231 research outputs found
A Common Platform for Graphical Models in R: The gRbase Package
No full textThe gRbase package is intended to set the framework for computer packages for data analysis using graphical models. The gRbase package is developed for the open source language, R, and is available for several platforms. The package is intended to be widely extendible and flexible so that package developers may implement further types of graphical models using the available methods. The gRbase package consists of a set of S version 3 classes and associated methods for representing data and models. The package is linked to the dynamicGraph package (Badsberg 2005), an interactive graphical user interface for manipulating graphs. In this paper, we show how these building blocks can be combined and integrated with inference engines in the special cases of hierarchical loglinear models. We also illustrate how to extend the package to deal with other types of graphical models, in this case the graphical Gaussian models.
Package giRaph for graph representation in R
No full textThis paper presents the giRaph package for R, providing formal classes and methods to handle a broad family of graphs, including graphs with loops, multiple edges and hyperedges (i.e. edges involving more than two vertices) both directed and undirected. Since there is no unique way to represent a graph that is optimal for all computations, four different representations are considered: incidence list, incidence matrix, adjacency list and adjacency matrix. Simple methods to set and retrieve information using these representationsare made available
Gorst-Rasmussen et al. Respond to "Dietary Pattern Analysis"
No full textWe thank Imamura and Jacques (1) for their insightful commentary on our article (2), in which they go beyond the treelet transform (TT) to critically discuss the relevance of sparsity in dietary pattern analysis. ... (1) Imamura F, Jacques PF. Invited commentary: dietary pattern analysis. Am J Epidemiol 2011;173(0):000-000. (2) Gorst-Rasmussen A, Dahm CC, Dethlefsen C, et al. Exploring dietary patterns by using the treelet transform. Am J Epidemiol 2011;173(0):000-000
deal: A Package for Learning Bayesian Networks
No full textdeal is a software package for use with R. It includes several methods for analysing data using Bayesian networks with variables of discrete and/or continuous types but restricted to conditionally Gaussian networks. Construction of priors for network parameters is supported and their parameters can be learned from data using conjugate updating. The network score is used as a metric to learn the structure of the network and forms the basis of a heuristic search strategy. deal has an interface to Hugin.
Phantom study for comparison between computed tomography- and C-Arm computed tomography-guided puncture applied by residents in radiology
No full textPurpose Comparison of puncture deviation and puncture duration between computed tomography (CT)- and C-arm CT (CACT)-guided puncture performed by residents in training (RiT). Methods In a cohort of 25 RiTs enrolled in a research training program either CT- or CACT-guided puncture was performed on a phantom. Prior to the experiments, the RiT’s level of training, experience playing a musical instrument, video games, and ball sports, and self-assessed manual skills and spatial skills were recorded. Each RiT performed two punctures. The first puncture was performed with a transaxial or single angulated needle path and the second with a single or double angulated needle path. Puncture deviation and puncture duration were compared between the procedures and were correlated with the self-assessments. Results RiTs in both the CT guidance and CACT guidance groups did not differ with respect to radiologic experience (p = 1), angiographic experience (p = 0.415), and number of ultrasound-guided puncture procedures (p = 0.483), CT-guided puncture procedures (p = 0.934), and CACT-guided puncture procedures (p = 0.466). The puncture duration was significantly longer with CT guidance (without navigation tool) than with CACT guidance with navigation software (p < 0.001). There was no significant difference in the puncture duration between the first and second puncture using CT guidance (p = 0.719). However, in the case of CACT, the second puncture was significantly faster (p = 0.006). Puncture deviations were not different between CT-guided and CACT-guided puncture (p = 0.337) and between the first and second puncture of CT-guided and CACT-guided puncture (CT: p = 0.130; CACT: p = 0.391). The self-assessment of manual skills did not correlate with puncture deviation (p = 0.059) and puncture duration (p = 0.158). The self-assessed spatial skills correlated positively with puncture deviation (p = 0.011) but not with puncture duration (p = 0.541). Conclusion The RiTs achieved a puncture deviation that was clinically adequate with respect to their level of training and did not differ between CT-guided and CACT-guided puncture. The puncture duration was shorter when using CACT. CACT guidance with navigation software support has a potentially steeper learning curve. Spatial skills might accelerate the learning of image-guided puncture. Key Points: Citation FormatZiel Vergleich der Punktionsabweichung und -dauer zwischen Computertomografie (CT) – und C-Arm-CT (CACT) -gesteuertem Punktionsverfahren bei Anwendung durch Assistenzärzte in Weiterbildung (AiW). Material und Methode In einer Kohorte von 25 AiW, die Teil einer wissenschaftlichen Förderung waren, wurden entweder CT- oder CACT-gesteuerte Punktionen an einem Phantom durchgeführt. Vor Beginn wurden der Weiterbildungsstand, die Erfahrung mit Spielen eines Musikinstruments, mit Videospielen und mit Ballsportarten und die Selbsteinschätzung von manueller Geschicklichkeit und räumlichem Denkvermögen abgefragt. Jede/r AiW führte 2 Punktionen durch, wobei die 1. Punktion mit einem transaxialen bzw. einfach angulierten Nadelpfad und die 2. Punktion mit einem einfach bzw. doppelt angulierten Nadelpfad erfolgte. Punktionsabweichung und -dauer wurden zwischen den Verfahren verglichen und mit den Selbsteinschätzungen korreliert. Ergebnisse Die beiden Gruppen der AiW zeigten keine Unterschiede in der Erfahrung in der Radiologie (p = 1), in der Angiografie (p = 0.415) und in der Anzahl bereits durchgeführter Punktionen gesteuert durch Ultraschall (p = 0,483), CT (p = 0,934) und CACT (p = 0,466). In der CT (ohne Navigationssoftware) war die Punktionsdauer signifikant länger als mit der CACT-Bildsteuerung mit Navigationssoftware (p < 0,001). Bei der Punktionsdauer zeigten sich keine signifikanten Unterschiede zwischen der 1. und 2. Punktion im CT (p = 0,719), während die 2. Punktion mit CACT schneller durchgeführt werden konnte (p = 0,006). Die Punktionsabweichung war weder signifikant zwischen CT- und CACT-Bildsteuerung (p = 0,337), noch zwischen der 1. und 2. Punktion der jeweiligen Verfahren (CT: p = 0,130; CACT: p = 0,391). Die Selbsteinschätzung der manuellen Geschicklichkeit korrelierte nicht mit der Punktionsabweichung (p = 0,059) und -dauer (p = 0,158). Das subjektive räumliche Denkvermögen zeigte eine moderate positive Korrelation zur Punktionsabweichung (p = 0,011), aber nicht zur -dauer (p = 0,541). Schlussfolgerung Die AiW erreichten eine dem Ausbildungsstand entsprechende, klinisch adäquate Punktionsabweichung unter CT- und CACT-Bildsteuerung. Die CACT-gesteuerten Punktionen mit Unterstützung durch Navigationssoftware wurden schneller durchgeführt, und auch die Lernkurve war mit CACT-Bildsteuerung steiler. Räumliches Denkvermögen kann möglicherweise das Erlernen bildgesteuerter Punktionen beschleunigen. Kernaussagen: ZitierweisePurpose Comparison of puncture deviation and puncture duration between computed tomography (CT)- and C-arm CT (CACT)-guided puncture performed by residents in training (RiT). Methods In a cohort of 25 RiTs enrolled in a research training program either CT- or CACT-guided puncture was performed on a phantom. Prior to the experiments, the RiT’s level of training, experience playing a musical instrument, video games, and ball sports, and self-assessed manual skills and spatial skills were recorded. Each RiT performed two punctures. The first puncture was performed with a transaxial or single angulated needle path and the second with a single or double angulated needle path. Puncture deviation and puncture duration were compared between the procedures and were correlated with the self-assessments. Results RiTs in both the CT guidance and CACT guidance groups did not differ with respect to radiologic experience (p = 1), angiographic experience (p = 0.415), and number of ultrasound-guided puncture procedures (p = 0.483), CT-guided puncture procedures (p = 0.934), and CACT-guided puncture procedures (p = 0.466). The puncture duration was significantly longer with CT guidance (without navigation tool) than with CACT guidance with navigation software (p < 0.001). There was no significant difference in the puncture duration between the first and second puncture using CT guidance (p = 0.719). However, in the case of CACT, the second puncture was significantly faster (p = 0.006). Puncture deviations were not different between CT-guided and CACT-guided puncture (p = 0.337) and between the first and second puncture of CT-guided and CACT-guided puncture (CT: p = 0.130; CACT: p = 0.391). The self-assessment of manual skills did not correlate with puncture deviation (p = 0.059) and puncture duration (p = 0.158). The self-assessed spatial skills correlated positively with puncture deviation (p = 0.011) but not with puncture duration (p = 0.541). Conclusion The RiTs achieved a puncture deviation that was clinically adequate with respect to their level of training and did not differ between CT-guided and CACT-guided puncture. The puncture duration was shorter when using CACT. CACT guidance with navigation software support has a potentially steeper learning curve. Spatial skills might accelerate the learning of image-guided puncture. Key Points: Citation FormatZiel Vergleich der Punktionsabweichung und -dauer zwischen Computertomografie (CT) – und C-Arm-CT (CACT) -gesteuertem Punktionsverfahren bei Anwendung durch Assistenzärzte in Weiterbildung (AiW). Material und Methode In einer Kohorte von 25 AiW, die Teil einer wissenschaftlichen Förderung waren, wurden entweder CT- oder CACT-gesteuerte Punktionen an einem Phantom durchgeführt. Vor Beginn wurden der Weiterbildungsstand, die Erfahrung mit Spielen eines Musikinstruments, mit Videospielen und mit Ballsportarten und die Selbsteinschätzung von manueller Geschicklichkeit und räumlichem Denkvermögen abgefragt. Jede/r AiW führte 2 Punktionen durch, wobei die 1. Punktion mit einem transaxialen bzw. einfach angulierten Nadelpfad und die 2. Punktion mit einem einfach bzw. doppelt angulierten Nadelpfad erfolgte. Punktionsabweichung und -dauer wurden zwischen den Verfahren verglichen und mit den Selbsteinschätzungen korreliert. Ergebnisse Die beiden Gruppen der AiW zeigten keine Unterschiede in der Erfahrung in der Radiologie (p = 1), in der Angiografie (p = 0.415) und in der Anzahl bereits durchgeführter Punktionen gesteuert durch Ultraschall (p = 0,483), CT (p = 0,934) und CACT (p = 0,466). In der CT (ohne Navigationssoftware) war die Punktionsdauer signifikant länger als mit der CACT-Bildsteuerung mit Navigationssoftware (p < 0,001). Bei der Punktionsdauer zeigten sich keine signifikanten Unterschiede zwischen der 1. und 2. Punktion im CT (p = 0,719), während die 2. Punktion mit CACT schneller durchgeführt werden konnte (p = 0,006). Die Punktionsabweichung war weder signifikant zwischen CT- und CACT-Bildsteuerung (p = 0,337), noch zwischen der 1. und 2. Punktion der jeweiligen Verfahren (CT: p = 0,130; CACT: p = 0,391). Die Selbsteinschätzung der manuellen Geschicklichkeit korrelierte nicht mit der Punktionsabweichung (p = 0,059) und -dauer (p = 0,158). Das subjektive räumliche Denkvermögen zeigte eine moderate positive Korrelation zur Punktionsabweichung (p = 0,011), aber nicht zur -dauer (p = 0,541). Schlussfolgerung Die AiW erreichten eine dem Ausbildungsstand entsprechende, klinisch adäquate Punktionsabweichung unter CT- und CACT-Bildsteuerung. Die CACT-gesteuerten Punktionen mit Unterstützung durch Navigationssoftware wurden schneller durchgeführt, und auch die Lernkurve war mit CACT-Bildsteuerung steiler. Räumliches Denkvermögen kann möglicherweise das Erlernen bildgesteuerter Punktionen beschleunigen. Kernaussagen: Zitierweis
Mytilicola intestinalis, parasitism
No full textMytilicola intestinalis primarily affects the marine mussels Mytilus edulis and M. gall provincialis. M. intestinalis has also been shown to affect Ostrea edulis and Crassostrea gigas in both field and laboratory studies (Baird, R.H. et al., 1951; Dare, 1982; Aguirre Macedo, M. L., and Kennedy, C. R. 1999).
Revision and update of the original leaflet by V. Dethlefsen, 1985.</p
A review of Nearctic and some related Anthribidae (Coleoptera)
No full textTaxonomy, synonymy, distribution, and biologies of Nearctic (and a few Neotropical and Pale arctic) Anthribidae are reviewed, new keys are provided, and four new genera and eleven new species are described. Allandrus Leconte, 1876 (=Tropiderinus Reitter, 1916). Anthribus Geoffrey, 1762 (=Pseudobrachytarsus Pierce, 1930). Araecerus Schoenherr, 1823 (=Araeocorynus Jekel, 1855); Araecerus coffeae Fabricius, 1801 (=Tropideres (Rhaphitropis) mateui Cobos, 1954). Brachycorynus n. gen., type species Tropideres rectus Leconte, 1876; congeneric: Homocloeus distentus Frieser, 1983 from Cuba and Florida, and B. hirsutus n. sp. from Texas. Choragus major n. sp., Ohio, etc., striolatus n. sp., Ohio, and exophthalmus n. sp., Virginia. Corrhecerus Schoenherr, 1826 (=Paranthribus Jordan, 1904) resulting in Corrhecerus rufescens (Jordan, 1904), new combination. Eurymycter Leconte, 1876, and Gonotropis Leconte, 1876, are removed from synonymy with Tropideres Schoenherr, 1823, and returned to full generic rank. Eusphyrus Leconte, 1876 is removed from synonymy with Ormiscus Waterhouse, 1845, and returned to full generic rank; Tropideres (Opisthotropis) vasconicus Hoffmann and Tempere, 1954, from France is transferred to Eusphyrus, with Opisthotropis a generic synonym; Eusphyrus pulicarius Boheman, 1859, Brasil, is transferred from Brachytarsus, and the species eusphyroides Schaeffer and quercus Schaeffer are transferred from Ormiscus. Gymnognathus triangularis n. sp., Texas. Habroxenus n. gen., type species H. politus n. sp., Texas and Maryland, also H. fuscus n. sp., Guatemala, and H. sarmenticola n. sp., Haiti. Neoxenus n. gen., type species N. versicolor n. sp., Texas, etc.; congeneric: Notioxenus ater and polius Jordan, 1907, Central America, andpallipes Suffrian, 1870, Cuba. Phoenicobiella trituberculata (Suffrian, 1870, Cuba) transferred from Toxonotus Lacordaire, 1866. Piesocorynus lateralis Jordan, 1906 (=P. virginicus Leng, 1918). Sicanthus n. gen., type species S. rhizophorae n. sp., Florida. Toxonotus bipunctatus Schaeffer, 1904 (=Neanthribus obtusus Jordan, 1906); Toxonotus penicellatus Schaeffer, 1906 (=Neanthribus segregus Jordan, 1906); Toxonotus vagus Horn, 1894 (=Neanthribus hieronymus Jordan, 1906). Trigonorhinus lepidus n. sp., California; Trigonorhinus limbatus Say, 1827 (=Brachytarsus plumbeus and B. vestitus Leconte, 1876, and Brachytarsoides minor, quadratus, quadratus ssp. nigrinus and rufodorsalis Dethlefsen, 1954); Trigonorhinus grise us Leconte, 1876 (=Brachytarsus riddelliae Schaeffer, 1906, and Brachytarsoides cylindratus, elongatus, nevadensis, nevadensis ssp. tigrinus, and vulgaris Dethlefsen, 1954); Trigonorhinus tomentosus Say, 1827 (=Brachytarsus paululus Casey, 1884, B. beyeri Schaeffer, 1906, B. franseria Barrett, 1931, and B. irregularis Tanner, 1934); Trigonorhinus zeae Wolfrum, 1931 (=Opanthribus trimaculatus Senoh, 1986); Trigonorhinus areolatus Boheman, 1845 (=Tropideres (Tropideres), bagueni Cobos, 1954, Spain). Introgressive hybridization is invoked for the Trigonorhinus limbatus-griseus complex. New keys are provided for the species of Brachycorynus, Choragus, Habroxenus, Neoxenus, Phoenicobiella, Trigonorhinus, and Eusphyrus, plus a new key to Nearctic tribes and genera, and a new Nearctic checklist. New distribution and life-history data are given for many species
Inverse analysis in non-parametric multivariate analyses: distinguishing groups of associated species which covary coherently across samples
No full textFor decades multivariate analysis has been recognised as being appropriate for the analysis and description of complex ecological datasets, such as are routinely generated in studies of biota along gradients in time or space. The main focus of analyses tends to be the description and analysis of patterns among samples and groups of samples. Early applications of multivariate analyses to ecological data also recognised the importance of, and gave equal weight to, understanding how variables (species or taxa, in biotic datasets) varied among samples and groups of samples, but such analyses have inherent difficulties. Among these are the facts that species do not vary independently of each other, that responses of species to gradients may not be monotonic, that there are generally many more species than samples, that abundances vary widely within and among species, and that some species are rare. Although some methods are routinely applied to explore species responses across and among samples to environmental gradients, few explicitly recognise that species do not vary independently. Within a very widely-used framework for the nonparametric multivariate analysis of ecological data we demonstrate how Similarity Profiles (SIMPROF) analysis and other approaches may be combined to analyse associations among species and to visualise those relationships. Type 2 SIMPROF determines whether observed associations could have arisen by chance. Type 3 SIMPROF detects statistically distinct subsets of species which respond to gradients in a coherent manner. How different groups respond is visualised using component line plots (coherent curves). We illustrate the method using a range of datasets. We show how the method discriminates groups of species which respond differently to a single gradient, or respond coherently to different environmental or anthropogenic pressure gradients. We demonstrate how these approaches extend naturally to analyses of other types of multivariate data where the identification of coherent groups of variables is of interest
Principal Coordinates Analysis of unweighted UniFrac distances for 16S rDNA V1–V3 sequence data.
No full text<p>Beta diversity patterns were explored using Principal Coordinates Analysis (PCoA). Samples were rarefied to 6,596 reads/sample for <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053838#pone-0053838-g002" target="_blank">Figs. 2A and 2C</a> and rarefied to 427 reads/sample for 2B due to the smaller number of available reads per U.S. adult. The near full-length 16S rDNA data were not included in this analysis. (A) The sample symbols for Bangladeshi and U.S. children are colored by country. Only the data from the children (with the exception of BK8F and BK9F) were included in this PCoA plot. (B) Nine U.S. adults were included in this analysis (one time point per adult). The fecal communities for all three subjects (Subjects A, B, and C) in the Eckburg <i>et al.</i> study (near full-length 16S rDNA sequences) and all 6 subjects (Subjects A, B, C, D, E, F) in the Dethlefsen <i>et al.</i> studies (V1–V3 16S rDNA sequences) were included in the analysis <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053838#pone.0053838-Dethlefsen1" target="_blank">[11]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053838#pone.0053838-Eckburg1" target="_blank">[25]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053838#pone.0053838-Dethlefsen2" target="_blank">[26]</a>. The near full-length 16S rDNA sequences were filtered <i>in silico</i> to the V1–V3 regions using ARB. Data from all of the children were included in this analysis. (C) Same as (A) but with each sample symbol colored-coded by subject.</p
- …
