bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum mechanical study of the conformational behavior of proline and 4R‐hydroxyproline dipeptide analogues in vacuum and in aqueous solution
Authors: Benzi Caterina , Improta Roberto , Scalmani Giovanni , Barone Vincenzo 
Published: August 2002

AbstractThe conformational behavior of the title compounds has been investigated by Hartree–Fock, MP2, and DFT computations on the most significant structures related to variations of the backbone dihedral angles, cis/trans isomerism around the peptide bond, and diastereoisomeric puckering of the pyrrolidine ring. In vacuum the reversed γ turn (γl), characterized by an intramolecular hydrogen bridge, corresponds to the absolute energy minimum for both puckerings (up and down) of the pyrrolidine ring. An additional energy minimum is found in the helix region, but only for an up puckering of the pyrrolidine ring. When solvent effects are included by means of the polarizable continuum model the conformer observed experimentally in condensed phases becomes the absolute minimum. The down puckering is always favored over its up counterpart, albeit by different amounts (0.4–0.5 kcal/mol for helical structures and about 2 kcal/mol for γl structures). In helical structures cis arrangements of the peptide bond are only slightly less stable than their trans counterparts. This is no longer true for γl structures, because the formation of an intramolecular hydrogen bond is possible only for trans peptide bonds. In most cases, proline and hydroxyproline show the same general trends; however, the electronegative 4(R) substituent of hydroxyproline leads to a strong preference for up puckerings irrespective of the backbone conformation. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 341–350, 2002
Identifying native‐like protein structures using physics‐based potentials
Authors: Dominy Brian N. , Brooks, Charles L. 
Published: August 2002

AbstractAs the field of structural genomics matures, new methods will be required that can accurately and rapidly distinguish reliable structure predictions from those that are more dubious. We present a method based on the CHARMM gas phase implicit hydrogen force field in conjunction with a generalized Born implicit solvation term that allows one to make such discrimination. We begin by analyzing pairs of threaded structures from the EMBL database, and find that it is possible to identify the misfolded structures with over 90% accuracy. Further, we find that misfolded states are generally favored by the solvation term due to the mispairing of favorable intramolecular ionic contacts. We also examine 29 sets of 29 misfolded globin sequences from Levitt's “Decoys ‘R’ Us” database generated using a sequence homology‐based method. Again, we find that discrimination is possible with approximately 90% accuracy. Also, even in these less distorted structures, mispairing of ionic contacts results in a more favorable solvation energy for misfolded states. This is also found to be the case for collapsed, partially folded conformations of CspA and protein G taken from folding free energy calculations. We also find that the inclusion of the generalized Born solvation term, in postprocess energy evaluation, improves the correlation between structural similarity and energy in the globin database. This significantly improves the reliability of the hypothesis that more energetically favorable structures are also more similar to the native conformation. Additionally, we examine seven extensive collections of misfolded structures created by Park and Levitt using a four‐state reduced model also contained in the “Decoys ‘R’ Us” database. Results from these large databases confirm those obtained in the EMBL and misfolded globin databases concerning predictive accuracy, the energetic advantage of misfolded proteins regarding the solvation component, and the improved correlation between energy and structural similarity due to implicit solvation. Z‐scores computed for these databases are improved by including the generalized Born implicit solvation term, and are found to be comparable to trained and knowledge‐based scoring functions. Finally, we briefly explore the dynamic behavior of a misfolded protein relative to properly folded conformations. We demonstrate that the misfolded conformation diverges quickly from its initial structure while the properly folded states remain stable. Proteins in this study are shown to be more stable than their misfolded counterparts and readily identified based on energetic as well as dynamic criteria. In summary, we demonstrate the utility of physics‐based force fields in identifying native‐like conformations in a variety of preconstructed structural databases. The details of this discrimination are shown to be dependent on the construction of the structural database. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 147–160, 2002
Thermodynamics and kinetics of initial gas phase reactions in chemical vapor deposition of titanium nitride. Theoretical study of TiCl4 ammonolysis
Authors: Umanskii Stanislav Ya. , Novoselov Konstantin P. , Minushev Airat Kh. , Siodmiak Magdalena , Frenking Gernot , Korkin Anatoli A. 
Published: August 2002

AbstractThermodynamic equilibrium and kinetics of the gas‐phase reaction between TiCl4 and NH3 have been studied computationally using results from recent quantum mechanical calculations of titanium tetrachloride ammonolysis.1 These calculations were based upon the transition state theory for the direct reactions and RRKM theory for the reactions proceeding via intermediate complex. Rate constants for the barrierless reactions were expressed through the thermodynamic characteristics of the reagents and products using a semiempirical variational method. The kinetic simulation of the gas‐phase steps of CVD was performed within a model of a well‐stirred reactor at temperatures 300–1200 K and residence times between 0.1–2 s. At temperatures below 450 K formation of donor–acceptor complexes between TiCl4 and NH3 is the dominating process. At higher temperatures sequential direct ammonolysis takes place. At typical LPCVD conditions the only product of the first step of ammonolysis, TiCl3NH2, is formed in substantial amount. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1366–1376, 2001
The elastic net algorithm and protein structure prediction
Authors: Ball Keith D. , Erman Burak , Dill Ken A. 
Published: August 2002

AbstractPredicting protein structures from their amino acid sequences is a problem of global optimization. Global optima (native structures) are often sought using stochastic sampling methods such as Monte Carlo or molecular dynamics, but these methods are slow. In contrast, there are fast deterministic methods that find near‐optimal solutions of well‐known global optimization problems such as the traveling salesman problem (TSP). But fast TSP strategies have yet to be applied to protein folding, because of fundamental differences in the two types of problems. Here, we show how protein folding can be framed in terms of the TSP, to which we apply a variation of the Durbin–Willshaw elastic net optimization strategy.1 We illustrate using a simple model of proteins with database‐derived statistical potentials and predicted secondary structure restraints. This optimization strategy can be applied to many different models and potential functions, and can readily incorporate experimental restraint information. It is also fast; with the simple model used here, the method finds structures that are within 5–6 Å all‐Cα‐atom RMSD of the known native structures for 40‐mers in about 8 s on a PC; 100‐mers take about 20 s. The computer time τ scales as τ∼n, where n is the number of amino acids. This method may prove to be useful for structure refinement and prediction. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 77–83, 2002
A comparison of the short and long forms of the Multiple Affect Adjective Check List—Revised (MAACL‐R)
Authors: Lubin Bernard , Van Whitlock Rodney , Reddy Deepika , Petren Suzanne 
Published: August 2002

AbstractBrief, reliable, and valid assessment instruments are very important for clinical psychology research and practice. The possible equivalency of a short form and the long form of the Multiple Affect Adjective Check List—Revised (MAACL‐R; Zuckerman & Lubin,1985) was studied by correlating both forms of the MAACL‐R with the State Trait Personality Inventory (Spielberger,1995); the Affect Balance Scale (Bradburn,1969); and the Sensation Seeking Scale (Zuckerman,1978). Reliability and validity of the two forms were equivalent. © 2001 John Wiley & Sons, Inc. J Clin Psychol 57: 411–416, 2001.
Exercise in treating depression: Broadening the psychotherapist's role
Authors: Pollock Kenneth M. 
Published: August 2002

AbstractResearch findings over the past two decades strongly indicate that moderate exercise can have a beneficial effect upon depression, yet suggestions to depressed patients that they exercise rarely are followed. Despite the research, few psychotherapists employ exercise promotion and maintenance as part of their treatment. An approach to integrating exercise promotion into psychotherapy treatment is presented. It incorporates a therapist–patient collaborative process involving joint assessment of biopsychosocial barriers and facilitators for exercise initiation and maintenance that are unique to the patient. Based upon the assessment, a collaborative exercise plan is developed and implemented. © 2001 John Wiley & Sons, Inc. J Clin Psychol/In Session 57: 1289–1300, 2001.
Heterogeneity of the signal transduction pathways for VEGF‐induced MAPKs activation in human vascular endothelial cells
Authors: Yashima Rei , Abe Mayumi , Tanaka Katsuhiro , Ueno Hikaru , Shitara Kenya , Takenoshita Seiichi , Sato Yasufumi 
Published: August 2002

AbstractVascular endothelial growth factor (VEGF) activates ERK and p38 MAPK in endothelial cells (ECs). The present study was aimed to compare its intracellular signal transduction pathways between three primary cultures of human ECs including human aortic ECs (HAECs), human umbilical vein ECs (HUVECs), and human microvascular ECs (HMVECs). VEGF activated ERK and p38 MAPK in all of three ECs. Isoforms of p38 MAPK that were activated by VEGF in HUVECs were p38‐α and p38‐δ. GF109203X, a specific inhibitor of PKC, markedly inhibited VEGF‐induced activation of ERK and p38 MAPK in HAECs and HUVECs, whereas it exhibited little effect in HMVECs. In contrast, dominant negative mutant of Ha‐Ras almost completely abrogated VEGF‐induced activation of ERK and p38 MAPK in HMVECs. Although dominant negative mutant of Ha‐Ras substantially inhibited the basal activities of ERK and p38 MAPK, it exhibited marginal effect on VEGF‐induced activation of ERK and p38 MAPK in HUVECs and HAECs. The activation of Ras by VEGF appeared to be most prominent in HMVECs. These results indicate that intracellular signal transduction pathways for VEGF‐induced activation of MAPKs are heterogeneous and vary depending on the origin of ECs.© 2001 Wiley‐Liss, Inc.
Oxidation of several chlorophenolic derivatives by UV irradiation and hydroxyl radicals
Authors: Benitez F Javier , Beltran‐Heredia Jesus , Acero Juan L , Rubio F Javier 
Published: August 2002

AbstractThe oxidation of some chlorophenols: 4‐chlorophenol, 2,4‐dichlorophenol, 2,4,6‐trichlorophenol, 2,3,4,6‐tetrachlorophenol, tetrachlorocatechol (3,4,5,6‐tetrachloro‐2‐hydroxy phenol) and 4‐chloroguaiacol (4‐chloro‐2‐methoxy phenol) has been studied via single photodecomposition produced by polychromatic UV irradiation, oxidation by hydroxyl radicals generated by Fenton's reagent (hydrogen peroxide plus ferrous ions), and degradation by hydroxyl radicals produced by combinations of UV irradiation plus hydrogen peroxide, and UV irradiation plus hydrogen peroxide and ferrous ions (photo‐Fenton system). These organics have been selected as models of chloro‐phenolic derivative pollutants present in wastewaters and groundwaters. The degradation levels obtained in each process are reported. The quantum yields in the single photodecomposition reaction and the rate constants between the chlorophenols and the hydroxyl radicals in the reaction with Fenton's reagent are determined. Finally, the additional contributions to the photodecomposition promoted by the radical reaction in the combined UV/H2O2 and photo‐Fenton systems are also evaluated.© 2001 Society of Chemical Industry
Effect of amino acids containing sulfur on the corrosion of mild steel in phosphoric acid solutions polluted with Cl−, F− and Fe3+ ions–behaviour near and at the corrosion potential
Authors: Morad Mohamed Samir S , Hermas Abo El‐Hagag A , Aal Mohamed S Abdel 
Published: August 2002

AbstractResearch on non‐toxic inhibitors is of considerable interest in investigations into the replacement of hazardous classical molecules. This paper reports the action of four amino acids containing sulfur on the corrosion of mild steel in phosphoric acid solution with and without Cl−, F− and Fe3+ ions near and at the corrosion potential (Ecorr) using both the polarization resistance method and electrochemical impedance spectroscopy (EIS). Both cysteine and N‐acetylcysteine (ACC) showed higher inhibition efficiency than methionine and cystine. Adsorption of methionine onto a mild steel surface obeys the Frumkin adsorption isotherm and has a free energy of adsorption value (ΔG °ads) lower than those obtained in the presence of cystine, cysteine and ACC whose adsorption isotherms follow that of Langmuir. Both F− and Fe3+ ions stimulate mild steel corrosion while Cl− ions inhibit it. The binary mixtures of methionine, cysteine or ACC with Cl− or F− ions are effective inhibitors (synergism) while the combinations of the amino acid with Fe3+ or the ternary Cl−/F−/Fe3+ mixture have low inhibitive action (antagonism). EIS measurements revealed that the charge transfer process mainly controls the mechanism of mild steel corrosion in phosphoric acid solution in the absence and presence of the investigated additives. The mechanism of corrosion inhibition or acceleration is discussed.© 2002 Society of Chemical Industry
Production of L‐methionine by immobilized pellets of Aspergillus oryzae in a packed bed reactor
Authors: Yuan Ying‐Jin , Wang Shu‐hao , Song Zheng‐xiao , Gao Rui‐chang 
Published: August 2002

AbstractProduction of L‐methionine by immobilized pellets of Aspergillus oryzae in a packed bed reactor was investigated. Based on the determination of relative enzymatic activity in the immobilized pellets, the optimum pH and temperature for the resolution reaction were 8.0 and 60 °C, respectively. The effects of substrate concentration on the resolution reaction were also investigated and the kinetic constants (Km and Vm) of immobilized pellets were found to be 7.99 mmol dm−3 and 1.38 mmol dm−3 h−1, respectively. The maximum substrate concentration for the resolution reaction without inhibition was 0.2 mol dm−3. The L‐methionine conversion rate reached 94% and 78% when substrate concentrations were 0.2 and 0.4 mol dm−3, respectively, at a flow rate of 7.5 cm3 h−1 using the small‐scale packed bed reactor developed. The half‐life of the L‐aminoacylase in immobilized pellets was 70 days in continuous operation. All the results obtained in this paper exhibit a practical potential of using immobilized pellets of Aspergillus oryzae in the production of L‐methionine.© 2002 Society of Chemical Industry
Preoperative evaluation of periampullary tumors by endoscopic sonography, transabdominal sonography, and computed tomography
Authors: Chen Chien‐Hua , Tseng Li‐Jung , Yang Chi‐Chieh , Yeh Yung‐Hsiang 
Published: August 2002

AbstractPurposeThe purpose of this retrospective study was to compare the sensitivity of endoscopic sonography (EUS), transabdominal sonography (US), and CT in the detection of, local staging of, and prediction of vascular involvement by or distant metastasis from periampullary tumors.MethodsSeventy‐four consecutive patients with presumed periampullary tumors were evaluated by EUS, US, and CT during a 3.25‐year period. The local staging accuracy of the modalities was assessed in the 36 patients with solid tumors who underwent surgery. The sensitivity of the modalities in predicting vascular involvement and distant metastasis was assessed in the 56 patients with carcinomas.ResultsEUS was the most sensitive modality in the detection (EUS, 97%; US, 24%; and CT, 39%; p < 0.001 for EUS versus US or CT) and T classification (EUS, 72%; US, 11%; CT, 22%; p < 0.001 for EUS versus US or CT) of periampullary tumors. EUS also had better sensitivity than US in detecting lymph node metastasis from periampullary cancers (EUS, 47%; US, 7%; and CT, 33%; p = 0.02 for EUS versus US; p = 0.7 for EUS versus CT). The accuracy of EUS in determining the T classification (without stent, 81%; with stent, 65%) and N classification (without stent, 80%; with stent, 70%) tended to decrease in the presence of an endobiliary stent, but the differences were not significant. EUS was the most sensitive modality in demonstrating vascular involvement (EUS, 100%; US, 0%; and CT, 33%; p = 0.002 for EUS versus US; p = 0.03 for EUS versus CT) but was not significantly different in detecting distant metastasis (EUS, 11%; US, 44%; and CT, 44%).ConclusionsEUS is superior to US and CT in the local assessment of periampullary tumors. The staging accuracy of EUS is minimally but not significantly affected by the presence of an endobiliary stent. © 2001 John Wiley & Sons, Inc. J Clin Ultrasound 29:313–321, 2001.
Homologies of process and modular elements of embryonic construction
Authors: Gilbert Scott F. , Bolker Jessica A. 
Published: August 2002

AbstractThere are several signal transduction pathways that integrate embryonic development. We find that both within species and between species, these pathways constitute homologous modules. The processes, themselves, can be considered homologous, just as structures can be considered homologous. Just like vertebrate limbs, these pathways are composed of homologous parts (in this case, the proteins of the pathway) that are organized in homologous ways. These pathways are conserved through evolutionary time, and they undergo descent with modification. Such homologies of processes become critical to the discussion of evolution and development when we consider (1) that evolution depends on heritable changes in development, (2) that development is modular such that different modules can change without affecting other modules, (3) that modules can be co‐opted into new functions, and (4) that modules depend on intercellular communication. J. Exp. Zool. (Mol. Dev. Evol.) 291:1–12, 2001. © 2001 Wiley‐Liss, Inc.
Effects of plasma from bivalve mollusk species on the in vitro proliferation of the protistan parasite Perkinsus marinus
Authors: Gauthier Julie D. , Vasta Gerardo R. 
Published: August 2002

AbstractThe in vitro culture of the Eastern oyster parasite Perkinsus marinus has provided a unique opportunity to examine its susceptibility to putative recognition and effector defense mechanisms operative in refractory bivalve species. In this study, we report the effect of supplementing the culture medium with plasma from: (1) uninfected to heavily infected Eastern oysters; (2) oyster species considered to be disease‐resistant; and (3) bivalve mollusk species that are naturally exposed to the parasite but show no signs of disease. We also examined in vitro the interaction between hemocytes from Crassostrea virginica and C. gigas and P. marinus trophozoites. Our results revealed a significant decrease (32%) in proliferation of P. marinus in the presence of plasma from heavily infected C. virginica oysters. The inhibitory effects were less pronounced with plasma from moderately infected and uninfected oysters. In contrast, plasma from C. rivularis and C. gigas enhanced P. marinus proliferation. Proliferation was significantly reduced in media supplemented with plasma from Mytilus edulis, Mercenaria mercenaria, and Anadara ovalis. The highest inhibitory activity was apparent in M. edulis, for which 5% plasma‐supplemented medium reduced growth by 35% relative to the controls. M. edulis active component(s) was heat‐stable, yet pronase‐sensitive. The significantly higher uptake of live P. marinus trophozoites by hemocytes from C. virginica, relative to those from C. gigas, suggests a certain level of specificity in the recognition/endocytosis of the parasite by its natural bivalve host species. J. Exp. Zool. 292:221–230, 2002. © 2002 Wiley‐Liss, Inc.
Egg‐jelly structure promotes efficiency of internal fertilization in the newt, Cynops pyrrhogaster
Authors: Itoh Tokuko , Kamimura Saori , Watanabe Akihiko , Onitake Kazuo 
Published: August 2002

AbstractEgg‐jelly is composed of a network of fibrous components and contains substances regulating the sperm‐egg interaction. Many studies on the latter have been conducted, whereas the role of the egg‐jelly structure in fertilization has not yet been fully assessed. In this study, we examined the fertilization efficiency in the presence and absence of the structure around the egg of the newt, Cynops pyrrhogaster, using a gelatin gel system. Although de‐jellied eggs of C. pyrrhogaster can be fertilized with an adequate number of sperm, the fertilization rate was dramatically increased through the use of the gelatin gel. Sperm showed forward motility with straight morphology in the gel, whereas they swam in circles in solution. This result indicates that the gel structure is significant for sperm guidance to the egg surface, and its presence raises the fertilization efficiency in C. pyrrhogaster. When sperm were entangled in the gel structure, they were immediately folded and never showed any forward motility. Sperm with zigzag morphology were observed in the gelatin gel as well as in the egg‐jelly, indicating the elimination of sperm by the gel structure. The effect of sperm elimination on successful fertilization was estimated using gelatin gels of different thickness. Though the variation did not affect the fertilization rate, the rate of normal development gradually increased in the thicker gels. This result indicates that sperm elimination in egg‐jelly can function in the fertilization system. The roles of sperm guidance and sperm elimination under the physiological condition of internal fertilization of the newt are discussed. J. Exp. Zool. 292:314–322, 2002. © 2002 Wiley‐Liss, Inc.
Effects of the purified IGF‐I complex on the capacitation and acrosome reaction of rabbit spermatozoa
Authors: Minelli Alba , Liguori Lavinia , Collodel Giulia , Lattaioli Paolo , Castellini Cesare 
Published: August 2002

AbstractA protein complex containing IGF‐I, purified from rabbit seminal plasma, was used to investigate its effects on the capacitation and acrosome reaction of rabbit spermatozoa. Uncapacitated sperm (Pattern F), capacitated sperm (Pattern B), and acrosome‐reacted sperm (Pattern AR) were determined by CTC staining, and the results were validated by PSA‐staining. The addition of the IGF‐I complex to the capacitative medium directed the spermatozoa to spontaneous acrosome reaction. On the other hand, IGF‐I complex, added to capacitated spermatozoa, acted as inducer of the acrosome reaction. Results of IVF experiments showed high rates of fertilization with capacitated spermatozoa, acrosome‐reacted by either A23187 or IGF I complex, whereas significantly lower rates were obtained with spermatozoa capacitated in the presence of IGF‐I complex. J. Exp. Zool. 290:311–317, 2001. © 2001 Wiley‐Liss, Inc.