bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of polyphosphate parameters for use with the AMBER force field
Authors: Meagher Kristin L. , Redman Luke T. , Carlson Heather A. 
Published: May 2003

AbstractAccurate force fields are essential for reproducing the conformational and dynamic behavior of condensed‐phase systems. The popular AMBER force field has parameters for monophosphates, but they do not extend well to polyphorylated molecules such as ADP and ATP. This work presents parameters for the partial charges, atom types, bond angles, and torsions in simple polyphosphorylated compounds. The parameters are based on molecular orbital calculations of methyldiphosphate and methyltriphosphate at the RHF/6‐31+G* level. The new parameters were fit to the entire potential energy surface (not just minima) with an RMSD of 0.62 kcal/mol. This is exceptional agreement and a significant improvement over the current parameters that produce a potential surface with an RMSD of 7.8 kcal/mol to that of the ab initio calculations. Testing has shown that the parameters are transferable and capable of reproducing the gas‐phase conformations of inorganic diphosphate and triphosphate. Also, the parameters are an improvement over existing parameters in the condensed phase as shown by minimizations of ATP bound in several proteins. These parameters are intended for use with the existing AMBER 94/99 force field, and they will permit users to apply AMBER to a wider variety of important enzymatic systems. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1016–1025, 2003
Methyl dynamics in crystalline amino acids: MD and NMR
Authors: Chatfield David C. , Augsten Alberto , D'Cunha Cassian , Wong Sergio E. 
Published: May 2003

AbstractCorrelation times for rotation of deuterated methyls in crystalline leucine, valine, and cyclo‐L‐alanyl‐L‐alanine are calculated with molecular dynamics and compared with NMR data. The simulations distinguish between methyls having different steric environments in the crystal, yielding correlation times differing by a factor of up to 30 for methyls within a given crystal. MD and NMR correlation times agree to within a factor of 2. However, averaging over nonequivalent methyls can yield correlation functions that, although actually multiexponential, are well fit by single exponentials. This may have significance for interpreting NMR data; previous NMR data did not distinguish between the methyls in these crystals. Adiabatic rotational barriers calculated with the X‐ray structure differ from effective barriers during simulation by up to ±1 kcal/mol; the difference indicates that dynamical effects have a significant role in determining rotational correlation times. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1052–1058, 2003
Peptide models. XXXIII. Extrapolation of low‐level Hartree–Fock data of peptide conformation to large basis set SCF, MP2, DFT, and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory
Authors: Perczel András , Farkas Ödön , Jákli Imre , Topol Igor A. , Csizmadia Imre G. 
Published: May 2003

AbstractAt the dawn of the new millenium, new concepts are required for a more profound understanding of protein structures. Together with NMR and X‐ray‐based 3D‐stucture determinations in silico methods are now widely accepted. Homology‐based modeling studies, molecular dynamics methods, and quantum mechanical approaches are more commonly used. Despite the steady and exponential increase in computational power, high level ab initio methods will not be in common use for studying the structure and dynamics of large peptides and proteins in the near future. We are presenting here a novel approach, in which low‐ and medium‐level ab initio energy results are scaled, thus extrapolating to a higher level of information. This scaling is of special significance, because we observed previously on molecular properties such as energy, chemical shielding data, etc., determined at a higher theoretical level, do correlate better with experimental data, than those originating from lower theoretical treatments. The Ramachandran surface of an alanine dipeptide now determined at six different levels of theory [RHF and B3LYP 3‐21G, 6‐31+G(d) and 6‐311++G(d,p)] serves as a suitable test. Minima, first‐order critical points and partially optimized structures, determined at different levels of theory (SCF, DFT), were completed with high level energy calculations such as MP2, MP4D, and CCSD(T). For the first time three different CCSD(T) sets of energies were determined for all stable B3LYP/6‐311++G(d,p) minima of an alanine dipeptide. From the simplest ab initio data (e.g., RHF/3‐21G) to more complex results [CCSD(T)/6‐311+G(d,p)//B3LYP/6‐311++G(d,p)] all data sets were compared, analyzed in a comprehensive manner, and evaluated by means of statistics. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1026–1042, 2003
Complete graph conjecture for inner‐core electrons: Homogeneous index case
Authors: Pogliani Lionello 
Published: May 2003

AbstractThe complete graph conjecture that encodes the inner‐core electrons of atoms with principal quantum number n ≥ 2 with complete graphs, and especially with odd complete graphs, is discussed. This conjecture is used to derive new values for the molecular connectivity and pseudoconnectivity basis indices of hydrogen‐suppressed chemical pseudographs. For atoms with n = 2 the new values derived with this conjecture are coincident with the old ones. The modeling ability of the new homogeneous basis indices, and of the higher‐order terms, is tested and compared with previous modeling studies, which are centered on basis indices that are either based on quantum concepts or partially based on this new conjecture for the inner‐core electrons. Two similar algorithms have been proposed with this conjecture, and they parallel the two “quantum” algorithms put forward by molecular connectivity for atoms with n > 2. Nine properties of five classes of compounds have been tested: the molecular polarizabilities of a class of organic compounds, the dipole moment, molar refraction, boiling points, ionization energies, and parachor of a series of halomethanes, the lattice enthalpy of metal halides, the rates of hydrogen abstraction of chlorofluorocarbons, and the pED50 of phenylalkylamines. The two tested algorithms based on the odd complete graph conjecture give rise to a highly interesting model of the nine properties, and three of them can even be modeled by the same set of basis indices. Interesting is the role of some basis indices all along the model. © 2003 Wiley Periodicals, Inc. J Comput Chem 9: 1097–1109, 2003
Self‐efficacy changes in groups: effects of diversity, leadership, and group climate
Authors: Choi Jin Nam , Price Richard H. , Vinokur Amiram D. 
Published: May 2003

AbstractSelf‐efficacy belief is a significant predictor of behavioral choices in terms of goal setting, the amount of effort devoted to a particular task, and actual performance. This study conceives of formation and change of self‐efficacy as a social and context‐dependent process. We hypothesized that different group factors (discretionary and ambient group stimuli) influence changes in members' self‐efficacy through differing routes (individual‐level and cross‐level processes). We tested our hypotheses using data from individuals in 169 training groups who attended a 5‐day workshop designed to increase participants' job‐search skills and efficacy. Specifically, we examined the degree of change in participants' job‐search efficacy before and after the workshop. The results showed that (a) membership diversity in education was positively related to increases in job‐search efficacy, (b) supportive leadership contributed to job‐search efficacy at the individual level of analysis with no cross‐level effects, and (c) open group climate contributed to job‐search efficacy through both individual‐level and cross‐level processes. Limitations and directions for future research are discussed. Copyright © 2003 John Wiley & Sons, Ltd.
Becoming an undercover police officer: a note on fairness perceptions, behavior, and attitudes
Authors: Farmer Suzanne J. , Beehr Terry A. , Love Kevin G. 
Published: May 2003

AbstractReactions to an undercover police officer selection system were analyzed for 271 officers. Officers given undercover assignments had higher procedural justice perceptions and outcome satisfaction than others awaiting assignment in a qualified applicant pool. Procedural and distributive justice perceptions were subsequently related to the undercover officer's job performance, job satisfaction, and organizational commitment. Copyright © 2003 John Wiley & Sons, Ltd.
Relationships between psychological climate perceptions and work outcomes: a meta‐analytic review
Authors: Parker Christopher P. , Baltes Boris B. , Young Scott A. , Huff Joseph W. , Altmann Robert A. , LaCost Heather A. , Roberts Joanne E. 
Published: May 2003

AbstractIn this study, meta‐analytic procedures were used to examine the relationships between individual‐level (psychological) climate perceptions and work outcomes such as employee attitudes, psychological well‐being, motivation, and performance. Our review of the literature generated 121 independent samples in which climate perceptions were measured and analyzed at the individual level. These studies document considerable confusion regarding the constructs of psychological climate, organizational climate, and organizational culture and reveal a need for researchers to use terminology that is consistent with their level of measurement, theory, and analysis. Our meta‐analytic findings indicate that psychological climate, operationalized as individuals' perceptions of their work environment, does have significant relationships with individuals' work attitudes, motivation, and performance. Structural equation modeling analyses of the meta‐analytic correlation matrix indicated that the relationships of psychological climate with employee motivation and performance are fully mediated by employees' work attitudes. We also found that the James and James (1989) PCg model could be extended to predict the impact of work environment perceptions on employee attitudes, motivation, and performance. Despite the number of published individual‐level climate studies that we found, there is a need for more research using standardized measures so as to enable analyses of the organizational and contextual factors that might moderate the effects of psychological climate perceptions. Finally, we argue for a molar theory of psychological climate that is rooted in the psychological processes by which individuals make meaning or their work experiences. Copyright © 2003 John Wiley & Sons, Ltd.
Reducing subjectivity in the assessment of the job environment: development of the Factual Autonomy Scale (FAS)
Authors: Spector Paul E. , Fox Suzy 
Published: May 2003

AbstractSelf‐report measures of job stressors have been criticized for being too subjective, rendering relations with other variables inconclusive. The Factual Autonomy Scale (FAS) was developed to reduce subjectivity by careful choice of fact‐based items. Results of two studies showed that when compared to the Job Diagnostic Survey autonomy scale, the FAS demonstrated superior convergent validity with alternate sources (supervisors in Study 1 and coworkers in Study 2), and discriminant validity when correlated with the remaining JDS core characteristics subscales. In addition, the FAS was correlated to a lesser extent than the JDS autonomy scale with job satisfaction. Incumbent FAS scores and not JDS scores correlated significantly with job performance as assessed by supervisors. It is suggested that it is feasible to develop fact‐based items for scales of the work environment that reduce the degree of subjectivity of responses. Copyright © 2003 John Wiley & Sons, Ltd.
Microflora involved in textile dye waste removal
Authors: Abd El–Rahim Wafaa M. , Moawad Hassan , Khalafallah M. 
Published: May 2003

AbstractTextile dyes are heavily used in factories for coloring different cloth materials. This work was designed to identify microorganisms capable of removing textile dyes, either by biodegradation or by biosorption.We expected to isolate microorganisms adapted to high dye concentrations from sites near textile industry complex. An experiment was conducted to study the efficiency of the isolates in removing textile dyes. The tested dyes were used as carbon and nitrogen sources for isolation of soil and/or water microorganisms capable of removing textile dyes wastes from factories effluent. The results indicated the low efficiency of both bacteria and actinomycetes in clean‐up the effluent from the waste dyes in 10–21 days. On the other hand six fungal isolates were obtained by plating factory effluent on Martin's medium and media containing dyes as the sole source of carbon and nitrogen for growth. These isolates fell in two genera, Aspergillus and Trichoderma. Results of these studies revealed the potential capacity of these fungi to decolorize the tested dyes in comparatively short time (2–24 hours) indicating strong efficiency of dye bioremediation by the fungal isolates. Since the process involved is mostly fast interaction between the fungal mycelium and the dye in the media, the possible mechanism could be based on a biosorption of such chemicals on the intact fungal biomass, rather than direct biodegradation of the compounds.
Distribution of zoosporic fungi in the mud of major Egyptian lakes
Authors: Ali Esam H. , Abdel–Raheem Ahmed 
Published: May 2003

AbstractTwenty‐six identified and three unidentified species belonging to eight genera of zoosporic fungi were recovered from seventy‐six mud samples of Egyptian lakes using sesame seeds as baits. Nineteen samples were collected along the borders of four major lakes. Pythium, Phytophthora and Allomyces, yielded the highest spectra of zoosporic species, while Aqualinderella, Blastocladia and Dictyuchus, had one species. Pythium, Aphanomyces, Allomyces, Aqualinderella, Phytophthora and Saprolegnia were the dominant zoosporic genera while Blastocladia and Dictyuchus were rare. The most prevalent species of zoosporic fungi were Aqualinderella fermentans, Aphanomyces laevis and unidentified Pythium species while the other isolated species in this study were rare. Menzalah was the richest lake with zoosporic species followed by Borolous and Karoon. Some zoosporic fungal genera were recovered from the mud of the four tested lakes (participator genera) and others from three lakes or from only two lakes. Physicochemical characteristics of the mud samples (pH, total soluble salts and organic matter) revealed no correlation with the fungal occurrence and distribution in these lakes.
Occurrence of yeasts in municipal wastes and their behaviour in presence of cadmium, copper and zinc
Authors: Balsalobre Luz , De Silóniz María‐Isabel , Valderrama María‐José , Benito Teresa , Larrea María‐Teresa , Peinado José‐Martínez 
Published: May 2003

AbstractSeven yeasts strains have been isolated from sewage sludge. Also six samples of compost with different sieving, composting times and origins, have been analysed. Apparently, composting processes negatively affect the viability of yeasts, as none could be isolated from the compost samples. The margins of tolerance of the yeasts to Cd, Cu and Zn have been determined. The physiological response to metals was similar in all the species studied, and in general, kinetic parameters (μ and lag) were affected. Metal uptake ability was also studied and inter‐ and intra‐specific heterogeneity was detected, thus indicating that both the tolerance to metals and the capacity of the uptake were dependent on ionic metal and yeast species. The effect of the presence of multi‐metal ions on the uptake capacity of each individual metal was assayed for two selected yeasts, Pichia guilliermondii and Torulaspora delbrueckii. The uptake of each individual metal varied with the combination assayed, and when both strains were compared different results were also found.
Evaluation of SDS‐polyacrylamide gel systems for the study of outer membrane protein profiles of clinical strains of Acinetobacter baumannii
Authors: Cuenca Felipe Fernández , Pascual Alvaro , Martínez Luis Martínez , Conejo Ma Carmen , Perea Evelio J. 
Published: May 2003

AbstractThe outer membrane protein (OMP) profiles of 23 blood isolates of Acinetobacter baumannii representing all the different antimicrobial susceptibility patterns observed during a 3‐year period in a Spanish hospital were studied. OMPs extracted from envelopes of sonicated cells after solubilisation with 2% of N‐lauryl‐sarcosinate were analysed by sodium dodecyl sulphate‐polyacrylamide gel electrophoresis (SDS‐PAGE) using the Laemmli's buffers. Eight running gel systems differing in the concentration of polyacrylamide (8%, 10% and 12%) and in the absence or presence of urea (4 M and 6 M) were used in a preliminary study analysing the OMP profiles of four clonally unrelated strains of A. baumannii. When this study was completed, the OMPs of the 23 A. baumannii were analysed in 10% SDS‐polyacrylamide gels with 6 M urea and in 12% SDS‐polyacrylamide gels. Ten OMP profiles were observed in 10% SDS‐polyacrylamide gels with 6 M urea, whereas only 5 OMP profiles were visualised using 12% SDS‐polyacrylamide gels. The OMP profiles obtained in 10% SDS‐polyacrylamide gels with 6 M urea only partially correlated with those observed in 12% SDS‐polyacrylamide gels. In conclusion, the use of 10% SDS‐polyacrylamide gels with 6 M urea is recommended for the study of OMP profiles of A. baumannii.
Molecular diversity of mesophilic and thermophilic bacteria in a membrane bioreactor determined by fluorescent in situ hybridization with mxaF‐ and rRNA‐targeted probes
Authors: Dias João Carlos T. , Silva Cláudio M. , Mounteer Ann H. , Passos Flavia M. L. , Linardi Valter R. 
Published: May 2003

AbstractAn evaluation of the efficiency of treatment of kraft mill foul condensates in a membrane bioreactor was carried out in the laboratory. Efficiency and rate of methanol removal were quantified at operating temperatures of 35, 45 and 55 °C. The structure of the bacterial community present in the reactor biomass at the different operating temperatures was evaluated by in situ hybridization of the biomass samples with fluorescently‐labelled probes (FISH) targeting the Eubacteria, the alpha, beta and gamma subclasses of the Proteobacteria, the low G + C content Gram‐positive bacteria (Bacillus spp.), while community function was evaluated by in situ hybridization with a methanol dehydrogenase gene (mxaF) probe. Methanol removal efficiency decreased from 99.4 to 92%, and removal rate from 2.69 mg MeOH/l × min to 2.49 mg MeOH/l × min when the operating temperature was increased from 35 to 55 °C. This decrease in methanol removal was accompanied by a decrease (from 58% to 42%) in the relative proportion of cells that hybridized with the mxaF probe. The relative proportion of Bacillus spp. increased from 5 to 20% while the proportion of members of the alpha subclass of Proteobacteria decreased from 16% to 6% when the bioreactor operating temperature was raised from 35 to 55 °C. The relative proportions of bacteria belonging to the beta (22–25%) and gamma (18–20%) subclasses of the Proteobacteria remained relatively constant regardless of operating temperature. Proteobacteria (alpha, beta and gamma subclasses) and Bacillus spp. represented 61, 67 and 71% of the Eubacteria in the biomass sampled at 35, 45 and 55 °C, respectively. The FISH technique was shown to be an efficient method for detection of both structural and functional changes in the bacterial communities that could be related to efficiency of methanol removal in a membrane bioreactor operating at different temperatures.
Effect of carbon source on alkaline phosphatase production and excretion in Aspergillus caespitosus
Authors: Guimarães Luis Henrique Souza , Jorge João Atilio , Terenzi Héctor Francisco , Jamur Maria Célia , Oliver Constance , De Lourdes Teixeira De Moraes Polizeli Maria 
Published: May 2003

AbstractThe effect of several carbon sources on the production of alkaline phosphatase by the thermotolerant Aspergillus caespitosus was analysed. The fungus released high levels of alkaline phosphatases into the medium after being cultured for long periods with xylan or industrial residues such as wheat raw and sugar cane bagasse in the culture media. In contrast, the alkaline phosphatase activities were found only intracellulary when the fungus was cultured in glucose‐supplemented media. The pH of the medium likely affects the process of enzyme secretion according to the carbon source used. Addition of xylan or industrial residues in the culture medium stimulated the secretion of phosphatases. In contrast, media supplemented with glucose or disaccharides promoted retention of these enzymes into the cells. The subcellular location activities of alkaline phosphatases were studied using histochemical and immunochemical methods and showed that alkaline phosphatases were present in the mycelial walls and septa.
Evaluation of biotoxicity of textile dyes using two bioassays
Authors: Moawad Hassan , El–Rahim Wafaa M. Abd , Khalafallah M. 
Published: May 2003

AbstractThe toxicity of eight textile dyes was evaluated using two bioassays namely: Ames test and seed germination test. The Ames test is widely used for the evaluation of hazardous mutagenic effect of different chemicals, as a short‐term screening test for environmental impact assessment. The eight‐textile dyes and Eithidium bromide dye (as positive control) were tested with five “his” Salmonella typhimurium strains: TA 100; TA 98; TA 1535; TA 1537; TA 1538. Using six concentrations of each dye (2.5 μg/ml, 4.5 μg/ml, 9 μg/ml, 13.5 μg/ml, 18 μg/ml, and 22.5 μg/ml) revealed that, most of the dyes were mutagenic for the test strains used in this study. The high concentrations of dye eliminated microbial colonies due to the high frequency of mutation causing lethal effect on the cells.In this work the phytotoxicity of different soluble textile dyes was estimated by measuring the relative changes in seed germination of four plants: clover, wheat, tomato and lettuce. The changes in shooting percentages and root length as affected by dye were also measured. Seed germination percent and shoot growth as well as root length were recorded after 6 days of exposure to different concentrations of textile dyes in irrigation water. The results show that high concentrations of dyes were more toxic to seed germination as compared with the lower concentrations. However, the low concentrations of the tested dyes adversely affected the shooting percent significantly.
Biomass and exopolysaccharide production in submerged cultures of Pleurotus ostreatoroseusSing. and Pleurotus ostreatus “florida” (Jack.: Fr.) Kummer
Authors: Rosado Fábio Rogério , Germano Sandro , Carbonero Elaine R. , da Costa Sandra Maria Gomes , Iacomini Marcello , Kemmelmeier Carlos 
Published: May 2003

AbstractThe species of the genus Pleurotus produce large amounts of biomass and exopolysaccharide (EPS) in submerged cultures, which may be used for biotechnological purposes. In the present work two Brazilian autochthonous strains of edible Pleurotus (P. ostratoroseus Sing. and P. ostreatus “florida”) were used. The fungi grown in liquid Potato Dextrose medium (PD) were used as inocula to cultivate those microorganisms in the POL culture medium. After a 9‐day incubation, the optimal growth time for biomass production, P. ostreatus “florida” presented higher biomass production (22.8 g d.w./l) than P. ostreatoroseus (16.8 g d.w./l). After a 7‐day incubation, the optimal growth time for EPS production, P. ostreatoroseus produced higher amounts of crude EPS (5.8 g d.w./l) than P. ostreatus “florida” (1.4 g d.w./l). Relative carbohydrate composition for P. ostreatoroseus and P. ostreatus “florida” EPS were: glucose (95.5–87.7), galactose (traces – 4.9), mannose (traces – 3.1), xylose (1.3–2.5), and arabinose (3.2–1.8). Lower ammonium sulfate concentration in the POL culture medium increased the exopolysaccharides production by P. ostreatoroseus.