A data base of data banks for toxicological information

The procedures necessary to find the appropriate data banks in seeking particular information or data are much less systematic than the way in which the information is stored at some data banks. Based on the information taken from several hundred direct-mailed questionnaires, a conceptual design is proposed for a data base of toxicological data banks relating to other areas such as medicine, pharmacology, biology, chemistry and environmental science. The system (not yet implemented) contains nearly 150 data banks (both computerized and manual) all over the world with data on the type of information, the way to obtain it, its cost, etc.     

An information theoretical evaluation of the applicability of the ASTM infrared data base for retrieval purposes

Summary The information content of the identification by retrieval with binary coded infrared spectra (ASTM infrared datafile), taking into account the correlations between the speaks and the errors in the coded spectra, amounts to about 21 bits. This amount of information can be obtained when use is made of not more than 93 wavelength intervals, selected from the total number of 140 intervals that are available for retrieval. The information content can be raised to about 29 bits when for the retrieval procedure a window of 0.3 is introduced, thereby requiring only 72 intervals. The influence of the composition of the dataset upon the information content is considerable; for hydrocarbons an amount of information of only 15 bits is obtained with a search using 79 intervals.The probability of the match between the spectrum of the unknown compound and the right reference spectrum being superior to all other possible matches will increase from virtually zero to about 88% when a window of 0.3 is used.

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Eine informationstheoretische Auswertung der Anwendung der ASTM-Sammlung — Infrarotspektren für die Bibliothekssuche

Zusammenfassung Der Informationsgehalt für die Identifizierung durch Vergleich binÄr codierter Infrarotspektren (ASTM-Sammlung Infrarotspektren) betrÄgt unter Berücksichtigung der Ungenauigkeiten und der Korrelation zwischen den Banden etwa 21 Bits. Diese Informationsmenge kann erhalten werden aus dem Vergleich von nur 93 WellenlÄngen-Intervallen, die aus einer Gesamtzahl von 140 verfügbaren selektiert wurden.Der Informationsgehalt für die Bibliothekssuche kann bis zu 29 Bits zunehmen, wenn für die Suche ein Fenster von 0,3 angewendet wird; die Zahl der benötigten Intervalle betrÄgt dann nur 72. Aus verschiedenen Spektrensammlungen erhÄlt man verschiedene Informationsmengen; zum Beispiel betrÄgt der Informationsgehalt für Kohlenwasserstoffe nur 15 Bits unter Benutzung von 79 Intervallen. Die Wahrscheinlichkeit, da\ der Vergleich des Spektrums einer unbekannten Verbindung mit dem richtigen Vergleichsspektrum eine bessere übereinstimmung liefert als der Vergleich mit allen anderen Vergleichsspektren, nimmt von ungefÄhr null bis 88% zu, wenn ein Fenster von 0,3 angewendet wird.

     

Calculation of the information content of retrieval procedures applied to mass spectral data bases

A procedure has been developed for estimating the information content of retrieval systems with binary-coded mass spectra, as well as mass spectra coded by other methods, from the statistical properties of a reference file. For a reference file, binary-coded with a threshold of 1% of the intensity of the base peak, this results typically in an estimated information content of about 50 bits for 200 selected $\text{m}\text{z}$ values. It is shown that, because of errors occurring in the binary-coded spectra, the actual information content is only about 12 bits. This explains the poor performance observed for retrieval systems with binary-coded mass spectra.     

The origins of the base peak in the electron impact spectrum of limonene

The origins and nature of the [C₅H₈]⁺? ions which form the base peak in the electron impact spectrum of limonene, at nominal electron energies greater than 11 eV, have been investigated. Linked scan techniques were used to study unimolecular and collision induced fragmentation reactions. No fragmentation pathway leading to [C₅H₈]⁺? could be found. Measurement of ionization efficiency curves indicated that the threshold for formation of C₅H₈[⁺?] lies above the range of internal energies deposited in incident ions by collisional activation. By a combination of comparisons of collisionally activated spectra and energetic considerations, the [C₅H₈]⁺? ions formed from limonene were shown to resemble those of the molecular ion of isoprene, while the neutral fragment is most likely isoprene also. Deuterium labelling experiments yielded evidence of extensive scrambling prior to fragmentation. The most probable mechanism of formation of [C₅H₈]⁺? appears to involve a retro Diels–Alder reaction of a structurally intact molecular ion of limonene.     

Origin and information content of the compensation effect

An attempt is made to assess: (i) The conditions under which a compensation effect should be observable, (ii) The associated physical properties affected by such compensation. (iii) The nature of the information which can be gleaned from studies of compensation. Specific attention is given to simple desorption processes and the main conclusion is that the compensation law in adsorption indicates a phenomenon involving many molecules. However the Meyer-Neldel rule in semiconductors is also embraced, as well as observations of the compensation effect in liquids.Dedicated to Professor J. Koutecký on the occasion of his 65th birthday     

New algorithms for processing and peak detection in liquid chromatography/mass spectrometry data

Two new algorithms for automated processing of liquid chromatography/mass spectrometry (LC/MS) data are presented. These algorithms were developed from an analysis of the noise and artifact distribution in such data. The noise distribution was analyzed by preparing histograms of the signal intensity in LC/MS data. These histograms are well fit by a sum of two normal distributions in the log scale. One new algorithm, median filtering, provides increased performance compared to averaging adjacent scans in removing noise that is not normally distributed in the linear scale. Another new algorithm, vectorized peak detection, provides increased robustness with respect to variation in the noise and artifact distribution compared to methods based on determining an intensity threshold for the entire dataset. Vectorized peak detection also permits the incorporation of existing algorithms for peak detection in ion chromatograms and/or mass spectra. The application of these methods to LC/MS spectra of complex biological samples is described.     

Automation of the information content analysis of kinetic parameters

The aim of this work has been to automate the analysis of kinetic measurements in solving inverse problems in order to recognize the number and form of the independent combinations of reaction rate constants. Software for determining the basis of nonlinear parametric functions of the kinetic parameters of a mathematical model for the mechanism of a complex chemical reaction has been developed and described. The main stages of program construction with the use of a search algorithm for the independent combinations of the rate constants of elementary steps in the mechanism of a complex chemical reaction based on experimental data on the concentrations of reactants are considered.     

Note on the topological information content of simple graphs

It is shown that simple graphs gave equal topological information content if their automorphism groups are isomorphic. Further, if the automorphism groups of two graphs are represented by wreath products of which the inner groups are isomorphic, then the two graphs possess equal topological information content. Three graphs which correspond to organic molecules illustrate this finding.Dedicated to Professor Dr.Karl Schlögl on the occasion of his 60th birthday.     

Reduction of the information space for data collections

Reduction of infrared spectra representation by using fast Fourier and fast Hadamard transforms is discussed. It is shown that the information content for different truncations varies in the same way for both transformations, while the execution of FHT is about 8 times faster than that of FFT. The reduction of the information content is illustrated by comparing the hierarchical ordering of clusters of the same set of infrared spectra using representations of different lengths. The same basic pattern of three clusters was obtained even when the representations were reduced by more than 96% of the original representations.     

Evaluation of the sensitivity of the ‘Wiley registry of tandem mass spectral data,MSforID’ with MS/MS data of the ‘NIST/NIH/EPA mass spectral library’

Tandem mass spectral libraries are versatile tools for small molecular identification finding application in forensic science, doping control, drug monitoring, food and environmental analysis, as well as metabolomics. Two important libraries are the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’ (Wiley Registry MSMS) and the collection of MS/MS spectra part of the 2011 edition of the ‘NIST/NIH/EPA Mass Spectral Library’ (NIST 11 MSMS). Herein, the sensitivity and robustness of the Wiley Registry MSMS were evaluated using spectra extracted from the NIST 11 MSMS library. The sample set was found to be heterogeneous in terms of mass spectral resolution, type of CID, as well as applied collision energies. Nevertheless, sensitive compound identification with a true positive identification rate ≥95% was possible using either the MSforID Search program or the NIST MS Search program 2.0g for matching. To rate the performance of the Wiley Registry MSMS, cross‐validation experiments were repeated using subcollections of NIST 11 MSMS as reference library and spectra extracted from the Wiley Registry MSMS as positive controls. Unexpectedly, with both search algorithms tested, correct results were obtained in less than 88% of cases. We examined possible causes for the results of the cross validation study. The large number of precursor ions represented by a single tandem mass spectrum only was identified as the basic cause for the comparably lower sensitivity of the NIST library. Copyright © 2013 John Wiley & Sons, Ltd.     

Visualization and interpretation of high content screening data

High content screening is a method for identifying small molecule modulators of mammalian cell biology. The nature of the experiment generates an enormous amount of data in the form of photographic images of cells after treatment with compounds of interest. The interpretation of data from these experiments is challenging both in terms of automatically perceiving the images, extracting, and understanding differences between screened compounds and visualizing the results. This paper discusses the application of statistical and visual methods that have been used to interpret data from a simplified DNA stain (DAPI) screen to quickly identify compounds of interest. An understanding of the mechanism of action of the screened compounds can be obtained by comparing them to control compounds of known mechanism of action. Statistical and visual methods will be shown that facilitate easy comparison of screened compounds against these control compounds. As an example, a subset of the internal repository at ArQule was screened, together with control compounds that were known to induce characteristic mitotic arrest. Subsequent data processing described in this paper permitted the easy identification of compounds that were similar to (and very different from) the control compounds.     

Enhancing the information content of vibrational spectra through sample perturbation

Infrared and Raman band frequencies, intensities and line shapes are often sensitive to the local molecular environment determined by molecular conformation, surrounding matrix, temperature, pressure, etc. The variety of local environments experienced by a condensed-phase molecule can lead to vibrational spectra with broad bands containing many overlapped spectral features. The spectral resolution of these overlapped features can be enhanced by making perturbations to the sample environment. Examples of perturbations which can be applied to the sample to enhance the information content of infrared spectra are changes in temperature, concentration and mechanical strain. In each instance, the spectra obtained as a function of the perturbation can be cross-correlated to produce a two-dimensional correlation map defined by two independent wavenumber axes. in this representation, infrared bands which respond to the perturbation in a similar or different manner can be clearly identified. This information can be used to help resolve overlapped bands and make unambiguous band assignments.     

Optimization of information properties of NAA with respect to information content and profitability of results

Information properties of analytical results together with other important parameters especially economic ones can be used for the optimization of analytical procedures. Therefore, we have proposed a computational technique for the optimization of multielement neutron activation analysis (NAA) based on the information content and profitability. The optimization starts with the prediction of the -ray spectra to be expected during analysis under given experimental conditions (sample size, irradiation, decay and counting times etc.) and with the calculation of detection and determination limits. In the next step, the information contents for the determination of particular elements and for the simultaneous determination of element groups are computed. The information content depends or is closely connected with such properties of the method as selectivity, sensitivity, precision, accuracy and, as in the other cases of trace analysis, also with the detection limit. Then, the information profitability (IP) taking into account the information content and relevance (appreciation of specific information according to its contribution to the solution of a given problem) together with economic aspects can be calculated. This function can be used for the optimization of a particular NAA procedure, for the mutual comparison of different variants of NAA and also for the comparison with other analytical methods. The use of information profitability for the optimization of NAA is shown on a practical example of the INAA analysis of urban particulate matter SRM 1648 produced by NBS (USA).     

An expedient protocol for conversion of olefins to α-bromo/iodoketones using IBX and NBS/NIS

A variety of olefins have been shown to undergo conversion to the corresponding α-bromo/iodoketones when reacted with NBS/NIS and IBX in DMSO at room temperature. While the reaction is found to occur rapidly with e-rich arylolefins leading to the corresponding haloketones in 65-95% yields in 0.3-3.0 h, those containing e-withdrawing groups are found to yield diketones concomitantly, such that the latter are the exclusive products over extended duration of the reactions.     

Preliminary study of scientific data base,the distributed chemical engineering library

The design principles, system architecture and functions, as well as an application example, of the distributed chemical engineering library (CLIB) are presented. Common characteristics among scientific data bases and common problems in their development, with on-line services, are discussed.