bluuebunny/crossref_metadata_2025_split huggingface dataset:
Viscoelastic characterization of polymers using instrumented indentation. I. Quasi‐static testing*
Authors: VanLandingham M. R. , Chang N.‐K. , Drzal P. L. , White C. C. , Chang S.‐H. 
Published: June 2005

AbstractThe use of instrumented indentation to characterize the mechanical response of polymeric materials was studied. A model based on contact between a rigid probe and a linear viscoelastic material was used to calculate values for the creep compliance and stress relaxation modulus for two glassy polymeric materials, epoxy and poly(methyl methacrylate), and two poly(dimethyl siloxane) (PDMS) elastomers. Results from bulk rheometry studies were used for comparison with the indentation stress relaxation results. For the two glassy polymers, the use of sharp pyramidal tips produced responses that were considerably more compliant (less stiff) than the rheometry values. Additional study of the deformation remaining in epoxy after indentation creep testing as a function of the creep hold time revealed that a large portion of the creep displacement measured was due to postyield flow. Indentation creep measurements of the epoxy with a rounded conical tip also produced nonlinear responses, but the creep compliance values appeared to approach linear viscoelastic values with decreasing creep force. Responses measured for the unfilled PDMS were mainly linear elastic, with the filled PDMS exhibiting some time‐dependent and slight nonlinear responses in both rheometry and indentation measurements. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 1794–1811, 2005
Perceptions of changes in weight among African American breast cancer survivors
Authors: Weathers Benita , Barg Frances K. , Collier Aliya , Halbert Chanita Hughes 
Published: June 2005

AbstractBack ground: Although African American breast cancer survivors are most likely to gain weight following diagnosis and treatment compared to women from other ethnic groups, limited information is available on psychological and behavioral reactions to weight change in this population.Objectives: To explore perceptions and reactions to weight change in African American breast cancer survivors.Methodology: A parallel mixed methods approach was used to explore experiences with and reactions to weight change following breast cancer diagnosis and treatment. Participants were 16 short‐ and long‐term African American breast cancer survivors.Results: Nine out of 16 participants gained weight following diagnosis and treatment and most participants were concerned about these changes. Most participants were also interested in diet and exercise programs; however, a holistic and common sense approach to diet and physical activity emerged as key themes.Conclusions: Although prior reports have found that African American women in the general population report a greater tolerance for larger body sizes, most participants in this study were concerned about changes in their weight and were actively trying to minimize weight gain. Several themes emerged regarding physical activity and dietary behaviors; overall, participants described a holistic and practical approach to these behaviors. Copyright © 2005 John Wiley & Sons, Ltd.
Soft Plasma Treated Surfaces: Tailoring of Structure and Properties for Biomaterial Applications
Authors: Förch Renate , Zhang Zhihong , Knoll Wolfgang 
Published: June 2005

AbstractSummary: This paper aims to discuss and review developments in plasma surface modification techniques which have been seen over the past few years, with particular emphasis on low energy or soft plasma assisted surface polymerisation processes. While early work focussed mainly on protective coatings and surface activation, the advancements in microtechnology in the 1980s followed by those in nanotechnology in the 1990s and 2000s have resulted in new challenges for surface processing and surface modification processes. The latest advancements in plasma polymer chemistry have shown tremendous potential for the synthesis of reasonably well defined molecular structures with a high retention of functional groups. Some of the latest achievements and newest insights into the behaviour of such deposits in a liquid environment will be discussed, with a particular focus on bio‐nanotechnological applications. Utilising novel approaches in surface and interface analysis, it will be shown that plasma polymers can be tailored to have considerable elasticity with reversible swelling characteristics, offering a three‐dimensional interface for biomolecular immobilisation procedures in a liquid environment.SPR data suggesting the elastic and reproducible swelling and shrinking of pp‐allylamine under a humid nitrogen environment.magnified imageSPR data suggesting the elastic and reproducible swelling and shrinking of pp‐allylamine under a humid nitrogen environment.
RF Plasma Sputtering Deposition of Hydroxyapatite Bioceramics: Synthesis, Performance, and Biocompatibility
Authors: Xu Shuyan , Long Jidong , Sim Lina , Diong Cheong Hoong , Ostrikov Kostya (Ken) 
Published: June 2005

AbstractSummary: Hydroxyapatite (HA) coatings have numerous applications in orthopedics and dentistry, owing to their excellent ability to promote stronger implant fixation and faster bone tissue ingrowth and remodeling. Thermal plasma spray and other plasma‐assisted techniques have recently been used to synthesize various calcium phosphate‐based bioceramics. Despite notable recent achievements in the desired stoichiometry, phase composition, mechanical, structural, and biocompatible properties, it is rather difficult to combine all of the above features in a single coating. For example, many existing plasma‐sprayed HA coatings fall short in meeting the requirements of grain size and crystallinity, and as such are subject to enhanced resorption in body fluid. On the other hand, relatively poor interfacial bonding and stability is an obstacle to the application of the HA coatings in high load bearing Ti6Al4V knee joint implants. Here, we report on an alternative: a plasma‐assisted, concurrent, sputtering deposition technique for high performance biocompatible HA coatings on Ti6Al4V implant alloy. The plasma‐assisted RF magnetron co‐sputtering deposition method allows one to simultaneously achieve most of the desired attributes of the biomimetic material and overcome the aforementioned problems. This article details the film synthesis process specifications, extensive analytical characterization of the material's properties, mechanical testing, simulated body fluid assessments, biocompatibility and cytocompatibility of the HA‐coated Ti6Al4V orthopedic alloy. The means of optimization of the plasma and deposition process parameters to achieve the desired attributes and performance of the HA coating, as well as future challenges in clinical applications are also discussed.SEM image of differentiated cells on HA bioceramics deposited by plasma sputtering, after a two‐day incubation period.magnified imageSEM image of differentiated cells on HA bioceramics deposited by plasma sputtering, after a two‐day incubation period.
Transmission Fluctuation Spectrometry in Concentrated Suspensions. Part Three: Measurements
Authors: Shen Jianqi , Riebel Ulrich 
Published: June 2005

AbstractThe theory of transmission fluctuation spectrometry (TFS) was developed for particle size analysis in flowing particle suspensions, whereby the statistical transmission fluctuations are used to extract the particle size distribution (PSD) and particle concentration.In the previous parts of this publication high concentration effects on TFS were investigated theoretically and by simulation. This work presents a study on TFS measurements in concentrated suspensions. By introducing an empirical correction to include the high concentration effects from both the monolayer structure and particle overlapping in the inversion algorithm, it is possible to obtain the particle size distribution and particle concentration over broad ranges of particle sizes and concentrations.
Transmission Fluctuation Spectrometry with Spatial Correlation
Authors: Shen Jianqi , Riebel Ulrich , Guo Xiaoai 
Published: June 2005

AbstractTransmission fluctuation spectrometry (TFS) is being developed as a new method of particle size analysis. In the early approaches, the particle suspension was illuminated by one beam with finite beam diameter and the transmission signals underwent a process with variable spatial and/or temporal averaging and a subsequent nonlinear operation. The transmission fluctuations were obtained as a spectrum which included the information on particle size distribution and particle concentration.A new approach presented here employs two narrow parallel beams. While changing the beam separation, the transmission fluctuations of these two beams are expressed in terms of the expectancy of the transmission product (ETP). The analytical expression of the ETP through a monolayer is derived and the ETP of a 3‐dimensional suspension is formulated based on the layer model. The deviation between the transition functions of 3‐dimensional suspensions and monolayers is found to be affected by effects from particle overlapping and monolayer structure.
Statistical Analysis of Pellet Size Variation in Commercial Catalysts
Authors: Wu Dongfang , Zhou Jiancheng , Li Yongdan 
Published: June 2005

AbstractThe size of commercial catalyst pellets is distributed over a range of values. The suitability of the normal, lognormal and Weibull distributions to model pellet size variation was judged by three quality‐of‐fit criteria: the coefficient of determination, Akaike information criterion and Kolmogorov‐Smirnov test, respectively. It is concluded that the normal distribution is most appropriate to represent the diameter distribution of the spherical pellets, though the lognormal distribution also gives a satisfactory fit. The Weibull distribution is the best one to represent the length distribution of the catalyst tablets. It is elucidated that a downward tail of the tablet length distribution results from the fluctuating characteristics of feeding for the individual tablets. It is also pointed out that pellet size distributed in a narrow window is beneficial to the industrial application of solid catalysts.
Various strategies of using residual dipolar couplings in NMR‐driven protein docking: Application to Lys48‐linked di‐ubiquitin and validation against 15N‐relaxation data
Authors: van Dijk Aalt D.J. , Fushman David , Bonvin Alexandre M.J.J. 
Published: June 2005

AbstractWhen classical, Nuclear Overhauser Effect (NOE)‐based approaches fail, it is possible, given high‐resolution structures of the free molecules, to model the structure of a complex in solution based solely on chemical shift perturbation (CSP) data in combination with orientational restraints from residual dipolar couplings (RDCs) when available. RDCs can be incorporated into the docking following various strategies: as direct restraints and/or as intermolecular intervector projection angle restraints (Meiler et al., J Biomol NMR 2000;16:245–252). The advantage of the latter for docking is that they directly define the relative orientation of the molecules. A combined protocol in which RDCs are first introduced as intervector projection angle restraints and at a later stage as direct restraints is shown here to give the best performance. This approach, implemented in our information‐driven docking approach HADDOCK (Dominguez et al., J Am Chem Soc 2003;125:1731–1737), is used to determine the solution structure of the Lys48‐linked di‐ubiquitin, for which chemical shift mapping, RDCs, and 15N‐relaxation data have been previously obtained (Varadan et al., J Mol Biol 2002;324:637–647). The resulting structures, derived from CSP and RDC data, are cross‐validated using 15N‐relaxation data. The solution structure differs from the crystal structure by a 20° rotation of the two ubiquitin units relative to each other. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Comparing protein–ligand docking programs is difficult
Authors: Cole Jason C. , Murray Christopher W. , Nissink J. Willem M. , Taylor Richard D. , Taylor Robin 
Published: June 2005

AbstractThere is currently great interest in comparing protein–ligand docking programs. A review of recent comparisons shows that it is difficult to draw conclusions of general applicability. Statistical hypothesis testing is required to ensure that differences in pose‐prediction success rates and enrichment rates are significant. Numerical measures such as root‐mean‐square deviation need careful interpretation and may profitably be supplemented by interaction‐based measures and visual inspection of dockings. Test sets must be of appropriate diversity and of good experimental reliability. The effects of crystal‐packing interactions may be important. The method used for generating starting ligand geometries and positions may have an appreciable effect on docking results. For fair comparison, programs must be given search problems of equal complexity (e.g. binding‐site regions of the same size) and approximately equal time in which to solve them. Comparisons based on rescoring require local optimization of the ligand in the space of the new objective function. Re‐implementations of published scoring functions may give significantly different results from the originals. Ostensibly minor details in methodology may have a profound influence on headline success rates. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Structural and immunological reactivity of the principal neutralizing determinant V3 of glycoprotein gp 120 of HIV‐1
Authors: Borbe Harald C. , Stuber György , Wagner Ralf , Wolf Hans , Modrow Susanne 
Published: May 2005

AbstractThe variable domain V3 in the outer glycoprotein gp 120 of HIV‐1 is a highly important region with respect to immune response during the course of viral infection. Neutralizing antibodies are produced against this domain; in addition, it has been shown to be a functionally active epitope for T helper and cytotoxic T cells. The high degree of amino acid variability in individual HIV‐isolates, however, limits the use of the V3‐domain in approaches to vaccine development. In order to characterize the residues important for antibody interaction and binding to MHC class I proteins, we constructed a consensus sequence of the V3‐domain with broad reactivity [1] and used synthetic peptides derived from this consensus with individual residues altered to alanine. These peptides were used as antigens in ELISA tests to define the amino acids which are important for binding to human and rabbit/anti‐peptide immunoglobulins. In addition, we used these alanine‐derived peptides in interaction studies with human HLA‐A2.1 and mouse H‐2Dd by testing their capacity to stabilize the respective MHC class I protein complexes on the surface of mutant cell lines T2 and RMA‐S transfected with Dd gene. The experimental tests allowed us to define individual residues involved in antibody and MHC‐protein interaction, respectively. In a further approach, we used those results to design interaction models with HLA‐A2.1 and H‐2Dd. Therefore, a structural model for H‐2Dd was built that exhibits an overall similar conformation to the parental crystal structure of HLA‐A2.1. The resulting interaction models show V3‐peptide bound in an extended β‐conformation with a bulge in its centre for both H‐2Dd and HLA‐A2.1 complexes. The N‐ and C‐termini of V3 peptide reside in conserved pockets within both MHC‐proteins. Anchoring residues could be determined that are crucial for the binding of the respective MHC class I haplotype. The cross‐reactivity of V3‐peptide in enhancing the expression of two different MHC class I molecules (H‐2Dd and HLA‐A2.1) is shown to be based on similar peptide binding that induces an almost identical peptide conformation.
The use of N‐urethane‐protected N‐carboxyanhydrides (UNCAs) in amino acid and peptide synthesis
Authors: Fehrentz Jean‐Alain , Genu‐Dellac Corine , Amblard Muriel , Winternitz Franclois , Loffet Albert , Martinez Jean 
Published: May 2005

AbstractN‐Urethane‐protected N‐carboxyanhydrides (UNCAs) are very reactives. They have been successfully used in peptide synthesis, in both solution and solid phase. We have demonstrated that UNCAs are interesting starting materials for the synthesis of various amino acid derivatives. Chemoselective reduction of UNCAs with sodium borohydride led the corresponding N‐protected β amino alcohols. Reaction of UNCAs with Meldrum's acid, followed by cyclisation, yielded enantiomerially pure tetramic acid derivatives. Diastereoselective reduction of tetramic acid derivatives produced (4S,5S)‐N‐alkoxycarbonyl‐4‐hydroxy‐5‐alkylpyrrolidin‐2‐ones derived from amino acids, which after hydrolysis yielded statine and statine analogues. Tetramic acid derivatives could also be obtained by reaction of UNCAs with benzyl ethyl followed by hydrogenolytic deprotection and decarboxylation. UNCAs also reacted with phosphoranes to produce the ketophosphorane in excellent yields. Subsequent oxidation with oxone or with [bis(acetoxy)‐iodol]‐benzene produced vicinal tricarbonyl derivatives. These reactions usually proceeded smoothly and with high yields.
Proteinogenic amino acids labelled with 15N and/or 13C for application in peptide synthesis: A short review with a comprehensive list of published derivatives
Authors: Ragnarsson Ulf 
Published: May 2005

AbstractA review is given of the literature dealing with the most common protected derivatives of 15N‐ and/or 13C‐labelled amino acids of interest in peptide synthesis. The list contains all such Boc‐, Z‐ and Fmoc‐amino acids as well as published methyl, ethyl, t‐butyl and benzyl esters.
Synthesis and properties of the first all‐aza analogue of a biologically active peptide
Authors: Gante Joachim , Krug Michael , Lauterbach Günter , Weitzel Reinhard , Hiller W. 
Published: May 2005

AbstractThe synthesis of the first all‐aza‐amino acid analogue (2) of a peptidic renin inhibitor is described. The X‐ray structural analysis and molecular modelling investigations of this novel compound reveal interesting conformational features which have a significant impact on its biological activity. In addition, insight into conformational features of azapeptides in general in comparison with the corresponding purely peptidic compounds is given.
Solid‐phase Synthesis of ω‐Agatoxin IVA, a P‐type Calcium Channel Blocker
Authors: Najib Jamila , Letailleur Thierry , Gesquière Jean‐Claude , Tartar André 
Published: May 2005

Abstractω‐Agatoxin IVA, isolated from the venom of funnel web spider Agelenopsis aperta, blocks potently and selectively P‐type calcium channels. This toxin, composed of 48 amino acids and containing 8 cysteine residues, was synthesized by the solid‐phase procedure. The Cys residues were protected by acetamidomethyl (Acm) groups which were removed by mercuric acetate. During treatment with mercuric acetate, a by‐product was detected, involving modification of tryptophan residues by the Acm groups. This side reaction can be completely prevented by addition of an excess of tryptophan in the reaction medium during Acm deprotection.The resulting peptide was submitted to an oxidative refolding, in different conditions, in order to determine the most favourable protocol. After formation of the four disulphide bonds, the toxin was purified by successive preparative HPLC, on two different supports, and fully characterized by analytical HPLC, capillary electrophoresis, amino acid analysis, mass spectrometry and Edman degradation. It was found to block the P‐type calcium channel with a similar biological potency as described for the natural product.
The Use of Proton Chemical Shifts to Define the Solution Structure of a Dimeric Peptide
Authors: Busetta Bernard , Picard Philippe 
Published: May 2005

AbstractFor flexible peptides, nuclear Overhauser Effects (NOE) experiments do not provide enough information to ensure a correct definition of their solution structure. The use of distance constraints, derived from the knowledge of proton chemical shifts, is developed to restrict the number of possible conformations. In the case of flexible molecules, randomization appears as an important factor of the correct estimation of the chemical shifts from the 3D structure. The refinement of the solution structure of the highly flexible AVP‐like parallel dimer is described to illustrate this process.
The Use of Crown Ethers in Peptide Chemistry – V. Solid‐phase Synthesis of Peptides by the Fragment Condensation Approach using Crown Ethers as Non‐covalent Protecting Groups
Authors: Botti Paolo , Ball Haydn L. , Lucietto Pierluigi , Pinori Massimo , Rizzi Emanuele , Mascagni Paolo 
Published: May 2005

AbstractWe have previously described the conditions by which peptide synthesis by the solid‐phase fragment condensation approach can be carried out using crown ethers as non‐covalent protection for the Nα ‐amino group. Here we demonstrate that the procedure can be extended to large, partially protected peptide fragments possessing free Lys and/or Arg residues. The first step was to ensure that complex formation on the side chain of amino acids was not detrimental to the methodology and exhibited the same solubility and coupling properties as Nα ‐complexed peptides. Thus, a model hexapeptide was synthesized using Fmoc chemistry containing Lys and Arg residues, which, when complexed with 18‐Crown‐6, was readily soluble in DCM and coupled quantitatively to a resin‐bound tetrapeptide. Two tripeptides were then prepared, one containing a free Ser residue, the other free Tyr, to examine the possible occurrence of side reactions. After coupling using standard conditions only the former tripeptide exhibited the formation of the O‐acylation by‐product (5%). Another model hexapeptide containing Lys, Tyr, Ser and Asp protected with a TFA‐stable adamantyl group was complexed with 18‐Crown‐6 and coupled to the resin‐bound tetrapeptide with near quantative yield. Extending the length of the peptide to 21 and 40 residues, which represent sequences Gly52 to Leu72 (21‐mer) and Pro33 to Leu72 (40‐mer) from Rattus norvegicus chaperonin 10 protein, respectively, resulted in partially protected fragments that were readily soluble in water, thus enabling purification by RP‐HPLC. Complexation with 18‐Crown‐6 gave two highly soluble products that coupled to resin‐board tetramer with 68% and 50% coupling efficiencies for the 21‐mer and 40‐mer, respectively. Treatment with 1% DIEA solutions followed by acidolytic cleavage and purification of the major product confirmed that the correct product had been formed, when analysed by amino acid analysis and ESI‐MS. These results served to extend the methodology of non‐covalent protection of large partially protected peptide fragments for the stepwise fragment condensation of polypeptides.
Application of entropy calculations to the determination of transition temperature in zirconium
Authors: Srepusharawoot Pornjuk , Pinsook Udomsilp 
Published: June 2005

AbstractThe Helmholtz free energy is determined in order to calculate the bcc–hcp phase transition temperature in zirconium. The molecular dynamics method is employed to calculate the vibrational entropy which comprises both the harmonic and anharmonic vibrational entropy. Electronic effects are estimated and taken into account. The anharmonic vibrational entropy is determined from the anharmonic free energy and the electronic entropy is calculated via the electronic density of states. By considering the Helmholtz free energy, the bcc–hcp transition temperature from our simulations is 1047 ± 210 K compared to 1135 K from experimental results. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)