Bulking II: Classifications of Cellular Automata

This paper is the second part of a series of two papers dealing with bulking: a way to define quasi-order on cellular automata by comparing space-time diagrams up to rescaling. In the present paper, we introduce three notions of simulation between cellular automata and study the quasi-order structures induced by these simulation relations on the whole set of cellular automata. Various aspects of these quasi-orders are considered (induced equivalence relations, maximum elements, induced orders, etc) providing several formal tools allowing to classify cellular automata

Optimality of the genetic code with respect to protein stability and amino acid frequencies

How robust is the natural genetic code with respect to mistranslation errors? It has long been known that the genetic code is very efficient in limiting the effect of point mutation. A misread codon will commonly code either for the same amino acid or for a similar one in terms of its biochemical properties, so the structure and function of the coded protein remain relatively unaltered. Previous studies have attempted to address this question more quantitatively, namely by statistically estimating the fraction of randomly generated codes that do better than the genetic code regarding its overall robustness. In this paper, we extend these results by investigating the role of amino acid frequencies in the optimality of the genetic code. When measuring the relative fitness of the natural code with respect to a random code, it is indeed natural to assume that a translation error affecting a frequent amino acid is less favorable than that of a rare one, at equal mutation cost. We find that taking the amino acid frequency into account accordingly decreases the fraction of random codes that beat the natural code, making the latter comparatively even more robust. This effect is particularly pronounced when more refined measures of the amino acid substitution cost are used than hydrophobicity. To show this, we devise a new cost function by evaluating with computer experiments the change in folding free energy caused by all possible single-site mutations in a set of known protein structures. With this cost function, we estimate that of the order of one random code out of 100 millions is more fit than the natural code when taking amino acid frequencies into account. The genetic code seems therefore structured so as to minimize the consequences of translation errors on the 3D structure and stability of proteins.Comment: 31 pages, 2 figures, postscript fil

Variable density sampling based on physically plausible gradient waveform. Application to 3D MRI angiography

Performing k-space variable density sampling is a popular way of reducing scanning time in Magnetic Resonance Imaging (MRI). Unfortunately, given a sampling trajectory, it is not clear how to traverse it using gradient waveforms. In this paper, we actually show that existing methods [1, 2] can yield large traversal time if the trajectory contains high curvature areas. Therefore, we consider here a new method for gradient waveform design which is based on the projection of unrealistic initial trajectory onto the set of hardware constraints. Next, we show on realistic simulations that this algorithm allows implementing variable density trajectories resulting from the piecewise linear solution of the Travelling Salesman Problem in a reasonable time. Finally, we demonstrate the application of this approach to 2D MRI reconstruction and 3D angiography in the mouse brain.Comment: IEEE International Symposium on Biomedical Imaging (ISBI), Apr 2015, New-York, United State

A Catalog of Patterns for Concept Lattice Interpretation in Software Reengineering

International audienceFormal Concept Analysis (FCA) provides an important approach in software reengineering for software understanding, design anomalies detection and correction. However, FCA-based approaches have two problems: (i) they produce lattices that must be interpreted by the user according to his/her understanding of the technique and different elements of the graph; and, (ii) the lattice can rapidly become so big that one is overwhelmed by the mass of information and possibilities. In this paper, we present a catalogue of important patterns in concept lattices, which can allow automating the task of lattice interpretation. The approach helps the reengineer to concentrate on the task of reengineering rather than understanding a complex lattice. We provide interpretation of these patterns in a generalized manner and illustrate them on various contexts constructed from program information of different open-source systems. We also present a tool that allows automated extraction of the patterns from concept lattices

Mutualistic interactions shape global spatial congruence and climatic niche evolution in Neotropical mimetic butterflies

Understanding the mechanisms underlying species distributions and coexistence is both a priority and a challenge for biodiversity hotspots such as the Neotropics. Here, we highlight that Mullerian mimicry, where defended prey species display similar warning signals, is key to the maintenance of biodiversity in the c. 400 species of the Neotropical butterfly tribe Ithomiini (Nymphalidae: Danainae). We show that mimicry drives large-scale spatial association among phenotypically similar species, providing new empirical evidence for the validity of Muller's model at a macroecological scale. Additionally, we show that mimetic interactions drive the evolutionary convergence of species climatic niche, thereby strengthening the co-occurrence of co-mimetic species. This study provides new insights into the importance of mutualistic interactions in shaping both niche evolution and species assemblages at large spatial scales. Critically, in the context of climate change, our results highlight the vulnerability to extinction cascades of such adaptively assembled communities tied by positive interactions

L’étude de cas face à l’exemple : pratiques et enjeux dans l’enseignement de la géographie et de l’aménagement à l’université

L’enseignement de la géographie et de l’aménagement renvoie à l’espace, d’un point de vue général et théorique mais aussi de façon plus spécifique, appuyé sur des espaces singuliers. Dans cette perspective la mobilisation d’exemples ou d’études de cas semble incontournable dans les pratiques pédagogiques de l’enseignement en géographie. Cette représentation est largement construite dans un héritage disciplinaire où une géographie empirique s’est construite autour d’études de cas régionaux. Alors que la géographie a connu différentes évolutions épistémologiques, il semble intéressant d’interroger la réalité des pratiques enseignantes de cette géographie contemporaine à l’université. C’est ce que cet article propose de faire par le biais de l’analyse d’un corpus d’entretiens menés auprès d’enseignants- chercheurs français de géographie ou aménagement.Geography and Urban planning teaching is focused on space in a general and theoretical point of view but it also deals with specific places. Using examples or case studies to teach geography or urban planning seems to be natural. This fact is largely based on a disciplinary legacy for which empirical geography is built around regional case studies. While geography has experienced different epistemological developments, it seems interesting to question the reality of teaching practices in contemporary geography education in the university. That is what this article proposes to do through the analysis of a corpus of interviews with French teacher-researchers in the geography or urban planning field

Pemodelan Numerik Tsunami untuk Mengestimasi Waktu Tiba dan Ketinggian Maksimum Gelombang Tsunami di Teluk Amurang

Amurang Bay is a coastal area of South Minahasa Regency which is densely populated but faces the subduction zone of North Sulawesi which has the potential to generate earthquakes that trigger a tsunami. The process of the tsunami disaster occurred quickly, but the impact was very destructive and caused many casualties. This study aims to determine the propagation of tsunami waves with the worst scenario Mw 8.5 in Amurang Bay. Numerical methods in COMCOT software are used to model the propagation of tsunami waves in order to obtain an estimate of arrival time and maximum height of tsunami waves. Based on this modeling, the estimated arrival time of tsunami waves at the virtual tide gauge point in Amurang Bay is in the range of 8–11 minutes. The maximum height of tsunami waves is included in the alert category, which is 9.55 meters to 11.44 meters. The fastest estimated arrival time was recorded in Amurang Barat District and maximum height of tsunami waves was found in Tumpaan District. The results of this modeling can be used as one of the steps for mitigating tsunami disaster by preparing the surrounding community and assisting the evacuation process when a tsunami disaster occurs

Participation of TRPV1 in the activity of the GnRH system in male rats

GnRH neuron activity is under the influence of multiple stimuli, including those coming from the endocannabinoid and the immune systems. Since it has been previously suggested that some of the main elements controlling the GnRH pulse generator possess the TRPV1 receptor, the aim of the present study was to evaluate the participation of the hypothalamic TRPV1, through its pharmacological blockade, in the activity of the hypothalamic-pituitary-testicular axis in male rats under basal or acute inflammatory conditions. Our hypothesis was based on the idea that the hypothalamic TRPV1 participates in the synthesis of the main neuromodulatory signals controlling GnRH, and therefore the reproductive axis. Our results showed that the hypothalamic TRPV1 blockade induced pro-inflammatory effects by increasing Tnfα and Il-1β mRNA Hypothalamic levels, and inhibited the reproductive axis by affecting Gnrh, Kiss1 and Rfrp3 mRNA levels and decreasing plasma levels of luteinizing hormone and testosterone under basal conditions, without significant additive effects in rats exposed to systemic LPS. Altogether, these results suggest that the hypothalamic TRPV1 receptor participates in the regulation of the GnRH system, probably by modulating immune-dependent mechanisms.Fil: Surkin, Pablo Nicolas. Universidad de Buenos Aires. Facultad de Odontología. Cátedra de Fisiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Dmytrenko, Ganna. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Centro de Estudios Farmacológicos y Botánicos. Universidad de Buenos Aires. Facultad de Medicina. Centro de Estudios Farmacológicos y Botánicos; ArgentinaFil: Di Giorgio, Noelia Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; ArgentinaFil: Bizzozzero, Marianne. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; ArgentinaFil: de Laurentiis, Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Centro de Estudios Farmacológicos y Botánicos. Universidad de Buenos Aires. Facultad de Medicina. Centro de Estudios Farmacológicos y Botánicos; ArgentinaFil: Fernández Solari, José Javier. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Odontología. Cátedra de Fisiología; Argentin

Mid-infrared predictions of cheese yield from bovine milk

audience: researcher, professiona