Simulating Tritrophic Interactions by Means of P Systems

P systems provide a high level computational modelling framework that combines the structural and dynamical aspects of ecosystems in a compressive and relevant way. The inherent randomness and uncertainty in biological systems is captured by using probabilistic strategies. The design of efficient simulation algorithms in order to reproduce the behavior of these computational models over conventional computers is fundamental for the validation and virtual experimentation processes. In this paper, we describe the modelling framework and two different simulation algorithms. As a case study, a P system based model of an ideal ecosystem with three trophic levels is designed and simulated by both simulation algorithms, providing comparisons of efficiency between them

Comparing simulation algorithms for multienvironment probabilistic P systems over a standard virtual ecosystem

Membrane Computing has recently proved to be a suitable framework for addressing the modelling of dynamical biological systems in general, and ecosystems in particular. Due to the inherent randomness and uncertainty in biological systems, when designing a model the relevant tasks to be addressed are the validation and virtual experimentation processes, rather than the formal verification. It is therefore crucial to rely on software implementations of efficient simulation algorithms. This paper presents a simple (but realistic enough) ecosystem where a carnivore and several herbivorous species interact. The model of this ecosystem has been used to compare experimentally the performance of two different simulation algorithms.Ministerio de Ciencia e Innovación TIN2009–13192Junta de Andalucía P08-TIC-0420

MeCoSim: A general purpose software tool for simulating biological phenomena by means of P Systems

In recent years, the increasing importance of the computational systems biology is leading to an impressive growth of the knowledge of several real-life phenomena. In this framework, membrane computing is an emergent branch within natural computing that has been succesfully used to model biological phenomena. The study of these phenomena usually requires the execution of virtual experiments using mechanisms of simulation, implying the development of ad-hoc tools to simulate. However, the advance of the research is demanding general solutions to avoid the necessity of custom software developments for each matter of study, when there are some common problems to resolve. MeCoSim (Membrane Computing Simulator) is a first step in this direction providing the users a customizable application to generate custom simulators based on membrane computing by simply writing a configuration file.Ministerio de Educación y Ciencia TIN2009–13192Junta de Andalucía P08–TIC-0420

A new simulation algorithm for multienvironment probabilistic P systems

Multienvironment P systems are the base of a general framework for modeling ecosystems dynamics. On one hand, this modeling framework represents the structural and dynamical aspects of real ecosystems in a discrete, modular and compressive way. On the other hand, the inherent randomness and uncertainty of biological systems are captured by using probabilistic strategies. Nowadays, the simulation of these P systems based models is fundamental for experimentation and validation. In this paper, we introduce a new simulation algorithm, called DNDP, which performs object distribution and maximal consistency in the application of rules, that are crucial aspects of these systems. The paper also depicts a parallel implementation of the algorithm, and a comparison with the existing algorithm in PLinguaCore is provided. In order to test the performance of the presented algorithm, several experiments (simulations) have been carried out over four simple P systems with the same skeleton and different number of environments.Ministerio de Ciencia e Innovación TIN2009–13192Junta de Andalucía P08–TIC-0420

A uniform framework for modeling based on P Systems

In this paper, a P systems based general framework for modeling the dynamics of a population biology is presented. Multienvironment probabilistic functional P systems with active membranes provide the syntactical specification, and the semantics is captured by using stochastic or probabilistic strategies implemented through simulation algorithms.Ministerio de Ciencia e Innovación TIN2009–13192Junta de Andalucía P08–TIC-0420

A new approach for the treatment of CLL using chlorambucil/hydroxychloroquine-loaded anti-CD20 nanoparticles

Current approaches for the treatment of chronic lymphocytic leukemia (CLL) have greatly improved the prognosis for survival, but some patients remain refractive to these therapeutic regimens. Hence, in addition to reducing the long-term sideeffects of therapeutics for all leukemia patients, there is an urgent need for novel therapeutic strategies for difficult-to-treat leukemia cases. Due to the cytotoxicity of drugs, the major challenge currently is to deliver the therapeutic agents to neoplastic cells while preserving the viability of non-malignant cells. In this study, we propose a therapeutic approach in which high doses of hydroxychloroquine and chlorambucil were loaded into biodegradable polymeric nanoparticles coated with an anti-CD20 antibody.We first demonstrated the ability of the nanoparticles to target and internalize in tumor B-cells. Moreover, these nanoparticles could kill not only p53-mutated/deleted leukemia cells expressing a low amount of CD20, but also circulating primary cells isolated from chronic lymphocytic leukemia patients. The safety of these nanoparticles was also demonstrated in healthy mice, and their therapeutic effects were shown in a new model of aggressive leukemia. These results showed that anti-CD20 nanoparticles containing hydroxychloroquine and chlorambucil can be effective in controlling aggressive leukemia and provided a rationale for adopting this approach for the treatment of other B-cell disorders. [Figure not available: see fulltext.

Evaluación física y clínica de sementales bovinos en dos municipios de la costa chica de Guerrero, México

Objective: To evaluate the reproductive physical characteristics and general health of stallions in two municipalities of Costa Chica of Guerrero, Mexico. Design/methodology/approach: The study was carried out in the municipalities of Ometepec and Cuajinicuilapa. Thirty bulls between 2 and 10 years of age were evaluated. In the physical reproductive and clinical examination were performed by direct observation, using ultrasound to evaluate attached reproductive glands and testicular parenchyma. Blood samples were taken to determine the blood profile. Descriptive statistics was used to present the results. Results: The 86% of the bulls had adequate legs and feet as well as preputial length. Scrotal circumference was according to the age and breed of the animals. Testicular defects were showed for 30% of the bulls, the most common was hypoplasia and unilateral tumors of testicular parenchyma and epididymis, as well as calcifications of the testicular parenchyma. The 93% of the bulls had normal accessory genital glands. Clinically 24% of the bulls with signs suggestive of anaplasmosis were found. The 76% of the bulls, apparently healthy, presented monocytosis, thrombocytopenia and anemia. Limitations on study/implications: the lack of knowledge of the producers about the need for a comprehensive evaluation of the bulls allows them to suffer from diseases without receiving any type of treatment, decreasing their reproductive efficiency. Findings/conclusions: Most of the bulls evaluated had the minimum physical characteristics required, although the presence of anemia and respiratory diseases may have an indirect negative impact on the reproductive efficiency of the bulls.Objetivo: Evaluar las características físicas reproductivas y la salud general de los sementales en dos municipios de Costa Chica de Guerrero, México. Diseño/metodología/aproximación: Se evaluaron reproductiva y clínicamente 30 sementales, de entre 2 y 10 años. El examen reproductivo, se realizó por observación directa, empleándose ecografía para evaluar glándulas reproductivas anexas y el parénquima testicular. La evaluación clínica se realizó por medio del examen físico y perfil hemático. Se empleó estadística descriptiva para la presentación de los resultados. Resultados: El 86% de los sementales tuvieron aplomos y largo prepucial adecuado, así como circunferencia escrotal acorde a la edad y raza de los animales. El 30% de los sementales presentaron defectos testiculares, siendo los más comunes, hipoplasia y tumores unilaterales de parénquima testicular y epidídimos, así como calcificaciones del parénquima testicular. El 93% de las glándulas anexas fueron normales. Clínicamente se encontró un 24% de los sementales con signos sugerentes a anaplasmosis. El 76% de los toros, aparentemente sanos, presentaron monocitosis, trombocitopenia y anemia. Limitaciones del estudio/implicaciones: El desconocimiento de los productores sobre la necesidad de una evaluación integral de los sementales permite que éstos padezcan enfermedades que no son tratadas, disminuyendo su eficiencia reproductiva. Hallazgos/conclusiones: La mayoría de los sementales evaluados tuvieron las características físicas mínimas requeridas, aunque la presencia de anemia y enfermedades respiratorias pueden tener incidencia negativa indirecta sobre la eficiencia reproductiva de los sementales

DCBA: Simulating Population Dynamics P Systems with Proportional Object Distribution

Population Dynamics P systems refer to a formal framework for ecological modelling. The semantics of the model associates probabilities to rules, but at the same time, the model is based on P systems, so the rules are applied in a maximally parallel way. Since the success of the rst model using this framework [5], initially called multienvironment probabilistic P systems, several simulation algorithms have been de ned in order to better reproduce the behaviour of the ecosystems with the models. BBB and DNDP are previous attempts, which de ne blocks of rules having the same left-hand side, but do not de ne a deterministic behaviour when di erent rules are competing for the same resources. That is, di erent blocks of rules present in their lefthand side common objects, being applicable at the same time. In this paper, we introduce a new simulation algorithm, called DCBA, which performs a proportional distribution of resources.Junta de Andalucía P08-TIC04200Ministerio de Educación y Ciencia TIN2009-1319

Methods to estimate aboveground wood productivity from long-term forest inventory plots

Forest inventory plots are widely used to estimate biomass carbon storage and its change over time. While there has been much debate and exploration of the analytical methods for calculating biomass, the methods used to determine rates of wood production have not been evaluated to the same degree. This affects assessment of ecosystem fluxes and may have wider implications if inventory data are used to parameterise biospheric models, or scaled to large areas in assessments of carbon sequestration. Here we use a dataset of 35 long-term Amazonian forest inventory plots to test different methods of calculating wood production rates. These address potential biases associated with three issues that routinely impact the interpretation of tree measurement data: (1) changes in the point of measurement (POM) of stem diameter as trees grow over time; (2) unequal length of time between censuses; and (3) the treatment of trees that pass the minimum diameter threshold (“recruits”). We derive corrections that control for changing POM height, that account for the unobserved growth of trees that die within census intervals, and that explore different assumptions regarding the growth of recruits during the previous census interval. For our dataset we find that annual aboveground coarse wood production (AGWP; in Mg ha−1 year−1 of dry matter) is underestimated on average by 9.2% if corrections are not made to control for changes in POM height. Failure to control for the length of sampling intervals results in a mean underestimation of 2.7% in annual AGWP in our plots for a mean interval length of 3.6 years. Different methods for treating recruits result in mean differences of up to 8.1% in AGWP. In general, the greater the length of time a plot is sampled for and the greater the time elapsed between censuses, the greater the tendency to underestimate wood production. We recommend that POM changes, census interval length, and the contribution of recruits should all be accounted for when estimating productivity rates, and suggest methods for doing this.European UnionUK Natural Environment Research CouncilGordon and Betty Moore FoundationCASE sponsorship from UNEP-WCMCRoyal Society University Research FellowshipERC Advanced Grant “Tropical Forests in the Changing Earth System”Royal Society Wolfson Research Merit Awar