bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple protein folding nuclei and the transition state ensemble in two‐state proteins
Authors: Klimov D.K. , Thirumalai D. 
Published: August 2002

AbstractUsing exhaustive simulations of lattice models with side‐chains, we show that optimized two‐state folders reach the native state by a nucleation‐collapse mechanism with multiple folding nuclei (MFN). For both the full model and the Go version, there are certain contacts that on an average participate in the critical nuclei with higher probability than the others. The high‐ (≳0.5) probability contacts are largely determined by the structure of the native state. Comparison of the results for the full sequence and the Go model shows that non‐native interactions compromise the degree of cooperativity and stability of the native state. From an extremely detailed analysis of the folding kinetics, we find that non‐native interactions are present in the folding nuclei. The folding times decrease if the non‐native interactions in the folding nuclei are made neutral or repulsive. Using cluster analysis and making no prior assumption about reaction coordinate, we show that both full and Go models have three distinct transition states that give a structural description for the MFN. In the transition states, on an average, about two‐thirds of the sequence is structured, whereas the rest is disordered, reminiscent of the polarized transition state in the SH3 domain. Our studies show that Go models cannot describe the transition state characteristics of two‐state folders at the molecular level. As a byproduct of our investigations, we establish that our method of computing the transition state ensemble is numerically equivalent to the technique based on the stochastic separatrix, which also does not require a priori knowledge of the folding reaction coordinate. Proteins 2001;43:465–475. © 2001 Wiley‐Liss, Inc.
The insecticide target in the PSST subunit of complex I
Authors: Schuler Franz , Casida John E 
Published: August 2002

AbstractCurrent insecticides have been selected by sifting and winnowing hundreds of thousands of synthetic chemicals and natural products to obtain commercial preparations of optimal effectiveness and safety. This process has often ended up with compounds of high potency as inhibitors of the electron transport chain and more specifically of complex I (NADH:ubiquinone oxidoreductase). Many classes of chemicals are involved and the enzyme is one of the most complicated known, with 43 subunits catalyzing electron transfer from NADH to ubiquinone through flavin mononucleotide and up to eight iron–sulfur clusters. We used a potent photoaffinity ligand, (trifluoromethyl)diazirinyl‐[3H]pyridaben, to localize the insecticide target to a single high‐affinity site in the PSST subunit that couples electron transfer from iron–sulfur cluster N2 to ubiquinone. Most importantly, all of the potent complex I‐inhibiting pesticides, despite their great structural diversity, compete for this same specific binding domain in PSST. Finding their common mode of action and target provides insight into shared toxicological features and potential selection for resistant pests.© 2001 Society of Chemical Industry
Molluscicidal and anti‐feedant activities of diterpenes from Euphorbia paralias L
Authors: Abdelgaleil Samir A M , El‐Aswad Ahmed F , Nakatani Munehiro 
Published: August 2002

AbstractNine known diterpene polyesters of segetanes, jatrophenes and paralianes have been isolated from the aerial parts of Euphorbia paralias L. The molluscicidal activity of isolated compounds was evaluated on Biomphalaria alexandrina (Ehrenberg). Paraliane diterpene, (2S,3S,4R,5R,6R,8R, 12S,13S,14R,15R)‐5,8,14‐triacetoxy‐3‐benzoyloxy‐15‐hydroxy‐9‐oxo‐paraliane, was the most potent compound against the snail. Anti‐feedant activity was tested by a conventional leaf disc method against third‐instar larvae of Spodoptera littoralis (Boisd). Jatrophene diterpene, (2R,3R,4S,5R,7S,8R,13R, 15R)‐2,3,5,7,15‐pentaacetoxy‐8‐angeloyloxy‐14,15‐dioxojatropha‐6(17)‐11E‐diene, had the highest anti‐feedant activity among the compounds tested.© 2002 Society of Chemical Industry
Ship structural safety and reliability
Authors: Paik J K , Frieze P A 
Published: August 2002

AbstractRecent research and development in the area of design methodologies related to safety and reliability of ship structures is reviewed, focusing on some relevant probabilistic approaches used for the load and resistance factor design (LRFD) of ship hulls against collapse. Important insights and findings previously obtained in the literature are summarized, and recommendations are made with respect to both technologically improved design procedures and those needed for future development.
Augmentation of natural killer cell activity in vivo against tumour cells by some wild plants from Jordan
Authors: Abuharfeil N. M. , Salim Maher , Von Kleist S. 
Published: August 2002

AbstractTwelve aqueous extracts prepared from Jordanian plants that are currently used in traditional medicine to treat various types of cancer were tested in mice for their augmentation of natural killer cells in vivo in generating cytotoxicity against YAC tumour targets. After 1 week of oral administration of aqueous extracts of fresh Nigella sativum (N.s.) seeds and Allium sativum (A.s.) bulbs significant augmentation of splenic natural killer (NK) cells (62.3% ± 6.4% and 52.6% ±5.4% cytotoxicity, respectively), was obtained in comparison with spontaneous activity (24.5% ± 1.6%) at 200:1 effector:target ratio. Onopordum acanthium (O.a.) stem and leaves and Allium cepa (A.c.) bulbs showed intermediate augmentation (38.6% ± 3.8% and 30.6% ± 3.4% cytotoxicity, respectively) while the rest showed insignificant augmentation activity. The fresh aqueous extract of a mixture of the plants with high and intermediate activity showed little insignificant augmentation activity (72.7% ± 6.7% cytotoxicity) of NK cells compared with that obtained with each plant alone. Copyright © 2001 John Wiley & Sons, Ltd.
Analgesic and antiinflammatory activities of vernonioside B2 from Vernonia condensata
Authors: Valverde A. L. , Cardoso G. L. C. , Pereira N. A. , Silva A. J. R. , Kuster R. M. 
Published: August 2002

AbstractVernonioside B2 isolated from the methanol extract of the Brazilian herb Vernonia condensata Baker was evaluated in vivo for analgesic and antiinflammatory activities. The compound reduced writhings (93.28%) and Evans blue dye diffusion (91.80%) induced by acetic acid (0.1 N) in a dose‐dependent manner. Copyright © 2001 John Wiley & Sons, Ltd.
The first clinical trial of topical application of procyanidin B‐2 to investigate its potential as a hair growing agent
Authors: Takahashi Tomoya , Kamimura Ayako , Yokoo Yoshiharu , Honda Shinkichi , Watanabe Yasushi 
Published: August 2002

AbstractProcyanidin B‐2 is a compound we have identified in apple which acts as a growth‐promoting factor on murine hair epithelial cells. This report describes our investigation of the hair‐growing effects of 1% procyanidin B‐2 tonic after sequential use for 4 months. A double‐blind clinical trial was performed, involving a total of 29 subjects (procyanidin B‐2, 19 men; placebo, 10 men). No adverse side effects were observed in either group. In the procyanidin B‐2 group, 78.9% showed an increased mean value of hair diameter, whereas only 30.0% in the placebo group showed any increase (p < 0.02, Fisher's exact probability test). The increased ratio of hairs measuring more than 40 μm in diameter after 4 months of procyanidin B‐2 treatment was significantly higher than that of the placebo controls (p < 0.05, two‐sample­t‐test). The increase in number of total hairs in the designated scalp area (0.25 cm2) of procyanidin B‐2 subjects after a 4 month trial was significantly greater than that of the placebo controls (procyanidin­B‐2, 3.67 ± 4.09 (mean ± SD)/0.25 cm2; placebo, −2.54 ± 4.00/0.25 cm2; p < 0.001, two‐sample t‐test). Procyanidin B‐2 therapy shows potential as a promising cure for male pattern baldness. Copyright © 2001 John Wiley & Sons, Ltd.
Morphologic and morphometric analyses of acetic acid‐induced colitis in rats after treatment with enemas from Myracrodruon urundeuva Fr. All. (Aroeira do Sertão)
Authors: Rodrigues Lusmar Veras , Ferreira Francisco Valdeci , Regadas F. Sérgio P. , Matos Délcio , Viana Glauce Socorro de Barros 
Published: August 2002

AbstractThe present work showed the effects of Myracrodruon urundeuva Fr. All., popularly known as ‘aroeira’ (AE), in the form of enemas prepared from the stem bark, on several morphologic and morphometric parameters after acetic acid‐induced colitis in rats. Enemas from 5‐ASA were used as standard while the vehicle, carboxymethylcellulose, was used as a control. The results of the morphological evaluation showed that on day 1 acetic acid produced significantly more necrosis in the groups treated with AE (10% and 20%) or 5‐ASA than the controls. However, on day 60, there were more caliciform and absorptive cells in the treated groups compared with the controls. A significantly higher number of eosinophil and mononuclear cells and also collagen deposition in the controls compared with the treated groups were observed on day 60. However, a higher number of polymorphonuclear cells was detected on day 60 only in the AE treated group but not in the 5‐ASA group. These data indicate that animals treated with AE or 5‐ASA showed complete epithelial tissue regeneration, while in the controls chronic inflammatory exudate persisted and tissue regeneration occurred through fibrosis. Copyright © 2002 John Wiley & Sons, Ltd.
Phytochemical and antioedematogenic studies of commercial copaiba oils available in Brazil
Authors: Veiga Valdir F. , Zunino Luciano , Calixto João B. , Patitucci Maria L. , Pinto Ângelo C. 
Published: August 2002

AbstractThe composition of eight samples of commercial copaiba oils, used in the Amazonian region as antiinflammatory agents and available in popular markets, were analysed by gas chromatography/mass spectrometry (HRGC‐MS). Major differences were observed in their chemical composition and some adulterations were pointed out. When tested in vivo oils 1 and 3, and to a lesser extent oil 6, significantly inhibited bradykinin‐induced oedema formation. The other tested oils had no effect. When assessed in carrageenan‐induced oedema formation, oils 1, 2 and 6, but not oil 3, significantly attenuated the oedema formation. The other tested oils failed to affect carrageenan‐induced paw oedema. Oils 1 and 6 were further fractionated and several sesquiterpenes and diterpenes were detected. It is suggested that the naturally occurring sesquiterpenes present in the copaiba oils seem to be responsible for the antiinflammatory action reported in the folk medicine. Furthermore, our results clearly show an adulteration in copaiba oils available in Brazil. Copyright © 2001 John Wiley & Sons, Ltd.
Odorous compounds in paperboard as influenced by recycled material and storage
Authors: Ziegleder Gottfried 
Published: August 2002

AbstractMany volatile compounds can be identified in unprinted paperboard by means of steam distillation in combination with capillary gas chromatography, mass spectrometry and olfactometry. Paperboards produced with recycled material exhibit additional volatiles which partly contribute to off‐odours. Using sniffing techniques, benzaldehyde, acetophenone, 1‐octen‐3‐ol, 1‐octen‐3‐one, 2‐nonenal, methylguajacol, butanoic and 3‐methyl butanoic acid were identified as the most odorous volatiles. The aromatic substances mainly exude from inks and printing solvents in waste materials used for paperboard manufacturing. During storage under controlled conditions, the microbial load of paperboard decreased slightly, and no odorous metabolic products were generated. Copyright © 2001 John Wiley & Sons, Ltd.
A constraint‐based approach to the modelling and analysis of packaging machinery
Authors: Hicks B. J. , Medland A. J. , Mullineux G. 
Published: August 2002

AbstractTo enable packaging machinery manufacturers to compete at an international level, it is necessary to introduce them to more advanced design methods and technologies. For years, the evolution of packaging machinery has relied heavily on trial‐and‐error methods. The demands for continual increases in the performance capabilities of the machines, escalating legislation, environmental directives and changes in the characteristics of the product require rapid development of existing machine designs and the creation of new machines. This paper discusses the needs of SME packaging machinery manufacturers and identifies their requirements for methods in support of the design and redesign of packaging machinery. The need to identify, capture and manipulate design knowledge is critical for SMEs, where all too often design records are incomplete. Furthermore, a systems modelling approach that provides for support over the conceptual, embodiment and detailed design phases is essential for the rapid and effective development of designs. In order to meet these requirements, a methodology is proposed which incorporates ‘constraint modelling’ techniques. The methodology provides for experimental investigation and computer‐based modelling, which together aid the designer in gaining a fundamental understanding of the design problem. This enables the identification and representation of design knowledge, the determination of the limitations of an existing design, the evaluation of alternative designs and redesign strategies, as well as the embodiment, refinement and optimization of design solutions. The theory of ‘constraint modelling’ is discussed and the various phases of the methodology described. The applications of the methodology to a new machine design and a redesign program are also detailed. Copyright © 2001 John Wiley & Sons, Ltd.
Robustness of Chi‐square and Canberra distance metrics for computer intrusion detection
Authors: Emran Syed Masum , Ye Nong 
Published: August 2002

AbstractIntrusion detection complements intrusion prevention mechanisms, such as firewalls, cryptography, and authentication, to capture intrusions into an information system while they are acting on the information system. We develop two multivariate quality control techniques based on chi‐square and Canberra distance metrics, respectively, to detect intrusions by building a long‐term profile of normal activities in the information system (norm profile) and using the norm profile to detect anomalies. We investigate the robustness of these two distance metrics by comparing their performance on a number of data sets involving different noise levels in data. The performance results indicate that the Chi‐square distance metric is much more robust to noises than the Canberra distance metric. Copyright © 2002 John Wiley & Sons, Ltd.
Protein interaction property similarity analysis
Authors: Wade R. C. , Gabdoulline R. R. , De Rienzo F. 
Published: August 2002

AbstractWe describe how similarity indices may be applied to semiquantitatively compare the molecular interaction fields, such as electrostatic and hydrophobic potentials, of proteins. We then review ways in which this approach has been used to investigate protein interaction properties in diverse applications ranging from in‐depth comparison of pairs of proteins to large‐scale analysis of hundreds of modeled protein structures. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 122–127, 2001
Modeling zinc sulfhydryl bonds in zinc fingers
Authors: Bredenberg Johan , Nilsson Lennart 
Published: August 2002

AbstractMolecular dynamics simulations have been carried out employing three different model descriptions of the zinc sulfhydryl interactions in class II fingers. One bonded and two nonbonded models were studied. Two variant structures of the glucocorticoid receptor DNA‐binding domain and a NMR structure from a fragment of methionyl‐tRNA synthetase were subjected to long‐time MD simulations with these models. Our analysis is focused on comparison with experimental and quantum mechanical data, concerning the local Zn‐finger and overall structural and dynamic properties for these models. All models performed well, but the nonbonded models appeared to reproduce the protein dynamics in better agreement with experimental data than does the bonded description. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 230–244, 2001
Theoretical studies on the spectroscopy of the 7‐azaindole monomer and dimer
Authors: Serrano‐Andrés Luis , Merchán Manuela , Borin Antonio Carlos , Stålring Jonna 
Published: August 2002

AbstractThe absorption and the emission spectra, both fluorescence and phosphorescence, of the 7‐azaindole molecule have been studied by means of the complete active space (CAS) SCF method and multiconfigurational second‐order perturbation theory (CASPT2). Excitation energies, oscillator strengths, dipole moments, transition dipole moments, and their directions have been computed and the results compared to those of analogous molecules such as indene, indole, and benzimidazole, to get a homogeneous picture of the photophysics of the systems. The absorption and emission of the 7‐azaindole dimer and its related tautomer have also been computed in order to get further insight into the double fluorescence phenomenon, which was first observed in highly concentrated media. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem 84: 181–191, 2001
Characterization of dehydroascorbic acid solutions by liquid chromatography/mass spectrometry
Authors: Pastore Paolo , Rizzetto Tania , Curcuruto Ornella , Cin Michele Dal , Zaramella Alessio , Marton Daniele 
Published: August 2002

AbstractThe composition of a commercial dehydroascorbic acid (DA) solution at pH 2 was investigated by liquid chromatography/mass spectrometry (LC/MS) and liquid chromatography/tandem mass spectrometry (LC/MS/MS) to establish the nature of its different forms and its decomposition products. In freshly prepared solutions, dimeric forms of DA and the hydrated bicyclic hemiketal of DA are the species mainly present in solution. In the presence of light, the initial dimeric species disappears over time to give other dehydrated dimers some of which decompose to the monomer. The comparison of these data with similar data obtained for ascorbic acid (AA) solutions under the same experimental conditions revealed that, in the presence of light, the aging of such AA solutions gives rise to only the hemiketal form of DA, and that no dimeric species of DA were formed. The presence of the hemiketal form of DA was not revealed by analysis of the same AA solutions using the conventional LC/UV technique. The natural form of DA from the oxidation of AA is the hydrated bicyclic form. Copyright © 2001 John Wiley & Sons, Ltd.
Implications of matrix effects in ultra‐fast gradient or fast isocratic liquid chromatography with mass spectrometry in drug discovery
Authors: Tiller Philip R. , Romanyshyn Leslie A. 
Published: August 2002

AbstractIn the analysis of biological samples it is important to reduce the risk of interferences from the matrix itself, other analytes, the dosing vehicle (commonly PEG), and from the MS/MS transitions used for the analysis. Rapid analysis is essential for drug discovery, and even though the requirements for separation may be minimized for speed, the integrity of the analysis is still dependent on the separation. This paper focuses on the potential for interferences from various endogenous and exogenous matrix components commonly encountered in quantitation of analytes and their metabolites from biological matrices. We demonstrate that neither high organic isocratic nor ballistic gradient ultra‐fast HPLC show a clearly defined advantage in regards to complex biological matrices. The critical factor in the resolution of matrix interferences still remains in sample preparation. Copyright © 2001 John Wiley & Sons, Ltd.
The pathogenesis of febrile seizures: Is there a role for specific infections?
Authors: van Zeijl J.H. , Mullaart R.A. , Galama J.M.D. 
Published: August 2002

AbstractAlthough fever is regarded as the main trigger in the pathogenesis of febrile seizures (FS), it is not supposed to be the unique causative factor. In FS, there is a strong familial predisposition. This does not exclude infections as a causative factor because subtle genetic polymorphisms have been demonstrated to affect the course of infections. We review the literature on: (1) the role of fever, especially the height of temperature, its cause, and metabolic effects induced by temperature; (2) the role of heredity; (3) the role of cytokines which play a role in the induction of fever; and (4) the role of type of infection, with emphasis on newly identified agents and improved diagnostic techniques. With modern molecular techniques such as PCR, viruses have been detected in the CSF far more often than previously thought, even in the absence of pleocytosis of the CSF. This makes it difficult to distinguish FS from acute encephalitis. FS may be caused by neuroinvasion or intracerebral activation of viruses. Further studies should focus on these options because therapeutic intervention is possible and may prevent late sequelae such as recurrent FS and subsequent epilepsy. Copyright © 2002 John Wiley & Sons, Ltd.
Chattering‐free sliding mode control for a class of nonlinear mechanical systems
Authors: Parra‐Vega Vicente , Hirzinger Gerd 
Published: August 2002

AbstractSecond‐order sliding mode control (2‐smc) and dynamic sliding mode control (dsmc) eliminate the disturbing characteristic of chattering in static sliding mode control under the assumption that the derivative of the sliding surface is available or complex inequalities at the acceleration level can be constructed. In this paper, passivity‐based adaptive and non‐adaptive chattering‐free sliding mode controllers are proposed assuming that the upper bound of the norm of the derivative of the sliding surface is available, a weaker and easy to implement assumption in comparison to those of 2‐smc and dsmc. The closed‐loop system accounts explicitly for the invariance condition without reaching phase, and therefore for a desired transient response with global exponential convergence of tracking errors. Preliminary experiments are presented. Copyright © 2001 John Wiley & Sons, Ltd.
Effects of habitat enhancement on 0‐group fishes in a lowland river
Authors: Langler Glenn J. , Smith Carl 
Published: August 2002

AbstractLoss of habitat complexity through river channelization can have adverse affects on riverine fauna and flora through reductions in abundance and diversity of species. Habitat enhancement schemes are used to improve the physical and biological heterogeneity of riverine habitats. Between 1996 and 1997 the Environment Agency undertook a habitat enhancement scheme on the Huntspill River, Somerset, England to improve conditions for coarse (non‐salmonid) fishes. The scheme involved reducing bank gradients and the construction of off‐channel bays in parts of the channel, all of which were planted with willow (Salix sp.) and common reed (Phragmites australis). The effectiveness of the enhancement scheme was investigated by comparing 0‐group fish assemblages in manipulated and unmanipulated sites. Abundance and diversity of 0‐group fishes was significantly higher in manipulated habitats. There was no significant difference detected in the effects of the different types of enhancement measure used. The significance of microhabitats produced by habitat enhancement schemes is discussed with respect to spawning, nursery and refuge sites for 0‐group coarse fish assemblages. Copyright © 2001 John Wiley & Sons, Ltd.