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At least 451 records · Page 25Linked to original sources
PubMed2006

Characterizing the potential energy surface of the water dimer with DFT: failures of some popular functionals for hydrogen bonding.

Ten stationary points on the water dimer potential energy surface have been examined with ten density functional methods (X3LYP, B3LYP, B971, B98, MPWLYP, PBE1PBE, PBE, MPW1K, B3P86, and BHandHLYP). Geometry optimizations and vibrational frequency calculations were carried out with the TZ2P(f,d)+dif basis set. All ten of the density functionals correctly describe the relative energies of the ten stationary points. However, correctly describing the curvature of the potential energy surface is far more difficult. Only one functional (BHandHLYP) reproduces the number of imaginary frequencies from CCSD(T) calculations. The other nine density functionals fail to correctly characterize the nature of at least one of the ten (H(2)O)(2) stationary points studied here.

Journal Article↗
PubMed2001

Reproducing the conformations of protein-bound ligands: a critical evaluation of several popular conformational searching tools.

Several programs (Catalyst, Confort, Flo99, MacroModel, and Omega) that are commonly used to generate conformational ensembles have been tested for their ability to reproduce bioactive conformations. The ligands from thirty-two different ligand-protein complexes determined by high-resolution (< 2.0 A) X-ray crystallography have been analyzed. The Low-Mode Conformational Search method (with AMBER* and the GB/SA hydration model), as implemented in MacroModel, was found to perform better than the other algorithms. The rule-based method Omega, which is orders of magnitude faster than the other methods, also gave reasonable results but were found to be dependent on the input structure. The methods supporting diverse sampling (Catalyst, Confort) performed least well. For the seven ligands in the set having eight or more rotatable bonds, none of the bioactive conformations were ever found, save for one exception (Flo99). These ligands do not bind in a local minimum conformation according to AMBER*\GB/SA. Taking these last two observations together, it is clear that geometrically similar structures should be collected in order to increase the probability of finding the bioactive conformation among the generated ensembles. Factors influencing bioactive conformational retrieval have been identified and are discussed.

Algorithms↗
PubMed1997

Cancer coverage and tobacco advertising in African-American women's popular magazines.

Mass circulating magazines offer an opportunity to inform large segments of the population about preventive health behaviors relevant for cancer control. We collected information about the number and type of cancer articles from January 1987 through December 1994 in Jet, Ebony and Essence magazines. These magazines each have a principal readership of African-American women and a paid circulation of 1,000,000 or more annually. Cancer articles were counted if the content was gender neutral or specifically targeted for women. There were 84 articles on cancer including 6 on lung cancer and 3 on other tobacco-related cancers. Nine additional references to lung cancer were mentioned under the general cancer category, but lung cancer was not the primary focus of the articles. There were 24 articles on breast cancer and 9 on cervical cancer over the 8 year period. Most of the articles (> 70%) were short fillers of less than one page in length. A prevention focus was included in 42.2%, 75.0%, and 71.0% of the cancer articles in Jet, Ebony, and Essence respectively. Of the 649 health articles, 116 were on cardiovascular disease. In contrast, there were 1,477 tobacco advertisements over the 8 years. The number of cancer articles was not significantly associated with the number of tobacco advertisements. Because tobacco-related cancers are entirely preventable and contribute to the significant cancer burden, the lack of coverage of tobacco-related cancers is a missed opportunity for health promotion among African-American females.

Adult↗
PubMed2002

Correlation and examiner agreement between a new method of plaque scoring and a popular established plaque index, modelled in vitro.

BACKGROUND, AIMS: Scoring of supragingival plaque is common to epidemiological studies, oral hygiene assessments and clinical trials of oral hygiene products. These clinical practices utilize indices such as the Turesky et al. (1970, Journal of Periodontology 41, pp. 41-43) modification [Turesky Plaque Index (TPI)] of the Quigley & Hein (1962, Journal of the American Dental Association 65, pp. 26-29) plaque index for evaluating plaque extension. Whilst this index is in common use by clinicians, there is potential for ambiguity in the interpretation of scores by different examiners. The aims of this study were to compare examiner agreement between a new method of plaque scoring (NMPS) and TPI, and to determine if there was a correlation between the two indices. METHODS: Simulated plaque was scored from eight study casts, each consisting of 14 teeth. The two indices were both scored twice from the study casts by eight examiners experienced in plaque scoring. The first readings obtained were analysed for a correlation between the indices and between-examiner variability. Within-examiner variability was assessed using both first and second readings of each index. RESULTS: A positive correlation was found between the two indices (r = 0.717). The NMPS was found to have better inter- and intra-examiner agreement than TPI. CONCLUSION: The NMPS was found to have less variability within and between examiners than TPI: evaluation of NMPS in a clinical setting would now appear warranted.

Analysis of Variance↗
PubMed1986

The relation between popularity and achievement: a longitudinal test of the lateral transmission of value hypothesis.

Data from a longitudinal study of school desegregation were used to examine the relation between normative social influence processes and academic achievement in order to test theoretical models of how school desegregation produces benefit. Subjects were white, Mexican-American, and black elementary school children who were measured once prior to and twice after desegregation of their schools. For all groups, analyses using structural equation techniques showed that, contrary to the lateral transmission of values hypothesis, which views social influence processes as shaping academic achievement, "causal influence" did not flow from social acceptance to academic achievement; instead, achievement appeared to affect subsequent social acceptance.

Achievement↗