pathmatrix: a geographical information system tool to compute effective distances among samples

pathmatrix is a tool used to compute matrices of effective geographical distances among samples using a least‐cost path algorithm. This program is dedicated to the study of the role of the environment on the spatial genetic structure of populations. Punctual locations (e.g. individuals) or zones encompassing sample data points (e.g. demes) are used in conjunction with a species‐specific friction map representing the cost of movement through the landscape. Matrices of effective distances can then be exported to population genetic software to test, for example, for isolation by distance. pathmatrix is an extension to the geographical information system (GIS) software arcview 3.x.     

Assessment of Optimal Selected Prognostic Factors

The identification and assessment of prognostic factors is one of the major tasks in clinical research. The assessment of one single prognostic factor can be done by recently established methods for using optimal cutpoints. Here, we suggest a method to consider an optimal selected prognostic factor from a set of prognostic factors of interest. This can be viewed as a variable selection method and is the underlying decision problem at each node of various tree building algorithms. We propose to use maximally selected statistics where the selection is defined over the set of prognostic factors and over all cutpoints in each prognostic factor. We demonstrate that it is feasible to compute the approximate null distribution. We illustrate the new variable selection test with data of the German Breast Cancer Study Group and of a small study on patients with diffuse large B‐cell lymphoma. Using the null distribution for a p‐value adjusted regression trees algorithm, we adjust for the number of variables analysed at each node as well. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Conditional and Unconditional Simulation of Healthy Patients' Visual Fields

This paper describes a simulation problem, motivated by the study of glaucoma, a very serious and widespread ocular illness. To ascertain whether a patient suffers from glaucoma, a perimetric test is done, but the evolution of the disease is very slow, and large longitudinal sets of tests taken on the same patient are needed to study its evolution, to analyze the efficiency of existing methods to detect the progression of glaucoma and to develop new ones. Simulation can be a very useful procedure to get appropriate data sets to work with. Our aim in this work is to simulate several VFs in a healthy patient to reflect his evolution in time. We use a spatio‐temporal model to simulate from, taking into account the correlation existing between the observed (or simulated) values in space and time. Two different simulation procedures (unconditional and conditional) are studied, and applied to obtain the simulations we are interested in. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Reaction mechanism of surfactant‐sensitized chemiluminescence of bis(2,4,6‐trichlorophyenyl) oxalate and hydrogen peroxide induced by gold nanoparticles

The chemiluminescence (CL) of bis(2,4,6‐trichlorophyenyl) oxalate with hydrogen peroxide in the present of cationic surfactant and gold nanoparticles was studied. The CL emission was obviously enhanced in the presence of surfactant at a suitable concentration, with a synergetic catalysis effect exhibited. Different sizes of gold nanoparticles (15 and 50 nm) showed different effects on CL intensity. Mechanisms of the CL reaction and sensitization effect are discussed. Copyright © 2008 John Wiley & Sons, Ltd.     

Effects of hatchling body colour and rearing density on body colouration in last-stadium nymphs of the desert locust, Schistocerca gregaria

Abstract.  The influences of hatchling character and rearing density on body colour at the last-nymphal stadium are investigated for the desert locust, Schistocerca gregaria . Hatchlings are divided into five groups based on the darkness of the body colour and reared either under isolated or crowded conditions. Two types of body colour variation at the last-nymphal stadium are separately analysed (i.e. the background colour and black patterns). Under isolated conditions, the background body colour is either greenish or brownish. Most individuals are greenish and the highest percentage of brownish insects is obtained from hatchlings with the darkest body colour. Under crowded conditions, the background colour is yellow or orange and the percentage of yellowish nymphs tends to decrease when they are darker at hatching. The intensity of black patterns differs depending on the body colour at hatching and subsequent rearing density. Most isolated-reared nymphs exhibit few or no black patterns but nymphs with some black patterns also appear, particularly among those that had been dark at hatching. Under crowded conditions, the black patterns become more intense when they are darker at hatching. Therefore, last-stadium nymphs with typical solitarious or gregarious body colouration appear when they have the phase-specific body colouration at hatching as well. The present results demonstrate that both body colour at hatching and rearing density during nymphal development influence body colouration at the last-nymphal stadium.     

Presence of haemocyte-like cells in coccinellid reflex blood

Abstract.  Contrary to current assumptions, the reflex blood of two-spot ladybirds, Adalia bipunctata , and seven-spot ladybirds, Coccinella septempunctata , contains haemocyte-like cells. Furthermore, DNA can be extracted and amplified from coccinellid reflex blood, confirming the presence of haemocyte-like cells and demonstrating a nondestructive method of DNA extraction.     

Describing Ordinal Odds Ratios for Stratified r × c Tables

For an r × ctable with ordinal responses, odds ratios are commonly used to describe the relationship between the row and column variables. This article shows two types of ordinal odds ratios where local‐global odds ratios are used to compare several groups on a c‐category ordinal response and a global odds ratio is used to measure the global association between a pair of ordinal responses. When there is a stratification factor, we consider Mantel‐Haenszel (MH) type estimators of these odds ratios to summarize the association from several strata. Like the ordinary MH estimator of the common odds ratio for several 2 × 2 contingency tables, the estimators are used when the association is not expected to vary drastically among the strata. Also, the estimators are consistent under the ordinary asymptotic framework in which the number of strata is fixed and also under sparse asymptotics in which the number of strata grows with the sample size. Compared to the maximum likelihood estimators, simulations find that the MH type estimators perform better especially when each stratum has few observations. This article provides variances and covariances formulae for the local‐global odds ratios estimators and applies the bootstrap method to obtain a standard error for the global odds ratio estimator. At the end, we discuss possible ways of testing the homogeneity assumption.     

Hidden smectic properties of a chiral side-chain co-oligomer

We recently showed that a side-chain industrial co-oligosiloxane presents a quenchable enlarged blue phase behaviour at the cholesteric-isotropic phase transition. In this paper, we present the results of a structural study based on X-ray diffraction, differential scanning calorimetry and optical measurements. In particular, the smectic A organisation is demonstrated in the lower temperature domain, which was hitherto understood as a cholesteric phase. A structural model for this phase is proposed on the basis of the analysis of the anisotropic scattering of stretched fibers. Our results also suggest that the observed glass transition is indeed a rather complex phenomenon, which seems to involve not only the freezing of the main chains, but also smectic correlations at the side-chain level. Moreover, the calorimetric study indicates that, notwithstanding the conservation of the processed film's optical properties, low kinetic reorganisations occur at room temperature.     

Direct evidence for Ca++-induced lateral phase separation in black membranes of lipid mixtures by the analysis of gramicidin A single-channels

Single-channel conductance fluctuations are analysed for gramicidin A incorporated into binary-mixed black lipid membranes of charged phosphatidic acid and neutral lecithin in different molar ratios. At very low Ca⁺⁺ concentrations in the electrolyte (i.e. in the presence of EDTA) homogeneous lipid mixtures are identified through their conductance and life time probability distributions for integral gramicidin pores. As for the pure lipid components, the conductance histograms each show a single maximum with regular width and for all channels a single mean lifetime is found.For Ca⁺⁺-levels (10^-6–10^-5 M) that are close to the critical demixing concentration (10^-4 M) unusually broad conductance distributions and reduced lifetimes are found provided the PC content, x, of the membrane is close to the critical mixture (x _crit0.5). We interpret this as a first example of the coupling of a membrane function (the transport of ions) to a lipid matrix with locally fluctuating composition close to a critical demixing point.For the conductance histogram of gramicidin A in an equimolar mixture of PA and PC shows two well-separated maxima. A correlation analysis between conductance and lifetime of the single pores shows that the two channel populations also differ significantly in their mean channel lifetime, ^*. This finding is interpreted as being direct evidence for Ca⁺⁺-induced lateral phase separation in black lipid membranes, as has been postulated recently.Abbreviations used HEPES N-2-hydroxyethyl-piperazine-N-2-ethane-sulfonic acid - EDTA ethylenediaminetetraacetic acid     

The modulating influence of the fluidity of cell membrane on excision repair of DNA in UV-irradiated Escherichia coli

When the extent of liquid holding recovery (LHR) was measured as a function of the temperature at the time of liquid holding and the Arrhenius plot was made, two distinctive phases for the LHR were demonstrated in UV-irradiated RecA- derivative of E. coli ole28E1, which are unable to synthesize and degrade unsaturated fatty acids. The inflection temperatures were 17-18 degrees C, 23-24 degrees C and 28-30 degrees C for linoleate-, oleate- and elaidate-grown cells, respectively. These temperatures well corresponded to the phase transition temperatures of the cell membrane supplemented with the fatty acid. It is therefore concluded that at least a component involved in in vivo excision repair in E. coli is associated with cell membrane.