bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of diphenyl iodonium salt (DPI) in three‐component photoinitiator systems containing methylene blue (MB) and an electron donor
Authors: Kim Dongkwan , Scranton Alec 
Published: October 2004

AbstractThree‐component initiators generally include a light‐absorbing photosensitizer, an electron donor that is often an amine, and the third component, which is usually an iodonium salt. To characterize the role of diphenyl iodonium chloride (DPI) in three‐component photoinitiator systems containing methylene blue (MB) as the photosensitizer, a systematic series of electron donors was used. The Rhem–Weller equation was used to verify the thermodynamic feasibility for photo‐induced electron transfer from the electron donors to the MB. Comparison of the photopolymerization rates of each two‐component initiator system (containing the photosensitizer and amine) to those of the corresponding three‐component system (with the addition of (DPI) allowed fundamental information regarding the role of the DPI to be obtained. It was concluded that the DPI enhances the photopolymerization kinetics in two ways: (1) it consumes an inactive MB neutral radical and produces an active phenyl radical, thereby regenerating the original methylene blue, and (2) it reduces the recombination reaction of the MB neutral radical and amine radical/cation. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5863–5871, 2004
Effect of high electric fields on the isotropic phase of a lyotropic liquid‐crystalline system
Authors: Menna T. J. , Filisko F. E. 
Published: October 2004

AbstractThe effect of high (>1000 V/mm) electric fields on solutions of a lyotropic liquid‐crystalline polymer, poly(n‐hexyl isocyanate) in p‐xylene, is presented. The concentrations are adjusted such that the solutions are strictly within the isotropic phase domain region, thus exhibiting no spontaneous liquid crystallinity. The effects of field strength, frequency, and concentration are varied and the morphological changes are noted. The results are analyzed with birefringence measurements via comparison with the optical Kerr effect. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 4116–4125, 2004
Swelling of a polymer brush by a poor solvent
Authors: Gallagher P. D. , Satija S. K. , Karim A. , Douglas J. F. , Fetters L. J. 
Published: October 2004

AbstractThe addition of a small amount of a poor solvent impurity (methanol) to a theta solvent (cyclohexane) is found to cause appreciable swelling (≈30% increase of the average brush height) in a model end‐grafted polystyrene (PS) brush layer. This unusual type of swelling is not observed if octadecyltrichlorosilane (OTS) is first grafted to the portion of the silicon substrate uncovered by the grafting end‐groups of the PS chains. Brush swelling in the absence of OTS surface protection is interpreted as arising from a segregation of methanol to the solid substrate and the resulting modification of the polymer–surface interaction. We also observe that the addition of a small amount of methanol to an adsorbed PS layer exposed to cyclohexane causes rapid film delamination from the silicon substrate. Together these observations imply a strong influence of surface active impurities on the structure and adhesive stability of polymer layers. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 4126–4131, 2004
Determinants of cysteine pKa values in creatine kinase and α1‐antitrypsin
Authors: Naor Mor M. , Jensen Jan H. 
Published: October 2004

AbstractThe structural determinants of the unusually low pKa values of Cys282 in human creatine kinase and Cys232 in α1‐antitrypsin were studied computationally. We have demonstrated that hydrogen bonding to the cysteine residue is the prime determinant for both proteins. In the case of creatine kinase, the hydrogen bond donors are a serine side chain and an amide NH‐group, while in α1‐antitrypsin the donor is an amide NH. Each hydrogen bond lowers the pKa by between 0.8 and 1.5 pH units. The 1.1‐unit lowering due to the Ser284–Cys282 hydrogen bond is in good agreement with the 1.2‐unit difference between the Cys282 pKa value of wild‐type and the S284A mutant of creatine kinase. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Measurements of protein sequence–structure correlations
Authors: Crooks Gavin E. , Wolfe Jason , Brenner Steven E. 
Published: October 2004

AbstractCorrelations between protein structures and amino acid sequences are widely used for protein structure prediction. For example, secondary structure predictors generally use correlations between a secondary structure sequence and corresponding primary structure sequence, whereas threading algorithms and similar tertiary structure predictors typically incorporate interresidue contact potentials. To investigate the relative importance of these sequence–structureinteractions,we measured the mutual information among the primary structure, secondary structure and side‐chain surface exposure, both for adjacent residues along the amino acid sequence and for tertiary structure contacts between residues distantly separated along the backbone. We found that local interactions along the amino acid chain are far more important than non‐local contacts and that correlations between proximate amino acids are essentially uninformative. This suggests that knowledge‐based contact potentials may be less important for structure predication than is generally believed. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Scoring function for automated assessment of protein structure template quality
Authors: Zhang Yang , Skolnick Jeffrey 
Published: October 2004

AbstractWe have developed a new scoring function, the template modeling score (TM‐score), to assess the quality of protein structure templates and predicted full‐length models by extending the approaches used in Global Distance Test (GDT)1 and MaxSub.2 First, a protein size‐dependent scale is exploited to eliminate the inherent protein size dependence of the previous scores and appropriately account for random protein structure pairs. Second, rather than setting specific distance cutoffs and calculating only the fractions with errors below the cutoff, all residue pairs in alignment/modeling are evaluated in the proposed score. For comparison of various scoring functions, we have constructed a large‐scale benchmark set of structure templates for 1489 small to medium size proteins using the threading program PROSPECTOR_3 and built the full‐length models using MODELLER and TASSER. The TM‐score of the initial threading alignments, compared to the GDT and MaxSub scoring functions, shows a much stronger correlation to the quality of the final full‐length models. The TM‐score is further exploited as an assessment of all ‘new fold’ targets in the recent CASP5 experiment and shows a close coincidence with the results of human‐expert visual assessment. These data suggest that the TM‐score is a useful complement to the fully automated assessment of protein structure predictions. The executable program of TM‐score is freely downloadable at http://bioinformatics.buffalo.edu/TM‐score. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Enzyme classification by ligand binding
Authors: Izrailev Sergei , Farnum Michael A. 
Published: October 2004

AbstractThe problem of assigning a biochemical function to newly discovered proteins has been traditionally approached by expert enzymological analysis, sequence analysis, and structural modeling. In recent years, the appearance of databases containing protein–ligand interaction data for large numbers of protein classes and chemical compounds have provided new ways of investigating proteins for which the biochemical function is not completely understood. In this work, we introduce a method that utilizes ligand‐binding data for functional classification of enzymes. The method makes use of the existing Enzyme Commission (EC) classification scheme and the data on interactions of small molecules with enzymes from the BRENDA database. A set of ligands that binds to an enzyme with unknown biochemical function serves as a query to search a protein–ligand interaction database for enzyme classes that are known to interact with a similar set of ligands. These classes provide hypotheses of the query enzyme's function and complement other computational annotations that take advantage of sequence and structural information. Similarity between sets of ligands is computed using point set similarity measures based upon similarity between individual compounds. We present the statistics of classification of the enzymes in the database by a cross‐validation procedure and illustrate the application of the method on several examples. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Sequence patterns associated with disordered regions in proteins
Authors: Lise S. , Jones D. T. 
Published: October 2004

AbstractThe relationship between amino acid sequence and intrinsic disorder in proteins is investigated. Two databases, one of disordered proteins and the other of globular proteins, are analyzed and compared in order to extract simple sequence patterns of a few amino acids or amino acid properties that characterize disordered segments. It is found that a number of reliable, nonrandom associations exists. In particular, two types of patterns appear to be recurrent: a proline‐rich pattern and a (positively or negatively) charged pattern. These results indicate that local sequence information can determine disordered regions in proteins. The derived patterns provide some insights into the physical reasons for disordered structures. They should also be helpful in improving currently available prediction methods. Proteins 2005. © 2004 Wiley‐Liss, Inc.
Biochemical evidence that an S431F mutation in acetylcholinesterase‐1 of Aphis gossypii mediates resistance to pirimicarb and omethoate
Authors: Benting Jürgen , Nauen Ralf 
Published: October 2004

AbstractMolecular changes in acetylcholinesterase (AChE) leading to target‐site resistance to carbamate and organophosphate insecticides have recently been identified. Of particular interest is the S431F mutation in ace2 and its orthologue ace1 of Myzus persicae Sulzer and Aphis gossypii Glover, respectively. This mutation has been correlated with resistance to pirimicarb, but biochemical evidence has not yet been provided. Here, we describe for the first time that recombinantly expressed AChE1 from A gossypii carrying the S431F mutation is insensitive to pirimicarb and omethoate, but sensitive to demeton‐S‐methyl and hypersensitive to carbofuran. Furthermore, site‐directed mutagenesis of the serine residue at position 431 in ace1 from a pirimicarb‐susceptible clone of A gossypii conferred insensitivity to pirimicarb. We conclude that AChE1 of A gossypii is the target of toxicological relevance of carbamates and organophosphates. Copyright © 2004 Society of Chemical Industry
A covalent model of the optical spectra and EPR parameters for CdS:Ti2+
Authors: Chen Jia‐Jun , Du Mao‐Lu 
Published: October 2004

AbstractIn this paper, formulas for the optical spectrum and the EPR parameters calculated for d2 ions in Td symmetry are established by using a covalent model, in which the covalence contribution has been considered. Using the model, we have calculated the optical spectra and the ground‐state gyromagnetic factor and zero‐field splitting of CdS:Ti2+. The calculated results could explain well the experimental findings. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Neuroprotective effect of Ginkgo biloba L. extract in a rat model of Parkinson's disease
Authors: Kim M.‐S. , Lee J.‐I. , Lee W.‐Y. , Kim S.‐E. 
Published: October 2004

AbstractThe neuroprotective effects of a standardized extract of Ginkgo biloba L. (EGb 761) were investigated on 6‐hydroxydopamine (6‐OHDA)‐induced neurotoxicity in the nigrostriatal dopaminergic system of the rat brain. Rats were given a week of pretreatment with daily administrations of EGb 761. Unilateral striatal injection of 6‐OHDA was followed by treatment with EGb 761 for a week. Serial measurement of contralateral forepaw adjusting steps revealed a progressive deﬁcit in motor activity. At 8 weeks after 6‐OHDA lesion the number of contralateral forepaw adjusting steps was signiﬁcantly higher in rats that were treated with high doses of EGb 761 (100 mg/kg daily) than in those treated with low doses (50 mg/kg) or with the vehicle. Dopamine neuron loss in the substantia nigra and a depletion in striatal dopamine corresponded with behavioural deﬁcit. These data suggest that the neuroprotective effects of EGb 761 reduce the behavioural deﬁcit in 6‐OHDA lesions in rat and also indicates a possible role for the extract in the treatment of Parkinson's disease. Copyright © 2004 John Wiley & Sons, Ltd.
Two ellagitannins from the leaves of Terminalia triﬂora with inhibitory activity on HIV‐1 reverse transcriptase
Authors: Martino V. , Morales J. , Martínez‐Irujo J. J. , Font M. , Monge A. , Coussio J. 
Published: October 2004

AbstractThe bioassay‐ guided fractionation of the aqueous extract of Terminalia triﬂora leaves afforded punicalin and 2‐O‐galloylpunicalin, isolated for the ﬁrst time from this species. These compounds showed inhibitory activity on HIV‐1 reverse transcriptase in a dose dependant manner. Punicalin showed an IC50 of 0.11 µg/ml (0.14 µM) and 2‐O‐galloylpunicalin an IC50 of 0.10 µg/ml (0.11 µM). Copyright © 2004 John Wiley & Sons, Ltd.
The rediscovery of ancient Chinese herbal formulas
Authors: Jia Wei , Gao Wen‐yuan , Yan Yong‐qing , Wang Jie , Xu Zhao‐hui , Zheng Wen‐jie , Xiao Pei‐gen 
Published: October 2004

AbstractThis review presents some recent discoveries of ancient Chinese herbal formulas evolved through thousands of years of clinical practice. It appears that many of the ancient combination formulas have sound scientiﬁc basis through modern pharmacological evaluation. Signiﬁcant chemical changes occurred during the preparation (decoction) process of a prescribed herbal formula. For example, some toxic ingredients were signiﬁcantly reduced and new active compounds generated due to the chemical interactions among the ingredients. Many combination formulas showed signiﬁcantly better pharmacological results than individual herbal medicines participated in the formula. These ﬁndings suggest that the current drug screening and regulatory methodology will not be appropriate for the development of a botanical drug containing a group of phytochemicals, in which a synergistic interaction from chemical ingredients plays a fundamental role in the treatment of disease. If we view a diseased state in a holistic and dynamic way, i.e. it involves interactions among many biological systems in human body and these interactions change as the disease improves or worsens, the treatment of such disease with a single chemical entity may not be logical or technically feasible. Combination formulas may hold the potential to become the therapeutics of choice in the future due to the synergistic effect and dynamic adjustment achieved by the multiple ingredients that will restore the balance of an imbalanced or diseased human body. Copyright © 2004 John Wiley & Sons, Ltd.
Identiﬁcation of the antibacterial component of an ethanolic extract of the Australian medicinal plant, Eremophila duttonii
Authors: Shah Arvind , Cross Reg F. , Palombo Enzo A. 
Published: October 2004

AbstractActivity‐guided fractionation was used to determine the antibacterial component of an ethanolic extract of the leaves of an Australian native medicinal plant, Eremophila duttonii F. Muell. (Myoporaceae). The extract, previously shown to have activity against Gram positive bacteria, was shown to have activity against additional Gram positive bacteria, including Clostridium perfringens, C. sporogenes and Listeria monocytogenes. Thin layer chromatography (TLC) was used to separate the extract into seven coloured fractions in visible light, one of which was shown by bioautography to contain antibacterial activity. Recovery of the component from the TLC plate and testing for antibacterial activity using a plate‐hole diffusion assay supported this result. The purity of the component was veriﬁed by high‐performance liquid chromatography and a time‐kill experiment indicated that the puriﬁed component showed identical bactericidal activity to the whole extract. TLC spray reagents indicated that the component was a sterol, terpene or sugar but not a ﬂavonoid, while the pigmented nature suggested a carotenoid. Copyright © 2004 John Wiley & Sons, Ltd.
Polyherbal extract of septilin protects mice against whole body lethal dose of gamma radiation
Authors: Jagetia Ganesh Chandra , Baliga Manjeshwar Shrinath 
Published: October 2004

AbstractThe effect of various doses (5, 10, 20, 40, 60, 80, 100, 120, 140 and 160 mg/kg b. wt.) of 50% ethanolic extract of Septilin (a herbal preparation) was studied on the radiation‐induced mortality in mice exposed to 10 Gy of γ‐irradiation. Treatment of mice with different doses of Septilin, consecutively for 5 days before irradiation, delayed the onset of mortality and reduced the symptoms of radiation sickness when compared with the non‐drug treated irradiated controls. All doses of Septilin provided protection against gastrointestinal (GI) deaths (death within 10 days of irradiation). However, the best protection was observed at 100 mg/kg b. wt. of Septilin, as the number of survivors after 30 days post‐irradiation was highest (58.33%) in this group when compared with the other doses of Septilin. The number of survivors was 1.75 fold greater for 100 mg/kg Septilin when compared with the 2‐mercaptopropionylglycine (MPG, 33.33%) which was used as a positive control. The LD50 of Septilin was 1250 mg/kg as against the optimum protective dose of 100 mg/kg. Our study demonstrates Septilin as a good radioprotective agent. Copyright © 2004 John Wiley & Sons, Ltd.
Antimalarial activity of Bidens pilosa L. (Asteraceae) ethanol extracts from wild plants collected in various localities or plants cultivated in humus soil
Authors: Andrade‐Neto Valter F. , Brandão Maria G. L. , Oliveira Francielda Q. , Casali Vicente W. D. , Njaine Brian , Zalis Mariano G. , Oliveira Luciana A. , Krettli Antoniana U. 
Published: October 2004

AbstractBidens pilosa (Asteraceae), a medicinal plant used worldwide, has antimalarial activity as shown in previous work. This study tested ethanol extracts from wild plants collected in three different regions of Brazil and from plants cultivated in various soil conditions. The extracts were active in mice infected with P. berghei: doses of ≤500 mg/kg administered by oral route reduced malaria parasitaemia and mouse mortality; higher doses were found to be less effective. Tested in vitro against three P. falciparum isolates, two chloroquine resistant and one meﬂoquine resistant, the plants cultivated under standard conditions, and in humus enriched soil, were active; but the wild plants were the most active. Analysis using thin layer chromatography demonstrated the presence of ﬂavonoids (compounds considered responsible for the antimalarial activity) in all plants tested, even though at different proﬁles. Because B. pilosa is proven to be active against P. falciparum drug‐resistant parasites in vitro, and in rodent malaria in vivo, it is a good candidate for pre‐clinical tests as a phytotherapeutic agent or for chemical isolation of the active compounds with the aim of ﬁnding new antimalarial drugs. Copyright © 2004 John Wiley & Sons, Ltd.
Oxygen activation by photoexcited protoberberinium alkaloids from Mahonia aquifolium
Authors: Brezová Vlasta , Dvoranová Dana , Košt'álová Daniela 
Published: October 2004

AbstractProtoberberinium salts, i.e. berberine (I), palmatine (II) and jatrorrhizine (III) prepared from Mahonia aquifolium (Pursh) Nutt. belong to isoquinoline alkaloids possessing interesting biological activity (e.g. antibacterial, antimalarial, antitumor). The characteristic UV/Vis absorption band maxima of I–III iodide salts were found in regions 350 and 425 nm in dimethylsulfoxide (DMSO) and ethanol solvents, and were only negligibly inﬂuenced by substitution changes on the C‐2 and C‐3 positions. The ﬂuorescence intensity of protoberberinium salts monitored in ethanol solutions was signiﬁcantly lowered by iodide counter‐ions, and decreased in the order berberine > palmatine > jatrorrhizine. EPR spectroscopy supplied evidence of the formation of super‐oxide anion radicals and singlet oxygen upon irradiation of berberine in oxygenated DMSO solvent. The photochemical generation of O2·− and 1O2 in DMSO solutions of palmatine and jatrorrhizine was substantially lower, and probably reﬂected the replacement of a photolabile methylenedioxy group at C‐2 and C‐3 positions in the berberine molecule by two methoxy groups in palmatine, and methoxyl (C‐2) and hydroxyl (C‐3) substitution in jatrorrhizine. Additionally, the powder EPR spectra of protoberberinium iodides I–III measured at 290 K revealed the presence of single‐line EPR signals (geff = 2.0044), which were attributed to hydroperoxidic structures produced by the autoxidation process. The photochemical reactions of protoberbenium salts producing reactive oxygen species after UVA excitation should be integrated in biological activity investigations, as well as in their applications in skin disorder treatment. Copyright © 2004 John Wiley & Sons, Ltd.
Antimicrobial activity of Mahonia aquifolium crude extract and its major isolated alkaloids
Authors: Slobodníková Lívia , KoSt'álová Daniela , Labudová Darina , Kotulová Daniela , Kettmann Viktor 
Published: October 2004

AbstractThe crude extract of Mahonia aquifolium (Pursh) Nutt. stem bark and its two main protoberberine alkaloids, berberine and jatrorrhizine, were tested for their in vitro antimicrobial activity. Twenty strains of coagulase‐negative staphylococci and 20 strains of Propionibacterium acnes isolated from skin lesions of patients with a severe form of acne, and 20 strains of Candida sp. isolated from chronic vulvovaginal candidoses were tested for their susceptibility to crude extract and two isolated alkaloids. The minimum inhibitory concentrations obtained in this study illustrate the varying degrees of antibacterial and antifungal activity of the tested agents. The results indicate a rational basis for the traditional use of Mahonia aquifolium for localized skin and mucosal infection therapy, as well as for the possible development of a preparation for supportive therapy of the diseases mentioned above. Copyright © 2004 John Wiley & Sons, Ltd.
In vitro anti‐β‐secretase and dual anti‐cholinesterase activities of Camellia sinensis L. (tea) relevant to treatment of dementia
Authors: Okello Edward J. , Savelev Sergey U. , Perry Elaine K. 
Published: October 2004

AbstractThe primary target of licensed drugs for the treatment of Alzheimer's disease is the inhibition of the enzyme acetylcholinesterase, although preventing β‐amyloidosis is a prime target for drugs in development. The in vitro dual anti‐cholinesterase and β‐secretase activities of Camellia sinensis L. extract (tea) is reported. Green and black tea inhibited human acetylcholinesterase (AChE) with IC50 values of 0.03 mg/mL and 0.06 mg/mL respectively, and human butyrylcholinesterase (BuChE) with IC50 values 0.05 mg/mL. Green tea at a ﬁnal assay concentration of 0.03 mg/mL inhibited β‐secretase by 38%. These novel ﬁndings suggest that tea infusions contain biologically active principles, perhaps acting synergistically, that may be used to retard the progression of the disease assuming that these principles, yet to be identiﬁed, reach the brain. Copyright © 2004 John Wiley & Sons, Ltd.