bluuebunny/crossref_metadata_2025_split huggingface dataset:
Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins
Authors: Dennis S. , Vajda S. 
Published: August 2002

AbstractThe classical simplex method is extended into the Semiglobal Simplex (SGS) algorithm. Although SGS does not guarantee finding the global minimum, it affords a much more thorough exploration of the local minima than any traditional minimization method. The basic idea of SGS is to perform a local minimization in each step of the simplex algorithm, and thus, similarly to the Convex Global Underestimator (CGU) method, the search is carried out on a surface spanned by local minima. The SGS and CGU methods are compared by minimizing a set of test functions of increasing complexity, each with a known global minimum and many local minima. Although CGU delivers substantially better success rates in simple problems, the two methods become comparable as the complexity of the problems increases. Because SGS is generally faster than CGU, it is the method of choice for solving optimization problems in which function evaluation is computationally inexpensive and the search region is large. The extreme simplicity of the method is also a factor. The SGS method is applied here to the problem of finding the most preferred (i.e., minimum free energy) solvation sites on a streptavidin monomer. It is shown that the SGS method locates the same lowest free energy positions as an exhaustive multistart Simplex search of the protein surface, with less than one‐tenth the number of minizations. The combination of the two methods, i.e., multistart simplex and SGS, provides a reliable procedure for predicting all potential solvation sites of a protein. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 319–334, 2002
On the irrelevance of electrostatics for the crystal structures and polymorphism of long even n‐alkanes
Authors: Van de Streek Jacco , Verwer Paul , Bennema Piet , Vlieg Elias 
Published: August 2002

AbstractIt is known that the experimental triclinic crystal structures of even n‐alkanes are not well reproduced upon energy minimization with current force fields. The inclusion of electrostatics does not solve this, and, moreover, some charge schemes show unphysical features such as positively charged carbon atoms or charge alternation. The effect of the electrostatics on the energies of the crystal structures of the even n‐alkanes, and thereby on their polymorphism, has never been established. A new charge scheme is introduced that yields physically sensible charges without constraints. It will also be shown, however, that electrostatics are relevant neither for the structures of the crystals, nor for their energies. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 365–370, 2002
Parametrization of the Becke3‐LYP hybrid functional for a series of small molecules using quantum molecular similarity techniques
Authors: Poater Jordi , Duran Miquel , Solà Miquel 
Published: August 2002

AbstractThe a0, ax, and ac semiempirical parameters of the original Becke three‐parameter method have been optimized by minimizing the difference between the density given by this method and the singles and doubles quadratic configuration interaction (QCISD) generalized density using quantum molecular similarity measures. The optimization is performed including the hybrid energy functional in a self‐consistent fashion and employing the relaxed geometry at each set of a0, ax, and ac parameters. This method has been applied to a series of 16 small molecules with different bonding patterns. Results show that, at least in diatomic molecules, it is possible to obtain a set of parameters that reproduces almost exactly the QCISD electron density. The optimized parameters for the studied molecules follow two main general trends: (a) the parameters governing the amount of gradient corrections for exchange and correlation have similar values (ac≈ax); and (b) the larger the exact exchange included, the smaller the gradient correction for exchange needed (a0≈1−ax). Especially interesting are the values obtained for the a0 parameter, which reflect how much exact exchange should be included in the description of a particular system. Finally, for H2 and LiH, we have carried out a search for other possible local minima on the quadratic error integral surface concluding that for these molecules there is not a unique set of parameters that produces a B3LYP density of QCISD quality. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1666–1678, 2001
Artificial neural networks applied for studying metallic complexes
Authors: de Viterbo V. D. , Belchior J. C. 
Published: August 2002

AbstractMetallic complexes of multimetal and multiligand systems are complicated for calculating equilibrium concentrations in solutions. An artificial neural network has been developed for studying Al3+ and EDTA complexes in solution with an initial concentration of 0.01 mol L−1 for these species. In this system there are 20 compounds and may exist 18 simultaneous reactions. The neural network has been trained and the simulated data of different concentrations as a function of pH are predicted with an accuracy of about 1% for all species simultaneously. A general analytical formula is presented, which directly relates all the concentrations as a function of pH. The analysis showed that predictions closer to the boundary of the input and output data are quantitative while out of these limits these are not even qualitative. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1691–1701, 2001
Localization function study of excitation processes in a set of small isoelectronic molecules
Authors: Chesnut D. B. 
Published: August 2002

AbstractElectron localization function (ELF) theory is used to characterize changes that occur upon excitation from ground singlet to first excited triplet states in a series of isoelectronic 16‐electron molecules including H2CCH2, HNCH2, H2CO, HNNH, HNO, and O2 (ground triplet to excited singlet). ELF allows one to visualize lone pair or nonbonding electrons, and in these cases the π→π* or n→π excitation processes involved lead to an effective 90° rotation of the electronic structure about one heavy atom center and consequent distortion towards pyramidal symmetry about both heavy atom centers. The heavy atom bond lengths change very little in those cases where effectively two‐center three‐electron bonds can be formed (HNNH, HNO, and O2) while a significant lengthening occurs in those cases where hydrogen atoms prevent such interactions (H2CCH2, HNCH2, and H2CO). It is shown that both ELF basin populations and atoms‐in‐molecules (AIM) delocalization indices reflect expected bond orders for conventional single and double bonds provided one compares the ratio of the molecular quantities rather than their absolute magnitudes. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1702–1711, 2001
Docking of small ligands to low‐resolution and theoretically predicted receptor structures
Authors: Wojciechowski Marek , Skolnick Jeffrey 
Published: August 2002

AbstractWe have developed a simple docking procedure that is able to utilize low‐resolution models of proteins created by structure prediction algorithms such as threading or ab initio folding to predict the conformation of receptor–small ligand complexes. In our approach, using only approximate, discretized models of both molecules, we search for the steric and quasi‐chemical complementarity between a ligand and the receptor molecules. This averaging procedure allows for the compensation of numerous structural inaccuracies resulting from the theoretical predictions of the receptor structure. The best relative orientation of these two models is obtained by an exhaustive scan over the rigid body's six‐dimensional translational and rotational degrees of freedom. The search method is based on a real space grid‐searching algorithm, unlike docking methods based on the fast Fourier Transform algorithm. We have applied this algorithm to rebuild structures of several complexes available in the Protein Data Bank. The structures of the receptors are produced by means of our threading algorithm PROSPECTOR, subsequently refined, and then utilized in the docking experiment. In many cases, not only is the localization of the binding site on the receptor surface correctly identified, but the proper orientation of the bounded ligand is also reasonably well reproduced within the level of accuracy of the modeled receptor itself. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 189–197, 2002
A complete classification of (12,4,3)‐RBIBDs
Authors: Morales Luis B. , Velarde Carlos 
Published: August 2002

AbstractUsing a parallel class by parallel class backtracking algorithm we classify (12,4,3)‐RBIBDs. The size of the search space is reduced by combinatorial arguments. Five nonisomorphic RBIBDs are found and listed. © 2001 John Wiley & Sons, Inc. J Combin Designs 9: 385–400, 2001
Heart rate variability as an outcome measure for Thought Field Therapy in clinical practice
Authors: Pignotti Monica , Steinberg Mark 
Published: August 2002

AbstractThe need for empirical, objective, clear, and practical outcome measures for therapy has long been recognized by clinicians and researchers. Pragmatic tools for objective determination of the efficacy of therapy have been scarce in clinical practice settings. Heart rate variability (HRV) is increasing in popularity for use in clinical settings as a measure of treatment success. Since HRV is stable and placebo‐free, it has the potential to meet this need. Thirty‐nine cases are presented from the clinical practices of the authors and three other clinicians where HRV was used as an outcome measure for Thought Field Therapy (TFT). The cases included TFT treatments which addressed a wide variety of problems including phobias, anxiety, trauma, depression, fatigue, attention deficit hyperactivity disorder, learning difficulties, compulsions, obsessions, eating disorders, anger, and physical pain. A lowering of subjective units of distress was in most cases related to an improvement in HRV. © 2001 John Wiley & Sons, Inc. J Clin Psychol 57: 1193–1206, 2001.
Coping, meaning in life, and suicidal manifestations: Examining gender differences
Authors: Edwards Melanie J. , Holden Ronald R. 
Published: August 2002

AbstractLife meaning and coping strategies were investigated as statistical predictors of suicidal manifestations in a sample of 298 university undergraduates. Participants completed measures of hopelessness, sense of coherence, purpose in life, coping for stressful situations, suicide ideation, prior suicide attempts, and self‐reported likelihood of future suicidal behavior. Moderated multiple regression techniques examined the incremental validity of life meaning by coping interactions for predicting each suicide variable separately by gender. The interaction of sense of coherence and emotion‐oriented coping made a unique, significant contribution to the statistical prediction of all suicide variables for women. For men, the interaction between sense of coherence and emotion‐oriented coping contributed significantly to the statistical prediction of suicide ideation. All interactions remained significant when hopelessness was statistically controlled. The hypothesis that life meaning acts as a buffer between coping style and suicidal manifestations was partially supported. Implications for suicide prevention and intervention are discussed. © 2001 John Wiley & Sons, Inc. J Clin Psychol 57: 1517–1534, 2001.
Morphine inhibits indolactam V‐induced U937 cell adhesion and gelatinase secretion
Authors: Weeks Benjamin S. , Goldman Steven , Touma Salwa , Payne Malique , Cadet Patrick , Stefano George B. 
Published: August 2002

AbstractWe demonstrate that indolactam V, a non‐phorbol protein kinase C activator, promotes U937 cell attachment to fibronectin, type IV collagen and laminin. In the absence of indolactam V, 2–4% of U937 cells attach to all test substrates, however, in the presence of 100 nM indolactam V, 25, 16 and 11% of U937 cells attach to fibronectin, type IV collagen and laminin, respectively. When added concomitantly, 90 μM H‐7, a protein kinase C inhibitor, reduces indolactam V‐induced U937 cell adhesion to fibronectin by 91%. Monoclonal antibodies directed against both the β1 and α5 integrin subunits inhibit indolactam V‐induced U937 cell adhesion to fibronectin by 62 and 52%, respectively. Indolactam V also promotes homotypic aggregation in U937 cells, which is blocked with either anti‐ICAM or anti‐LFA‐1 antibodies. In addition, indolactam V promotes U937 cell secretion of a 92 kDa gelatinase as demonstrated by zymography. In the presence of low levels of morphine (10 nM–1.0 μM), the U937 cell attachment to matrix proteins was not significantly affected. However, in the presence of 10 μM morphine, the indolactam V treated cells exhibit a 71–74% reduction in cell adhesion to the matrix proteins. Further, 10 μM morphine also blocks indolactam V‐induced homotypic aggregation and gelatinase secretion. The inhibitory effect of morphine on cell‐matrix adhesion and gelatinase secretion was not inhibited by the opiate receptor antagonist naloxone (1 μM). While 10 μM naloxone did partially counteract the effect of 10 μM morphine on U937 cell attachment, this effect was likely non‐specific since 10 μM naloxone alone increased cell adhesion. Supporting this conclusion, PCR analysis revealed that U937 cells do not express the μ high affinity morphine receptor. Also, indolactam V did not induce μ receptor expression, suggesting that morphine acts on U937 cells in a non‐specific fashion. © 2001 Wiley‐Liss, Inc.
Human T cell leukemia virus type I and neurologic disease: Events in bone marrow, peripheral blood, and central nervous system during normal immune surveillance and neuroinflammation
Authors: Grant Christian , Barmak Kate , Alefantis Timothy , Yao Jing , Jacobson Steven , Wigdahl Brian 
Published: August 2002

AbstractHuman T cell lymphotropic/leukemia virus type I (HTLV‐I) has been identified as the causative agent of both adult T cell leukemia (ATL) and HTLV‐I‐associated myelopathy/tropical spastic paraparesis (HAM/TSP). Although the exact sequence of events that occur during the early stages of infection are not known in detail, the initial route of infection may predetermine, along with host, environmental, and viral factors, the subset of target cells and/or the primary immune response encountered by HTLV‐I, and whether an HTLV‐I‐infected individual will remain asymptomatic, develop ATL, or progress to the neuroinflammatory disease, HAM/TSP. Although a large number of studies have indicated that CD4+ T cells represent an important target for HTLV‐I infection in the peripheral blood (PB), additional evidence has accumulated over the past several years demonstrating that HTLV‐I can infect several additional cellular compartments in vivo, including CD8+ T lymphocytes, PB monocytes, dendritic cells, B lymphocytes, and resident central nervous system (CNS) astrocytes. More importantly, extensive latent viral infection of the bone marrow, including cells likely to be hematopoietic progenitor cells, has been observed in individuals with HAM/TSP as well as some asymptomatic carriers, but to a much lesser extent in individuals with ATL. Furthermore, HTLV‐I+ CD34+ hematopoietic progenitor cells can maintain the intact proviral genome and initiate viral gene expression during the differentiation process. Introduction of HTLV‐I‐infected bone marrow progenitor cells into the PB, followed by genomic activation and low level viral gene expression may lead to an increase in proviral DNA load in the PB, resulting in a progressive state of immune dysregulation including the generation of a detrimental cytotoxic Tax‐specific CD8+ T cell population, anti‐HTLV‐I antibodies, and neurotoxic cytokines involved in disruption of myelin‐producing cells and neuronal degradation characteristic of HAM/TSP. J. Cell. Physiol. 190: 133–159, 2002. © 2002 Wiley‐Liss, Inc.
Obesity modulates the expression of haptoglobin in the white adipose tissue via TNFα
Authors: Chiellini Chiara , Bertacca Anna , Novelli Silvia E. , Görgün Cem Z. , Ciccarone Annamaria , Giordano Antonio , Xu Haiyan , Soukas Alexander , Costa Mario , Gandini Daniele , Dimitri Roberto , Bottone Pietro , Cecchetti Paolo , Pardini Ennia , Perego Lucia , Navalesi Renzo , Folli Franco , Benzi Luca , Cinti Saverio , Friedman Jeffrey M. , Hotamisligil Gökhan S. , Maffei Margherita 
Published: August 2002

AbstractIncrease in adipose mass results in obesity and modulation of several factors in white adipose tissue (WAT). Two important examples are tumor necrosis factor α (TNFα) and leptin, both of which are upregulated in adipose tissue in obesity. In order to isolate genes differentially expressed in the WAT of genetically obese db/db mice compared to their lean littermates, we performed RNA fingerprinting and identified haptoglobin (Hp), which is significantly upregulated in the obese animals. Hp is a glycoprotein induced by a number of cytokines, LPS (Lipopolysaccharide), and more generally by inflammation. A significant upregulation of WAT Hp expression was also evident in several experimental obese models including the yellow agouti (/) Ay, ob/ob and goldthioglucose‐treated mice (10‐, 8‐, and 7‐fold, respectively). To identify the potential signals for an increase in Hp expression in obesity, we examined leptin and TNFα in vivo. Wild type animals treated with recombinant leptin did not show any alteration in WAT Hp expression compared to controls that were food restricted to the level of intake of the treated animals. On the other hand, Hp expression was induced in mice transgenically expressing TNFα in adipose tissue. Finally, a significant downregulation of WAT Hp mRNA was observed in ob/ob mice deficient in TNFα function, when compared to the ob/ob controls. These results demonstrate that haptoglobin expression in WAT is increased in obesity in rodents and TNFα is an important signal for this regulation. J. Cell. Physiol. 190: 251–258, 2002. © 2002 Wiley‐Liss, Inc.
Angiotensin II type1 receptor regulation and differential trophic effects on rat cardiac myofibroblasts after acute myocardial infarction
Authors: Staufenberger Sibylle , Jacobs Martina , Brandstätter Katja , Hafner Mathias , Regitz‐Zagrosek Vera , Ertl Georg , Schorb Winfried 
Published: August 2002

AbstractFibroblast growth in the scar and surviving tissue is a key element of the remodeling post myocardial infarction. The regulation of fibroblast growth after acute myocardial infarction remains to be determined. Recently, Angiotensin II has been demonstrated to be a mitogen for neonatal cardiac fibroblasts. In this study adult rat cardiac fibroblasts were isolated from different regions of the infarcted rat heart and Angiotensin II effects examined. Adult Wistar‐rats were sham operated or left coronary artery ligated. After 4 days, hearts were removed and fibroblasts from sham operated, infarct‐ and non‐infarct regions of the left ventricle isolated. Radioligand binding studies were performed and cell number, cell area, total protein, and AT1 receptor mRNA after stimulation determined. Radioligand binding studies demonstrated that myofibroblasts expressed a single class of high affinity Angiotensin II AT1 receptors. Myofibroblasts from the infarct area revealed a lower maximal binding capacity, compared to sham operated myocardium. Conversely, myofibroblasts from the non‐infarct area had a higher expression of Angiotensin II AT1 receptor mRNA compared to sham operated myofibroblasts. Angiotensin II (1 μM, 48 h) increased cell‐number in sham operated and non‐infarct, but not in infarct myofibroblasts. Angiotensin II elevated total protein in sham operated, non‐infarct, and infarct myofibroblasts. In addition, Angiotensin II increased cell area in sham operated and infarct myofibroblasts. These data demonstrate that Angiotensin II acted as a mitogen in sham operated and non‐infarct myofibroblasts and stimulated hypertrophy in infarct myofibroblasts. These regional different effects of Angiotensin II might participate in the remodeling post myocardial infarction. © 2001 Wiley‐Liss, Inc.
Improvement of a fed‐batch process for high level xylanase production by aBacillusstrain
Authors: Schneider Gerhard , Strehaiano Pierre , Taillandier Patricia 
Published: August 2002

AbstractIn this paper, the improvement of a fed‐batch fermentation from the point of view of an industrial xylanase production process is described. TheBacillusstrain chosen for this study is able to produce high quantities of a xylanase that is suitable to be used as bleach boost agent in chlorine‐free bleaching sequences of paper pulp. It was found that xylo‐oligosaccharides (hydrolysis products from xylan by xylanase action) were indispensable for induction of the enzyme synthesis, but that their presence in quantities of only 0.1 g dm−3xylose equivalents led to catabolite repression. A substrate‐limited fed‐batch process, that is the most adapted, was furthermore improved with regard to nutrient requirement of the microorganism, especially the nitrogen source. A process with constant supply of a culture medium containing xylan, peptone and mineral nitrogen was able to produce 20 240 nkat cm−3with a productivity of 910 nkat cm−3 h−1, which places the process among the best ever reported.© 2001 Society of Chemical Industry
In situ reactive extraction of lactic acid from fermentation media
Authors: Tik Nurcan , Bayraktar Emine , Mehmetoglu Ülkü 
Published: August 2002

AbstractExtractive lactic acid fermentation was investigated in the presence of sunflower oil and Alamine‐336 (with oleyl alcohol as the diluent solvent). Lactic acid was produced in various media at 37 °C using Lactobacillus delbrueckii (NRRL‐B 445). First, the effects of oleyl alcohol (33.3%, v/v), immobilisation, and immobilisation in the presence of sunflower oil (5, 10, 15%, v/v) on lactic acid production were investigated. It was found that oleyl alcohol did not affect production while addition of sunflower oil increased lactic acid production from 10.22 to 16.46 gdm−3. On the other hand, a toxic effect was observed for oleyl alcohol solutions containing 15–50% (v/v) Alamine‐336. A maximum total lactic acid concentration of 25.59 gdm−3 was obtained when an oleyl alcohol solution containing 15% (v/v) Alamine together with immobilised cells with 15% (v/v) sunflower oil was used. This value was about 2.5 times that obtained from fermentation without organic solutions.© 2001 Society of Chemical Industry
Biotechnology, Volume 8B, Biotransformations II, 2nd edn Edited by DR Kelly, Series Editors H‐J Rehm, G Reed, A Pühler and P Stadler, John Wiley & Sons Ltd, Chichester, UK, 2000, 533 pp, Price UK £175.00, ISBN 3527 283242
Authors: Bucke C 
Published: August 2002

Abstract© 2001 Society of Chemical Industry
Comprehensive utilization of acidic wastewater from 3,3′‐dichlorobenzidine hydrochloride manufacture
Authors: Zhiqian Jia , Changqing Zhu , Qun Zhang , Huijuan Liu , Zhongzhou Liu , Jiuhul Qu , Dianpo Fu 
Published: August 2002

AbstractIn the commercial manufacture of 3,3′‐dichlorobenzidine hydrochloride, substantial quantities of acidic industrial effluents were generated. A combination of ultrafiltration and evaporation processes was investigated for the recovery of products and dilute hydrochloric acid. In a novel purification method, waste sulfuric acid is purified and reused four or five times in the hydrazobenzene–benzidine transformation step, resulting in a 75% reduction in the consumption of sulfuric acid, minimization of wastewater discharge and environmental hazards risk and significant economic, environmental and social benefits.© 2001 Society of Chemical Industry