bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein domain assignment from the recurrence of locally similar structures
Authors: Tai Chin‐Hsien , Sam Vichetra , Gibrat Jean‐Francois , Garnier Jean , Munson Peter J. , Lee Byungkook 
Published: October 2010

AbstractDomains are basic units of protein structure and essential for exploring protein fold space and structure evolution. With the structural genomics initiative, the number of protein structures in the Protein Databank (PDB) is increasing dramatically and domain assignments need to be done automatically. Most existing structural domain assignment programs define domains using the compactness of the domains and/or the number and strength of intra‐domain versus inter‐domain contacts. Here we present a different approach based on the recurrence of locally similar structural pieces (LSSPs) found by one‐against‐all structure comparisons with a dataset of 6373 protein chains from the PDB. Residues of the query protein are clustered using LSSPs via three different procedures to define domains. This approach gives results that are comparable to several existing programs that use geometrical and other structural information explicitly. Remarkably, most of the proteins that contribute the LSSPs defining a domain do not themselves contain the domain of interest. This study shows that domains can be defined by a collection of relatively small locally similar structural pieces containing, on average, four secondary structure elements. In addition, it indicates that domains are indeed made of recurrent small structural pieces that are used to build protein structures of many different folds as suggested by recent studies. Proteins 2011. Published 2010 Wiley‐Liss, Inc.
The effects of the L29F mutation on the ligand migration kinetics in crystallized myoglobin as revealed by molecular dynamics simulations
Authors: Anselmi Massimiliano , Di Nola Alfredo , Amadei Andrea 
Published: October 2010

AbstractBy using multiple molecular dynamics (MD) trajectories, a quantitative description of carbon monoxide (CO) migration within crystal of L29F myoglobin mutant (L29F‐Mb) was obtained. The aim was to provide a detailed model for ligand diffusion in the protein to be compared to the available L29F‐Mb experimental‐computational data and to the corresponding model kinetics we previously obtained for photolyzed CO within crystallized wild‐type myoglobin (wt‐Mb). Results suggest a clear migration pathway from distal pocket to the proximal site, similar to the one observed in wt‐Mb, with a relaxation kinetics differing from the wt‐Mb one essentially for the escape rate which is much higher in the mutant. Moreover MD data indicated a clear correlation between CO location within the protein and the conformation adopted by Phe29, well matching the available experimental data as obtained by time‐resolved X‐ray density maps. Such data, further validating the model used in the simulations, point out the subtle mutual effect between ligand diffusion and protein functional motions possibly explaining the observed dramatic variation of CO exit rate in L29F‐Mb. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Induction effects of host plants on insecticide susceptibility and detoxification enzymes of Bemisia tabaci (Hemiptera: Aleyrodidae)
Authors: Xie Wen , Wang Shaoli , Wu Qingjun , Feng Yuntao , Pan Huipeng , Jiao Xiaoguo , Zhou Long , Yang Xin , Fu Wei , Teng Haiyuan , Xu Baoyun , Zhang Youjun 
Published: October 2010

AbstractBACKGROUND: The polyphagous B‐biotype Bemisia tabaci (Gennadius) has developed a high resistance to commonly used insecticides in China. To illustrate the induced changes by host plant, bioassay and biochemical research on five different host populations were investigated.RESULTS: Except for bifenthrin, all tested insecticides showed lower toxicity to the B. tabaci poinsettia population compared with other host populations. Moreover, four insecticides, the exceptions being abamectin and fipronil, showed highest toxicity towards the tomato population. The LC50 values of the poinsettia population, particularly towards acetamiprid, were 14.8‐, 10.3‐ and 7.29‐fold higher than those of tomato, cucumber and cabbage respectively. The CarE activities of B. tabaci cabbage and cucumber populations were all significantly higher than those of poinsettia, cotton and tomato populations. The ratio of the cabbage population was 1.97‐, 1.79‐ and 1.30‐fold higher than that of poinsettia, cotton and tomato respectively. The frequency profiles for this activity also have obvious differences. The GST and P450 activities of the cucumber population were the lowest in the five host populations.CONCLUSION: Long‐term induction of host plants for B‐biotype B. tabaci could influence their susceptibilities to several insecticides. Rational selection and usage of insecticides for particular hosts will be helpful for resistance management and control of this species. Copyright © 2010 Society of Chemical Industry
High resolution angle‐resolved photoemission spectroscopy on Cu‐based and Fe‐based high‐Tc superconductors
Authors: Zhou Xingjiang , Liu Guodong , Meng Jianqiao , Zhang Wentao , Liu Haiyun , Zhao Lin , Jia Xiaowen 
Published: October 2010

AbstractResearch on high temperature superconductivity has been a prominent topic in condensed matter physics. Angle‐resolved photoemission spectroscopy (ARPES) is a powerful technique in probing the electronic structure, energy gap and many‐body effects in high temperature superconductors, and other materials. In this paper, we first introduce our effort in developing vacuum ultra‐violet (VUV) laser‐based photoemission techniques, including angle‐resolved, spin‐resolved, time‐of‐flight electron energy analyzer‐based ones. Then, we highlight some of our recent results on Cu‐based high temperature superconductors utilizing our VUV laser‐based ARPES including many‐body effects in hole‐ and electron‐doped cuprates, superconducting gap and pseudogap, and the observation of Fermi pockets. In the last part of this paper, we briefly introduce our ARPES study on band structure, Fermi surface, superconducting gap, and many‐body effects in the newly discovered Fe‐based compounds.
Oscillatory clusterings in compartmentalized granular systems
Authors: Hou Meiying , Li Yinchang , Liu Rui , Zhang Yin , Lu Kunquan 
Published: October 2010

AbstractA review is given of our previous work on the clustering, especially the oscillatory clustering for shaken fluidized granular matter in connected compartments, as examples for pattern formation and bifurcations in far from equilibrium systems. Flux model is presented and discussed for mono‐disperse and bi‐disperse granular systems. Comparison of the flux model with simulation results is given. They show reasonably well agreements. Besides the homogeneous (HOM), segregation (SEG), and oscillatory (OSC) states, two new stationary states (d‐OSC and s‐HOM) in the bi‐disperse granular system are predicted by our simulation. In our recent work these two new states are observed experimentally, and their flow diagrams are obtained based on the flux model, which shows qualitative agreement with the experimental results. Discussions of variations of the above system are also given, such as adding an asymmetric structure, changing the number of compartments from two to three, and adding more than two types of particles. This compartmentalized fluidized granular system turns out to be a good model system for studying nonlinear dynamics and pattern formation of far from equilibrium systems.
Glabridin, a phytoestrogen from licorice root, up‐regulates manganese superoxide dismutase, catalase and paraoxonase 2 under glucose stress
Authors: Yehuda Itamar , Madar Zecharia , Szuchman‐Sapir Andrea , Tamir Snait 
Published: October 2010

AbstractThe risk of death from cardiovascular diseases (CVDs), which are exacerbated by oxidative stress, is higher in diabetic women. This phenomenon has been attributed to the loss of estradiol‐vascular protection. Such knowledge led us to examine the potential of glabridin, a phytoestrogen, to substitute estradiol up‐regulation of antioxidant enzymes under high glucose conditions. Chronic glucose stress was found to down‐regulate catalase (CAT) and paraoxonase 2 (PON2) mRNA expression by 20% and 17%, respectively, and to decrease PON2 activity by 83% in macrophages. Inflammatory conditions had an additive effect on PON2 expression in a time‐dependent manner. Treatment with glabridin, under high glucose stress, increased PON2 activity by 60% and up‐regulated its mRNA expression by 3.5 fold. Furthermore, glabridin up‐regulated the expression of manganese superoxide dismutase (Mn‐SOD) and CAT in monocytes. In conclusion, glabridin has the potential of strengthening the antioxidant defense mechanism and may serve as an antiatherogenic agent in diabetes. Copyright © 2010 John Wiley & Sons, Ltd.
Grape seed extract enhances neurogenesis in the hippocampal dentate gyrus in C57BL/6 mice
Authors: Yoo Dae Young , Kim Woosuk , Yoo Ki‐Yeon , Lee Choong Hyun , Choi Jung Hoon , Yoon Yeo Sung , Kim Dong‐Woo , Won Moo‐Ho , Hwang In Koo 
Published: October 2010

AbstractThe effects of grape seed extract (GSE), a major source of phenolic compounds, were examined on cell proliferation, neuroblast differentiation and integration into granule cells in the hippocampal dentate gyrus (DG) of middle‐aged (12 month‐old) mice using Ki67, doublecortin (DCX) immunohistochemistry and 5′‐bromo‐2‐deoxyguanosine (BrdU)/calbindin D‐28k (CB) double immunofluorescence study, respectively. GSE (25, 50 and 100 mg/kg) was administered orally for 28 days, and the animals were treated with 50 mg/kg BrdU intraperitoneally on the day of first GSE treatment. In the vehicle‐treated group, Ki67 and DCX immunoreactivity was detected in the subgranular zone of the DG (SZDG). GSE treatment dose‐dependently increased the number of Ki67 and DCX immunoreactive cells, particularly the number of DCX immunoreactive neuroblasts with well‐developed (tertiary) dendrites. GSE also dose‐dependently increased DCX protein levels. In addition, GSE treatment increased significantly the number of BrdU/CB double labeled granule cells. These results suggest that GSE significantly increases cell proliferation, neuroblast differentiation and integration into granule cells in the DG, and the consumption of GSE enhances the plasticity of hippocampus in middle‐aged mice. Copyright © 2010 John Wiley & Sons, Ltd.
Protective effect of a polysaccharide isolated from a cultivated Cordyceps mycelia on hydrogen peroxide‐induced oxidative damage in PC12 cells
Authors: Shen Wenbin , Song Dan , Wu Jianyong , Zhang Weiyun 
Published: October 2010

AbstractCordyceps sinensis as a well‐known traditional Chinese tonic has many therapeutic functions. In the present study, an acid polysaccharide (APS) was isolated from cultivated Cordyceps mycelia by ion‐exchange and sizing chromatography. The protective capacity of APS against H2O2‐induced oxidative damage in rat pheochromocytoma PC12 cells was investigated by measuring cell viability, lactate dehydrogenase (LDH) release, antioxidant enzyme activity, malondialdehyde (MDA) levels and intracellular accumulation of reactive oxygen species (ROS) and Ca2+. The results demonstrated that pretreatment of PC12 cells with APS, prior to H2O2 exposure, significantly increased the survival of cells and the activities of glutathione peroxidase (GSH‐Px), catalase (CAT) and superoxide dismutase (SOD), and reduced the levels of LDH and MDA. Intracellular accumulation of reactive oxygen species (ROS) and Ca2+ were also inhibited by APS treatment. In conclusion, APS was found to increase the cellular antioxidant defence capacity, thereby protecting PC12 cells against oxidative stress. Copyright © 2010 John Wiley & Sons, Ltd.
Effect of ginsenosides Rg3 and Re on glucose transport in mature 3T3‐L1 adipocytes
Authors: Lee Ok‐Hwan , Lee Hee‐Hyun , Kim Ji‐Hyup , Lee Boo‐Yong 
Published: October 2010

AbstractGinsenosides, the active component of Panax ginseng, have been shown to evidence a variety of biological activities associated with hyperglycemia, obesity and type 2 diabetes mellitus. This study evaluated the effects of the ginsenosides, Rg3 and Re, on glucose uptake and the glucose transport system in mature 3T3‐L1 cells. The results demonstrated that the glucose uptake of ginsenosides Rg3 and Re at concentrations of 1–10 µM significantly increased by approximately ∼10% and ∼12%, respectively. Furthermore, the glucose transporter 4 (GLUT4) mRNA expression of ginsenosides Rg3 and Re at 10 µM was increased by approximately ∼1.73 and 1.43 fold, respectively. It was further confirmed in a series of experiments that ginsenosides Rg3 and Re stimulated the mRNA expression of insulin receptor substrate (IRS‐1) and the expression of phosphatidylinositol 3‐kinase (PI3K)‐110α protein, which is involved in downstream events in the insulin signaling pathway. These findings demonstrate that ginsenosides Rg3 and Re may stimulate glucose uptake via the PI3K pathways involving IRS‐1. Further, our results suggest that both of these ginsenosides might prove useful as effective antidiabetic and antihyperglycemic agents. Copyright © 2010 John Wiley & Sons, Ltd.
Sampling distributions of the Brier score and Brier skill score under serial dependence
Authors: Wilks D.S. 
Published: October 2010

AbstractRelatively little attention has been given to the effects of serial correlation of forecasts and observations on the sampling properties of forecast verification statistics. An assumption of serial independence for low‐quality forecasts may be reasonable. However, forecasts of sufficient quality for autocorrelated events must themselves be autocorrelated: as quality approaches the limit of perfect forecasts, the forecasts become increasingly similar to the corresponding observations.The effects of forecast serial correlation on the sampling properties of the Brier Score (BS) and Brier Skill Score (BSS), for probability forecasts of dichotomous events, are examined here. As in other settings, the effect of serial correlation is to inflate the variances of the sampling distributions of the two statistics, so that uncorrected confidence intervals are too narrow, and uncorrected hypothesis tests yield p‐values that are too small. Expressions are given for ‘effective sample size’ corrections for the sampling variances of both BS and BSS, in which it can be seen that the effects of serial correlation on the sampling variances increase with increasing forecast accuracy, and with decreasing climatological event probability. The sampling variance of BSS is more robust to serial correlation than that of BS. Hypothesis tests based on BSS are seen to be more powerful (i.e. more sensitive) than those based on BS, and substantially so for lower‐accuracy forecasts of lower‐probability events, for both serially correlated and temporally independent forecasts. Copyright © 2010 Royal Meteorological Society
A simulation model for improving the maintenance of high cost systems, with application to an offshore oil installation
Authors: Conn Andrew R. , Deleris Léa A. , Hosking Jonathan R. M. , Thorstensen Tom Anders 
Published: October 2010

AbstractWe describe a Generalized Semi‐Markov Model paired with Monte Carlo simulation that represents the evolution of the systems that constitute an offshore installation. We use the model to assess the performance of a maintenance plan in terms of a production penalty and unplanned shutdowns. In addition to estimating, comparing and improving maintenance plans, our approach enables the determination of the consequences of planning capital expenditures and installation modifications and the value of process improvements. Moreover, the entire framework is designed to be sufficiently flexible to accommodate various ‘what if’ scenarios in addition to other modifications. The simulation model was tested on data from an offshore oil installation, and was well received by the installation's operations personnel. Copyright © 2010 John Wiley & Sons, Ltd.
Isoelectric points of plasma‐modified and aged silicon oxynitride surfaces measured using contact angle titrations
Authors: Trevino Kristina J. , Shearer Jeffrey C. , McCurdy Patrick R. , Pease‐Dodson Shannon E. , Okegbe Christabel C. , Fisher Ellen R. 
Published: October 2010

AbstractAcid‐base properties of metal oxides and polymers can control adhesion properties between materials, electrical properties, the physical structure of the material and gas adsorption behavior. To determine the relationships between surface isoelectric point, chemical composition and aging effects, plasma‐surface treatment of amorphous silicon oxynitride (SiOxNy) substrates was explored using Ar, H2O vapor, and NH3 inductively coupled rf plasmas. Overall, the Ar plasma treatment resulted in nonpermanent changes to the surface properties, whereas the H2O and NH3 plasmas introduced permanent chemical changes to the SiOxNy surfaces. In particular, the H2O plasma treatments resulted in formation of a more ordered SiO2 surface, whereas the NH3 plasma created a nitrogen‐rich surface. The trends in isoelectric point and chemical changes upon aging for one month suggest that contact angle and composition are closely related, whereas the relationship between IEP and composition is not as directly correlated. Copyright © 2010 John Wiley & Sons, Ltd.
Site‐oriented immobilization of fusion antigen directed by an affinity ligand, and its validation in an immunoassay
Authors: Feng Bo , Luo Yueping , Ge Fei , Wang Lu , Huang Liqun , Dai Youzhi 
Published: October 2010

AbstractImmobilizing proteins on a solid surface in a site‐specific orientation and maintaining their bioactivity are crucial to the construction of high‐performance immunoassays. In this study, an affinity ligand for polystyrene (PS) surface screened from a phage display peptide library, named Lig1, was genetically fused to the N/C‐terminus of chimeric antigen HCV that could be recognized by specific antibodies against hepatitis C virus (HCV). Immunoassay characteristics of lig1‐fused HCVs immobilized on PS surface were compared to that of original HCV in both direct and indirect enzyme‐linked immunosorbent assay (ELISA). The results indicated that HCV‐Lig1 (Lig1 fused to HCV C‐terminus) was preferentially adsorbed on PS surface in a site‐oriented manner and would expose specific antibody‐binding sites well, which resulted in a substantial enhancement of detection sensitivity. AFM images showed that, compared to the original one, HCV‐Lig1 was arranged on PS surface in an ordered state and its conformational and steric distortions induced during the interfacial binding process were much slighter. As long as the specific epitope of a coating antigen is not located on both its N and C‐terminus, the ligand fusion approach could be an ideal strategy for site‐oriented protein immobilization. Copyright © 2010 John Wiley & Sons, Ltd.
Simplified column shortening analysis of a multi‐storey reinforced concrete frame
Authors: Kim Han‐Soo , Jeong Se‐Hun , Shin Seung‐Hak , Park Jae‐Pyo 
Published: October 2010

AbstractAn improved column shortening analysis method which can be used at the design stage of a tall building has been proposed. The proposed analysis method considers construction sequences, the restraining effect of horizontal members, as well as creep and shrinkage. The whole analysis period is divided into two phases: before completion and after completion, and correction factors are applied only to the before‐completion phase to consider the gradual nature of construction sequences. Age‐adjusted effective moduli of the horizontal members considering the long‐term behaviour of the members are used for more exact internal forces. Column shortenings of a 70‐storey reinforced concrete frame–shear wall building were investigated as a numerical example. It is shown that the proposed analysis method can be used effectively to evaluate the effects of the differential column shortening to the horizontal members at the design stage. Copyright © 2010 John Wiley & Sons, Ltd.
Computational Fluid Dynamics study on the performance and mechanism of suction control over a high‐rise building
Authors: Zheng Chao‐Rong , Zhang Yao‐Chun 
Published: October 2010

SUMMARYIn order to reduce the wind‐induced drag and improve the wind‐resistance performance of a high‐rise building, active suction control was proposed to investigate its drag‐reducing property through Computational Fluid Dynamics (CFD) method. The numerical method was validated by the experiment of suction control over a backward‐facing step flow. Effects of the dimensionless suction flux, the suction angle and the slot size on drag reduction for a high‐rise building model were analysed, and the detailed flow fields (including the time‐averaged stream and vorticity fields), the boundary layer development and turbulence characteristics like turbulent kinetic energy for the suction models were presented to discuss the mechanism of suction control. The results indicate that suction is very effective in reducing the wind‐load of a high‐rise building model, and only the dimensionless suction flux is important, while the orifice geometrical parameters and the suction velocities show little influence on drag reduction. The mechanism of suction control is concluded that suction can bring more flows around the windward face, restrain the flow separation and decrease the width of the wake for the suction models. Copyright © 2010 John Wiley & Sons, Ltd.
Effectiveness of active multiple‐tuned mass dampers for asymmetric structures considering soil–structure interaction effects
Authors: Li Chunxiang 
Published: October 2010

SUMMARYBased on recent researches by Li et al. in 2009, the optimum parameter criterion of the AMTMD here is selected as minimizing the translational and torsional displacement mean square responses of the asymmetric structure with the AMTMD taking into account the SSI. The effectiveness criterion of the AMTMD is the ratio of the minimization of the translational and torsional displacement mean square responses of the asymmetric structure with the AMTMD to the translational and torsional displacement mean square responses of the asymmetric structure without the AMTMD considering the SSI. The investigations for the influences of the normalized eccentricity ratio (NER), torsional to translational frequency ratio (TTFR), relative stiffness of the soil to the structure (RSSS), and height‐to‐base ratio (HBR) of the soil‐asymmetric structure interaction system are then carried out on both the effectiveness and robustness of the AMTMD. A new basic result is that when an asymmetric structure is built on soft soil sites, the SSI needs to be considered to determine the optimal parameters of the AMTMD to avoid overestimating or underestimating its effectiveness. Likewise, the robustness of the AMTMD for asymmetric structures is underestimated if the SSI effect is left out of consideration. Copyright © 2010 John Wiley & Sons, Ltd.