bluuebunny/crossref_metadata_2025 huggingface dataset:
Biological Receptor Maps. 2 Steric Maps of Benzoate Antibody and Carbonic Anhydrase
Authors: Motoc Ioan
Published: October 2006

SIBIS calculations for hapten‐antibody interactions (i.e., substituted benzoates in the anti‐p‐(p′‐azophenylazo)benzoate system) and sulfonamide binding to carbonic anhydrase are reported. The antibody active site steric map, supported by an excellent QSAR (n = 18, r = 0.99, s = 0.17, F = 156.25), demonstrates that the receptor consists of two regions with distinct steric features: one region exhibits stringent steric requirements and the other one is lax. The steric map of the carbonic anhydrase receptor (based on a very good correlation, n = 33, R = 0.96, s = 0.35, F = 126.64) is confirmed by pattern recognition calculations, and shows that the binding of sulfonamides depends mainly on steric effects.
Some Critical Remarks Concerning the Inductive Parameter σI Part III: Parametrization of the Ortho Effect in Benzoic Acids and Phenols
Authors: Bijloo Greetje J. , Rekker Roelof F.
Published: October 2006

Correlation analysis was applied to pKa values of a series of 63 benzoic acids and a series of 64 phenols in order to obtain more evidence for the correct rules of parametrization of orthosubstituents as suggested by Fujita and Nishioka in 1976.

For the inductive effect parameter σI‐used in this type of equations ‐ again a σI = 0.00 parametrization for alkyl groups is applied. The results are in agreement with the findings for aliphatic amines and aliphatic carboxylic acids as discussed in previous papers in this series.

Good correlation with r = 0.9982 for benzoic acids and r = 0.9987 for phenols could be made.
Specificities of Subtilisin BPN' and Intracellular Proteinase from Bacillus Amyloliquefaciens in Reaction with Organophosphorus Inhibitors
Authors: Aaviksaar Aavo , Peips Mart , Sikk Peeler , Strongin Alexander Y. A. , Markaryan Adham N. , Stepanov Valentin M.
Published: October 2006

The kinetics of irreversible inhibition of two proteinases from Bacillus amyloliquefaciens, i.e. an intracellular serine proteinase and subtilisin BPN', by O‐n‐alkyl‐p‐nitrophenyl methyl‐phosphonates, (n‐CnH2n+1O)(CH3)P(O)OC6H4NO2‐p, n from 2 to 8, have been studied. The inhibitory activity of these compounds significantly depended upon the length of the alkoxy group in their acid moieties. The dependence of the second‐order rate constant of the enzyme active site phosphorylation upon the Hansch hydrophobicity parameter π of the substituent ‐CnH2n+1 is described by the equation log ki = const. + φ, where φ is 1.1 for the intracellular proteinase and 0.7 for subtilisin BPN′. In subtilisin BPN′ the straight line holds up to n = 6, in the intracellular proteinase up to n = 5. The data point of a difference between the structures of nonpolar substrate‐binding areas in the active sites of the two enzymes.
Multivariate structure‐activity relationships between data from a battery of biological tests and an ensemble of structure descriptors: The PLS method
Authors: Dunn W. J. , Wold S. , Edlund U. , Hellberg S. , Gasteiger J.
Published: October 2006

Quantitative structure‐activity relationships (QSAR) are discussed for the case when the chemical structure is characterised by a multitude of structure descriptors and the biological activity measured as the values of several tests.

The use of the multivariate data analytical method PLS (partial least squares modelling with latent variables) in this type of problems is described. PLS has some advantages before regression methods, notably the ability to handle both multivariate activity and structure descriptor data and the ability to handle more variables (descriptors) than compounds.

As an illustration, a battery of five measures of the mutagenicity of seven chlorinated aliphatic hydrocarbons is analysed in relation to eleven structure descriptors.
A Quantum Chemical QSAR Study of Carbonic Anhydrase Inhibition by Sulfonamides Sulfonamide Carbonic Anhydrase Inhibitors: Quantum Chemical QSAR
Authors: De Benedetti Pier G. , Menziani M. Cristina , Frassineti Chiara
Published: October 2006

Molecular Orbital (MO) indices were computed (CNDO/2) for three series of sulfonamide carbonic anhydrase inhibitors, in their neutral and anionic forms.

Linear regression analyses between the calculated indices and both physico‐chemical and enzyme inhibition data provide good correlations which enable us to test the predictive and diagnostic aspects of the quantitative structure‐activity relationships employing quantum chemical indices.

In particular:

The molecular size affects the inhibitory power among the different sulfonamide derivatives (aliphatic, arylic and bridged diarylic) but not significantly within each molecular series;

the MO indices are good predictors of the various experimental molecular properties and suggest that the less electron‐rich the sulfamoyl group is, the more favoured are both the hydrophobic and hydrophilic steps leading to enzyme inhibition.
Topological Pharmacophores New Methods and Their Application to a Set of Antimalarials Part 2: Results from LOGANA
Authors: Franke Rainer , Streich W. Jürgen
Published: October 2006

The LOGANA procedure described in part 1 of this series is applied to a set of antimalarials as a test case. Its principle consists in the stepwise combination of binary descriptors characterizing the presence or absence of substructural features into conjunctions using the logical operator “and”, such that the structural patterns described by these conjunctions are typical of the class of high activity compounds. Clear substructural patterns for antimalarial activity are obtained which are consistent with corresponding Hansch equations taken from the literature.
Topological Pharmacophores New Methods and Their Application to a Set of Antimalarials Part 3: Results from LOCON
Authors: Franke Rainer , Streich W. Jürgen
Published: October 2006

The LOCON procedure described in the first part of this series is applied to a set of antimalarials as a test case. Its principle consists in the stepwise evaluation of conjunctions such that sets of compounds characterized by these conjunctions have high mean values of biological activity. The conjunctions are obtained from binary descriptors which characterize the presence or absence of predefined substructural features using the logical operator “and”. Clear substructural patterns typical of the highly active compounds are obtained which supplement the LOGANA results presented in Part 2 of this series. There is very good agreement with corresponding Hansch equations taken from the literature so that similar predictions result from both approaches.
The Prediction of Substituent Interactions in the Lipophilicity of Disubstituted Benzenes using RP‐HPLC
Authors: El Tayar Nabil , van De Waterbeemd Han , Testa Bernard
Published: October 2006

A number of papers have recently appeared investigating interactions between substituents on aromatic rings, in particular their lack of additivity in terms of hydrophobic constants. In the present study, chromatographic capacity factors (log kw i.e. extrapolated to 100% water composition of the mobile phase) obtained from reversed‐phase high‐performance liquid chromatography (RP‐HPLC) are reported. For the exploration of functional group interactions these values provide a more consistent and precise data set than logP values collected in the literature. A series of 43 disubstituted benzenes was investigated. Substituent interactions are expressed in terms of a previously reported hydration factor ω and the general equation derived is log k = log k + mw · ω, where mw, is a multiplicity factor having an integer value. The physical background of the term mw · ω is discussed by considering the number of water molecules involved in the partitioning process.
Physical Factors Contributing to Hydrophobic Constant π
Authors: Yang Guang‐Zhong , Lien Eric J. , Guo Zong‐Ru
Published: October 2006

The hydrophobicity constants (μ) of different aromatic substituents have been factored into three major components, a volume factor (MW, or Vw), an electronic factor as represented by dipole moment (μ), and H‐bonding factor. The following general equation has been shown to be applicable to a wide range of nonpolar to polar substituents, with only a few notable outliers: π = a · MW (or Vw) ‐ b · HB ‐ c · μ + d.

The usefulness and the limitations of such a general correlation are discussed.
Distribution Coefficients by Curve Fitting: Application to Ionogenic Nonsteroidal Antiinflammatory Drugs
Authors: Barbato F. , Caliendo G. , La Rotonda M. I. , Silipo C. , Toraldo G. , Vittoria A.
Published: October 2006

A thorough investigation on the dependence of distribution coefficients of acidic drugs on pH and pKa values has been carried out. The results give evidence that the Henderson‐Hasselbach equation is an idealization and only an approximation for real systems.

It is shown that a multiparametric curve‐fitting technique may constitute a useful alternative to the previously reported methods to describe the hydrophilic/lipophilic pH‐profiles of ionogenic substances. Calculated values at any given pH value are in very good agreement with the experimental partition (log P) and distribution coefficients determined by shake‐flask method and reversed‐phase high performance liquid chromatography.
Application of the ORMUCS Method to Structure‐Activity Studies on the Fungicidal Activity of Mepronil Derivatives
Authors: Takahashi Yoshimasa , Sasaki Shin‐Ichi , Tamaru Masatoshi , Shimazaki Isao , Ito Shigetoshi , Kawada Seigo , Suda Yoshitaka
Published: October 2006

Application of the ORMUCS method, proposed by the authors in the previous work, to structure‐activity studies is discussed in comparison with the Hansch approach. Using this method, the correlation between chemical structures of a series of mepronil derivatives and their fungicidal activity were examined with rating score data obtained by green house tests (in vivo test). The activity was highly correlated with the largest width and hydrogen accepting property of a substituent on the benzoyl moiety. This is consistent with the best QSAR equation obtained from Hansch analysis using in vitro data for mycelial growth inhibition on the same series.
A Quantum Chemical Study of Insect Juvenile Hormone Mimics: The Active Conformation and the Electrostatic Similarities
Authors: Nakayama Akira , Richards W. Graham
Published: October 2006

The stable conformations and the electrostatic properties of insect juvenile hormone (JH) mimics are studied using semi‐empirical molecular orbital methods. One of the minimum energy conformations of JH active diphenylethers, a new class of JH mimics, is found to be superimposable on the stable extended structure of methoprene which is one of the most highly active JH mimics within the series of terpenoid compounds. As well as the superimposability of the diphenylether and terpenoid structures, JH active functional groups such as esters, carbamates and oxime O‐ethers are also shown to be superimposable. The electrostatic potentials of these functional groups which are commonly found in the diphenylethers and the terpenoid JH mimics are similar to each other in terms of potential contours and the similarity indices of electrostatic potentials. This may account for the bioisosterism of these active functional groups. Here we postulate a model of molecular recognition at the JH receptor in which the electrostatic interaction is important as well as the size and shape of the molecule. The molecular similarities between different classes of JH mimics in terms of steric and electrostatic properties, which are derived from quantum chemical methods, may help to understand the universality of active structures and aid in the design of new active generations.
Multiple Regression Analysis of Antimalarial Activities of Sulfones and Sulfonamides in Cell‐Free Systems and Principal Component Analysis to Compare with Antibacterial Activities
Authors: Wiese M. , Seydel J. K. , Pieper H. , Krüger G. , Noll K. R. , Keck J.
Published: October 2006

The inhibition of dihydropteroate synthase extracts by sulfones and sulfonamides has been determined. Structural dependency of the observed I50‐values has been quantitatively explained by multiple regression and principal component analysis. New highly active sulfones have been synthesized guided by the derived QSAR. The analysis leads to the conclusion that electronic and steric substituent effects are decisive and that sulfones and sulfonamides are binding to the same receptor site. The LFE‐descriptors used are correlated with the minimal conformational entropy. The results are also compared with the results obtained in cell‐free and whole cell systems of bacteria. The additional influence of cell‐wall permeability on inhibitory efficacy is demonstrated.
Description of Heterocyclic Substituents: A Free‐Wilson Type Approach Using D‐Optimal Designs
Authors: Cativiela Carlos , García José I. , Elguero José , Mathieu Didier , Luu Roger Phan Tan
Published: October 2006

In order to test the hypothesis that structural characteristics in a Free‐Wilson type model can be used to describe heterocyclic substituents, a set of heterocyclic compounds (eighteen carboxaldehydes and their corresponding carboxylic acids) containing only one heteroatom was prepared and some spectroscopical properties were used as experimental responses. Fedorov's algorithm has been used to choose D‐optimal designs. The validity of this methodology is discussed.
Quantum Chemical Studies of H2‐Antagonist‐Receptor Complexes. Cimetidine and Related Compounds
Authors: den Kelder Gabriëlle M. Donneé‐Op , Haaksma Eric E. J. , Timmerman Hendrik
Published: October 2006

Molecular and conformational properties of H2‐receptor antagonists were studied by means of the semiempirical MNDO (Modified Neglect of Differential Overlap) approximation. The compounds investigated were cimetidine (N″‐cyano‐N‐methyl‐N′‐[2‐[(5‐methylimidazol‐4‐yl methyl)thio]ethyl]guanidine) analogues, in which the cyanoguanidine moiety was replaced by various other neutral dipolar groups. A strong relation was found between, H2‐antagonistic activity as measured in vitro on the histamine stimulated guinea pig right atrium, one of the components of the overall MNDO dipole moment, and the lipophilic character of the different substituent groups. The dipole moment component points along the direction of the amidine N′H‐bond suggesting the relevance of hydrogen bond formation upon binding of the ligand to the H2‐receptor molecule. This theoretical study demonstrates that the semiempirical quantum chemical MNDO method might be helpful in calculating molecular properties as e.g. dipole moments, both in cases were experimental data are lacking, and in cases where experimental data are obtained under conditions which deviate strongly from the situation in which the ligand most probably is present when bound to the receptor macromolecule. An incorrect use of quantum chemical properties is discussed.
Electronic and Hydrophobic Constants of Azoxy Groups Containing Electron Withdrawing Functions
Authors: Calvino Rosella , Fruttero Roberta , Garrone Adele , Gasco Alberto
Published: October 2006

σ and π constants for azoxy groups containing electron withdrawing functions have been evaluated. The electrical influence of these groups was separated into an induction and a resonance parameter. A new scale of π substituent constants has been derived analysing log P values of phenyldiazenecarbonitrile 2‐oxide derivatives. It is closely parallel with the π scale obtained from the nitrophenyl substituted system.
QSAR Studies on Mifentidine and Related Compounds
Authors: den Kelder G. M. Donné‐Op , Haaksma E. E. J. , van der Schaar M. W. G. , Veenstra D. M. J. , Timmerman H. , Cereda E. , Dubini E.
Published: October 2006

The MNDO semiempirical SCF‐MO method has been used to calculate charge distributions of a series of histamine H2‐receptor antagonists. The investigated compounds concern mifentidine (N‐isopropyl‐N′‐(4‐1H‐imidazol‐4‐yl‐phenyl)formamidine) analogues, in which the imidazole moiety has been substituted or replaced by various aromatic heterocyclic groups. A correlation has been found between H2‐antagonistic activity as determined by inhibition of specific [3H]‐tiotidine binding to the H2 receptors of a guinea pig cortex preparation, and the net atomic charges of two of the atoms (X‐H bond in which X is a nitrogen or carbon atom) in the heterocycle. The binding capacity of the ligand molecule to the receptor is enhanced when the electronic population of atom X and the positive charge on the proton are higher. Assuming that the difference between both charges might effectively serve as a valuable substitute for the hydrogen bond forming capacity of the X‐H group, the conclusion can be drawn that this property of the heterocycle plays an important role in the interaction process of the ligand with its H2‐receptor. The obtained regression equation(s) suggest that the monocation (formamidine moiety protonated) is the species related to pharmacological activity.
Solubility Properties in Biological Media. 12. Regarding the Mechanism of Nonspecific Toxicity or Narcosis by Organic Nonelectrolytes
Authors: Kamlet Mortimer J. , Doherty Ruth M. , Abraham Michael H. , Taft Robert W.
Published: October 2006

Narcotic effects of organic nonelectrolytes to the tadpole (logC), minimum blocking concentrations for stoppage of electrical activity in the muscle of the frog, Rana pipiens (logMBC), and binding of nonelectrolytes to bovine serum albumin (log1/C) are well correlated by the following equations, magnified image where VI is the intrinsic (van der Waals) molar volume, and π*, βm and αm are the solvatochromic parameters that scale solute dipolarity/polarizability, hydrogen bond acceptor basicity, and hydrogen bond donor acidity.

That increasing solute π* leads to lesser partition into the biosystem compared with its aqueous environment, but also leads to greater toxicity or anesthetic effect is suggested to implicate in the mechanism of toxicity or narcosis a specific association effect between the more dipolar solutes (toxicants) and a molecule involved in the transmission of nervous impulses.
An Index of Molecular Flexibility from Kappa Shape Attributes
Authors: Kier Lemont B.
Published: October 2006

An index encoding the structural attribute known as flexibility has been devised based upon the chemical graph. The flexibility definition is based upon the role of molecular size, branching, cycles and heteroatom content. The calculation of the index, phi, uses information from the kappa indexes to encode these contributions. The flexibility index is made equal to the product of kappa‐one and kappa‐two, normalized to the number of atoms in the graph. Examples reveal the structure‐activity potential for the index.
pKa, Log P and MedChem CLOGP Fragment Values of Acidic Heterocyclic Potential Bioisosteres
Authors: Lipinski Christopher A. , Fiese Eugene F. , Korst Robert J.
Published: October 2006

Log P values have been measured for twenty phenyl and benzyl five membered heterocycles and alicyclic analogs that might function as acidic bioisosteres. pKa's have been measured by potentiometric titration in water and 1:1 dioxane‐water. From this experimental data, twelve missing fragmental CLOGP values are derived for use in calculating Log P values according to the Pomona College MedChem program. Log P values of some of the simple benzyl and phenyl heterocycles are compared to those measured for four clinically used drugs containing the same acidic moieties. Sulfonyl urea and acyl sulfonamide moieties have similar pKa and Log P values suggesting that these groups might be explored as bioisosteres.
Comprehensive Analysis of Quantitative Structure‐Activity Relationships of Catecholamine‐Uptake Inhibitors
Authors: Terada Yukimasa , Tomita Tatsuya , Inami Yoshiharu
Published: October 2006

Quantitative Structure‐Activity Relationships (QSAR) of inhibitors of dopamine (DA)‐ and norepinephrine (NE)‐uptake have been analyzed quantitatively. Previously, we reported that several series of congeners are susceptible to similar substituent effects, and these structurally diverse compounds interact with common receptor points by the hydrophobic interaction of a phenyl group and the hydrogen bonding of a nitrogen atom. In this report, we extended this concept to derive an equation that quantitatively interprets the activity of 113 compounds comprising 6 skeletal groups.

Excellent QSAR equations were obtained in which all parameters used were physicochemically significant. Of the parameters adopted therein, the root mean square (rms) of the distances between corresponding pharmacophore was an especially valuable parameter to compare the activity of the structurally diverse compounds. On the other hand, a substituent existing in a specific region of the inhibitor molecule causes steric hindrance with the receptor and interferes with an effective binding of the inhibitor. Lastly, it was concluded that a degree of correspondence of proper pharmacophore to the receptor points, as well as the volume of that specific region, principally determines the binding ability of that congener, and the substituent effect of each compound is added to that fundamental affinity.
Studies of Performance of Graph Theoretical Indices in QSAR Analysis
Authors: Ośamiałowski Krzysztof , Kaliszan Roman
Published: October 2006

Comparative studies of performance in exemplary QSAR of the most commonly used structural descriptors derived from molecular graphs were performed. Three diverse series of test compounds were selected for which various property measures existed. One group of compounds were polychlorinated dibenzofurans of determined gas chromatographic retention indices. The second group comprised isomers of general formula C4H8O of known boiling points, refractivity indices and densities. Third set of agents consisted of 2‐substituted isonicotinic acid hydrazides of determined antibacterial activity. The following graph theoretical indices were considered: the Kier and Hall [22] generalized molecular connectivity indices, the Balaban distance sum connectivity index calculated after Barysz et al. [23], the indices of molecular shape of Kier [24], the information indices of neighbourhood symmetry of Sarkar et al. [25] and of Basak et al. [26]. Auxiliary structural parameters, e.g., molecular surface area, were also employed. Significant correlation with molecular mass and intercorrelations among the graph theoretical indices were observed excepting the group of information content indices. For the compounds and properties studied the graph theoretical indices considered appeared unable to provide a size‐independent, meaningful input to property description.
H‐Bond Contribution to Octanol‐Water Partition Coefficients of Polar Compounds
Authors: Raevsky Oleg A. , Schaper Klaus‐J. , Seydel Joachim K.
Published: October 2006

A quantitative description of the hydrogen bond contribution to logP is presented for carbonyl and hydroxyl compounds. A two parameter Eq. correlating the hydrophobicity with molecular volume and sum of free energy H‐bond acceptor ability is derived for carbonyl compounds. If compounds with hydroxyl groups are included also H‐bond donor abilities have to be considered. It can be concluded that hydrogen bonds play a very important role for the formation/presentation of hydrophobic properties of polar compounds. A quantitative description of the hydrogen bond contribution to logP values of such compounds is possible by means of free energy H‐bond acceptor and donor factor values only. Negative logP values result from the negative contribution of H‐bond acceptor ability.
SD‐modelling and Prediction by WHIM Descriptors. Part 5. Theory Development and Chemical Meaning of WHIM Descriptors
Authors: Todeschini Roberto , Gramatica Paola
Published: October 2006

WHIM descriptors are 3‐dimensional molecular indices that represent different sources of chemical information. WHIM descriptors contain information about the whole 3D‐molecular structure in terms of size, shape, symmetry and atom distribution. These indices are calculated from (x, y, z)‐coordinates of a molecule within different weighting schemes in a straightforward manner and represent a very general approach to describe molecules in a unitary conceptual framework. A set of 40 simple heterogeneous compounds is used to show the main characteristics, some properties and the modelling power of WHIM descriptors by using simple scatter plots of the descriptors, Principal Component Analysis and predictions of simple physicochemical properties.
A general approach for the quantitative analysis of bisphosphonates in human serum and urine by high‐performance liquid chromatography/tandem mass spectrometry
Authors: Zhu Lee S. , Lapko Veniamin N. , Lee Jean W. , Basir Yousef J. , Kafonek Chris , Olsen Richard , Briscoe Chad
Published: October 2006

Bisphosphonates are extremely hydrophilic and structurally similar to many endogenous phosphorylated compounds, making their selective extraction from serum or urine very challenging. Many bisphosphonates lack strong chromophores for sensitive UV or fluorescence detection. We report here the first general approach to enable sensitive and selective quantitation of N‐containing bisphosphonates by liquid chromatography/tandem mass spectrometry (LC/MS/MS) following derivatization with diazomethane. The novelty of the strategy lies in performing the derivatization on silica‐based anion‐exchange sorbents as an integrated step in the sample purification by solid‐phase extraction (SPE). The ‘on‐cartridge’ reaction with diazomethane not only led to higher efficiency of derivatization, but also enabled a more discriminatory recovery of the drug's derivatives. The derivatized bisphosphonates demonstrated improved chromatographic separation and increased sensitivity of the detection. The general applicability of the approach was demonstrated by validation of bioanalytical methods for risedronate and alendronate in human serum and urine. Sensitivity was achieved at the pg/mL level with merely 100–200 µL of sample. Copyright © 2006 John Wiley & Sons, Ltd.
Design and experimental evaluation of a QFT contact task controller for electro‐hydraulic actuators
Authors: Niksefat N. , Sepehri N. , Wu Q.
Published: October 2006

This paper presents design and experimental evaluation of a robust contact task controller for an electro‐hydraulic actuator that operates under significant system uncertainties and nonlinearities. The designed controller allows the actuator to follow a free space trajectory, and upon contact with an uncertain environment exert a desired force, by stably passing through the transition phase from free space to constrained space. The scheme is essentially the combination of two distinct control laws that are individually designed for position regulation in free space and force regulation during sustained contact. Both controllers are designed, using a nonlinear approach within the framework of quantitative feedback theory (QFT), to satisfya priorispecified stability, tracking and disturbance rejection specifications. They are then combined with a simple switching law to form a contact task controller. Due to the existence of a switching, the resulting control system is non‐smooth. The stability of the controller is then analysed using an extended version of Lyapunov's second method under the condition of existence and uniqueness of Filippov's solution. Experiments, performed on a typical industrial hydraulic actuator, include motion through free space, contact with the environment and the transition between the two. The proposed QFT contact task control scheme enjoys the simplicity of fixed‐gain controllers, is easy to implement, requires very little computational effort, is robust to the variation of hydraulic functions as well as environmental stiffness, and results in responses with good performance in both transient and steady‐state periods. Additionally, the controller only requires measured contact force and actuator position as feedback; this makes the controller attractive for industrial implementation. Copyright © 2006 John Wiley & Sons, Ltd.
Output feedback stabilization of nonlinear networked control systems with non‐decreasing nonlinearities: a matrix inequalities approach
Authors: Cheng Teddy M. , Savkin Andrey V.
Published: October 2006

This paper addresses an output feedback stabilization problem of a class of nonlinear systems with nonlinearities satisfying the non‐decreasing propertyvialimited‐capacity communication channels. Using ideas from absolute stability theory, we propose an algorithm that consists of an observer and a coder/decoder‐controller pair. Sufficient conditions for the stabilization problem are provided and presented in terms of linear matrix inequalities. Copyright © 2006 John Wiley & Sons, Ltd.
The visual compass: Performance and limitations of an appearance‐based method
Authors: Labrosse Frédéric
Published: October 2006

In this article we present an algorithm to estimate the orientation of a robot relative to an orientation specified at the beginning of the process. This is done by computing the rotation of the robot between successive panoramic images, grabbed on the robot while it moves, using a subsymbolic method to match the images. The context of the work is simultaneous localization and mapping (SLAM) in unstructured and unmodified environments. As such, very few assumptions are made about the environment and the robot's displacement. The algorithm's performance depends on the value of a number of parameters being determined to provide overall good performance of the system. The performance is evaluated in different situations (trajectories and environments) with the same parameters and the results show that the method performs adequately for its intended use. In particular, the error is shown to be drifting slowly, in fact much slower than unprocessed inertial sensors, thus only requiring infrequent realignment, for example, when relocalizing in a topological map. Limitations of the proposed methods are also shown and discussed. © 2006 Wiley Periodicals, Inc.
Transient binding of plastocyanin to its physiological redox partners modifies the copper site geometry
Authors: Díaz-Moreno Irene , Díaz-Quintana Antonio , Díaz-Moreno Sofía , Subías Gloria , De la Rosa Miguel A.
Published: October 2006

The transient complexes of plastocyanin with cytochrome f and photosystem I are herein used as excellent model systems to investigate how the metal sites adapt to the changes in the protein matrix in transient complexes that are involved in redox reactions. Thus, both complexes from the cyanobacterium Nostoc sp. PCC 7119 (former Anabaena sp. PCC 7119) have been analysed by X‐ray absorption spectroscopy. Our data are consistent with a significant distortion of the trigonal pyramidal geometry of the Cu coordination sphere when plastocyanin binds to cytochrome f, no matter their redox states are. The resulting tetrahedral geometry shows a shortening of the distance between Cu and the Sδ atom of its ligand Met‐97, with respect to the crystallographic structure of free plastocyanin. On the other hand, when plastocyanin binds to photosystem I instead of cytochrome f, the geometric changes are not significant but a displacement in charge distribution around the metal centre can be observed. Noteworthy, the electronic density around the Cu atom increases or decreases when oxidised plastocyanin binds to cytochrome f or photosystem I, respectively, thus indicating that the protein matrix affects the electron transfer between the two partners during their transient interaction.
Effects of dietary lysine supplementation in cats with enzootic upper respiratory disease
Authors: Maggs David J. , Sykes Jane E. , Clarke Heather E. , Yoo Seung H. , Kass Philip H. , Lappin Michael R. , Rogers Quinton R. , Waldron Mark K. , Fascetti Andrea J.
Published: October 2006

To determine the effectiveness of dietary lysine supplementation in cats with enzootic upper respiratory disease (URD), 50 cats were fed a ration containing 11 or 51 g lysine/kg diet for 52 days. Food intake, body weight, clinical signs, plasma amino acid concentrations and presence of Chlamydophila felis or feline herpesvirus (FHV)-1 DNA within the conjunctival fornix were assessed. Food and lysine intake of both dietary groups decreased between days 17 and 22, coinciding with peak disease and viral presence. Mean disease score for cats fed the supplemented ration (0.94) was higher than for those fed the basal diet (0.21); however, this could be attributed to a small subset of male cats which demonstrated fighting behavior that may have contributed to stress within that cage. FHV-1 DNA was detected on 12 occasions in six cats receiving the supplemented diet and on one occasion in one cat fed the basal diet. C felis DNA was never detected. Mean plasma arginine concentration was lower and plasma lysine concentration was higher in supplemented cats. Mean plasma arginine concentration declined throughout the study in both dietary groups. Data from the present study raise important questions but do not permit a definitive conclusion regarding the efficacy of dietary lysine supplementation in cats with enzootic URD.
Cochlear implantation in the irradiated temporal bone
Authors: Adunka O F , Buchman C A
Published: October 2006

Objective: To demonstrate the feasibility and complexities of cochlear implantation in the setting of bilateral temporal bone osteoradionecrosis.

Study design: Case report.

Setting: Tertiary care referral centre.

Case description: A 66-year-old woman with bilateral temporal bone osteoradionecrosis and profound hearing loss, following treatment for tonsillar cancer, underwent cochlear implantation. Prior canal wall down mastoidectomy and subsequent temporal bone resection with free flap reconstruction had been performed on the implanted ear. The contralateral ear received a canal wall down mastoidectomy. A completely dehiscent mastoid segment of the facial nerve and extensive fibrosis were evident in the implanted ear. Only minimal fibrous reaction was found within the cochlea, allowing for full electrode insertion. At three months, speech recognition testing documented a consonant-nucleus-consonant (CNC) word score of 54 per cent.

Conclusions: This report demonstrates the feasibility of cochlear implantation after temporal bone surgery and free flap reconstruction in the setting of diffuse osteoradionecrosis. The patient's excellent open-set speech understanding using the cochlear implant implies that radiation did not severely damage the central auditory pathways. Thus, some patients with radiation-induced hearing loss may be appropriate cochlear implant candidates. Special attention should be paid to surgical planning, as complications related to wound healing, electrode insertion and facial nerve injury may be more likely.
New reports and combinations in the family Pannariaceae (Lecanorales, lichenized Ascomycota)
Authors: PASSO Alfredo , CALVELO Susana
Published: October 2006

Two Psoroma species, P. calophyllum and P. contortum, described from southern South America have been studied. The morphology, anatomy and chemistry of the two species are described together with notes on their ecology and taxonomy. The placing of these taxa in Pannaria is discussed, and the new combinations Pannaria calophylla and Pannaria contorta are proposed.
Waynea cretica, a new species from the Mediterranean Region
Authors: LLOP Esteve
Published: October 2006

A new Mediterranean species, Waynea cretica, is described. The species is so far known only from Crete (Greece). Waynea cretica has flat to scarcely ascending squamules, an upper cortex being a paraplectenchymatous eucortex, and long, narrow, acicular ascospores with (5–)7 septa. The new taxon is compared with the hitherto known species of Waynea.
Soil surface lichens on a 1500 kilometre climatic gradient in subtropical eastern Australia
Authors: ROGERS R. W.
Published: October 2006

Soil lichens are taxonomically diverse in subtropical eastern Australia. A total of 61 species in 25 genera is reported from a transect 1500 km long, running from the humid sub-tropical coast to the arid interior of the continent. The distribution of the lichen species and genera is associated with climatic pattern and with the growth form of the species. The total number of species found in bands of one degree of longitude along the transect decreases from the wet coastal region to the arid interior. Fruticose and foliose species dominated the flora in wetter regions and squamulose species in the dry interior.
Pannaria isidiosa, a new Australian lichen with a new chemosyndrome
Authors: ELVEBAKK Arve , ELIX John A.
Published: October 2006

Pannaria isidiosa sp. nov. is newly described from montane forests in New South Wales, Australia. It is characterized by abundant globose to coralloid isidia, long-ellipsoid spores with a verrucose and citriform perispore. It is related to P. xanthomelana, but in addition to pannarin and porphyrilic acid, it contains methylplacodiolic acid and a chemosyndrome of four unidentified terpenoids.
Caloplaca sorediella Arup, a new sorediate species from western Britain
Authors: ARUP Ulf
Published: October 2006

Caloplaca sorediella Arup is described as a new species. It is so far known only from extreme maritime situations on seashore rocks in western England, Scotland and Wales.
The constructive use of ‘vernacular religion’
Authors: Monteith W. Graham
Published: October 2006

The study of vernacular religion is often confined to the discussion of ‘folk religion’ in a rather derogatory and sterile manner. An attempt is made to correct this by describing seven ideal-typical ways in which vernacular religion can be studied and defined. The seven types or discussions are: 1) whether vernacular religion represents elitist or popular religious practices and the nature of New Religious Movements; 2) the study of cults and New Religious Movements; 3) vernacular religion as folklore; 4) Bellah's concept of ‘civil religion’ and its application to modern British culture particularly as it relates to public expressions of mourning; 5) ecclesiastical historians' use of the concept in historical studies; 6) Küng's use of paradigm as formulated by Kuhn, discussed in the context of two examples of modern usage of the term in vernacular religion; and 7) vernacular religion and modern hermeneutics as preachers attempt to relate local practices to their congregations. In order to use any combinations of these constructions in a positive manner, it is suggested that we develop a diagnostic technique which recognises that people have an inherent desire to discover ways of relating everyday experience to their religious expression. Such a method is developed using both Murphy and Tracy to show how attention may be paid to vernacular religion without succumbing to the trap of relativism.
Influence of target plasma nuclei collisions on correlated motion of fragmented H2+protons
Authors: BARRIGA-CARRASCO MANUEL D.
Published: October 2006

The aim of this paper is to describe the influence of target plasma nuclei on the correlated motion of H2+protons traversing classical plasma matter. Electronic stopping of the protons pair is treated by means of the dielectric formalism, while nuclear collisions are dealt within the classical dispersion theory through a Monte Carlo method. It is shown that vicinage electronic forces screen Coulomb repulsion between the two protons from H2+ion decelerating the increase of their relative distance. Vicinage forces also align the interproton vector along the motion direction. However, proton interactions with plasma nuclei mask most of these vicinage effects. These nuclear collisions hide the screening effect produced by the vicinage forces, increasing the proton relative distance even faster than for bare Coulomb repulsion. The interproton vector along motion direction is also misaligned due to nuclear collisions. Nuclear collisions effects are more significant in reducing projectile velocity. In particular, all these effects are studied in a deuterium (D) plasma with temperatureTe= 10 eV and electronic densityn= 1023cm−3.
Effective collision strengths for electron-impact excitation of Al10+
Authors: STANCALIE V. , PAIS V.
Published: October 2006

Electron collision strengths for electron-impact excitation of Li-like and Al ion are evaluated in close-coupling approximation using the multi-channel R-matrix method. Five LS target eigenstates are included in the expansion of the total wave function, consisting of the twon= 2 states withconfigurationsof 1s22s, 1s22p, and threen= 3 states withconfigurations1s23s, 1s23p, and 1s23d. Collision strengths are obtained in LS coupling using FARM code and in intermediate coupling scheme using the SUPERSTRUCTURE program. The effective collision strengths are calculated as function of temperature, up to a temperature that does not exceed half of the maximum energy in the R-matrix run.
Laser-induced plasma spectroscopy for mine detection and verification
Authors: SCHADE WOLFGANG , BOHLING CHRISTIAN , HOHMANN KONRAD , SCHEEL DIRK
Published: October 2006

Laser-induced breakdown spectroscopy (LIBS) in combination with a conventional mine prodder is applied for remote detection of explosives and mine housing materials. High power subnanosecond laser pulses (pulse powerEp= 0.6 mJ and pulse duration Δt= 650 ps) at 1064 nm with a typical repetition rate of 10 kHz are generated by using a passively Q-switched Cr4+:Nd3+:YAG microchip-laser as seed-laser for an Yb-fiber amplifier. In the present investigation, the ratios of “late” and “early” LIBS intensities for the cyanide (CN) plasma emission at 388 nm and for the C-emission at 248 nm are used for data analysis. This allows the classification of different explosives and mine casing materials under real time conditions and also similar applications to materials processing.
Potential of Kα radiation by energetic ionic particles for high energy density plasma diagnostics
Authors: KAWAMURA TOHRU , HORIOKA KAZUHIKO , KOIKE FUMIHIRO
Published: October 2006

In this paper, potential of diagnostics with the use ofKα radiation for an energy deposition process from an intense ion-beam to background plasma is considered quantitatively.Kα radiation is a good candidate for the purpose. The wavelength ofKα radiation is varied according to the charge state of an emitter atom, and the diagnostics spatially resolved with radiations from various kinds of charge states can give us a profile of plasma temperature in a target material. For the calculation ofKα yield, an atomic population kinetics code is developed, and the result shows thatKα radiation has potential to get information of a plasma profile heated by an intense ion-beam.
High-energy-density attosecond electron beam production by intense short-pulse laser with a plasma separator
Authors: SAKAI KEI , MIYAZAKI SHUJI , KAWATA SHIGEO , HASUMI SHOTARO , KIKUCHI TAKASHI
Published: October 2006

An attosecond electron beam generation is studied by an intense short-pulse TEM (1,0) + TEM (0,1)-mode laser with a plasma separator in vacuum. The TEM (1,0) + TEM (0,1)-mode laser has a ring-shaped intensity peak in the radial direction. Electrons are accelerated and compressed near the focus point of the TEM (1,0) + TEM (0,1)-mode laser. However, after the focus point, some electrons move to its deceleration phase of the laser pulse and are decelerated. As a result, a longitudinal velocity deference of electrons generated causes a density lowering. In order to suppress the deceleration and the density lowering, we set an overdense plasma-foil separator before the electrons move to the deceleration phase of the laser pulse. Since only the laser is reflected by the plasma separator, the electrons do not experience the deceleration phase and the density of the electron bunch is kept high after passing through the plasma separator. Consequently, a high-density electron beam is generated and at the same time, the pulse length of the electron bunch becomes sub-femto second.
The Alfvén limit revisited and its relevance to laser-plasma interactions
Authors: DAVIES J.R.
Published: October 2006

Alfvén's derivation of his current limit is given. It demonstrates that it does not give the maximum possible current of a beam, but the maximum current that can propagate for an indefinite distance and time, from a source, in a charge neutral beam. Furthermore, the value Alfvén obtained applies to a uniform current density and to particles initially moving in the direction of the beam. It is also shown that Alfvén predicted that beams which exceed the limit will filament as a result of the particles that are turned back by the magnetic field. His work is extended to beams with particles that have transverse momentum, to beams with non-uniform current densities, to beams that are not charge neutral and to the time dependent case. These extensions of Alfvén's work are found to require numerical calculations in most cases and to give ambiguous results in some cases. A general formula for the current limit is given based on the conservation of energy. It is calculated for the cases considered previously and found to confirm the accuracy of Alfvén's original estimate. The relevance of the current limit to high intensity laser-solid interactions and fast ignition is then discussed.
Reactive pulsed laser ablation: Plasma studies
Authors: THAREJA RAJ K. , SHARMA A.K.
Published: October 2006

We report on the pulsed laser ablation of aluminum (Al) plasma in presence of ambient nitrogen to understand the formation of aluminum nitride (AlN). Formation of carbon nitride (CN) and titanium oxide (TiO) by pulsed laser-ablation of graphite and titanium targets in presence of ambient nitrogen and oxygen is also compared. We discuss the dynamics of plasma expansion based on existing models, shock and drag models, and the plasma gas interface distortion, Rayleigh-Taylor instability at various ambient pressures of nitrogen. Since Rayleigh-Taylor instability may give rise to self-generated magnetic field in the plasma, an attempt is made to understand the mechanism of generation as well as the estimation of this field near the focal spot using the information from the images of the expanding plasma. This is the first time images of the expanding plume are used to estimate self generated magnetic fields. At the irradiance level used in the experiment the field is high very close to the target surface therefore we expect splitting of the energy levels thus giving rise to emissions that may be anisotropic in nature. We discuss the extent of anisotropy by measuring the degree of polarization using emission intensity in optical emission spectrum of selected Al III transition 4s2S1/2–4p2P3/2oat 569.6 nm using both nanosecond and picosecond pulses.
Guest Editor's Preface: 8th Workshop on Fast Ignition of
Fusion Targets
Authors: Honrubia J.J.
Published: October 2006

This issue of Laser and Particle Beams includes papers
presented at the 8th Workshop on Fast Ignition of Fusion Targets,
held in Tarragona, Spain, from June 29 to July 1, 2005 as part of the
32nd Conference on Plasma Physics organized by the European
Physical Society.
Can self-managed systems be trusted? Some views and trends
Authors: MCCANN JULIE A. , DE LEMOS ROGEŔIO , HUEBSCHER MARKUS , RANA OMER F. , WOMBACHER ANDREAS
Published: October 2006

Self-managing or autonomic computing is a highly emerging field having been championed by industry and academia alike. Essentially the management of the system is being handed to the system itself, therefore the issue of trust in terms of the decisions the system makes regarding itself, is of paramount interest. This paper considers four aspects of trust in self-adaptive computing systems with the aim to identify trends and pinpoint areas that require more investigation.