bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated QSAR with a Hierarchy of Global and Local Models
Authors: Wood David J. , Buttar David , Cumming John G. , Davis Andrew M. , Norinder Ulf , Rodgers Sarah L. 
Published: November 2011

AbstractWe present an automated QSAR procedure that is used in AstraZeneca’s AutoQSAR system. The approach involves automatically selecting the most predictive models from pools of both global and local models. The effectiveness of this QSAR modelling strategy is demonstrated with a retrospective study that uses a diverse selection of 9 early stage AstraZeneca drug discovery projects and 3 physicochemical endpoints: LogD; solubility and human plasma protein binding. We show that the strategy makes a statistically significant improvement to the accuracy of predictions when compared to an updating global strategy, and that the systematic biases inherent in the global model predictions are almost completely removed. This improvement is attributed to the model selection aspect of the strategy.
Boiling peanut Ara h 1 results in the formation of aggregates with reduced allergenicity
Authors: Blanc Fany , Vissers Yvonne M. , Adel‐Patient Karine , Rigby Neil M. , Mackie Alan R. , Gunning A. Patrick , Wellner Nikolaus K. , Skov Per S. , Przybylski‐Nicaise Laetitia , Ballmer‐Weber Barbara , Zuidmeer‐Jongejan Laurian , Szépfalusi Zsolt , Ruinemans‐Koerts Janneke , Jansen Ad P. H. , Bernard Hervé , Wal Jean‐Michel , Savelkoul Huub F. J. , Wichers Harry J. , Mills E. N. Clare 
Published: November 2011

AbstractScope: Roasting rather than boiling and Maillard modifications may modulate peanut allergenicity. We investigated how these factors affect the allergenic properties of a major peanut allergen, Ara h 1.Methods and results: Ara h 1 was purified from either raw (N‐Ara h 1) or roasted (R‐Ara h 1) peanuts. Boiling (100°C 15 min; H‐Ara h 1) resulted in a partial loss of Ara h 1 secondary structure and formation of rod‐like branched aggregates with reduced IgE‐binding capacity and impaired ability to induce mediator release. Glycated Ara h 1 (G‐Ara h 1) formed by boiling in the presence of glucose behaved similarly. However, H‐ and G‐Ara h1 retained the T‐cell reactivity of N‐Ara h 1. R‐Ara h 1 was denatured, comprised compact, globular aggregates, and showed no evidence of glycation but retained the IgE‐binding capacity of the native protein.Conclusion: Ara h 1 aggregates formed by boiling were morphologically distinct from those formed by roasting and had lower allergenic activity. Glycation had no additional effect on Ara h 1 allergenicity compared with heating alone. Taken together with published data on the loss of Ara h 2/6 from boiled peanuts, this supports the hypothesis that boiling reduces the allergenicity of peanuts.
The protective role of natural phytoalexin resveratrol on inflammation, fibrosis and regeneration in cholestatic liver injury
Authors: Chan Che‐Chang , Cheng Ling‐Yi , Lin Chin‐Lung , Huang Yi‐Hsiang , Lin Han‐Chieh , Lee Fa‐Yauh 
Published: November 2011

AbstractLiver injuries can trigger a cascade of inflammatory responses and as a result, initiate the process of hepatic regeneration and fibrogenesis. Resveratrol (RSV) has multiple health‐promoting benefits. This study evaluated the potential protective effects and mechanism of RSV as related to cholestatic liver injury. RSV was given (4 mg/kg/day, i.p.) for either 3 days or 7 days after bile duct ligation (BDL) injury. RSV significantly reduced serum ALT, AST but not T‐bil on Day 3. At this early stage of injury, RSV significantly reduced TNF‐α and IL‐6 mRNA and decreased the number of Kupffer cells (CD68+) recruited in the injured liver. RSV decreased hepatic fibrosis and reduced collagen Iα1 and TIMP‐1 mRNA on Day 7. At the later stages of injury, RSV increased the number of Ki67+ hepatocytes indicating that RSV promoted hepatocyte proliferation. Additionally, it resulted in decreased expression of 4‐hydroxynonenal and increased expression of the hepatocyte growth factor protein and mRNA in the RSV‐treated BDL group. Meanwhile, RSV reduced the mortality rate of BDL mice. In conclusion, RSV attenuated inflammation and reduced Kupffer cells activation. RSV decreased fibrosis and promoted hepatocyte regeneration, which increased the survival of BDL mice. RSV was beneficial for the treatment of cholestatic liver injury.
Contrast at high field: Relaxation times, magnetization transfer and phase in the rat brain at 16.4 T
Authors: Pohmann Rolf , Shajan G. , Balla D. Z. 
Published: November 2011

AbstractParameter maps: Relaxation times T1, T2 and T*2, MTR and frequency for one exemplary slice. All images represent different rats and slice positions. All maps were generated by a pixel‐by‐pixel fit of the corresponding parameters; SNR differences are caused by the varying fitting accuracies. The arrows in the T*2 image (c) point out cortical veins. The increased MTR on the left side of image (d) is due to B1 inhomogeneity. From the article by Pohmann et al (pp 1572–1581).
Restricted additive Schwarz methods for Markov chains
Authors: Benzi Michele , Kuhlemann Verena 
Published: November 2011

SUMMARYThe restricted additive Schwarz method is adapted to the problem of computing the stationary probability distribution vector of large, sparse, and irreducible stochastic matrices. Inexact and two‐level variants are also considered as well as acceleration by Krylov subspace methods. The convergence properties are analyzed, and extensive numerical experiments aimed at assessing the effect of varying the number of subdomains and the amount of overlap are discussed. Copyright © 2011 John Wiley & Sons, Ltd.
Improved mathematical modeling for the sheet reheat phase during thermoforming
Authors: Khan Sohail Akbar , Girard Patrick , Bhuiyan Nadia , Thomson Vince 
Published: November 2011

AbstractIn any thermoforming process, plastic sheet heating is the most important phase as it is responsible for final part quality as well as overall process efficiency and productivity. The goal of the study reported here was to improve existing mathematical models to accurately predict the temperature profile inside a heated sheet, where the model could be used to better control the overall thermoforming process. A mathematical model with temperature dependent, variable sheet material properties including density, thermal diffusivity, specific heat, and thermal conductivity was developed and validated against experimental data. Models with constant and variable plastic sheet properties were created, simulated, and compared in Matlab. The models were validated by experiments which obtained temperature profiles at different depths within a plastic sheet by inserting thermocouples and recording temperatures. Further, the effect of sheet color on heating was investigated by considering two extreme cases: white (transparent) and black (opaque) colored sheets, and the effect of oven air temperature and velocity on sheet heating was also investigated. Results indicated that a variable properties model was needed to control sheet reheating especially with narrow forming windows, and that the heating profiles required for colored and noncolored sheets were very different. POLYM. ENG. SCI., 2012. © 2011 Society of Plastics Engineers
Nanoparticle encapsulation by a polymer via in situ polymerization in supercritical conditions
Authors: Esmaeili Babak , Chaouki Jamal , Dubois Charles 
Published: November 2011

AbstractThe encapsulation of aluminum nanoparticles by polyvinylidene fluoride (PVDF) was carried out in supercritical conditions via in situ polymerization. The aluminum particles possessed an average diameter of 43.7 nm. The presence of PVDF on the particles was validated by thermogravimetric analysis (TGA). This result was further approved by X‐ray photoelectron spectroscopy (XPS), which showed high intensity peaks of fluorine and carbon on the particles after the encapsulation process, which are associated with the presence of hydrocarbon‐based PVDF. As observed by transmission electron microscopy (TEM) images, the nanoparticles were uniformly coated by a polymer of a few nanometers in thickness. The results showed that there is a good consistency between the calculated thickness of the polymer coating and the results obtained by TEM. In addition, the effect of polymerization time on the kinetics of the reaction was investigated. Finally, it was found that the thickness of the polymer layer can be controlled by the duration of the encapsulation process. POLYM. ENG. SCI., 2012. © 2011 Society of Plastics Engineers
Shear‐induced crystallization of isotactic polypropylene studied by simultaneous light intensity and rheological measurements
Authors: Tiang Jen Shueng , Dealy John M. 
Published: November 2011

AbstractWe investigate the effects of high shear rate and a melt‐insensitive, organophosphate nucleating agent on shear‐induced crystallization of four isotactic polypropylenes using a sliding plate rheometer under isothermal, low‐supercooling conditions. We used a bifurcated optical fiber probe to measure light intensity and a shear stress transducer to monitor the simultaneous viscoelastic response to small‐amplitude oscillatory shear. The two techniques complement each other; at early times of crystallization, large attenuation in the light intensity is observed, whereas during the later stages, a major change in the viscoelastic response occurs due to the growing volume fraction of spherulites. In contrast to quiescent crystallization, the nucleation pathway of nucleated polymers after a brief, strong shear is little influenced by the nucleating agent but strongly affected by molecular weight. The early kinetics of non‐nucleated polymers is more strongly enhanced by shear than that of nucleated polymers. Increasing either shear rate or strain accelerates crystallization, and we found the product of shear rate and strain to be useful for correlating our data. POLYM. ENG. SCI., 2011. © 2011 Society of Plastics Engineers
Synthesis, characterization of an epoxy‐terminated carbosiloxane and its application as a modifier in epoxy systems
Authors: Kang Nianjun , Du Zhongjie , Li Hangquan , Zhang Chen 
Published: November 2011

AbstractAn epoxy‐terminated carbosiloxane has been designed and synthesized as a modifier to improve toughness and stiffness of epoxy resins simultaneously. The modifier was rubbery in nature and possessed several epoxy groups. When co‐cured with a conventional epoxy precursor, diglycidyl ether of bisphenol‐A (DGEBA), it would phase separate as individual domains and thus act as a toughener. Through participating in curing reaction with its multiple epoxy groups, the crosslinking density of the system was increased and thus resulted in reinforcing of cured epoxy system. The modifier was synthesized via hydrosilylation and cohydrolysis reactions. The chemical structures of the carbosiloxane were confirmed by FTIR and 1H NMR spectra. The cured epoxy products were characterized by dynamic mechanical thermal analysis (DMTA), thermogravimetric analysis (TGA), impact strength testing, and atomic force microscopy (AFM). POLYM. ENG. SCI., 2011. ©2011 Society of Plastics Engineers
The effects of radiation cross‐linking and process parameters on the behavior of polyamide 12 in vacuum thermoforming
Authors: Seefried A. , Drummer D. 
Published: November 2011

AbstractCompared to amorphous thermoplastics, semi‐crystalline thermoplastics usually have a smaller processing range for thermoforming, due to their narrow temperature window for the transition from viscoelastic to viscous material behavior. On the other hand, semi‐crystalline thermoplastics offer superior properties for applications like ductility or chemical resistance. Within this article, modification of semi‐crystalline polyamide 12 by radiation cross‐linking with respect to its suitability for vacuum thermoforming as well as the effects of processing parameters and sheet thickness on the resulting strain distributions in thermoformed parts are shown. Experimental thermoforming processing studies in combination with digital image correlation measurements, thermo‐mechanical and elongational rheometry were performed to characterize the behavior of cross‐linked semi‐crystalline thermoplastics in the vacuum thermoforming process. POLYM. ENG. SCI., 2011. ©2011 Society of Plastics Engineers
Poly(lactic acid)/low‐density polyethylene blends and its nanocomposites based on sepiolite
Authors: Nuñez K. , Rosales C. , Perera R. , Villarreal N. , Pastor J.M. 
Published: November 2011

AbstractPoly(lactic acid) (PLA) nanocomposite ternary blends based on unmodified sepiolite were prepared by melt blending using a corotating twin‐screw extruder. Two grafted polymers were used as compatibilizer agents, in an effort to increase the PLA tensile toughness. The influence of incorporating a low‐cost commodity low‐density polyethylene, as dispersed phase to the composites on thermal degradation, and rheological and tensile properties was studied. The morphology of the blends and composites was determined through transmission and scanning electron microscopy techniques. Results showed that the compatibilized blends prepared without clay have higher thermal degradation susceptibility and tensile toughness than those prepared with sepiolite and significant changes in complex viscosity and melt elasticity values were observed between them. The nanocomposite blends exhibited similar thermal degradation, lower tensile strength, and Young's modulus values and increased elongation at break and tensile toughness, complex viscosity, and storage modulus compared with those of the nanocomposite of PLA. These results are related to the clay dispersion, to the type of morphology of the different blends, to the localization of the sepiolite in the different phases, the thermomechanical degradation of the PLA matrix phase during melt blending and the grafting degree of the compatibilizers used. POLYM. ENG. SCI., 2012. © 2011 Society of Plastics Engineers
Cavitation‐induced rupture in high‐density polyethylene copolymers
Authors: Ben Jar P.‐Y. , Muhammad Souvenir 
Published: November 2011

AbstractUsing cylindrical specimens with short gauge length, bulk cavitation is successfully generated in high‐density polyethylene copolymers (HDPE) under tensile loading. The bulk cavitation is generated without the presence of sharp notch, and therefore, crack growth is not involved in the rupture process. The bulk cavitation is investigated in two types of HDPE that have different molecular characteristics. Test results indicate that bulk cavitation can be introduced in both the types of HDPE, for which the loading level is most easily identified using plots of true axial stress versus stroke. The main difference in the rupture process occurs during the postcavitation stretch. Using specimens of sufficiently long gauge length, constitutive equations for the HDPEs are determined and applied to finite element modeling of specimens with short gauge length. The results show that the hydrostatic stress level in specimens of short gauge length is about twice as high as that in specimens of long gauge length, supporting the conclusion on bulk cavitation from rubber testing. For HDPE, this study shows that the rise of hydrostatic stress level leads to the suppression of necking, to allow the bulk cavitation to dominate the deformation process. POLYM. ENG. SCI., 2012. © 2011 Society of Plastics Engineers
Identification of the bile salt binding site on ipad from Shigella flexneri and the influence of ligand binding on IpaD structure
Authors: Barta Michael L. , Guragain Manita , Adam Philip , Dickenson Nicholas E. , Patil Mrinalini , Geisbrecht Brian V. , Picking Wendy L. , Picking William D. 
Published: November 2011

AbstractType III secretion (TTS) is an essential virulence factor for Shigella flexneri, the causative agent of shigellosis. The Shigella TTS apparatus (TTSA) is an elegant nano‐machine that is composed of a basal body, an external needle to deliver effectors into human cells, and a needle tip complex that controls secretion activation. IpaD is at the tip of the nascent TTSA needle where it controls the first step of TTS activation. The bile salt deoxycholate (DOC) binds to IpaD to induce recruitment of the translocator protein IpaB into the maturing tip complex. We recently used spectroscopic analyses to show that IpaD undergoes a structural rearrangement that accompanies binding to DOC. Here, we report a crystal structure of IpaD with DOC bound and test the importance of the residues that make up the DOC binding pocket on IpaD function. IpaD binds DOC at the interface between helices α3 and α7, with concomitant movement in the orientation of helix α7 relative to its position in unbound IpaD. When the IpaD residues involved in DOC binding are mutated, some are found to lead to altered invasion and secretion phenotypes. These findings suggest that adoption of a DOC‐bound structural state for IpaD primes the Shigella TTSA for contact with host cells. The data presented here and in the studies leading up to this work provide the foundation for developing a model of the first step in Shigella TTS activation. Proteins 2011. © 2012 Wiley Periodicals, Inc.
An advanced cost estimation methodology for engineering systems
Authors: Hart C.G. , He Z. , Sbragio R. , Vlahopoulos N. 
Published: November 2011

AbstractA mathematically advanced method for improving the fidelity of cost estimation for an engineering system is presented. In this method historical cost records can be expanded either through the use of local metamodels or by using an engineering build‐up model. In either case, the expanded data set is analyzed using principal component analysis (PCA) in order to identify the physical parameters, and the principal components (PCs) which demonstrate the highest correlation to the cost. A set of predictor variables, composed of the physical parameters and of the multipliers of the principal components which demonstrate the highest correlation to the cost, is developed. This new set of predictor variables is regressed, using the Kriging method, thus creating a cost estimation model with a high level of predictive capability and fidelity. The new methodology is used for analyzing a set of cost data available in the literature, and the new cost model is compared to results from a neural network based analysis and to a cost regression model. Further, a case study addressing the fabrication of a submarine pressure hull is developed in order to illustrate the new method. The results from the final regression model are presented and compared to results from other cost regression methods. The technical characteristics of the new novel general method are presented and discussed. © 2011 Wiley Periodicals, Inc. Syst Eng
Chip‐interleaving direct sequence spread spectrum system over Rician multipath fading channels
Authors: Gui Xiang 
Published: November 2011

ABSTRACTChip interleaving (CI) is a unique technique to exploit time diversity in direct sequence spread spectrum (DS/SS)‐based systems operating in fading environments. In order to facilitate design of CI systems in various fading situations, we present a performance analysis for CI DS/SS system over Rician multipath time‐varying fading channels. We derive the analytical bit error rate (BER) expression for CI DS/SS to allow fast and accurate evaluation of BER performance based on the interleaving depth selected, spreading codes employed, and the time correlation function of the channel. We then discuss some ideal cases by using the analytical results to reveal some of the insights presented in the performance analysis. For the purpose of comparison, we also obtain the BER expression for conventional DS/SS system as a special case of CI system with an interleaving depth of one. Using numerical examples, we verify the analytical results with computer simulations and illustrate the BER performance behavior of CI DS/SS system with varying interleaving depth for all possible combinations of two sets of spreading codes of different type and two different time correlation functions of the channel. Copyright © 2011 John Wiley & Sons, Ltd.
Diversity of animal small RNA pathways and their biological utility
Authors: Okamura Katsutomo 
Published: November 2011

AbstractHigher eukaryotes employ extensive post‐transcriptional gene regulation to accomplish fine control of gene expression. The microRNA (miRNA) family plays important roles in the post‐transcriptional gene regulation of broad networks of target mRNA expression. Most miRNAs are generated by a conserved mechanism involving two RNase III enzymes Drosha and Dicer. However, work from the past few years has uncovered diverse noncanonical miRNA pathways, which exploit a variety of other RNA processing enzymes. In addition, the discovery of another abundant small RNA family, endogenous short interfering RNAs (endo‐siRNAs), has also broadened the catalogs of short regulatory RNAs. This review highlights recent studies that revealed novel small RNA biogenesis pathways, and discusses their relevance to gene regulatory networks. WIREs RNA 2012, 3:351–368. doi: 10.1002/wrna.113This article is categorized under:

Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs
RNA Processing > Processing of Small RNAs
Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
Factors affecting chemical‐based purification of DNA from Saccharomyces cerevisiae
Authors: Lee Christopher K. , Araki Naoko , Sowersby Drew S. , Lewis L. Kevin 
Published: November 2011

ABSTRACTExtraction of high molecular weight chromosomal DNA from yeast cells is a procedure that is performed frequently for experiments involving polymerase chain reaction (PCR), Southern blotting and other DNA analysis techniques. We have investigated several parameters affecting DNA yield and quality, using a simple chemical‐based purification procedure that was modelled on alkaline lysis methods developed for bacterial cells. The three major steps of the procedure, cell lysis, protein removal and DNA precipitation, were optimized by testing the impacts of several chemicals, including sodium dodecyl sulphate (SDS), sodium hydroxide, Tris buffer, sodium acetate and potassium acetate. Other parameters, such as the effect of elevated temperatures on cell lysis, were also investigated. A rapid, optimized protocol was derived for the purification of DNA from small cell cultures that can be readily digested with restriction enzymes and used as a template for PCR. Average yield was calculated to be approximately 1.7 µg DNA/108 cells, which is similar to the theoretical maximum amount obtainable from haploid yeast cells. Copyright © 2011 John Wiley & Sons, Ltd.
Reversible Wettability of Tungsten Trioxide Films with Novel Dandelion‐like Structures
Authors: Wang Xinmin , Wei Zhihua , Yu Chengqun , Zhang Xianzhou , Zhang Yidong 
Published: November 2011

Abstract Tungsten trioxide (WO3) films with novel dandelion‐like structures were prepared by spin‐coating a sol of WO3 with CTAB (cetyltrimethyl ammonium bromides) on quartz substrates. The resultant WO3 films were characterized by X‐ray diffraction (XRD), FT‐IR spectroscopy, scanning electron microscopy (SEM), and X‐ray photoelectron spectroscopy (XPS). The wettabilities of the WO3 films were evaluated by contact angle (CA) measurements. It was found that the WO3 film exhibited superhydrophilicity under UV light irradiation, whereas after storage in the dark for a certain time, it turned to be superhydrophobic.