On P Systems as a Modelling Tool for Biological Systems

We introduce a variant of P systems where rules have associated a real number providing a measure for the “intrinsic reactivity”of the rule and roughly corresponding to the kinetic coefficient which, in bio-chemistry, is usually associated to each molecular reaction. The behaviour of these P systems is then defined according to a strategy which, in each step, randomly selects the next rule to be applied depending upon a certain distribution of probabilities. As an application, we present a P system model of the quorum sensing regulatory networks of the bacterium Vibrio Fischeri. In this respect, a formalisation of the network in terms of P systems is provided and some simulation results concerning the behaviour of a colony of such bacteria are reported. We also briefly describe the implementation techniques adopted by pointing out the generality of our approach which appears to be fairly independent from the particular choice of P system variant and the language used to implement it.Ministerio de Ciencia y Tecnología TIC2002-04220-C03-0

Longitudinal changes in wellbeing amongst breastfeeding women in Australia and New Zealand during the COVID-19 pandemic

The COVID-19 pandemic has impacted new mothers’ wellbeing and breastfeeding experience. Women have experienced changes in birth and postnatal care and restricted access to their support network. It is unclear how these impacts may have changed over time with shifting rates of infection and policies restricting movement and access to services in Australia and New Zealand. This study investigated the longitudinal effect of the COVID-19 pandemic on breastfeeding and maternal wellbeing in Australia and New Zealand. Mothers (n = 246) completed an online survey every 4 weeks for 6 months that examined feeding methods, maternal mental wellbeing, worries, challenges, and positive experiences during the pandemic. Mothers maintained high full breastfeeding rates at 4 months (81%) which decreased to 37% at 6 months. Perceived low milk supply contributed to the earlier cessation of full breastfeeding. Poor infant sleep was associated with stress, perinatal anxiety, mental wellbeing, and breastfeeding status. Although mothers initially reported that lockdowns helped with family bonding and less pressure, prolonged lockdowns appeared to have adverse effects on access to social networks and extended family support. Conclusion: The results highlight the changing dynamic of the pandemic and the need for adaptable perinatal services which allow mothers access to in-person services and their support network even in lockdowns. Similarly, access to continuous education and clinical care remains critical for women experiencing concerns about their milk supply, infant sleep, and their own wellbeing

Parity-Violating Interaction Effects I: the Longitudinal Asymmetry in pp Elastic Scattering

The proton-proton parity-violating longitudinal asymmetry is calculated in the lab-energy range 0--350 MeV, using a number of different, latest-generation strong-interaction potentials--Argonne V18, Bonn-2000, and Nijmegen-I--in combination with a weak-interaction potential consisting of rho- and omega-meson exchanges--the model known as DDH. The complete scattering problem in the presence of parity-conserving, including Coulomb, and parity-violating potentials is solved in both configuration- and momentum-space. The predicted parity-violating asymmetries are found to be only weakly dependent upon the input strong-interaction potential adopted in the calculation. Values for the rho- and omega-meson weak coupling constants $h^{pp}_\rho$ and $h^{pp}_\omega$ are determined by reproducing the measured asymmetries at 13.6 MeV, 45 MeV, and 221 MeV.Comment: 24 pages, 8 figures, submitted to Physical Review

From microscopic to macroscopic descriptions of cell\ud migration on growing domains

Cell migration and growth are essential components of the development of multicellular organisms. The role of various cues in directing cell migration is widespread, in particular, the role of signals in the environment in the control of cell motility and directional guidance. In many cases, especially in developmental biology, growth of the domain also plays a large role in the distribution of cells and, in some cases, cell or signal distribution may actually drive domain growth. There is a ubiquitous use of partial differential equations (PDEs) for modelling the time evolution of cellular density and environmental cues. In the last twenty years, a lot of attention has been devoted to connecting macroscopic PDEs with more detailed microscopic models of cellular motility, including models of directional sensing and signal transduction pathways. However, domain growth is largely omitted in the literature. In this paper, individual-based models describing cell movement and domain growth are studied, and correspondence with a macroscopic-level PDE describing the evolution of cell density is demonstrated. The individual-based models are formulated in terms of random walkers on a lattice. Domain growth provides an extra mathematical challenge by making the lattice size variable over time. A reaction-diffusion master equation formalism is generalised to the case of growing lattices and used in the derivation of the macroscopic PDEs

The Attributed Pi Calculus with Priorities

International audienceWe present the attributed $\pi$-calculus for modeling concurrent systems with interaction constraints depending on the values of attributes of processes. The $\pi$-calculus serves as a constraint language underlying the $\pi$-calculus. Interaction constraints subsume priorities, by which to express global aspects of populations. We present a nondeterministic and a stochastic semantics for the attributed $\pi$-calculus. We show how to encode the $\pi$-calculus with priorities and polyadic synchronization $\pi$@ and thus dynamic compartments, as well as the stochastic $\pi$-calculus with concurrent objects spico. We illustrate the usefulness of the attributed $\pi$-calculus for modeling biological systems at two particular examples: Euglena’s spatial movement in phototaxis, and cooperative protein binding in gene regulation of bacteriophage lambda. Furthermore, population-based model is supported beside individual-based modeling. A stochastic simulation algorithm for the attributed $\pi$-calculus is derived from its stochastic semantics. We have implemented a simulator and present experimental results, that confirm the practical relevance of our approach

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

Jet size dependence of single jet suppression in lead-lead collisions at sqrt(s(NN)) = 2.76 TeV with the ATLAS detector at the LHC

Measurements of inclusive jet suppression in heavy ion collisions at the LHC provide direct sensitivity to the physics of jet quenching. In a sample of lead-lead collisions at sqrt(s) = 2.76 TeV corresponding to an integrated luminosity of approximately 7 inverse microbarns, ATLAS has measured jets with a calorimeter over the pseudorapidity interval |eta| < 2.1 and over the transverse momentum range 38 < pT < 210 GeV. Jets were reconstructed using the anti-kt algorithm with values for the distance parameter that determines the nominal jet radius of R = 0.2, 0.3, 0.4 and 0.5. The centrality dependence of the jet yield is characterized by the jet "central-to-peripheral ratio," Rcp. Jet production is found to be suppressed by approximately a factor of two in the 10% most central collisions relative to peripheral collisions. Rcp varies smoothly with centrality as characterized by the number of participating nucleons. The observed suppression is only weakly dependent on jet radius and transverse momentum. These results provide the first direct measurement of inclusive jet suppression in heavy ion collisions and complement previous measurements of dijet transverse energy imbalance at the LHC.Comment: 15 pages plus author list (30 pages total), 8 figures, 2 tables, submitted to Physics Letters B. All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HION-2011-02

Model Revision from Temporal Logic Properties in Computational Systems Biology

International audienceSystems biologists build models of bio-molecular processes from knowledge acquired both at the gene and protein levels, and at the phenotype level through experiments done in wildlife and mutated organisms. In this chapter, we present qualitative and quantitative logic learning tools, and illustrate how they can be useful to the modeler. We focus on biochemical reaction models written in the Systems Biology Markup Language SBML, and interpreted in the Biochemical Abstract Machine BIOCHAM. We first present a model revision algorithm for inferring reaction rules from biological properties expressed in temporal logic. Then we discuss the representations of kinetic models with ordinary differential equations (ODEs) and with stochastic logic programs (SLPs), and describe a parameter search algorithm for finding parameter values satisfying quantitative temporal properties. These methods are illustrated by a simple model of the cell cycle control, and by an application to the modelling of the conditions of synchronization in period of the cell cycle by the circadian cycle