Bayesian analysis and inference from QSAR predictive model results

QSAR models have been under development for decades but acceptance and utilization of model results have been slow, in part, because there is no widely accepted metric for assessing their reliability. We reapply a method commonly used in quantitative epidemiology and medical decision-making for evaluating the results of screening tests to assess reliability of a QSAR model. It quantifies the accuracy (expressed as sensitivity and specificity) of QSAR models as conditional probabilities of correct and incorrect classification of chemical characteristic, given a true characteristic. Using Bayes formula, these conditional probabilities are combined with prior information to generate a posterior distribution to determine the probability a specific chemical has a particular characteristic, given a model prediction. As an example, we apply this approach to evaluate the predictive reliability of a CATABOL model and base on it a "ready" and "not ready" biodegradability classification. Finally, we show how predictive capability of the model can be improved by sequential use of two models, the first one with high sensitivity and the second with high specificity.     

A mathematical evaluation of dose-dependent PpIX fluorescence kinetics in vivo

The in vivo pharmacokinetics of protoporphyrin IX (PpIX) after administration of 5-aminolevulinic acid (ALA) cannot be described accurately by mathematical models using first-order rate processes. We have replaced first-order reaction rates by dose-dependent (Michaelis-Menten [MM]) reaction rates in a mathematical compartment model. Different combinations of first-order and dose-dependent reaction rates were evaluated to see which one would improve the goodness-of-fit to experimentally determined in vivo PpIX fluorescence kinetics as a function of concentration. The mathematical models that were evaluated are all based on a three-compartment model for drug distribution, conversion to PpIX and subsequent conversion to heme. Implementation of dose-dependent reaction rates improved the goodness-of-fit and enabled interpolation to other drug doses. For most data sets the time constant for delivery to the target cells turned out to be dose dependent. For all data sets the use of MM rates for the conversion of ALA to PpIX yielded better fits. The clearance of PpIX turned out to be a first-order process for all doses and types of administration. Fluorescence curves measured on a specific tissue type but obtained in different studies with different measurement techniques could be described with a single set of parameters.     

Benzolactams. 4. Reaction of 3',4'- or 4',5'-dialkoxy-substituted 1-(2'-Bromobenzyl)-2-ethoxycarbonyl-1,2,3,4-tetrahydroisoquinolines with alkyllithium. 1,2 and 1,4 additions of alkyllithium to benzolactams

Treatment of 1-(2'-bromo-3',4'-dialkoxybenzyl)-1,2,3, 4-tetrahydroisoquinoline carbamates, 1a,c, with excess alkyllithium gave 8-oxoberbines, 2a,c, which were successively attacked in situ with another molecule of alkyllithium to give 1,2 and/or 1,4 addition products. A primary alkyllithium, such as MeLi or BuLi, gave a 1,2 addition product, 8-methyleneberbine 9a or 8-butylideneberbine 3a. t-BuLi preferred 1,4 addition, followed by elimination of the alkoxy group, to give 9-tert-butyl-8-oxoberbine 6a or 7c. s-BuLi gave a mixture of 1,2 and 1,4 addition products, 1-[2'-(2' '-methylbutyryl)benzyl]-1,2,3,4-tetrahydroisoquinoline 4a and 9-s-butyl-8-oxoberbine 5a. Similar treatments of carbamate 1b having no alkoxy group at its 3' position gave 1,2 addition products, 8-butylideneberbine 3b, 1-[2'-(2' '-methylbutyryl)benzyl]-1,2,3, 4-tetrahydroisoquinoline 4b, and 1-(2'-pivaloylbenzyl)-1,2,3, 4-tetrahydroisoquinoline 6b, in all cases. Reactions of 1a with s-BuMgCl and isoPrMgCl also gave the 1,4 adduct, 5a, and its 9-isoPr analogue, 12a. Treatment of 9a with excess NaBH(4) in AcOH gave (+/-)-coralydine (10b).     

Coordination Complexes of Some Group(IV) Halides with Monodentate Schiff Bases

Coordination compounds resulting from the interaction of N-(phenyl)benzalaldimine and its derivatives containing a methyl group in different positions of the aniline ring and group(IV) halides, MX₄ (where M = Si or Sn and X = Cl or Br), have been prepared and characterized by elemental analyses and electronic, infrared and Raman spectra.     

Infrared spectroscopic study of the structure of the tetrabutyl S-dithiopyrophosphate complex of silver

The structure of the complex Ag·TBDTPP (tetrabutyl S-dithiopyrophosphate) formed in HNO₃ medium was studied by IR and NMR methods. The complex is involved in the isomerization of TBDTPP in the presence of Ag⁺ and NO ₃ ⁻ ions. In the IR spectra, we observe the disappearance of P−O−P band and the occurrence of new absorption bands associated with P−S−P and P=O bonds. The silver ion is coordinated to the thiophosphoryl group of the isomer molecule. The influence of HNO₃ concentration on complex formation is discussed.     

The stability of silver iodide sols in the presence of polyacrylic acids of various molecular weights

Summary The effect of a series of polyacrylic acids, ranging in molecular weight from 1.67×10⁴ to 2.36×10⁶, on the stability of positively charged silver iodide particles has been examined. Flocculation of the sol occurred at a well defined concentration of polyacrylic acid,c _f , and a further increase in concentration of the polyelectrolyte caused restabilization of the sol. Over the range examinedc _f appeared to be related to the viscosity average molecular weight of the acid,M _v , by an equation of the form,c _f =a ·M _v ^{– b} wherea andb are constants.     

Action of photoreactivating light on pyrimidine heteroadduct in bacteria

Abstract— In stationary-phase Escherichia coli B/r, photoreactivation (PR) at 313 nm of ultraviolet (u.v.) killing is inefficient compared with PR at 405 nm, and can be explained solely by photoenzymatic reversal of pyrimidine dimers. In Staphylococcus epidermidis, PR shows a maximum at 313 nm, suggesting that this organism shows the Type III PR proposed by Jagger et al.[5] for Streptomyces strains. Reversal of pyrimidine dimers is not sufficient to explain this PR. The mechanism of Type III PR remains unknown. With both S. epidermidis and E. coli B/r, the amount of uracil–thymine heteroadduct in DNA hydrolysates decreases if the cells are given a post-u.v. treatment at 313 nm, but no decrease is observed if the post-u.v. treatment is at 405 nm. The biological significance of this adduct and of its removal is not clear. It may play a role in Type III PR.     

Direkte fluorimetrische Bestimmung von 3,4-Benzpyren im w?\rigen Medium

Zusammenfassung Es wurde eine direkte Bestimmung des 3,4-Benzpyrens in wä\riger Lösung beschrieben, die auf der Löslichkeitserhöhung beruht, die das in Wasser schwer lösliche 3,4-Benzpyren durch Coffein erfährt. Es können so noch 4 ng/ml bei der angegebenen Standardisierung bestimmt werden. Bei der Direktbestimmung des 3,4-Benzpyrens im System Coffein-Wasser ist ein p_H >6,0 einzuhalten, da bei höheren Wasserstoffionenkonzentrationen die Fluorescenzintensität stark abnimmt.

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Direct fluorimetric determination of benzo(a)pyrene in aqueous medium

A method for the direct determination of benzo(a)pyrene in aqueous solution is based on the increase of its solubility by coffeine. 4 ng of benzo(a)pyrene/ml can be determined by the procedure described. In this direct determination in the system coffeine-water the p_H has to be adjusted to >6.0, as the fluorescence intensity considerably decreases with higher H⁺ concentrations.

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Eine ausführliche Darstellung findet sich in der Dissertation von G. Becker, Univ. Karlsruhe 1968.

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Die Messungen zu dieser Arbeit -wurden an dem Chemischen Untersuchungsamt für das Saarland, Saarbrücken, mit einem Spektralphotometer der Deutschen Forschungsgemeinschaft ausgeführt. Beiden Institutionen sind wir zu Dank verpflichtet.     

THE EFFECTS OF HOST-CELL REACTIVATION ON ASSAY OF U.V.-IRRADIATED HAEMOPHILUS INFLUENZAE TRANSFORMING DNA

Abstract— The host cell reactivation (HCR) mechanism in Haemophilus influenzae cells is inhibited by sub-microgram concentrations of acriflavine (as is already known to be true for Escherichia coli ). Exposure of these cells to similar concentrations of the drug during bacterial transformation increases the apparent ultraviolet light (u.v.) sensitivity of previously irradiated transforming DNA, indicating a repair of this DNA after uptake by the cells under normal conditions. Repair is inhibited by applying acriflavine at any time up to one hour after competent cells contact the irradiated transforming DNA. The fraction of the u.v. damage repaired by HCR is very different for different genetic markers. Those markers which are most u.v. sensitive when assayed in the absence of acriflavine are most poorly repaired, suggesting that this is the reason for their higher sensitivity. For all markers the fraction of the damage repairable by in vitro photoreactivation is approximately constant, and strongly overlaps the damage repairable by HCR. The degree of HCR achieved can be altered by experimental treatment of the H. influenzae DNA prior to transformation. Thus treatment of irradiated DNA with an enzyme from Micrococcus lysodeikticus –known to attack u.v. damaged, but not undamaged DNA–prevents subsequent intracellular repair of the same u.v. lesions whose repair is inhibited by acriflavine. Similarly, partial replacement of the thymine in transforming DNA by 5-bromouracil (BU) strongly inhibits repair of subsequent u.v. damage. As in bacteriophage, the BU effect is relieved if the u.v. exposure occurs in the presence of cysteamine. It is clear that intracellular repair must be considered in interpreting experiments with u.v.-irradiated transforming DNA.     

Austausch von Chrom(III) mit Chrom(II) und Szilard—Chalmers-Reaktion von Kaliumchromat

Zusammenfassung Durch Versuche mit⁵¹Cr wird gezeigt, daß Cr³⁺ mit Cr²⁺ austauscht, wenn man ein Chrom(III)-Salz in wässeriger Cr²⁺-Lösung auflöst, d. h. die Hydratation zum reaktionsträgen [Cr(H₂O)₆]³⁺ verläuft relativ langsam. Die Bedeutung dieses Austausches für dieSzilard—Chalmers-Reaktion von Chromat wird diskutiert.

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Experiments with⁵¹Cr prove the exchange of Cr³⁺ with Cr²⁺ when a Cr(III)-salt is dissolved in an aqueous solution of Cr²⁺. This indicates that the hydration to the inert [Cr(H₂O)₆]³⁺ is relatively slow. The importance of this exchange for theSzilard—Chalmers reaction of chromate is discussed.