A Fuzzy Logic Programming Environment for Managing Similarity and Truth Degrees

FASILL (acronym of "Fuzzy Aggregators and Similarity Into a Logic Language") is a fuzzy logic programming language with implicit/explicit truth degree annotations, a great variety of connectives and unification by similarity. FASILL integrates and extends features coming from MALP (Multi-Adjoint Logic Programming, a fuzzy logic language with explicitly annotated rules) and Bousi~Prolog (which uses a weak unification algorithm and is well suited for flexible query answering). Hence, it properly manages similarity and truth degrees in a single framework combining the expressive benefits of both languages. This paper presents the main features and implementations details of FASILL. Along the paper we describe its syntax and operational semantics and we give clues of the implementation of the lattice module and the similarity module, two of the main building blocks of the new programming environment which enriches the FLOPER system developed in our research group.Comment: In Proceedings PROLE 2014, arXiv:1501.0169

The spatial ultimatum game revisited

We revisit the issue of the emergence of fair behavior in the framework of the spatial Ultimatum game, adding many important results and insights to the pioneering work by Page et al. [2000. The spatial Ultimatum game. Proc. R. Soc. London B 267, 2177], who showed in a specific example that on a two dimensional setup evolution may lead to strategies with some degree of fairness. With in this spatial framework, we carry out a thorough simulation study and show that the emergence of altruism is a very generic phenomenon whose details depend on the dynamics considered. A very frequent feature is the spontaneous emergence and fixation of quasiempathetic individuals,whose offers are very close to their acceptance thresholds. We present analytical arguments that allow an understanding of our results and give insights on the manner in which local effects in evolution may lead to such non rational or apparently maladaptive behaviors.This work was supported in part by MICINN (Spain) through grants MOSAICO and RESINEE, and by Comunidad de Madrid (Spain) through grant MODELICO. J. I. is supported by a contract from the Consejería de Educación of the Comunidad de Madrid (Spain) and from the European Social Fund.Publicad

Determinación del estrés hídrico de una planta mediante sensores ZIM y técnicas de aprendizaje automático

El estrés hídrico refleja el nivel de hidratación de una planta. Medirlo adecuadamente permite ajustar el agua de riego para maximizar el rendimiento de la planta, obteniendo la máxima producción con el menor consumo de agua, así como monitorizar su estado de salud. En este sentido, se han propuesto numerosos métodos para realizar la medida. Este proyecto se centra en uno de ellos, enmarcado dentro de la investigación realizada por parte del IRNAS-CSIC, en el que se emplean sensores ZIM para medir el nivel de estrés hídrico a través de la turgencia de las hojas, centrándose por el momento en el olivo de la variedad arbequina, con el fin de aplicar técnicas de aprendizaje automático donde actualmente se necesita el análisis manual de un experto.Universidad de Sevilla. Máster en Ingeniería Electrónica, Robótica y Automátic

Evolutionary responses of fast adapting populations to opposing selection pressures

This thesis deals with the mathematical modeling of evolutionary processes that take place in heterogeneous populations. Its leitmotif is the response of complex ensembles of replicating entities to multiple (and often opposite) selection pressures. Even though the specific problems addressed in different chapters belong to different organizational levels—genome, population, and community—all of them can be conceptualized as the evolution of a heterogeneous population—let it be a population of genomic elements, viruses, or prokaryotic hosts and phages—facing a complex environment. As a result, the mathematical tools required for their study are quite similar. In contrast, the strategies that each population has discovered to perpetuate vary according to the different evolutionary challenges and environmental constraints that the population experiences. Along this thesis, there has been a special interest on connecting theoretical models with experimental results. To that end, most of the work presented here has been motivated either by laboratory findings or by the bioinformatic analysis of sequenced genomes. We strongly believe that such a multidisciplinary approach is necessary in order to improve our knowledge on how evolution works. Moreover, experiments are a must when it comes to propose antiviral strategies based on theoretical predictions, as we do in Chapter 3. This thesis is structured in two main blocks. The first one focuses on studying instances of viral evolution under the action of mutagenic drugs, paying particular attention to their possible application to the development of novel antiviral therapies. This block comprises chapters 2 and 3; the former dicussing the phenomenon of lethal defection and stochastic viral extinction; the latter dealing with the optimal way to combine mutagens and inhibitors in multidrug antiviral treatments. The second block is devoted to the study of the evolutionary forces underlying genome structure. In chapter 4, we propose a mechanism through which multipartite viruses could have originated. Interestingly, the pathway leading to genome segmentation shares some steps with lethal defection, but each outcome is reached at specific environmental conditions. Chapter 5 analyses the abundance distributions of transposable elements in prokaryotic genomes, with the aim of determining the key processes involved in their spreading. We explicitly explore the hypothesis that transposable elements follow a neutral dynamics, with a negligible fitness cost for their host genomes. A higher level of organization is studied in Chapter 6, where an agent based coevolutionary model based on Lotka-Volterra interactions is used to investigate the evolutionary dynamics of the prokaryotic antiviral immunity system CRISPR-Cas. This chapter also examines the environmental factors that are responsible for its maintenance or loss. Finally, Chapter 7 summarizes the main results obtained along the thesis and sketches possible lines of work based on them

Assessment of the shear strength of polyolefin and steel fibre-reinforced concrete

Ponencia presentada al congreso de innovación tecnológica en edificación analizando la evaluación resistente de hormigones reforzados con diferentes tipos de fibras a esfuerzo cortant

Disentangling the effects of selection and loss bias on gene dynamics

We combine mathematical modeling of genome evolution with comparative analysis of prokaryotic genomes to estimate the relative contributions of selection and intrinsic loss bias to the evolution of different functional classes of genes and mobile genetic elements (MGE). An exact solution for the dynamics of gene family size was obtained under a linear duplication-transfer-loss model with selection. With the exception of genes involved in information processing, particularly translation, which are maintained by strong selection, the average selection coefficient for most nonparasitic genes is low albeit positive, compatible with observed positive correlation between genome size and effective population size. Free-living microbes evolve under stronger selection for gene retention than parasites. Different classes of MGE show a broad range of fitness effects, from the nearly neutral transposons to prophages, which are actively eliminated by selection. Genes involved in antiparasite defense, on average, incur a fitness cost to the host that is at least as high as the cost of plasmids. This cost is probably due to the adverse effects of autoimmunity and curtailment of horizontal gene transfer caused by the defense systems and selfish behavior of some of these systems, such as toxin-antitoxin and restriction modification modules. Transposons follow a biphasic dynamics, with bursts of gene proliferation followed by decay in the copy number that is quantitatively captured by the model. The horizontal gene transfer to loss ratio, but not duplication to loss ratio, correlates with genome size, potentially explaining increased abundance of neutral and costly elements in larger genomes

High density of unrepaired genomic ribonucleotides leads to Topoisomerase 1-mediated severe growth defects in absence of ribonucleotide reductase

Cellular levels of ribonucleoside triphosphates (rNTPs) are much higher than those of deoxyribonucleoside triphosphates (dNTPs), thereby influencing the frequency of incorporation of ribonucleoside monophosphates (rNMPs) by DNA polymerases (Pol) into DNA. RNase H2-initiated ribonucleotide excision repair (RER) efficiently removes single rNMPs in genomic DNA. However, processing of rNMPs by Topoisomerase 1 (Top1) in absence of RER induces mutations and genome instability. Here, we greatly increased the abundance of genomic rNMPs in Saccharomyces cerevisiae by depleting Rnr1, the major subunit of ribonucleotide reductase, which converts ribonucleotides to deoxyribonucleotides. We found that in strains that are depleted of Rnr1, RER-deficient, and harbor an rNTP-permissive replicative Pol mutant, excessive accumulation of single genomic rNMPs severely compromised growth, but this was reversed in absence of Top1. Thus, under Rnr1 depletion, limited dNTP pools slow DNA synthesis by replicative Pols and provoke the incorporation of high levels of rNMPs in genomic DNA. If a threshold of single genomic rNMPs is exceeded in absence of RER and presence of limited dNTP pools, Top1-mediated genome instability leads to severe growth defects. Finally, we provide evidence showing that accumulation of RNA/DNA hybrids in absence of RNase H1 and RNase H2 leads to cell lethality under Rnr1 depletion