Solving the riddle of codon usage preferences: a test for translational selection

Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of molecular evolution, yet, establishing the underlying causes for its idiosyncratic behaviour across living kingdoms has proven elusive to researchers over the past 20 years. In this study, a statistical model for measuring translational selection in any given genome is developed, and the test is applied to 126 fully sequenced genomes, ranging from archaea to eukaryotes. It is shown that tRNA gene redundancy and genome size are interacting forces that ultimately determine the action of translational selection, and that an optimal genome size exists for which this kind of selection is maximal. Accordingly, genome size also presents upper and lower boundaries beyond which selection on codon usage is not possible. We propose a model where the coevolution of genome size and tRNA genes explains the observed patterns in translational selection in all living organisms. This model finally unifies our understanding of codon usage across prokaryotes and eukaryotes. Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model

Solving the riddle of codon usage preferences: a test for translational selection

Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of molecular evolution, yet, establishing the underlying causes for its idiosyncratic behaviour across living kingdoms has proven elusive to researchers over the past 20 years. In this study, a statistical model for measuring translational selection in any given genome is developed, and the test is applied to 126 fully sequenced genomes, ranging from archaea to eukaryotes. It is shown that tRNA gene redundancy and genome size are interacting forces that ultimately determine the action of translational selection, and that an optimal genome size exists for which this kind of selection is maximal. Accordingly, genome size also presents upper and lower boundaries beyond which selection on codon usage is not possible. We propose a model where the coevolution of genome size and tRNA genes explains the observed patterns in translational selection in all living organisms. This model finally unifies our understanding of codon usage across prokaryotes and eukaryotes. Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model

Early stopping for statistical inverse problems via truncated SVD estimation

We consider truncated SVD (or spectral cut-off, projection) estimators for a prototypical statistical inverse problem in dimension $D$. Since calculating the singular value decomposition (SVD) only for the largest singular values is much less costly than the full SVD, our aim is to select a data-driven truncation level $\widehat m\in\{1,\ldots,D\}$ only based on the knowledge of the first $\widehat m$ singular values and vectors. We analyse in detail whether sequential {\it early stopping} rules of this type can preserve statistical optimality. Information-constrained lower bounds and matching upper bounds for a residual based stopping rule are provided, which give a clear picture in which situation optimal sequential adaptation is feasible. Finally, a hybrid two-step approach is proposed which allows for classical oracle inequalities while considerably reducing numerical complexity.Comment: slightly modified version. arXiv admin note: text overlap with arXiv:1606.0770

Adaptation to criticality through organizational invariance in embodied agents

Many biological and cognitive systems do not operate deep within one or other regime of activity. Instead, they are poised at critical points located at phase transitions in their parameter space. The pervasiveness of criticality suggests that there may be general principles inducing this behaviour, yet there is no well-founded theory for understanding how criticality is generated at a wide span of levels and contexts. In order to explore how criticality might emerge from general adaptive mechanisms, we propose a simple learning rule that maintains an internal organizational structure from a specific family of systems at criticality. We implement the mechanism in artificial embodied agents controlled by a neural network maintaining a correlation structure randomly sampled from an Ising model at critical temperature. Agents are evaluated in two classical reinforcement learning scenarios: the Mountain Car and the Acrobot double pendulum. In both cases the neural controller appears to reach a point of criticality, which coincides with a transition point between two regimes of the agent's behaviour. These results suggest that adaptation to criticality could be used as a general adaptive mechanism in some circumstances, providing an alternative explanation for the pervasive presence of criticality in biological and cognitive systems.Comment: arXiv admin note: substantial text overlap with arXiv:1704.0525

INFLUENCE OF MATERIAL CHARACTERIZATION IN THE DESIGN OF TUNNEL LIGHTING INSTALLATIONS

The paper describes the influence of the characterisation of reflectance behaviour of tunnel pavements and wall materials on the tunnel lighting design. CIE 189 document suggests considering lambertian behaviour for inter-reflection calculations for road luminance evaluation at design stage, because, unfortunately, no bi-directional reflection data for tunnel surfaces are commonly available. This simplification is supported by the low impact of inter- reflection contribution to road luminance. A European funded research project ha the task of developing the metrological support for the road surface characterisation in new geometries of measurements. The paper suggests to apply the outcomes on new geometries to tunnel wall materials characterisation suggesting that the suggested SURFACE observation angle of 2.29° can be useful for short tunnel too, including wall surfaces