bluuebunny/crossref_metadata_2025_split huggingface dataset:
Meshless thermo‐elastoplastic analysis by triple‐reciprocity boundary element method
Authors: Ochiai Yoshihiro 
Published: September 2009

AbstractIn general, internal cells are required to solve thermo‐elastoplasticity problems by a conventional boundary element method (BEM). However, in this case, the merit of BEM, which is the easy preparation of data, is lost. A conventional multiple‐reciprocity boundary element method (MRBEM) cannot be used to solve elastoplasticity problems, because the distribution of initial strain or stress cannot be determined analytically. In this study, it is shown that without the use of internal cells, two‐dimensional thermo‐elastoplasticity problems can be solved by a triple‐reciprocity BEM using a thin plate spline. Initial strain and stress formulations are adopted and the initial strain or stress distribution is interpolated using boundary integral equations. A new computer program was developed and applied to solve several problems. Copyright © 2009 John Wiley & Sons, Ltd.
Non‐linear model reduction for uncertainty quantification in large‐scale inverse problems
Authors: Galbally D. , Fidkowski K. , Willcox K. , Ghattas O. 
Published: September 2009

AbstractWe present a model reduction approach to the solution of large‐scale statistical inverse problems in a Bayesian inference setting. A key to the model reduction is an efficient representation of the non‐linear terms in the reduced model. To achieve this, we present a formulation that employs masked projection of the discrete equations; that is, we compute an approximation of the non‐linear term using a select subset of interpolation points. Further, through this formulation we show similarities among the existing techniques of gappy proper orthogonal decomposition, missing point estimation, and empirical interpolation via coefficient‐function approximation. The resulting model reduction methodology is applied to a highly non‐linear combustion problem governed by an advection–diffusion‐reaction partial differential equation (PDE). Our reduced model is used as a surrogate for a finite element discretization of the non‐linear PDE within the Markov chain Monte Carlo sampling employed by the Bayesian inference approach. In two spatial dimensions, we show that this approach yields accurate results while reducing the computational cost by several orders of magnitude. For the full three‐dimensional problem, a forward solve using a reduced model that has high fidelity over the input parameter space is more than two million times faster than the full‐order finite element model, making tractable the solution of the statistical inverse problem that would otherwise require many years of CPU time. Copyright © 2009 John Wiley & Sons, Ltd.
Variationally consistent computational homogenization of transient heat flow
Authors: Larsson Fredrik , Runesson Kenneth , Su Fang 
Published: September 2009

AbstractA framework for variationally consistent homogenization, combined with a generalized macro‐homogeneity condition, is exploited for the analysis of non‐linear transient heat conduction. Within this framework the classical approach of (model‐based) first‐order homogenization for stationary problems is extended to transient problems. Homogenization is then carried out in the spatial domain on representative volume elements (RVE), which are (in practice) introduced in quadrature points in standard fashion. Along with the classical averages, a higher order conservation quantity is obtained. An iterative FE2‐algorithm is devised for the case of non‐linear diffusion and storage coefficients, and it is applied to transient heat conduction in a strongly heterogeneous particle composite. Parametric studies are carried out, in particular with respect to the influence of the ‘internal length’ associated with the second‐order conservation quantity. Copyright © 2009 John Wiley & Sons, Ltd.
Assessing the impact of organizational learning and innovation on performance in cultural organizations
Authors: Garrido M. José , Camarero Carmen 
Published: September 2009

AbstractProduct innovation, technological innovation and organizational innovations are the key to helping cultural organizations achieve their social mission and achieve efficiency. This innovation strategy and the outcomes depend on introducing learning orientation into the organization. The current work analyses the relationship between learning orientation, innovativeness and performance for the case of 386 British, French and Spanish museums. Findings indicate that learning orientation significantly influences both innovativeness and performance. Further, whereas technological and organizational innovations are related to economic performance, product innovations have a greater impact on social performance.Copyright © 2009 John Wiley & Sons, Ltd.
Removal of Pb2+ and Cd2+ ions from aqueous solutions using guanidine modified hydrogels
Authors: Yetimoğlu Ece Kök , Fırlak Melike , Kahraman Memet Vezir , Deniz Sabahattin 
Published: September 2009

AbstractIn this study, experimental measurements have been made on the batch adsorption of cadmium and lead ions from aqueous solutions using poly(guanidine modified 2‐acrylamido‐2‐methylpropan sulfonic acid/acrylic acid/N‐vinylpyrrolidone/2‐Hydroxyethyl methacrylate), P(AMPSG/AAc/NVP/HEMA) hydrogels. The guanidyl end group bearing AMPSG monomer was synthesized from the reaction of AMPS and guanidine. The hydrogels were prepared by UV‐curing technique. The morphology of the dry H10‐hydrogel sample was examined by SEM. The influence of the uptake conditions, such as pH, functional monomer per cent, contact time, initial feed concentration, and foreign metal ions on the metal ion binding capacity of hydrogel, was also tested. The selectivity of the hydrogel toward the different metal ions tested was Hg(II) > Pb(II) > Au(III) > Cd(II). The adsorption isotherm models were applied to the experimental data, and it was seen that the Langmuir isotherm model was the best fit for the adsorption of Cd(II) and Pb(II) ions on P(AMPSG/AAc/NVP/HEMA) hydrogel. It was found that adsorbed lead and cadmium ions on P(AMPSG/AAc/NVP/HEMA) hydrogel can be effectively desorbed by acid leaching and the regenerated P(AMPSG/AAc/NVP/HEMA) hydrogel can be reused almost five times less without any loss of adsorption capacity. Copyright © 2009 John Wiley & Sons, Ltd.
High Quality SiO2‐like Layers by Large Area Atmospheric Pressure Plasma Enhanced CVD: Deposition Process Studies by Surface Analysis
Authors: Premkumar Peter Antony , Starostin Sergey A. , de Vries Hindrik , Paffen Roger M. J. , Creatore Mariadriana , Eijkemans Tom J. , Koenraad Paul M. , de Sanden Mauritius C. M. van 
Published: September 2009

AbstractThis work reports on the main competing processes and their contribution to the properties of SiO2 layers on polymers in large area AP‐PE‐CVD from ArN2O2‐HMDSO mixtures. The detailed space resolved surface analysis on the statically deposited films showed smooth SiOx films in the vicinity of the gas injection, as deposited by HMDSO radicals. At the gas effluent, due to HMDSO depletion, non‐depositing species interact with the polymer and induce rough deposits with high carbon content. The competition of plasma–polymer surface interaction with HMDSO radicals deposition, is further confirmed from the analysis of films grown on polymers with a “protecting” layer and with reverse gas flow direction. Under web roll conditions, HMDSO radicals deposition is dominant, resulting in high quality SiOx layers along the whole electrode length.magnified image
Understanding the Roughening and Degradation of 193 nm Photoresist during Plasma Processing: Synergistic Roles of Vacuum Ultraviolet Radiation and Ion Bombardment
Authors: Nest Dustin , Chung Ting‐Ying , Graves David B. , Engelmann Sebastian , Bruce Robert L. , Weilnboeck Florian , Oehrlein Gottlieb S. , Wang Deyan , Andes Cecily , Hudson Eric A. 
Published: September 2009

AbstractWe have identified a synergistic roughening mechanism of 193 nm photoresist, where simultaneous ion bombardment, vacuum ultraviolet (VUV) radiation, and moderate substrate heating in a well‐characterized beam system results in a similar level of surface roughness observed during conditions typical of plasma etching. VUV radiation (147 nm) results in bulk modification of the photoresist polymer, witnessed by the loss of carbon–oxygen bonds through transmission FTIR. Ion bombardment (150 eV) results in the formation of a densified surface layer on the order of a few nanometers in depth. We have shown that elevated levels of roughness are observed only during simultaneous exposure and that sequential exposure is not sufficient to produce surface roughness. In addition, through the use of transmission FTIR we have shown that an etching synergy does not exist and that etch rates are nearly independent of temperature. We propose that the observed roughness could be due to the drastically different mechanical properties of the ion‐modified near‐surface region and VUV‐modified bulk photoresist, where the difference is exaggerated at elevated temperatures. A more complete understanding of plasma‐induced surface roughness will require further study, resulting in the improvement of existing pattern transfer technologies and possibly novel new technologies as well.magnified image
Recombinant human DNase in children with airway malacia and lower respiratory tract infection
Authors: Boogaard Ruben , de Jongste Johan C. , Vaessen‐Verberne Anja A.P.H. , Hop Wim C.J. , Merkus Peter J.F.M. 
Published: September 2009

AbstractBackgroundChildren with airway malacia often have protracted courses of airway infections, because dynamic airway collapse during coughing results in impaired mucociliary clearance. The aim of this study was to determine the effect of the mucolytic drug recombinant human deoxyribonuclease (rhDNase) on the recovery of respiratory symptoms in children with airway malacia and lower respiratory tract infection (LRTI).MethodsIn a randomized double‐blind controlled clinical trial, 40 children with airway malacia and LRTI were randomly assigned to receive either 2.5 mg nebulized rhDNase or placebo twice daily for 2 weeks. The primary endpoint was the change in the cough diary score (CDS) (scale 0–5) from baseline to the second week of treatment. Secondary endpoints were VAS symptom scores for cough, dyspnea, and difficulty in expectorating sputum, need for an antibiotic course, and lung function data (FVC, FEV1, FEF75, R).ResultsThere was no significant difference in the mean change in CDSs from baseline between the rhDNase group and the placebo group (mean difference for daytime 0.19 (95% CI −0.53 to 0.90); for nighttime 0.38 (95% CI −0.30 to 1.05). Proportions of patients requiring antibiotics, and the mean changes in symptom scores and lung function from baseline did not significantly differ between both groups.ConclusionTreatment with 2 weeks of nebulized rhDNase does not enhance recovery or reduce the need for antibiotics in children with airway malacia and LRTI. (Controlled‐trials.com number, ISRCTN85366144). Pediatr Pulmonol. 2009; 44:962–969. ©2009 Wiley‐Liss, Inc.
Respiratory health in overweight and obese Chinese children
Authors: He Qi‐qiang , Wong Tze‐wai , Du Lin , Jiang Zhuo‐qin , Qiu Hong , Gao Yang , Liu Jia‐wei , Wu Jia‐gang , Yu Ignatius Tak‐sun 
Published: September 2009

AbstractObjectivesChildhood obesity has been suggested to be associated with asthma and impairment of pulmonary functions, but the findings are conflicting. The aim of this study was to examine the relationship of body mass index (BMI) with asthma, asthma‐like symptoms, and lung functions in Chinese schoolchildren.MethodsData from a survey of 2,179 children aged 10.04 ± 0.85 years in Guangzhou, China were analyzed. Children's history of respiratory symptoms/diseases and other potential confounders were obtained by standardized questionnaires. Anthropometric and spirometry tests were performed in all subjects. Children were categorized as “normal weight,” “overweight,” and “obesity” using Chinese Obesity cut‐off points based on age‐ and gender‐specific BMI values.ResultsBeing overweight was significantly associated with an increased risk of cough with cold (odds ratio, OR 1.60; 95% CI 1.01–2.55) in boys, and phlegm with cold (OR 2.46; 95% CI 1.25–4.85) and cough without cold (OR 2.91; 95% CI 1.05–8.08) in girls. Being obese was positively associated with an increased risk of phlegm with cold (OR 1.69; 95% CI 1.04–2.87) in boys, and wheezing (OR 3.82; 95% CI 1.28–11.42) and wheezing with cold in girls (OR 8.75; 95% CI 2.11–36.34). The forced vital capacity (FVC) increased with BMI in all children, overweight boys and obese girls also had significantly higher forced expiratory volume in 1 sec (FEV1) than those with normal weight.ConclusionsOur findings demonstrate that overweight and obesity are high risks for children's respiratory symptoms and diseases. Pulmonary function was not adversely affected by obesity in schoolchildren. Pediatr Pulmonol. 2009; 44:997–1002. ©2009 Wiley‐Liss, Inc.
Pulmonary function changes in children after transcatheter closure of atrial septal defect
Authors: Lee Yu‐Sheng , Jeng Mei‐Jy , Tsao Pei‐Chen , Yang Chia‐Feng , Soong Wen‐Jue , Hwang Betau , Tang Ran‐Bin 
Published: September 2009

AbstractThis study was performed to assess changes in pulmonary function test (PFT) and pulmonary outcome after transcatheter closure of atrial septal defect (ASD) in pediatric patients. A total 55 pediatric patients undergoing transcatheter ASD closure received PFT at baseline (day before ASD closure), and at 3 days and 6 months after procedure. Forced vital capacity (FVC), forced expired volume in 1 sec (FEV1), FEV1 to FVC ratio (FEV1/FVC), peak expiratory flow (PEF), and mean forced expiratory flow during the middle half of FVC (FEF25–75) were measured. Individually, subjects were classified by spirometry as normal, obstructive or restrictive, to evaluate the effect of transcatheter closure on pulmonary outcome. These 55 children had significantly reduced mean PEF and FEF25–75 (84 ± 24%, P = 0.040 and 76 ± 22%, P = 0.010, respectively) at baseline, with FEF25–75 reduced significantly at 3 days and 6 months (78 ± 24%, P = 0.010 and 81 ± 24%, P = 0.040, respectively) after transcatheter closure. Six months after transcatheter closure of ASD, significant improvement was observed in mean FVC (94 ± 19% vs. 98 ± 15%, P = 0.034) and FEV1 (90 ± 20% vs. 96 ± 19%, P = 0.008). Assessed individually, better pulmonary outcome was found in patients without pulmonary hypertension (PH) (χ2 = 8.333, P = 0.044). PFT disturbance was observed in significant flow limitation in the peripheral airway of ASD patients. Improved PFT was found after transcatheter closure and better pulmonary outcome was observed in patients without PH. ASD children need monitoring pulmonary function and should receive transcatheter closure before PH develops. Pediatr Pulmonol. 2009; 44:1025–1032. ©2009 Wiley‐Liss, Inc.
Effect of Nano‐Aluminum and Fumed Silica Particles on Deflagration and Detonation of Nitromethane
Authors: Sabourin Justin L. , Yetter Richard A. , Asay Blaine W. , Lloyd Joseph M. , Sanders Victor E. , Risha Grant A. , Son Steven F. 
Published: September 2009

AbstractThe heterogeneous interaction between nitromethane (NM), particles of nanoscale aluminum (38 and 80 nm diameter), and fumed silica is examined in terms of the deflagration and detonation characteristics. Burning rates are quantified as functions of pressure using an optical pressure vessel up to 14.2 MPa, while detonation structure is characterized in terms of failure diameter. Nitromethane is gelled using fumed silica (CAB‐O‐SIL®), as well as by the nanoaluminum particles themselves. Use of nanoaluminum particles with fumed silica slightly increases burning rates compared to the use of larger diameter Al particles; however distinct increases in burning rates are found when CAB‐O‐SIL is removed and replaced with more energetic aluminum nanoparticles, whose high surface area allows them to also act as the gellant. Mixtures including fumed silica yield a reduced burning rate pressure exponent compared to neat NM, while mixtures of aluminum particles alone show a significant increase. Failure diameters of mixture detonations are found to vary significantly as a function of 38 nm aluminum particle loading, reducing more than 50% from that of neat nitromethane with 12.5% (by mass) aluminum loading. Failure diameter results indicate a relative minimum with respect to particle separation (% loading) which is not observed in other heterogeneous mixtures.
Structural model of ρ1 GABAC receptor based on evolutionary analysis: Testing of predicted protein–protein interactions involved in receptor assembly and function
Authors: Adamian Larisa , Gussin Hélène A. , Tseng Yan Yuan , Muni Niraj J. , Feng Feng , Qian Haohua , Pepperberg David R. , Liang Jie 
Published: September 2009

AbstractThe homopentameric ρ1 GABAC receptor is a ligand‐gated ion channel with a binding pocket for γ‐aminobutyric acid (GABA) at the interfaces of N‐terminal extracellular domains. We combined evolutionary analysis, structural modeling, and experimental testing to study determinants of GABAC receptor assembly and channel gating. We estimated the posterior probability of selection pressure at amino acid residue sites measured as ω‐values and built a comparative structural model, which identified several polar residues under strong selection pressure at the subunit interfaces that may form intersubunit hydrogen bonds or salt bridges. At three selected sites (R111, T151, and E55), mutations disrupting intersubunit interactions had strong effects on receptor folding, assembly, and function. We next examined the role of a predicted intersubunit salt bridge for residue pair R158–D204. The mutant R158D, where the positively charged residue is replaced by a negatively charged aspartate, yielded a partially degraded receptor and lacked membrane surface expression. The membrane surface expression was rescued by the double mutant R158D–D204R, where positive and negative charges are switched, although the mutant receptor was inactive. The single mutants R158A, D204R, and D204A exhibited diminished activities and altered kinetic profiles with fast recovery kinetics, suggesting that R158–D204 salt bridge perhaps stabilizes the open state of the GABAC receptor. Our results emphasize the functional importance of highly conserved polar residues at the protein–protein interfaces in GABAC ρ1 receptors and demonstrate how the integration of computational and experimental approaches can aid discovery of functionally important interactions.
Controllable protein cleavages through intein fragment complementation
Authors: Volkmann Gerrit , Sun Wenchang , Liu Xiang‐Qin 
Published: September 2009

AbstractIntein‐based protein cleavages, if carried out in a controllable way, can be useful tools of recombinant protein purification, ligation, and cyclization. However, existing methods using contiguous inteins were often complicated by spontaneous cleavages, which could severely reduce the yield of the desired protein product. Here we demonstrate a new method of controllable cleavages without any spontaneous cleavage, using an artificial S1 split‐intein consisting of an 11‐aa N‐intein (IN) and a 144‐aa C‐intein (IC). In a C‐cleavage design, the IC sequence was embedded in a recombinant precursor protein, and the small IN was used as a synthetic peptide to trigger a cleavage at the C‐terminus of IC. In an N‐cleavage design, the short IN sequence was embedded in a recombinant precursor protein, and the separately produced IC protein was used to catalyze a cleavage at the N‐terminus of IN. These N‐ and C‐cleavages showed >95% efficiency, and both successfully avoided any spontaneous cleavage during expression and purification of the precursor proteins. The N‐cleavage design also revealed an unexpected and interesting structural flexibility of the IC protein. These findings significantly expand the effectiveness of intein‐based protein cleavages, and they also reveal important insights of intein structural flexibility and fragment complementation.
KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program
Authors: Chen Vincent B. , Davis Ian W. , Richardson David C. 
Published: September 2009

AbstractProper visualization of scientific data is important for understanding spatial relationships. Particularly in the field of structural biology, where researchers seek to gain an understanding of the structure and function of biological macromolecules, it is important to have access to visualization programs which are fast, flexible, and customizable. We present KiNG, a Java program for visualizing scientific data, with a focus on macromolecular visualization. KiNG uses the kinemage graphics format, which is tuned for macromolecular structures, but is also ideal for many other kinds of spatially embedded information. KiNG is written in cross‐platform, open‐source Java code, and can be extended by end users through simple or elaborate “plug‐in” modules. Here, we present three such applications of KiNG to problems in structural biology (protein backbone rebuilding), bioinformatics of high‐dimensional data (e.g., protein sidechain chi angles), and classroom education (molecular illustration). KiNG is a mature platform for rapidly creating and capitalizing on scientific visualizations. As a research tool, it is invaluable as a test bed for new methods of visualizing scientific data and information. It is also a powerful presentation tool, whether for structure browsing, teaching, direct 3D display on the web, or as a method for creating pictures and videos for publications. KiNG is freely available for download at http://kinemage.biochem.duke.edu.
The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of α + β fold
Authors: Wang Shuren , Kirillova Olga , Chruszcz Maksymilian , Gront Dominik , Zimmerman Matthew D. , Cymborowski Marcin T. , Shumilin Igor A. , Skarina Tatiana , Gorodichtchenskaia Elena , Savchenko Alexei , Edwards Aled M. , Minor Wladek 
Published: September 2009

AbstractThe structure of AF2331, a 11‐kDa orphan protein of unknown function from Archaeoglobus fulgidus, was solved by Se‐Met MAD to 2.4 Å resolution. The structure consists of an α + β fold formed by an unusual homodimer, where the two core β‐sheets are interdigitated, containing strands alternating from both subunits. The decrease in solvent‐accessible surface area upon dimerization is unusually large (3960 Å2) for a protein of its size. The percentage of the total surface area buried in the interface (41.1%) is one of the largest observed in a nonredundant set of homodimers in the PDB and is above the mean for nearly all other types of homo‐oligomers. AF2331 has no sequence homologs, and no structure similar to AF2331 could be found in the PDB using the CE, TM‐align, DALI, or SSM packages. The protein has been identified in Pfam 23.0 as the archetype of a new superfamily and is topologically dissimilar to all other proteins with the “3‐Layer (BBA) Sandwich” fold in CATH. Therefore, we propose that AF2331 forms a novel α + β fold. AF2331 contains multiple negatively charged surface clusters and is located on the same operon as the basic protein AF2330. We hypothesize that AF2331 and AF2330 may form a charge‐stabilized complex in vivo, though the role of the negatively charged surface clusters is not clear.