and intrachain charge dynamics. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On the application of the Edwards–Anderson order parameter to the Coulomb glass
Authors: Matulewski J. , Baranovskii S. D. , Thomas P. 
Published: February 2008

AbstractIt has been suggested in the literature to use a kind of a modified Edwards–Anderson (EA) order parameter borrowed from the field of spin glasses in order to characterize the correlated distribution of electrons governed by the long‐range many‐body interactions in a disordered system with localized states (the Coulomb glass). So far this idea has been applied to the lattice model of the disordered media. We show by straight‐forward Monte Carlo computer simulations that such an order parameter is of little use for interacting charge systems with spatial disorder. It turns out that the EA parameter for the spatially disordered system tends to zero at much higher temperatures than in the case of the lattice. Furthermore, the value of the modified EA parameter appears dependent on the system size, which makes this parameter rather useless. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A simple topological factor determining the allowance of pericyclic reactions
Authors: Gineityte V. 
Published: February 2008

AbstractThe study is aimed at revealing the possible manifestation of the overlap topology of AOs at early stages of pericyclic reactions. To this end, formation of an evenmembered cycle of carbon atoms is considered as a unified model, wherein relatively strong (CC) bonds alternate with weak ones. A direct perturbative method is applied to derive algebraic expressions for energy and bond order corrections due to cyclization. To represent the overlap topology of 2pz AOs over the cycle, a new concept of the roundabout interaction is introduced. The relevant definition contains a product of resonance parameters (or overlap integrals) between orbitals of all neighboring pairs of CC bonds and a certain N‐dependent parity factor, where N coincides with the total number of these bonds. The principal result of the study consists in demonstration of proportionality of both energy and bond order corrections to the roundabout interaction of the given cycle and thereby of a direct dependence between these corrections and the overlap topology of AOs. Moreover, the sign of the roundabout interaction is shown to determine the allowance of the given way of the process, viz. cycles described by positive (negative) roundabout interactions refer to allowed (forbidden) ways. Thus, an analog of the famous Woodward‐Hoffmann rule is obtained, wherein the overlap topology of AOs stands instead of symmetry of molecular orbitals. Along with stabilization of the cycle vs. the initial open chain, the allowed processes also are necessarily characterized by growing uniformity of all bond orders over the cycle, while the forbidden ones are accompanied by both destabilization and an increasing distinction between strong and weak bonds. The results obtained also yield a new definition of the concerted nature of pericyclic processes. The general conclusions of the study are illustrated by consideration of specific examples including the electrocyclic closure of polyene chains. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Exactly solvable quantum potentials with special functions solutions
Authors: Peña J. J. , Ovando G. , Morales J. , García‐Ravelo J. , García J. 
Published: February 2008

AbstractIn this work, a canonical point and a gauge transformation applied to theg(x) times differential equations (DE) for special functions (SF) is used to convert it into a Schrödinger‐like equation. This method leads to exactly solvable potentials allowing special functions solutions. For specific applications, keeping in mind the general DE for SF, the choice of the coefficients that identify the SF under study allows to find the equivalent of the Witten superpotential and wavefunctions for eachg(x). That is, the choice of a particularg(x) leads straightforwardly to those exactly solvable potentials having as wavefunctions the SF under consideration. As a useful application of the proposed method, we considered explicitly the potentials associated to the standard Hermite, Laguerre, Legendre, and Bessel SF in the case of some particular forms ofg(x). However, the proposed approach can be directly applied to any other standard SF with the aim to obtain exactly solvable potentials that can be used in the modelling of quantum chemical applications. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
A classification of cranial implants based on the degree of difficulty in computer design and manufacture
Authors: Poukens Jules , Laeven Paul , Beerens Maikel , Nijenhuis Gerard , Sloten Jos Vander , Stoelinga Paul , Kessler Peter 
Published: February 2008

AbstractBackgroundSkull defects usually create aesthetic and functional disturbances to the patient. These defects are currently reconstructed by using computer‐aided design and manufacturing processes. Classification of skull defects becomes important in discussing the complexity of reconstruction in clinical practice or comparing clinical results in scientific articles.MethodsA more comprehensive classification, which takes into account not only the anatomical location but also the degree of difficulty in designing and manufacturing the implant, is presented here. It is not our intention to describe the different treatment modalities; therefore, only two clinical examples are presented to demonstrate the purpose of classification.ResultsThe new classification enables a more detailed comparison of the clinical outcome of different modes of treatment for skull defects.ConclusionsThe proposed classification reflects the degree of difficulty in designing and manufacturing of implants and can be very useful when comparing treatment results of skull defects for clinical or scientific purposes. Copyright © 2008 John Wiley & Sons, Ltd.
Securing the next generation mobile network
Authors: Hashim Fazirulhisyam , Kibria M. Rubaiyat , Jamalipour Abbas 
Published: February 2008

AbstractDespite well‐defined security models to prevent fraudulent intrusion, a number of security attacks have been reported in literature for legacy networks. While a section of these attacks are due to inherent design limitations, others stem from the pervasive introduction of Internet Protocol (IP)‐based applications and external attacks. The former can be addressed by the continual evolution of the system (as is the case with existing systems) whereas the latter requires careful designing. With the advent of all‐IP next generation mobile network (NGMN) inter‐connecting disparate access technologies, the design process assumes paramount importance in relation to detecting/preventing/eliminating migration of attacks through infected terminals. Taking into consideration the fact that standardization bodies are responsible for individual network evolution, a cooperative NGMN security architecture is proposed in this paper that identifies and isolates/eliminates security attacks. The cooperation is encased by the network elements within the NGMN hierarchy and utilizes an anomaly‐based attack detection mechanism. Several dominant security attacks are simulated to demonstrate the effectiveness of the proposed architecture. Copyright © 2008 John Wiley & Sons, Ltd.
A design of optimal key management scheme for secure and survivable wireless sensor networks
Authors: Qian Yi , Lu Kejie , Rong Bo , Tipper David 
Published: February 2008

AbstractIn this paper, we investigate optimal key management design for secure and survivable heterogeneous wireless sensor networks (HWSNs). In particular, we formulate the key management problem as a multi‐objective optimization problem, in which the cost of the sensor network, and the security and survivability metrics of the sensor network are taken into account. To solve the multi‐objective optimization model, we develop a genetic algorithm (GA)‐based approach that can efficiently obtain near‐optimal solutions. We show the performance of our scheme through extensive numerical results. With a small amount of powerful sensor nodes in HWSN, we can balance the cost of the sensor network and the resilience of the sensor network with the required security constraint in different hostile environment. Copyright © 2008 John Wiley & Sons, Ltd.
Interactions at the interface between thermoplastic rubber and polychloroprene adhesive
Authors: Navarro‐Bañón M. Virtudes , Pastor‐Blas M. Mercedes , Martín‐Martínez José Miguel 
Published: February 2008

AbstractThe interface produced between a chlorinated thermoplastic styrene‐butadiene‐styrene rubber and a polychloroprene (PCP) adhesive has been studied and compared to the interface produced using a polyurethane (PU) adhesive. Chlorination of the rubber was produced by spin coating solutions of trichloroisocyanuric acid in methyl ethyl ketone. The adhesive solution was spin coated on to the chlorinated rubber and the interface between the chlorinated rubber and the adhesive was analyzed by infrared spectroscopy.Chlorination of the rubber produces cross‐linking of the outermost chlorinated and oxidized rubber surface, which becomes insoluble in toluene. The chlorinated rubber chains are able to migrate through the chlorinated rubber/adhesive interface and produce a cross‐linked interface. Similar interfaces are obtained with PU or PCP adhesive. However it is the addition of a thermoreactive phenolic tackifier resin to the PCP adhesive, which imparts appropriate rheological properties to the PCP adhesive, responsible for the increased adhesion properties. Copyright © 2008 John Wiley & Sons, Ltd.