Structural Sensitivity of Neural and Genetic Networks

International audienceThis paper aims at giving new results on the structural sensitivity of biological networks represented by threshold Boolean networks and ruled by Hopfield-like evolution laws classically used in the context of neural and genetic networks. Indeed, the objective is to present how certain changes and/or perturbations in such networks can modify signicantly their asymptotic behaviour. More precisely, this work has been focused on three diferent kinds of what we think to be relevant in the biological area of robustness (in both theoretical and applied frameworks): the boundary sensitivity (external fields, hormone flows, ...), the state sensitivity (axonal or somatic modulations, microRNAs actions, ...) and the updating sensitivity

A guided tour of asynchronous cellular automata

Research on asynchronous cellular automata has received a great amount of attention these last years and has turned to a thriving field. We survey the recent research that has been carried out on this topic and present a wide state of the art where computing and modelling issues are both represented.Comment: To appear in the Journal of Cellular Automat

Implementation and Performance of the ATLAS Second Level Jet Trigger

ATLAS is one of the four major LHC experiments, designed to cover a wide range of physics topics. In order to cope with a rate of 40 MHz and 25 interactions per bunch crossing, the ATLAS trigger system is divided in three different levels. The first one (LVL1, hardware based) identifies signatures in 2 microseconds that are confirmed by the the following trigger levels (software based). The Second Level Trigger (LVL2) only looks at a region of the space around the LVL1 signature (called Region of Interest or ROI), confirming/rejecting the event in about 10 ms, while the Event Filter (Third Level Trigger, EF) has potential full event access and larger processing times, of the order of 1 s. The jet selection starts at the LVL1 with dedicated processors that search for high ET hadronic energy depositions. At the LVL2, the jet signatures are verified with the execution of a dedicated, fast jet reconstruction algorithm. Given the fact that the main jet's background are jets,the energy calibration at the LVL2 is one of the major dificulties of this trigger, allowing to distinguish low/high energy jets. The algorithm for the calibration has been chosen to be fast and robust, with a good performance. The other major dificulty is the execution time of the algorithm,dominated by the data unpacking time due to the large sizes of the jet ROI. In order to reduce the execution time, three possible granularities have been proposed and are being evaluated: cell based (standard), energy sums calculated at each Fron-End Board (FEB) and the use of the LVL1 Trigger Towers. The FEB and Trigger Tower granularities are also being used/evaluated for the reconstruction of the missing ET triggers at the Event Filter, given the short times available to process the full event. In this presentation, the design and implementation of the jet trigger of ATLAS will be discussed in detail, emphasasing the major dificulties of each selection step. The performance of the jet algorithm, including timing, eficiencies and rates will also be shown, with detailed comparisons of the different unpacking modes

Asynchronous simulation of Boolean networks by monotone Boolean networks

International audienceWe prove that the fully asynchronous dynamics of a Boolean network f : {0, 1}^n → {0, 1}^n without negative loop can be simulated, in a very specific way, by a monotone Boolean network with 2n components. We then use this result to prove that, for every even n, there exists a monotone Boolean network f : {0, 1}^n → {0, 1}^n , an initial configuration x and a fixed point y of f such that: (i) y can be reached from x with a fully asynchronous updating strategy, and (ii) all such strategies contains at least 2^{n/2} updates. This contrasts with the following known property: if f : {0, 1}^n → {0, 1}^n is monotone, then, for every initial configuration x, there exists a fixed point y such that y can be reached from x with a fully asynchronous strategy that contains at most n updates

Characterization of Reachable Attractors Using Petri Net Unfoldings

International audienceAttractors of network dynamics represent the long-term behaviours of the modelled system. Their characterization is therefore crucial for understanding the response and differentiation capabilities of a dynamical system. In the scope of qualitative models of interaction networks, the computation of attractors reachable from a given state of the network faces combinatorial issues due to the state space explosion. In this paper, we present a new algorithm that exploits the concurrency between transitions of parallel acting components in order to reduce the search space. The algorithm relies on Petri net unfoldings that can be used to compute a compact representation of the dynamics. We illustrate the applicability of the algorithm with Petri net models of cell signalling and regulation networks, Boolean and multi-valued. The proposed approach aims at being complementary to existing methods for deriving the attractors of Boolean models, while being %so far more generic since it applies to any safe Petri net

Association Between Toenail Selenium and Risk of Acute Myocardial Infarction in European Men: The EURAMIC Study

The association between selenium status and risk of acute myocardial infarction was examined in a multicenter case-control study in 10 centers from Europe and Israel in 1991-1992. Selenium in toenails was assessed for 683 nonfatal male cases with first acute myocardial infarction and 729 controls less than 70 years of age. Median toenail selenium content was 0.553 μg/g for cases and 0.590 μg/g for controls. After adjustment for age, center, and smoking, the odds ratio for myocardial infarction in the highest quintile of selenium as compared with the lowest was 0.63 . The observed inverse trend was somewhat stronger when the authors adjusted for vitamin E status (p = 0.05). Analysis stratified for smoking habits showed an inverse association in former smokers (odds ratio for the 75th-25th percentile contrast = 0.63 (95 percent confidence interval 0.43-0.94)), but not in current smokers (odds ratio = 0.97 ( 0.71-1.32)) or in those who had never smoked (odds ratio = 1.55 (0.87-2.76)). Analysis stratified by center showed a significant inverse association between selenium levels and risk of myocardial infarction for Germany (Berlin) only (75th to 25th percentile odds ratio = 0.62 (95 percent confidence interval 0.42-0.91)), which was the center with the lowest selenium levels. It appears that the increased risk of acute myocardial infarction at low levels of selenium intake is largely explained by cigarette smoking; selenium status does not appear to be an important determinant of risk of myocardial infarction at the levels observed in a large part of Europe. Am J Epidemiol 1997; 145: 373-

Attraction Basins as Gauges of Robustness against Boundary Conditions in Biological Complex Systems

One fundamental concept in the context of biological systems on which researches have flourished in the past decade is that of the apparent robustness of these systems, i.e., their ability to resist to perturbations or constraints induced by external or boundary elements such as electromagnetic fields acting on neural networks, micro-RNAs acting on genetic networks and even hormone flows acting both on neural and genetic networks. Recent studies have shown the importance of addressing the question of the environmental robustness of biological networks such as neural and genetic networks. In some cases, external regulatory elements can be given a relevant formal representation by assimilating them to or modeling them by boundary conditions. This article presents a generic mathematical approach to understand the influence of boundary elements on the dynamics of regulation networks, considering their attraction basins as gauges of their robustness. The application of this method on a real genetic regulation network will point out a mathematical explanation of a biological phenomenon which has only been observed experimentally until now, namely the necessity of the presence of gibberellin for the flower of the plant Arabidopsis thaliana to develop normally

Single hadron response measurement and calorimeter jet energy scale uncertainty with the ATLAS detector at the LHC

The uncertainty on the calorimeter energy response to jets of particles is derived for the ATLAS experiment at the Large Hadron Collider (LHC). First, the calorimeter response to single isolated charged hadrons is measured and compared to the Monte Carlo simulation using proton-proton collisions at centre-of-mass energies of sqrt(s) = 900 GeV and 7 TeV collected during 2009 and 2010. Then, using the decay of K_s and Lambda particles, the calorimeter response to specific types of particles (positively and negatively charged pions, protons, and anti-protons) is measured and compared to the Monte Carlo predictions. Finally, the jet energy scale uncertainty is determined by propagating the response uncertainty for single charged and neutral particles to jets. The response uncertainty is 2-5% for central isolated hadrons and 1-3% for the final calorimeter jet energy scale.Comment: 24 pages plus author list (36 pages total), 23 figures, 1 table, submitted to European Physical Journal

Measurement of χ c1 and χ c2 production with s√ = 7 TeV pp collisions at ATLAS

The prompt and non-prompt production cross-sections for the χ c1 and χ c2 charmonium states are measured in pp collisions at s√ = 7 TeV with the ATLAS detector at the LHC using 4.5 fb−1 of integrated luminosity. The χ c states are reconstructed through the radiative decay χ c → J/ψγ (with J/ψ → μ + μ −) where photons are reconstructed from γ → e + e − conversions. The production rate of the χ c2 state relative to the χ c1 state is measured for prompt and non-prompt χ c as a function of J/ψ transverse momentum. The prompt χ c cross-sections are combined with existing measurements of prompt J/ψ production to derive the fraction of prompt J/ψ produced in feed-down from χ c decays. The fractions of χ c1 and χ c2 produced in b-hadron decays are also measured

Measurement of the production of a W boson in association with a charm quark in pp collisions at √s = 7 TeV with the ATLAS detector

The production of a W boson in association with a single charm quark is studied using 4.6 fb−1 of pp collision data at s√ = 7 TeV collected with the ATLAS detector at the Large Hadron Collider. In events in which a W boson decays to an electron or muon, the charm quark is tagged either by its semileptonic decay to a muon or by the presence of a charmed meson. The integrated and differential cross sections as a function of the pseudorapidity of the lepton from the W-boson decay are measured. Results are compared to the predictions of next-to-leading-order QCD calculations obtained from various parton distribution function parameterisations. The ratio of the strange-to-down sea-quark distributions is determined to be 0.96+0.26−0.30 at Q 2 = 1.9 GeV2, which supports the hypothesis of an SU(3)-symmetric composition of the light-quark sea. Additionally, the cross-section ratio σ(W + +c¯¯)/σ(W − + c) is compared to the predictions obtained using parton distribution function parameterisations with different assumptions about the s−s¯¯¯ quark asymmetry