bluuebunny/crossref_metadata_2025_split huggingface dataset:
Description of the Reversed‐Phase High‐Performance Liquid Chromatography (RP‐HPLC) Capacity Factors and Octanol‐Water Partition Coefficients of 2‐Pyrazine and 2‐Pyridine Analogues Directly from the Three‐Dimensional Structures Using Comparative Molecular Field Analysis (CoMFA) Approach
Authors: Kim Ki Hwan 
Published: October 2006

AbstractExcellent correlations were obtained between the logarithm of capacity factors (log k′) previously measured from the reverse‐phase high‐performance liquid chromatography (RP‐HPLC) and the octanol‐water partition coefficients (log P) of 2‐substituted pyrazine and 2‐substituted pyridine derivatives and the descriptors obtained directly from the three‐dimensional structures using comparative molecular field analysis (CoMFA) approach. The results presented in this study illustrate the applicability of CoMFA in calculating log k′ and log P values directly from the three‐dimensional structures of the molecules.
Quantitative Structure‐Activity Relationships for Antimicrobial Nitroheterocyclic Drugs
Authors: Rozenski Jef , De Ranter Camiel J. , Verplanken Hilda 
Published: October 2006

AbstractThe antimicrobial activity of a series of nitro‐heterocyclic drugs was determined and correlated with a number of physicochemical properties. The best correlation is found with the polarographic half‐wave potential, while the partition coefficient and LUMO‐values contribute poorly to the relationship. The value of the dipole moments can be used to discriminate between active 2‐nitro and 5‐nitroimidazoles and inactive 4‐nitroimidazoles. Free‐Wilson analysis emphasizes the need of structural parameters like the presence of the nitro group in position 2 or 5 or a methyl substituent on the imidazole ring. The activity is enhanced by a vinyl group in position 2 and is decreased by the presence of a phenyl substituent.
Physicochemical Significance of Topological Parameters: Molecular Connectivity Index and Information Content: Part 2. Correlation Studies With Molar Refractivity and Lipophylicity
Authors: Saxena Anil K. 
Published: October 2006

AbstractThe studies on physicochemical significance of molecular connectivity index (1χ, 2χv) have shown that connectivity indices correlate to a greater extent with MR than with hydrophobicity (π). In order to verify these results, a set of 183 compounds of different chemical classes viz. alcohols, amines, esters, hydrocarbons, ethers, carboxylic acids etc. was chosen. In the earlier studies on this set of compounds, molecular connectivity (1χ) had been found to correlate with Log P. The correlation of valence molecular connectivity (1χ) with MR and Log P has been studied where MR showed better correlation with 2χv than Log P. The comparative correlation studies of 1χ with Log P and MR has also been carried out where 1χ shows better correlation with MR than with Log P for the total set of 183 compounds.
QSAR in Toxicology. 3. Prediction of Chronic Toxicities
Authors: Cronin Mark T. D. , Dearden John C. 
Published: October 2006

AbstractA critical review is given of quantitative and qualitative structure‐activity relationships (QSAR) for the prediction of some chronic toxicological endpoints required for regulatory purposes. Many methodological approaches have been applied to the prediction of carcinogenicity and mutagenicity based on either identification of the molecular substructures that account for electrophilic reactivity or quantitative description of the hydrophobicity and reactivity of the molecule. A recent blind trial, however, found the opinion of human experts still to be most successful. Analyses of the interrelationship between carcinogenicity and mutagenicity data are also discussed.Relatively little work has been performed in the QSAR analysis of developmental toxicity. This whole area is hindered by a lack of quality in vivo toxicity data to model, and by the mechanisms of action not being fully understood.
A Fast Algorithm For Selecting Sets Of Dissimilar Molecules From Large Chemical Databases
Authors: Holliday John D. , Ranade Sonia S. , Willett Peter 
Published: October 2006

AbstractCurrent algorithms for the selection of a set of n dissimilar molecules from a dataset of N molecules have an expected time complexity of O(n2N). This paper describes an improved algorithm that has an expected time complexity of O(nN) and that will identify exactly the same set of molecules as the normal algorithm if the cosine coefficient is used for the calculation of the inter‐molecular (dis)similarities. The algorithm is applicable to any type of representation that characterises a molecule by a set of attribute values and to any procedure that involves calculating a sum of inter‐molecular similarities. It is also both more effective and more efficient than our implementation of a genetic algorithm for the selection of maximally‐dissimilar sets of molecules.
A New Set of Principal Properties for Heteroaromatics Obtained by GRID
Authors: Clementi Sergio , Cruciani Gabriele , Fifi Paola , Riganelli Daniela , Valigi Roberta , Musumarra Giuseppe 
Published: October 2006

AbstractA set of 40 heteroaromatic systems was multivariately characterized by 13 descriptors derived by GRID. From this data matrix a second generation of Principal Properties for heteroaromatics was derived. Such Principal Properties are suitable for designing series of molecules of biological interest containing heteroaromatic moieties.
QSAR Study of Phenols: Relation between the Phenoxyl Radical Formation and the Antiinflammatory Activity via an Antioxidant Mechanism
Authors: Ruiz Juan , Pérez Angel , Pouplana Ramon 
Published: October 2006

AbstractThe antiinflammatory mechanism of phenols as radical scavengers was analyzed. The biradical formation process Ph‐OH → Ph‐O + H was studied by the reaction coordinate method using the semiempirical AM1 quantum‐mechanical method. The enthalpies of formation of ground, transition, and radical states were determined; other parameters like the reaction, stabilization and activation enthalpies for phenoxyl radical formation of fifteen phenolic compounds were also calculated and correlated with their antiinflammatory activities.The results suggest that the ability of phenols to form the phenoxyl radical and the stability of this derived radical are important in the antiinflammatory activities of phenols via neutralization of harmful radicals.
Estimation of Caco‐2 Cell Permeability using Calculated Molecular Descriptors
Authors: van De Waterbeemd Han , Camenisch Gian , Folkers Gerd , Raevsky Oleg A. 
Published: October 2006

AbstractPermeability of a compound by passive diffusion through a biological membrane such as Caco‐2 cell monolayers depends mainly on lipophilicity, molecular size and hydrogen bonding capacity of the solute. Since these properties are often used in structure‐permeability correlations, we have evaluated different calculated descriptors for size and hydrogen bonding, as well as their intercorrelations. A new descriptor for hydrogen bonding potential is introduced. It is demonstrated that a combination of appropriate size and H‐bonding descriptors using graphical or Eq.‐based approaches may be of potential use for membrane permeation estimation.
Application of Molecular Quantum Similarity to QSAR
Authors: Fradera Xavier , Amat Lluís , Besalü Emili , Carbó‐Dorca Ramon 
Published: October 2006

AbstractMolecular Quantum Similarity Measures (MQSM), which allow quantitative comparison between molecular electronic density distributions, are investigated as a potential source of QSAR parameters. By computing the MQSM for all possible molecular pairs in a given molecular set, a Similarity Matrix is obtained, containing relevant information about the structural relationships within the set. Approximate Overlap‐like MQSM using several computational levels are employed to obtain similarity matrices for three molecular sets, taken as test cases: (1) non‐branched alkanes, (2) Baker triazines, (3) indole derivatives. The similarity matrices have been analyzed by means of PCA and PLS techniques. QSAR regression models were derived in order to fit available property or biological activity data. A reasonably good correlation between properties or activities and the similarity measures has been found.
Description of Vapour Pressures of Polycyclic Aromatic Compounds by Graph Theoretical Indices
Authors: Niederfellner J. , Lenoir D. , Matuschek G. , Rehfeldt F. , Utschick H. , Brüggemann R. 
Published: October 2006

AbstractThe vapour pressure (VP) is an important physical property of organic compounds for the description of fate and distribution of xenobiotics in the environment. This property was measured for 30 polycyclic aromatic hydrocarbons (PAH) and formulas for VP based on molecular weight and topological indices, respectively, were derived using the technique of Kubinyi and as a second step by regression analysis. A formula for the 30 PAH, considered here, is given.magnified imageTherein the VP is related to the information theoretical index IdWmean and with a chain‐connectivity index. More specific results are derived for three groups of PAHs. The robustness of the equations is tested by bootstrap analysis. In addition a formula is discussed, which is based on four different incremental factors, a method widely used in physical organic chemistry.
Three‐valued logic for reasoning from an inconsistent knowledge base
Authors: Tahara Ikuo , Nobesawa Shiho 
Published: October 2006

AbstractNontrivial reasoning under inconsistency, called paraconsistent reasoning, has been discussed mainly in two frameworks; one is the classical logic (consistency‐based) framework and the other is the three‐valued logic framework. In this paper, we propose a new entailment relation based on three‐valued logic for reasoning from an inconsistent knowledge base, and discuss the relation between the previous two frameworks. A U‐minimum model of the inconsistent knowledge base is defined in accordance with a principle of uncertainty minimization for three‐valued models. We show that every set of atomic formulas assigned the additional third value in the U‐minimum model is the minimum hitting set for the collection of sets each of which consists of atomic formulas occurring in the minimal inconsistent set of the knowledge base. Based on this result, we present an algorithm to compute the paraconsistent entailment relation by reducing the three‐valued entailment relation to a two‐valued classical entailment relation. © 2006 Wiley Periodicals, Inc. Syst Comp Jpn, 37(14): 44–51, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.20539
Autonomous motion recognition by combining reinforcement learning and hidden Markov model
Authors: Morooka Ken'ichi , Hamamoto Kazuhisa , Nagahashi Hiroshi 
Published: October 2006

AbstractA robot needs the abilities of recognizing motion in the world (“other‐motion”), and generating “self‐motion” to adaptively behave in a real environment. We have been currently developing a system composed of an “other‐motion” recognition module and a “self‐motion” generation module. This paper focuses on “other‐motion” recognition that is based on “self‐motion.” The recognition and generation modules are each constructed by reinforcement learning and a Hidden Markov Model (HMM). In this case, the HMM estimation needs many sample data of the motion to be learned. However, there is no guarantee that a sufficient amount of motion data can be acquired in the real world, and the reliability of the HMM may therefore be low. In order to solve this problem, this paper presents a new estimation method of an HMM based on the learning results of reinforcement learning. The state value function of the reinforcement learning is divided into some clusters, and each cluster is made to correspond to a state of the HMM. An output distribution can thereby be estimated on the basis of the value of the value function. Some experimental results show that our method can estimate HMM's model parameters not only from few sample data but also from value functions of the generation module, and that the reliability of the estimated HMM can be improved. © 2006 Wiley Periodicals, Inc. Syst Comp Jpn, 37(14): 34–43, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.20586.
Chemical force microscopy of chemical and biological interactions
Authors: Noy Aleksandr 
Published: October 2006

AbstractInteractions between chemical functionalities define outcomes of the vast majority of important events in chemistry, biology, and materials science. Chemical force microscopy (CFM)—a technique that uses direct chemical functionalization of atomic force microscopy (AFM) probes with specific functionalities—allows researchers to investigate these important interactions directly. We review the basic principles of CFM, some examples of its application, and theoretical models that provide the basis for understanding the experimental results. We also emphasize application of modern kinetic theory of noncovalent interactions to the analysis of CFM data. Copyright © 2006 John Wiley & Sons, Ltd.
Advances in time‐of‐flight secondary ion mass spectrometry analysis of protein films
Authors: Michel Roger , Castner David G. 
Published: October 2006

AbstractThis article reviews the advances made in the analysis of protein films by time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS). ToF‐SIMS has been used extensively to analyze biological samples owing to its high surface sensitivity, high mass resolution, molecular specificity and imaging capabilities. The fact that its information depth for molecular fragments is typically 1–2 nm, which is smaller than the dimensions of most proteins, makes it an ideal technique for analyzing protein films. Multivariate analysis (MVA) techniques are well suited for analyzing the large, complex data sets generated from ToF‐SIMS experiments on biological samples and have become widely used for interpreting ToF‐SIMS spectra and images. In recent years, new advances in polyatomic or cluster ion sources have improved spectral quality, reduced sample damage and enabled depth profiling of some organic samples. Also, cationization and other matrix enhancement methods have been developed, which significantly increase the yield of molecular fragments from biological samples. This review will cover the modern ToF‐SIMS analysis methods that are currently employed to characterize protein films along with the opportunities and challenges for future advances in ToF‐SIMS analysis of these films. Copyright © 2006 John Wiley & Sons, Ltd.
Coupling evanescent‐wave fluorescence imaging and spectroscopy with scanning probe microscopy: challenges and insights from TIRF–AFM
Authors: Shaw James E. , Oreopoulos John , Wong Daniel , Hsu Jenny C. Y. , Yip Christopher M. 
Published: October 2006

AbstractRecent work has demonstrated that imaging platforms based on the integration of total internal reflection fluorescence microscopy (TIRFM)/spectroscopy with scanning probe microscopy are well‐suited for investigations of biological phenomena, ranging from lipid bilayer dynamics and membrane protein assembly to cellular dynamics and structures. We have shown that this approach is particularly compelling for studies of protein‐membrane interactions. While this functional imaging strategy has proved to be very useful for studies of cell dynamics, and most recently, in the study of single‐molecule dynamics by TIRF‐AFM‐based force spectroscopy, a number of key challenges remain to be resolved. Copyright © 2006 John Wiley & Sons, Ltd.
Anti‐microbial coatings by agent entrapment in coatings deposited via atmospheric pressure plasma liquid deposition
Authors: O'Hare Lesley‐Ann , O'Neill Liam , Goodwin Andrew J. 
Published: October 2006

AbstractBy injecting a liquid aerosol precursor directly into a non‐equilibrium atmospheric pressure plasma (APP), a controlled, free‐radical‐induced polymerisation reaction can be initiated with minimal fragmentation of the precursor molecules. This can be used to chemically graft highly complex chemical functionalities directly onto a variety of substrates. This process normally proceeds through polymerisation of unsaturated functional groups on the precursor molecules. In this work, it has been found that compounds that lack such polymerisable groups can be physically dissolved in the liquid precursor and that these chemicals are not directly involved in the plasma reaction. Instead, these chemicals become physically entrapped within the resultant plasma polymer and retain much of their biological and chemical properties. As a preliminary example of such a reaction, the entrapment of various anti‐microbial species (quaternary ammonium salts) within glycol and acrylic acid plasma polymers is described. The biological and chemical reactivity of these chemicals is examined using a combination of anti‐microbial and XPS investigations. Copyright © 2006 John Wiley & Sons, Ltd.
Current and possible alternate indicators of fecal contamination in tropical waters: A short review
Authors: Toranzos Gary A. 
Published: October 2006

AbstractBacteria that belong to the total and fecal coliform groups have been used for several decades as indicators of fecal pollution of waters and other systems. The prevailing idea behind this is that these two groups of bacteria cannot replicate outside the gastrointestinal tract of warm‐blooded animals. Several studies conducted by this and other laboratories have indicated that these bacteria may be naturally present in certain areas of the world. Naturally occurring fecal coliforms (the genera Escherichia and Klebsiella) have been isolated from pristine sites and from sites where there was no apparent fecal contamination. All these results lead us to the conclusion that these groups of bacteria are not adequate indicators of fecal contamination in tropical areas of the world. Alternate indicators are being tested. This laboratory and others around the world are testing the adequacy of bacteriophages (more specifically, coliphages) for this purpose. In Puerto Rico coliphages have been detected only in areas known to be contaminated with domestic sewage, but not in pristine areas, although high levels of fecal coliforms can be detected at the latter sites. All these results suggest that coliphages may be used as indicators that more realistically demonstrate fecal contamination of waters in tropical areas of the world. In addition, newer techniques, although still in the trial stages, can be used to directly detect pathogens in the environment. Of all the techniques currently available, the polymerase chain reaction is the most promising for the direct detection of pathogens and therefore for the unequivocal evaluation of the biological quality of waters.
Toxicity testing of synthetic and biogenic surfactants on marine microorganisms
Authors: Poremba K. , Gunkel W. , Lang S. , Wagner F. 
Published: October 2006

AbstractThe toxicity of four synthetic surfactants, two commercial oil dispersants, and six biosurfactants have been examinated. The test systems were (a) bacterial growth inhibition, (b) microalgae growth inhibition, (c) microflagellate growth inhibition, (d) biodegradation, and (e) bioluminescence inhibition (Microtox test). The multiplication of bacteria was stimulated by surfactants, while that of microflagellates and microalgae was inhibited. This may be due to the metabolic usage of surfactants, especially biosurfactants, by bacteria. The bioluminescence was very sensitive to surfactants. No toxicity could be detected with glucose‐lipid, produced by the marine bacterium Alcaligenes sp. MM1. Most biosurfactants were degraded faster and possessed higher EC50 values than synthetic dispersants.
Soil: The environmental source of Escherichia coli and enterococci in Hawaii's streams
Authors: Hardina C. M. , Fujioka R. S. 
Published: October 2006

AbstractThe concentrations and sources of Escherichia coli and enterococci in a typical stream (Manoa) in Hawaii were determined. The concentrations of these two sanitary indicator bacteria in Manoa Stream consistently exceeded the new U.S. Environment Protection Agency recreational water standard in freshwater of 126E. coli/100 mL or 33 enterococci/ 100 mL. Escherichia coli but not enterococci was shown to multiply in stream water samples. Soil samples obtained near the stream bank, 10 m from the stream bank as well as from a grassy area on the university campus, were determined to be sources of both E. coli and enterococci. These indicator bacteria were recovered from the surface of the soil as well as from soil samples at depths down to 36 cm. Soil is considered the most likely source for the high concentrations of indicator bacteria naturally present in the freshwater streams of Hawaii.
Use of bioassays to evaluate river water and sediment quality
Authors: Dutka B. J. , Kwan K. K. , Rao S. S. , Jurkovic A. , McInnis R. , Palmateer G. A. , Hawkins B. 
Published: October 2006

AbstractIn trying to establish the extent and degree of impact of point and nonpoint source contaminants on riverine systems, it is important to know the implications of the data obtained from various sampling points in a riverine system. Spatial variability between water and/or sediment samples collected in close approximation at the same sites was assessed by the battery of tests approach. In these samples there appeared to be no consistent relationship between sediment structure, microbial population, and toxicant concentrations. Furthermore the ATP‐TOX System and Mutatox tests were the most responsive tests in all types of samples. Since sediments with their bound contaminants may be an important factor in this data interpretation, different methods for releasing and concentrating the sediment bound contaminants were evaluated. The results and implications of these results are described.
Detection of toxicity of cyanobacteria by Artemia salina bioassay
Authors: Kiviranta J. , Sivonen K. , Niemelä S. I. , Huovinen K. 
Published: October 2006

AbstractA bioassay for the detection of neuro‐ and hepatotoxins of cyanobacteria was developed. Larvae of a small shrimp, Artemia salina, were used as the test organism. Two pure toxins, 44 natural bloom samples, and 29 laboratory strains of cyanobacteria were studied. The toxicity of the samples had earlier been tested by mouse bioassay and in most cases by chemical analysis of the toxins. Moderate and high concentrations of toxins in bloom samples can be reliably detected by the Artemia salina method. Out of 29 toxic bloom samples, 4 were found nontoxic to Artemia. According to mouse bioassay, the toxicity of these samples was very low. The pure laboratory‐grown strains contained some compounds that were toxic to A. salina but nontoxic to mouse. Because of these compounds, 1 out of 15 nontoxic bloom samples was erroneously analyzed to be toxic. EC50 for hepatotoxin desmethyl 7‐microcystin‐RR was 5.0 μ/mL. Pure anatoxin‐a‐hydrochloride was not toxic to larvae, but when added to nontoxic cyanobacterial samples, anatoxin‐a was toxic.
A novel bioassay approach: Direct application of the toxi‐chromotest and the SOS chromotest to sediments
Authors: Kwan K. K. , Dutka B. J. 
Published: October 2006

AbstractRoutine testing of sediments or suspended sediments for toxicant or genotoxicants by the bioassay route often involves time‐consuming and expensive organic extraction procedures. In most instances these extraction procedures are more time‐consuming and costly than the bioassays that will be used on these extracts. A direct sediment test procedure (DSTP) was developed to alleviate the problem and thus returning bioassays to one of their original roles, i.e., short, quick, screening tests to identify priority samples for more intensive chemical analysis. The DSTP was developed in conjunction with the Toxi‐Chromotest and SOS Chromotest kits. The SOS Chromotest can be used with or without S9. Our results presented in this paper indicate the sensitivity of DSTP and cost effectiveness compared to some commonly used sediment extraction procedures.