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

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

Vibrio neptunius produces piscibactin and amphibactin and both siderophores contribute significantly to virulence for clams

Vibrio neptunius is an inhabitant of mollusc microbiota and an opportunistic pathogen causing disease outbreaks in marine bivalve mollusc species including oysters and clams. Virulence of mollusc pathogenic vibrios is mainly associated with the production of extracellular products. However, siderophore production is a common feature in pathogenic marine bacteria but its role in fitness and virulence of mollusc pathogens remains unknown. We previously found that V. neptunius produces amphibactin, one of the most abundant siderophores in marine microbes. In this work, synthesis of the siderophore piscibactin was identified as the second siderophore produced by V. neptunius. Single and double mutants in biosynthetic genes of each siderophore system, piscibactin and amphibactin, were constructed in V. neptunius and their role in growth ability and virulence was characterized. Although the High Pathogenicity Island encoding piscibactin is a major virulence factor in vibrios pathogenic for fish, the V. neptunius wild type did not cause mortality in turbot. The results showed that amphibactin contributes more than piscibactin to bacterial fitness in vitro. However, infection challenges showed that each siderophore system contributes equally to virulence for molluscs. The V. neptunius strain unable to produce any siderophore was severely impaired to cause vibriosis in clams. Although the inactivation of one of the two siderophore systems (either amphibactin or piscibactin) significantly reduced virulence compared to the wild type strain, the ability to produce both siderophores simultaneously maximised the degree of virulence. Evaluation of the gene expression pattern of each siderophore system showed that they are simultaneously expressed when V. neptunius is cultivated under low iron availability in vitro and ex vivo. Finally, the analysis of the distribution of siderophore systems in genomes of Vibrio spp. pathogenic for molluscs showed that the gene clusters encoding amphibactin and piscibactin are widespread in the Coralliilyticus clade. Thus, siderophore production would constitute a key virulence factor for bivalve molluscs pathogenic vibriosThis work was supported by grants AGL2017-86183-R (AEI/ FEDER, EU), RTI2018-093634-B-C21/C22 (AEI/FEDER, EU) and PID2019-103891RJ-100 (AEI) from the State Agency for Research (AEI) of Spain. AGL2017-86183-R and RTI2018- 093634-B-C21/C22 were co-funded by the FEDER Programme from the European Union. Work in University of Santiago de Compostela was also supported by grants GRC2018/018 and 2021-CP112, and in University of A Coruña by grant GRC2018/ 039 from Xunta de Galicia (Spain). FG was financed with a fellowship ‘Programa de formación de recurso humano de alto nivel doctorado en el exterior’ granted by Colciencias and the government of Norte de Santander, Colombia. LA was financed with a fellowship (ED481A-2019/081) from Xunta de Galicia (Spain), co-financed by ESF (European Social Fund)S

PCI-AER interface for Neuro-inspired Spiking Systems

Address event representation (AER) is a neuromorphic interchip communication protocol that allows for real-time connectivity between huge number neurons located on different chips. By exploiting high speed digital communication circuits (nano-seconds), synaptic neural connections can be time multiplexed (mili-seconds). When building multi-chip muti-layered AER systems it is absolutely necessary to have a computer interface that allows: (a) to read AER interchip traffic; and (b) inject a sequence of events to the AER structure. This paper presents a PCI to AER interface, that dispatches a sequence of events with timing information. It is able to recovery the possible delays introduced by AER bus. It has been implemented in real time hardware using VHDL and tested in a PCI-AER board, developed by authors, that currently capable to send and receive events at a peak rate of 16 Mev/sec, and a typical rate of 10 Mev/secEuropean Commission IST-2001-34124Ministerio de Ciencia y Tecnología TIC-2003-08164-C03-0

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

Strained SrMnO3 thin films: engineering multiferroic properties

Resumen del trabajo presentado al "European Congress and Exhibition on Advanced Materials Processes" celebrado en Sevilla (España) del 8 al 13 de septiembre de 2013.-- et al.Multiferroic materials showing simultaneous magnetic and ferroelectric ordering have become the subject of intensive research in recent years. The scarcity of these materials due to the different phenomena responsible for both properties [1], and also, the weak magnetoelectric coupling in most of them force to develop new methods to avoid the excluding mechanisms of ferroelectricity and magnetism. Recent theoretical predictions suggested that epitaxially strained SrMnO3 should become multiferroic [2] by means of the interplay of spins, lattice phonons and strain of the perovskite unit cell. In this system, Mn4+ (d3 ion) is expected to drive both the magnetic order (Mn-O-Mn magnetic superexchange interaction) and the required non-centrosymmetric distortion for ferroelectric order (Mn4+ off-centers from MnO6 octahedra), and therefore a strong magnetoelectric coupling with similar ordering temperatures is expected. Here, we have investigated the effect of epitaxial strain on the structure, electrical and magnetic properties of SrMnO3 (SMO) thin films. Pulsed laser deposition technique was used to grow strained SMO thin films onto different substrates ranging from -1% compressive to 4% tensile mismatch. Coherent cube-on-cube growth is borne out by X-ray diffraction measurements, which also show that under appropriate deposition conditions and substrate selection the perovskite pseudo-cubic phase is stabilized in thin films. The growth of the samples has been monitored by in situ RHEED measurements. Selected films were observed by scanning transmission electron microscopy, which prove the homogeneity and defect-free crystal quality of films. Chemical composition mapping, stoichiometry and 4+ oxidation state of Mn were corroborated by electron energy loss spectroscopy. Nonlinear optics measurements reveal that SMO films, under epitaxial stress, emitt optical second harmonic generation signal, pointing to inversion symmetry being broken (necessary condition for ferroelectricity). Electric measurements were carried out to further investigate the ferroelectric nature of SMO films, thus assessing the possibility of non-d0 cations off-centring.Peer Reviewe

Prevalence of Multi-Resistant Microorganisms and Antibiotic Stewardship among Hospitalized Patients Living in Residential Care Homes in Spain: A Cross-Sectional Study

Antimicrobial resistance is a growing global health problem. Patients living in care homes are a vulnerable high-risk population colonized by multidrug-resistant organisms (MDRO). We identified a case series of 116 residents of care homes from a cohort of 540 consecutive patients admitted to the internal medicine service of our hospital. We performed early diagnostic tests of MDRO through anal exudates in our sample. The prevalence of MDRO colonization was 34.5% of residents and 70% of them had not been previously identified in the clinical records. Previous hospitalizations and in-hospital antibiotic administration were significantly associated with the presence of MDRO. Our results emphasize the need to consider care homes in the planning of regional and national infection control measures and for implementing surveillance systems that monitor the spread of antimicrobial resistance in Spain. Systematic early testing upon admission to hospital services with a high prevalence of patients with MDRO colonization (e.g., internal medicine) could contribute to the adoption of adequate prevention measures. Specific educational programs for care home staff should also be implemented to address this increasing problem.Catedra de Docencia e Investigacion SEMERGEN-Medicina de Familia, University of Granada, Spai