bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of compression molding of stand‐alone microlenses: Simulation and experimental results
Authors: Mirkhalaf M. , Tor S.B. , Murukeshan V.M. , Loh N.H. , Lye S.W. 
Published: July 2010

AbstractHot compression molding is a promising method to fabricate polymer stand‐alone microlenses. A reliable theoretical as well as statistical analysis is required for the optimization of the process to minimize the residual stresses and to predict the amount of springback to achieve a better replication of the mold profile. This article in this context focuses on the finite element simulation (FES), optimization as well as experimental validation of hot compression molding of polymer stand‐alone microlenses. Three steps such as molding, cooling, and demolding, under different molding parameters, were analyzed using ABAQUS/standard solver and the results were compared with experimental results. Compression test and compression relaxation test have been conducted at different temperatures and strain rates to characterize the rheological behavior of material. Two material models, linear viscoelastic and hyperelastic–viscoelastic models, were developed and used for compression test simulations. Hyperelastic–viscoelastic model is found to predict the material behavior in low strain rates better and, thus, is used for the simulation of actual lens compression molding. Good agreement is found between the FES‐predicted curve and the lens profile molded at different molding temperatures. POLYM. ENG. SCI., 2010. © 2010 Society of Plastics Engineers
Numerical simulation of the self‐assembly of a polymer–polymer–solvent ternary system on a heterogeneously functionalized substrate
Authors: Shang Yingrui , Kazmer David , Wei Ming , Barry Carol , Mead Joey 
Published: July 2010

AbstractThe spinodal decomposition of a polymer–polymer–solvent ternary blend spin coated on heterogeneously functionalized substrate is studied in a three‐dimensional numerical model. The Cahn‐Hilliard equation was used to describe the free energy profile of the domain. The mechanism of the morphology evolution was studied quantitatively. The well‐established linear relationship of the characteristic length, R(t), with t1/3 can be observed in the simulation results. The functionalized substrate greatly affected the morphology evolution of blends with different solvent concentrations. The results indicated that a critical time can be observed, at which the evolution rate changes abruptly, also after which the compatibility of the surface morphology to the functionalized substrate pattern increases at a much lower pace in the diluted solution. In the condensed solution, the compatibility actually decreases beyond the critical time. The influence of solvent evaporation is investigated and a sharper interface was observed in the case with solvent evaporation and film thickness reduction. POLYM. ENG. SCI., 2010. © 2010 Society of Plastics Engineers
Linear and nonlinear melt rheology and extrudate swell of acrylonitrile‐butadiene‐styrene and organoclay‐filled acrylonitrile‐butadiene‐styrene nanocomposite
Authors: Saadat Amir , Nazockdast Hossein , Sepehr Fatemeh , Mehranpour Milad 
Published: July 2010

AbstractMelt viscoelastic behavior and the die swell of Acrylonitrile‐Butadiene‐Styrene (ABS) and ABS/clay nanocomposites varying in organoclay loading were studied. A pronounced low‐frequency nonterminal behavior exhibited in linear viscoelastic experiments along with an apparent yield stress in transient startup flow tests suggested the existence of a network type, because of interconnection of rubber particles in ABS matrix. From the results of linear and nonlinear viscoelastic measurements, it was found that the incorporation of organoclay can lead to the formation of an additional network formed between organoclay tactoids that caused reduced temperature dependency of linear viscoelastic properties of the nanocomposite samples compared with ABS matrix. The swelling behavior of samples was interpreted using the results of stress relaxation experiments after cessation of steady shear flow. The great reduction in the die swell of nanocomposite samples could be explained in terms of great surface area and anisometric nature of organoclay tactoids and/or platelets, which promote energy consumption and less energy to be stored in chains. POLYM. ENG. SCI., 2010. © 2010 Society of Plastics Engineers
Microwave absorption of poly‐N‐vinylcarbazole–polyaniline composites
Authors: Basavaraja C. , Jo Eun Ae , Kim Bong Seong , Kim Dae Gun , Huh Do Sung 
Published: July 2010

AbstractPoly‐N‐vinylcarbazole–polyaniline (PANI) composites were synthesized using different loading concentration of aniline (0.025–0.1 M) for their microwave absorption characteristics. The obtained composites were studied by Fourier transform infrared spectroscopy, thermogravimetric analysis technique, and atomic force microscope for their chemical structure, thermal stability, and the surface modifications, respectively. The conductivity increased much with the increase of aniline concentration in the composites. The composite sheets exhibited a strong microwave absorption in the microwave range of 1–10 GHz and achieved a maximum absorption value of 33 dB. The position of absorbing peak shows a mixed trend moving from lower to higher and again to lower with an increasing the concentration of aniline in the poly‐N‐vinylcarbazole–PANI. The new polymer composite exhibited an appreciable electromagnetic interference shielding efficiency compared with the previously reported PANI composites. POLYM. ENG. SCI., 2011. © 2010 Society of Plastics Engineers
Power output fluctuations in large scale pv plants: One year observations with one second resolution and a derived analytic model
Authors: Marcos Javier , Marroyo Luis , Lorenzo Eduardo , Alvira David , Izco Eloisa 
Published: July 2010

AbstractThe variable nature of the irradiance can produce significant fluctuations in the power generated by large grid‐connected photovoltaic (PV) plants. Experimental 1 s data were collected throughout a year from six PV plants, 18 MWp in total. Then, the dependence of short (below 10 min) power fluctuation on PV plant size has been investigated. The analysis focuses on the study of fluctuation frequency as well as the maximum fluctuation value registered. An analytic model able to describe the frequency of a given fluctuation for a certain day is proposed. Copyright © 2010 John Wiley & Sons, Ltd.
Comparative study of ZnO thin films prepared by plasma deposition and electron beam evaporation for use in photovoltaic devices
Authors: Falcão V. D. , Miranda D. O. , Sabino M. E. L. , Moura T. D. O. , Diniz A. S. A. C , Cruz L. R. , Branco J. R. T. 
Published: July 2010

AbstractUndoped zinc oxide thin films were grown at room temperature using two techniques: plasma deposition (PD) and electron beam evaporation in an argon atmosphere. PD offers some advantages, such as low ion damage and low deposition temperature. The optical transmittance of the films deposited by both methods was higher than 80% in the near UV–VIS range; the energy band gap and index of refraction agree with values reported in the literature. The resistivity of films grown by PD was 3.1 × 10−2 Ω cm, lower than the value of 1.2 × 10−1 Ω cm found for plasma assisted e‐beam evaporated films. Copyright © 2010 John Wiley & Sons, Ltd.
GIAO‐HDFT scaling factor for 13C NMR chemical shifts calculation
Authors: Costa Fabio Luiz Paranhos , de Albuquerque Ana Carolina Ferreira , dos Santos Fernando Martins , de Amorim Mauro Barbosa 
Published: July 2010

AbstractIn this paper, we present a GIAO‐HDFT scaling factor study, in which we intent to investigate the ability of GIAO‐HDFT/cc‐pVDZ to achieve a high cost‐effectiveness ratio. A set of 22 small molecules providing 27 different 13C chemical shifts determined in the gas phase was used. Geometry optimizations were performed for a single molecule in a gas phase using B3LYP/cc‐pVDZ, B3LYP/aug‐cc‐pVDZ, B3PW91/cc‐pVDZ and B3PW91/aug‐cc‐pVDZ level of theory. NMR chemical shifts were computed at the B3LYP and B3PW91 with cc‐pVnZ (n = 2–3) and augment aug‐cc‐pVnZ (n = 2–3) levels using the GIAO method and are given relative to that of TMS calculated at the same level of theory. Despite the calculation approximations the chemical shifts calculated at the B3PW91/cc‐pVDZ//B3PW91/cc‐pVDZ using a simple relationship (δscalc = 1.02 δcalc − 0.92, where δcalc and δscalc are the calculated and the linearly scaled values of the 13C chemical shifts, respectively) were able to yield MAD and RMS errors as small as those obtained with other GIAO‐HDFT (B3LYP, B3PW91 and OPBE) with bigger basis sets, such as 6‐311 + G(2d,p) and cc‐pVTZ. The used approach also proved successful in distinguishing regioisomers, but, unfortunately, it lacks the ability to distinguish between diastereoisomers, a task otherwise proved to be very difficult to accomplish. Copyright © 2010 John Wiley & Sons, Ltd.
Surfactant protein C gene (SFTPC) mutation‐associated lung disease: High‐resolution computed tomography (HRCT) findings and its relation to histological analysis
Authors: Mechri M. , Epaud R. , Emond S. , Coulomb A. , Jaubert F. , Tarrant A. , Feldmann D. , Flamein F. , Clement A. , de Blic J. , Taam R. Abou , Brunelle F. , le Pointe H. Ducou 
Published: July 2010

AbstractAim of the StudyDetermine high‐resolution tomography (HRCT) scan characteristics in children with SFTPC mutation and correlate them to histological findings.Patients and MethodsThis retrospective multicenter study included 15 children (7 females and 8 males) with SFTPC mutations. HRCT scans have been performed in all the children and lung biopsies in 8 children.ResultsFrom all signs assessed on initial HRCT scans, ground‐glass opacities (n = 14, 93%) and lung cysts (n = 6, 40%) were predominant. Interlobular septal thickening (n = 1, 7%), air space consolidation (n = 1, 7%), paraseptal emphysema (n = 2, 13%), and pulmonary nodules (n = 1, 7%) were also found. Histological analysis revealed accumulation of macrophages in the alveolar lumen, type II pneumocyte hyperplasia, and alveolar septal thickening. Dilatation of the respiratory bronchiole and alveolar duct associated with muscular hyperplasia were also described. Interestingly, lung cysts on HRCT scans were associated with dilatation of terminal bronchioli and alveolar duct in lung biopsies.ConclusionIn children with SFTPC mutations, HRCT scan finding was highly correlated to the histological findings and, as such, represent a useful tool to identify patients that may require SFTPC gene sequencing. Pediatr Pulmonol. 2010; 45:1021–1029. © 2010 Wiley‐Liss, Inc.
Aerosolized amphotericin for the treatment of allergic bronchopulmonary aspergillosis
Authors: Hayes Don , Murphy Brian S. , Lynch James E. , Feola David J. 
Published: July 2010

AbstractAllergic bronchopulmonary aspergillosis (ABPA) is a complex hypersensitivity reaction to Aspergillus fumigatus that occur frequently in patients with cystic fibrosis (CF). Recurrent episodes of bronchial obstruction, inflammation, and mucoid impaction occur in ABPA and results in bronchiectasis, fibrosis, and respiratory failure. The treatment of ABPA includes corticosteroids to reduce the acute inflammation and intraconazole to reduce the fungal colonization load in order to reduce lung injury. This case discusses the successful use of aerosolized amphotericin B for the treatment of ABPA in a 14‐year‐old patient with CF listed for lung transplant. The patient required fewer hospitalizations, and both oral corticosteroids and anti‐fungal therapy were eventually stopped. Pediatr Pulmonol. 2010;45:1145–1148. © 2010 Wiley‐Liss, Inc.
Sop‐GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors
Authors: Zhmurov A. , Dima R. I. , Kholodov Y. , Barsegov V. 
Published: July 2010

AbstractTheoretical exploration of fundamental biological processes involving the forced unraveling of multimeric proteins, the sliding motion in protein fibers and the mechanical deformation of biomolecular assemblies under physiological force loads is challenging even for distributed computing systems. Using aCα‐based coarse‐grained self organized polymer (SOP) model, we implemented the Langevin simulations of proteins on graphics processing units (SOP‐GPU program). We assessed the computational performance of an end‐to‐end application of the program, where all the steps of the algorithm are running on a GPU, by profiling the simulation time and memory usage for a number of test systems. The ∼90‐fold computational speedup on a GPU, compared with an optimized central processing unit program, enabled us to follow the dynamics in the centisecond timescale, and to obtain the force‐extension profiles using experimental pulling speeds (vf= 1–10 μm/s) employed in atomic force microscopy and in optical tweezers‐based dynamic force spectroscopy. We found that the mechanical molecular response critically depends on the conditions of force application and that the kinetics and pathways for unfolding change drastically even upon a modest 10‐fold increase invf. This implies that, to resolve accurately the free energy landscape and to relate the results of single‐molecule experimentsin vitroandin silico, molecular simulations should be carried out under the experimentally relevant force loads. This can be accomplished in reasonable wall‐clock time for biomolecules of size as large as 105residues using the SOP‐GPU package. Proteins 2010; © 2010 Wiley‐Liss, Inc.
Structural origins of pH‐dependent chemical shifts in the B1 domain of protein G
Authors: Tomlinson Jennifer H. , Green Victoria L. , Baker Patrick J. , Williamson Mike P. 
Published: July 2010

AbstractWe report chemical shifts for HN, N, and C′ nuclei in the His‐tagged B1 domain of protein G (GB1) over a range of pH values from pH 2.0 to 9.0, which fit well to standard pH‐dependent equations. We also report a 1.2 Å resolution crystal structure of GB1 at pH 3.0. Comparison of this crystal structure with published crystal structures at higher pHs provides details of the structural changes in GB1 associated with protonation of the carboxylate groups, in particular a conformational change in the C‐terminus of the protein at low pH. An additional change described recently is not seen in the crystal structure because of crystal contacts. We show that the pH‐dependent changes in chemical shifts can be almost entirely understood based on structural changes, thereby providing insight into the relationship between structure and chemical shift. In particular, we describe through‐bond effects extending up to five bonds, affecting N and C′ but not HN; through‐space effects of carboxylates, which fit well to a simple electric field model; and effects due to conformational change, which have a similar magnitude to many of the direct effects. Finally, we discuss cooperative effects, demonstrating a lack of cooperative unfolding in the helix, and the existence of a β‐sheet “iceberg” extending over three of the four strands. This study therefore extends the application of chemical shifts to understanding protein structure. Proteins 2010; © 2010 Wiley‐Liss, Inc.
Structural facets of disease‐linked human prion protein mutants: A molecular dynamic study
Authors: Rossetti Giulia , Giachin Gabriele , Legname Giuseppe , Carloni Paolo 
Published: July 2010

AbstractPrion propagation in transmissible spongiform encephalopathies involves the conversion of the cellular prion protein, PrPC, into the pathogenic conformer PrPSc. Human familial forms of the disease are linked to specific mutations in the PrP gene, PRNP, and include Gerstmann‐Sträussler‐Scheinker syndrome (GSS), familial Creutzfeldt‐Jakob disease (fCJD), and fatal familial insomnia. To gain insights into the molecular basis of these disorders, we performed 200 ns of classical molecular dynamic simulations in aqueous solution on wild type (WT) human PrP (HuPrP), and on three HuPrP variants located in the globular HuPrP domain: two pathological mutations, HuPrP(Q212P) and HuPrP(E200K), linked to GSS and to fCJD respectively, and one protective polymorphism, HuPrP(E219K) (total time‐scale simulated 800 ns). A comparison between the predicted structural determinants of WT HuPrP and HuPrP(E200K) with their NMR structures established the accuracy of the methods used. Strikingly, the analyzed disease‐linked variants produced their major effect on the α2‐α3 region and the β2‐α2 loop, regardless of the mutation position. The conformational change of the latter might affect the interactions with cellular partners in the fibrillation process. The protocol proposed here represents a powerful approach for reproducing the structural effects of genetic mutations located in the globular domain of HuPrP, such as the GSS‐related HuPrP(Q212P) and the protective polymorphism HuPrP(E219K). Proteins 2010. © 2010 Wiley‐Liss, Inc.
Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13–19
Authors: Kozakov Dima , Hall David R. , Beglov Dmitri , Brenke Ryan , Comeau Stephen R. , Shen Yang , Li Keyong , Zheng Jiefu , Vakili Pirooz , Paschalidis Ioannis Ch. , Vajda Sandor 
Published: July 2010

AbstractOur approach to protein—protein docking includes three main steps. First, we run PIPER, a rigid body docking program based on the Fast Fourier Transform (FFT) correlation approach, extended to use pairwise interactions potentials. Second, the 1000 best energy conformations are clustered, and the 30 largest clusters are retained for refinement. Third, the stability of the clusters is analyzed by short Monte Carlo simulations, and the structures are refined by the medium‐range optimization method SDU. The first two steps of this approach are implemented in the ClusPro 2.0 protein–protein docking server. Despite being fully automated, the last step is computationally too expensive to be included in the server. When comparing the models obtained in CAPRI rounds 13–19 by ClusPro, by the refinement of the ClusPro predictions and by all predictor groups, we arrived at three conclusions. First, for the first time in the CAPRI history, our automated ClusPro server was able to compete with the best human predictor groups. Second, selecting the top ranked models, our current protocol reliably generates high‐quality structures of protein–protein complexes from the structures of separately crystallized proteins, even in the absence of biological information, provided that there is limited backbone conformational change. Third, despite occasional successes, homology modeling requires further improvement to achieve reliable docking results. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Liquiritigenin induces mitochondria‐mediated apoptosis via cytochrome c release and caspases activation in heLa Cells
Authors: Liu Changwei , Wang Yu , Xie Sirou , Zhou Yijing , Ren Xiangmei , Li Xiaoting , Cai Yunqing 
Published: July 2010

AbstractIt has been demonstrated that many flavonoids possess a potent and broad spectrum of antitumor activity. Liquiritigenin is a flavanone extracted from Glycyrrhizae. This study investigated the effects of liquiritigenin on cell viability and apoptosis induction in human cervical carcinoma (HeLa) cells. The results show that liquiritigenin significantly suppressed cell proliferation in a dose‐ and time‐dependent manner in HeLa cells. In addition, liquiritigenin promoted apoptosis in HeLa cells, evidenced by apoptotic morphological changes and Annexin‐V binding. The apoptosis induction with liquiritigenin is associated with the up‐regulation of p53 and Bax, along with down‐regulation of Bcl‐2 and survivin. Finally, examination of the mitochondrial pathway of apoptosis revealed that cytochrome c is released from mitochondria to cytosol, associated with the activation of caspase‐9 and ‐3, and the cleavage of poly (ADP‐ribose) polymerase (PARP). Overall, the results indicate that liquiritigenin induces apoptosis in part via the mitochondrial pathway, which is associated with p53 up‐regulation, release of cytochrome c and elevated activity of caspase‐9 and ‐3 in HeLa cells. Copyright © 2010 John Wiley & Sons, Ltd.
Sensitivity study for mesoscale simulations of gravity waves above Antarctica during Vorcore
Authors: Plougonven Riwal , Arsac Antonin , Hertzog Albert , Guez Lionel , Vial François 
Published: July 2010

AbstractThe observations from the Vorcore campaign (September 2005– January 2006) provide a unique dataset for the study of gravity waves in the lower stratosphere because of their wide coverage (150 000 observations from the South Pole to about 40°S) and of the quasi‐Lagrangian nature of the superpressure balloons used. Numerical simulations with a mesoscale model are undertaken in order to investigate further the observed gravity waves, their sources and the induced momentum fluxes. The need for a high spatial resolution makes it necessary to find a compromise between the size of the model domain and the length of the simulations. We describe preliminary simulations used to determine the best configuration of the model for this purpose, and show that the simulations compare reasonably well with the observations. Model results complement the observations and provide new insights into orographic and non‐orographic wave sources. Copyright © 2010 Royal Meteorological Society
Additional information from array comparative genomic hybridization technology over conventional karyotyping in prenatal diagnosis: a systematic review and meta‐analysis
Authors: Hillman S. C. , Pretlove S. , Coomarasamy A. , Mcmullan D. J. , Davison E. V. , Maher E. R. , Kilby M. D. 
Published: July 2010

AbstractObjectiveArray comparative genomic hybridization (CGH) is transforming clinical cytogenetics with its ability to interrogate the human genome at increasingly high resolution. The aim of this study was to determine whether array CGH testing in the prenatal population provides diagnostic information over conventional karyotyping.MethodsMEDLINE (1970 to December 2009), EMBASE (1980 to December 2009) and CINAHL (1982 to December 2009) databases were searched electronically. Studies were selected if array CGH was used on prenatal samples or if array CGH was used on postnatal samples following termination of pregnancy for structural abnormalities that were detected on an ultrasound scan. Of the 135 potential articles, 10 were included in this systematic review and eight were included in the meta‐analysis. The pooled rate of extra information detected by array CGH when the prenatal karyotype was normal was meta‐analyzed using a random‐effects model. The pooled rate of receiving an array CGH result of unknown significance was also meta‐analyzed.ResultsArray CGH detected 3.6% (95% CI, 1.5–8.5) additional genomic imbalances when conventional karyo‐typing was ‘normal’, regardless of referral indication. This increased to 5.2% (95% CI, 1.9–13.9) more than karyotyping when the referral indication was a structural malformation on ultrasound.ConclusionsThere appears to be an increased detection rate of chromosomal imbalances, compared with conventional karyotyping, when array CGH techniques are employed in the prenatal population. However, some are copy number imbalances that are not clinically significant. This carries implications for prenatal counseling and maternal anxiety. Copyright © 2010 ISUOG. Published by John Wiley & Sons, Ltd.