Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.

Modelos de viento aplicados a la mejora en la predicción de incendios forestales

La predicción de incendios forestales es uno de los grandes retos de la comunidad científica debido al impacto medioambiental, humano y económico que tienen en la sociedad. El comportamiento de este fenómeno es difícil de modelar debido a la gran cantidad de variables que intervienen y la dificultad que implica su correcta medición. Los simuladores de fuego son herramientas muy útiles pero, actualmente, los resultados que obtenemos tienen un alto grado de imprecisión. Desde nuestro grupo se ha trabajado en la predicción en dos etapas, donde antes de realizar cualquier predicción, se incorpora una etapa de ajuste de los parámetros de entrada para obtener mejores predicciones. Pese a la mejora que supone este nuevo paradigma de predicción, las simulaciones sobre incendios reales tienen un alto grado de error por el efecto de las condiciones meteorológicas que, usualmente, varían de manera notable durante el transcurso de la simulación. Uno de los factores más determinantes en el comportamiento de un incendio, junto con las características del terreno, es el viento. Los modelos de predicción son extremadamente sensibles al cambio en los componentes de dirección y velocidad del viento por lo que cualquier mejora que podamos introducir para mejorar la calidad de estas componentes influye directamente en la calidad de la predicción. Nuestro sistema de predicción utiliza la dirección y velocidad del viento de forma global en todo el terreno, y lo que proponemos con este trabajo es introducir un modelo de vientos que nos permita generar vientos locales en todas las celdas en las que se divide el terreno. Este viento local dependerá del viento general y de las características del terreno de dichas celdas. Consideramos que la utilización de un viento general no es suficiente para realizar una buena predicción del comportamiento de un incendio y hemos comprobado que la inclusión de un simulador de campo de vientos en nuestro sistema puede llegar a mejorar nuestras predicciones considerablemente. Los resultados obtenidos en los experimentos sintéticos que hemos realizado nos hacen ser optimistas, puesto que consideramos que la inclusión de componentes de viento locales permitirá mejorar nuestras predicciones en incendios reales.

The Rapakivi texture of feldspars in a plutonic mixing environment - A dissolution-recrystallization process

A new hypothesis is formulated to explain the development of rapakivi texture in and around the mafic enclaves of porphyritic granitoids, i.e. in environments involving magma mixing and mingling. The formation of a plagioclase mantle around alkali feldspar megacrysts is attributed to the localized presence of a melt resulting from the reaction of these megacrysts, with host hybrid magma with which they are in disequilibrium. This feldspathic melt adheres to the resorbed crystals and is virtually immiscible with the surrounding magma. Its composition is modified in terms of the relative proportions of K2O, Na2O, and CaO through selective diffusion of these elements, thus allowing the specific crystallization of andesine. With decreasing temperature, the K-feldspar, again stable, crystallizes along with the plagioclase, leading to mixed mantle structures.

IPH response to the Environmental Protection Agency Consultation on Stategic Environmental Assessment (SEA) Process Checklist

The Institute of Public Health in Ireland is an all-island body which aims to improve health in Ireland by working to combat health inequalities and influence public policies in favour of health. The Institute promotes co-operation in research, training, information and policy in order to contribute to policies which tackle inequalities in health. Over the past six years the Institute has worked closely with the Department of Health and Children and the Department of Health, Social Services and Public Safety in Northern Ireland to build capacity for Health Impact Assessment. The Institute takes the view that health is determined by policies, plans and programmes in many sectors outside the health sector as well as being dependent on access to and availability of first class health services. The importance of other sectors is encapsulated in a social determinants of health perspective which recognises that health is largely shaped and influenced by the physical, social, economic and cultural environments in which people live, work and play. Figure 1 illustrates these multi-dimensional impacts on health and also serves to highlight the clear and inextricable links between health and sustainable development. Factors that impact on long-term sustainability will thus also impact on health.

Nonclassical measurement error with applications to labor and development issues

Zero correlation between measurement error and model error has been assumed in existing panel data models dealing specifically with measurement error. We extend this literature and propose a simple model where one regressor is mismeasured, allowing the measurement error to correlate with model error. Zero correlation between measurement error and model error is a special case in our model where correlated measurement error equals zero. We ask two research questions. First, we wonder if the correlated measurement error can be identified in the context of panel data. Second, we wonder if classical instrumental variables in panel data need to be adjusted when correlation between measurement error and model error cannot be ignored. Under some regularity conditions the answer is yes to both questions. We then propose a two-step estimation corresponding to the two questions. The first step estimates correlated measurement error from a reverse regression; and the second step estimates usual coefficients of interest using adjusted instruments.

Monitoring the domiciliary and peridomiciliary invasion process of Triatoma rubrovaria in the State of Rio Grande do Sul, Brazil

The presence of Triatoma rubrovaria in Brazil has only been confirmed in the States of Paraná and Rio Grande do Sul (RS), where it is found naturally infected with Trypanosoma cruzi. In the wild environment it occurs in rocky habitats and has an eclectic diet, feeding from cockroaches, reptiles and mammals. Data from the Chagas Disease Control Program obtained by the Fundação Nacional de Saúde, between 1975 and 1997, indicate a growing domiciliary and peridomiciliary invasion of T. rubrovaria in RS, where it has become the most frequently Triatominae species captured in this state since the control of Triatoma infestans. In order to monitor this process, we analyzed collection data derived from 22 years of control campaigns against T. infestans. Collection data for triatomines from domestic habitats show an inverse relationship, with high numbers of T. infestans and low numbers of T. rubrovaria during 1976-1987, compared to the following ten years, 1986-1997, when the number of T. infestans dropped drastically and that of T. rubrovaria increased. There are no consistent indications of intradomiciliary colonization by T. rubrovaria, since only low numbers of nymphs have been captured in the intradomiciliary ecotopes. Nevertheless, this species appears to have preadaptive characteristics for anthropic ecotopes, and should be kept under constant epidemiological surveillance.

Productivity in southern European small firms: When and how work organization complements process innovation

The aim of this paper is to analyse the effects of human capital, advanced manufacturing technologies (AMT), and new work organizational practices on firm productivity, while taking into account the synergies existing between them. This study expands current knowledge in this area in two ways. First, in contrast with previous works, we focus on AMT and not ICT (information and communication technologies). Second, we use a unique employer-employee data set for small firms in a particular area of southern Europe (Catalonia, Spain). Using a small firm data set, allows us to analyse the particular case of small and medium enterprises, since we cannot assume they have the same characteristics as large firms. The results provide evidence in favor of the complementarity hypothesis between human capital, advanced manufacturing technologies, and new work organization practices, although we show that the complementarity effects depend on what type of work organization practices are used by a firm. For small and medium Catalan firms, the only set of work organization practices that improve the benefits of human capital and technology investment are those practices which are more quality oriented, such as quality circles, problem-solving groups or total quality management.

Quantificació de l'error comès pels models de níxol ecològic al predir la distribució d'especies generalistes

Report for the scientific sojourn carried out at the University of California at Berkeley, from September to December 2007. Environmental niche modelling (ENM) techniques are powerful tools to predict species potential distributions. In the last ten years, a plethora of novel methodological approaches and modelling techniques have been developed. During three months, I stayed at the University of California, Berkeley, working under the supervision of Dr. David R. Vieites. The aim of our work was to quantify the error committed by these techniques, but also to test how an increase in the sample size affects the resultant predictions. Using MaxEnt software we generated distribution predictive maps, from different sample sizes, of the Eurasian quail (Coturnix coturnix) in the Iberian Peninsula. The quail is a generalist species from a climatic point of view, but an habitat specialist. The resultant distribution maps were compared with the real distribution of the species. This distribution was obtained from recent bird atlases from Spain and Portugal. Results show that ENM techniques can have important errors when predicting the species distribution of generalist species. Moreover, an increase of sample size is not necessary related with a better performance of the models. We conclude that a deep knowledge of the species’ biology and the variables affecting their distribution is crucial for an optimal modelling. The lack of this knowledge can induce to wrong conclusions.

Error estimate and control in the MSFV method for multiphase flow in porous media

n this paper the iterative MSFV method is extended to include the sequential implicit simulation of time dependent problems involving the solution of a system of pressure-saturation equations. To control numerical errors in simulation results, an error estimate, based on the residual of the MSFV approximate pressure field, is introduced. In the initial time steps in simulation iterations are employed until a specified accuracy in pressure is achieved. This initial solution is then used to improve the localization assumption at later time steps. Additional iterations in pressure solution are employed only when the pressure residual becomes larger than a specified threshold value. Efficiency of the strategy and the error control criteria are numerically investigated. This paper also shows that it is possible to derive an a-priori estimate and control based on the allowed pressure-equation residual to guarantee the desired accuracy in saturation calculation.