Quantifying robustness of biochemical network models

BACKGROUND: Robustness of mathematical models of biochemical networks is important for validation purposes and can be used as a means of selecting between different competing models. Tools for quantifying parametric robustness are needed. RESULTS: Two techniques for describing quantitatively the robustness of an oscillatory model were presented and contrasted. Single-parameter bifurcation analysis was used to evaluate the stability robustness of the limit cycle oscillation as well as the frequency and amplitude of oscillations. A tool from control engineering – the structural singular value (SSV) – was used to quantify robust stability of the limit cycle. Using SSV analysis, we find very poor robustness when the model's parameters are allowed to vary. CONCLUSION: The results show the usefulness of incorporating SSV analysis to single parameter sensitivity analysis to quantify robustness

The Socio-Economic Evaluation of a European Project: The Diylab Case

This paper builds on the results of a 3-year long European project, the main aim of which was to deeply and sustainably transform teaching and learning practice in primary and secondary schools and higher education, by introducing Do it Yourself (DIY) philosophy in order to expand digital competence and foster students' agency and collaborative learning. Three universities and three primary and secondary schools have been involved in a Collaborative Action Research (CAR) process in order to analyse their current institutional context and perceive needs, strengths and weaknesses; to undertake professional development activities and the design of DIYLabs; implement DIYLabs in the selected courses; and reflect upon ways of improving the institution's performance. This paper offers a global vision of the research and implementation processes and the results achieved, from the perspective of the socio-economic dimensions involved in a project aiming to make a difference in teaching and learning to meet the challenges of a society highly permeated by digital technology (DT). Keywords: educational change; digital competence; DIY digital objects; autonomous learning; action research; student agency; collaborative researc

Contribution of cropland to the spread of Shiga toxin phages and the emergence of new Shiga toxin-producing strains

A growing interest in healthy eating has lead to an increase in the consumption of vegetables, associated with a rising number of bacterial outbreaks related to fresh produce. This is the case of the outbreak in Germany, caused by a O104:H4 enteroaggregative E. coli strain lysogenic for a Stx phage. Temperate Stx phages released from their hosts occur as free particles in various environments. This study reports the occurrence of Stx phages in vegetables (lettuce, cucumber, and spinach) and cropland soil samples. Infectious Stx2 phages were found in all samples and many carried also Stx1 phages. Their persistence in vegetables, including germinated sprouts, of Stx phage 933 W and an E. coli C600 (933 W∆stx::gfp-cat) lysogen used as surrogate, showed reductions below 2 log10 units of both microorganisms at 23 °C and 4 °C over 10 days. Higher reductions (up to 3.9 log10) units were observed in cropland soils at both temperatures. Transduction of a recombinant 933 W∆stx::kan phage was observed in all matrices. Protecting against microbial contamination of vegetables is imperative to ensure a safe food chain. Since the emergence of new Stx strains by Stx phage transduction is possible in vegetable matrices, methods aimed at reducing microbial risks in vegetables should not neglect phages

A Probabilistic Approach to the Existence of Solutions to Semilinear Elliptic Equations

We study a semilinear elliptic equation with a pure power nonlinearity with exponent $p>1$, and provide sufficient conditions for the existence of positive solutions. These conditions involve expected exit times from the domain, $D$, where a solution is defined, and expected occupation times in suitable subdomains of $D$. They provide an alternative new approach to the geometric or topological sufficient conditions given in the literature for exponents close to the critical Sobolev exponent. Moreover, unlike standard results, in our probabilistic approach no \emph{a priori} upper bound restriction is imposed on $p$, which might be supercritical. The proof is based on a fixed point argument using a probabilistic representation formula. We also prove a multiplicity result and discuss possible extensions to the existence of sign changing solutions. Finally, we conjecture that necessary conditions for the existence of solutions might be obtained using a similar probabilistic approach. This motivates a series of natural questions related to the characterisation of topological and geometrical properties of a domain in probabilistic terms.Comment: 13 page

Visualidades contemporáneas, ciudadanía y sabiduría digital: Afrontar las posibilidades sin eludir las tensiones

En los últimos años la proliferación de tecnologías digitales (TD) para crear, almacenar, transformar, mezclar, transmitir y acceder a todo tipo de información ha supuesto una auténtica revolución en distintos ámbitos de la vida. La información visual (re)crea estereotipos, modelos, deseos, mundos irreales, posibles e imposibles, que constituyen y proyectan nuestros imaginarios y permean nuestras realidades. Esta revolución de lo visual, esta creciente facilidad, tanto para crear imágenes, como para transmitirlas y acceder a ellas, está teniendo un impacto considerable en la redefinición de los conceptos de ciudadanía y sabiduría y por tanto de la educación. En este contexto, discutimos las cuestiones relacionadas con lo que se ha dado en llamar la ciudadanía y la sabiduría digital, sobre todo en sus dimensiones relacionadas con un uso prudente de las mismas y el derecho (y el deber) del ciudadano de contar con una educación que le permita entender y participar en la sociedad, defender sus derechos y cumplir con sus obligaciones. En este artículo nos centraremos en la caracterización de las visualidades en la era digital, las nociones de ciudadanía y sabiduría en este contexto y sus implicaciones para la educación

On competitive bidding: scoring and position probability graphs

Iso-score curves graph (iSCG) and mathematical relationships between Scoring Parameters (SP) and Forecasting Parameters (FP) can be used in Economic Scoring Formulas (ESF) used in tendering to distribute the score among bidders in the economic part of a proposal. Each contracting authority must set an ESF when publishing tender specifications and the strategy of each bidder will differ depending on the ESF selected and the weight of the overall proposal scoring. The various mathematical relationships and density distributions that describe the main SPs and FPs, and the representation of tendering data by means of iSCGs, enable the generation of two new types of graphs that can be very useful for bidders who want to be more competitive: the scoring and position probability graphs

Near-field photocurrent nanoscopy on bare and encapsulated graphene

Opto-electronic devices utilizing graphene have already demonstrated unique capabilities, which are much more difficult to realize with conventional technologies. However, the requirements in terms of material quality and uniformity are very demanding. A major roadblock towards high-performance devices are the nanoscale variations of graphene properties, which strongly impact the macroscopic device behaviour. Here, we present and apply opto-electronic nanoscopy to measure locally both the optical and electronic properties of graphene devices. This is achieved by combining scanning near-field infrared nanoscopy with electrical device read-out, allowing infrared photocurrent mapping at length scales of tens of nanometers. We apply this technique to study the impact of edges and grain boundaries on spatial carrier density profiles and local thermoelectric properties. Moreover, we show that the technique can also be applied to encapsulated graphene/hexagonal boron nitride (h-BN) devices, where we observe strong charge build-up near the edges, and also address a device solution to this problem. The technique enables nanoscale characterization for a broad range of common graphene devices without the need of special device architectures or invasive graphene treatment

Terahertz epsilon-near-zero graded-index lens

An epsilon-near-zero graded-index converging lens with planar faces is proposed and analyzed. Each perfectly-electric conducting (PEC) waveguide comprising the lens operates slightly above its cut-off frequency and has the same length but different cross-sectional dimensions. This allows controlling individually the propagation constant and the normalized characteristic impedance of each waveguide for the desired phase front at the lens output while Fresnel reflection losses are minimized. A complete theoretical analysis based on the waveguide theory and Fermat’s principle is provided. This is complemented with numerical simulation results of two-dimensional and three-dimensional lenses, made of PEC and aluminum, respectively, and working in the terahertz regime, which show good agreement with the analytical work.Effort sponsored by Spanish Government under contracts Consolider “Engineering Metamaterials” CSD2008-00066 and TEC2011-28664-C02-01. P.R.-U. is sponsored by the Government of Navarra under funding program “Formación de tecnólogos” 055/01/11. M.N.- C. is supported by the Imperial College Junior Research Fellowship. M. B. acknowledges funding by the Spanish Government under the research contract program Ramon y Cajal RYC-2011-08221. N.E. acknowledges the support from the US Office of Naval Research (ONR) Multidisciplinary University Research Initiatives (MURI) grant number N00014-10-1- 0942

The Convex Relaxation Barrier, Revisited: Tightened Single-Neuron Relaxations for Neural Network Verification

We improve the effectiveness of propagation- and linear-optimization-based neural network verification algorithms with a new tightened convex relaxation for ReLU neurons. Unlike previous single-neuron relaxations which focus only on the univariate input space of the ReLU, our method considers the multivariate input space of the affine pre-activation function preceding the ReLU. Using results from submodularity and convex geometry, we derive an explicit description of the tightest possible convex relaxation when this multivariate input is over a box domain. We show that our convex relaxation is significantly stronger than the commonly used univariate-input relaxation which has been proposed as a natural convex relaxation barrier for verification. While our description of the relaxation may require an exponential number of inequalities, we show that they can be separated in linear time and hence can be efficiently incorporated into optimization algorithms on an as-needed basis. Based on this novel relaxation, we design two polynomial-time algorithms for neural network verification: a linear-programming-based algorithm that leverages the full power of our relaxation, and a fast propagation algorithm that generalizes existing approaches. In both cases, we show that for a modest increase in computational effort, our strengthened relaxation enables us to verify a significantly larger number of instances compared to similar algorithms