bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid typing of Moraxella catarrhalis subpopulations based on outer membrane proteins using mass spectrometry
Authors: Schaller André , Troller Rolf , Molina Daniel , Gallati Sabina , Aebi Christoph , Stutzmann Meier Patricia 
Published: November 2005

AbstractMoraxella catarrhalis is a major mucosal pathogen of the human respiratory tract both in children and in adults. Two subpopulations of this organism have been described that differ in 16S rRNA gene sequence and virulence traits. Three 16S rRNA types have been defined. 2‐DE followed by protein identification by MS revealed significant differences in the outer membrane protein (OMP) patterns of each M. catarrhalis 16S rRNA type. Approximately 130 features were detected on the 2‐DE map of each M. catarrhalis 16S rRNA type. However, only 50 features were expressed by all strains. Furthermore, direct profiling of isolated OMP using MALDI‐TOF MS resulted in a characteristic spectral fingerprint for each 16S rRNA type. Fingerprints remained identical when intact cells instead of isolated OMP were analyzed. This finding suggests that the source of desorbed ions is the outer membrane. Based on the fingerprint we were able to assign 18 well‐characterized clinical M. catarrhalis isolates to the correct subpopulation. Therefore, MALDI‐TOF of intact M. catarrhalis provides a rapid and robust tool for M. catarrhalis strain typing that could be applied in epidemiological studies.
Nonaqueous synthesis of nanosilica in epoxy resin matrix and thermal properties of their cured nanocomposites
Authors: Lee Tzong‐Ming , Ma Chen‐Chi M. 
Published: November 2005

AbstractNonaqueous synthesis of nanosilica in diglycidyl ether of bisphenol‐A epoxy (DGEBA) resin has been successfully achieved in this study by reacting tetraethoxysilane (TEOS) directly with DGEBA epoxy matrix, at 80 °C for 4 h under the catalysis of boron trifluoride monoethylamine (BF3MEA). BF3MEA was proved to be an effective catalyst for the formation of nanosilica in DGEBA epoxy under thermal heating process. FTIR and 29Si NMR spectra have been used to characterize the structures of nanosilica obtained from this direct thermal synthetic process. The morphology of the nanosilica synthesized in epoxy matrix has also been analyzed by TEM and SEM studies. The effects of both the concentration of BF3MEA catalyst and amount of TEOS on the diameters of nanosilica in the DGEBA epoxy resin have been discussed in this study. From the DSC analysis, it was found that the nanosilica containing epoxy exhibited the same curing profile as pure epoxy resin, during the curing reaction with 4,4′‐diaminodiphenysulfone (DDS). The thermal‐cured epoxy–nanosilica composites from 40% of TEOS exhibited high glass transition temperature of 221 °C, which was almost 50 °C higher than that of pure DGEBA–DDS–BF3MEA‐cured resin network. Almost 60 °C increase in thermal degradation temperature has been observed during the TGA of the DDS‐cured epoxy–nanosilica composites containing 40% of TEOS. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 757–768, 2006
Transition states for deactivation reactions in the modeled 2,2,6,6‐tetramethyl‐1‐piperidinyloxy‐mediated free‐radical polymerization of acrylonitrile
Authors: Kaim Andrzej , Megiel Elżbieta 
Published: December 2005

AbstractThe geometries and energetics of transition states (TS) for radical deactivation reactions, including competitive combination and disproportionation reactions, have been studied for the modeled 2,2,6,6‐tetramethyl‐1‐piperidinyloxy (TEMPO)‐mediated free‐radical polymerization of acrylonitrile with quantum mechanical calculations at the DFT/UB3‐LYP/6‐311+G(3df,2p)//(U)AM1 level of theory (where DFT is density functional theory, AM1 is Austin model 1, and UAM1 is unrestricted Austin model 1). A method providing reasonable starting geometries for an effective search for TS between the TEMPO radical and 1‐cyanopropyl radical mimicking the growing polyacrylonitrile macroradical is shown. For the hydrogen atom abstraction reaction by the TEMPO radical from the 1‐cyanopropyl radical, practically one TS has been found, whereas for the combination reaction of the radicals, several TS have been found, mainly differing in out‐of‐plane angle α of the NO bond in the TEMPO structure. α in the TS is correlated with the activation energy, ΔE, determined from the single‐point calculation at the DFT UB3‐LYP/6‐311+G(3df, 2p)//UAM1 level for the combination reaction of CH3AN· with the TEMPO radical. The theoretical activation energy for the coupling reaction from DFT UB3‐LYP/6‐311+G(3df, 2p)//UAM1 calculations has been estimated to be 11.6 kcal mol−1, that is, only about 4.5 times smaller than ΔE for the disproportionation reaction obtained with the DFT UB3‐LYP/6‐311+G(3df, 2p)//(U)AM1 approach. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 914–927, 2006
A contact mechanics method for characterizing the elastic properties and permeability of gels
Authors: Hui Chung‐Yuen , Lin Yu Yun , Chuang Fu‐Chin , Shull Kenneth R. , Lin Wei‐Chun 
Published: November 2005

AbstractWhen a saturated gel immersed in the same liquid is suddenly brought into contact with a smooth rigid indenter, the liquid cannot immediately flow out of the pores, and so the gel initially behaves as an incompressible material. This gives rise to a pressure gradient in the liquid phase and the liquid flows until the pressure in it goes to zero everywhere, and all the stresses are transferred to the elastic network. As a result of the flow, the force needed to maintain a constant contact area relaxes with time. In this work, we study the feasibility of using an indentation test to measure this time‐dependent force and to determine the elastic modulus, the Poisson's ratio, and the permeability, Dp, of the network. Specifically, we consider a two‐dimensional Hertz contact problem of a rigid circular cylinder indenting on a half space consisting of an elastic gel. The network of the gel is assumed to be linearly elastic and isotropic, and liquid flow within the gel is assumed to obey Darcy's law, which states that the flux is proportional to the pressure gradient. Exact expressions are obtained for the initial and final force required to maintain a given contact length. These expressions allow us to determine the elastic constants of the network. The permeability of the network can be obtained from the time‐dependent relaxation of the load, which is obtained by solving the exact continuum equations. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 359–370, 2006
Exploiting sequence and structure homologs to identify protein–protein binding sites
Authors: Chung Jo‐Lan , Wang Wei , Bourne Philip E. 
Published: December 2005

AbstractA rapid increase in the number of experimentally derived three‐dimensional structures provides an opportunity to better understand and subsequently predict protein–protein interactions. In this study, structurally conserved residues were derived from multiple structure alignments of the individual components of known complexes and the assigned conservation score was weighted based on the crystallographic B factor to account for the structural flexibility that will result in a poor alignment. Sequence profile and accessible surface area information was then combined with the conservation score to predict protein–protein binding sites using a Support Vector Machine (SVM). The incorporation of the conservation score significantly improved the performance of the SVM. About 52% of the binding sites were precisely predicted (greater than 70% of the residues in the site were identified); 77% of the binding sites were correctly predicted (greater than 50% of the residues in the site were identified), and 21% of the binding sites were partially covered by the predicted residues (some residues were identified). The results support the hypothesis that in many cases protein interfaces require some residues to provide rigidity to minimize the entropic cost upon complex formation. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Solution structure of YggX: A prokaryotic protein involved in Fe(II) trafficking
Authors: Cui Qiu , Thorgersen Michael P. , Westler William M. , Markley John L. , Downs Diana M. 
Published: December 2005

AbstractWe report the three‐dimensional structure of YggX from Salmonella enterica, determined by solution nuclear magnetic resonance (NMR) spectroscopy from protein labeled with carbon‐13 and nitrogen‐15 produced by Escherichia coli cells. The protein has a β1β2α1α2α3 fold that is unique to YggX and one of its homologs, a protein from Pseudomonas aeruginosa with 45% sequence identity whose X‐ray structure [Protein Data Bank (PDB) 1T07] was determined by a structural genomics center. The NMR structure, which revealed that the C‐terminal region of YggX is dynamically disordered, explains why electron density from the corresponding region was missing in the X‐ray structure of the Pseudomonas protein. Because it has been hypothesized that YggX has a role in iron trafficking, we investigated the influence of Fe(II) on the 1H‐15N NMR fingerprint region of nitrogen‐15‐labeled YggX. Several signals shifted or broadened upon the addition of excess Fe(II) under anoxic conditions, with His81 showing the largest effect. These results indicate that Fe(II) binds weakly to this protein at a region of the sequence conserved only in the subset of the YggX proteins from organisms similar to Salmonella. The finding that iron binds only weakly to YggX, and not to a highly conserved region of the structure, suggests that the role of this protein in iron homeostasis is more complex than previously thought. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Electronic structure and parity effects in correlated nanosystems
Authors: Rycerz Adam , Spałek Jozef 
Published: December 2005

AbstractWe discuss the spectral, transport and magnetic properties of quantum nanowires composed of N ≤ 13 atoms and containing either even or odd numbers of valence electrons. In our approach we combine Exact Diagonalization and Ab Initio calculations (EDABI method). The analysis is performed as a function of the interatomic distance. The momentum distribution differs drastically for those obtained for even N with those for odd N , whereas the Drude weight evolve smoothly. A role of boundary conditions is stressed. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Frequency dependent mobility of charge carriers along polymer chains with finite length
Authors: Prins P. , Grozema F. C. , Schins J. M. , Siebbeles L. D. A. 
Published: December 2005

AbstractThe effect of the chain length of conjugated polymers on the real and imaginary components of the frequency dependent mobility of charge carriers is studied. A theoretical model for one‐dimensional diffusive motion of charges between reflecting chain ends is presented. It is shown that the model can be used to describe the measured ratio of the imaginary and real components of the microwave (30 GHz) mobility of charge carriers moving along ladder‐type polymer chains with different lengths. From comparison of theoretical and experimental data it is inferred that an intra‐chain mobility of 30 cm2/Vs can be achieved for ladder‐type polymer chains, which are sufficiently long so that chain ends do not limit the mobility. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interactions between aroma compounds and latex films: partition coefficients and influence on latex film formation
Authors: Nestorson A. , Leufvén A. , Järnström L. 
Published: November 2005

AbstractThe potential of various latex grades to take up, retain and release different types of aroma compound has been explored. The latex grades used included two styrene–acrylate latices and two styrene–butadiene latices, of which one contained talc. The aroma compounds used were ethyl butyrate, 1‐hexanol, heptanal, 3‐octanone, α‐pinene and limonene dissolved in propylene glycol. It was shown that talc improves both the uptake of aroma compounds in the dispersion phase and the retention during the film formation process. However, the styrene–acrylate latex had a greater ability than the styrene–butadiene latex to hold the aroma compounds once the films were formed. These results have been compared to calculated solubility parameters. The uptake of 1‐hexanol and propylene glycol in the latex dispersions were higher than expected from the theoretical calculations, probably because of the amphiphilic nature of these molecules. In addition, the influence of aroma compounds on the film formation was evaluated. Copyright © 2005 John Wiley & Sons, Ltd.
Allosteric Modulation of Family 3 GPCRs
Authors: Noeske Tobias , Gutcaits Aleksandrs , Parsons Christopher G. , Weil Tanja 
Published: December 2005

AbstractThis article reviews recent advances towards an understanding of the transmembrane structure, its activation and binding sites of family 3 G‐Protein‐Coupled Receptors (3‐GPCRs). First, the prediction of their 3D structureviahomology models based on the crystal structure of bovine rhodopsin will be discussed. Then, different kinetic mechanisms of ligand‐binding inside the heptahelical domain are presented before an overview of most common structural motifs of 3‐GPCR allosteric modulators will be given. Here, special focus lies in the characterization of their binding pocket within the transmembrane domain as well as their interaction with crucial amino acids. The overview of available mutation data inside the ligand‐binding domains as well as the influence of exchanged amino acids on the activity of different receptors leads to the question whether allosteric ligands of family 3 GPCRs bind to the same binding pocket and if there exists a common binding site of family 1 GPCRs and family 3 GPCRs.
Plant dispersal along rivers fragmented by dams
Authors: Merritt David M. , Wohl Ellen E. 
Published: November 2005

AbstractTo understand the influence of dams on connectivity of riparian plant communities along rivers, we examined plant dispersal by water (hydrochory) and riparian plant community attributes upstream and downstream from dams on two rivers in the southern Rocky Mountains, Colorado, USA. Drifting plant propagules were collected from the water column along reaches upstream and downstream from dams to examine the longitudinal and temporal variation in seed‐pool species composition and concentration of water‐transported seeds. Similarities between species composition of the hydrochoric seed pool and local standing riparian vegetation were used to evaluate the degree of longitudinal connectivity along river corridors and to isolate the relative contributions of local versus regional species pools to hydrochoric species composition. Furthermore, several synthetic attributes (longevity, origin, life‐form and dispersal mode) and species composition of riparian plant communities were examined to explore the effects of interrupted propagule dispersal on standing vegetation.We estimated that as many as 120 million seeds were transported via hydrochory along free‐flowing reaches of the Rocky Mountain streams in a single growing season. Seed concentration (seeds/m3) in the water column was reduced by 70–94% along reaches downstream from dams compared to free‐flowing reaches. The similarity in species composition of hydrochoric seeds and local standing vegetation was nearly two times greater downstream from reservoirs compared to upstream. This suggests that hydrochory complements local species pools by importing seeds from throughout the upstream catchment area along free‐flowing river reaches, but that hydrochoric seeds are derived primarily from local sources along regulated river reaches. Species richness recovers as a function of downstream distance from contributions of standing vegetation and seeds from tributary streams. Hydrochory may extend the period over which viable seeds of a parent population are dispersed. Even after dispersal of parent populations has terminated, seeds may continue to be available due to residence time in water transport. This extension of the ‘effective dispersal window’ of some species may exceed two weeks or more and may influence the likelihood of successful establishment.In this study, synthetic attributes of riparian vegetation did not differ significantly between free‐flowing and regulated reaches, whereas formal statistical comparisons of community composition upstream and downstream from reservoirs indicate that there are differences in community composition upstream and downstream from dams. These findings suggest that the consequences of 50 to 100 years of fragmentation result in community‐wide effects along Rocky Mountain streams and that these effects may be partially explained by dam‐caused disruption in connectivity of plant populations. Copyright © 2005 John Wiley & Sons, Ltd.
Accommodation of additional non‐randomly sampled cases in a study of Helicobacter pylori infection in families
Authors: Kivi Mårten , Johansson Anna L. V. , Salim Agus , Tindberg Ylva , Reilly Marie 
Published: November 2005

AbstractEpidemiological studies with two‐stage designs typically gather information about some covariates from all study subjects in the first sampling stage, while additional data from only a subset of the subjects are collected in the second sampling stage. Appropriate analysis of two‐stage studies maintains validity and can also improve precision. We describe an application of a weighted likelihood method, mean‐score logistic regression, to accommodate data from a cross‐sectional study of Helicobacter pylori infection in children, where the study sample was enriched with additional non‐randomly sampled cases. The present work exemplifies how careful analysis of epidemiological data from complex sampling schemes can adjust for potential selection bias, improve precision and enable a more complete investigation of factors of interest. Our results highlight the importance of H. pylori infected mothers and siblings as risk factors for the infection in children in Sweden. Copyright © 2005 John Wiley & Sons, Ltd.
Modelling intervention effects after cancer relapses
Authors: González Juan R. , Peña Edsel A. , Slate Elizabeth H. 
Published: November 2005

AbstractThis article addresses the problem of incorporating information regarding the effects of treatments or interventions into models for repeated cancer relapses. In contrast to many existing models, our approach permits the impact of interventions to differ after each relapse. We adopt the general model for recurrent events proposed by Peña and Hollander, in which the effect of interventions is represented by an effective age process acting on the baseline hazard rate function. To accommodate the situation of cancer relapse, we propose an effective age function that encodes three possible therapeutic responses: complete remission, partial remission, and null response. The proposed model also incorporates the effect of covariates, the impact of previous relapses, and heterogeneity among individuals. We use our model to analyse the times to relapse for 63 patients with a particular subtype of indolent lymphoma and compare the results to those obtained using existing methods. Copyright © 2005 John Wiley & Sons, Ltd.
Re‐use of case–control data for analysis of new outcome variables
Authors: Reilly Marie , Torrång Anna , Klint Åsa 
Published: November 2005

AbstractCase–control studies are usually defined to investigate risk factors for a single disease of interest. However, subsequent to data collection, investigators may wish to examine as an ‘outcome’ a variable that was an exposure in the original study. A naive analysis that disregards the sampling strategy that gave rise to the data is clearly prone to bias. We present here a simple approach to the analysis of such data using an appropriately weighted regression model. Viewing the problem as a two‐stage design provides a unified framework for recognizing and defining the necessary weights when confronted with a variety of real data problems that at first seem unrelated. We provide illustrations that highlight the generality of the approach and demonstrate that the method gives essentially the same results as more specialized methods that require non‐standard tools for analysis. Copyright © 2005 John Wiley & Sons, Ltd.
Eliciting and using expert opinions about influence of patient characteristics on treatment effects: a Bayesian analysis of the CHARM trials
Authors: White Ian R. , Pocock Stuart J. , Wang Duolao 
Published: November 2005

AbstractWhen randomized trial results are available for several different groups of patients, neither applying the overall results to each type of patient nor using group‐specific results is entirely satisfactory. Instead, we estimate group‐specific treatment effects using a Bayesian approach with informative priors for the treatment × group interactions. We describe how we elicited these prior beliefs about the effects of a new drug for the treatment of heart failure in three different patient groups. Using results from three trials, one in each patient group, the posterior mean treatment effects are very similar to the trial‐specific maximum likelihood estimates, showing that in this case each trial effectively stands by itself. Our methods can also be applied to subgroup analyses in a single clinical trial, where subgroup‐specific posterior means are likely to lie between the subgroup‐specific maximum likelihood estimates and the pooled maximum likelihood estimates. Copyright © 2005 John Wiley & Sons, Ltd.
Prenatal diagnosis of thrombosed aneurysm of vein of Galen
Authors: Vijayaraghavan S. Boopathy , Vijay S. , Kala M. R. , Neha D. 
Published: November 2005

AbstractAneurysm of the vein of Galen in the fetus is a rare malformation that has been described in a small number of case reports. Thrombosis of aneurysm of the vein of Galen is a rare occurrence reported in postnatal cases. We report a case of thrombosis of vein of Galen aneurysm occurring in a fetus of 21 weeks' gestation. The fetus showed an echogenic mass posterior and superior to the thalamus. It also showed dilated dural venous sinuses, dilated neck vessels, cardiomegaly and minimal ascites. The pregnancy was terminated and autopsy confirmed the diagnosis. The present case is the first report of the prenatal sonographic features of this condition in the literature. Copyright © 2005 ISUOG. Published by John Wiley & Sons, Ltd.
Fluor‐Kohlenstoff‐Nanoschichten zur gezielten Oberflächenfunktionalisierung. Fluorine‐Carbon Nano Coatings for Specific Surface Functionalization
Authors: Haupt Michael , Barz Jakob , Vohrer Uwe , Hilgers Heinz , Oehr Christian 
Published: November 2005

AbstractDer Artikel beschreibt einige Aspekte aus den Entwicklungs‐ und Forschungsarbeiten, die im Rahmen des BMBF Projektes “Nano‐Funktionalisierung von Grenzflächen für Daten‐, Textil‐, Gebäude‐, Medizin‐, Bio‐, und Raumfahrttechnik” durchgeführt werden. Es wird auf die verschiedenen, breit gefächerten Anwendungsgebiete von plasmamodifizierten Oberflächen eingegangen und ein Überblick über die Charakterisierungsmethoden an den Schichten gegeben.Mit Hilfe der Niederdruck‐Plasmatechnologie lassen sich Oberflächen physikalisch‐chemisch funktionalisieren und gezielt auf ihre Anwendung anpassen, ohne die Grundeigenschaften des Volumenmaterials zu verändern. Die Oberflächen der zu modifizierenden Werkstücke werden in einem Plasmaprozess mit einer ultra dünnen, d.h. nur wenige Nanometer dicken Fluor‐Kohlenstoff‐Polymerschicht beschichtet. Die physikalisch‐chemischen Eigenschaften der Oberflächen, wie z.B. die Oberflächenenergie, die Rauheit (auf der Nanometerskala), das dynamische Benetzungsverhalten oder die Adhäsionseigenschaft gegenüber anderen Materialien lassen sich durch Veränderung der Plasmaprozessparameter einstellen. Es wird gezeigt, dass diese Art der Oberflächenmodifizierung in Zukunft ein breites Anwendungsfeld eröffnet.