Parallel simulation of Population Dynamics P systems: updates and roadmap

Population Dynamics P systems are a type of multienvironment P systems that serve as a formal modeling framework for real ecosystems. The accurate simulation of these probabilisticmodels, e.g. with Direct distribution based on Consistent Blocks Algorithm, entails large run times. Hence, parallel platforms such as GPUs have been employed to speedup the simulation. In 2012, the first GPU simulator of PDP systems was presented. However, it was able to run only randomly generated PDP systems. In this paper, we present current updates made on this simulator, involving an input modu le for binary files and an output module for CSV files. Finally, the simulator has been experimentally validated with a real ecosystem model, and its performance has been tested with two high-end GPUs: Tesla C1060 and K40.Ministerio de Economía y Competitividad TIN2012-37434Junta de Andalucía P08-TIC-0420

Simulating FRSN P Systems with Real Numbers in P-Lingua on sequential and CUDA platforms

Fuzzy Reasoning Spiking Neural P systems (FRSN P systems, for short) is a variant of Spiking Neural P systems incorporating fuzzy logic elements that make it suitable to model fuzzy diagnosis knowledge and reasoning required for fault diagnosis applications. In this sense, several FRSN P system variants have been proposed, dealing with real numbers, trapezoidal numbers, weights, etc. The model incorporating real numbers was the first introduced [13], presenting promising applications in the field of fault diagnosis of electrical systems. For this variant, a matrix-based algorithm was provided which, when executed on parallel computing platforms, fully exploits the model maximally parallel capacities. In this paper we introduce a P-Lingua framework extension to parse and simulate FRSN P systems with real numbers. Two simulators, implementing a variant of the original matrix-based simulation algorithm, are provided: a sequential one (written in Java), intended to run on traditional CPUs, and a parallel one, intended to run on CUDAenabled devices.Ministerio de Economía y Competitividad TIN2012-3743

Parallel Simulation of PDP Systems: Updates and Roadmap

PDP systems are a type of multienvironment P systems, which serve as a formal modeling framework for Population Dynamics. The accurate simulation of these probabilistic models entails large run times. Hence, parallel platforms such as GPUs has been employed to speedup the simulation. In 2012 [14], the rst GPU simulator of PDP systems was presented. In this paper, we present current updates made on this simulator, and future developments to consider.Ministerio de Economía y Competitividad TIN2012-3743

SAGT: Aplicación informática para análisis de generalizabilidad

Se presenta un nuevo software para realizar análisis de generalizabilidad. Las características del mismo superan las limitaciones de programas anteriores (GENOVA, TG o EduG), tanto a nivel de tratamiento numérico como gráfico y en la importación/exportación de datos. El entorno del programa es más amigable. Para demostrar su eficacia se utiliza en el análisis de datos y valoración de resultados de un programa de intervención para la reducción de discriminación de género en las clases de educación física (EF). Se utiliza un diseño observacional y un diseño de generalizabilidad ortogonal con 6 facetas parcialmente anidado. El programa se desarrolla durante seis meses. La muestra está compuesta por 100 alumnos (51 chicas y 49 chicos) con edades comprendidas entre los 10 y los 12 años que cursaban 5º de Educación Primaria y se encontraban distribuidos en cuatro grupos. Los resultados del anàlisis de generalizabilidad señalan que la herramienta de observación es fiable, válida y precisa y que los observadores son altamente fiables (k = 0.73-0.81, G = 1). El ANOVA realizado señala que el programa de intervención ha sido eficaz. Además, se ha demostrado la eficacia y usabilidad del programa SAGT

The role of the direction in tissue P systems with cell separation

Tissue P systems with cell separation where the communication among cells is performed by means of symport and antiport rules are able to efficiently solve computationally hard problems in a feasible time by a space-time trade off. Symport and antiport rules formally capture the cases where a number of chemical substances pass through a membrane at the same time, with the help of each other, either in the same direction (symport) or in opposite directions (antiport). The present paper investigates the role of the direction in communication rules from a computational complexity point of view. More precisely, the efficiency of tissue P systems with cell separation is analyzed in the case when their communication rules are all of the same type: either symport rules or antiport rules. The main result is that in the framework of tissue P systems with cell separation, passing from using only symport rules to using only antiport rules amounts to passing from non-efficiency to efficiency, assuming that P ≠ NP.Ministerio de Economía y Competitividad TIN2012-37434Junta de Andalucía P08 – TIC 0420

Antifungal activity against Fusarium culmorum of stevioside, Silybum marianum seed extracts, and their conjugate complexes

Fusarium head blight (FHB) is a disease that poses a major challenge in cereal production that has important food and feed safety implications due to trichothecene contamination. In this study, the effect of stevioside—a glycoside found in the leaves of candyleaf (Stevia rebaudiana Bertoni)—was evaluated in vitro against Fusarium culmorum (W.G. Smith) Sacc., alone and in combination (in a 1:1 molar ratio) with polyphenols obtained from milk thistle seeds (Silybum marianum (L.) Gaertn). Different concentrations, ranging from 32 to 512 µg·mL−1, were assayed, finding EC50 and EC90 inhibitory concentrations of 156 and 221 µg·mL−1, respectively, for the treatment based only on stevioside, and EC50 and EC90 values of 123 and 160 µg·mL−1, respectively, for the treatment based on the stevioside–polyphenol conjugate complexes. Colony formation inhibition results were consistent, reaching full inhibition at 256 µg·mL−1. Given that synergistic behavior was observed for this latter formulation (SF = 1.43, according to Wadley’s method), it was further assessed for grain protection at storage, mostly directed against mycotoxin contamination caused by the aforementioned phytopathogen, confirming that it could inhibit fungal growth and avoid trichothecene contamination. Moreover, seed tests showed that the treatment did not affect the percentage of germination, and it resulted in a lower incidence of root rot caused by the pathogen in Kamut and winter wheat seedlings. Hence, the application of these stevioside–S. marianum seed extract conjugate complexes may be put forward as a promising and environmentally friendly treatment for the protection of cereal crops and stored grain against FHB

Antifungal activity of chitosan oligomers-amino acid conjugate complexes against Fusarium culmorum in spelt (Triticum spelta L.)

Fusarium head blight (FHB) is a complex disease of cereals caused by Fusarium species, which causes severe damages in terms of yield quality and quantity worldwide, and which produces mycotoxin contamination, posing a serious threat to public health. In the study presented herein, the antifungal activity against Fusarium culmorum of chitosan oligomers (COS)–amino acid conjugate complexes was investigated both in vitro and in vivo. The amino acids assayed were cysteine, glycine, proline and tyrosine. In vitro tests showed an enhancement of mycelial growth inhibition, with EC50 and EC90 effective concentration values ranging from 320 to 948 µg·mL−1 and from 1107 to 1407 µg·mL−1 respectively, for the conjugate complexes, as a result of the synergistic behavior between COS and the amino acids, tentatively ascribed to enhanced cell membrane damage originating from lipid peroxidation. Tests on colonies showed a maximum percentage reduction in the number of colonies at 1500 µg·mL−1 concentration, while grain tests were found to inhibit fungal growth, reducing deoxynivalenol content by 89%. The formulation that showed the best performance, i.e., the conjugate complex based on COS and tyrosine, was further investigated in a small-scale field trial with artificially inoculated spelt (Triticum spelta L.), and as a seed treatment to inhibit fungal growth in spelt seedlings. The field experiment showed that the chosen formulation induced a decrease in disease severity, with a control efficacy of 83.5%, while the seed tests showed that the treatment did not affect the percentage of germination and resulted in a lower incidence of root rot caused by the pathogen, albeit with a lower control efficacy (50%). Consequently, the reported conjugate complexes hold enough promise for crop protection applications to deserve further examination in larger field trials, with other Fusarium spp. pathogens and/or Triticum species

Identification, capsular typing and virulence factors of Pasteurella multocida isolates from Merino lambs in Extremadura (Southwestern Spain)

En el presente informe se describen la prevalencia, el tipo de cápsula y los factores de virulencia de Pasteurella multocida aislados de las vías respiratorias de corderos sanos y enfermos. Para este estudio se analizaron quinientos noventa y ocho corderos de engorde procedentes de diferentes cebaderos de la comunidad de Extremadura. El aislamiento e identificación de P. multocida se realizó mediante técnicas bacteriológicas y bioquímicas convencionales, mientras que la confirmación de la identificación de P. multocida, el tipo de cápsula y los factores de virulencia se realizó mediante la técnica de reacción en cadena de la polimerasa (PCR). De 598 corderos estudiados (410 corderos clínicamente sanos y 188 enfermos), se aisló P. multocida de 37 animales (6,2%), con tasas de prevalencia del 0,49% (2/410) en corderos sanos y del 18,62% (35/188) en corderos enfermos, lo que confirma una estrecha relación entre la presencia de bacterias y la enfermedad. La tipificación capsular de los aislados de P. multocida demostró dos tipos de cápsulas: A (15) y D (22), con tasas de prevalencia general del 40,5% y 59,5%, respectivamente, y con la presencia exclusiva del tipo D en animales sanos (100%) y de los tipos D y A en animales enfermos (42,9% y 57,1%, respectivamente). Entre los cuatro genes de virulencia investigados (pfhA, hgbB, tbpA y toxA), se encontró una notable alta prevalencia de los genes tbpA (100%) (37/37) en P. multocida; el toxA sólo se detectó en algunos corderos enfermos (11/37), mientras que el resto de los genes estudiados no se detectaron. La alta prevalencia de toxA entre las cepas aisladas de animales enfermos puede implicar un papel importante de este gen en la virulencia de las cepas de P. multocida en las ovejas, especialmente en los corderos enfermos.This report describes the prevalence, capsular type and virulence factors of Pasteurella multocida isolated from the respiratory tracts of healthy and diseased lambs. For this study, five hundred and ninety-eight fattening lambs from different feedlots of the community of Extremadura were analysed. Isolation and identifica¬tion of P. multocida were performed using conventional bacteriological and biochemical techniques, while con¬firmation of P. multocida identification, capsular type and virulence factors was done using the polymerase chain reaction technique (PCR). Of 598 studied lambs (410 clinically healthy and 188 diseased sheep), P. multocida was isolated from 37 animals (6.2%), with prevalence rates of 0.49% (2/410) in healthy lambs and 18.62% (35/188) in diseased lambs confirming a close relationship between the presence of bacteria and disease. Capsular typing of P. multocida isolates demonstrated two capsular types: A (15) and D (22), with general prevalence rates of 40.5% and 59.5%, respectively, and with the exclusive presence of type D in healthy animals (100%) and types D and A among diseased animals (42.9% and 57.1%, respectively). Among four virulence genes investigated (pfhA, hgbB, tbpA and toxA), we found a remarkable high prevalence of tbpA (100%) (37/37) genes in P. multocida; toxA was only detected in some diseased lambs (11/37), while the rest of the studied genes were not detected. The high prevalence of toxA among isolates from diseased animals may imply an important role of this gene in the virulence of P. multocida isolates in sheep, especially in diseased lambs.• Junta de Extremadura y Programa FEDER. Proyecto PCE1007, del programa PRI IV + DT + I para cooperación sectorial estratégica entre grupos de investigación y empresas, proporcionada por el grupo de investigación GRU10142 • Junta de Extremadura y el Fondo Social Europeo. Proyecto PD12131 y GRU10110 • Ministerio de Ciencia e Innovación. Proyecto AGL2009-10136peerReviewe

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

Bone mineral density, bone remodeling and osteoprotegerin in patients with acute coronary syndrome

Producción CientíficaThe objective of this study was to evaluate the relationship between coronary disease and osteoporosis and determine the effect of osteoprotegerin (OPG) on bone remodeling and bone mineral density (BMD) in a group of patients with acute coronary syndrome. Eightythree patients (52 males and 31 women) with acute coronary syndrome (75 patients with acute myocardial infarction and 8 with unstable angina) with an average age of 61±10 years were studied. Levels of osteocalcin, urinarydeoxypyridinoline, OPG and the receptor activator of nuclear factor-κB ligand (RANKL) were determined during the hospital stay. Femoral neck, trochanter and lumbar spine densitometry was carried out using a DXA densitometer. Thirty percent of patients presented osteoporosis (39% of females and 26% of males). Osteoporotic patients were older and had a lower weight and height and elevated serum levels of osteocalcin (3.6±2.25 2.63 versus ±1.55, p=0.05). Levels of OPG and RANKL were similar in both groups and showed no relationship with BMD. In conclusion, no relationship was observed between the OPG/RANKL system and BMD in these patients