bluuebunny/crossref_metadata_2025_split huggingface dataset:
The interrupter technique to assess airway responsiveness in children with cystic fibrosis
Authors: Davies Philip L. , Doull Iolo J. , Child Frances 
Published: November 2006

AbstractThe aim of this study was to assess the validity of the interrupter technique (Rint) in measuring airway responsiveness in children with cystic fibrosis. Fifty children (aged 6–16 years) with cystic fibrosis performed six Rint measurements followed by three acceptable forced expiratory maneuvers. Each child then inhaled 5 mg of nebulized salbutamol by facemask. After 20 min the Rint and forced expiratory measurements were repeated. In the population as a whole a moderate but significant correlation between inverse Rint and FEV1 values was observed, both before and after inhaled bronchodilator (r = 0.71 and 0.72, respectively, P < 0.001). However, when changes in Rint and FEV1 readings following inhaled bronchodilator were examined, no relationship was seen. Indeed, the two methods identified completely different subsets of children as being bronchodilator responsive. These results indicate that although a relationship exists between Rint and FEV1 in the whole population, this is not the case in individual children. Rint and FEV1 reflect different aspects of lung function. It is not appropriate to use Rint as a simple alternative for FEV1 in children with cystic fibrosis when assessing airway responsiveness. Pediatr Pulmonol. 2007; 42:23–28. © 2006 Wiley‐Liss, Inc.
Endoscopic Nd:YAG laser therapy of infantile subglottic hemangioma
Authors: Fu Chia‐Hsiang , Lee Li‐Ang , Fang Tuan‐Jen , Wong Kin‐Sun , Li Hsueh‐Yu 
Published: November 2006

AbstractOf the many therapeutic modalities that have been developed for infantile subglottic hemangioma (ISH), the most common technique is endoscopic excision with carbon dioxide laser, used alone or combined with other therapeutic techniques. A staged procedure has been proposed as the preferred choice for patients with severe airway obstruction. Nevertheless, ever since the neodymium: yttrium‐aluminum‐garnet (Nd:YAG) laser was developed, this modality has been considered feasible to treat vascular tumor in the airway due to good hemostasis power. We present two cases of ISH with severe airway obstruction that underwent endoscopic surgery using an one‐stage Nd:YAG laser approach. Details of the laser characteristics and surgery techniques are described in this article. Pediatr Pulmonol. 2007; 42:89–92. © 2006 Wiley‐Liss, Inc.
Standardizing lung function laboratories for multicenter trials
Authors: Beardsmore C.S. , Paton J.Y. , Thompson J.R. , Laverty A. , King C. , Oliver C. , Stocks J. 
Published: November 2006

AbstractMulti‐center studies provide advantages in clinical research but differences between centers can introduce bias. Three specialist pediatric respiratory laboratories standardized their methodology and examined differences between centers. The specific aims were to (i) assess the variability of measurements on adults within and between centers and (ii) to exchange and cross‐analyze data from children to assess the extent of agreement between centers. Each laboratory used identical equipment and software. Inter‐laboratory visits were used to (i) standardize protocols for data collection and analysis and (ii) make spirometric and plethysmographic measurements on participating staff at each location. Staff also had repeat measurements in their home laboratories. Measurements from children in each laboratory were exchanged on disk, cross‐analyzed, and data compared by ANOVA. There were no significant within‐subject, between‐center differences in FVC, FEV1, FEF50, FRCpleth, or VC. There was a slight trend for TLC and RV (P = 0.07) to be higher at one center. The 95% limits of agreement within and between centers were similar for all parameters. There were no differences between centers in cross‐analyzed data from 10 children. By standardizing hardware, software, and protocol, potential inter‐laboratory differences can be minimized. We recommend that this approach be adopted prior to multi‐center studies. Pediatr Pulmonol. 2007; 42:51–59. © 2006 Wiley‐Liss, Inc.
MUPRED: A tool for bridging the gap between template based methods and sequence profile based methods for protein secondary structure prediction
Authors: Bondugula Rajkumar , Xu Dong 
Published: November 2006

AbstractPredicting secondary structures from a protein sequence is an important step for characterizing the structural properties of a protein. Existing methods for protein secondary structure prediction can be broadly classified into template based or sequence profile based methods. We propose a novel framework that bridges the gap between the two fundamentally different approaches. Our framework integrates the information from the fuzzy k‐nearest neighbor algorithm and position‐specific scoring matrices using a neural network. It combines the strengths of the two methods and has a better potential to use the information in both the sequence and structure databases than existing methods. We implemented the framework into a software system MUPRED. MUPRED has achieved three‐state prediction accuracy (Q3) ranging from 79.2 to 80.14%, depending on which benchmark dataset is used. A higher Q3 can be achieved if a query protein has a significant sequence identity (>25%) to a template in PDB. MUPRED also estimates the prediction accuracy at the individual residue level more quantitatively than existing methods. The MUPRED web server and executables are freely available at http://digbio.missouri.edu/mupred. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Automatic procedure for using models of proteins in molecular replacement
Authors: Raimondo Domenico , Giorgetti Alejandro , Giorgetti Alejandro , Bosi Stefania , Tramontano Anna 
Published: November 2006

AbstractIn a crystallography experiment, a crystal is irradiated with X‐rays whose diffracted waves are collected and measured. The reconstruction of the structure of the molecule in the crystal requires knowledge of the phase of the diffracted waves, information that is lost in the passage from the three‐dimensional structure of the molecule to its diffraction pattern. It can be recovered using experimental methods such as heavy‐atom isomorphous replacement and anomalous scattering or by molecular replacement, which relies on the availability of an atomic model of the target structure. This can be the structure of the target protein itself, if a previous structure determination is available, or a computational model or, in some cases, the structure of a homologous protein. It is not straightforward to predict beforehand whether or not a computational model will work in a molecular replacement experiment, although some rules of thumb exist. The consensus is that even minor differences in the quality of the model, which are rather difficult to estimate a priori, can have a significant effect on the outcome of the procedure. We describe here a method for quickly assessing whether a protein structure can be solved by molecular replacement. The procedure consists in submitting the sequence of the target protein to a selected list of freely available structure prediction servers, cluster the resulting models, select the representative structures of each cluster and use them as search models in an automatic phasing procedure. We tested the procedure using the structure factors of newly released proteins of known structure downloaded from the Protein Data Bank as soon as they were made available. Using our automatic procedure we were able to obtain an interpretable electron density map in more than half the cases. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Theoretical model of human apolipoprotein B100 tertiary structure
Authors: Kriško Anita , Etchebest Catherine 
Published: November 2006

AbstractLow density lipoprotein (LDL) particles are the main cholesterol carriers in human plasma. The organization of the particle, composed of apolar lipids and phospholipid monolayer stabilized by apolipoprotein B100 (apoB), is highly complex and still unknown. ApoB is an extremely large protein (4563 amino acids) and very little is known about its structure. A 3D model of the N‐terminal region has been recently proposed and has provided interesting insights about the physico‐chemical properties of the protein and putative interaction zones with lipids. In the present article, we propose the first tentative 3D modelling for most remaining residues. All predicted features emerging from the models are confronted with agreement to experimental data available. Using different up‐to‐date prediction methods, we decomposed the protein into eight domains and predicted 3D structure for each of them. The analysis of hydrophobic patches, polar regions, coupled with functional predictions based on the 3D models, gives new clues to understanding of the functional role of apoB. We suggest precise regions putatively involved in the lipid interactions, and discuss the position of apoB on the LDL particle. Finally, we propose relative organization of the domains, providing a shape quite compatible with the low resolution electron microscopy map. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Compton profiles and band structure calculations of CdS and CdTe
Authors: Heda N. L. , Mathur S. , Ahuja B. L. , Sharma B. K. 
Published: November 2006

AbstractIn this paper we present the isotropic Compton profiles of zinc‐blende CdS and CdTe measured at an intermediate resolution of 0.39 a.u. using our 20 Ci 137Cs Compton spectrometer. The electronic band structure calculations for both the zinc‐blende structure compounds and also wurtzite CdS have been undertaken using various schemes of ab‐initio linear combination of atomic orbitals calculations implemented in CRYSTAL03 code. The band structure and Mulliken's populations are reported using density functional scheme. In case of wurtzite CdS, our theoretical anisotropies in directional Compton profiles are compared with available experimental data. In case of both the zinc‐blende compounds, the isotropic experimental profiles are found to be in better agreement with the present Hartree–Fock calculations. A study of the equal‐valence‐electron‐density experimental profiles of zinc‐blende CdS and CdTe shows that the CdS is more ionic than CdTe. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Influence of ligand spin–orbit coupling to the g ‐shift in NaCl:V2+ and NaBr:V2+
Authors: Lei Y. , Zu X. T. , Zhao M. G. 
Published: November 2006

AbstractThe paper presents a molecular orbital calculation of the optical spectra and g ‐shift in NaCl:V2+ and NaBr:V2+, in which the contribution due to the electrostatic parameter A0, the Trees correction, the spin–orbit coupling of the central transition metal ion and the ligand are included. The calculated optical spectra and g ‐shift agree well with the available experimental data. The results show that the contribution due to the 3s of the ligand and the conjunct action between the center metal ion and the ligand can not be neglected. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Competing magnetic interactions in (Dy0.375Y0.625)2Cu2O5 solid solution studied by EPR
Authors: Typek J. 
Published: November 2006

Abstract(Dy0.375Y0.625)2Cu2O5 is an antiferromagnet below TN = 11 K, displaying many signs of low‐dimensional magnetism. Electron paramagnetic resonance (EPR) investigation of different magnetic interactions in (Dy0.375Y0.625)2Cu2O5 solid solution is carried out by analysis of thermal evolution of EPR spectral parameters (integrated intensity, effective resonance field, effective linewidth) evaluated in the paramagnetic phase. A model, proposed earlier to explain metamagnetic transitions in the anntiferromagnetic phase was used to interpret the observed magnetic behaviour. Manifestations of copper chains existing in the (Dy0.375Y0.625)2Cu2O5 structure has been found in the EPR spectrum and the values of appropriate exchange constants connected with a hierarchy of exchange interactions has been calculated. At about 40 K a dimensional crossover from 2D to 3D behaviour has been observed in the temperature dependence of the product of the EPR integrated intensity and temperature. At high temperatures (T > 200 K) the EPR spectrum is suggestive of the presence of defect centres consisting of antferromagnetically coupled copper spins, forming dimers with the S = 0 ground state. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Integral equations and complex resonance energies for analytical potentials
Authors: Kapshai V. , Alferova Tatjana , Elander Nils 
Published: November 2006

AbstractIt is shown that the Volterra integral equation in combination with complex scaling gives a formalism capable to solve Schrödinger‐type problems concerning bound states and resonances. The regular solution of the Schrödinger equation presented at the Volterra integral equation allows us to define the explicit form of the Jost function analytically continued into the lower half complex momentum plane. The resulting formalism is used to develop a numerical method for finding resonances defined as zeros of the Jost function. The numerical method is tested on several analytical potentials; it gives good results for arbitrary orbital momentum l. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Quantum chemical investigation of linear hydrogen bonding in ONCCN···HX (X = F, Cl, Br) dimers
Authors: Varadwaj Pradeep R. 
Published: November 2006

AbstractLinear hydrogen bonding formed between the nitrogen end of cyanogen‐N‐oxide (ONCCN) and hydrogen halides HX (X = F, Cl, Br) has been observed in their ground Σ states. The order of agreement of energetic stabilities between the correlated functionals used in this calculation is: B3LYP < PBE0 <PBE< PW91 in conjunction with the 6–311++G(3df,3pd) basis set. Analysis of various parameters describing the existence of H‐bonds in these dimers follows the conventional trend: ONCCN···HF > ONCCN···HCl > ONCCN···HBr in the series, except H‐bond lengths and static dipole polarizabilities which are in reverse order. The atomic charges obtained from the Mulliken and natural population analysis is used to assess the charge transfer effects that accompany the dimer formation. It is found from the investigation that the dimers having highest binding energy are accompanied by the highest transfer of charge. The14N nuclear quadrupole coupling constants of the monomer ON1CCN2are found to be decreased upon complection and in the series it increases from F through Br. We observed enhancements in the values of the dimer dipole moment and intrinsic dipole polarizabilities compared with the sum of the monomer values by intermolecular electrical interaction. Investigation reveals vibrational spectral shifts of HX and CN stretching modes similar to the conventional red‐shifted H‐bonded dimers; for the former case, the infrared band intensity increases significantly. Finally, the new vibrational modes originated from the intermolecular interaction are outlined. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Theoretical study of the gas‐phase SN2 reactions of X− with CH3OY (X, Y = Cl, Br, I)
Authors: Gai Jing‐Gang , Ren Yi 
Published: November 2006

AbstractThe gas‐phase nucleophilic substitution reactions at saturated oxygen X− + CH3OY (X, Y = Cl, Br, I) have been investigated at the level of CCSD(T)/6‐311+G(2df,p)//B3LYP/6‐311+G(2df,p). The calculated results indicate that X− preferably attacks oxygen atom of CH3OY via a SN2 pathway. The central barriers and overall barriers are respectively in good agreement with both the predictions of Marcus equation and its modification, respectively. Central barrier heights (ΔH and ΔH) correlate well with the charges (Q) of the leaving groups (Y), Wiberg bond orders (BO) and the elongation of the bonds (OY and OX) in the transition structures. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Theoretical studies of structures and stabilities of endohedral fullerenes X0/n+ @C32 (X = H, Li, Na, K, Be, Mg, Ca, B, Al, C, Si, N, P, n = 1–3)
Authors: Sun Lili , Chang Yingfei , Hong Bo , Wang Rongshun 
Published: November 2006

AbstractBased on the D3 C32 fullerene, the equilibrium geometries, electronic structures, and binding energies of the endohedral fullerenes X0/n+@C32 (X = H, Li, Na, K, Be, Mg, Ca, B, Al, C, Si, N, P, n = 1–3) have been calculated using the DFT/B3LYP/6‐31G(d) method. The results show that the C32 cages are slightly enlarged due to encapsulation, and the sizes of non‐neutral molecules are smaller than the corresponding neutral ones. Cages containing Li, Na, and Ca and most of the cations, except Na+ and K+, are energetically favorable. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Some continuous geometry transitions and the consequences for a transition‐metal atom
Authors: Springborg Michael , Hegetschweiler Kaspar 
Published: November 2006

AbstractBy considering a transition‐metal ion in the field of some symmetrically placed ions, we illustrate the consequences of a continuous change of the structure of the ligands on the energies of the 3d electrons of the transition‐metal atom. Both a rigorous mathematical derivation and an analysis based on group theory are presented. For six ions surrounding the transition‐metal atom, a continuous D∞h → D3d → Oh→ D3d→ D6d transition is observed, whereas for four ions, a continuous D∞ h→ D2d→ Td→ D2d→ D4d transition results. Although the two systems possess many similarities, interesting differences are found as well. Finally, we demonstrate that when including orbital interactions between the ligands and the transition‐metal atom, quantitative differences occur. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Electron attachment to the DNA bases adenine and guanine and dehydrogenation of their anionic derivatives: Density functional study
Authors: Xie Hujun , Cao Zexing 
Published: November 2006

AbstractDensity functional theory (DFT) calculations have been used to explore electron attachment to the purines adenine and guanine and their hydrogen atom loss. Calculations show that the dehydrogenation at the N9 site in the adenine and guanine transient anions is the lowest‐cost channel of hydrogen loss, and the N9H bond scission has Gibbs free energies of dissociation ΔG° of 8.8 kcal mol−1 for the anionic adenine and 13.9 kcal mol−1 for the anionic guanine. The relatively high feasibility of low‐energy electron (LEE)‐induced N9H bond cleavage in the purine nucleobases arises from high electron affinities of their H‐deleted counterparts. Unlike adenine, other NH bond dissociations are competitive with the N9H bond fission in the anionic guanine. The replacement of hydrogen in the ring of purine has a significant effect on the N9H bond fragmentation. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
DFT study of rearrangements in cyclopentylheptenyl carbocations
Authors: Vrcek Valerije 
Published: November 2006

AbstractCarbocation rearrangements relevant to sterol biosynthesis were investigated computationally by using the model cyclopentylheptenyl carbocations 1A and 1B. Five different rearrangement pathways of these equilibrating cations were located at the potential energy surface (PES), all calculated at the B3LYP/6‐31G(d) level of theory. Each of these five distinct pathways differs from previous mechanistic proposals, and each involves new and unusual intermediates. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
The W algorithm and the D transformation for the numerical evaluation of three‐center nuclear attraction integrals
Authors: Duret Stefan , Safouhi Hassan 
Published: November 2006

AbstractThree‐center nuclear attraction integrals over exponential‐type functions are required for ab initio molecular structure calculations and density functional theory (DFT). These integrals occur in many millions of terms, even for small molecules, and they require rapid and accurate numerical evaluation. The use of a basis set of B functions to represent atomic orbitals, combined with the Fourier transform method, led to the development of analytic expressions for these molecular integrals. Unfortunately, the numerical evaluation of the analytic expressions obtained turned out to be extremely difficult due to the presence of two‐dimensional integral representations, involving spherical Bessel integral functions. % The present work concerns the development of an extremely accurate and rapid algorithm for the numerical evaluation of these spherical Bessel integrals. This algorithm, which is based on the nonlinear D transformation and the W algorithm of Sidi, can be computed recursively, allowing the control of the degree of accuracy. Numerical analysis tests were performed to further improve the efficiency of our algorithm. The numerical results section demonstrates the efficiency of this new algorithm for the numerical evaluation of three‐center nuclear attraction integrals. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Exact‐mass library for pesticides using a molecular‐feature database
Authors: Ferrer Imma , Fernandez‐Alba Amadeo , Zweigenbaum Jerry A. , Thurman E. Michael 
Published: November 2006

AbstractAn automated molecular‐feature database (MFD) consisting of the exact monoisotopic mass of 100 compounds, at least one exact mass product ion for each compound, and chromatographic retention time were used to identify pesticides in food and water samples. The MFD software compiles a list of accurate mass ions, excludes noise, and compares them with the monoisotopic exact masses in the database. The screening criteria consisted of ±5 ppm accurate mass window, ±0.2 min retention time window, and a minimum 1000 counts (signal‐to‐noise (S/N) ratio of ∼10:1). The limit of detection for 100 tested compounds varied from <0.01 mg/kg for 72% of the compounds to <0.1 mg/kg for 95% of the compounds. The MFD search was useful for rapid screening and identification of pesticides in food and water, as shown in actual samples. The combined use of accurate mass and chromatographic retention time eliminated false positives in the automated analysis. The major weakness of the MFD is matrix interferences and loss of mass accuracy. Strengths of the MFD include rapid screening of 100 compounds at sensitive levels compared with a manual approach and the ease of use of the library for any accurate mass spectrometer instrumentation capable of routine sub‐5‐ppm mass accuracy. Copyright © 2006 John Wiley & Sons, Ltd.
Improved matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry of carboxymethyl cellulose
Authors: Enebro Jonas , Karlsson Sigbritt 
Published: November 2006

AbstractA refined sample preparation procedure for matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry (MALDI‐TOFMS) was developed for the evaluation of the degree of substitution (DS) in partially depolymerised carboxymethyl cellulose (CMC). By adding ammonium sulphate to the sample mixture prior to the analysis, good quality mass spectra could be acquired. The usual time‐consuming search for ‘sweet‐spots’ at the crystalline rim of the MALDI target spot was also avoided. This quality improvement made it possible to investigate whether various positions on the target spot generated mass spectra in which the measured DS varied. The accuracy and reproducibility of the sample preparation procedure were tested by applying it on three commercial CMCs. The study shows that the DS values that were calculated from the spectra acquired from the centre region of the MALDI target spot were in better agreement with the DS provided by the supplier than were the values obtained from the large crystals at the target spot rim. This observation could be one reasonable explanation for the higher DS values reported in other publications. By applying our refined MALDI sample preparation procedure DS values that were in good agreement with the values provided by the manufacturer could be obtained. This indicates that MALDI‐TOFMS of partially depolymerised CMCs can be used for an estimation of the DS as a complement to the more established methods, e.g. NMR, titrimetry, and chromatographic techniques. Copyright © 2006 John Wiley & Sons, Ltd.