Evaluation of properties over phylogenetic trees using stochastic logics

Background: Model checking has been recently introduced as an integrated framework for extracting information of the phylogenetic trees using temporal logics as a querying language, an extension of modal logics that imposes restrictions of a boolean formula along a path of events. The phylogenetic tree is considered a transition system modeling the evolution as a sequence of genomic mutations (we understand mutation as different ways that DNA can be changed), while this kind of logics are suitable for traversing it in a strict and exhaustive way. Given a biological property that we desire to inspect over the phylogeny, the verifier returns true if the specification is satisfied or a counterexample that falsifies it. However, this approach has been only considered over qualitative aspects of the phylogeny. Results: In this paper, we repair the limitations of the previous framework for including and handling quantitative information such as explicit time or probability. To this end, we apply current probabilistic continuous-time extensions of model checking to phylogenetics. We reinterpret a catalog of qualitative properties in a numerical way, and we also present new properties that couldn't be analyzed before. For instance, we obtain the likelihood of a tree topology according to a mutation model. As case of study, we analyze several phylogenies in order to obtain the maximum likelihood with the model checking tool PRISM. In addition, we have adapted the software for optimizing the computation of maximum likelihoods. Conclusions: We have shown that probabilistic model checking is a competitive framework for describing and analyzing quantitative properties over phylogenetic trees. This formalism adds soundness and readability to the definition of models and specifications. Besides, the existence of model checking tools hides the underlying technology, omitting the extension, upgrade, debugging and maintenance of a software tool to the biologists. A set of benchmarks justify the feasibility of our approach

Importance of Vanadium-Catalyzed Oxidation of SO2 to SO3 in Two-Stroke Marine Diesel Engines

Low-speed marine diesel engines are mostly operated on heavy fuel oils, which have a high content of sulfur and ash, including trace amounts of vanadium, nickel, and aluminum. In particular, vanadium oxides could catalyze in-cylinder oxidation of SO2 to SO3, promoting the formation of sulfuric acid and enhancing problems of corrosion. In the present work, the kinetics of the catalyzed oxidation was studied in a fixed-bed reactor at atmospheric pressure. Vanadium oxide nanoparticles were synthesized by spray flame pyrolysis, i.e., by a mechanism similar to the mechanism leading to the formation of the catalytic species within the engine. Experiments with different particle compositions (vanadium/sodium ratio) and temperatures (300–800 °C) show that both the temperature and sodium content have a major impact on the oxidation rate. Kinetic parameters for the catalyzed reaction are determined, and the proposed kinetic model fits well with the experimental data. The impact of the catalytic reaction is studied with a phenomenological zero-dimensional (0D) engine model, where fuel oxidation and SOx formation is modeled with a comprehensive gas-phase reaction mechanism. Results indicate that the oxidation of SO2 to SO3 in the cylinder is dominated by gas-phase reactions and that the vanadium-catalyzed reaction is at most a very minor pathway

Estudio de la oxidación de SO2 a SO3 con catalizadores basados en vanadio. Aplicación a motores marinos diésel de dos tiempos

Los grandes barcos utilizan generalmente motores diesel de dos tiempos, funcionan con fuelóleo pesado, que contiene grandes cantidades de azufre y vanadio. Por ello, es posible que se de lugar a la formación de ácido sulfúrico y que lleve a la llamada corrosión fría. Este trabajo pretende determinar la influencia de la presencia de vanadio sobre la conversión de SO2 y, por tanto, sobre la corrosió fría

Construction of data streams applications from functional, non-functional and resource requirements for electric vehicle aggregators. the COSMOS vision

COSMOS, Computer Science for Complex System Modeling, is a research team that has the mission of bridging the gap between formal methods and real problems. The goal is twofold: (1) a better management of the growing complexity of current systems; (2) a high quality of the implementation reducing the time to market. The COSMOS vision is to prove this approach in non-trivial industrial problems leveraging technologies such as software engineering, cloud computing, or workflows. In particular, we are interested in the technological challenges arising from the Electric Vehicle (EV) industry, around the EV-charging and control IT infrastructure

Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA

This paper examines the influence of the Raf Kinase Inhibitor Protein (RKIP) on the Extracellular signal Regulated Kinase (ERK) signalling pathway [5] through modelling in a Markovian process algebra, PEPA [11]. Two models of the system are presented, a reagent-centric view and a pathway-centric view. The models capture functionality at the level of subpathway, rather than at a molecular level. Each model affords a different perspective of the pathway and analysis. We demonstrate the two models to be formally equivalent using the timing-aware bisimulation defined over PEPA models and discuss the biological significance

Anatomo-functional organization in brain networks

There are several studies focused on comparing rsFC networks with their structural substrate \cite{hagmann2008, honey2010}. However an accurate description of how anatomo-­functional connections are organized, both at physical and topological levels, is still to be defined. Here we present an approach to quantify the anatomo-functional organization and discuss its consistency

Efficient bleaching of non-woody high-quality paper pulp using lacasse-mediator systems

aDepartment of Molecular Microbiology, CIB, Consejo Superior de Investigaciones Científicas (CSIC), Velázquez 144, E-28006 Madrid, Spain; bDepartment of Textile and Paper Engineering, ETSII, Polytechnic University of Catalunya (UPC), Colón 11, E-08222 Terrassa, Spain; cDepartment of Biogeochemistry, IRNAS, CSIC, PO Box 1052, E-41080, Seville, Spain; dCelulosas de Levante SA (CELESA), Ctra. C-237, km 4.5, E-43500 Tortosa, SpainHigh-quality flax pulp was bleached in a totally-chlorine-free (TCF) sequence using a laccase-mediator system. Three fungal laccases (from Pycnoporus cinnabarinus, Trametes versicolor and Pleurotus eryngii) and two mediators, 2,2´-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) and 1-hydroxybenzotriazole (HBT), were compared. P. cinnabarinus and T. versicolor laccases in the presence of HBT gave the best results in terms of high brightness and low lignin content (kappa number). The former laccase also resulted in the best preservation of cellulose and the largest removal of residual lignin as revealed by analytical pyrolysis, and was selected for subsequent TCF bleaching. Up to 90% delignification and strong brightness increase were attained after a laccase-mediator treatment followed by H2O2 bleaching. This TCF sequence was further improved by applying H2O2 under pressurized O2. In this way, we obtained up to 82% ISO brightness (compared with 37% in the initial pulp, and 60% in the peroxide-bleached control) and very low kappa number (near 1). Good results were also found when the laccase-mediator treatment was performed in a bioreactor under pressurized oxygen. The pulp properties obtained, which could not be attained by conventional TCF bleaching of flax pulp, demonstrate the feasibility of enzymatic bleaching to substitute chlorine-containing reagents in manufacturing of these high-price paper pulps.This study was supported by the European Commission (contract QLK3-99-590), the Spanish CICYT (FEDER project 2FD97-0896-C02, and projects AGL2002-00393, BIO2002-1166 and PPQ2000-1068-C02-02), the Comunidad de Madrid, and the CSIC network on “Bioremediation and Phytoremediation”.Peer reviewe

Population pharmacokinetics of ganciclovir after intravenous ganciclovir and oral valganciclovir administration in solid organ transplant patients infected with cytomegalovirus

A population pharmacokinetics analysis was performed after intravenous ganciclovir and oral valganciclovir in solid organ transplant patients with cytomegalovirus. Patients received ganciclovir at 5 mg/kg of body weight (5 days) and then 900 mg of valganciclovir (16 days), both twice daily with dose adjustment for renal function. A total of 382 serum concentrations from days 5 and 15 were analyzed with NONMEM VI. Renal function given by creatinine clearance (CL(CR)) was the most influential covariate in CL. The final pharmacokinetic parameters were as follows: ganciclovir clearance (CL) was 7.49.(CL(CR)/57) liter/h (57 was the mean population value of CL(CR)); the central and peripheral distribution volumes were 31.9 liters and 32.0 liters, respectively; intercompartmental clearance was 10.2 liter/h; the first-order absorption rate constant was 0.895 h(-1); bioavailability was 0.825; and lag time was 0.382 h. The CL(CR) was the best predictor of CL, making dose adjustment by this covariate important to achieve the most efficacious ganciclovir exposure

Eliminación de la hepatitis C. Documento de posicionamiento de la Asociación Española para el Estudio del Hígado (AEEH)

La Asociación Española para el Estudio del Hígado (AEEH) está convencida de que la eliminación de la hepatitis C en España es posible siempre y cuando seamos capaces de emplear los recursos y las herramientas necesarias para la misma. Este documento refleja la posición de la AEEH respecto a la eliminación del virus de la hepatitis C (VHC), estableciendo una amplia serie de recomendaciones que se pueden agrupar en cinco categorías: 1) cribado del VHC en función de la edad, de la existencia de factores de riesgo clásicos de adquisición de la infección, búsqueda activa de pacientes diagnosticados con anterioridad y desarrollo de estrategias de microeliminación en poblaciones vulnerables; 2) simplificación del diagnóstico del VHC (diagnóstico en un solo paso y diagnóstico en el punto de atención del paciente); 3) simplificación del tratamiento de los pacientes y mejora de los circuitos asistenciales; 4) medidas de política sanitaria, y, finalmente, 5) establecimiento de indicadores de eliminación del VHC. The Spanish Association for the Study of the Liver (AEEH) is convinced that the elimination of hepatitis C virus (HCV) in Spain is possible as long as we are able to use the resources and tools necessary for it. This document reflects the position of the AEEH regarding the elimination of HCV, establishing a wide range of recommendations that can be grouped into five categories: 1) Screening of HCV according to age, of the existence of classic acquisition risk factors of infection, active search of previously diagnosed patients and development of microelimination strategies in vulnerable populations; 2) Simplification of HCV diagnosis (one-step diagnosis and diagnosis at the point of patient care); 3) Simplification of patient treatment and improvement of care circuits; 4) Health policy measures, and, finally, 5) Establishment of HCV elimination indicators