bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interactive measurement and characterization of DNA molecules by analysis of AFM images
Authors: Marek J. , Demjénová E. , Tomori Z. , Janáček J. , Zolotová I. , Valle F. , Favre M. , Dietler G. 
Published: January 2005

AbstractBackgroundIn the past few years, computer‐based analysis of atomic‐force microscopic images has acquired increasing importance for studying biomolecules such as DNA. On the one hand, fully automated methods do not allow analysis of complex shapes; on the other hand, manual methods are usually time consuming and inaccurate. The semiautomated approach presented in this report overcomes the drawbacks of both methods.MethodsTwo kinds of images were analyzed: computer‐generated filaments that modeled circular DNA molecules on a surface and real atomic‐force microscopic images of DNA molecules adsorbed on an appropriate substrate surface.ResultsThe algorithm was tested on a group of 140 simulated and 189 real plasmids with a nominal length of 913 nm. The accuracy of the length measurement was statistically evaluated on the ensemble of molecules, with particular attention to the influence of the noise. Mean contour lengths of 912 ± 5 nm and 910 ± 47 nm were found for simulated and real plasmids, respectively. The measured end‐to‐end distance of λ‐DNA molecules as a function of their contour length is reported, from which it is possible to estimate the stiffness of the DNA molecules adsorbed onto a surface; the value obtained for the DNA persistence length (42 ± 5 nm) is consistent with values measured by other imaging techniques.ConclusionsAn interactive algorithm for DNA molecule measurements based on the detection of the filament ridge line in a digitized image is presented. The simulation of artificial filaments combined with the experimental data demonstrates that the proposed method can be a valuable tool for the DNA contour length evaluation, especially in the case of complex shapes where the use of automatic methods is not possible. © 2005 Wiley‐Liss, Inc.
Quantification of gliadin levels to the picogram level by flow cytometry
Authors: Capparelli Rosanna , Ventimiglia Ilaria , Longobardo Luigi , Iannelli Domenico 
Published: January 2005

AbstractBackgroundCeliac disease is a widely prevalent enteropathy caused by intolerance to gliadin, one of the gluten proteins. We developed two methods for the analysis of gliadin levels. Both methods use flow cytometry and rat antibodies against a 16‐residue peptide of gliadin. The peptide is common to the α‐, β‐, γ‐, and ω‐gliadins.MethodsIn the one‐site assay, the antigen (gliadin standard or food extract) was adsorbed on 3‐μm latex particles. Sensitized particles were then incubated, in this order, with rat anti‐gliadin peptide antibodies and anti‐rat immunoglobulin G antibodies labeled with fluorescein isothiocyanate. In the two‐site assay, the antigen was trapped on the latex particles by rat anti‐gliadin antibodies and then measured by the same antibodies labeled with fluorescein.ResultsDetection limits were 1 ng/ml for the one‐site assay and 10 pg/ml for the two‐site assay. The two‐site assay displayed gliadin at concentrations above the limit proposed by the Codex Alimentarius in 2 of 40 gluten‐free products.ConclusionThere is a growing concern that gliadin, even when present in gluten‐free foods within the limit fixed by the Codex Alimentarius, over the long term may become toxic to patients with celiac disease. The techniques described in this study provide an opportunity to further decrease the acceptable limit of gliadin in gluten‐free foods. © 2005 Wiley‐Liss, Inc.
Variational data assimilation for Hamiltonian problems
Authors: Watkinson L. R. , Lawless A. S. , Nichols N. K. , Roulstone I. 
Published: January 2005

AbstractWe investigate the conservation properties of Hamiltonian systems in variational data assimilation. We set up a four‐dimensional data assimilation scheme for the two‐body (Kepler) system using a symplectic scheme to model the non‐linear problem. We use our completed scheme to investigate the observability of the system and the effect of different background constraints. We find that the addition of these constraints gives an improved solution for the cases we have investigated. Copyright © 2005 John Wiley & Sons, Ltd.
Laboratory for internal gravity‐wave dynamics: the numerical equivalent to the quasi‐biennial oscillation (QBO) analogue
Authors: Wedi Nils P. , Smolarkiewicz Piotr K. 
Published: January 2005

AbstractWe have extended the classical terrain‐following coordinate transformation of Gal–Chen and Somerville to a broad class of time‐dependent vertical domains. The proposed extension facilitates modelling of undulating vertical boundaries in various areas of computational fluid dynamics. The theoretical development and the efficient numerical implementation have been documented in the context of the generic Eulerian/semi‐Lagrangian, non‐oscillatory forward in time (NFT), nonhydrostatic model framework. In particular, it allows the simulation of stratified flows with intricate geometric, time‐dependent boundary forcings, either at the top or at the bottom of the domain. We have applied our modelling framework in the direct numerical simulation of the celebrated laboratory experiment of Plumb and McEwan creating the numerical equivalent to their quasi‐biennial oscillation (QBO) analogue. The QBO represents a conspicuous example of a fundamental dynamical mechanism with challenging detail, which is difficult to deduce from experimental evidence alone. A series of 2D and 3D simulations demonstrate the ability to reproduce the laboratory results. The numerical experiments identify the developing periodically reversing mean flow pattern primarily as a wave–wave mean flow interaction‐driven phenomenon. The results not only enhance the confidence in the numerical approach but further elevate the importance of the laboratory setup in its fundamental similarity to the atmosphere, while allowing the study of the principal atmospheric mechanisms and their numerical realizability in a confined ‘laboratory’ environment. Copyright © 2005 John Wiley & Sons, Ltd.
Angiopoietin 1 prevents retinal detachment in an aggressive model of proliferative retinopathy, but has no effect on established neovascularization
Authors: Nambu Hiroyuki , Umeda Naoyasu , Kachi Shu , Oshima Yuji , Akiyama Hideo , Nambu Rie , Campochiaro Peter A. 
Published: January 2005

AbstractVascular endothelial growth factor (VEGF) plays a central role in vasoproliferative diseases in the retina, however, other gene products modulate its effects. The angiopoietins are particularly important in this regard. Angiopoietin 2 (Ang2) collaborates with VEGF to stimulate neovascularization (NV) in some situations, but in other situations causes regression of NV. Ang2 also causes a transient increase in vascular density during retinal vascular development. In this study, we sought to determine if Ang1 has similar activities. The effects of Ang1 were tested in double transgenic mice with inducible expression of Ang1. Increased expression of Ang1 in the retina during retinal vascular development did not cause a detectable alteration in vascular density. Also, unlike Ang2, increased expression of Ang1 had no effect on established retinal or choroidal NV. However, when Ang1 expression was initiated simultaneously with that of VEGF, it strongly suppressed VEGF‐induced NV and prevented retinal detachment. These data indicate that the timing of Ang1 expression is a critical determinate of its effects on VEGF‐induced NV in the retina; it effectively blocks the initiation and progression of NV, but cannot reverse established NV or reduce leakage from NV. These data suggest that increased expression of Ang1 may be a good strategy for prophylaxis of retinal NV, but is unlikely to be effective as monotherapy of established NV. © 2005 Wiley‐Liss, Inc.
Catalytic 1,3‐Cyclohexadiene Homopolymerization and Regioselective Copolymerization with Ethylene
Authors: Heiser Dirk E. , Okuda Jun , Gambarotta Sandro , Mülhaupt Rolf 
Published: January 2005

AbstractSummary: 1,3‐Cyclohexadiene (CHD) was homo‐ and copolymerized by means of diimine nickel complexes and various substituted titanium based half‐sandwich complexes activated with methylaluminoxane (MAO). Soluble polycyclohexadienes were produced with the constrained geometry catalyst [Me2Si(NtBu)(Me4Cp)]TiCl2 (CBT) (Cp = cyclopentadienyl, Me = methyl). Only in the presence of CBT/MAO soluble high molecular weight CHD copolymers with ethylene were obtained. The CHD incorporation was varied between 0 and 12.3 mol‐%. According to NMR analysis the CHD/ethylene copolymerization is highly regioselective, accounting for exclusive formation of 1,4‐cyclohexene units randomly distributed in the polyethylene backbone.13C NMR spectra of 1,4‐poly(1,3‐cyclohexadiene‐co‐ethylene) with 6.8 mol‐% CHD content in the copolymer.magnified image13C NMR spectra of 1,4‐poly(1,3‐cyclohexadiene‐co‐ethylene) with 6.8 mol‐% CHD content in the copolymer.
Novel Partially Fluorinated Copolymers: Evidence of the Effect of Fluorine on the Reactivity of the Unfluorinated Comonomer Units
Authors: Lazzari Massimo , Scalarone Dominique , Castelvetro Valter , Signori Francesca , Chiantore Oscar 
Published: January 2005

AbstractSummary: A conventional free‐radical polymerization of vinyl or propenyl ethers with acrylic or methacrylic monomers with fluorine substitution either in the main chain or in the ester groups has permitted us to obtain a series of copolymers with substantially different fluorine contents and distributions to be obtained. Such copolymers were considered as model compounds to offer new valuable insights as to the influence of fluorinated moieties on the overall stability and, more specifically, on their reactivity with atmospheric oxygen under environmental‐like conditions. Depending on the relative position of the fluorine atoms with respect to the common active center of oxidation, the influence ranges from a simple slowing down of the process to a complete redirection towards an otherwise secondary mechanism of oxidation.FT‐IR spectra of the carbonyl region of three novel fluorinated copolymers after oxidation.imageFT‐IR spectra of the carbonyl region of three novel fluorinated copolymers after oxidation.
Differential pattern of hand‐tapping compromise in vascular versus idiopathic parkinsonism: A study based on computerized movement analysis
Authors: Bäzner Hansjörg , Schanz Jurik , Blahak Christian , Grips Eva , Wöhrle Johannes C. , Hennerici Michael 
Published: January 2005

AbstractWe tested the characteristics and the differential pattern of upper extremity motor compromise, comparing hand tapping in patients with subcortical vascular encephalopathy (SVE; n = 18), idiopathic Parkinson's disease (PD; n = 18), and in healthy controls (n = 18). Both patient groups showed significant compromise in hand tapping compared with that in controls, with higher coefficients of variability (CV) regarding tapping amplitude and angular velocity, determined using a computerized movement analysis system. A differential tapping pattern in both patient groups could be demonstrated in that patients with PD showed lower tapping amplitudes than patients with SVE. Both patient groups displayed abnormalities in tapping rhythmicity compared with that in the control group. © 2005 Movement Disorder Society
Model density approach to the Kohn–Sham problem: Efficient extension of the density fitting technique
Authors: Birkenheuer Uwe , Gordienko Aleksei B. , Nasluzov Vladimir A. , Fuchs‐Rohr Monika K. , Rösch Notker 
Published: January 2005

AbstractWe present a novel procedure for treating the exchange‐correlation contributions in the Kohn–Sham procedure. The approach proposed is fully variational and closely related to the so‐called “fitting functions” method for the Coulomb Hartree problem; in fact, the method consistently uses this auxiliary representation of the electron density to determine the exchange‐correlation contributions. The exchange‐correlation potential and its matrix elements in a basis set of localized (atomic) orbitals can be evaluated by reusing the three‐center Coulomb integrals involving fitting functions, while the computational cost of the remaining numerical integration is significantly reduced and scales only linearly with the size of the auxiliary basis. We tested the approach extensively for a large set of atoms and small molecules as well as for transition‐metal carbonyls and clusters, by comparing total energies, atomization energies, structure parameters, and vibrational frequencies at the local density approximation and generalized gradient approximation levels of theory. The method requires a sufficiently flexible auxiliary basis set. We propose a minimal extension of the conventional auxiliary basis set, which yields essentially the same accuracy for the quantities just mentioned as the standard approach. The new method allows one to achieve substantial savings compared with a fully numerical integration of the exchange‐correlation contributions. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Elongation method with cutoff technique for linear SCF scaling
Authors: Korchowiec Jacek , Gu Feng Long , Imamura Akira , Kirtman Bernard , Aoki Yuriko 
Published: January 2005

AbstractThe elongation method uses the concept of locality and works in a regionally localized molecular orbital basis set. In this method the system is partitioned into several frozen fragments and an active one. If the coupling between a given frozen fragment and the active space is small enough, one can develop a cutoff scheme for effectively discarding the former in all further calculations. At the Hartree–Fock level many two‐electron integrals are thereby eliminated, leading to a reduction in self‐consistent field computation time. In test calculations on four polyglycine conformers, with an appropriate default threshold for coupling, the cutoff error is very small and/or comparable to that of a normal elongation calculation. On the other hand, the computation time for 20 residues is a factor of 5 less than that of a normal Hartree–Fock treatment and scales linearly (or even sublinearly) with the number of residues. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
MCD of non‐aromatic cyclic π‐electron systems. Part 6: Pentalenes and heptalenes
Authors: Fleischhauer Jörg , Raabe Gerhard , Klingensmith Kenneth A. , Höweler Udo , Chatterjee Prabir K. , Hafner Klaus , Vogel Emanuel , Michl Josef 
Published: January 2005

AbstractThe magnetic circular dichroism (MCD) spectra of several stable derivatives of pentalene (1) and heptalene (2) have been recorded. The lowest energy transition (from the ground to the S state in perimeter model nomenclature) is extremely weak in MCD and in absorption. The sign patterns of the B terms for the first three strong transitions—N1, N2, P1—in the order of increasing energy, are −−+ for 1 and ++− for 2. These findings are in perfect agreement with numerical results obtained at the SACCI level and with expectations based on the perimeter model of Parts 1–4 of this series, both of which lead to the conclusion that the magnetic mixing of the S excited state with the ground state is dominant. This is an extremely rare situation for an organic molecule, in which B term signs are normally determined by the mutual magnetic mixing of excited states. It can be expected to occur in other conjugated systems derived from 4N‐electron perimeters that have a low‐energy first excitation, which is of intrashell nature in the perimeter model and therefore is magnetic‐dipole allowed. In contrast, all low‐energy transitions in the much more common systems derived from (4N + 2)‐electron perimeters are of intershell nature and are magnetic‐dipole forbidden. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Can the Fulleride superconducting model (FSM) be extended?
Authors: Squire R. H. 
Published: January 2005

AbstractThe Fulleride superconducting model (FSM) is based on the existence of an electron (or Cooper) pair density wave localized on a single Fulleride molecule. Interaction of the wave with itinerant electrons at low temperature creates a pseudo‐gap above the superconducting state. In addition, the interaction of the electron and the bosonic pair create a net attraction between two Fulleride molecules resulting in an intermolecular Cooper pair. This pairing interaction appears to have all the aspects of a spin liquid. This study extends the model to high‐temperature superconductors and suggests that superconductivity may exist with considerably fewer molecules than in BCS theory. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
A method for carbon stable isotope analysis of methyl halides and chlorofluorocarbons at pptv concentrations
Authors: Archbold Marie E. , Redeker Kelly R. , Davis Simon , Elliot Trevor , Kalin Robert M. 
Published: January 2005

AbstractA pre‐concentration system has been validated for use with a gas chromatography/mass spectrometry/isotope ratio mass spectrometer (GC/MS/IRMS) to determine ambient air 13C/12C ratios for methyl halides (MeCl and MeBr) and chlorofluorocarbons (CFCs). The isotopic composition of specific compounds can provide useful information on their atmospheric budgets and biogeochemistry that cannot be ascertained from abundance measurements alone. Although pre‐concentration systems have been previously used with a GC/MS/IRMS for atmospheric trace gas analysis, this is the first study also to report system validation tests. Validation results indicate that the pre‐concentration system and subsequent separation technologies do not significantly alter the stable isotopic ratios of the target methyl halides, CFC‐12 (CCl2F2) and CFC‐113 (C2Cl3F3). Significant, but consistent, isotopic shifts of −27.5‰ to −25.6‰ do occur within the system for CFC‐11 (CCl3F), although the shift is correctible. The method presented has the capacity to separate these target halocarbons from more than 50 other compounds in ambient air samples. Separation allows for the determination of stable carbon isotope ratios of five of these six target trace atmospheric constituents within ambient air for large volume samples (≤10 L). Representative urban air analyses from Belfast City are also presented which give carbon isotope results similar to published values for 13C/12C analysis of MeCl (−39.1‰) and CFC‐113 (−28.1‰). However, this is the first paper reporting stable carbon isotope signatures for CFC‐11 (−29.4‰) and CFC‐12 (−37.0‰). Copyright © 2005 John Wiley & Sons, Ltd.
Carbon isotope analyses of cellulose using two different on‐line techniques (elemental analysis and high‐temperature pyrolysis)—a comparison
Authors: Knöller Kay , Boettger Tatjana , Weise Stephan M. , Gehre Matthias 
Published: January 2005

AbstractEven though the recent development in on‐line methods for the stable isotope determination in cellulose has led to a significant increase in sample throughput and decrease in sample preparation expenditure, there still is a large potential for optimizing the analytical procedures by simultaneously measuring the isotope ratios of two or even more elements. Therefore, the main objective of this study was to answer the question whether high‐temperature pyrolysis (HTP) is a suitable and reliable technique for the determination of the carbon isotopic composition of cellulose simultaneously during the well‐known conventional oxygen isotope analysis. This study shows that HTP of cellulose is a technique that can produce reasonable δ13C values, matching the requirements of most research problems related to paleoclimatology. The reproducibility of the delta values for 13C/12C is better than 0.2‰. Some deficiencies of the method are related to the incomplete conversion of the organic carbon in the sample to carbon monoxide. A clear isotope effect seems to be related to the non‐statistical conversion of the carbon in the cellulose to CO. The extent of this effect appears to be controlled by the relative proportion of crystallized and amorphous matter in the cellulose structure. Those deficiencies can be eliminated by using an appropriate normalization and by applying the principles of identical treatment for reference materials and samples. In general, a very good agreement is achieved for carbon isotope values determined by HTP and elemental analysis (EA). Copyright © 2005 John Wiley & Sons, Ltd.
The carbon isotope composition of CO2 respired by trunks: comparison of four sampling methods
Authors: Damesin C. , Barbaroux C. , Berveiller D. , Lelarge C. , Chaves M. , Maguas C. , Maia R. , Pontailler J.‐Y. 
Published: January 2005

AbstractThe 13C natural abundance of CO2 respired by plants has been used in the laboratory to examine the discrimination processes that occur during respiration. Currently, field measurements are being expanded to interpret the respiration δ13C signature measured at ecosystem and global levels. In this context, forests are particularly important to consider as they represent 80% of the continental biomass. The objective of this investigation was to compare four methods of sampling the CO2 respired by trunks for the determination of its carbon isotope composition: three in situ methods using chambers placed on the trunk, and one destructive method using cores of woody tissues. The in situ methods were based either on a Keeling plot approach applied at the tissue level or on an initial flush of the chamber with nitrogen or with CO2‐free air. In parallel, we investigated the possibility of an apparent discrimination during tissue respiration by comparing the δ13C signature of the respired CO2 and that of the organic matter. The study was performed on six tree species widely distributed in temperate and mediterranean areas. The four methods were not significantly different when overall means were considered. However, considering the individual data, the Keeling plot approach and the nitrogen flush methods gave fairly homogeneous results, whereas the CO2‐free air method produced more variable results. The core method was not correlated with any of the chamber methods. Regardless of the methodology, the respired CO2 generally was enriched in 13C relative to the total organic matter. This apparent enrichment during respiration was variable, reaching as much as 3–5‰. This study showed that, on the whole, the different sampling techniques gave similar results, but one should be aware of the variability associated with each method. Copyright © 2005 John Wiley & Sons, Ltd.
Halogeno‐substituted 2‐aminobenzoic acid derivatives for negative ion fragmentation studies of N‐linked carbohydrates
Authors: Harvey David J. 
Published: January 2005

AbstractNegative ion electrospray mass spectra of high‐mannose N‐linked glycans derivatised with 2‐aminobenzoic acids and ionised from solutions containing ammonium hydroxide gave prominent [M–H]− ions accompanied by weaker [M–2H]2− ions. Fragmentation of both types of ions gave prominent singly charged glycosidic cleavage ions containing the derivatised reducing terminus and ions from the non‐reducing terminus that appeared to be products of cross‐ring cleavages. Differentiation of these two groups of ions was conveniently achieved in a single spectrum by use of chloro‐ or bromo‐substituted benzoic acids in order to label ions containing the derivative with an atom with a distinctive isotope pattern. Fragmentation of the doubly charged ions gave more abundant fragments, both singly and doubly charged, than did fragmentation of the singly charged ions, but information of chain branching was masked by the appearance of prominent ions produced by internal cleavages. Copyright © 2005 John Wiley & Sons, Ltd.