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

An Information-Theoretic Characterization of the Optimal Gradient Sensing Response of Cells

Many cellular systems rely on the ability to interpret spatial heterogeneities in chemoattractant concentration to direct cell migration. The accuracy of this process is limited by stochastic fluctuations in the concentration of the external signal and in the internal signaling components. Here we use information theory to determine the optimal scheme to detect the location of an external chemoattractant source in the presence of noise. We compute the minimum amount of mutual information needed between the chemoattractant gradient and the internal signal to achieve a prespecified chemotactic accuracy. We show that more accurate chemotaxis requires greater mutual information. We also demonstrate that a priori information can improve chemotaxis efficiency. We compare the optimal signaling schemes with existing experimental measurements and models of eukaryotic gradient sensing. Remarkably, there is good quantitative agreement between the optimal response when no a priori assumption is made about the location of the existing source, and the observed experimental response of unpolarized Dictyostelium discoideum cells. In contrast, the measured response of polarized D. discoideum cells matches closely the optimal scheme, assuming prior knowledge of the external gradient—for example, through prolonged chemotaxis in a given direction. Our results demonstrate that different observed classes of responses in cells (polarized and unpolarized) are optimal under varying information assumptions

Study of a market model with conservative exchanges on complex networks

Many models of market dynamics make use of the idea of conservative wealth exchanges among economic agents. A few years ago an exchange model using extremal dynamics was developed and a very interesting result was obtained: a self-generated minimum wealth or poverty line. On the other hand, the wealth distribution exhibited an exponential shape as a function of the square of the wealth. These results have been obtained both considering exchanges between nearest neighbors or in a mean field scheme. In the present paper we study the effect of distributing the agents on a complex network. We have considered archetypical complex networks: Erdös–Rényi random networks and scale-free networks. The presence of a poverty line with finite wealth is preserved but spatial correlations are important, particularly between the degree of the node and the wealth. We present a detailed study of the correlations, as well as the changes in the Gini coefficient, that measures the inequality, as a function of the type and average degree of the considered networks.Fil: Braunstein, Lidia A.. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mar del Plata. Instituto de Investigaciones Físicas de Mar del Plata; Argentina. Boston University; Estados UnidosFil: Macri, Pablo Alejandro. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mar del Plata. Instituto de Investigaciones Físicas de Mar del Plata; ArgentinaFil: Iglesias, José Roberto. Universidade Federal do Rio Grande do Sul; Brasi

Principios de elaboración redaccional de noticias en el periodismo de Internet

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Ciencias de la Información, Departamento de Periodismo II, leída el 09-03-2009Internet ha revolucionado los medios tradicionales pero todavía no ha transformado el modo de redactar las noticias a publicar en este nuevo soporte. De la misma manera que los periódicos de papel, la radio y la televisión buscaron en su momento un estilo propio para contar las noticias, Internet debe encontrar también el lenguaje más acorde a este nuevo soporte. A través de una exhaustiva investigación, del análisis de los principales diarios digitales, de entrevistas a expertos del sector, del caso práctico de LaSemana.es y de los resultados obtenidos en el trabajo de campo, esta tesis doctoral concluye cuál es la estructura más acorde para escribir noticias en la Red, cómo serán los periódicos digitales del futuro, cómo sacar el máximo partido a los distintos elementos informativos y qué lenguaje es el más acorde para redactar las noticias a publicar en Internet.Depto. de Periodismo y Nuevos MediosFac. de Ciencias de la InformaciónTRUEunpu

Principios de elaboración redaccional de noticias en el periodismo de Internet

Internet ha revolucionado los medios tradicionales pero todavía no ha transformado el modo de redactar las noticias a publicar en este nuevo soporte. De la misma manera que los periódicos de papel, la radio y la televisión buscaron en su momento un estilo propio para contar las noticias, Internet debe encontrar también el lenguaje más acorde a este nuevo soporte. A través de una exhaustiva investigación, del análisis de los principales diarios digitales, de entrevistas a expertos del sector, del caso práctico de LaSemana.es y de los resultados obtenidos en el trabajo de campo, esta tesis doctoral concluye cuál es la estructura más acorde para escribir noticias en la Red, cómo serán los periódicos digitales del futuro, cómo sacar el máximo partido a los distintos elementos informativos y qué lenguaje es el más acorde para redactar las noticias a publicar en Internet

Dynamic Properties of Network Motifs Contribute to Biological Network Organization

Biological networks, such as those describing gene regulation, signal transduction, and neural synapses, are representations of large-scale dynamic systems. Discovery of organizing principles of biological networks can be enhanced by embracing the notion that there is a deep interplay between network structure and system dynamics. Recently, many structural characteristics of these non-random networks have been identified, but dynamical implications of the features have not been explored comprehensively. We demonstrate by exhaustive computational analysis that a dynamical property—stability or robustness to small perturbations—is highly correlated with the relative abundance of small subnetworks (network motifs) in several previously determined biological networks. We propose that robust dynamical stability is an influential property that can determine the non-random structure of biological networks

A method for determining the robustness of bio-molecular oscillator models

Abstract Background Quantifying the robustness of biochemical models is important both for determining the validity of a natural system model and for designing reliable and robust synthetic biochemical networks. Several tools have been proposed in the literature. Unfortunately, multiparameter robustness analysis suffers from computational limitations. Results A novel method for quantifying the robustness of oscillatory behavior to parameter perturbations is presented in this paper. This method relies on the combination of Hopf bifurcation and Routh-Hurwitz stability criterion, which is widely applied in control system design. The proposed method is employed to calculate the robustness of two oscillating biochemical network models previously analyzed in the literature. The robustness bounds here obtained are tighter than what was previously obtained in the literature for both models. Conclusion The method here proposed for quantifying the robustness of biochemical oscillator models is computationally less demanding than similar multiparamter variation techniques available in the literature. It also provides tighter bounds on two models previously analyzed in the literature.http://deepblue.lib.umich.edu/bitstream/2027.42/112631/1/12918_2009_Article_363.pd

Geant4-GATE Simulation of a Large Plastic Scintillator for Muon Radiography

Envisaging the possibility of using large-area plastic scintillator slabs as robust detectors for high spatial resolution muon radiography, and prior to prototype development, we study expected basic performance by Monte Carlo simulation. We present preliminary results for a scalable square footprint detector unit of similar to 1 m(2), defining a representative simulation model volume of 50 cm x 50 cm, with reflective surfaces and a light readout by direct coupling of 4 small PMTs (in a square arrangement) at one face of the scintillator slab. Light detection efficiency is calculated for several light collection configurations, considering different values of surface roughness, reflectivity, optical coupling index and scintillator thickness. Values maximizing photon detection have been identified. The light response function of 2.5-3.5 cm diameter PMTs for the proposed configuration has been determined. A detector intrinsic spatial resolution of the order of 1 cm is estimated for muon interactions at the center region of the detector module, using a simple centroid positioning algorithm (Anger logic)

Avoiding communication barriers in the classroom: the APEINTA project

Education is a fundamental human right, however unfortunately not everybody has the same learning opportunities. For instance, if a student has hearing impairments, s/he could face communications barriers in the classroom, which could affect his/her learning process. APEINTA is a Spanish educational project that aims for inclusive education for all. This project proposes two main accessible initiatives: (1) real-time captioning and text-to-speech (TTS) services in the classroom and (2) accessible Web-learning platform out of the classroom with accessible digital resources. This paper presents the inclusive initiatives of APEINTA. Also an evaluation of the into-the-classroom initiative (real-time captioning and TTS services) is presented. This evaluation has been conducted during a regular undergraduate course at a university and during a seminar at an integration school for deaf children. Forty-five hearing students, 1 foreign student, 3 experts in captioning, usability and accessibility, and 20 students with hearing impairments evaluated these services in the classroom. Evaluation results show that these initiatives are adequate to be used in the classroom and that students are satisfied with them.Publicad