An iterated Radau method for time-dependent PDE's

This paper is concerned with the time integration of semi-discretized, multi-dimensional PDEs of advection-diffusion-reaction type. To cope with the stiffness of these ODEs, an implicit method has been selected, viz., the two-stage, third-order Radau IIA method. The main topic of this paper is the efficient solution of the resulting implicit relations. First a modified Newton process has been transformed into an iteration process in which the 2 stages are decoupled and, moreover, can exploit the same LU-factorization of the iteration matrix. Next, we apply a so-called Approximate Matrix Factorization (AMF) technique to solve the linear systems in each Newton iteration. This AMF approach is very efficient since it reduces the `multi-dimensional' system to a series of `one-dimensional' systems. The total amount of linear algebra work involved is reduced enormously by this approach. The idea of applying AMF to two-dimensional problems is quite old and goes back to Peaceman and Rachford in the early fifties. The situation in three space dimensions is less favourable and will be analyzed here in more detail, both theoretically and experimentally. Furthermore, we analyze a variant in which the AMF-technique has been used to really solve (`until convergence') the underlying Radau IIA method so that we can rely on its excellent stability and accuracy characteristics. Finally, the method has been tested on several examples. Also a comparison has been made with the existing codes VODPK and IMEXRKC, and the efficiency (CPU time versus accuracy) is shown to be at least competitive with the efficiency of these solvers

Analysis of the legume–rhizobia symbiosis in shrubs from central western Spain

s. rodríguez-echeverría, m.a. pérez-fernández, s. vlaar and t. finnan. 2003.Aims: This work analyses the diversity of rhizobia associated with some of the predominant shrubby legumes in central-western Spain. Symbiotic promiscuity and effectiveness were studied using cross-inoculation experiments with shrubby species.Material and Results: Six new bradyrhizobia strains were isolated from nodules collected from wild plants of six leguminous species, Cytisus balansae, C. multiflorus, C. scoparius, C. striatus, Genista hystrix and Retama sphaerocarpa. These isolates were genetically characterized by 16S rDNA partial sequencing and random amplification of polymorphic DNA2013PCR fingerprinting. The phylogenetic analysis revealed that these isolates could represent three new Bradyrhizobium species. Shrubby legumes and bradyrhizobia displayed a high symbiotic promiscuity both for infectivity and effectiveness. Symbioses were effective in more than 70% of the associations established by four of the six plant species.Conclusions: Native woody legumes in western Spain are nodulated by Bradyrhizobium strains. The high degree of symbiotic promiscuity and effectiveness highlights the complex dynamics of these communities in wild ecosystems under a Mediterranean-type climate. Furthermore, the results from this study suggest a potential importance of inoculation for these legume species in soil-restoration projects.Significance and Impact of the Study: This is the first study, to our knowledge, that combines both molecular analysis and pot trials to study the rhizobia2013legume symbiosis for wild legumes

Characterization of plant growth promoting bacteria isolated from red fruits. Studies on growth promotion and fruit quality in strawberry plants

Microorganisms associated to the rizosphere of plants cultivated plants for human consumption are scarcely analyzed. However,nowadays, organic farming  where the use of microbial inoculants is essential, has arisenas emergent alternative with a great commercial interest.In this study, the characterization of the bacterial microbiotic presents in the rhizosphere of strawberry and blueberry plants has been carried out. In particular, three relevant characteristics have been determined order  to classify he isolated strains as plant growth promoting bacteria (PGPB). These characteristics are: 1) the ability to produce auxins, 2) siderophores and 3)  the solubilization of phosphates presents in the medium.On the other hand, the behavior of bacterial strains previously identified as PGPB has been studied in strawberry plants  both in greenhouse and field trials. The plants located in the greenhouse, were inoculated with the endophytic strawberries isolated strains: LTE1, LTE2, LTE3, LTE4, LTE6, EF12a, EF35 and EF113, as well as with three blueberries insolated bacteria which possess a high leves of auxin production, named AC8, ACH2 and ACH7. The strawberries plants located in the field, were inoculated with the strains Hv16, Hvs8 and Rec3.At the greenhouse trials, production parameters (precocity in flowering, number and weight of fruits) as well as biometrical parameters at the end of the trial, the fresh and dry weigth of root and shoots will be analyzed. At the field trial, the following production parameters will be evaluated: number and weight of extra-early fruit (February), number and weight of early fruit (March) and number and weight of total fruit. Quality fruit parameters as color, shape, sugar content (ºBrix), acidity, pH, vitamin C and anthocyanin content will be determined twice, once in February and again at the end of the experiment. By the time, the micro and macro-nutrient will also be analyzaed

On vector measures with values in ℓ∞\ell_\infty

We study some aspects of countably additive vector measures with values in $\ell_\infty$ and the Banach lattices of real-valued functions that are integrable with respect to such a vector measure. On the one hand, we prove that if $W \subseteq \ell_\infty^*$ is a total set not containing sets equivalent to the canonical basis of $\ell_1(\mathfrak{c})$, then there is a non-countably additive $\ell_\infty$-valued map $\nu$ defined on a $\sigma$-algebra such that the composition $x^* \circ \nu$ is countably additive for every $x^*\in W$. On the other hand, we show that a Banach lattice $E$ is separable whenever it admits a countable positively norming set and both $E$ and $E^*$ are order continuous. As a consequence, if $\nu$ is a countably additive vector measure defined on a $\sigma$-algebra and taking values in a separable Banach space, then the space $L_1(\nu)$ is separable whenever $L_1(\nu)^*$ is order continuous

Factors affecting mortality of shearwaters stranded by light pollution

Every year and across the world, thousands of fledglings of different petrel species crash into human structures because they are disorientated by artificial lights during their first flights. As this phenomenon is rather predictable, rescue cam- paigns are organized to help birds to reach the ocean, but unfortunately, a low proportion gets hurt or dies. Despite the huge number of affected individuals, and the fact that the problem was detected a long time ago, little is known on this source of mortality. We have studied the factors (i.e. body condition, plumage development, fledging date and sex) influencing the mortality of Cory’s Shearwa- ter Calonectris diomedea fledglings stranded inland due to light pollution in Ten- erife (Canary Islands) during two consecutive breeding seasons (2009 and 2010). Late fledglings showed lower values of a body condition index than early ones. No sex biases were detected, neither considering stranded birds overall, nor for recov- ery dates or in the body condition of rescued fledglings. Our results indicate that late birds stranded by lights showing abundant down are more susceptible to fatal collisions and that the lights do not selectively kill birds with lower body condition indices. An enhancement of veterinary care should be done during the last part of the fledging period when more fatal collisions occur, especially focused on fledg- lings with abundant down. More research to determine why some individuals end up disoriented around artificial lights and others do not is urgently needed to minimize or prevent fallouts.Peer reviewe

A New Simulated Annealing Algorithm for the Multiple Sequence Alignment Problem: The approach of Polymers in a Random Media

We proposed a probabilistic algorithm to solve the Multiple Sequence Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits the representation of the Multiple Alignment between $D$ sequences as a directed polymer in $D$ dimensions. Within this representation we can easily track the evolution in the configuration space of the alignment through local moves of low computational cost. At variance with other probabilistic algorithms proposed to solve this problem, our approach allows for the creation and deletion of gaps without extra computational cost. The algorithm was tested aligning proteins from the kinases family. When D=3 the results are consistent with those obtained using a complete algorithm. For $D>3$ where the complete algorithm fails, we show that our algorithm still converges to reasonable alignments. Moreover, we study the space of solutions obtained and show that depending on the number of sequences aligned the solutions are organized in different ways, suggesting a possible source of errors for progressive algorithms.Comment: 7 pages and 11 figure

Empleo de la composición química de minerales ferromagnesianos como indicadores de variables termodinámicas y químicas en la cristalización de rocas igneas: aplicación a los casos particulares de biotitas y granitoides del centro oeste de España

Se establecen en biotitas las relaciones entre: Rb y K/Rb y la naturaleza del granito, funciones de los contenidos en Al, Fe y Mg y la alcalinidad y temperatura en la cristalización, y finalmente, paragénesis de minerales alumínicos, grado de influencia en los diversos elementos en las esferasde coordinación tetraédrica y octaédrica, y variaciones de contenidos en elementos trazas con la alcalinidad. Las conclusiones se vinculan a la génesis de yacimientos típicamente asociados a granitos

On the succinctness of query rewriting over shallow ontologies

We investigate the succinctness problem for conjunctive query rewritings over OWL2QL ontologies of depth 1 and 2 by means of hypergraph programs computing Boolean functions. Both positive and negative results are obtained. We show that, over ontologies of depth 1, conjunctive queries have polynomial-size nonrecursive datalog rewritings; tree-shaped queries have polynomial positive existential rewritings; however, in the worst case, positive existential rewritings can be superpolynomial. Over ontologies of depth 2, positive existential and nonrecursive datalog rewritings of conjunctive queries can suffer an exponential blowup, while first-order rewritings can be superpolynomial unless NP �is included in P/poly. We also analyse rewritings of tree-shaped queries over arbitrary ontologies and note that query entailment for such queries is fixed-parameter tractable

Interaction Effects on the Magneto-optical Response of Magnetoplasmonic Dimers

The effect that dipole-dipole interactions have on the magneto-optical (MO) properties of magnetoplasmonic dimers is theoretically studied. The specific plasmonic versus magnetoplasmonic nature of the dimer's metallic components and their specific location within the dimer plays a crucial role on the determination of these properties. We find that it is possible to generate an induced MO activity in a purely plasmonic component, even larger than that of the MO one, therefore dominating the overall MO spectral dependence of the system. Adequate stacking of these components may allow obtaining, for specific spectral regions, larger MO activities in systems with reduced amount of MO metal and therefore with lower optical losses. Theoretical results are contrasted and confirmed with experiments for selected structures

Reproducible science: What, why, how

Most scientific papers are not reproducible: it is really hard, if not impossible, to understand how results are derived from data, and being able to regenerate them in the future (even by the same researchers). However, traceability and reproducibility of results are indispensable elements of highquality science, and an increasing requirement of many journals and funding sources. Reproducible studies include code able to regenerate results from the original data. This practice not only provides a perfect record of the whole analysis but also reduces the probability of errors and facilitates code reuse, thus accelerating scientific progress. But doing reproducible science also brings many benefits to the individual researcher, including saving time and effort, improved collaborations, and higher quality and impact of final publications. In this article we introduce reproducible science, why it is important, and how we can improve the reproducibility of our work. We introduce principles and tools for data management, analysis, version control, and software management that help us achieve reproducible workflows in the context of ecology.Peer Reviewe