bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phase changes of poly(alkoxyphosphazenes), and their behavior in the presence of oligoisobutylene
Authors: Weikel Arlin L. , Lee David K. , Krogman Nicholas R. , Allcock Harry R. 
Published: July 2011

AbstractA series of closely related polyphosphazenes with propoxy, pentoxy, hexoxy, octoxy, isostearyloxy, and 2‐(2‐methoxyethoxy)ethoxy (MEE) side groups, together with cosubstituent species with both the alkoxy and MEE side chains, were studied for their morphology and miscibility with oligoisobutylene (OIB). All the pure polymers except one had a single glass transition temperature. The exception was the species with both isostearyloxy and MEE side groups, which underwent two low‐temperature second‐order transitions, even though 31P NMR spectra indicated the absence of a block‐type structure. For the single‐substituent macromolecules, the solubility at 80°C in OIB increased as the length of the unbranched alkoxy side groups rose from propoxy to octoxy (from 1 to 11 wt/wt%). However, the polymer with two isostearyloxy side chains per repeat unit had a low solubility in OIB (3 wt/wt%), and the species with the two MEE side groups on every repeat unit was totally insoluble. When both alkoxy and MEE side groups were present, the solubility in OIB was also low (0–3%), except for the species with both isostearyloxy and MEE side groups, which was soluble in OIB at a level of 21 wt/wt% at 80°C, and showed Tg evidence of polymer/oligomer miscibility even at −80°C. Explanations are suggested for the unusual behavior of this polymer. POLYM. ENG. SCI., 2011. © 2011 Society of Plastics Engineers
Stochastic modeling and simulation of photopolymerization process
Authors: Altun‐Çiftçioğlu Gökçen A. , Ersoy‐Meriçboyu Ayşegül , Henderson Clifford L. 
Published: July 2011

AbstractIn this study, the effect of photoinitiator concentration on the gelation time of different resins were studied in the absence of oxygen in the reaction volume by using passive microrheology technique. Four different monomers which are ethoxylated pentaerythritol tetraacrylate (SR494), trimethylolpropane triacrylate (SR351), triethylene glycol diacrylate (SR272), and 2(2‐ethoxyetoxy) ethyl acrylate (SR256) were used in these experiments. Resins were prepared from these four different monomers by mixing them with various amount of 2,2‐dimethoxy 1,2‐diphenylethanone photoinitiator molecule with high absorption coefficient at the frequency of UV light used in these experiment. The simulations of the results obtained from microrheology experiments were carried out with the new model based on the stochastic Monte Carlo approach in order to account for the inherently random and discrete nature of the photopolymerization reactions. The model captures the nonlinear decrease of gelation time with increasing photoinitator concentration and number of acrylate fragments on each monomer. POLYM. ENG. SCI., 2011. © 2011 Society of Plastics Engineers
Optimization of froth flotation procedure for poly(ethylene terephthalate) recycling industry
Authors: Carvalho M. Teresa , Ferreira Célia , Santos Liliana R. , Paiva M. Conceição 
Published: July 2011

AbstractThis article addresses the separation of polyethylene terephthalate (PET) from ternary blends with polyvinyl chloride (PVC) and polystyrene (PS) by froth flotation. The experimental work was carried out with representative samples from post‐consumer waste packages collected at drop‐off‐points. Previous to froth flotation, PET selective wetting was achieved by alkaline treatment followed by surfactant adsorption. For this purpose, an aqueous solution of NaOH and an industrial detergent commonly used for waste plastic washing were tested as alkaline treatment, and calcium lignosulphonate and Hostaphat were tested as surfactants. An enriched product with 98.9% grade in PET and only 0.6% in PVC was recovered in the nonfloated product. The PET recovery in this product was 97% while ∼96% of PVC and 91% of PS were recovered in the floated product. An analytical method was developed for the quantification of the waste plastic composition. The method was based on the selective dissolution of the plastics in the mixture. POLYM. ENG. SCI., 2012. © 2011 Society of Plastics Engineers
Investigating the role of FGF‐2 in stem cell maintenance by global phosphoproteomics profiling
Authors: Zoumaro‐Djayoon Adja D. , Ding Vanessa , Foong Leong‐Yan , Choo Andre , Heck Albert J. R. , Muñoz Javier 
Published: July 2011

AbstractHuman embryonic stem cells (hESCs) are of immense interest for regenerative medicine as a source of tissue replacement. Expansion of hESCs as a pluripotent population requires a balance between survival, proliferation and self‐renewal signals. One of the key growth factors that maintains this balance is fibroblast growth factor‐2 (FGF‐2). However, the underlying molecular mechanisms are poorly understood. We recently profiled specifically tyrosine phosphorylation events that occur during FGF‐2 stimulation of hESCs (Ding et al., J. Cell. Physiol. 2010, 225, 417–428). Here, we complement this phosphoproteome profiling by analyzing temporal dynamics of mostly serine and threonine protein phosphorylation events. Our multi‐dimensional strategy combines strong cation exchange chromatography to reduce the sample complexity followed by titanium dioxide off‐line for the enrichment of phosphopeptides and dimethylation‐based stable isotope labeling for quantification. This approach allowed us to identify and quantify 3261 unique proteins from which 1064 proteins were found to be phosphorylated in one or more residues (representing 1653 unique phosphopeptides). Approximately 40% of the proteins (553 unique phosphopeptides) showed differential phosphorylation upon FGF‐2 treatment. Among those are several members of the canonical pathways involved in pluripotency and self‐renewal (e.g. Wnt and PI3K/AKT), hESC‐associated proteins such as SOX2, RIF1, SALL4, DPPA4, DNMT3B and 53 proteins that are target genes of the pluripotency transcription factors SOX2, OCT4 and NANOG. These findings complement existing pluripotency analyses and provide new insights into how FGF‐2 assists in maintaining the undifferentiated state of hESCs.
A universally applicable process for preparing stoichiometrically 1:1 labelled functional proteins
Authors: Friedrich Achim , Hoheisel Jörg D. , Knemeyer Jens‐Peter , Marmé Nicole 
Published: July 2011

AbstractA universally applicable labelling and purification process was established to prepare biologically active proteins with a stoichiometric 1:1 ratio of attached dye‐label. The dye‐label is linked to a specific DNA sequence, which acts as a barcode‐like tag for affinity purification. The DNA‐dye tag is covalently bound to the target protein, which is present in excess to assure the binding of not more than one dye per molecule. Affinity purification occurs at magnetic beads that are functionalized with oligonucleotides that are complementary to the DNA‐tag of the labelled proteins but for one or two mismatches. Washing removes all unbound, unlabelled molecules. The labelled protein is subsequently released by the addition of a fully complementary oligonucleotide. This process allows a gentle purification of a protein fraction that has exactly one label attached to each molecule under conditions that preserve protein structure.
Identification of core–attachment complexes based on maximal frequent patterns in protein–protein interaction networks
Authors: Yu Liang , Gao Lin , Kong ChuiLiang 
Published: July 2011

AbstractIn this paper, we present a method for core–attachment complexes identification based on maximal frequent patterns (CCiMFP) in yeast protein–protein interaction (PPI) networks. First, we detect subgraphs with high degree as candidate protein cores by mining maximal frequent patterns. Then using topological and functional similarities, we combine highly similar protein cores and filter insignificant ones. Finally, the core–attachment complexes are formed by adding attachment proteins to each significant core. We experimentally evaluate the performance of our method CCiMFP on yeast PPI networks. Using gold standard sets of protein complexes, Gene Ontology (GO), and localization annotations, we show that our method gains an improvement over the previous algorithms in terms of precision, recall, and biological significance of the predicted complexes. The colocalization scores of our predicted complex sets are higher than those of two known complex sets. Moreover, our method can detect GO‐enriched complexes with disconnected cores compared with other methods based on the subgraph connectivity.
A Cloud Rise Model for Dust and Soot from High Explosive Detonations
Authors: Cao Xiaoying , Roy Gilles , Brousseau Patrick , Erhardt Lorne , Andrews William 
Published: July 2011

AbstractTraditionally, the evolution and rise of the dust and soot cloud resulting from high explosive detonations has been divided into two stages, with specific models used for each stage. In this study, based on the assumption that cloud formation progresses smoothly from stage to stage, a simple cloud rise model has been developed based on three sets of field tests of high explosive detonations (25×10−3 to 4.5 kg of detasheet and C‐4). This model provides a good fit to observations and measurements of clouds from detonations both at ground level and 1 m above the ground. It was also found that the detonation height has a noticeable influence on cloud rise before reaching its effective height, but the influence is minor on the subsequent cloud rise.
Applications of High‐Nitrogen Energetics in Pyrotechnics: Development of Perchlorate‐Free Red Star M126A1 Hand‐Held Signal Formulations with Superior Luminous Intensities and Burn Times
Authors: Sabatini Jesse J. , Nagori Amita V. , Latalladi Eric A. , Poret Jay C. , Chen Gary , Damavarapu Reddy , Klapötke Thomas M. 
Published: July 2011

AbstractPerchlorate‐free hand‐held signal illuminant formulations for the M126A1 red star parachute have been developed. The formulations exhibited longer burn times and higher luminous intensities compared to the US Army in‐service M126A1 formulation. The perchlorate‐free formulations derive their enhanced performance from the inclusion of strontium bis‐(1‐methyl‐5‐nitriminotetrazolate) monohydrate, the choice of magnesium used, and replacing a polyester binder system with an epoxy binder system.
A combinatorial histidine scanning library approach to engineer highly pH‐dependent protein switches
Authors: Murtaugh Megan L. , Fanning Sean W. , Sharma Tressa M. , Terry Alexandra M. , Horn James R. 
Published: July 2011

AbstractThere is growing interest in the development of protein switches, which are proteins whose function, such as binding a target molecule, can be modulated through environmental triggers. Efforts to engineer highly pH sensitive protein–protein interactions typically rely on the rational introduction of ionizable groups in the protein interface. Such experiments are typically time intensive and often sacrifice the protein's affinity at the permissive pH. The underlying thermodynamics of proton‐linkage dictate that the presence of multiple ionizable groups, which undergo a pKachange on protein binding, are necessary to result in highly pH‐dependent binding. To test this hypothesis, a novel combinatorial histidine library was developed where every possible combination of histidine and wild‐type residue is sampled throughout the interface of a model anti‐RNase A single domain VHH antibody. Antibodies were coselected for high‐affinity binding and pH‐sensitivity using anin vitro, dual‐function selection strategy. The resulting antibodies retained near wild‐type affinity yet became highly sensitive to small decreases in pH, drastically decreasing their binding affinity, due to the incorporation of multiple histidine groups. Several trends were observed, such as histidine “hot‐spots,” which will help enhance the development of pH switch proteins as well as increase our understanding of the role of ionizable residues in protein interfaces. Overall, the combinatorial approach is rapid, general, and robust and should be capable of producing highly pH‐sensitive protein affinity reagents for a number of different applications.
Histidine in continuum electrostatics protonation state calculations
Authors: Couch Vernon , Stuchebrukhov Alexei 
Published: July 2011

AbstractA modification to the standard continuum electrostatics approach to calculate protein pKas, which allows for the decoupling of histidine tautomers within a two‐state model, is presented. Histidine with four intrinsically coupled protonation states cannot be easily incorporated into a two‐state formalism, because the interaction between the two protonatable sites of the imidazole ring is not purely electrostatic. The presented treatment, based on a single approximation of the interrelation between histidine's charge states, allows for a natural separation of the two protonatable sites associated with the imidazole ring as well as the inclusion of all protonation states within the calculation. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Is the prediction of pKavalues by constant‐pH molecular dynamics being hindered by inherited problems?
Authors: Machuqueiro Miguel , Baptista António M. 
Published: July 2011

AbstractIn this study, we investigate two factors that can hinder the performance of constant‐pH molecular dynamics methods in predicting protein pKavalues, using hen egg white lysozyme as a test system. The first factor is related to the molecular definition and pKavalue of model compounds in the Poisson‐Boltzmann framework. We address this by defining the model compound as a molecular fragment with an associated pKavalue that is calibrated against experimental data, which results in a decrease of 0.12 units in pKaerrors. The second addressed factor is the possibility that detrimental structural distortions are being introduced in the simulations by the underlying molecular mechanics force field. This issue is investigated by analyzing how the gradual structural rearrangements affect the predicted pKavalues. The two GROMOS force fields studied here (43A1 and 53A6) yield good pKapredictions, although a time‐dependent performance is observed: 43A1 performs better after a few nanoseconds of structural reorganization (pKaerrors of ∼0.45), while 53A6 gives the best prediction right at the first nanosecond (pKaerrors of 0.42). These results suggest that the good performance of constant‐pH molecular dynamics methods could be further improved if these force field limitations were overcome. Proteins 2011;. © 2011 Wiley‐Liss, Inc.
A new residue‐nucleotide propensity potential with structural information considered for discriminating protein‐RNA docking decoys
Authors: Li Chun Hua , Cao Li Bin , Su Ji Guo , Yang Yong Xiao , Wang Cun Xin 
Published: July 2011

AbstractUnderstanding the key factors that influence the preferences of residue‐nucleotide interactions in specific protein‐RNA interactions has remained a research focus. We propose an effective approach to derive residue‐nucleotide propensity potentials through considering both the types of residues and nucleotides, and secondary structure information of proteins and RNAs from the currently largest nonredundant and nonribosomal protein‐RNA interaction database. To test the validity of the potentials, we used them to select near‐native structures from protein‐RNA docking poses. The results show that considering secondary structure information, especially for RNAs, greatly improves the predictive power of pair potentials. The success rate is raised from 50.7 to 65.5% for the top 2000 structures, and the number of cases in which a near‐native structure is ranked in top 50 is increased from 7 to 13 out of 17 cases. Furthermore, the exclusion of ribosomes from the database contributes 8.3% to the success rate. In addition, some very interesting findings follow: (i) the protein secondary structure element π‐helix is strongly associated with RNA‐binding sites; (ii) the nucleotide uracil occurs frequently in the most preferred pairs in which the unpaired and non‐Watson‐Crick paired uracils are predominant, which is probably significant in evolution. The new residue‐nucleotide potentials can be helpful for the progress of protein‐RNA docking methods, and for understanding the mechanisms of protein‐RNA interactions. Proteins 2012; © 2011 Wiley Periodicals, Inc.
Automated tertiary structure prediction with accurate local model quality assessment using the intfold‐ts method
Authors: McGuffin Liam J. , Roche Daniel B. 
Published: July 2011

AbstractThe IntFOLD‐TS method was developed according to the guiding principle that the model quality assessment (QA) would be the most critical stage for our template‐based modeling pipeline. Thus, the IntFOLD‐TS method firstly generates numerous alternate models, using in‐house versions of several different sequence‐structure alignment methods, which are then ranked in terms of global quality using our top performing QA method—ModFOLDclust2. In addition to the predicted global quality scores, the predictions of local errors are also provided in the resulting coordinate files, using scores that represent the predicted deviation of each residue in the model from the equivalent residue in the native structure. The IntFOLD‐TS method was found to generate high quality 3D models for many of the CASP9 targets, whilst also providing highly accurate predictions of their per‐residue errors. This important information may help to make the 3D models that are produced by the IntFOLD‐TS method more useful for guiding future experimental work. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid‐binding function
Authors: Aramini James M. , Rossi Paolo , Fischer Markus , Xiao Rong , Acton Thomas B. , Montelione Gaetano T. 
Published: July 2011

AbstractProtein domain family PF09905 (DUF2132) is a family of small domains of unknown function that are conserved in a wide range of bacteria. Here we describe the solution NMR structure of the 80‐residue VF0530 protein from Vibrio fischeri, the first structural representative from this protein domain family. We demonstrate that the structure of VF0530 adopts a unique four‐helix motif that shows some similarity to the C‐terminal double‐stranded DNA (dsDNA) binding domain of RecA, as well as other nucleic acid binding domains. Moreover, gel shift binding data indicate a potential dsDNA binding role for VF0530. Proteins 2011; © 2011 Wiley‐Liss, Inc.
MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease
Authors: Gunner M. R. , Zhu Xuyu , Klein Max C. 
Published: July 2011

AbstractThe pKas of 96 acids and bases introduced into buried sites in the staphylococcal nuclease protein (SNase) were calculated using the multiconformation continuum electrostatics (MCCE) program and the results compared with experimental values. The pKas are obtained by Monte Carlo sampling of coupled side chain protonation and position as a function of pH. The dependence of the results on the protein dielectric constant (ϵprot) in the continuum electrostatics analysis and on the Lennard–Jones non‐electrostatics parameters was evaluated. The pKas of the introduced residues have a clear dependence on ϵprot, whereas native ionizable residues do not. The native residues have electrostatic interactions with other residues in the protein favoring ionization, which are larger than the desolvation penalty favoring the neutral state. Increasing ϵprot scales both terms, which for these residues leads to small changes in pKa. The introduced residues have a larger desolvation penalty and negligible interactions with residues in the protein. For these residues, changing ϵprot has a large influence on the calculated pKa. An ϵprot of 8–10 and a Lennard–Jones scaling of 0.25 is best here. The X‐ray crystal structures of the mutated proteins are found to provide somewhat better results than calculations carried out on mutations made in silico. Initial relaxation of the in silico mutations by Gromacs and extensive side chain rotamer sampling within MCCE can significantly improve the match with experiment. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Optical spectra of nitride quantum‐dot systems: From tight‐binding states to many‐body effects
Authors: Seebeck J. , Lorke M. , Schulz S. , Schuh K. , Gartner P. , Jahnke F. 
Published: July 2011

AbstractA microscopic theory for optical properties of self‐assembled quantum‐dot systems is presented. For nitride‐based material systems, the single‐particle states are determined from atomistic tight‐binding (TB) calculations. This includes not only localized quantum‐dot states but also delocalized wetting‐layer states, since both contribute to the optical properties and are coupled via interaction processes. The TB wave functions are used to calculate matrix elements for optical dipole transitions as well as Coulomb and LO–phonon interaction of carriers. Absorption and gain spectra are investigated via a solution of the semiconductor Bloch equations including Coulomb interaction effects as well as dephasing due to carrier interaction with LO–phonons. Numerical results are presented for InN/GaN QD‐WL systems and allow to investigate the excitation‐density dependence of the optical spectra for this particular system.
Depth profile characterization of spin‐coated poly(3,4‐ethylenedioxythiophene): poly(styrene sulfonic acid) (PEDOT:PSS) films by spectroscopic ellipsometry
Authors: Ino Tomohisa , Hayashi Tatsuya , Fukuda Takeshi , Ueno Keiji , Shirai Hajime 
Published: July 2011

AbstractDepth profiles of the optical constants, carrier mobility, and carrier density of spin‐coated poly(3,4‐ethylene‐dioxythiophene):(polystyrene sulfonic acid) (PEDOT:PSS) films were investigated by real‐time spectroscopic ellipsometry (SE) characterization during argon plasma etching at atmospheric pressure. Spectra analysis revealed that homogeneous etching occurred within 10‐20 nm of the top surface, followed by the appearance of conductive PEDOT phase with a surface roughening. These findings originated from the depth profile of the PEDOT‐to‐PSS molar concentration ratio. The use of a 10‐20‐nm etched PEDOT:PSS layer improved relatively the performance of a hole‐transport layer for CuPc/C60 organic thin‐films solar cells with higher optical transmittance (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Large area thin film silicon modules with 10% efficiency for production
Authors: Klein Stefan , Wieder Stephan , Buschbaum Susanne , Rohde Martin , Schwanitz Konrad , Stolley Tobias , Stömmer Christian , Severin Daniel , Straub Axel , Schmidt Ursula I. , Ahmed Khaled 
Published: July 2011

AbstractA stabilized total‐area efficiency above 10% (ISC = 1.46 A, VOC = 148 V, FF = 67%, Pmpp = 145W, total area of 1.43m2) has been achieved on Gen 5 modules for the first time with an amorphous/microcrystalline silicon solar cell. The efficiency was enhanced by improving the light management and reducing the light induced degradation. The short circuit current density Jsc was enhanced by the introduction of internal light trapping using textured ZnO as the front transparent conductor, the implementation of an innovative µc‐SiOx based p‐layer and by an optical filter between the top and bottom cells of the tandem junction. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Control of a chain of integrators subject to actuator saturation and disturbances
Authors: Wang Xu , Saberi Ali , Stoorvogel Anton A. , Grip Håvard Fjær 
Published: July 2011

SUMMARYIn this paper, we study control of a chain of integrators under actuator saturation and non‐additive disturbances. We shall show that boundedness of the states can be ensured if the disturbances are matched and integral‐bounded, misaligned and magnitude‐bounded, or a combination of the two, using either a static or a dynamic low‐gain state feedback. This result is an extension of our earlier work on double integrator. Copyright © 2011 John Wiley & Sons, Ltd.