bluuebunny/crossref_metadata_2025_split huggingface dataset:
Homozygosity for a CHEK2*1100delC mutation identified in familial colorectal cancer does not lead to a severe clinical phenotype
Authors: van Puijenbroek Marjo , van Asperen Christi J , van Mil Anneke , Devilee Peter , van Wezel Tom , Morreau Hans 
Published: April 2005

AbstractIt has recently been suggested that the frequency of the germline CHEK2*1100delC mutation is higher among breast cancer families with colorectal cancer, although the mutation does not seem to be significantly associated with familial colorectal cancer. Five hundred and sixty‐four familial colorectal tumours were studied for expression of CHEK2 using tissue microarrays and an antibody against the NH2‐terminal SQ regulatory domain of the CHEK2 protein. Normal colonic tissue from patients whose tumours showed loss of CHEK2 expression was investigated further using fragment and sequence analysis for the presence of a CHEK2*1100delC mutation and five other (R117G, R137Q, R145W, I157T, and R180H) known germline variants in CHEK2. Twenty‐nine tumours demonstrated loss of expression for CHEK2. Analysis of matched normal colonic tissue from these patients revealed germline CHEK2*1100delC mutation in three cases. In two of these, the mutation was heterozygous but, interestingly, the third patient proved to be homozygous for the deletion, using six different primer pair combinations. None of the other tested germline variants were identified. No CHEK2*1100delC mutations were found in patients whose tumours stained positive. Homozygosity for the CHEK2*1100delC mutation appears not to be lethal in humans. No severe clinical phenotype was apparent, although the patient died from colonic carcinoma at age 52 years. This observation is in line with recent knockout mouse models, although in the latter, cellular defects in apoptosis and increased resistance to irradiation seem to exist. It is also concluded that CHEK2 protein abrogation is not caused by the CHEK2 germline variants R117G, R137Q, R145W, I157T, and R180H in familial colorectal cancer. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Ultrafast single‐electron‐transfer/degenerative‐chain‐transfer mediated living radical polymerization of acrylates initiated with iodoform in water at room temperature and catalyzed by sodium dithionite
Authors: Percec Virgil , Ramirez‐Castillo Ernesto , Popov Anatoliy V. , Hinojosa‐Falcon Luis A. , Guliashvili Tamaz 
Published: April 2005

AbstractSodium dithionite in the presence of NaHCO3 in water acts as a single‐electron‐transfer agent and facilitates the single‐electron‐transfer/degenerative‐chain‐transfer mediated living radical polymerization (SET–DTLRP) of acrylates initiated with iodoform at room temperature. The resulting α,ω‐di(iodo)polyacrylates can be used as macroinitiators for the SET–DTLRP of other acrylates. Ultrahigh‐molar‐mass poly(tert‐butyl acrylate) can be synthesized via the SET–DTLRP of tert‐butyl acrylate and has a very low weight‐average molecular weight/number‐average molecular weight ratio of 1.15. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 2178–2184, 2005
Synthesis and characterization of alt‐copoly(carbosiloxane)s containing oligodiphenylsiloxane segments
Authors: Gädda Thomas M. , Weber William P. 
Published: April 2005

AbstractNovel α,ω‐divinyloligodiphenylsiloxanes (1,9‐divinyldecaphenylpentasiloxane, 1,7‐divinyloctaphenyltetrasiloxane, 1,5‐divinylhexaphenyltrisiloxane, and 1,3‐divinyltetraphenyldisiloxane) were prepared and copolymerized by Pt‐catalyzed hydrosilylation with α,ω‐dihydridopentasiloxanes. The molecular weights of the copolymers were measured with gel permeation chromatography, and their thermal properties were characterized with differential scanning calorimetry and thermogravimetric analysis. The polymers had high thermal stability in air and nitrogen. The oligomer and polymer structures were determined with 1H, 13C, 19F, and 29Si NMR and IR spectrometry. The molecular weights of the oligomers were measured with high‐resolution mass spectrometry. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 2155–2163, 2005
Ethylene polymerization over supported catalysts [2,6‐bis(imino)pyridyl iron dichloride/magnesium dichloride] with AlR3 as an activator
Authors: Mikenas Tatiana B. , Zakharov Vladimir A. , Echevskaya Lyudmila G. , Matsko Michail A. 
Published: April 2005

AbstractData on ethylene polymerization over supported LFeCl2/MgCl2 catalysts {L = 2,6‐bis[1‐(2,6‐dimethylphenylimino)ethyl]pyridyl} containing AlR3 (R = Me, Et, i‐Bu, or n‐Oct) as an activator are presented. These catalysts are highly active (100–300 kg of polyethylene/g of Fe h bar of C2H4) and stable in ethylene polymerization at 70–80 °C. Data on the effects of the iron content, AlR3 type, Al(i‐Bu)3 concentration, and hydrogen presence on the catalyst activity are presented. The molecular structure of polyethylene produced with these catalysts (including the molecular masses, molecular mass distribution, branching, and number of CC bonds) has been studied; data on the effects of AlR3 and hydrogen on the molecular structure are presented. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 2128–2133, 2005
Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles
Authors: Snyder David A. , Montelione Gaetano T. 
Published: April 2005

AbstractAn important open question in the field of NMR‐based biomolecular structure determination is how best to characterize the precision of the resulting ensemble of structures. Typically, the RMSD, as minimized in superimposing the ensemble of structures, is the preferred measure of precision. However, the presence of poorly determined atomic coordinates and multiple “RMSD‐stable domains”—locally well‐defined regions that are not aligned in global superimpositions—complicate RMSD calculations. In this paper, we present a method, based on a novel, structurally defined order parameter, for identifying a set of core atoms to use in determining superimpositions for RMSD calculations. In addition we present a method for deciding whether to partition that core atom set into “RMSD‐stable domains” and, if so, how to determine partitioning of the core atom set. We demonstrate our algorithm and its application in calculating statistically sound RMSD values by applying it to a set of NMR‐derived structural ensembles, superimposing each RMSD‐stable domain (or the entire core atom set, where appropriate) found in each protein structure under consideration. A parameter calculated by our algorithm using a novel, kurtosis‐based criterion, the ϵ‐value, is a measure of precision of the superimposition that complements the RMSD. In addition, we compare our algorithm with previously described algorithms for determining core atom sets. The methods presented in this paper for biomolecular structure superimposition are quite general, and have application in many areas of structural bioinformatics and structural biology. Proteins 2005. © 2005 Wiley‐Liss, Inc.
How does nitrous oxide reductase interact with its electron donors?—A docking study
Authors: Mattila Kimmo , Haltia Tuomas 
Published: April 2005

AbstractElectron transfer reactions are crucial for respiration and denitrification. In this article, we analyze the interaction of nitrous oxide reductase with its electron donors cytochrome c550 and pseudoazurin. Our docking protocol comprises generation of candidate complexes followed by a selection step based on the distance of the donor and acceptor groups in each partner protein. Finally, the structures of the candidate complexes were optimized using a force field calculation, together with a second distance filtering step. The prediction power of this protocol was studied using the crystal structure of the cytochrome c2/photosynthetic reaction center of Rhodobacter sphaeroides as a reference. The results suggest that both cytochrome c550 and pseudoazurin bind at the same hydrophobic surface patch residing near the CuA center of nitrous oxide reductase. The central, well‐conserved interaction surface of the donors is hydrophobic, but it is surrounded by numerous lysine side‐chains, which interact electrostatically with analogously positioned side‐chain carboxylates of the acceptor. The prediction output is an ensemble of energetically similar structures that are rotationally related to each other. While such an ensemble may reflect incomplete prediction power of the docking protocol, it may also manifest a biological situation where there are multiple ways of forming a productive electron transfer complex. Analyses of the predicted structures and the conservation pattern of the amino acid residues suggest the existence of specific electron transfer pathways to and from the CuA center of nitrous oxide reductase. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Quantifying allosteric effects in proteins
Authors: Ming Dengming , Wall Michael E. 
Published: April 2005

AbstractIn allosteric regulation, protein activity is altered when ligand binding causes changes in the protein conformational distribution. Little is known about which aspects of protein design lead to effective allosteric regulation, however. To increase understanding of the relation between protein structure and allosteric effects, we have developed theoretical tools to quantify the influence of protein–ligand interactions on probability distributions of reaction rates and protein conformations. We define the rate divergence, $\bar{D}$k, and the allosteric potential, $\bar{D}$x, as the Kullback–Leibler divergence between either the reaction‐rate distributions or protein conformational distributions with and without the ligand bound. We then define Dx as the change in the conformational distribution of the combined protein/ligand system, derive Dx in the harmonic approximation, and identify contributions from 3 separate terms: the first term, D, results from changes in the eigenvalue spectrum; the second term, D, results from changes in the mean conformation; and the third term, D, corresponds to changes in the eigenvectors. Using normal modes analysis, we have calculated these terms for a natural interaction between lysozyme and the ligand tri‐N‐acetyl‐D‐glucosamine, and compared them with calculations for a large number of simulated random interactions. The comparison shows that interactions in the known binding‐site are associated with large values of D. The results motivate using allosteric potential calculations to predict functional binding sites on proteins, and suggest the possibility that, in Nature, effective ligand interactions occur at intrinsic control points at which binding induces a relatively large change in the protein conformational distribution. Proteins 2005. Published 2005 Wiley‐Liss, Inc.
Computational analysis of molecular basis of 1:1 interactions of NRG‐1β wild‐type and variants with ErbB3 and ErbB4
Authors: Luo Cheng , Xu Lingfei , Zheng Suxin , Luo Xiaomin , Shen Jianhua , Jiang Hualiang , Liu Xifu , Zhou Mingdong 
Published: April 2005

AbstractThe neuregulin/ErbB system is a growth factor/receptor cascade that has been proven to be essential in the development of the heart and the sympathetic nervous system. However, the basis of the specificity of ligand–receptor recognition remains to be elucidated. In this study, the structures of NRG‐1β/ErbB3 and NRG‐1β/ErbB4 complexes were modeled based on the available structures of the homologous proteins. The binding free energies of NRG‐1β to ErbB3 and ErbB4 were calculated using the molecular mechanics Poisson–Boltzmann surface area (MM‐PBSA) computational method. In addition, computational alanine‐scanning mutagenesis was performed in the binding site of NRG‐1β and the difference in the binding free energies between NRG‐1β mutants and the receptors was calculated. The results specify the contribution of each residue at the interaction interfaces to the binding affinity of NRG‐1β with ErbB3 and ErbB4, identifying several important interaction residue pairs that are in agreement with previously acquired experimental data. This indicates that the presented structural models of NRG‐1β/ErbB3 and NRG‐1β/ErbB4 complexes are reliable and could be used to guide future studies, such as performing desirable mutations on NRG‐1β to increase the binding affinity and selectivity to the receptor and discovering new therapeutic agents for the treatment of heart failure. Proteins 2005. © 2005 Wiley‐Liss, Inc.
O‐raffinose crosslinked hemoglobin lacks site‐specific chemistry in the central cavity: Structural and functional consequences of β93Cys modification
Authors: Boykins Robert A. , Buehler Paul W. , Jia Yiping , Venable Richard , Alayash Abdu I. 
Published: April 2005

AbstractReacting human deoxyHbA0with oxidized raffinose (O‐raffinose), a trisaccharide, results in a low oxygen affinity “blood substitute,” stabilized in a noncooperative T‐conformation and possesses readily oxidizable rhombic heme. In this study, we fractionated theO‐raffinose–modified HbA0heterogeneous polymer (O‐R‐PolyHbA0) into six distinct fractions with a molecular weight distribution ranging from 64 to ∼600 kDa using size‐exclusion chromatography (SEC). Oxygen equilibrium and kinetics binding parameters of all fractions were nearly identical, reflecting a lack of heterogeneity in ligand binding properties amongO‐R‐PolyHbA0species (Hill coefficientnequal to 1.0). Several mass spectrometry techniques were used to evaluate undigested and digested HbA0,O‐R‐PolyHbA0, andO‐R‐PolyHbA0fractions. Proposed sites of intramolecular crosslinking (i.e., β1Lys82, β2Lys82, and β1Val1) were not found to be the predominant site of crosslinking within the central cavity. Intermolecular crosslinking withO‐raffinose results in no discernible site of amino acids modifications with the exception of β93Cys and α104Cys. Based on accessible surface area (ASA) calculations in intact deoxyHbA0, slight conformational changes are required to allow for the S on α104Cys to be modified during the reaction withO‐raffinose or its partially oxidized product(s). The stabilization of HbA0in the T‐conformation may not be a direct correlate ofO‐raffinose induced changes, but an indirect consequence of changing hydration in the water‐filled central cavity and/or the distal heme pocket leading in the latter case to accelerated iron oxidation. Structural data presented here when taken together with the oxidative instability ofO‐R‐PolyHbA0may provide some basis for the reported toxicity of this oxygen carrier. Proteins 2005. Published 2005 Wiley‐Liss, Inc.
Amphipathic α‐helices in proteins: Results from analysis of protein structures
Authors: Sharadadevi Ambure , Sivakamasundari Chandrasekaran , Nagaraj Ramakrishnan 
Published: April 2005

AbstractAmphipathic α‐helices play a crucial role in mediating the interaction of peptides and proteins with membranes. We have analyzed protein structures for the occurrence of 18‐residue amphipathic helices. We find several of these α‐helices having average hydrophobic moments and average hydrophobicities that would favor their interaction with membranes. We have analyzed the distribution of net charge, helix length, normalized frequency of occurrence, and propensities of the 20 amino acids in the delineated 18‐residue helices. We have observed distinct differences in the frequencies of occurrence of polar and hydrophobic amino acids at positions 1–18 in amphipathic and nonamphipathic helices. There are also differences in propensities of the 20 amino acids to occur at positions 1–18 of amphipathic and nonamphipathic helices. Synthetic peptides corresponding to some of these surface‐seeking helices do possess antibacterial and/or hemolytic activities. Knowledge of the distribution of charges in 18‐residue surface‐seeking amphipathic α‐helices, as well as propensity of occurrence of amino acids at various positions, would be useful inputs in the de novo design of amphipathic peptides. Proteins 2005. © 2005 Wiley‐Liss, Inc.
High accuracy prediction of β‐turns and their types using propensities and multiple alignments
Authors: Fuchs Patrick F.J. , Alix Alain J.P. 
Published: April 2005

AbstractWe have developed a method that predicts both the presence and the type of β‐turns, using a straightforward approach based on propensities and multiple alignments. The propensities were calculated classically, but the way to use them for prediction was completely new: starting from a tetrapeptide sequence on which one wants to evaluate the presence of a β‐turn, the propensity for a given residue is modified by taking into account all the residues present in the multiple alignment at this position. The evaluation of a score is then done by weighting these propensities by the use of Position‐specific score matrices generated by PSI‐BLAST. The introduction of secondary structure information predicted by PSIPRED or SSPRO2 as well as taking into account the flanking residues around the tetrapeptide improved the accuracy greatly. This latter evaluated on a database of 426 reference proteins (previously used on other studies) by a sevenfold crossvalidation gave very good results with a Matthews Correlation Coefficient (MCC) of 0.42 and an overall prediction accuracy of 74.8%; this places our method among the best ones. A jackknife test was also done, which gave results within the same range. This shows that it is possible to reach neural networks accuracy with considerably less computional cost and complexity. Furthermore, propensities remain excellent descriptors of amino acid tendencies to belong to β‐turns, which can be useful for peptide or protein engineering and design. For β‐turn type prediction, we reached the best accuracy ever published in terms of MCC (except for the irregular type IV) in the range of 0.25–0.30 for types I, II, and I′ and 0.13–0.15 for types VIII, II′, and IV. To our knowledge, our method is the only one available on the Web that predicts types I′ and II′. The accuracy evaluated on two larger databases of 547 and 823 proteins was not improved significantly. All of this was implemented into a Web server called COUDES (French acronym for: Chercher Où Une Déviation Existe Sûrement), which is available at the following URL: http://bioserv.rpbs.jussieu.fr/Coudes/index.html within the new bioinformatics platform RPBS. Proteins 2005;59. © 2005 Wiley‐Liss, Inc.
An explosion caused by mixing incompatible liquids
Authors: Lacoursiere PE J. P. 
Published: April 2005

AbstractTwo workers of a waste handling contractor lost their lives as a result of the explosion of a vacuum truck where they had inadvertently mixed sulfuric acid and hydrogen peroxide. The consequences of the explosion were simulated and documented. Root causes and contributing factors were identified and, in particular, failure of the management systems are underlined: (1) inadequate procedures, (2) poor training, and (3) poor management controls. Improved procedures, training, and management controls will prevent accidents of this type. © 2005 American Institute of Chemical Engineers Process Saf Prog, 2005
Investigation of a naphtha storage tank fire
Authors: Rodante Thomas V. 
Published: April 2005

AbstractIn October 1988, one of the world's largest combined loss storage tank fires occurred at a refinery located on the island of Pulau Merlimau, Singapore. At the height of the incident, the blaze involved three floating roof naphtha storage tanks, each approximately 134 feet in diameter and containing a total of 294,500 barrels of product. The resultant property loss was estimated at over USD 6.6 million in 1988 dollars.At several stages, the fire threatened to involve tankage in adjacent dikes containing kerosene, reformate, motor gasoline, and diesel product. Because the refinery was located on an island, equipment and manpower were ferried to the site. Despite the size of the fire and adverse logistics, fire‐fighting efforts were successful in containing the incident to the primary dike tankage.This paper investigates the incidents leading up to the fire, operational and design engineering considerations, and analyzes the basic fire‐fighting strategy, prefire and emergency response plans, fire water management, and fixed/semifixed foam systems. © 2005 American Institute of Chemical Engineers Process Saf Prog, 2005
Lessons learned from fires and explosions involving air pollution control systems
Authors: Ogle Russell A. , Carpenter Andrew R. , Morrison Delmar “Trey” 
Published: April 2005

AbstractSix case studies of fires or explosions involving air pollution control (APC) systems are reviewed in this paper. These case studies have been generalized from actual accident investigations performed by the authors.The case studies cover the APC technologies of thermal oxidation, catalytic oxidation, gas scrubbers, adsorption, and condensation. Each of the technologies was used to control emissions of volatile organic compounds (VOCs). The accidents encompass a broad range of industries, ignition sources, and circumstances. The causal factors for these accidents are compared with applicable safety guidelines and standards to show how safeguards could have prevented or mitigated these accidents.The common theme that emerges from these accident investigations is that APC systems should not be specified and installed strictly by intuition or experience, but rather through careful engineering design. The key findings of this study are:
Characterize the waste stream to be treated.
Conduct a process hazard analysis for each APC system, with particular emphasis on fire and explosion hazards.
Design the APC system using good engineering practices.
Operate the APC system within its design specifications.
Periodically verify that the APC system performance satisfies its technical and regulatory objectives.
Perform maintenance activities in accordance with manufacturer's recommendations.
Each of the accidents was the direct result of the omission of one or more of these basic tenets. © 2005 American Institute of Chemical Engineers Process Saf Prog, 2005
Large quasi‐linear electro‐optical response of BaZr0.75Hf0.25O3 thin films by pulsed laser deposition
Authors: Tian H. Y. , Wang D. Y. , Zhou X. Y. , Wang Y. , Chan H. L. W. , Choy C. L. 
Published: April 2005

AbstractEpitaxial BaZr0.75Hf0.25O3 (BZH) thin films were grown successfully on MgO (100) substrates by pulsed laser deposition. The FWHM of the rocking curve of the BZH thin film deposited at 650 °C is about 0.6°, and the pole‐figure shows that the BZH thin film has fourfold symmetry with 0.5–1.1° FWHM in the ϕ‐scanning. A large quasi‐linear electro‐optic effect was observed under an external electric field in a transverse geometry at 633 nm. The electric‐optic coefficient Rc and birefringence shift are found to be 9.145 × 10–11 m/V and 4 × 10–3 at 10 kV/mm, respectively. The microstructure of the films and its relation to the observed electric‐optic properties is discussed. It is expected that BZH thin films will have various electric‐optic and microwave applications. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)