bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alpha sphere filter method: Application of pseudomolecular descriptors in virtual screening of 2D chemical structures
Authors: Muta Hajime , Hirayama Noriaki 
Published: March 2010

AbstractAlpha sphere filter (ASF) method is a novel previrtual screening method to undertake a rapid virtual screening of a huge chemical space. The small‐molecule binding site of a target molecule can be characterized by a set of alpha spheres generated at the site. Two types of pseudomolecules representing molecules that likely fit into the binding site were molded from the set of alpha spheres. Based on the pseudomolecules, pseudomolecular descriptors corresponding to the conventional two‐dimensional (2D) molecular descriptors were calculated. The correlations between the pseudomolecular descriptors and the 2D molecular descriptors were analyzed for a set of high‐quality X‐ray structures of the complexes between ligands and proteins. By use of these correlations, specific value ranges of the 2D molecular descriptors were determined. These value ranges were applied in virtual screening. In a trial to screen 200 active ligands out of a chemical database with 42,547 molecules, the enrichment rate of 5.8 was attained. The enrichment rate was good enough for a prescreening tool prior to docking simulations. As the ASF method screens molecules by 2D molecular descriptors, it is rapid enough to screen a huge chemical space and could significantly decrease the number of trivial compounds to be considered in the following docking simulations. Therefore, the ASF method can contribute to enlarge the possibility of virtual screening. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
A toolkit to assist ONIOM calculations
Authors: Tao Peng , Schlegel H. Bernhard 
Published: March 2010

AbstractA general procedure for quantum mechanics and molecular mechanics (QM/MM) studies on biochemical systems is outlined, and a collection of PERL scripts to facilitate ONIOM‐type QM/MM calculations is described. This toolkit is designed to assist in the different stages of an ONIOM QM/MM study of biomolecules, including input file preparation and checking, job monitoring, production calculations, and results analysis. An iterative procedure for refitting the partial charges of QM region atoms is described and yields a more accurate treatment of the electrostatic interaction between QM and MM regions during QM/MM calculations. The toolkit fully supports this partial charge‐refitting procedure. By using this toolkit for file conversions, structure manipulation, input sanity checks, parameter lookup, charge refitting, tracking optimizations, and analyzing results, QM/MM studies of large size biochemical systems can be much more convenient and practical. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
Parental relationships among three grape varieties studied by MALDI of grape seed protein profiles
Authors: Bertazzo Antonella , Rosso Mirko De , Vedova Antonio Dalla , Agnolin Fabio , Flamini Riccardo , Traldi Pietro 
Published: March 2010

AbstractTwo Raboso cultivars, i.e. Raboso Veronese and Raboso Piave, are two black Vitis vinifera varieties. A genetic study suggested that Raboso Veronese is the progeny of a spontaneous cross between Raboso Piave and Marzemina Bianca cultivars. Parental relationships are usually investigated by genetic studies, which are effective to establish genetic links among different cultivars. Considering that proteome is the genome expression, in this article we evaluated the power of seed protein profiles obtained by matrix‐assisted laser desorption/ionization (MALDI)/MS for parentage investigation. The three cultivars lead to very similar spectra with differences in the relative intensity of the most abundant species and the presence of very weak specific ions. In order to evaluate the analytical significance of these aspects, the variability due to instrumental factors and due to different harvesting areas and years of the same cultivars have been considered and measured by the calculation of discrepancy factor values. On one hand, the results obtained can be considered a valid confirmation of the genomic findings, whereas on the other hand, the results provide evidence for the ability of MALDI/MS to individuate minor differences in protein profiles of complex protein mixtures. Copyright © 2010 John Wiley & Sons, Ltd.
Hepatitis C virus core protein compromises iron‐induced activation of antioxidants in mice and HepG2 cells
Authors: Moriya Kyoji , Miyoshi Hideyuki , Shinzawa Seiko , Tsutsumi Takeya , Fujie Hajime , Goto Koji , Shintani Yoshizumi , Yotsuyanagi Hiroshi , Koike Kazuhiko 
Published: March 2010

AbstractOne of the characteristics of hepatitis C virus (HCV) infection is the unusual augmentation of oxidative stress, which is exacerbated by iron accumulation in the liver, as observed frequently in hepatitis C patients. Using a transgenic mouse model, the core protein of HCV was shown previously to induce the overproduction of reactive oxygen species (ROS) in the liver. In the present study, the impact of iron overloading on the oxidant/antioxidant system was examined using this mouse model and cultured cells. Iron overloading caused the induction of ROS as well as antioxidants. However, the augmentation of some antioxidants, including heme oxygenase‐1 and NADH dehydrogenase, quinone 1, was compromised by the presence of the core protein. The attenuation of iron‐induced augmentation of heme oxygenase‐1 was also confirmed in HepG2 cells expressing the core protein. This attenuation was not dependent on the Nrf2 transcription factor. Thus, HCV infection not only induces oxidative stress but also hampers the iron‐induced antioxidant activation in the liver, thereby exacerbating oxidative stress that would facilitate hepatocarcinogenesis. J. Med. Virol. 82: 776–782, 2010. © 2010 Wiley‐Liss, Inc.
Development and implementation of influenza a virus subtyping and detection of genotypic resistance to neuraminidase inhibitors
Authors: Ruiz‐Carrascoso Guillermo , Casas Inmaculada , Pozo Francisco , Pérez‐González Carmen , Reina Jordi , Pérez‐Breña Pilar 
Published: March 2010

AbstractInfluenza virus hemagglutinin and neuraminidase, surface glycoproteins with an essential role in viral pathogenesis, are important antigen determinants and essential markers for epidemiological surveillance. Neuraminidase is also a suitable target for designing antiviral drugs. The introduction into clinical practice of neuraminidase inhibitors and the development of random point mutations have increased the emergence of drug‐resistant viruses. A universal RT nested PCR‐based system has been developed for subtyping H1, H3, N1 and N2, in influenza A viruses of human or animal origin. The subsequent sequencing and analysis of the hemagglutinin and neuraminidase templates reveal antigenic and receptor binding changes in the HA1 subunit and mutations of clinical relevance concerning resistance to neuraminidase inhibitors. The specificity and sensitivity of the method were evaluated using 113 influenza A isolates, 105 influenza A positive respiratory samples obtained from patients and 29 prototype strains of both human and animal origin. The resulting analytical sensitivity of the subtyping techniques is one to at least 100 molecules of cloned DNA product in a final reaction volume of 50 µl. In the course of implementing the method, two H1N1 isolates with the H274Y mutation in the neuraminidase segment have been detected and their molecular features analyzed. The emergence of influenza virus resistance makes the neuraminidase genetic characterization and surveillance activities to detect antiviral resistance necessary. J. Med. Virol. 82: 843–853, 2010. © 2010 Wiley‐Liss, Inc.
New variations of Epstein–Barr virus‐encoded small RNA genes in nasopharyngeal carcinomas, gastric carcinomas, and healthy donors in northern China
Authors: Wang Yun , Zhang Xia , Chao Yan , Jia Yuping , Xing Xiaoming , Luo Bing 
Published: March 2010

AbstractIt has been generally believed that the Epstein–Barr virus (EBV)‐encoded small RNA 1 and 2 (EBER1 and EBER2) genes are conserved as two families that correlated with type 1 (B95‐8) and type 2 (AG876 or P3HR‐1) EBV strains. EBER polymorphism and its association with EBV‐associated disease have not received much attention. To explore the variations of EBER genes in different malignancies and healthy donors, the sequences of EBER genes were analyzed in 154 EBV‐positive samples, including 47 nasopharyngeal carcinoma (NPC), 50 EBV‐associated gastric carcinoma (EBVaGC) biopsies and 57 throat washing (TW) samples from healthy donors in northern China, where NPC is non‐endemic. Three main distinct variants of EBER genes, designated as EB‐6m, EB‐8m, and EB‐10m, were identified. EB‐6m had a previously identified EBER sequence identical to P3HR‐1 and was found in 33/47 (70.2%) NPC, 48/50 (96.0%) EBVaGC, and 54/57 (94.7%) TW isolates. EB‐8m and EB‐10m were new EBER variants with more mutations in EBER2 genes. They were found in 13/47 (27.7%) NPC cases, whereas in only 1/50 (2.0%) EBVaGC cases and not found in TW cases. The distributions were significantly different (P < 0.05). Other five isolates (one NPC, one EBVaGC and three TW cases) showed different sequences and could not be assigned to any of the three groups. Type 1 EBV strains showed heterogeneous in terms of EBER variants. These results suggest that EBER locus can be useful to identify different EBV isolates, and it would be interesting to evaluate the association of EBER polymorphisms with EBV‐associated tumors. J. Med. Virol. 82: 829–836, 2010. © 2010 Wiley‐Liss, Inc.
Geographical differences in the proportion of human group A rotavirus strains within New Zealand during one epidemic season
Authors: Chandrahasen Clarissa , Grimwood Keith , Redshaw Natalie , Rich Fenella J. , Wood Catherine , Stanley James , Kirman Joanna R. ,   on behalf of the New Zealand Rotavirus Study Group
Published: March 2010

AbstractThe prospect of future rotavirus vaccine programs means it is important to understand rotavirus strain diversity within New Zealand, especially if this was to influence vaccine effectiveness. The G‐genotype of 359 group A rotavirus strains isolated from 416 stool samples collected from June 2005 to May 2006 (inclusive) from children less than 5 years of age in multiple centers throughout New Zealand was determined. G1 was the dominant circulating strain (55.8%) followed by G4 (21.4%), G3 (3.4%), G9 (3.4%) G2 (1.0%), and mixed infection (1.0%). Two less common strains, G6 and G8, were identified for the first time in New Zealand. P genotypes were determined for a random 10% of samples containing the common G‐type strains, and all samples with an unusual G‐type. All samples able to be tested contained P[8] bearing strains, except for G1P[4], G2P[4], and G8P[14] strains. Importantly, significant differences in strain frequency were found between samples collected from the North and South Islands of New Zealand. G1 was the most commonly identified strain in the North Island (81.9%); whereas G4 predominated in the South Island (39.6%). Of note, no significant differences in the relative frequency of rotavirus strains were observed between samples collected from children treated in hospital compared to samples collected from children seen by their primary healthcare provider in the community. Regional strain variation highlights the importance of ensuring multi‐center surveillance to help monitor program effectiveness when rotavirus vaccines are introduced into New Zealand's national childhood immunization schedule. J. Med. Virol. 82: 897–902, 2010. © 2010 Wiley‐Liss, Inc.
Omega‐3 fatty acids reverse age‐related decreases in nuclear receptors and increase neurogenesis in old rats
Authors: Dyall Simon C. , Michael Gregory J. , Michael‐Titus Adina T. 
Published: March 2010

AbstractRetinoic acid receptors (RARs), retinoid X receptors (RXRs), and peroxisome proliferator‐activated receptors (PPARs) are transcription factors involved in many cellular processes, such as learning and memory. RAR and RXR mRNA levels decrease with ageing, and the decreases can be reversed by retinoic acid treatment, which also alleviates age‐related memory deficits. The omega‐3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) have neuroprotective effects in the aged brain and are endogenous ligands of RXR and PPAR. We investigated whether dietary EPA and DHA supplementation reverses age‐related declines in protein levels of these receptors in rat forebrain. Two studies were conducted comparing adult and old rats. In the first, old rats were fed standard or EPA/DHA‐enriched (270 mg/kg/day, EPA to DHA ratio 1.5:1) diets for 12 weeks. Analysis by Western blot revealed significant decreases in RARα, RXRα, RXRβ, and PPARγ in the forebrain with ageing, which were reversed by supplementation. Immunohistochemical analysis of the hippocampus showed significant age‐related decreases in RARα and RXRβ expression in CA1 and the dentate gyrus, which were restored by supplementation. Decreases in hippocampal doublecortin expression were also partially alleviated, suggesting a positive effect on neurogenesis. We also investigated the effects of DHA supplementation (300 mg/kg/day for 12 weeks) on RARα, RXRα, and RXRβ expression in the prefrontal cortex, striatum, and hippocampus. Overall, DHA supplementation appeared to increase receptor expression compared with the untreated old group. These observations illustrate additional mechanisms that might underlie the neuroprotective effects of omega‐3 fatty acids in ageing. © 2010 Wiley‐Liss, Inc.
Diverse roles of extracellular calcium‐sensing receptor in the central nervous system
Authors: Bandyopadhyay Sanghamitra , Tfelt‐Hansen Jacob , Chattopadhyay Naibedya 
Published: March 2010

AbstractThe G‐protein‐coupled calcium‐sensing receptor (CaSR), upon activation by Ca2+ or other physiologically relevant polycationic molecules, performs diverse functions in the brain. The CaSR is widely expressed in the central nervous system (CNS) and is characterized by a robust increase in its expression during postnatal brain development over adult levels throughout the CNS. Developmental increases in CaSR levels in brain correlate with myelinogenesis. Indeed, neural stem cells differentiating to the oligodendrocyte lineage exhibit the highest CaSR expression compared with those differentiating to astrocytic or neuronal lineages. In adult CNS, CaSR has broad relevance in maintaining local ionic homeostasis. CaSR shares an evolutionary relationship with the metabotropic glutamate receptor and forms heteromeric complexes with the type B‐aminobutyric acid receptor subunits that affects its cell surface expression, activation, signaling, and functions. In normal physiology as well as in pathologic conditions, CaSR is activated by signals arising from mineral ions, amino acids, polyamines, glutathione, and amyloid‐β in conjunction with Ca2+ and other divalent cationic ligands. CaSR activation regulates membrane excitability of neurons and glia and affects myelination, olfactory and gustatory signal integration, axonal and dendritic growth, and gonadotrophin‐releasing hormonal‐neuronal migration. Insofar as the CaSR is a clinically important therapeutic target for parathyroid disorders, development of its agonists or antagonists as therapeutics for CNS disorder could be a major breakthrough. © 2010 Wiley‐Liss, Inc.
A wavelet approach to the short‐term to pluri‐decennal variability of streamflow in the Mississippi river basin from 1934 to 1998
Authors: Massei N. , Laignel B. , Rosero E. , Motelay‐massei A. , Deloffre J. , Yang Z.‐L. , Rossi A. 
Published: March 2010

AbstractThe temporal variability of streamflow in the Mississippi river basin, including its major tributaries (Missouri, Upper Mississippi, Ohio and Arkansas rivers), was analysed using continuous wavelet methods in order to detect possible changes over the past 60 years. Long‐ to short‐term fluctuations were investigated. The results were compared with SOI, PDO and NAO indices and precipitation time series and were also processed by wavelet methods. A major change point around 1970, also reported in other works, was recovered in all climate and hydrological processes. It is characterised by the occurrence of an 8–16‐year mode for Upper Mississippi and Missouri and of a 3–6‐year mode for all rivers. Two other discontinuities around the mid‐1950s and 1985 were also detected. A strong power attenuation of the annual cycle in the Arkansas, Upper Mississippi and Missouri rivers was also found between 1955 and 1975. In general, the dominant modes of inter‐annual to pluri‐annual streamflow variability lay in the 2–4‐year, 4–8‐year and 10–16‐year ranges, which was typical of SOI for the period of study. A preferential link with the Mississippi basin headwater zone (i.e. Upper Mississippi and Missouri) was deduced during the ≈ 1934–1950 and ≈ 1970–1985 periods.Overall, the contribution of inter‐annual to pluri‐annual oscillations ranged from 6.6 to 26% of streamflow variance, while the short‐term scales (<2–3 weeks) explained from 1.1 to 6.4%. The annual cyclicity explained from 19.1 to 48.6% of streamflow variance. High‐frequency streamflow fluctuations linked to synoptic activity were also found to increase after 1955 for all basins except Upper and Lower Mississippi, apparently modulated by a ≈ 2–4‐yr oscillation. Copyright © 2010 Royal Meteorological Society
Screening and assessment of crime victimization and its effects
Authors: Hanson Rochelle F. , Self‐Brown Shannon 
Published: March 2010

AbstractThe authors provide a review of tools used to screen and assess history and mental health consequences of adult crime victimization. These measures can be utilized across a broad range of settings that may serve crime victims, including venues for first response (e.g., law enforcement offices or emergency departments), primary medical care, or mental health treatment facilities, regardless of whether or not the crime was reported. The authors conclude with a discussion on limitations in the field and directions for future research.
Preparation of Biodegradable Liquid Core PLLA Microcapsules and Hollow PLLA Microcapsules Using Microfluidics
Authors: Lensen Dennis , van Breukelen Kevin , Vriezema Dennis M. , van Hest Jan C. M. 
Published: March 2010

AbstractBiodegradable PLLA capsules with a narrow size distribution were prepared using a microfluidics platform. With this technique, an oil‐in‐water emulsion was produced in which the polymer, a hydrophobic non‐volatile non‐solvent and a hydrophobic model drug were dissolved in the organic phase. The polymer precipitated at the droplet interface, yielding a drug deliverable microcapsule of which the release of this model drug was investigated. These capsules with an organic phase in the core were also used to prepare hollow particles by conveniently removing the core phase by lyophilization. Optimal conditions for the preparation of biodegradable capsules were found with respect to the flow rate of the continuous phase and the molecular weight of the PLLA polymer. This approach of preparing biodegradable capsules is of potential interest for the field of drug delivery.
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Ring‐Opening Polymerization of Propylene Oxide Catalyzed by a Calcium‐Chloride‐Modified Zinc‐Cobalt Double Metal‐Cyanide Complex
Authors: Huang Yi‐Jun , Zhang Xing‐Hong , Hua Zheng‐Jiang , Chen Shi‐Liang , Qi Guo‐Rong 
Published: March 2010

AbstractHighly active CaCl2‐modified Zn‐Co(III) DMCs were prepared. XRD results showed that the modified catalyst Ca‐DMC containing 0.14 wt.‐% CaCl2 was amorphous. A higher polymer yield (>61 kg polymer/g catalyst) and a shorter induction period for ROP of PO were observed for Ca‐DMC than for unmodified DMC catalysts. An initiator had an inhibitory effect on the initiation and polymerization rate of PO ROP. As the molar ratio of the initiator functionality to the catalyst was increased, the reaction rate and polymer yield decreased, whereas the induction period increased. An increase in reaction temperature tended to reduce the polymer yield and broaden the MWD. The 13C NMR spectrum for an oligomer from a model polymerization without an initiator revealed that the main terminal unit of the polymer was CH2CH(CH3)OH because H2O in the system participated in reaction initiation. Cl− and t‐BuOH may also initiate the reaction according to the small amounts of terminal CH2Cl and OC(CH3)3 units observed by 13C NMR spectroscopy. On the basis of common characteristics and some new evidence for DMC catalysis, a mechanism similar to a classical coordination insertion process is proposed.magnified image
RAFT Polymerization Meets Coordination Chemistry: Synthesis of a Polymer‐Based Iridium(III) Emitter
Authors: Ulbricht Christoph , Becer Caglar Remzi , Winter Andreas , Schubert Ulrich S. 
Published: March 2010

AbstractA synthetic approach toward the synthesis of well‐defined copolymers with attached phosphorescent iridium(III) emitters is presented. A reactive µ‐hydroxy‐bridged precursor complex has been utilized to coordinate suitable ligand sites of a methacrylate‐based copolymer. The starting copolymer has been synthesized via the reversible addition fragmentation chain transfer (RAFT) polymerization technique. Using a reactive complex species, the coordination reaction at the copolymer could be performed under very mild conditions in the absence of any supporting additives.magnified image
Preparation of Stable Miniemulsions of Poly(2‐ethyl hexyl acrylate‐co‐vinyl acetate)
Authors: Fonseca Gabriela E. , McKenna Timothy F.L. , Dubé Marc A. 
Published: March 2010

AbstractSummary: This paper presents the results of the preparation of miniemulsions as well as the subsequent copolymerizations of 2‐ethyl hexyl acrylate and vinyl acetate. The miniemulsions were prepared using a mixture of an anionic and a non‐ionic surfactant. Sodium dodecyl sulfate (SDS) was used as the anionic surfactant and two non‐ionic surfactants were studied: Triton X‐405 and Disponil A3065. The miniemulsions prepared with a 90/10 mol.‐% Disponil A3065 were able to reach a kinetically‐stable state to yield latexes with 43 wt.‐% solids content with a maximum change in the number of particles (Np) with respect to the number of droplets (Nd) of ∼6%. A 23 factorial design was then used to discern the influence of monomer, chain transfer agent and surfactant concentration on the droplet size distribution (DSD) and particle size distribution (PSD). Pressure‐sensitive adhesive (PSA) properties were also examined.
Ionic Conductivity in Solutions of Poly(ethylene oxide) and Lithium Perchlorate
Authors: Nasir Noor Hidaya Abdul , Chan Chin Han , Kammer Hans‐Werner , Sim Lai Har , Yahya Muhd Zu Azahan 
Published: March 2010

AbstractSummary: Solution casting technique served to prepare solid solutions of lithium perchlorate and poly(ethylene oxide) (PEO) having different molecular masses. Salt concentrations of solutions were varied between around 2 and 13 wt%. Crystallinity and melting point depression served to determine composition and content of amorphous phase as well as thermodynamic behavior of the solutions. Conductivity as a function of salt concentration in the amorphous phase follows a power law at constant temperature (30 °C). It results that both exponent and mobility of charge carriers increase with ascending molecular mass of PEO. The mobility follows an increase with molecular mass proportional to M2.8 indicating dependence of mobility on interstitial volume between chain molecules. Deviation of solution from perfect behavior can be evaluated by melting point depression. Accordingly, increase in conductivity is preferably related to approach to perfect solution behavior. Determination of dielectric function allows some conclusion about ion pair formation in the systems under discussion. It turns out that probability of ion pair formation decreases with increasing molecular mass of PEO in agreement with thermodynamic behavior of the solutions.