bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ethnic differences in determinants of participation and non‐participation in prenatal screening for Down syndrome: A theoretical framework
Authors: Fransen Mirjam P. , Essink‐Bot Marie‐Louise , Oenema Anke , Mackenbach Johan P. , Steegers Eric A. P. , Wildschut Hajo I. J. 
Published: June 2007

AbstractObjective To develop a theoretical framework for analysing ethnic differences in determinants of participation and non‐participation in prenatal screening for Down syndrome.Methods We applied Weinstein's Precaution Adoption Process (PAP) Model to the decision of whether or not to participate in prenatal screening for Down syndrome. The prenatal screening stage model was specified by reviewing the empirical literature and by data from seven focus group interviews with Dutch, Turkish and Surinamese pregnant women in the Netherlands.Results We identified 11 empirical studies on ethnic differences in determinants of participation and non‐participation in prenatal screening for Down syndrome. The focus group interviews showed that almost all stages and determinants in the stage model were relevant in women's decision‐making process. However, there were ethnic variations in the relevance of determinants, such as beliefs about personal consequences of having a child with Down syndrome or cultural and religious norms.Discussion The prenatal screening stage model can be applied as a framework to describe the decision‐making process of pregnant women from different ethnic backgrounds. It provides scope for developing culturally sensitive, tailored methods to guide pregnant women towards informed decision‐making on participation or non‐participation in prenatal screening for Down syndrome. Copyright © 2007 John Wiley & Sons, Ltd.
Ethenyl indoles as neutral hydrophobic fluorescence probes
Authors: Singh Anil K. , Hota Prasanta K. 
Published: June 2007

Abstract3‐(4‐Nitrophenylethenyl‐E)‐NH‐indole (1), 3‐(4‐nitrophenyl ethenyl‐E)‐N‐acetylindole (2), and 3‐(4‐nitrophenylethenyl‐E)‐N‐benzenesulfonylindole (3) are relatively less fluorescent in organic solvents, with fluorescence quantum yield (Φf) in the range of 0.002 to 0.066 depending on the solvent polarity. However, in bovine serum albumin (BSA)‐phosphate buffer, the fluorescence of these compounds gets drastically enhanced with Φf in the range of 0.21 to 0.67, depending on the substituent on the indolic nitrogen atom. Additionally, linear increase in the fluorescence intensity of 2 and 3 occurs on increasing the BSA concentration. These fluorescence properties together with the neutral, hydrophobic nature of these compounds make these fluorophores good fluorescence probe for studying the micropolarity of proteins like BSA and in general the ligand–protein interactions. Copyright © 2007 John Wiley & Sons, Ltd.
Molecular dynamics study of polymer crystallization in the presence of a particle
Authors: Zhang Dongsheng , Meyer Hendrik 
Published: June 2007

AbstractWe have used molecular dynamics simulations with a coarse‐grained model to study the effect of a particle on the crystallization of polymer melt. We analyzed in particular a bond order parameter to characterize the nucleation and crystallization process. Our calculations show that the presence of a particle modifies the free energy landscape of polymer melts, locally induces the ordering of polymer melts near the particle surface, and thus enhances the polymer crystallization. Because the interaction between the particle and polymers is repulsive, our results suggest that the origin of the enhancement for polymer crystallization is entropic. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2161–2166, 2007
Pre‐analytical influence on the low molecular weight cerebrospinal fluid proteome
Authors: Berven Frode S. , Kroksveen Ann C. , Berle Magnus , Rajalahti Tarja , Flikka Kristian , Arneberg Reidar , Myhr Kjell‐Morten , Vedeler Christian , Kvalheim Olav M. , Ulvik Rune J. 
Published: June 2007

AbstractCerebrospinal fluid (CSF) is a perfect source to search for new biomarkers to improve early diagnosis of neurological diseases. Standardization of pre‐analytical handling of the sample is, however, important to obtain acceptable analytical quality. In the present study, MALDI‐TOF MS was used to examine the influence of pre‐analytical sample procedures on the low molecular weight (MW) CSF proteome. Different storage conditions like temperature and duration or the addition of as little as 0.2 µL blood/mL neat CSF caused significant changes in the mass spectra. The performance of different types of MW cut‐off spin cartridges from different suppliers used to enrich the low MW CSF proteome showed great variance in cut‐off accuracy, stability and reproducibility. The described analytical method achieved a polypeptide discriminating limit of approximately 800 pM, two to three orders of magnitude lower than reported for plasma. Based on this study, we recommend that CSF is centrifuged immediately after sampling, prior to storage at –80ºC without addition of protease inhibitors. Guanidinium hydrochloride is preferred to break protein‐protein interactions. A spin cartridge with cut‐off limit above the intended analytical mass range is recommended. Our study contributes to the important task of developing standardized pre‐analytical protocols for the proteomic study of CSF.
Simulated annealing exploration of an active‐site tyrosine in TEM‐1β‐lactamase suggests the existence of alternate conformations
Authors: Doucet Nicolas , Pelletier Joelle N. 
Published: June 2007

AbstractTEM‐1 is a class A β‐lactamase that contributes to the primary defensive measure used by bacteria to hydrolyze the clinically‐relevant β‐lactam antibiotics. Several crystal structures of this enzyme complexed with inhibitors display the active‐site residue Tyr105 in an alternate orientation relative to that assigned in the free or in the substrate‐bound forms. Thus, the alternate conformation may not be favored in the free enzyme and may be adopted only in the presence of inhibitor. As the residue at position 105 is a determinant of substrate specificity, we sought a better understanding of the relation between its conformation and its function in ligand binding. Here, we perform a molecular dynamics simulated annealing protocol to identify stable orientations adopted by Tyr105 in free TEM‐1. Our results demonstrate that, in the absence of substrate, structurally validated conformers of Tyr105 predominantly adopt either of the two rotameric orientations observed in the crystal structures. This suggests that adoption of either conformation in the free enzyme is energetically favored and is not strictly promoted by ligand binding. We propose that free TEM‐1 alternates between these two conformations of Tyr105 and that a dynamically heterogeneous population of both rotamers exists in solution. The conformational change significantly reshapes the active‐site cavity and modifies the potential for forming specific ligand contacts. Our results add to the body of evidence suggesting that Tyr105 displays a dynamical behavior resulting in alternate ligand binding modes and are consistent with the lower affinity of TEM‐1 for cephalosporins relative to penicillins. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Electronic activity of SiC precipitates in multicrystalline solar silicon
Authors: Bauer Jan , Breitenstein Otwin , Rakotoniaina Jean‐Patrice 
Published: June 2007

AbstractIn the upper part of block‐cast multicrystalline silicon one often finds silicon carbide and silicon nitride precipitates and inclusions. These contaminants can cause severe ohmic shunts in solar cells and thus decrease the efficiency of the solar cells very strongly. It is well known that the silicon carbide precipitates cause the ohmic shunts. However, the electrical properties of the silicon carbide was unknown so far. To study the electrical properties of these silicon carbide particles we isolated them from the silicon bulk material and performed different electrical measurements on them. The measurements show that the silicon carbide precipitates are highly conductive. An investigation of the heterojunction silicon–silicon carbide was also performed and a simulation of this heterojunction leads to a new model of the ohmic shunt mechanism. It is concluded that the shunt current flows inside of the filaments. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
High‐stress plasticity and the core structures of dislocations in silicon
Authors: Rabier J. 
Published: June 2007

AbstractThe recent observation of perfect dislocations at high stress and low temperature in silicon [J. Rabier, P. Cordier, J. L. Demenet, and H. Garem, Mater. Sci. Eng. A 309/310, 74 (2001)] in accordance with the calculations of Duesbery and Joos [M. S. Duesbery and B. Joos, Philos. Mag. A 74, 253 (1996)] has solved the apparent paradox regarding the nature of mobile dislocations in silicon under usual deformation conditions. However, although several experiments and calculations are consistent with those perfect dislocations being located in the shuffle set, little is known about the actual core structure of those dislocations which lie along unusual Peierls valleys: 〈112〉/30°, 〈123〉/41°. This paper aims to review and discuss recent results related to high‐stress plasticity and dislocation core structure in silicon. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Iberian thermal lows in a changed climate
Authors: Hoinka Klaus P. , Gaertner Miguel , de Castro Manuel 
Published: June 2007

AbstractRecent results from enhanced greenhouse‐gas scenarios over southern Europe suggest that climate change implies a summertime mean surface warming of up to 4 K over the Iberian Peninsula. It is suggested that thermal lows, the most prominent Iberian summer weather, will undergo significant modifications in a changed climate. This is studied in the present paper by determining statistical features of the Iberian thermal low, at first for today's climate using data provided by ERA‐40 and by the regional climate model PROMES. In general the analysed and simulated climatic structures compare well. However, the ERA‐40 data provide conditions more favourable for thermal lows than simulated with the model. Statistics in a changed climate are obtained by performing two 30‐year model simulations for 1961–1990 and 2071–2100. It is found that thermal lows strengthen by decreasing the central Iberian surface pressure from 1012.2 to 1010.5 hPa and increasing its daily variation by about 7% in magnitude. Associated with this is an increase in the number of thermal low days by more than 60%. A second finding is an enhancement of the sea breezes over the Iberian westerly and easterly coasts and a particularly significant strengthening of the sea breeze between Cadiz and Huelva. The westerly flow over the Strait of Gibraltar, observed during thermal low events, decreases. The increase in occurrence of the thermal low is associated with a significant increase in the number of dry spells of longer period, and could involve considerable impact on desertification, water resources and wildfire hazards around the Mediterranean basin. The results suggest that there is some evidence that the subtropical character of the Mediterranean climate strengthens. Copyright © 2007 Royal Meteorological Society
Characterization and determination of six aristolochic acids and three aristololactams in medicinal plants and their preparations by high‐performance liquid chromatography‐photodiode array detection/electrospray ionization mass spectrometry
Authors: Yuan Jinbin , Liu Qian , Wei Guobing , Tang Fei , Ding Li , Yao Shouzhuo 
Published: June 2007

AbstractAristolochic acid derivatives (AAs) and aristolactam derivatives (ALs) have been characterized by electrospray ionization mass spectrometry, and their fragmentation pathways are proposed. ALs exhibit a single ionization product [M+H]+, whereas AAs show multiple ionization products. By optimizing the chromatographic separation and mass spectrometric parameters, the precursor ions of the derivatives with the best responses were found, and the sensitivities in the determination of the nine derivatives were improved. Based on the investigation of ionization behaviour, a HPLC‐DAD/ESI‐MS (high‐performance liquid chromatography‐photodiode array detection/electrospray ionization mass spectrometry) method has been developed for simultaneous analysis of nine derivatives, i.e., AA I, AA II, AA C, AA D, 7‐OH AA I, aristolic acid I, AL AII, AL IIIa and AL IVa, in nine medicinal herbs and two preparations. The method appears to be suitable for safety assurance and quality control of commercially available samples with good selectivity and suitable sensitivity. Copyright © 2007 John Wiley & Sons, Ltd.
Scanning and Transmission Electron Microscopy for Evaluation of Order/Disorder in Bone Structure
Authors: Suvorova Elena I. , Petrenko Pavel P. , Buffat Philippe A. 
Published: June 2007

AbstractA comparative characterization of the structure of normal and abnormal (osteoporotic) human lumbar and thoracic vertebrae samples was carried out to reveal the type of possible disorder. Samples from the bone fragments extracted during the surgery due to vertebra fractures were examined by scanning electron microscopy (SEM), conventional and high resolution transmission electron microscopy (TEM and HRTEM), and X‐ray energy dispersive spectroscopy (EDS). Contrary to what might be expected in accordance with possible processes of dissolution, formation and remineralization of hard tissues, no changes in phase composition of mineral part, crystal sizes (length, width, and thickness), and arrangement of crystals on collagen fibers were detected in abnormal bones compared to the normal ones. The following sizes were determined by HRTEM for all bone samples: ≤ 20 nm in length, 3–15 nm in width, and 0.8 nm in thickness (the height of hexagonal HAP unit cell along the [2110] direction. Significant overgrowth of organic fibers filled up the former paths for blood vessels and nerves together with organic films covering the mineral part was revealed by SEM only in osteoporotic bones. EDS showed that this organic tissue was not mineralized. Penetration of such organic fibers inside bones can result in bone dilatation and lower the mineral density, deteriorating the mechanical properties and finally terminating in fracture.SCANNING 29: 000–000, 2007. © 2007 Wiley Periodicals, Inc.
The stoichiometry of the T cell antigen receptor and its implications for the signal transduction mechanism
Authors: Schamel Wolfgang W. A. 
Published: June 2007

AbstractThe T cell antigen receptor (TCR·CD3) is a multi‐subunit complex mediating T cell development and activation. The molecular mechanism of how this receptor transmits information across the membrane is still an enigma. The stoichiometry and architecture of this receptor in the membrane are under intense investigation, since they are important in deciphering the signal transduction mechanism of the TCR·CD3. This review highlights the evidence that TCR·CD3 is found on unstimulated T cells in monovalent (one ligand‐binding site per receptor) as well as in multivalent forms. Distinct detergents affect the integrity of the multivalent receptor differently, explaining controversial findings of TCR·CD3 stoichiometries as determined by biochemical means. The existence of multivalent receptors is not compatible with current models of TCR·CD3 triggering. Therefore, I discuss the novel “permissive geometry model” that combines multivalent TCR·CD3s, the requirement for multimeric ligands for receptor triggering and conformational changes at CD3.
Efficient Synthesis of α‐Monoglycerides via Solventless Condensation of Fatty Acids with Glycerol Carbonate
Authors: Ghandi Mehdi , Mostashari Abdoljalil , Karegar Mojgan , Barzegar Mina 
Published: June 2007

AbstractHighly pure α‐monoglycerides (5a–e) were successfully prepared in high yields by the condensation of fatty acids such as lauric, myristic, palmitic, stearic and oleic (2a–e) with glycerol carbonate (4‐hydroxymethyl‐1,3‐dioxolan‐2‐one) (1) in the presence of triethylamine as catalyst. Reaction conditions and spectroscopic identification of products will be presented in this article.
Nonlinear magnetoacoustic waves in a cold plasma
Authors: ROWLANDS G. , ALLEN M. A. 
Published: June 2007

AbstractThe equations describing planar magnetoacoustic waves of permanent form in a cold plasma are rewritten so as to highlight the presence of a naturally small parameter equal to the ratio of the electron and ion masses. If the magnetic field is not nearly perpendicular to the direction of wave propagation, this allows us to use a multiple-scale expansion to demonstrate the existence and nature of nonlinear wave solutions. Such solutions are found to have a rapid oscillation of constant amplitude superimposed on the underlying large-scale variation. The approximate equations for the large-scale variation are obtained by making an adiabatic approximation and in one limit, new explicit solitary pulse solutions are found. In the case of a perpendicular magnetic field, conditions for the existence of solitary pulses are derived. Our results are consistent with earlier studies which were restricted to waves having a velocity close to that of long-wavelength linear magnetoacoustic waves.
Anaerobic phenanthrene mineralization by a carboxylating sulfate-reducing bacterial enrichment
Authors: Davidova Irene A , Gieg Lisa M , Duncan Kathleen E , Suflita Joseph M 
Published: June 2007

Abstract
Information on the susceptibility of higher molecular weight polynuclear aromatic hydrocarbons to anaerobic biodegradation is relatively rare. We obtained a sulfate-reducing bacterial enrichment capable of phenanthrene metabolism from a hydrocarbon-contaminated marine sediment. Phenanthrene degradation was in stoichiometric agreement with the theoretically expected amount of sulfate reduction and inhibited by molybdate. Mineralization of 14C-phenanthrene by the enrichment was confirmed by the recovery of the expected amount of 14CO2. Stable isotope studies with protonated or deuterated phenanthrene resulted in the detection of the correspondingly labeled phenanthrene carboxylic acid by gas chromatography–mass spectrometry. Comparison of the metabolite profile with a synthesized standard confirmed that the parent molecule was carboxylated at the C-2 position. Incorporation of 13C-bicarbonate into the carboxyl group implicated a direct carboxylation of phenanthrene as a likely key initial reaction. Denaturing gradient gel electrophoresis analysis of the enrichment showed only two major bands and 16S rRNA sequences obtained by cloning clustered with known hydrocarbon-degrading sulfate-reducing δ-proteobacteria, indicating their possible involvement in the anaerobic oxidation of phenanthrene via carboxylation as the initial activation reaction.
Biological and chemical sulfide oxidation in a Beggiatoa inhabited marine sediment
Authors: Preisler André , de Beer Dirk , Lichtschlag Anna , Lavik Gaute , Boetius Antje , Jørgensen Bo Barker 
Published: June 2007

Abstract
The ecological niche of nitrate-storing Beggiatoa, and their contribution to the removal of sulfide were investigated in coastal sediment. With microsensors a clear suboxic zone of 2–10 cm thick was identified, where neither oxygen nor free sulfide was detectable. In this zone most of the Beggiatoa were found, where they oxidize sulfide with internally stored nitrate. The sulfide input into the suboxic zone was dominated by an upward sulfide flux from deeper sediment, whereas the local production in the suboxic zone was much smaller. Despite their abundance, the calculated sulfide-oxidizing capacity of the Beggiatoa could account for only a small fraction of the total sulfide removal in the sediment. Consequently, most of the sulfide flux into the suboxic layer must have been removed by chemical processes, mainly by precipitation with Fe2+ and oxidation by Fe(III), which was coupled with a pH increase. The free Fe2+ diffusing upwards was oxidized by Mn(IV), resulting in a strong pH decrease. The nitrate storage capacity allows Beggiatoa to migrate randomly up and down in anoxic sediments with an accumulated gliding distance of 4 m before running out of nitrate. We propose that the steep sulfide gradient and corresponding high sulfide flux, a typical characteristic of Beggiatoa habitats, is not needed for their metabolic performance, but rather used as a chemotactic cue by the highly motile filaments to avoid getting lost at depth in the sediment. Indeed sulfide is a repellant for Beggiatoa.
Penalized and weightedK-means for clustering with scattered objects and prior information in high-throughput biological data
Authors: Tseng George C. 
Published: June 2007

AbstractMotivation: Cluster analysis is one of the most important data mining tools for investigating high-throughput biological data. The existence of many scattered objects that should not be clustered has been found to hinder performance of most traditional clustering algorithms in such a high-dimensional complex situation. Very often, additional prior knowledge from databases or previous experiments is also available in the analysis. Excluding scattered objects and incorporating existing prior information are desirable to enhance the clustering performance.Results: In this article, a class of loss functions is proposed for cluster analysis and applied in high-throughput genomic and proteomic data. Two major extensions from K-means are involved: penalization and weighting. The additive penalty term is used to allow a set of scattered objects without being clustered. Weights are introduced to account for prior information of preferred or prohibited cluster patterns to be identified. Their relationship with the classification likelihood of Gaussian mixture models is explored. Incorporation of good prior information is also shown to improve the global optimization issue in clustering. Applications of the proposed method on simulated data as well as high-throughput data sets from tandem mass spectrometry (MS/MS) and microarray experiments are presented. Our results demonstrate its superior performance over most existing methods and its computational simplicity and extensibility in the application of large complex biological data sets.Availability: http://www.pitt.edu/~ctseng/research/software.htmlContact: ctseng@pitt.eduSupplementary information: Supplementary data are available at Bioinformatics online.