bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of respiratory illness on expiratory flow rates in normal, asthmatic, and allergic children
Authors: Rappaport Edward B. , Gilliland Frank D. , Linn William S. , Gauderman W. James 
Published: October 2002

AbstractWe examined the effects of current respiratory illness (RI) on pulmonary function (PF) in 1,103 subjects who underwent spirometry at schools twice within a 4‐month period. Before spirometry, subjects were asked if they had a “cold or other chest illness” during the previous month, and if so, whether they had fully recovered. Those who had not recovered were considered to have an RI.We found that children without RI at their first PF test who reported RI on retest had significantly lower forced expiratory volume in 1 sec (FEV1) (−0.8%), peak expiratory flow rate (PEFR) (−2.2%), forced expiratory flow between 25–75% of vital capacity (FEF25–75) (−3.5%), and forced expiratory flow at 75% of vital capacity (FEF75) (−5.1%) than those without RI on both test and retest. Restriction of subjects to those without a history of doctor‐diagnosed asthma did not appreciably change these findings. Children with hay fever had significantly larger RI‐associated decreases for FEV1, FEF25–75, and FEF75, but not PEFR, than those without hay fever. Among asthmatic subjects, those with active asthma had larger RI‐associated decreases in FEF25–75 and FEF75, but not PEFR, than those without asthma. There was limited evidence that small airway losses were greater in children less than 12.5 years old.We conclude that RI in children who are well enough to attend school may reduce expiratory flow rates. These effects are greater for children with active asthma or hay fever than in those without, and may be inversely related to age. Pediatr Pulmonol. 2002; 34:112–121. © 2002 Wiley‐Liss, Inc.
Prediagnostic toenail cadmium and zinc and subsequent prostate cancer risk
Authors: Platz Elizabeth A. , Helzlsouer Kathy J. , Hoffman Sandra C. , Morris J. Steven , Baskett Connie K. , Comstock George W. 
Published: October 2002

AbstractBACKGROUNDCadmium is a recognized human lung carcinogen that has also been positively associated with prostate cancer mainly in occupationally exposed men. The association between dietary and supplemental zinc intake and prostate cancer has not been consistent in epidemiologic studies. We evaluated the association between prediagnostic toenail cadmium and zinc concentrations and risk of prostate cancer in a cohort in which the primary route of exposure to cadmium and zinc is the diet.METHODSIncluded in the analysis were 115 prostate cancer cases and 227 age‐matched controls nested in the prospective CLUE II study located in Washington County, MD. Participants provided toenail samples at baseline in 1989. Furnace atomic absorption and flame atomic absorption were used to determine toenail cadmium and zinc concentrations, respectively. Odds ratios (OR) and 95% confidence intervals (CI) were estimated from conditional logistic regression models.RESULTSMedian toenail cadmium and zinc concentrations did not statistically significantly differ between prostate cancer cases (cadmium, 45.9 ppb; zinc, 155.3 ppm) and controls (cadmium, 54.5 ppb; zinc, 164.0 ppm). Prostate cancer risk did not increase with increasing concentrations of cadmium (P trend = 0.9) and did not decrease with increasing concentrations of zinc (P trend = 0.2). For both metals, the ORs for the top four fifths were each below 1.0 when compared with the bottom fifth.CONCLUSIONMen who have high toenail cadmium concentrations in the range observed in this general population sample were not at an increased risk for prostate cancer. Although there was no evidence of a linear dose‐response, these findings suggest that risk of prostate cancer may be slightly lower among men with moderate and higher zinc intake. Prostate 52: 288–296, 2002. © 2002 Wiley‐Liss, Inc.
Free‐energy simulations of the oxidation of c‐terminal methionines in calmodulin
Authors: Jas Gouri S. , Kuczera Krzysztof 
Published: October 2002

AbstractIn the course of aging or under conditions of oxidative stress, methionine residues of calmodulin undergo oxidation, leading to loss of biological activity of the protein. We have performed free‐energy simulations of the effects of C‐terminal methionine side‐chain oxidation on the properties of calmodulin. The simulation results indicate that oxidation should have a destabilizing effect on all three protein functional states: calcium free, calcium loaded, and with both calcium and target peptide bound. Because the different states are destabilized by different amounts, this leads to a more complex pattern in the observable effects on protein thermal stability, calcium affinity, and binding of a target peptide. The influence of oxidation on the free energy of CaM unfolding is estimated by comparing the free‐energy cost of oxidizing a Met residue in a Gly‐Met‐Gly peptide and in the protein. The protein thermal stability of the oxidized forms is lowered by a moderate amount 1–3 kcal/mol, in qualitative agreement with experimental results of 0.3 kcal/mol. The calculated changes in affinity for calcium and for the target peptide show opposing trends. Oxidation at position 144 is predicted to enhance peptide binding and weaken calcium binding, whereas oxidation at 145 weakens peptide binding and enhances affinity for calcium. The lower affinity of Met 145‐oxidized calmodulin toward the target peptide correlates with experimentally observed lowering of calmodulin‐activated Ca‐ATPase activity when oxidized calmodulin from aged rat brains is used. Thus, our simulations suggest that Met 145 is the oxidation site in the C‐terminal fragment of calmodulin. The microscopic mechanism behind the calculated free energy changes appears to be a greater affinity for water of the oxidized Met side‐chain relative to normal Met. Structures with Met exposed to solvent had consistently lower free energies than those with buried Met sidechains. Proteins 2002;48:257–268. © 2002 Wiley‐Liss, Inc.
The role of hydrophobic microenvironments in modulating pKa shifts in proteins
Authors: Mehler E.L. , Fuxreiter M. , Simon I. , Garcia‐Moreno E B. 
Published: October 2002

AbstractThe screened Coulomb potential (SCP) method, combined with a quantitative description of the microenvironments around titratable groups, based on the Hydrophobic Fragmental Constants developed by Rekker, has been applied to calculate the pKa values of groups embedded in extremely hydrophobic microenvironments in proteins. This type of microenvironment is not common; but constitutes a small class, where the protein's architecture has evolved to lend special properties to the embedded residue. They are of significant interest because they are frequently important in catalysis and in proton and electron transfer reactions. In the SCP treatment these special cases are treated locally and therefore do not affect the accuracy of the pKa values calculated for other residues in less hydrophobic environments. Here the calibration of the algorithm is extended with the help of earlier results from lysozyme and of three mutants of staphylococcal nuclease (SNase) that were specially designed to measure the energetics of ionization of titratable groups buried in extremely hydrophobic microenvironments. The calibrated algorithm was subsequently applied to a fourth mutant of SNase and then to a very large dimeric amine oxidase of 1284 residues, where 334 are titratable. The observed pKa shifts of the buried residues are large (up to 4.7 pK units), and all cases are well reproduced by the calculations with a root mean square error of 0.22. These results support the hypothesis that protein electrostatics can only be described correctly and self‐consistently if the inherent heterogeneity of these systems is properly accounted for. Proteins 2002;48:283–292. © 2002 Wiley‐Liss, Inc.
Atoms‐in‐molecules study of the genetically encoded amino acids. II. Computational study of molecular geometries
Authors: Matta Chérif F. , Bader Richard F. W. 
Published: October 2002

AbstractThe geometries of the 20 genetically encoded amino acids were optimized at the restricted Hartree–Fock level of theory using the 6‐31+G* basis set. A detailed comparison showed the calculated geometries to be in excellent agreement with those determined by X‐ray crystallography. The study demonstrated that the geometric parameters for the main‐chain group and for the bonds and common functional groups of the side‐chains exhibit a high degree of transferability among the members of this set of molecules. This geometric transferability is a necessary prerequisite for the corresponding transferability of their electron density distributions and hence of their bond and atomic properties. The transferability of the electron distributions will be demonstrated and exploited in the following paper of this series, which uses the topology of the electron density to define an atom within the quantum theory of atoms in molecules. Particular features of the geometries of the amino acids are discussed. It has been shown, for example, how the apparent anomaly of the CαN bond length in a peptide being shorter than in the charged species CαNHis resolved when the charge separation is gauged by the differences in the charges of the Cα and N atoms as opposed to the use of formal charges. A compilation of literature sources on experimental geometries covering each member of the 20 amino acids is presented. A set of rules for labeling the atoms and bonds, complementing the generally accepted IUPAC‐IUB rules, is proposed to uniquely identify every atom and bond in the amino acids. Proteins 2002;48:519–538. © 2002 Wiley‐Liss, Inc.
Aromatic side‐chain interactions in proteins. I. Main structural features
Authors: Thomas Annick , Meurisse Rita , Charloteaux Benoit , Brasseur Robert 
Published: October 2002

AbstractIn a data set of 593 nonhomologous proteins from the PDB, we have analyzed the pairing of phenylalanine, tyrosine, tryptophan, and histidine residues with their closest aromatic partner. The frequency distribution of the shortest interatomic distance of partners is bimodal with a sharp peak at ∼3.8 Å and a wider one at a longer distance. Only the 3.8 Å peak corresponds to direct ring–ring interactions thus aromatic pairs. The aromatic pairs were separated into two classes, near‐sequence pairs and far‐sequence pairs. Near sequence pairs stabilize local structure, and far‐sequence pairs stabilize tertiary structure. Far‐sequence pairs (74% of all pairs) mainly bridge two β‐strands, followed by pairs that bridge a β‐strand and a helix, and pairs that bridge a β‐strand and a random coil structure. Pairs that bridge helices are rare. The secondary structure of the near‐sequence pairs depends on the partner distance in the sequence. When the partners are 1, 3, or 4 residues apart in the sequence, pairs are mostly found in helical structures. When the partners are two apart, pairs are mostly found in the same β‐strand. Analysis of the frequency of near sequence pairs supports the hypothesis that aromatic pairing occurs after, rather than before, the formation of secondary structures. Proteins 2002;48:628–634. © 2002 Wiley‐Liss, Inc.
Information‐theoretic dissection of pairwise contact potentials
Authors: Cline Melissa S. , Karplus Kevin , Lathrop Richard H. , Smith Temple F. , Rogers Robert G. , Haussler David 
Published: October 2002

AbstractPairwise contact potentials have a long, successful history in protein structure prediction. They provide an easily‐estimated representation of many attributes of protein structures, such as the hydrophobic effect. In order to improve on existing potentials, one should develop a clear understanding of precisely what information they convey. Here, using mutual information, we quantified the information in amino acid potentials, and the importance of hydropathy, charge, disulfide bonding, and burial. Sampling error in mutual information was controlled for by estimating how much information cannot be attributed to sampling bias. We found the information in amino acid contacts to be modest: 0.04 bits per contact. Of that, only 0.01 bits of information could not be attributed to hydropathy, charge, disulfide bonding, or burial. Proteins 2002;49:7–14. © 2002 Wiley‐Liss, Inc.
CysxHisyZn2+ interactions: Thiol vs. thiolate coordination
Authors: Simonson Thomas , Calimet Nicolas 
Published: October 2002

AbstractIn zinc proteins, the Zn2+ cation frequently binds with a tetrahedral coordination to cysteine and histidine side chains, for example, in many DNA‐binding proteins, where it plays primarily a structural role. We examine the possibility of thiolate protonation in CysxHisyZn2+ groups, both in proteins and in solution, through a combination of theoretical calculations and database analysis. Seventy‐five percent of the thiolate‐coordinated zincs in the Cambridge Structural Database are tetrahedral, while di‐alkanethiol coordination always involves five or more ligands. Ab initio quantum calculations are performed on (ethanethiol/thiolate)3imidazole‐Zn2+ complexes in vacuum, yielding geometries and gas phase basicities. Protonating one (respectively two) thiolates increases the Zn‐S(thiol) distance by 0.4 Å (respectively 0.3 Å), providing a structural marker for protonation. The stabilities of the complexes in solution are compared by combining the gas phase basicities with continuum dielectric solvation calculations. In a continuum solvent with permittivity ε = 4, 20, or 80, one of three thiolates is predicted to be protonated at neutral pH. By extension, Cys4Zn2+ groups are expected to be protonated in the same conditions. In contrast, most Cys3His and Cys4 geometries in the Protein Data Bank (PDB) appear consistent with all‐thiolate Zn2+ coordination. This apparent discrepancy is resolved by two recent surveys of zinc protein structures, which suggest that these all‐thiolate sites are stabilized by charged and polar groups nearby in the protein, thus overcoming their intrinsic instability. However, the experimental resolution is not sufficient in all the PDB structures to rule out a thiol/thiolate mixture, and protonated thiolates may occur in some proteins not solved at high resolution or not represented in the PDB, as suggested by recent mass spectrometry experiments; this possibility should be allowed for in X‐ray structure refinement. Proteins 2002;49:37–48. © 2002 Wiley‐Liss, Inc.
Iron(III) photo‐induced degradation of isoproturon: correlation between degradation and toxicity
Authors: Galichet Frédéric , Mailhot Gilles , Bonnemoy Frédérique , Bohatier Jacques , Bolte Michèle 
Published: October 2002

AbstractThe degradation of isoproturon photoinduced by Fe(III) was investigated under both artificial and solar light. The monomeric species Fe(OH)2+ present under the experimental conditions ([Fe(III)] = 3 × 10−4 M) is the main Fe(III) species responsible for the degradation of isoproturon. The process involves the attack on the pollutant by ·OH radicals generated by irradiation of Fe(OH)2+. The major primary photoproducts were identified; they accumulate in the solution medium before being degraded. The toxicity of the solution to marine bacterium Vibrio fisheri (Beijerinck) Lehmann & Neumann was monitored during the degradation process. It increased in the early stages of the reaction and, among the photoproducts, the N‐formyl derivative appeared to be the major product responsible for the increase in toxicity.© 2002 Society of Chemical Industry
Preventative effects of the flowers of Inula britannica on autoimmune diabetes in C57BL/KsJ mice induced by multiple low doses of streptozotocin
Authors: Kobayashi Takao , Song Qing‐Hua , Hong Tie , Kitamura Hajime , Cyong Jong‐Chol 
Published: October 2002

AbstractWe have reported that an aqueous extract from the flowers of Inula britannica L. subsp. japonica Kitam. (IB) prevented immunologically induced experimental hepatitis in mice and suggested that the antihepatitic effect of IB is due to inhibition of IFN‐γ production. We then investigated the effects of IB on diabetes in mice induced by multiple low doses of streptozotocin (MLDSTZ), which is a mouse model for IFN‐γ‐dependent autoimmune diabetes. C57BL/KsJ mice (male, 7 weeks) were provided with IB extract (500 mg/ kg/ day) in drinking water ad libitum, starting 7 days before the first STZ injection. Autoimmune diabetes was induced by MLDSTZ (40 mg/kg/day for 5 daily doses, i.p.). The IB treatment significantly suppressed the increase of blood glucose levels. Histological analysis of the pancreas showed that the degree of insulitis and destruction of β‐cells were reduced by IB treatment. The IFN‐γ production from stimulated splenic T lymphocytes was inhibited by the IB treatment. Moreover, the proportion of IFN‐γ‐producing cells in the CD4+ population, which was increased by MLDSTZ, was significantly decreased by the IB treatment. These results suggest that IB has a preventative effect on autoimmune diabetes by regulating cytokine production. Copyright © 2002 John Wiley & Sons, Ltd.
Evaluation of antilipid peroxidative action of propolis ethanol extract
Authors: Shinohara Rikio , Ohta Yoshiji , Hayashi Takahiro , Ikeno Takeyuki 
Published: October 2002

AbstractThe antilipid peroxidative action of the ethanol extract of Brazilian propolis at a concentration of 47% (w/v) was evaluated by examining the inhibitory effect of the extract on the formation of hydroperoxide‐ and endoperoxide‐type lipid peroxides during heating of authentic polyunsaturated fatty acids and on Fe3+‐ADP/ascorbic acid‐ and Fe3+‐ADP/NADPH‐dependent lipid peroxidation reactions in rat liver microsomes. Hydroperoxide‐type lipid peroxides were measured by the haemoglobin–methylene blue method and endoperoxide‐type lipid peroxides by the thiobarbituric aicd (TBA), Fe3+‐TBA and LPO‐586 methods. Propolis ethanol extract inhibited dose‐dependently the formation of hydroperoxide‐ and endoperoxide‐type lipid peroxides during heating of linoleic acid, linolenic acid or arachidonic acid and the amount of the extract causing a half inhibition of these lipid peroxide formations ranged between 20 and 75 μg. Propolis ethanol extract inhibited dose‐dependently both Fe3+‐ADP/ascorbic acid‐ and Fe3+‐ADP/NADPH‐dependent lipid peroxidation reactions in rat liver microsomes when lipid peroxides produced in both reactions were measured by the TBA method. The amount of propolis extract causing a half inhibition of the Fe3+‐ADP/ascorbic acid‐dependent lipid peroxidation was about 5 μg, while that of the extract causing a half inhibition of the Fe3+‐ADP/NADPH‐dependent lipid peroxidation was about 0.15 μg. These results indicate that the propolis ethanol extract exerts an antilipid peroxidative action at very low doses. Copyright © 2002 John Wiley & Sons, Ltd.
Peroxynitrite scavenging activity of herb extracts
Authors: Choi Hye Rhi , Choi Jae Sue , Han Yong Nam , Bae Song Ja , Chung Hae Young 
Published: October 2002

AbstractPeroxynitrite (ONOO−) is a cytotoxicant with strong oxidizing properties toward various cellular constituents, including sulphydryls, lipids, amino acids and nucleotides and can cause cell death, lipid peroxidation, carcinogenesis and aging. The aim of this study was to characterize ONOO− scavenging constituents from herbs. Twenty‐eight herbs were screened for their ONOO− scavenging activities with the use of a fluorometric method. The potency of scavenging activity following the addition of authentic ONOO− was in the following order: witch hazel bark > rosemary > jasmine tea > sage > slippery elm > black walnut leaf > Queen Anne's lace > Linden flower. The extracts exhibited dose‐dependent ONOO− scavenging activities. We found that witch hazel (Hamamelis virginiana L.) bark showed the strongest effect for scavenging ONOO− of the 28 herbs. Hamamelitannin, the major active component of witch hazel bark, was shown to have a strong ability to scavenge ONOO−. It is suggested that hamamelitannin might be developed as an effective peroxynitrite scavenger for the prevention of ONOO− involved diseases. Copyright © 2002 John Wiley & Sons, Ltd.
Detection of microbial contamination of packaging for foodstuffs by gas chromatography–mass spectrometry method
Authors: Mielniczuk Zbigniew , Pogorzelska Zofia 
Published: October 2002

AbstractDetection of microbial contamination of packaging for foodstuffs and of the environment, using a gas chromatography–mass spectrometry (GC–MS) method, is described. Quantitative determination of muramic acid, a chemical marker of bacterial peptidoglycan, has been used for this purpose. Samples of dust collected from packaging material (plastic film in the store‐room), intended to come into contact with foodstuffs, and dust from a laboratory environment were hydrolysed in aqueous hydrochloric acid and next extracted with hexane to remove hydrophobic compounds. The aqueous phase was evaporated, heated in silylation reagent to trimethylsilyl derivatives and analysed by GC–MS. Internal standard (3‐hydroxytridecanoic methyl ester) was added before silylation procedure for quantification purposes. The method described is quick and simple, can be applied to study chemical markers directly without prior culturing, in complex
environmental samples (not only of packaging), and should therefore become widely used for measuring bacterial peptidoglycan. The method can be used for the detection of microbial infection in humans, hospitals, infusing fluids,
contamination of biochemical and fermentation processes, and for
monitoring of air, water, air‐conditioning systems, etc. Copyright © 2002 John Wiley & Sons, Ltd.
Detection of norbolethone, an anabolic steroid never marketed, in athletes' urine
Authors: Catlin Don H. , Ahrens Brian D. , Kucherova Yulia 
Published: October 2002

AbstractNorbolethone (13‐ethyl‐17‐hydroxy‐18,19‐dinor‐17α‐pregn‐4‐en‐3‐one) is a 19‐nor anabolic steroid first synthesized in 1966. During the 1960s it was administered to humans in efficacy studies concerned with short stature and underweight conditions. It has never been reported by doping control laboratories. Norbolethone was identified in two urine samples from one athlete by matching the mass spectra and chromatographic retention times with those of a reference standard. The samples also contained at least one likely metabolite. The samples were also unusual because the concentrations of endogenous steroids were exceptionally low. Since norbolethone is not known to be marketed by any pharmaceutical company, a clandestine source of norbolethone may exist. Copyright © 2002 John Wiley & Sons, Ltd.
9‐Aminoacridine as a matrix for negative mode matrix‐assisted laser desorption/ionization
Authors: Vermillion‐Salsbury Rachal L. , Hercules David M. 
Published: October 2002

Abstract9‐Aminoacridine (9AA) is introduced as a matrix for negative mode matrix‐assisted laser desorption/ionization (MALDI). While most traditional MALDI matrices have been acidic in character, 9AA is a moderately strong base. The mechanism by which 9AA brings about ionization in the negative mode appears to involve abstraction of a labile proton in an acid/base reaction. Most MALDI matrices readily donate protons; 9AA readily accepts them leading to the formation of [M − H]− species. 9AA was first examined as a matrix for low molecular weight compounds having acidic protons, such as phenols, carboxylic acids, sulfonates, amines and alcohols. Also studied were larger molecules frequently analyzed by MALDI including oligonucleotides, oligoamides and proteins. Spectra obtained from 9AA were compared with those recorded using more traditional matrices such as 2,5‐dihydroxybenzoic acid (DHB) and α‐cyano‐4‐hydroxycinnamic acid (α‐CHCA). Copyright © 2002 John Wiley & Sons, Ltd.