bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biodegradable fibrous scaffolds composed of gelatin coated poly(ϵ‐caprolactone) prepared by coaxial electrospinning
Authors: Zhao Pengcheng , Jiang Hongliang , Pan Hui , Zhu Kangjie , Chen Weiliam 
Published: April 2007

AbstractA facile coaxial electrospinning technique was devised to prepare biodegradable core‐shell fibrous scaffolds with poly(ϵ‐caprolactone) (PCL) comprising the core structure and gelatin forming the coating of the fibers. The effect of the feed rate of the inner dope on the electrospinning process and fiber morphology was investigated. The results indicated that core‐shell fibers with narrow size distribution and smooth surface morphology could be obtained when the feed rate was below 8 mL/h. An increase of the feed rate resulted in analogous increase in the diameters of both the inner PCL fiber core and the entire core‐shell fibers. XPS analyses revealed that the surface of the core‐shell fibers was tainted with a small amount of PCL. The outer gelatin layer in the core‐shell fibers was crosslinked with glutaraldehyde. By optimizing the glutaraldehyde/gelatin feed ratio, crosslinked scaffolds with high porosity were obtained. The mechanic strength of the hydrated, crosslinked core‐shell fibrous scaffolds was significantly enhanced because of the presence of hydrophobic PCL in the core region of the fibers. Results of cell culture studies suggested that the crosslinked, core‐shell fibrous scaffold were nontoxic and capable of supporting fibroblast adhesion and proliferation. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res 2007
In vitro biocompatibility of degradable biopolymers in cell line cultures from various ocular tissues: Direct contact studies
Authors: Huhtala A. , Pohjonen T. , Salminen L. , Salminen A. , Kaarniranta K. , Uusitalo H. 
Published: April 2007

AbstractSynthetic biodegradable polymers have many potential therapeutic applications. In ophthalmology, biodegradable polymers have been used as viscoelastic agents and surgical implants. Other potential applications include controlled release of drugs and growth factors, gene therapy, and tissue engineering. In the present study, in vitro biocompatibility of three biodegradable polymers, 50:50 PDLGA, 85:15 PDLGA, and Inion GTR™ membrane was evaluated in comparison to tissue culture polystyrene by investigating cell proliferation and potential acute toxicity by the WST‐1 cytotoxicity/cell proliferation test, the ATP test, and the lactate dehydrogenase (LDH) test. Evaluations were conducted with cell line cultures from various ocular tissues, human corneal epithelial cells (HCE), rabbit stromal fibroblasts (SIRC), bovine corneal endothelial cells (BCE), human conjunctival epithelial cells (IOBA‐NHC), and human retinal pigment epithelial cells (ARPE‐19) by direct contact studies by plating the cells on the polymer film specimens in 96‐wells. The proliferation results show that cell lines from various ocular tissues attached and grew on PDLGA 50:50, PDLGA 85:15, and Inion GTR™ membrane. Cytotoxicity experiments with the LDH and ATP tests showed no or extremely slight toxic adverse effects. These polymers have potential to be used as scaffolds in cell transplantation devices or as surgical implants. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res 2007
Computational chemistry comparison of stable/nonstable protein mutants classification models based on 3D and topological indices
Authors: González‐Díaz Humberto , Pérez‐castillo Yunierkis , Podda Gianni , Uriarte Eugenio 
Published: April 2007

AbstractIn principle, there are different protein structural parameters that can be used in computational chemistry studies to classify protein mutants according to thermal stability including: sequence, connectivity, and 3D descriptors. Connectivity parameters (called topological indices, TIs) are simpler than 3D parameters being then less computationally expensive. However, TIs ignore important aspects of protein structure and hence are expected to be inaccurate. In any case, a comparison of 3D and TIs has not been reported with respect to the power of discrimination of proteins according to stability. In this study, we compare both classes of indices in this sense by the first time. The best model found, based on 3D spectral moments correctly classified 507 out of 525 (96.6%) proteins while TIs model correctly classified 404 out of 525 (77.0%) proteins. We have shown that, in fact, 3D descriptor models gave more accurate results than TIs but interestingly, TIs give acceptable results in a timely way in spite of their simplicity. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
NLOPredict: Visualization and data analysis software for nonlinear optics
Authors: Moad Andrew J. , Moad Charles W. , Perry John M. , Wampler Ronald D. , Goeken G. Scott , Begue Nathan J. , Shen Tian , Heiland Randy , Simpson Garth J. 
Published: April 2007

AbstractA data analysis and visualization program was developed to assist in the interpretation of second‐order nonlinear optical (NLO) processes, including vibrational sum‐frequency generation and electronically resonant second harmonic generation. A novel diagrammatic approach allows concise visual representations of the resonant NLO molecular response. By mapping the predicted NLO response as a function of molecular orientation, molecular modeling results can be combined with experimental measurements for orientational analysis. A method is developed and implemented to predict the nonlinear optical properties of the amide backbones in complete proteins with known structures. NLOPredict is available for most computer operating systems from http://sda.iu.edu/nlopredict/. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Chiral discrimination via nuclear magnetic shielding polarisabilities from NMR spectroscopy: Theoretical study of (Ra)‐1,3‐dimethylallene, (2R)‐2‐methyloxirane, and (2R)‐N‐methyloxaziridine
Authors: Zanasi R. , Pelloni S. , Lazzeretti P. 
Published: April 2007

AbstractThree medium‐size optically active molecules have been studied to make a guess at candidates suitable for chiral discrimination in an isotropic medium via nuclear magnetic resonance spectroscopy. The criterion for experimental detection is given by the magnitude of the isotropic part of nuclear magnetic shielding polarisability tensors, related to a pseudoscalar of opposite sign for the two enantiomers. The pseudoscalar shielding polarisability at the 17O nucleus in N‐methyloxaziridine, calculated at the Hartree‐Fock level, is ≈7.8 ×10−17 mV−1. To obtain an experimentally observable magnetic field induced at the 17O nucleus in N‐methyloxaziridine, electric fields as large as ≈107–108 Vm−1 should be applied to the probe. The molecular electric dipole moment induced by precession of the magnetic dipole of the 17O nucleus in a magnetic field of 10 T is, in absolute value, ≈8.8 × 10−42 Cm. The estimated rf‐voltage at a resonance circuit is ≈10 nV. Smaller values have been estimated for N, C, and H nuclei in 1,3‐dimethylallene and 2‐methyloxirane. © 2007 Wiley Periodicals, Inc. J Comput Chem 2007
A computational investigation on the sequential rearrangement mechanism of 2‐allyl‐2,4,5‐hexatrienaldehyde involving [1,5]‐hydrogen migration and 8π‐electrocyclization
Authors: Zhu Yuanqiang , Guo Yong , Zhang Lidong , Xie Daiqian 
Published: April 2007

AbstractThe sequential rearrangement reaction mechanism of the 2‐allyl‐2,4,5‐hexatrienaldehyde has been studied at the unrestricted Becke three‐parameter hybrid functional combined with Lee–Yang–Parr correlation functional (UB3LYP)/6‐31G**, Complete Active Space Self‐Consistent Field (CAS (8,8))/6‐31G**, Configuration Interaction with Single and Double Excitations (CISD)//UB3LYP/6‐31G** and the second‐order perturbation theory based on the CASSCF reference wave function (CASPT2)//CAS(8,8)/6‐31G** levels. Two pathways have been found to be involved for this reaction. The first pathway includes four processes of the rotation of the C3C4 single bond, the stepwise [2 + 2] cycloaddition, the [1,5]‐hydrogen migration, and the ring opening isomerization, while the second pathway undergoes only two processes of the [1,5]‐hydrogen migration and the 8π‐electrocyclization. The calculation results indicate that the second pathway is favorable, in good agreement with the recent experimental observation. The whole reaction is stepwise and strong exothermic. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Algorithm to evaluate rate constants for polyatomic chemical reactions. II. Applications
Authors: González Javier , Giménez Xavier , Bofill Josep Maria 
Published: April 2007

AbstractA new implementation of the classical reaction path–Liouville algorithm, as developed by the authors in the preceding paper, is tested with several chemical reactions. It results in a simple algorithm, which may be used straightforwardly for the calculation of rate constants, as well as to extract dynamical information of the reactive process. Results for the rate constant have been compared to transition state calculations, confirming that it provides a new lower bound than traditional transition state estimates. In addition, the time‐dependence of the kinetic energy stored in vibrational modes has been studied, as a means of characterizing the importance of each normal mode inside the reaction mechanism. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Peptide reagent design based on physical and chemical properties of amino acid residues
Authors: Du Qi‐Shi , Huang Ri‐Bo , Wei Yu‐Tuo , Wang Cheng‐Hua , Chou Kuo‐Chen 
Published: April 2007

AbstractIt has tremendous values for both drug discovery and basic research to develop a solid bioinformatical tool for guiding peptide reagent design. Based on the physical and chemical properties of amino acids, a new strategy for peptide reagent design, the so‐called AABPD (amino acid based‐peptide design), is proposed. The peptide samples in a training dataset are described by a series of HMLP (heuristic molecular lipophilicity potential) parameters and other physicochemical properties of amino acid residues that form a three‐dimensional data matrix where each component is defined by three indexes: the first index refers to the peptide samples, the second to the amino acid positions, and the third to the amino acid parameters. The binding free energy between a peptide ligand and its protein receptor is calculated by a linear free energy equation through the physicochemical parameters, resulting in a set of simultaneous linear equations between the bioactivity of the peptides and the physicochemical properties of amino acids. An iterative double least square technique is developed for the solution of the three‐dimensional simultaneous linear equation set to determine the amino acid position coefficients of peptide sequence and the physicochemical parameter coefficients of amino acid residues alternately. The two sets of coefficients thus obtained are used for predicting the bioactivity of other query peptide reagents. Two calculation examples, the peptide substrate specificity of the SARS coronavirus 3C‐like proteinase and the affinity prediction for epitope‐peptides with Class I MHC molecules are studied by using the peptide reagent design strategy. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Genetic algorithm for the determination of binodal curves in ternary systems polymer–liquid(1)–liquid(2) and polymer(1)–polymer(2)–solvent
Authors: Milani G. , Milani F. 
Published: April 2007

AbstractA simple genetic algorithm for the numerical evaluation of binodal curves in ternary systems polymer–liquid (1)–liquid (2) and polymer (1)–polymer (2)–solvent is presented. The technique exploits a specifically developed restarting technique based on a combined elitist and zooming strategy on the last population at each iteration. The objective function (fitness) is represented by the weighted sum of the squared differences of chemical potentials of the two phases of each component, obtained evaluating first derivatives of Gibbs free energy of the mixture with respect to the number of moles of the components. The method proposed (a) is numerically stable since it does not require the evaluation of first derivatives of the objective function and (b) can be applied in a wide range of cases changing the equation of state. Several comparisons with simplified iterative procedures presented in the past in the technical literature both for mixtures of two polymers with identical characteristics in a solvent and for mixtures of solvent–nonsolvent–polymer with solvent–polymer interaction parameter equal to zero are reported. Finally, a comparison between present results and the “alternating tangent approach” is reported for two technically meaningful binary systems, when a simplified PC‐SAFT equation of state is adopted. The comparisons show that reliable results can be obtained by means of the algorithm proposed and suggest that the procedure presented can be used for practical purposes. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Prostacyclin inhibits endothelial cell XIAP ubiquitination and degradation
Authors: Liou Jun‐Yang , Matijevic‐Aleksic Nena , Lee Sang , Wu Kenneth K. 
Published: April 2007

AbstractTo understand the role of prostacyclin (PGI2) in protecting endothelial cells from apoptosis, we evaluated the effects of carbaprostacyclin (cPGI2) on H2O2‐induced human umbilical vein endothelial cell (HUVEC) apoptosis. cPGI2 suppressed H2O2‐induced annexin V‐positive cells in a concentration‐ and time‐dependent manner. Pre‐treatment of HUVEC with 50 µM cPGI2 for 4 h produced the maximal anti‐apoptotic effect. Authentic PGI2 generated by adenoviral transfer of PGI2 synthetic genes exerted a similar protective effect. cPGI2 inhibited Smac/DIABLO release from mitochondria, caspase 3 activation, focal adhesion protein degradation, and cell detachment. cPGI2 selectively protected X‐linked inhibitor of apoptosis protein (X‐linked IAP, XIAP) from H2O2‐induced ubiquitination, and preserved XIAP protein levels. PD‐98059 but not H‐89 abrogated the protective action of cPGI2. cPGI2 increased ERK phosphorylation which was blocked by PD‐98059. HUVEC stably transfected with dominant negative Ras abrogated XIAP preservation by cPGI2 while constitutive active Ras increased ERK phosphorylation and protected XIAP from degradation. Our results demonstrate for the first time that PGI2 inhibits XIAP ubiquitination and degradation via the Ras/MEK‐1/ERK signaling pathway. Preservation of XIAP proteins represents a key mechanism by which PGI2 protects endothelial cells from oxidant‐induced apoptosis. J. Cell. Physiol. 212:840–848, 2007. © 2007 Wiley‐Liss, Inc.
PAH biodegradation in surfactant‐water systems based on the theory of cohesive energy density (CED)
Authors: Chang Yi‐Tang , Lee Jiunn‐Fwu , Hung Chun‐Hsiung 
Published: April 2007

AbstractThe influence of two non‐ionic surfactant additives (Triton X‐100 and Brij 35) on polycyclic aromatic hydrocarbon (PAH) biodegradation was evaluated using the chemical molecular interaction method, which is based on the theory of cohesive energy density (CED). The results indicated that PAHs have relatively higher CED values because aromatic compounds with labile π are more polarized and this encourages molecular attractions involving induced dipole force. Under different PAH‐surfactant compositions, similar CED values, which facilitated their intermolecular attractions through π–π electron interactions, gave rise to a similar biodegradation pattern. For example, when induced enzymes were able to target the same molecular bonding on the PAH and Triton X‐100, rapid degradation rates were observed in both systems. The distribution of the PAH in the monomer or micelle surfactant bulk affected the rate of PAH biodegradation. Quantification of the bacterial activity by applying specific oxygen uptake requirements (SOUR) identified an effect involving chemical molecular interaction. Changes in the physiological characteristics as measured by BioLog GN microplate measurements were identifiable and also could be related to the chemical structure of the dual substrates. Community‐level physiological profiling (CLPP) changed when PAH biodegradation took place in the presence of the different surfactants. Cluster analysis using matching coefficient and carbon degradation potential values also varied with the different PAH‐surfactant compositions. Copyright © 2007 Society of Chemical Industry
Sequential optimization of culture medium composition for extracellular lipase production byBacillus sphaericususing statistical methods
Authors: Rajendran Aravindan , Thangavelu Viruthagiri 
Published: April 2007

AbstractAsequential optimization strategy with the aid of statistical design of experiments was used to enhance the lipase (triacylglycerol acylhydrolases, EC 3.1.1.3) production byBacillus sphaericusin submerged cultivation. A Plackett–Burman experimental design was used to evaluate the twelve medium components. Various vegetable oil inducers were tested for lipase production in the second step and the third step was to identify the optimal values of the significant medium components with sesame oil as the inducer using response surface methodology. A predictive model of the combined effects of the independent variables using response surface methodology and an artificial neural network was proposed. Unstructured kinetic models, a logistic model and a Luedeking–Piret model, were used to describe the cell mass and lipase production respectively. The significant variables affecting lipase production were found to be glucose, olive oil, peptone, NaCl and MnSO4.H2O. Sesame oil was found to be the best inducer for lipase production byBacillus sphaericus. The maximum lipase activity of 4.45 U mL−1, which was 1.5 times the maximum activity obtained in the Plackett–Burman experimental trials, was obtained at the optimum combination of medium constituents containing 12.695 g L−1glucose, 13.161 mL L−1sesame oil, 9.947 g L−1peptone, 3.25 g L−1NaCl, 0.5917 g L−1MnSO4.H2O and other insignificant components at the fixed level. The statistical design of experiments offers an efficient methodology to identify the significant variables and to optimize the factors with a minimum number of experiments for lipase production byBacillus sphaericus. Copyright © 2007 Society of Chemical Industry
Microbial metagenomes: moving forward industrial biotechnology
Authors: Ferrer Manuel , Beloqui Ana , Golyshin Peter N 
Published: April 2007

AbstractBiotechnology, in terms of exploitation of catalytic activities for industrial applications, is increasingly recognized as one of the pillars of the knowledge‐based economy that we are heading for. Comprehensive knowledge of enzymology should be of practical importance for effective intervention on whole cell processes and enzymatic networks. Over the last decade metagenome‐based technologies have been developed to take us farther and deeper into the enzyme universe from uncultivable microbes. This sophisticated platform, which identifies new enzymes from vast genetic pools available, and assesses their potential for novel chemical applications, should be increasingly important in the discovery of advanced biotechnological resources. Copyright © 2007 Society of Chemical Industry
Scientific collaboration and the Kerala model: does the internet make a difference?
Authors: Sooryamoorthy Radhamany , Duque Ricardo B. , Ynalvez Marcus Antonius , Shrum Wesley 
Published: April 2007

AbstractInformation and communication technologies (ICTs) have become the panacea for development for many developing countries in the modern, knowledge‐based world. Kerala, a state in India known for its model of development, has not only joined this bandwagon but has also selected ICTs as a means to pull the state out of its present crisis. The paper examines the institutions of knowledge production in Kerala (academic and scientific sectors), which are generally the forerunner of other sectors in terms of their use of ICTs. We examine the extent to which ICTs have affected research communication and collaboration, the processes, which are crucial in developing a knowledge‐based economy. Copyright © 2007 John Wiley & Sons, Ltd.
Mosaic versus regulation development in avian blastoderms depends on the spatial distribution of Rauber's sickle material
Authors: Callebaut Marc , Van Nueten Emmy , Harrisson, Fernand , Bortier Hilde 
Published: April 2007

AbstractWe describe how to prepare unincubated avian eggs to obtain a greater number of clearly visible Rauber's sickles for experimental embryology. After hemi‐sectioning of unincubated chicken (Gallus domesticus) blastoderms and cultivating both halves in vitro, two kinds of development can be discerned: (1) when the unincubated blastoderms were hemi‐sectioned according to the plane of bilateral symmetry, going through the middle region of Rauber's sickle, we obtained two hemi‐embryos (a left and a right one). Each contained a half primitive streak, localized at the cut edge (starting from the most median part of Rauber's sickle) giving rise to a half mesoblast mantle and half area vasculosa, thus indicating mosaic development (each part of the whole fertilized egg would be able to form independently on its own). (2) When the unincubated blastoderm is hemi‐sectioned more obliquely, going through a more lateral part of Rauber's sickle (sickle horn), two complete bilaterally symmetrically miniature embryos will form, indicating the so‐called regulation phenomena. We demonstrate that these two types of development are in reality due to the different spreading and concentration of Rauber's sickle tissue (containing γ ooplasm) around the area centralis. Embryonic regulation thus must not be considered as a kind of totipotent regeneration capacity of isolated parts of the unincubated avian blastoderm, but depends on the spatial distribution of a kind of extraembryonic tissue (Rauber's sickle) built up by the oblique uptake of γ ooplasm (ooplasmic mosaicism) at the moment of bilateral symmetrization (Callebaut [1994] Eur Arch Biol 105:111–123; Callebaut [2005] Dev Dyn 233:1194–1216). J. Morphol., 2007. © 2007 Wiley‐Liss, Inc.
The tachykinin tale: molecular recognition in a historical perspective
Authors: Werge Thomas 
Published: April 2007

AbstractCrystallography, mutational mapping and crosslinking are but a few of the experimental techniques that have helped to elucidate the underlying principles of molecular recognition between macromolecules and to improve our understanding of the evolution of the structure–activity relationship (SAR). While this development has been particularly successful for small and rigid ligands and substrates that bind to larger hydrophilic biomolecules, our understanding of membrane‐embedded proteins is still rather limited. This review uses the example of the neuropeptide family of tachykinins and their G‐protein coupled receptors (GPCR) to present how complementary experimental strategies over the past decades have nourished and modified conceptual models of the structural requisites of molecular recognition and function. Given the little we know, the pertinent question is how we proceed from here. Copyright © 2007 John Wiley & Sons, Ltd.