bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exhaled nitric oxide and asthma in young children
Authors: Avital Avraham , Uwyyed Kamal , Berkman Neville , Godfrey Simon , Bar‐Yishay Ephraim , Springer Chaim 
Published: August 2002

AbstractExhaled nitric oxide (eNO) has been used to diagnose asthma in adults and children using either the slow vital capacity method (SVCm) or, in younger children, the tidal breathing method (TBm). Adenosine 5′‐monophosphate (AMP) challenge also has been found to be a sensitive and specific test for the diagnosis of asthma. In the present study, we used the AMP provocation concentration that caused wheezing (PCW) to confirm the diagnosis of asthma (PCW ≤ 200 mg/mL). We studied 36 children (2–7 years) with mild intermittent asthma, 13 children (3–7 years) with moderate persistent asthma treated with inhaled steroids, 20 nonasthmatic children (2–7 years) with chronic cough and recurrent pneumonia, and 15 healthy children (4–6 years). Expired gas was collected in collection bags by the TBm, and eNO was measured. We evaluated the efficacy of eNO values in diagnosing asthma.The mean eNO level of the mild intermittent asthmatic children (5.6 ± 0.4 ppb) not receiving inhaled corticosteroids was significantly higher (ANOVA P < 0.0001) than that of the moderate persistent asthmatics who were treated with inhaled steroids, the nonasthmatic children with chronic cough, and the group of healthy children (3.7 ± 0.6 ppb, P < 0.05; 3.2 ± 0.3 ppb, P < 0.001; 2.2 ± 0.2 ppb, P < 0.001, respectively). The points of intersection for sensitivity and specificity curves of eNO to differentiate mild intermittent asthmatics from nonasthmatic children with chronic cough and from healthy children were 77% and 88% for eNO values of 3.8 ppb and 2.9 ppb, respectively.We conclude that eNO collected by the TBm can differentiate steroid‐naive young children with intermittent asthma from healthy children, from nonasthmatic children with chronic cough, and from asthmatic children treated with inhaled steroids. Pediatr Pulmonol. 2001; 32:308–313. © 2001 Wiley‐Liss, Inc.
Immunohistochemical studies on the distribution of nerve fibers in the human prostate with special reference to the anterior fibromuscular stroma
Authors: Iwata Tsuyoshi , Ukimura Osamu , Inaba Mitsuhiko , Kojima Munekado , Kumamoto Kenzo , Ozawa Hitoshi , Kawata Mitsuhiro , Miki Tsuneharu 
Published: August 2002

AbstractBACKGROUNDAlthough the anterior fibromuscular stroma (AFMS) comprises up to one third of the total bulk of the prostate, its physiological function remains unknown. We recently reported the possible contribution of the AFMS to micturition. The aim of this study is to reveal the differences in the distribution of innervation between the AFMS and the other regions of the prostate.METHODSWe performed immunohistochemical stainings using antibodies such as protein gene product (PGP) 9.5, tyrosine hydroxylase(TH), neuropeptide Y (NPY), and vasoactive intestinal peptide (VIP). Morphometric analysis was made to examine the density of peripheral nerve fibers containing PGP 9.5, TH, NPY, and VIP by using a computer‐assisted imaging system.RESULTSThe number of PGP 9.5‐immunoreactive (IR) nerve fibers and the smooth muscle in the AFMS decreased from the base to the apex of the prostate. TH‐IR nerve fibers were more abundant in the AFMS than in the transition zone. NPY‐ and VIP‐IR nerve fibers were less numerous in the AFMS than in the peripheral zone.CONCLUSIONSThis study is the first to demonstrate that the AFMS has peculiar neuronal innervation. We observed significantly different innervation in the AFMS compared with the other regions of the prostate. Prostate 48:242–247, 2001. © 2001 Wiley‐Liss, Inc.
Weak temperature dependence of the free energy surface and folding pathways of structured peptides
Authors: Cavalli Andrea , Ferrara Philippe , Caflisch Amedeo 
Published: August 2002

AbstractThe thermodynamics and energetics of a 20‐residue synthetic peptide with a stable three‐stranded antiparallel β‐sheet fold are investigated by implicit solvent molecular dynamics (MD) at 330 K (slightly above the melting temperature in the model) and compared with previous simulation results at 360 K. At both temperature values, the peptide folds reversibly to the NMR solution conformation, irrespective of the starting conformation. The sampling of the conformational space (2.3 μs and 25 folding events at 330 K, and 3 μs and 50 folding events at 360 K) is sufficient to obtain a thermodynamic description of minima and transition states on the free energy surface, which is determined near equilibrium by counting populations. The free energy surface, plotted as a function of two‐order parameters that monitor formation of either of the β‐hairpins, is similar at both temperature values. The statistically predominant folding pathway and its frequency (about two‐thirds of the folding events) are the same at 330 K and 360 K. Furthermore, the main unfolding route is the reverse of the predominant folding pathway. The effective energy and its electrostatic and van der Waals contributions show a downhill profile at both temperatures, implying that the free energy barrier is of entropic origin and corresponds to the freezing of about two‐thirds of the chain into a β‐hairpin conformation. The average folding rate is nearly the same at 330 K and 360 K, while the unfolding rate is about four times slower at 330 K than at 360 K. Taken together with previous MD analysis of α‐helices and β‐hairpins, the present simulation results indicate that the free energy surface and folding mechanism of structured peptides have a weak temperature dependence. Proteins 2002;47:305–314. © 2002 Wiley‐Liss, Inc.
A study on protein sequence alignment quality
Authors: Elofsson Arne 
Published: August 2002

AbstractOne of the most central methods in bioinformatics is the alignment of two protein or DNA sequences. However, so far large‐scale benchmarks examining the quality of these alignments are scarce. On the other hand, recently several large‐scale studies of the capacity of different methods to identify related sequences has led to new insights about the performance of fold recognition methods. To increase our understanding about fold recognition methods, we present a large‐scale benchmark of alignment quality. We compare alignments from several different alignment methods, including sequence alignments, hidden Markov models, PSI‐BLAST, CLUSTALW, and threading methods. For most methods, the alignment quality increases significantly at about 20% sequence identity. The difference in alignment quality between different methods is quite small, and the main difference can be seen at the exact positioning of the sharp rise in alignment quality, that is, around 15–20% sequence identity. The alignments are improved by using structural information. In general, the best alignments are obtained by methods that use predicted secondary structure information and sequence profiles obtained from PSI‐BLAST. One interesting observation is that for different pairs many different methods create the best alignments. This finding implies that if a method that could select the best alignment method for each pair existed, a significant improvement of the alignment quality could be gained. Proteins 2002;46:330–339. © 2002 Wiley‐Liss, Inc.
Optimizing the hydrogen‐bond network in Poisson–Boltzmann equation‐based pKa calculations
Authors: Nielsen Jens E. , Vriend Gerrit 
Published: August 2002

AbstractpKa calculation methods that are based on finite difference solutions to the Poisson–Boltzmann equation (FDPB) require that energy calculations be performed for a large number of different protonation states of the protein. Normally, the differences between these protonation states are modeled by changing the charges on a few atoms, sometimes the differences are modeled by adding or removing hydrogens, and in a few cases the positions of these hydrogens are optimized locally. We present an FDPB‐based pKa calculation method in which the hydrogen‐bond network is globally optimized for every single protonation state used. This global optimization gives a significant improvement in the accuracy of calculated pKa values, especially for buried residues. It is also shown that large errors in calculated pKa values are often due to structural artifacts induced by crystal packing. Optimization of the force fields and parameters used in pKa calculations should therefore be performed with X‐ray structures that are corrected for crystal artifacts. Proteins 2001;43:403–412. © 2001 Wiley‐Liss, Inc.
PRED‐CLASS: Cascading neural networks for generalized protein classification and genome‐wide applications
Authors: Pasquier Claude , Promponas Vassilis J. , Hamodrakas Stavros J. 
Published: August 2002

AbstractA cascading system of hierarchical, artificial neural networks (named PRED‐CLASS) is presented for the generalized classification of proteins into four distinct classes—transmembrane, fibrous, globular, and mixed—from information solely encoded in their amino acid sequences. The architecture of the individual component networks is kept very simple, reducing the number of free parameters (network synaptic weights) for faster training, improved generalization, and the avoidance of data overfitting. Capturing information from as few as 50 protein sequences spread among the four target classes (6 transmembrane, 10 fibrous, 13 globular, and 17 mixed), PRED‐CLASS was able to obtain 371 correct predictions out of a set of 387 proteins (success rate ∼ 96%) unambiguously assigned into one of the target classes. The application of PRED‐CLASS to several test sets and complete proteomes of several organisms demonstrates that such a method could serve as a valuable tool in the annotation of genomic open reading frames with no functional assignment or as a preliminary step in fold recognition and ab initio structure prediction methods. Detailed results obtained for various data sets and completed genomes, along with a web sever running the PRED‐CLASS algorithm, can be accessed over the World Wide Web at http://o2.biol.uoa.gr/PRED‐CLASS. Proteins 2001;44:361–369. © 2001 Wiley‐Liss, Inc.
Aromatic di‐alanine repeats (AdAR) are structural motifs characteristic of the soluble N‐ethylmaleimide‐sensitive factor attachment protein (SNAP) family
Authors: Bruckert Franz , Casavant Thomas , Satre Michel 
Published: August 2002

AbstractThe aromatic di‐alanine repeat is a novel 12‐amino acid‐long motif constituting alternate small and large hydrophobic residues that mediate the close packing of α‐helices. A hidden Markov model profile was constructed from the motifs initially described in Soluble N‐ethyl maleimide‐sensitive factor attachment proteins (SNAP), a family of soluble proteins involved in intracellular membrane fusion. Scanning different sets of protein sequences showed unambiguously that this profile defines a structural motif independent of the tetratrico peptide repeat, another widespread α‐helical motif. In addition to SNAP, aromatic di‐alanine repeats are found in selective LIM homeodomain binding proteins (SLB) and in proteins from the Pyrococcus and Archaeoglobus prokaryotes. Proteins 2001;45:40–46. © 2001 Wiley‐Liss, Inc.
Structure‐based inhibitor screening: A family of sulfonated dye inhibitors for malaria parasite triosephosphate isomerase
Authors: Joubert F. , Neitz A.W.H. , Louw A.I. 
Published: August 2002

AbstractThe crystal structure of malaria triosephosphate isomerase (TIM) was screened against the National Cancer Institute database of three‐dimensional molecular structures. Ten top‐scoring commercially available compounds were analyzed for inhibition of recombinant TIM. Two anionic dyes showed inhibition of TIM at concentrations of <100 mM. Four related sulfonated dyes were identified from the literature, docked, and screened in vitro. All showed inhibition of malaria TIM. Models indicate that these compounds bind in two suggested conformations to the active site region of the TIM enzyme. These compounds may be used in rational modification procedures for the synthesis of lead anti‐TIM drugs. Proteins 2001;45:136–143. © 2001 Wiley‐Liss, Inc.
Computer simulations aimed at structure prediction of supersecondary motifs in proteins
Authors: Forcellino François , Derreumaux Philippe 
Published: August 2002

AbstractIt is well established that protein structures are more conserved than protein sequences. One‐third of all known protein structures can be classified into ten protein folds, which themselves are composed mainly of α‐helical hairpin, β hairpin, and βαβ supersecondary structural elements. In this study, we explore the ability of a recent Monte Carlo–based procedure to generate the 3D structures of eight polypeptides that correspond to units of supersecondary structure and three‐stranded antiparallel beta sheet. Starting from extended or misfolded compact conformations, all Monte Carlo simulations show significant success in predicting the native topology using a simplified chain representation and an energy model optimized on other structures. Preliminary results on model peptides from nucleotide binding proteins suggest that this simple protein folding model can help clarify the relation between sequence and topology. Proteins 2001;45:159–166. © 2001 Wiley‐Liss, Inc.
RunMACRO: a program to facilitate sensitivity analyses using the water flow and solute movement model MACRO
Authors: Hansen Martin 
Published: August 2002

AbstractSensitivity analyses of pesticide leaching often involve a large range of simulations based on nearly identical set‐ups. Using RunMACRO it is possible to make large numbers of simulations with a minimum of exertion. Running many nearly identical model set‐ups is tedious and might introduce errors in selecting the correct values from a long range of parameter files that are appropriate to the model set‐up. RunMACRO makes the task easier and minimises the risk of errors in the generation of parameter files and model executions. Using RunMACRO, it is possible to create a suite of MACRO simulations based on a single parameter file where the range or a list of values for one to three parameters is specified. RunMACRO then creates a parameter file for each of the simulations and runs the simulations one by one. RunMACRO can easily be modified to be used with other simulation programs that use ASCII‐based parameter files and can be started from a command prompt. RunMACRO is available free to use and modify from the Geological Survey of Denmark and Greenland's home page.© 2001 Society of Chemical Industry
Long term effect of aflatoxin B1 on lipid peroxidation in rat liver and kidney: effect of picroliv and silymarin
Authors: Rastogi Ravi , Srivastava Arvind Kumar , Rastogi Anil Kumar 
Published: August 2002

AbstractAflatoxin B1 (AFB1) is a potent hepatotoxic and hepatocarcinogenic mycotoxin. The mechanism of cellular damage caused by AFB1 has not been fully elucidated. Lipid peroxidation is one of the main manifestations of oxidative damage and has been found to play an important role in the toxicity and carcinogenesis of many carcinogens. The present investigation aims at assessing the comparative antioxidant effet of picroliv, a standardized iridoid glycoside fraction of Picrorhiza kurroa and silymarin, a well known standard hepatoprotective, on aflatoxin B1 induced lipid‐peroxidation in rat liver and kidney. Marked increases in lipid peroxide levels and a concomitant decrease in enzymic antioxidant levels were observed in aflatoxin B1 (2 mg/kg, i.p) ‐toxicated rats, while drug (picroliv and silymarin both) treatment reversed the condition to near normal levels. The effects of picroliv and silymarin were comparable. Copyright © 2001 John Wiley & Sons, Ltd.
Experimental treatment of chronic Trypanosoma cruzi infection in mice with 2‐n‐propylquinoline
Authors: Nakayama Hector , Ferreira Maria Elena , Arias Antonieta Rojas de , Bilbao Ninfa Vera de , Torres Susana , Schinini Alicia , Fournet Alain 
Published: August 2002

AbstractIt was reported previously that 2‐n‐propylquinoline was active against the epimastigote form of Trypanosoma cruzi. The effects of oral treatments with benznidazole and 2‐n‐propylquinoline were evaluated in Balb/c mice infected with T. cruzi chronically. The reference drug and 2‐n‐propylquinoline were administered 60 days post‐infection for 30 days at 25 mg/mL. At 35 days post‐treatment, the serological tests (ELISA) of the 2‐n‐ propylquinoline‐treated mice were significantly different from the controls (p = 0.01) and the benznidazole‐treated mice (p = 0.03), while this was not the case at 85 days post‐treatment. These results are encouraging for continuing the investigation of other analogues of 2‐n‐propylquinoline in experimental chronic Chagas' disease. Copyright © 2001 John Wiley & Sons, Ltd.
The range of pro‐ecological activities concerning packaging in Poland against the background of the European Union (EU)
Authors: Lisińska‐Kuśnierz Małgorzata 
Published: August 2002

AbstractThe aim of this work was to present the legal status relating to fundamental issues of packaging ecology. Next, the fundamental requirements established for packaging from the point of view of environmental protection are analysed. For this reason requirements related to the manufacture of packaging and its raw material composition, to returnable packaging, suitability for various forms of processing, marking of packaging and the content of heavy metals in packaging are presented. These requirements may significantly influence the manufacturing technologies of packaging materials and packaging, as well as the packaging systems applied. It should be remembered that manufacturers and users of packaging are responsible for the quantity and types of packaging introduced to the market. The amount and the nature of waste depend on them. These links are of major influence on the final form of packaging as well as on creating and shaping consumer habits, which are not always justified in terms of ecological requirements established for packaging. Copyright © 2001 John Wiley & Sons, Ltd.
Coupling crystallography and computational biochemistry in understanding heme enzyme structure and function
Authors: Poulos Thomas L. , Barrows Tiffany , Bhaskar B. , Bonagura Christopher A. , Li Huiying 
Published: August 2002

AbstractComputational methods and crystallography have been coupled to study structure–function relationships in cytochrome c peroxidase (CCP) and nitric oxide synthase (NOS). NOS is an important drug target and the structural details of NOS–inhibitor interactions are essential if structure‐based drug design is to be of any use in the development of therapeutic agents targeted to NOS. The structure of 7‐nitroindazole, a potent NOS inhibitor, complexed to one NOS isoform left some ambiguity in the precise orientation of the inhibitor. Various computational approaches were used to resolve this ambiguity as well as revealing the energetic basis for tight binding. With CCP site directed mutagenesis, crystallography and various computational tools have been used to understand why CCP is unique among the peroxidases in its ability to stabilize a tryptophan cation radical during catalysis. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Unexpectedly large basis set effects on the binding of O2 to heme complexes
Authors: Barea Guada , Maseras Feliu , Lledós Agustí 
Published: August 2002

AbstractIMOMM(Becke3LYP:MM3) geometry optimizations on the Fe(P)(H2O)(O2) (P=porphyrin) system with different basis sets are shown to provide large differences in the iron–oxygen bond distance. This difference is found to be not in the basis set superposition error or in the description of the interaction between iron and dioxygen. Instead, the origin of the difference is shown to be in the relative energies of the FeII(P)(O2) and FeIII(P)(O2−) descriptions emerging from the stabilities of the separate FeII/O2 and FeIII/O2− fragments. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
New computational algorithm for the prediction of protein folding types
Authors: Štambuk Nikola , Konjevoda Paško 
Published: August 2002

AbstractWe present a new computational algorithm for the prediction of a secondary protein structure. The method enables the evaluation of α‐ and β‐protein folding types from the nucleotide sequences. The procedure is based on the reflected Gray code algorithm of nucleotide–amino acid relationships, and represents the extension of Swanson's procedure in Ref. 4. It is shown that six‐digit binary notation of each codon enables the prediction of α‐ and β‐protein folds by means of the error‐correcting linear block triple‐check code. We tested the validity of the method on the test set of 140 proteins (70 α‐ and 70 β‐folds). The test set consisted of standard α‐ and β‐protein classes from Jpred and SCOP databases, with nucleotide sequence available in the GenBank database. 100% accurate classification of α‐ and β‐protein folds, based on 39 dipeptide addresses derived by the error‐correcting coding procedure was obtained by means of the logistic regression analysis (p<0.00000001). Classification tree and machine learning sequential minimal optimization (SMO) classifier confirmed the results by means 97.1% and 90% accurate classification, respectively. Protein fold prediction quality tested by means of leave‐one‐out cross‐validation was a satisfactory 82.1% for the logistic regression and 81.4% for the SMO classifier. The presented procedure of computational analysis can be helpful in detecting the type of protein folding from the newly sequenced exon regions. The method enables quick, simple, and accurate prediction of α‐ and β‐protein folds from the nucleotide sequence on a personal computer. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 84: 13–22, 2001
Quantum Monte Carlo calculations for ground and excited states
Authors: Needs R. J. , Kent P. R. C. , Porter A. R. , Towler M. D. , Rajagopal G. 
Published: August 2002

AbstractA brief overview of the diffusion quantum Monte Carlo method is given. We illustrate the application to ground‐state calculations by a study of the relative stability of carbon clusters near the crossover to fullerene stability, thereby determining the smallest stable fullerene. The application to excited states is illustrated via a study of excitonic states in small hydrogenated silicon clusters. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Quantum manifestations of classical trajectories in molecular systems
Authors: Seidel L. , González‐Giralda C. , Benito R. M. , Borondo F. 
Published: August 2002

AbstractQuantum chaos, understood as the effect of the underlying classical dynamics on the stationary quantum properties in classically chaotic systems, is examined in two molecular floppy systems. Realistic models of two degrees of freedom for HO2 and HCN/HNC are considered. The structure of the classical phase space is studied using Poincaré surfaces of section and the dynamical characteristics of the corresponding wave functions analyzed also in phase space with the aid of Husimi functions. Some wave functions show strong localization along periodic orbits. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
The effect of water on the ion trap analysis of trimethylsilyl derivatives of long‐chain fatty acids and alcohols
Authors: Wood Karl V. , Bonham Connie C. , Jenks Matthew A. 
Published: August 2002

AbstractGas chromatography/mass spectrometry (GC/MS), with an ion trap mass analyzer, was used to examine the very‐long‐chain cuticular acid and certain non‐acid wax constituents on the leaf sheath surface of Sorghum bicolor before and during 36 hours of light exposure. The mass spectra of the trimethylsilylated acids and alcohols did not match any of those published in searchable mass spectral libraries. The observed differences can be related to the interaction between water and the trimethylsilylated acids and alcohols. Understanding the observed mass spectra of the very‐long‐chain plant waxes is critical for studies that employ GC/MS with the ion trap mass analyzer to elucidate cuticular wax compositions on plants. Copyright © 2001 John Wiley & Sons, Ltd.