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.     

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.     

Phylogeny and biogeography of the Vitrinidae (Gastropoda: Stylommatophora)

The phylogeny of the Vitrinidae is reconstructed in a cladistic analysis based on characters of the genitalia, the copulation behaviour and the radula. The genera with an atrial stimulator turned out to be the earliest branches of the Vitrinidae, whereas the genera with a glandula amatoria form a monophyletic, taxonomically apomorphic group. The differences between the proposed phylogeny and previous hypotheses are discussed. The ancestral areas of the Vitrinidae and its sister group, the limacoid slugs Boettgerillidae–Limacidae–Agriolimacidae, are estimated using weighted ancestral area analysis. The Vitrinidae and the limacoid slugs might have originated by a vicariance event between Central Europe and the Near East. © 2002 The Linnean Society of London. Zoological Journal of the Linnean Society , 2002, 134 , 347–358.     

Mathematical modelling of runoff and material transport from drainage areas into recipient water bodies

This paper describes a set of mathematical models to calculate runoff, soil erosion and chemical substance yields for drainage areas. The models represent different degrees of complexity and details of describing hydrological and hydrochemical processes. The availability of initial information and the requirements of the task determine the choice of a model for each particular case. These models have been written as PC/AT programs, to enable their use by a wide range of specialists. The models have been tested in different physical and geographical conditions, e.g. in some small watersheds on the Karelian Isthmus, west of Lake Ladoga, and in experimental catchment areas located in the Valdai Hills area in the southern part of Lake Ladoga drainage area. In further applications the drainage area models have been combined with models of the recipient water body, to obtain a single model of a watershed-lake system. The results of tests have proved that the models can be used for evaluation, simulation and forecasting of the processes of rainfall and snowmelt runoff, infiltration, evaporation, water erosion and pollutant wash-off from drainage areas.     

Effects of asexual reproduction on the neighborhood area of cyclical parthenogens

The habitat occupied by a subpopulation and withinwhich there is random mating is known as itsneighborhood area. Neighborhood area is dependenton dispersal rates and organisms with low rates ofdispersal are expected to have small neighborhoodareas. In the absence of evolutionary forces,neighborhood areas under sexual reproduction will beconstant in size as long as dispersal patterns do notchange. This scenario differs when reproduction is bycyclical parthenogenesis since recombination anddispersal may occur in different generations. Ingeneral, dispersal distances increase with the numberof parthenogenetic generations. We show that cyclicalparthenogenesis increases neighborhood area which,concomitantly, decreases the potential for geneticsubdivision. It is noteworthy, however, that theincrease in neighborhood area is a decreasing functionof the number of parthenogenetic generations.This mechanism may have important implications for thepopulation structure of planktonic rotifers living ina horizontally undifferentiated habitat. In suchhabitats organisms are effectively unrestricted intheir lateral movements. Because rotifers typicallyhave low dispersal rates spatial geneticdiscontinuities may develop that divide the populationinto genetically distinct subpopulations. Counteringthis tendency is the increased neighborhood areaproduced by dispersal during the parthenogeneticphase. Thus cyclical parthenogenesis in organismslike rotifers may have important and previouslyunreported effects on the population's geneticstructure.     

Habitat and distribution of perforatella rubiginosa (Gastropoda,Pulmonata) in the freshwater tidal region of the Scheldt estuary,Belgium

The amphibious land-molluse,Perforatella rubiginosa, is a common, wide-spread and characteristic inhabitant of the freshwater tidal region of the river Scheldt and its tributaries in NW Belgium. The species occupies a rather narrow zone in the uppermost intertidal area, which is characterized by large amounts of tidal drift covering the bottom, and usually by a luxuriant vegetation of tall, nitrophilous herbs, often withUrtica dioica dominant. Other characteristic molluscs of this zone areCarychium minimum, Oxyloma pfeifferi, O. sarsi, Deroceras laeve, Vitrea crystallina andZonitoides nitidus, locally alsoNesovitrea hammonis. Communication nr. 143 of the Delta Institute for Hydrobiological Research, Yerseke, The Netherlands     

Wood excavations of three species of subterranean termites

We compared the feeding excavations on wood blocks of three species of subterranean termites, Coptotermes formosanus Shiraki, Reticulitermes flavipes (Kollar), and R. virginicus (Banks). Feeding rate followed the order C. formosanus > R. flavipes > R. virginicus. Wood surface area (mm²) exposed per unit feeding was higher for C. formosanus and R. flavipes than for R. virginicus. This was caused by the tendency of C. formosanus and R. flavipes to make internally penetrating tunnels, thereby increasing surface area, whereas R. virginicus made trough- and bowl-like depressions on the outside of blocks, sometimes decreasing the size of blocks outwardly without a corresponding high increase in surface area typical with the tunnels of the other species. Consequently, wood surface area was sometimes reduced, rather than increased as a result of feeding by R. virginicus. Different patterns of wood excavation suggest that these termites have divergent roles in wood decay processes.

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Résumé Les organismes pionniers qui modifient le bois et le rendent acceptable par les insectes qui le perforent sont généralement des champignons du bois pourri. Cependant, une fois que les termites ou autres insectes perforant le bois ont pénétré, leurs galeries favorisent les bactéries fixatrices d'azote, permettent l'invasion d'autres organismes décomposeurs, et de ce fait régularisent la décomposition du bois (Ausmus, 1977). L'exposition de la surface à l'intérieur des perforations jouant un rôle très important dans le processus de pourrissement, il est souhaitable de pouvoir quantifier la surface des galeries dues à l'alimentation des termites. Une courbe type permettant de prédire l'aire de la surface perforée a été construite en perçant 109 morceaux de bois de trous cylindriques de différents diamètres, en calculant l'aire de la surface des morceaux de bois, en appliquant et pesant une couche de vernis pour bois au polyuréthane, et en divisant la masse de polyuréthane par l'aire de la surface. Le modèle prédictif qui en découle est: Y=0,01443×-3,51825 (P=0,0001; r=0,68), y étant la masse de polyuréthane (en g) et x la surface (en mm²) du morceau de bois. En traitant de la même façon au polyuréthane les morceaux de bois perforés par les termites, nous pourrions déduire leur surface.Une expérience a été effectuée avec 3 espèces de rhinotermitides,- Coptotermes formosanus Shiraki, Reticulitermes flavipes (Kollar) et R. virginicus (Banks). Des groupes de chaque espèce se sont alimentés pendant 11 ou 12 jours sur des morceaux de bois non contaminés par des champignons. Nous avons déterminé la survie, la consommation, la modification de la surface du morceau de bois (par utilisation du modèle prédictif) et le changement de surface par terminte.La survie est la même, mais la consommation est dans l'ordre suivant: C. formosanus > R. flavipes > R. virginicus. L'aire de la surface exposée par unité d'alimentation était plus élevée pour C. formosanus et R. flavipes que pour R. virginicus (Tab. 1). Ceci est dû à la tendance de C. formosanus et R. flavipes de creuser des galeries vers l'intérieur, tandis que R. virginicus fait des cuvettes à la surface du bois. Les attaques superficielles de R. virginicus réduisent parfois le volume du morceau de bois sans accroître proportionnellement la surface comme le font les espèces creusant des galeries. Ainsi, avec R. virginicus la surface peut être réduite au lieu d'augmenter. Des différences entre colonies s'observent avec toutes les variables (Tab. 2).Nos résultats suggèrent que C. formosanus et R. flavipes contribuent plus que R. virginicus à exposer le bois aux autres organismes décomposeurs. Cependant, ces résultats peuvent être modifiés par un conditionnement préalable du bois par des champignons.