Evidence of cryptic and pseudocryptic speciation in the Paracalanus parvus species complex (Crustacea, Copepoda, Calanoida), supplementary material

Introduction Many marine planktonic crustaceans such as copepods have been considered as widespread organisms. However, the growing evidence for cryptic and pseudo-cryptic speciation has emphasized the need of re-evaluating the status of copepod species complexes in molecular and morphological studies to get a clearer picture about pelagic marine species as evolutionary units and their distributions. This study analyses the molecular diversity of the ecologically important Paracalanus parvus species complex. Its seven currently recognized species are abundant and also often dominant in marine coastal regions worldwide from temperate to tropical oceans. Results COI and Cytochrome b sequences of 160 specimens of the Paracalanus parvus complex from all oceans were obtained. Furthermore, 42 COI sequences from GenBank were added for the genetic analyses. Thirteen distinct molecular operational taxonomic units (MOTU) and two single sequences were revealed with cladistic analyses (Maximum Likelihood, Bayesian Inference), of which seven were identical with results from species delimitation methods (barcode gaps, ABDG, GMYC, Rosenberg's P(AB)). In total, 10 to 12 putative species were detected and could be placed in three categories: (1) temperate geographically isolated, (2) warm-temperate to tropical wider spread and (3) circumglobal warm-water species. Conclusions The present study provides evidence of cryptic or pseudocryptic speciation in the Paracalanus parvus complex. One major insight is that the species Paracalanus parvus s.s. is not panmictic, but may be restricted in its distribution to the northeastern Atlantic.

Comparisons of observed ice properties and Envisat Advanced Synthetic Aperture Radar (ASAR) data during Nathanial B. Palmer cruise NBP09-01 and Oden cruise OSO08/09

Envisat Advanced Synthetic Aperture Radar (ASAR) Wide Swath Mode (WSM) images are used to derive C-band HH-polarization normalized radar cross sections (NRCS). These are compared with ice-core analysis and visual ship-based observations of snow and ice properties observed according to the Antarctic Sea Ice Processes and Climate (ASPeCt) protocol during two International Polar Year summer cruises (Oden 2008 and Palmer 2009) in West Antarctica. Thick first-year (TFY) and multi-year (MY) ice were the dominant ice types. The NRCS value ranges between -16.3 ± 1.1 and -7.6 ± 1.0 dB for TFY ice, and is -12.6 ± 1.3 dB for MY ice; for TFY ice, NRCS values increase from ~-15 dB to -9 dB from December/January to mid-February. In situ and ASPeCt observations are not, however, detailed enough to interpret the observed NRCS change over time. Co-located Advanced Microwave Scanning Radiometer-Earth Observing System (AMSR-E) vertically polarized 37 GHz brightness temperatures (TB37V), 7 day and 1 day averages as well as the TB37V difference between ascending and descending AMSR-E overpasses suggest the low NRCS values (-15 dB) are associated with snowmelt being still in progress, while the change towards higher NRCS values (-9dB) is caused by commencement of melt-refreeze cycles after about mid-January.

Análisis del comportamiento en servicio de los puentes de fábrica ante las nuevas condiciones de explotación

Los puentes arco de fábrica representan una parte importante del inventario de puentes en España y en Europa. De aquí, la importancia cuantitativa de estas estructuras y el interés que representa tanto para las Administraciones, organismos públicos y privados como para la sociedad en general, mantener estos puentes en servicio. Para poder alargar su vida útil, aún más si cabe, se plantea imprescindible llevar a cabo una labor de conservación y mantenimiento adecuada. La importancia de la evaluación estructural de los puentes de fábrica se basa en la conveniencia de conocer el comportamiento estructural tanto en condiciones de servicio como en agotamiento. El comportamiento en Estado Límite Último ha sido estudiado en profundidad y como resultado, la seguridad frente a agotamiento ha quedado definida con cierta confianza. Sin embargo, el comportamiento en Estado Límite de Servicio no es tan conocido. Se considera necesaria una revisión del concepto de ELS en puentes arco de fábrica puesto que muchos de ellos, cumpliendo las comprobaciones establecidas para ELU, presentan daños asociados a las actuales condiciones de explotación existentes actuales. El presente trabajo se enmarca dentro de un proyecto que está llevando a cabo la UIC (Union Internationale de Chemins de Fer) desde 2004. El objetivo general del mismo es conocer el comportamiento de los puentes arco de fábrica y mejorar los métodos de evaluación, mantenimiento y reparación existentes. Con este estudio, se pretende contribuir a mejorar la caracterización del comportamiento en servicio de estas estructuras. Para ello se ha realizado un análisis del estado tensional de la bóveda y el relleno estudiando la influencia de la configuración geométrica de los puentes y las propiedades de los materiales que los componen. Entender el funcionamiento de estas estructuras y conocer sus peculiares características ha sido el paso previo al desarrollo del estudio. Para ello, se ha acudido al minucioso trabajo desarrollado por diversos autores, desde los primeros análisis mediante la línea de presiones hasta los actuales métodos basados en elementos finitos. En primer lugar, se ha realizado un estudio paramétrico de diferentes configuraciones geométricas. El objetivo es comprobar la influencia de las dimensiones absolutas y las relaciones existentes entre las mismas en el comportamiento en servicio de los puentes. A continuación, se ha estudiado la influencia de las propiedades mecánicas de los rellenos rígido y granular (modificando su módulo de deformabilidad) en el estado tensional de la bóveda y el propio relleno. Para las dos etapas anteriores se emplea un modelo simplificado de puente arco de fábrica. A continuación, se crea un modelo más completo del mismo, para estudiar la influencia de las propiedades mecánicas del substrato de cimentación en el comportamiento estructural en servicio de la estructura. El objetivo final de este trabajo fin de máster, es conocer el comportamiento en servicio de los puentes arco de fábrica, para poder establecer las variables que condicionan el mismo. El siguiente paso en este campo de estudio, consiste en fijar unos valores límite para las mismas. Como síntesis de las conclusiones obtenidas, se menciona que el comportamiento estructural de los puente arco de fábrica, en mayor o menor medida, está influenciado por su geometría y las propiedades de los rellenos y substrato de cimentación que forman parte del mismo. Masonry arch bridges represent an important part of the total bridges, both in Spain and Europe. For this reason, these structures are so important in terms of quantity. They play an essential role for public administration and people in general. In order to remain those bridges serviceable, suitable inspections and repairs are required. It is necessary to have knowledge of the bridge condition so that an assessment can be made with confidence. It is therefore necessary to check that bridges behave properly under Ultimate Limit State criterion and Serviceability Limit State criterion. ULS has been studied thoroughly and as result, requirements under collapse are well described. However, structural behaviour under conditions of serviceability is not well evaluated. Serviceability Limit State criterion should be redefined for masonry arch bridges assessment. This is because many bridges that fulfil SLS criterion have damages. The purpose of this work is to take part in the improvement of assessment under serviceability. A vault and fill structural behaviour analysis has been performed from two points of view: geometry of the bridge and materials’ properties. The starting point was learning about masonry arch bridges behaviour and their special features. For this task, a revision of several authors’ thorough study has been made, from the line of thrust analysis to the current finite element analysis. Firstly, a parametric study of typologies of bridge has been made. The aim is to know how vault and fill behaviour changes modifying both absolute dimensions and relation between them. In the next step, a study of both surface fill and backfill properties has been done. The aim is to know how vault and fill behaviour changes modifying Young’s modulus. The principal conclusion achieved along this work is that the structural behaviour of masonry bridges depends of the bridge geometry and its material properties.

Efficient random variable generation: ratio of uniforms and polar rejection sampling

Monte Carlo techniques, which require the generation of samples from some target density, are often the only alternative for performing Bayesian inference. Two classic sampling techniques to draw independent samples are the ratio of uniforms (RoU) and rejection sampling (RS). An efficient sampling algorithm is proposed combining the RoU and polar RS (i.e. RS inside a sector of a circle using polar coordinates). Its efficiency is shown in drawing samples from truncated Cauchy and Gaussian random variables, which have many important applications in signal processing and communications. RESUMEN. Método eficiente para generar algunas variables aleatorias de uso común en procesado de señal y comunicaciones (por ejemplo, Gaussianas o Cauchy truncadas) mediante la combinación de dos técnicas: "ratio of uniforms" y "rejection sampling".

Probabilistic reasoning with an enzyme-driven DNA device

We present a biomolecular probabilistic model driven by the action of a DNA toolbox made of a set of DNA templates and enzymes that is able to perform Bayesian inference. The model will take single-stranded DNA as input data, representing the presence or absence of a specific molecular signal (the evidence). The program logic uses different DNA templates and their relative concentration ratios to encode the prior probability of a disease and the conditional probability of a signal given the disease. When the input and program molecules interact, an enzyme-driven cascade of reactions (DNA polymerase extension, nicking and degradation) is triggered, producing a different pair of single-stranded DNA species. Once the system reaches equilibrium, the ratio between the output species will represent the application of Bayes? law: the conditional probability of the disease given the signal. In other words, a qualitative diagnosis plus a quantitative degree of belief in that diagno- sis. Thanks to the inherent amplification capability of this DNA toolbox, the resulting system will be able to to scale up (with longer cascades and thus more input signals) a Bayesian biosensor that we designed previously.

Low-Cost Radar-Based Target Identification Prototype using an Expert System

Smart and green cities are hot topics in current research because people are becoming more conscious about their impact on the environment and the sustainability of their cities as the population increases. Many researchers are searching for mechanisms that can reduce power consumption and pollution in the city environment. This paper addresses the issue of public lighting and how it can be improved in order to achieve a more energy efficient city. This work is focused on making the process of turning the streetlights on and off more intelligent so that they consume less power and cause less light pollution. The proposed solution is comprised of a radar device and an expert system implemented on a low-cost platform based on a DSP. By analyzing the radar echo in both the frequency and time domains, the system is able to detect and identify objects moving in front of it. This information is used to decide whether or not the streetlight should be turned on. Experimental results show that the proposed system can provide hit rates over 80%, promising a good performance. In addition, the proposed solution could be useful in kind of other applications such as intelligent security and surveillance systems and home automation.

Inputs to directionally selective simple cells in macaque striate cortex

It is clear that the initial analysis of visual motion takes place in the striate cortex, where directionally selective cells are found that respond to local motion in one direction but not in the opposite direction. Widely accepted motion models postulate as inputs to directional units two or more cells whose spatio-temporal receptive fields (RFs) are approximately 90° out of phase (quadrature) in space and in time. Simple cells in macaque striate cortex differ in their spatial phases, but evidence is lacking for the varying time delays required for two inputs to be in temporal quadrature. We examined the space-time RF structure of cells in macaque striate cortex and found two subpopulations of (nondirectional) simple cells, some that show strongly biphasic temporal responses, and others that are weakly biphasic if at all. The temporal impulse responses of these two classes of cells are very close to 90° apart, with the strongly biphasic cells having a shorter latency than the weakly biphasic cells. A principal component analysis of the spatio-temporal RFs of directionally selective simple cells shows that their RFs could be produced by a linear combination of two components; these two components correspond closely in their respective latencies and biphasic characters to those of strongly biphasic and weakly biphasic nondirectional simple cells, respectively. This finding suggests that the motion system might acquire the requisite temporal quadrature by combining inputs from these two classes of nondirectional cells (or from their respective lateral geniculate inputs, which appear to be from magno and parvo lateral geniculate cells, respectively).

Calculating the probability of multitaxon evolutionary trees: bootstrappers Gambit.

The reconstruction of multitaxon trees from molecular sequences is confounded by the variety of algorithms and criteria used to evaluate trees, making it difficult to compare the results of different analyses. A global method of multitaxon phylogenetic reconstruction described here, Bootstrappers Gambit, can be used with any four-taxon algorithm, including distance, maximum likelihood, and parsimony methods. It incorporates a Bayesian-Jeffreys'-bootstrap analysis to provide a uniform probability-based criterion for comparing the results from diverse algorithms. To examine the usefulness of the method, the origin of the eukaryotes has been investigated by the analysis of ribosomal small subunit RNA sequences. Three common algorithms (paralinear distances, Jukes-Cantor distances, and Kimura distances) support the eocyte topology, whereas one (maximum parsimony) supports the archaebacterial topology, suggesting that the eocyte prokaryotes are the closest prokaryotic relatives of the eukaryotes.

High resolution spectroscopic characterization of the FGK stars in the Solar neighborhood

We present the most recent results of our ongoing long-term high resolution spectroscopic study of nearby (d ≤ 25 pc) FGK stars which aim is to characterize the local properties of the Galaxy, in particular the star-formation history. A through analysis has been carried out for 253 cool stars in the solar neighborhood. This includes radial and rotational velocities determinations, chromospheric activity levels inference, kinematic analysis, and age estimates. This study does not only shed new light on the issue of stellar formation history but also contributes to any present or future mission aiming to detect extra-solar planets. Exo-planets are likely to be found orbiting around nearby cool stars and their detection and characterization is highly dependent on the precise determination of fundamental stellar parameters such as age, activity levels. Therefore, our study is of paramount importance to ensure the success of any such mission.

Estimação do índice de memória em processos estocásticos com memória longa: uma abordagem via ABC

Neste trabalho propomos o uso de um método Bayesiano para estimar o parâmetro de memória de um processo estocástico com memória longa quando sua função de verossimilhança é intratável ou não está disponível. Esta abordagem fornece uma aproximação para a distribuição a posteriori sobre a memória e outros parâmetros e é baseada numa aplicação simples do método conhecido como computação Bayesiana aproximada (ABC). Alguns estimadores populares para o parâmetro de memória serão revisados e comparados com esta abordagem. O emprego de nossa proposta viabiliza a solução de problemas complexos sob o ponto de vista Bayesiano e, embora aproximativa, possui um desempenho muito satisfatório quando comparada com métodos clássicos.

Image processing for safety assessment in Civil Engineering

Behaviour analysis of construction safety systems is of fundamental importance to avoid accidental injuries. Traditionally, measurements of dynamic actions in Civil Engineering have been done through accelerometers, but high-speed cameras and image processing techniques can play an important role in this area. Here, we propose using morphological image filtering and Hough transform on high-speed video sequence as tools for dynamic measurements on that field. The presented method is applied to obtain the trajectory and acceleration of a cylindrical ballast falling from a building and trapped by a thread net. Results show that safety recommendations given in construction codes can be potentially dangerous for workers.

Viajes, actuantes, escenarios e interacciones: un análisis de la publicidad turística de los destinos, a partir de sus semánticas visuales

El presente artículo se organiza a partir de un análisis de las semánticas visuales del turismo y la manera en que éstas contribuyen a la construcción de sentido en la comunicación turística. Para ello se aborda el tema desde la perspectiva de la teoría de sistemas de Niklas Luhmann, y particularmente desde el sistema de los medios masivos de comunicación. El análisis pone énfasis en el uso sistemático de esquematismos y las representaciones de interacciones sociales en la publicidad y como éstas se relacionan con la creación de expectativas a partir de sus representaciones en los medios masivos de comunicación. Por lo tanto se analiza la correspondencia de los significados y significantes en la creación de sentido a partir de los elementos que componen dichas representaciones del viaje o destino y que dotan de sentido a la comunicación turística.

Phylogeny and biogeography of the freshwater crayfish Euastacus (Decapoda : Parastacidae) based on nuclear and mitochondrial DNA

Euastacus crayfish are endemic to freshwater ecosystems of the eastern coast of Australia. While recent evolutionary studies have focused on a few of these species, here we provide a comprehensive phylogenetic estimate of relationships among the species within the genus. We sequenced three mitochondrial gene regions (COI, 16S, and 12S) and one nuclear region (28S) from 40 species of the genus Euastacus, as well as one undescribed species. Using these data, we estimated the phylogenetic relationships within the genus using maximum-likelihood, parsimony, and Bayesian Markov Chain Monte Carlo analyses. Using Bayes factors to test different model hypotheses, we found that the best phylogeny supports monophyletic groupings of all but two recognized species and suggests a widespread ancestor that diverged by vicariance. We also show that Eitastacus and Astacopsis are most likely monophyletic sister genera. We use the resulting phylogeny as a framework to test biogeographic hypotheses relating to the diversification of the genus. (c) 2005 Elsevier Inc. All rights reserved.

Searching for convergence in phylogenetic Markov chain Monte Carlo

Markov chain Monte Carlo (MCMC) is a methodology that is gaining widespread use in the phylogenetics community and is central to phylogenetic software packages such as MrBayes. An important issue for users of MCMC methods is how to select appropriate values for adjustable parameters such as the length of the Markov chain or chains, the sampling density, the proposal mechanism, and, if Metropolis-coupled MCMC is being used, the number of heated chains and their temperatures. Although some parameter settings have been examined in detail in the literature, others are frequently chosen with more regard to computational time or personal experience with other data sets. Such choices may lead to inadequate sampling of tree space or an inefficient use of computational resources. We performed a detailed study of convergence and mixing for 70 randomly selected, putatively orthologous protein sets with different sizes and taxonomic compositions. Replicated runs from multiple random starting points permit a more rigorous assessment of convergence, and we developed two novel statistics, delta and epsilon, for this purpose. Although likelihood values invariably stabilized quickly, adequate sampling of the posterior distribution of tree topologies took considerably longer. Our results suggest that multimodality is common for data sets with 30 or more taxa and that this results in slow convergence and mixing. However, we also found that the pragmatic approach of combining data from several short, replicated runs into a metachain to estimate bipartition posterior probabilities provided good approximations, and that such estimates were no worse in approximating a reference posterior distribution than those obtained using a single long run of the same length as the metachain. Precision appears to be best when heated Markov chains have low temperatures, whereas chains with high temperatures appear to sample trees with high posterior probabilities only rarely. [Bayesian phylogenetic inference; heating parameter; Markov chain Monte Carlo; replicated chains.]

Developments of the generative topographic mapping

The generative topographic mapping (GTM) model was introduced by Bishop et al. (1998, Neural Comput. 10(1), 215-234) as a probabilistic re- formulation of the self-organizing map (SOM). It offers a number of advantages compared with the standard SOM, and has already been used in a variety of applications. In this paper we report on several extensions of the GTM, including an incremental version of the EM algorithm for estimating the model parameters, the use of local subspace models, extensions to mixed discrete and continuous data, semi-linear models which permit the use of high-dimensional manifolds whilst avoiding computational intractability, Bayesian inference applied to hyper-parameters, and an alternative framework for the GTM based on Gaussian processes. All of these developments directly exploit the probabilistic structure of the GTM, thereby allowing the underlying modelling assumptions to be made explicit. They also highlight the advantages of adopting a consistent probabilistic framework for the formulation of pattern recognition algorithms.