bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast construction of assembly trees for molecular graphs
Authors: Artemova Svetlana , Grudinin Sergei , Redon Stephane 
Published: February 2011

AbstractA number of modeling and simulation algorithms using internal coordinates rely on hierarchical representations of molecular systems. Given the potentially complex topologies of molecular systems, though, automatically generating such hierarchical decompositions may be difficult. In this article, we present a fast general algorithm for the complete construction of a hierarchical representation of a molecular system. This two‐step algorithm treats the input molecular system as a graph in which vertices represent atoms or pseudo‐atoms, and edges represent covalent bonds. The first step contracts all cycles in the input graph. The second step builds an assembly tree from the reduced graph. We analyze the complexity of this algorithm and show that the first step is linear in the number of edges in the input graph, whereas the second one is linear in the number of edges in the graph without cycles, but dependent on the branching factor of the molecular graph. We demonstrate the performance of our algorithm on a set of specifically tailored difficult cases as well as on a large subset of molecular graphs extracted from the protein data bank. In particular, we experimentally show that both steps behave linearly in the number of edges in the input graph (the branching factor is fixed for the second step). Finally, we demonstrate an application of our hierarchy construction algorithm to adaptive torsion‐angle molecular mechanics. © 2011 Wiley Periodicals, Inc. J Comput Chem , 2011.
Predicting protein folding rates using the concept of Chou's pseudo amino acid composition
Authors: Guo Jianxiu , Rao Nini , Liu Guangxiong , Yang Yong , Wang Gang 
Published: February 2011

AbstractOne of the most important challenges in computational and molecular biology is to understand the relationship between amino acid sequences and the folding rates of proteins. Recent works suggest that topological parameters, amino acid properties, chain length and the composition index relate well with protein folding rates, however, sequence order information has seldom been considered as a property for predicting protein folding rates. In this study, amino acid sequence order was used to derive an effective method, based on an extended version of the pseudo‐amino acid composition, for predicting protein folding rates without any explicit structural information. Using the jackknife cross validation test, the method was demonstrated on the largest dataset (99 proteins) reported. The method was found to provide a good correlation between the predicted and experimental folding rates. The correlation coefficient is 0.81 (with a highly significant level) and the standard error is 2.46. The reported algorithm was found to perform better than several representative sequence‐based approaches using the same dataset. The results indicate that sequence order information is an important determinant of protein folding rates. ©2011 Wiley Periodicals, Inc. J Comput Chem 2011.
Pharmacophore alignment search tool: Influence of scoring systems on text‐based similarity searching
Authors: HÄhnke Volker , Schneider Gisbert 
Published: February 2011

AbstractThe text‐based similarity searching method Pharmacophore Alignment Search Tool is grounded on pairwise comparisons of potential pharmacophoric points between a query and screening compounds. The underlying scoring matrix is of critical importance for successful virtual screening and hit retrieval from large compound libraries. Here, we compare three conceptually different computational methods for systematic deduction of scoring matrices: assignment‐based, alignment‐based, and stochastic optimization. All three methods resulted in optimized pharmacophore scoring matrices with significantly superior retrospective performance in comparison with simplistic scoring schemes. Computer‐generated similarity matrices of pharmacophoric features turned out to agree well with a manually constructed matrix. We introduce the concept of position‐specific scoring to text‐based similarity searching so that knowledge about specific ligand‐receptor binding patterns can be included and demonstrate its benefit for hit retrieval. The approach was also used for automated pharmacophore elucidation in agonists of peroxisome proliferator activated receptor gamma, successfully identifying key interactions for receptor activation. © 2011 Wiley Periodicals, Inc. J Comput Chem 2011.
Specific interactions between lactose repressor protein and DNA affected by ligand binding: Ab initio molecular orbital calculations
Authors: Ohyama Tatsuya , Hayakawa Masato , Nishikawa Shin , Kurita Noriyuki 
Published: February 2011

AbstractTranscription mechanisms of gene information from DNA to mRNA are essentially controlled by regulatory proteins such as a lactose repressor (LacR) protein and ligand molecules. Biochemical experiments elucidated that a ligand binding to LacR drastically changes the mechanism controlled by LacR, although the effect of ligand binding has not been clarified at atomic and electronic levels. We here investigated the effect of ligand binding on the specific interactions between LacR and operator DNA by the molecular simulations combined with classical molecular mechanics and ab initio fragment molecular orbital methods. The results indicate that the binding of anti‐inducer ligand strengthens the interaction between LacR and DNA, which is consistent with the fact that the binding of anti‐inducer enhances the repression of gene transcription by LacR. It was also elucidated that hydrating water molecules existing between LacR and DNA contribute to the specific interactions between LacR and DNA. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Infinite basis set extrapolation for double hybrid density functional theory 1: Effect of applying various extrapolation functions
Authors: Chuang Yao‐Yuan , Chen Sheng‐Min 
Published: February 2011

AbstractWe applied the Infinite Basis (IB) set extrapolation and Double Hybrid Density Functional Theory (DHDF) to calculate the databases of atomization energies, ionization energies, electron affinities, reaction barrier heights, proton affinities, alkyl bond dissociation energies, and noncovalent interactions. The Complete Basis Set (CBS) limit is estimated by extrapolating the hybrid density functional theory and PT2 energies using extrapolation functions including exponential, inverse power, modified exponential, and the combination of the these functions. We found that the combination of B2KPLYP/cc‐pV[D|T]Z (which is the extrapolation based on the energies calculated in cc‐pVDZ and cc‐pVTZ) gives results in quadruple‐ζ quality. However, if we want to reach the ∼2 kcal/mol chemical accuracy limit, the cc‐pV[T|Q]Z is required. Similar results with various extrapolation functions obtained, because the IB parameters were determined by minimizing the averaged mean unsigned error of the calculated databases. We generalized the IB set extrapolation to include more than two basis sets, but we found that extrapolation with two basis sets is satisfactory to give reasonable results. The largest error occurred in the databases of the electron affinities and the weak interactions between the noble gas and the nonpolar molecules. We expect that performing the DHDF‐IB scheme with the basis sets augmented by diffuse basis functions will further improve the results. © 2011 Wiley Periodicals, Inc. J Comput Chem , 2011.
Engineering a mammalian super producer
Authors: Dietmair Stefanie , Nielsen Lars K. , Timmins Nicholas E. 
Published: February 2011

AbstractMammalian cells are the preferred host for the manufacture of a wide range of biopharmaceuticals, but production costs are high owing to low productivity. A range of rational engineering strategies have been pursued in order to increase volumetric product titres from mammalian cells, such as delaying apoptosis, manipulation of the cell cycle, and improving metabolism and protein processing. Unfortunately, outcomes from these strategies have been mixed, with few instances where significant improvements in product yield have been achieved. This article reviews and contrasts many of the engineering strategies attempted to date, highlighting the variability and context specificity in outcome. The paper argues that this is a reflection of the complexity of mammalian cells, and that a deeper understanding of the biology underpinning protein production for biotechnological purposes is required. Copyright © 2011 Society of Chemical Industry
Development of a control algorithm for air‐scour reduction in membrane bioreactors for wastewater treatment
Authors: Ferrero Giuliana , Monclús Hector , Buttiglieri Gianluigi , Gabarron Sara , Comas Joaquim , Rodríguez‐Roda Ignasi 
Published: February 2011

AbstractBACKGROUND: Membrane bioreactors are used in an increasing number of wastewater treatment facilities because of their compactness and efficiency in solid‐liquid separation, but energy requirements are still higher than other competitive technologies such as conventional activated sludge.RESULTS: In this paper the development of an air‐scour control algorithm based on short‐term and long‐term membrane permeability evolution is presented. An open loop calibration and partial validation was carried out in a semi‐industrial scale pilot plant where manual changes in air‐scour flow had been previously carried out. The control system was successfully tested in closed loop in an industrial scale pilot plant, defining a maximum daily air‐scour decrease or increase of 6% of the air‐scour recommended by membranes suppliers. An average air‐scour saving of 13% and a maximum of 20%, calculated in terms of air flow saved, were achieved during the validation test without any apparent long‐term effect on membrane permeability.CONCLUSION: It was proven that the air‐scour control system is an important tool capable of reducing operational costs in MBR systems. Copyright © 2011 Society of Chemical Industry
Testing evolutionary hypotheses about the phylotypic period of zebrafish
Authors: Schmidt Kai , Starck J. Matthias 
Published: February 2011

AbstractVertebrate embryos pass through a period of morphological similarity, the phylotypic period. Since Haeckel's biogenetic law of recapitulation, proximate and ultimate evolutionary causes of such similarity of embryos were discussed. We test predictions about changes in phenotypic and genetic variances that were derived from three hypotheses about the evolutionary origin of the phylotypic stage, i.e. random, epigenetic effects, and stabilizing selection. The random hypothesis predicts increasing values for phenotypic variances and stable or increasing values for genetic variances; the epigenetic effects hypothesis predicts declining values for phenotypic variances but stable or increasing values of genetic variances, and the stabilizing selection predicts stable phenotypic variances but decreasing genetic variances. We studied zebrafish as a model species, because it can be bred in large numbers as necessary for a quantitative genetics breeding design. A half‐sib breeding scheme provided estimates of additive genetic variances from 11 embryonic characters from 12 through to 24 hr after fertilization, i.e. before, during (15–19 hr), and after the phylotypic period. Because additive genetic variances are size dependent, we calculated narrow‐sense heritabilities as a size independent gauge of genetic contributions to the phenotype. The results show declining phenotypic variances and stable heritabilities. In conclusion, we reject the random and the stabilizing selection hypotheses and favor ideas about epigenetic effects that constrain the early embryonic development. Additive genetic variance during the phylotypic stage makes it accessible for evolution, thus explaining in a simple and straightforward way why the phylotypic period differs among vertebrates in timing, duration, and morphologies.J. Exp. Zool. (Mol. Dev. Evol.) 316:319–329, 2011. © 2011 Wiley‐Liss, Inc.
Complete restoration of phenylalanine oxidation in phenylketonuria mouse by a self‐complementary adeno‐associated virus vector
Authors: Yagi Hiroya , Ogura Tsuyoshi , Mizukami Hiroaki , Urabe Masashi , Hamada Hiromi , Yoshikawa Hiroyuki , Ozawa Keiya , Kume Akihiro 
Published: February 2011

AbstractBackgroundClassical phenylketonuria (PKU) arises from a deficiency of phenylalanine hydroxylase (PAH) that catalyses phenylalanine oxidation in the liver. Lack of PAH activity causes massive hyperphenylalaninemia and consequently severe brain damage. Preclinical studies showed that conventional adeno‐associated virus (AAV) vectors could correct hyperphenylalaninemia in a mouse model of PKU, although limitations such as very large dose requirement and relative inefficiency in female animals were recognized.MethodAn AAV8‐pseudotyped vector was constructed with a self‐complementary AAV (scAAV) genome for efficient liver transduction and expression. Following vector injection to PKU mice, blood Phe was periodically measured by an enzymatic fluorometric assay. In vivo Phe oxidation was evaluated by a non‐invasive breath test using [1‐13C]Phe. Vector copy number in the host tissues was determined by quantitative polymerase chain reaction.ResultsA single injection of 1 × 1011–1 × 1012 particles of the scAAV8 vector resulted in a reduction of blood Phe to normal or near‐normal levels for more than 1 year in both genders. The treated animals showed normal level of in vivo Phe oxidation. The presence of > 1 copy of vector DNA per diploid genome in the liver was associated with normal blood Phe in the AAV‐treated PKU mice.ConclusionsComplete phenotypic correction of PKU mice was achieved by the scAAV8 vector for the longest duration reported to date. The vector overcame the female‐specific disadvantage in AAV‐mediated liver transduction; thus, it offers a promising platform of long‐lasting gene therapy for PKU. Copyright © 2011 John Wiley & Sons, Ltd.
Sustained inhibition of IL‐6 and IL‐8 expression by decoy ODN to NF‐κB delivered through respirable large porous particles in LPS‐stimulated cystic fibrosis bronchial cells
Authors: De Stefano Daniela , Ungaro Francesca , Giovino Concetta , Polimeno Antonio , Quaglia Fabiana , Carnuccio Rosa 
Published: February 2011

AbstractBackgroundCystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Neutrophil‐dominated inflammation and chronic bacterial infection are still considered the primary cause of bronchioectasis, respiratory failure and consequent death in CF patients. Activation of nuclear factor (NF)‐κB is responsible for overproduction of cytokines, such as interleukin (IL)‐6 and IL‐8, in airways of CF patients. Thus, decoy oligodeoxynucleotides against NF‐κB (dec‐ODN) may limit lung inflammation in CF. In the present study, we studied the effects of dec‐ODN delivered through biodegradable and respirable poly(D,L‐lactide‐co‐glycolide) large porous particles (LPP) on IL‐6 and IL‐8 mRNA expression as well as NF‐κB/DNA binding activity in cystic fibrosis cells stimulated with lipopolysaccharide (LPS) from Pseudomonas aeruginosa.Methodsdec‐ODN LPP were prepared by a modified double emulsion technique and characterized in terms of size, morphology, tapped density and dec‐ODN loading. Human epithelial bronchial IB3‐1 (CFTR‐mutated) as well as S9 (CFTR‐corrected) were stimulated with LPS from P. aeruginosa for 24 and 72 h in the absence or presence of naked dec‐ODN or dec‐ODN LPP.ResultsStimulation of cells with LPS from P. aeruginosa caused an increase of IL‐6 and IL‐8 mRNA levels, which were significantly inhibited by dec‐ODN LPP at 24 and 72 h, whereas naked dec‐ODN inhibited those only at 24 h. Similar effects were exhibited by dec‐ODN LPP or naked dec‐ODN on NF‐κB/DNA binding activity.ConclusionsOur observations indicate that respirable biodegradable dec‐ODN LPP may represent a promising strategy for inhibiting NF‐κB transcriptional activity and related gene expression and, thus, reduce lung chronic inflammation in CF patients. Copyright © 2011 John Wiley & Sons, Ltd.
Wettability, surface microstructure and mechanical properties of films based on phosphorus oxychloride‐treated zein
Authors: Wu Lei‐Yan , Wen Qi‐Biao , Yang Xiao‐Quan , Xu Ming‐Sheng , Yin Shou‐Wei 
Published: February 2011

AbstractBACKGROUND: Zein, the predominant protein in corn, has been extensively studied as an alternative packaging material in edible and biodegradable films. However, films made from 100% zein are brittle under normal conditions. The aim of this investigation was to improve the film‐forming properties of zein by chemical phosphorylation. The surface hydrophobicity, surface microstructure and mechanical properties of films based on untreated and phosphorus oxychloride (POCl3)‐treated zein were evaluated and compared. The effect of POCl3 treatment on the rheological properties of zein solutions was also studied.RESULTS: POCl3 treatment, especially at pH 7 and 9, led to an increase in the apparent viscosity of zein solutions. Atomic force microscopy (AFM) analysis showed that the film based on POCl3‐treated zein at pH 7 had a stone‐like surface microstructure with a higher roughness (Rq) than the untreated zein film. The AFM data may partially account for the phenomenon that this film exhibited high surface hydrophobicity (H0). POCl3 treatment diminished the tensile strength (TS) of zein films from 4.83–6.67 to 1.3–2.29 MPa. However, the elongation at break (EAB) of the films at pH 7 and 9 increased from 3.0–4.5% (control film) to 150.1–122.7% (POCl3‐treated film), indicating the potential application of zein films in wrapping foods or in non‐food industries such as sugar, fruit or troche that need good extension packing materials.CONCLUSION: The data presented suggest that the properties of zein films could be modulated by chemical phosphorylation treatment with POCl3 at an appropriate pH value. Copyright © 2011 Society of Chemical Industry
Effect of amino acid level in the pig diet during growing and early finishing on growth response during the late finishing phase of lean meat type gilts
Authors: Millet Sam , Langendries Karolien , Aluwé Marijke , De Brabander Daniël L 
Published: February 2011

AbstractBACKGROUND: This experiment examined the influence of different amino acid levels during the growing and early finishing diet and the late finishing diet on growth performance and carcass quality of a lean meat type gilt. In a two by two factorial trial, 96 gilts were divided over four treatments. The two factors were (1) amino acid level in growing and early finishing and (2) amino acid level in late finishing. For the low amino acid diets we lowered the lysine, methionine, threonine and tryptophan levels by 20% and 30% in the growing and two finishing phases, respectively.RESULTS: Restricting amino acid levels in growing and early finishing led to a decreased growth rate but improved efficiency of amino acid use, which lasted into the subsequent phase. Pigs on a high amino acid diet in late finishing pigs were able to compensate to a large extent for amino acid restriction in growing and early finishing. Amino acid content in late finishing determined carcass quality.CONCLUSION: In the lean meat type gilts used in this experiment, restricting amino acid concentrations by 20% in the growing and 30% in the early finishing phase increased the growth rate and efficiency of growth in the subsequent late finishing phase. In order to obtain good carcass quality, it is crucial to provide the animals with a balanced diet during the late finishing phase. Copyright © 2011 Society of Chemical Industry
Effects of feeding salt‐tolerant forage cultivated in saline‐alkaline land on rumen fermentation, feed digestibility and nitrogen balance in lamb
Authors: Wang Cong , Hu Dong Kuan , Liu Qiang , Yang Wen Zhu , Zhao Xiang , Liu Sheng Qiang , Ting He Ting , Yu Liu Zhuang 
Published: February 2011

AbstractBACKGROUND: Mixing salt‐tolerant plants with other plants may affect rumen fermentation, which could result in an increase of feed conversion rate. The objective of this study was to evaluate the effects of partially or entirely replacing the corn stover with a mixture of salt‐tolerant forage (Dahurian wildrye grass, weeping alkaligrass and erect milkvetch) in the diet of lambs on ruminal fermentation, feed digestibility and nitrogen (N) balance. Ratios of corn stover to the mixture of salt‐tolerant forages in the four experimental diets were 100:0, 67:33, 33:67 and 0:100, respectively, for control, low (LF), medium (MF) and high (HF).RESULTS: Ruminal pH was lower (P = 0.048) with LF and MF than with control and HF diets. Total VFA concentration was consistently higher (P = 0.039) for LF and MF than for control and HF with increasing amount of salt‐tolerant forage. Ratio of acetate to propionate was linearly (P = 0.019) decreased due to the decrease in acetate production. Digestibilities of OM, NDF and CP in the whole tract linearly (P < 0.002) decreased with increasing amount of salt‐tolerant forage. Similarly, retained N and ratio of retained N to digestible N also linearly (P < 0.005) decreased.CONCLUSION: Feeding salt‐tolerant forage cultivated in saline‐alkaline land improved rumen fermentation with increased total VFA production, and changed the rumen fermentation pattern to increased butyrate production. However, the decreased feed digestibility in the whole digestive tract of lamb may reduce nutrient availability to animals and thus adversely affect animal productivity. Additionally, feeding salt‐tolerant forages may require more protein supplement to meet animal requirements, because of the low protein content and low protein digestibility of the salt‐tolerant forages. Copyright © 2011 Society of Chemical Industry
Functionalized polymeric stationary phases for ion chromatography
Authors: Buszewski Bogusław , Jaćkowska Magdalena , Bocian Szymon , Kosobucki Przemysław , Gawdzik Barbara 
Published: February 2011

AbstractSynthesis and properties of the multilayered stationary phases, which contain quaternary amine functional groups for the analysis of anions by ion chromatography, are described. The bonded phases were characterized by elemental analysis, solid‐state 13C NMR spectroscopy and chromatographic methods. The surface of 1,4‐di(2‐hydroxy‐3‐methacryloyloxypropoxy)phenol (solid support) was coated with polymeric layers formed by condensation polymerization of primary amine with diepoxide. Each layer of the anion exchange stationary phase consists of copolymer of methylamine (MA) and 1,4‐butanedioldiglycidyl ether (BDDE). A series of stationary phases with different numbers of polymerized layers were tested. The separation of an inorganic anions sample (F–, Cl−, NO2− Br−, NO3−, additionally HPO42− and SO42−) was performed. In the measurement, a hydroxide, carbonate, bicarbonate and their mixture were used as mobile phases.