bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recurrence quantification analysis reveals interaction partners in paramyxoviridae envelope glycoproteins
Authors: Giuliani Alessandro , Tomasi Maurizio 
Published: August 2002

AbstractThe paramyxovirus envelope fuses with the host cell membrane by cooperative interaction of two transmembrane glycoproteins: the hemagglutinin neuraminidase (HN) and the fusion (F) glycoprotein. The interaction appears to be finely regulated, as both proteins must derive from the same viral species to obtain a functional interaction. Because HN and F do not form stable complexes, this interaction is poorly characterized. This article demonstrates that a modification of a classical bioinformatic method based on the co‐evolution of interacting partners can detect the specificity of the HN and F interaction. The proposed approach relies on a relatively new nonlinear signal analysis technique, recurrence quantification analysis (RQA), applied to the hydrophobicity sequences of viral proteins. This technique is able to shed light on the interaction between HN and F proteins in the virus–cell fusion and, more generally, permits the quantitative comparison of nonhomologue protein systems. On the contrary, the same co‐evolution approach, based on the classical sequence alignment procedure, was unable to discriminate interacting partners from the general strict correlation existing between the evolution of viral proteins as a whole. The cooperation between HN and F in the fusion process is thus demonstrated by a bioinformatic, purely sequence‐dependent, perspective. Proteins 2002;46:171–176. © 2001 Wiley‐Liss, Inc.
Multiple linear regression for protein secondary structure prediction
Authors: Pan Xian‐Ming 
Published: August 2002

AbstractIn the present work, a novel method was proposed for prediction of secondary structure. Over a database of 396 proteins (CB396) with a three‐state‐defining secondary structure, this method with jackknife procedure achieved an accuracy of 68.8% and SOV score of 71.4% using single sequence and an accuracy of 73.7% and SOV score of 77.3% using multiple sequence alignments. Combination of this method with DSC, PHD, PREDATOR, and NNSSP gives Q3 = 76.2% and SOV = 79.8%. Proteins 2001;43:256–259. © 2001 Wiley‐Liss, Inc.
Generalized comparative modeling (GENECOMP): A combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement
Authors: Kolinski A. , Betancourt M.R. , Kihara D. , Rotkiewicz P. , Skolnick J. 
Published: August 2002

AbstractAn improved generalized comparative modeling method, GENECOMP, for the refinement of threading models is developed and validated on the Fischer database of 68 probe–template pairs, a standard benchmark used to evaluate threading approaches. The basic idea is to perform ab initio folding using a lattice protein model, SICHO, near the template provided by the new threading algorithm PROSPECTOR. PROSPECTOR also provides predicted contacts and secondary structure for the template‐aligned regions, and possibly for the unaligned regions by garnering additional information from other top‐scoring threaded structures. Since the lowest‐energy structure generated by the simulations is not necessarily the best structure, we employed two structure‐selection protocols: distance geometry and clustering. In general, clustering is found to generate somewhat better quality structures in 38 of 68 cases. When applied to the Fischer database, the protocol does no harm and in a significant number of cases improves upon the initial threading model, sometimes dramatically. The procedure is readily automated and can be implemented on a genomic scale. Proteins 2001;44:133–149. © 2001 Wiley‐Liss, Inc.
Chlorothalonil and chlorpyrifos degradation products in golf course leachate
Authors: Armbrust Kevin L 
Published: August 2002

AbstractChlorothalonil and chlorpyrifos are commonly used to control disease and insect pests on golf course greens. While they are relatively immobile in the soil profile, their respective soil degradation products, 4‐hydroxy‐2,5,6‐trichloroisophthalonitrile and 3,5,6‐trichloropyridin‐2‐ol are more polar and may be present in golf course green leachate. To investigate this possibility, six stainless steel lysimeters were constructed into two practice greens at a country club in a northern Atlanta, Georgia suburb. Over a period of 1 year after rainfall events, lysimeter leachate samples were collected into glass bottles, filtered and directly analyzed by HPLC with UV detection. Chlorpyrifos was not detected in any sample and chlorothalonil was detected only in one sample, at a concentration of 0.12 mg liter−1. With a limit of quantitation of 0.05 mg liter−1, hydroxychlorothalonil and trichloropyridinol were detected in 87% and 63% of the samples at maximum and median concentrations of 2.21 and 0.55 mg liter−1 for hydroxychlorothalonil and 1.77 and 0.15 mg liter−1 for trichloropyridinol. Golf course green leachate often mixes with surface water, thus more data may be warranted to determine the persistence and ecological significance of chronic exposure to these compounds of organisms in the aquatic environment.© 2001 Society of Chemical Industry
Dye injection for predicting pesticide movement in micro‐irrigated polyethylene film mulch beds
Authors: Csinos Alex S , Laska James E , Childers Stan 
Published: August 2002

AbstractA new method is described for tracing water movement in polyethylene film covered soil beds. Dye was delivered via a drip tape micro‐irrigation system which was placed in the bed as the soil beds were shaped and covered with polyethylene film. The dye was injected into the system and irrigated with water for 4–24 h at 0.41–1.38 bar (41–138 kPa) pressure depending on the experiment. The dye appeared as blue circles on the soil surface within 20 min of injection and produced a three‐dimensional pattern in the soil profile. Injection‐irrigation‐pressure scenarios were evaluated by measuring dye movement directly below and between emitters by sliding fabricated blades vertically into the bed at the desired examination point and excavating the soil away from the blade. The dye typically produced a U shape on the face of the bed and the area was calculated for each of these exposed faces. The area increased as the length of irrigation and water pressure increased. Interrupted irrigation (pulsing) scenarios did not alter the calculated areas encompassed by the dye compared to uninterrupted irrigation scenarios. The blue dye provided a direct, inexpensive and easy method of visualizing water movement in soil beds. This information will be used to optimize application of emulsifiable plant‐care products in polyethylene film mulch beds.© 2002 Society of Chemical Industry
A review of potential pathogens of sea lice and the application of cleaner fish in biological control
Authors: Treasurer James W 
Published: August 2002

AbstractThere are many examples of successful biological control of pest populations in aquatic environments. This approach to sea louse control has environmental benefits and is cost‐effective. The range of possible pathogens of lice is reviewed and epibionts recorded from sea lice, including the monogenean Udonella caligorum and ciliates, are examined. Baculoviruses when ingested by insects form occlusion bodies resulting in severe damage to the digestive system and subsequent death, and this may be a promising approach. Cleaner wrasse (Labridae) have been stocked commercially with farmed salmon since 1989, and recent work on improving the method is reviewed. Wrasse are sourced from a wild fishery and stocked at ratios of 1 to 25–150 salmon. Over 5 million wrasse are stocked annually in Norway and c 30% of smolts in Scotland were stocked with wrasse until 1998, when an outbreak of infections salmon anaemia (ISA) deterred many farmers from transferring wild fish to cages. A case study is given showing that salmon in cages stocked with wrasse had a burden of one to eight lice through the first year compared with up to 40 lice per fish on unprotected and untreated fish. Electivity indices were used to compare the relative composition of lice developmental stages on salmon in stocked and unstocked cages, and adult male and female lice were found to comprise only 6% of the population in cages with wrasse, compared with 49% adults on fish in control cages. Measures to improve the efficacy of wrasse as a way of cleaning salmon in the second production year include the use of refuges to assist over‐wintering survival, and stocking ballan wrasse. Health hygiene includes sourcing wrasse in the farm locality, testing for pathogens, vaccination of wrasse and ultimately rearing wrasse for stocking. The role of wrasse in an IPM strategy is described.© 2002 Society of Chemical Industry
Chemistry and pharmacology of the citrus bioflavonoid hesperidin
Authors: Garg A. , Garg S. , Zaneveld L. J. D. , Singla A. K. 
Published: August 2002

AbstractHesperidin, a bioflavonoid, is an abundant and inexpensive by‐product of Citrus cultivation. A deficiency of this substance in the diet has been linked with abnormal capillary leakiness as well as pain in the extremities causing aches, weakness and night leg cramps. No signs of toxicity have been observed with the normal intake of hesperidin or related compounds.Both hesperidin and its aglycone hesperetin have been reported to possess a wide range of pharmacological properties. This paper reviews various aspects of hesperidin and its related compounds, including their occurrence, physical and chemical properties, analysis, pharmacokinetics, safety and toxicity and the marketed products available. A special emphasis has been laid on the pharmacological properties and medicinal uses of these compounds. Copyright © 2001 John Wiley & Sons, Ltd.
In vitro cytotoxicity of flavonoids against MK2 and C6 tumour cells
Authors: Sánchez I. , Calderón J. , Ruiz B. , Tellez J. , Calzada L. , Taboada J. 
Published: August 2002

AbstractThe cytotoxic effect of five flavonoids isolated from the aerial parts of the Asteraceae family of plants were studied in vitro using LLC‐MK2 and C6 glial cells. Agehoustin A was shown to be cytotoxic for both cells (71% or 67% cell death). Agehoustin B and artemetin, which lack a methoxy group at C‐8 (RI), were not cytotoxic for the cells (19% and 16% cell death). The three flavonoids showed considerable suppressive effects on LLC‐MK2 and C6 cell growth. Lucidin‐dimethylether and gnaphaliin were also not cytotoxic for cells but they had no suppressive effect on cell growth. The results show a structure–cytostatic activity relationship. We suggest that the methoxy group on C‐8 and on the B ring are responsible for death cell. Copyright © 2001 John Wiley & Sons, Ltd.
Simple evaluation of Franck–Condon factors and non‐Condon effects in the Morse potential
Authors: López V. J. C. , Rivera A. L. , Smirnov Yu. F. , Frank A. 
Published: August 2002

AbstractThe calculation of Franck–Condon factors between different 1‐D Morse potential eigenstates using a formula derived from the Wigner function is discussed. Our numerical calculations using a simple program written in Mathematica are compared with other calculations. We show that our results have a similar accuracy as those calculations performed with more sophisticated methods. We discuss the extension of our method to include non‐Condon effects in the calculation. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem 88: 280–295, 2002
B3LYP studies of the formation of neutral tyrosyl radical Yz⋅ and regeneration of neutral tyrosine Yz in PSII
Authors: Wang Yan‐Ni , Eriksson Leif A. 
Published: August 2002

AbstractTyrosine Y161 (Yz) plays an important role in the charge separation of photosystem II (PSII) by reducing photooxidized P680+ and thus forming a neutral tyrosyl radical. The neutral tyrosyl radical then abstracts an electron and a proton from the manganese cluster (or other proton source) to regenerate neutral tyrosine. The production of the neutral tyrosyl radical is closely related to the oxidation of tyrosine by P680+ and deprotonation by a neighbouring histidine. The regeneration of neutral tyrosine is more complicated, involving the manganese cluster and other protein bases. Hybrid density functional calculations (B3LYP) show that the electron transfer between tyrosine and P680+ is coupled to the proton transfer between tyrosine and histidine. The proton is transferred from tyrosine to histidine spontaneously as tyrosine is oxidized, forming Yz⋅‐ ‐H+His state. The theoretical results of the formation of the neutral tyrosyl radical agrees with recent experimental and previous computational results. Neutral tyrosine is difficult to regenerate directly via abstraction of a hydrogen atom from water. The possible proton transfer from histidine cation directly to water or with glutamic acid assitance are both endothermic. In both cases, the proton lies between tyrosine and histidine and shifts back to tyrosine spontaneously when the tyrosyl radical is reduced. This result is consistent with Junge's electron transfer model. However, when glutamate anion is present, rather than glutamic acid, the proton transfers spontaneously via histidine to glutamate as tyrosine is oxidized, forming Yz⋅‐ ‐His‐ ‐Glu state. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 220–229, 2001
Role of electron–electron coalescence density in density functional theory
Authors: Valderrama E. , Ugalde J. M. 
Published: August 2002

AbstractAn expression for the evaluation of electron–electron coalescence density as a functional of the density for any electron system is proposed. The formula, clarifies previously advanced upper bounds for this quantity and provides a method to independently estimate the system‐averaged on‐top exchange–correlation hole. The relationship with the on‐top pair density shows that producing the true electron–electron coalescense should be considered as a leading physical requirement for trial wave functions in any energy minimization scheme. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Evaluation of mass discrimination effects in the quantitative analysis of polydisperse polymers by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry using uniform oligostyrenes
Authors: Shimada Kayori , Lusenkova Marina A. , Sato Keisuke , Saito Takeshi , Matsuyama Shigetomo , Nakahara Hisae , Kinugasa Shinichi 
Published: August 2002

AbstractMass discrimination effects in matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) were quantitatively investigated using equiweight and equimolar mixtures of uniform polystyrene (PS) oligomers. Uniform PS oligomers were separated by preparative super‐critical fluid chromatography (SFC) from commercial standard PS samples. The separated PS oligomers, with degrees of polymerization n = 2–25, have absolutely no molecular weight distributions. Equiweight and equimolar mixtures of uniform PS oligomers were accurately prepared by weighing by microbalance, and their spectra were recorded using a MALDI‐TOF mass spectrometer. In the lower molecular weight region (less than about 103) the oligomers with lower molecular weights give lower mass spectral intensities, with no correlation with laser power. In contrast, higher laser powers yield a decrease of mass spectral intensities in the higher molecular weight region. These results clearly show that mass discrimination effects occur at lower and higher molecular weights depending on the laser power, and provide quantitative information about the discrimination. Using the data on equiweight and equimolar mixtures of PS oligomers, it was possible to calibrate the MALDI‐TOF mass spectral data for an analysis of molecular weight distribution of a standard monodisperse PS sample with number‐averaged molecular weight of 103, and to compare it with the molecular weight distribution measured by analytical SFC. The result from the calibrated MALDI‐TOF mass spectrum, however, does not agree perfectly with that from the SFC results, because undetectable peaks in MALDI‐TOF mass spectra at lower and higher molecular weights could not be included in the calibration of peak intensities. Copyright © 2001 John Wiley & Sons, Ltd.
High‐throughput semi‐automated 96‐well liquid/liquid extraction and liquid chromatography/mass spectrometric analysis of everolimus (RAD 001) and cyclosporin a (CsA) in whole blood
Authors: Brignol Nastry , McMahon Louis M. , Luo Suyi , Tse Francis L. S. 
Published: August 2002

AbstractA semi‐automated high‐throughput liquid/liquid extraction (LLE) assay was developed for RAD001 and cyclosporin A (CsA) in human blood. After addition of internal standard and ammonium hydroxide, samples were extracted twice with methyl tert‐butyl ether (MTBE). The organic extract was evaporated to dryness and reconstituted in mobile phase. Where possible, sample transfer and LLE steps were automated using a Tomtec Quadra 96 workstation. Samples were analyzed using ESI‐LC/MS/MS employing the transitions of ([M + NH4]+ → [M + H]+) for CsA and ([M + NH4]+ → [M + H‐(CH3OH + H2O)]+) for RAD001, under isocratic chromatographic conditions (75:25, (v/v), acetonitrile/20 mM ammonium acetate) with a run time of 3.6 min. A lower limit of quantitation (LLOQ) of 0.368 ng/mL and 5.23 ng/mL was achieved for RAD001 and CsA, respectively, using a sample volume of 0.3 mL for the analysis. The method was validated over a 3‐day period and the resulting calibration curves had a correlation coefficient >0.99 over the concentration range 0.368 to 409 ng/mL and 5.24 to 1748 ng/mL for RAD001 and CsA, respectively. The inter‐day coefficient of variation (CV) was less than 15% at the LLOQ for both compounds. The method was applied to the analysis of clinical samples. Under normal working conditions four 96‐well plates could be extracted and LC/MS analysis completed in less than 28 h. A marked improvement in sample throughput efficiency was realized with this LLE method when compared to existing solid phase extraction (SPE) methods which deal with both RAD001 and CsA. Copyright © 2001 John Wiley & Sons, Ltd.
Consequence of boar edible tissue consumption on urinary profiles of nandrolone metabolites. II. Identification and quantification of 19‐norsteroids responsible for 19‐norandrosterone and 19‐noretiocholanolone excretion in human urine
Authors: De Wasch Katia , Bizec Bruno Le , Brabander Hubert De , André François , Impens Sandra 
Published: August 2002

AbstractIn previous work (Le Bizec et al., Rapid Commun. Mass Spectrom. 2000; 14: 1058), it was demonstrated that a boar meal intake could lead to possible false accusations of abuse of 17β‐nortestosterone in antidoping control. The aim of the present study was to identify and quantify endogenous 19‐norsteroids in boar edible tissue at concentrations that can alter the steroid urinary profile in humans, and lead to excretion of 19‐norandrosterone (19‐NA) and 19‐noretiocholanolone (19‐NE). The samples were analysed in two laboratories. The methodologies used for extraction and detection (GC/MS(EI) and LC/MS/MS(APCI+)) are compared and discussed. 19‐Norandrostenedione (NAED), 17β‐ and 17α‐nortestosterone (bNT, aNT), and 17β‐ and 17α‐testosterone (bT, aT) were quantified. The largest concentrations of NAED and bNT were observed in testicles (83 and 172 µg/kg), liver (17 and 63 µg/kg) and kidney (45 and 38 µg/kg). A correlation between the bNT and NAED content of a typical meal prepared with boar parts and the excreted concentrations of 19‐NA and 19‐NE in human urine was demonstrated. Copyright © 2001 John Wiley & Sons, Ltd.
Analysis of a basic drug by on‐line solid‐phase extraction liquid chromatography/tandem mass spectrometry using a mixed mode sorbent
Authors: Mallet Claude R , Lu Ziling , Mazzeo Jeff , Neue Uwe 
Published: August 2002

AbstractTwo on‐line configurations using multiple 6‐ and 10‐port valves were investigated for high‐flow on‐line extraction of a basic drug in rat plasma and human urine using a reversed‐phase and a cation‐exchange SPE sorbent. The first configuration studied was a single reversed‐phase extraction cartridge (2.1 × 20 mm, 25µm) using an optimized washing protocol. The results showed that up to 1.5 mL of sample (urine or plasma diluted 1:1) can be injected with limits of quantification (LOQs) as low as 100 pg/mL. The second configuration studied was the combination of a cation exchanger and a reversed‐phase cartridge using at‐column dilution. The results showed better LOQs than those obtained with the single cartridge at 10 pg/mL with the same injection volume. The mass spectrometer was operated in the multiple reaction monitoring (MRM) mode. All calibration curves gave an average of 5% relative standard deviation (RSD). Copyright © 2002 John Wiley & Sons, Ltd.
The cellular receptor for measles virus—elusive no more
Authors: Yanagi Yusuke 
Published: August 2002

AbstractThe identity of the measles virus receptor has been controversial. Several years ago CD46 was identified as a cellular receptor for the Edmonston strain of measles virus, but most clinical isolates of measles virus, which are most efficiently isolated in the marmoset B cell line B95a, cannot grow in many CD46+ cell lines. Although some researchers attributed it to post‐entry block in viral replication, others believed that there is a receptor other than CD46 for wild‐type measles viruses. A new study showed that human signalling lymphocytic activation molecule (SLAM; also known as CDw150) is a cellular receptor for measles virus, including the Edmonston strain. SLAM is expressed on lymphocytes and dendritic cells, and plays an important role in lymphocyte activation. The identification of SLAM as a measles virus receptor nicely explains the pathogenesis of measles virus infection. Copyright © 2001 John Wiley & Sons, Ltd.
Zeno hybrid systems
Authors: Zhang Jun , Johansson Karl Henrik , Lygeros John , Sastry Shankar 
Published: August 2002

AbstractThe interacting continuous and discrete dynamics in hybrid systems may lead to Zeno executions, which are solutions of the system having infinitely many discrete transitions in finite time. Although physical systems do not show Zeno behaviour, models of real systems may be Zeno due to modelling abstraction. It is hard to analyse such models with the existing theory. Since abstraction is an important tool in the hierarchical design of hybrid systems, one would like to determine when it may lead to Zeno models. Zeno hybrid systems are studied in detail in the paper. Necessary and sufficient conditions for the existence of Zeno executions are given. The Zeno set is introduced as the ω limit set of a Zeno execution. Properties of the Zeno set are derived for a fairly large class of hybrid systems. Copyright 2001 © John Wiley & Sons, Ltd.
Randomized metarounding
Authors: Carr Robert , Vempala Santosh 
Published: August 2002

AbstractLet P be a linear relaxation of an integer polytope Z such that the integrality gap of P with respect to Z is at most r, as verified by a polytime heuristic A, which on any positive cost function c returns an integer solution (an extreme point of Z) whose cost is at most r times the optimal cost over P. Then for any point x* in P (a fractional solution), rx* dominates some convex combination of extreme points of Z. A constructive version of this theorem is presented here, with applications to approximation algorithms, and can be viewed as a generalization of randomized rounding. © 2002 Wiley Periodicals, Inc. Random Struct. Alg., 20:343–352, 2002