Digging into acceptor splice site prediction : an iterative feature selection approach

Feature selection techniques are often used to reduce data dimensionality, increase classification performance, and gain insight into the processes that generated the data. In this paper, we describe an iterative procedure of feature selection and feature construction steps, improving the classification of acceptor splice sites, an important subtask of gene prediction. We show that acceptor prediction can benefit from feature selection, and describe how feature selection techniques can be used to gain new insights in the classification of acceptor sites. This is illustrated by the identification of a new, biologically motivated feature: the AG-scanning feature. The results described in this paper contribute both to the domain of gene prediction, and to research in feature selection techniques, describing a new wrapper based feature weighting method that aids in knowledge discovery when dealing with complex datasets

Iteratively regularized Newton-type methods for general data misfit functionals and applications to Poisson data

We study Newton type methods for inverse problems described by nonlinear operator equations $F(u)=g$ in Banach spaces where the Newton equations $F'(u_n;u_{n+1}-u_n) = g-F(u_n)$ are regularized variationally using a general data misfit functional and a convex regularization term. This generalizes the well-known iteratively regularized Gauss-Newton method (IRGNM). We prove convergence and convergence rates as the noise level tends to 0 both for an a priori stopping rule and for a Lepski{\u\i}-type a posteriori stopping rule. Our analysis includes previous order optimal convergence rate results for the IRGNM as special cases. The main focus of this paper is on inverse problems with Poisson data where the natural data misfit functional is given by the Kullback-Leibler divergence. Two examples of such problems are discussed in detail: an inverse obstacle scattering problem with amplitude data of the far-field pattern and a phase retrieval problem. The performence of the proposed method for these problems is illustrated in numerical examples

Innovation et gouvernance territoriale : une analyse par les dispositifs

International audienceCette communication vise à présenter les outils méthodologiques d'analyse/évaluation de la gouvernance territoriale élaborés dans le cadre du projet de recherche PSDR Gouv.Innov sur les innovations organisationnelles relatives à la gouvernance territoriale. Il s'agit d'étudier les transformations introduites par les politiques de développement durable au niveau des dispositifs de gouvernance territoriale visant à favoriser une gestion intégrée des espaces ruraux. Dans un contexte de recomposition de l'action publique où les procédures d'aménagement sont plutôt normées par des représentations urbaines, l'accent est mis sur la question des modalités de représentation des activités rurales, pour lesquelles nous faisons l'hypothèse qu'elles sont sous représentées. Les premiers résultats méthodologiques permettent, dans une première partie, de proposer une définition générique et pragmatique de la gouvernance territoriale et de préciser la notion de dispositifs de gouvernance comme objet d'observation. A partir de cette définition une grille d'analyse permettant d'appréhender l'ensemble des dimensions en jeu dans les processus de gouvernance territoriale est élaborée. Dans la deuxième partie nous explorons l'intérêt de la notion de dispositif pour observer les processus de gouvernance et proposons une grille de collecte et de structuration des informations pour constituer des chroniques des dispositifs étudiés. / This paper seeks to present the methodological tools used in the analysis/evaluation of territorial governance developed during research undertaken within the framework of the PSDR Gouv-Innov project on organisational innovations with respect to territorial governance. It involves the study of the changes resulting from the emergence of sustainable development policies in territorial governance systems aiming to implement the integrated management of rural areas. In a context of changes in the way in which public action is implemented (for instance, public-private partnerships), where development procedures are usually standardised by urban representations, the emphasis is placed on the issue of the representation of rural activities, the hypothesis being that they are under-represented. The initial methodological results lead, in the first instance, to a proposition for a generic and pragmatic definition of territorial governance and a clarification of the notion of governance systems as objects of observation. This definition can be used as the basis of a framework to address all the analytical dimensions of the territorial governance process. In the second part, the authors explore the idea of system in order to observe governance processes and suggest a matrix for the collection and structuring of information in order to report on the studied systems

Comment étudier (analyser) la gouvernance territoriale ? Mise à l'épreuve d'une grille de lecture

International audienceDans cet article nous présentons une grille d'analyse de la gouvernance territoriale que nous avons construite dans le cadre d'un projet de recherche pluridisciplinaire à partir d'une définition commune de la gouvernance territoriale. La gouvernance territoriale est devenue une question centrale dans le développement territorial et un enjeu pour l'élaboration des politiques publiques. Elaborer une grille d'analyse sur la gouvernance territoriale ne va pas de soi ; nous illustrerons son opérationnalisation à partir des travaux de terrain réalisés dans trois situations dans la région de Languedoc Roussillon. Les dispositifs et outils sont contextuels et les modes de gouvernances pluriels selon les objectifs et les dynamiques antérieures. Enfin nous en tirerons des enseignements pour l'étude de la gouvernance tant sur la production des connaissances que sur l'opérationnalité de cette grille. / In this paper we present an analytical framework of territorial governance that we built as part of a multidisciplinary research project based on a common definition of territorial governance. Territorial governance has become a central issue in regional development and a challenge for public policy. Develop an analytical framework on territorial governance does not just happen, and we illustrate its operationalization based on fieldwork conducted in three situations in Languedoc-Roussillon. Devices and tools are contextual and plural forms of governance based on the objectives and dynamics earlier. Finally we will draw lessons for the study of governance both in the production of knowledge about the operational capability of the grid

Aquaculture system diversity and sustainable development : fish farms and their representation

Initiatives for the sustainable development of aquaculture have so far focused on the production of codes of conduct, of best management practices, of standards etc., most of which have been developed by international organisations, the industrial sector and non governmental organisations. They were, to a large extent, produced using a "top down" process and inspired by models from intensive industrial shrimp and sea fish farming (mainly salmon). However, most of global aquaculture production comes from small-and medium-sized farms, essentially in Asia which contributes 92% of the total world aquaculture production volume. The objective of this article is to define the contours of systemic typologies that are able to express the sustainability conditions of aquaculture systems. The proposed approach builds on surveys of aquaculture systems which differ in terms of their biogeographical nature (temperate/tropical and north/south countries) or their farming techniques and their governance systems. This work is a prerequisite to any attempt at an individualised and comparative evaluation of specific aquaculture systems from either global or territorial viewpoints. In order to go beyond the cleavage of a typology based on the differentiation between developed and developing countries, three typologies were produced. These typologies allow for discriminatory variables to be identified such as for example the marketing methods or the pace of innovation: a structural typology, a functional typology and a systemic typology. Finally, the representations of aquaculture activity and of its sustainability that producers have of the 4 different types that emerge from the systemic typology were recorded and analyzed

Anomalous zipping dynamics and forced polymer translocation

We investigate by Monte Carlo simulations the zipping and unzipping dynamics of two polymers connected by one end and subject to an attractive interaction between complementary monomers. In zipping, the polymers are quenched from a high temperature equilibrium configuration to a low temperature state, so that the two strands zip up by closing up a "Y"-fork. In unzipping, the polymers are brought from a low temperature double stranded configuration to high temperatures, so that the two strands separate. Simulations show that the unzipping time, $\tau_u$, scales as a function of the polymer length as $\tau_u \sim L$, while the zipping is characterized by anomalous dynamics $\tau_z \sim L^\alpha$ with $\alpha = 1.37(2)$. This exponent is in good agreement with simulation results and theoretical predictions for the scaling of the translocation time of a forced polymer passing through a narrow pore. We find that the exponent $\alpha$ is robust against variations of parameters and temperature, whereas the scaling of $\tau_z$ as a function of the driving force shows the existence of two different regimes: the weak forcing ($\tau_z \sim 1/F$) and strong forcing ($\tau_z$ independent of $F$) regimes. The crossover region is possibly characterized by a non-trivial scaling in $F$, matching the prediction of recent theories of polymer translocation. Although the geometrical setup is different, zipping and translocation share thus the same type of anomalous dynamics. Systems where this dynamics could be experimentally investigated are DNA (or RNA) hairpins: our results imply an anomalous dynamics for the hairpins closing times, but not for the opening times.Comment: 15 pages, 9 figure

Troposphere-to-mesosphere microphysics of carbon dioxide ice clouds in a Mars Global Climate Model

We have implemented full CO ice cloud microphysics into the LMD Mars Global Climate Model (MGCM) and we have conducted the first global simulations. The microphysical model implementation follows the modal scheme used for water ice cloud microphysics in the MGCM, but includes specific aspects that need to be accounted for when dealing with CO ice clouds. These include nucleation of CO on water ice crystals and CO condensation theory adapted for the Martian conditions. The model results are compared to available observations globally, and separately for polar regions and equatorial mesosphere. The observed seasonal and latitudinal variability of the CO ice clouds is in general reproduced. The polar regions are covered by CO ice clouds during the winter as observed. Instead of forming only in the lowest 10–15 km of the atmosphere, they extend up to several tens of kilometers above the surface in the model, dictated by the modeled temperature structure. We have also quantified the contribution of the cloud microphysics to the surface CO ice deposits. Snowfall from these clouds contributes up to 10% of the atmosphere–surface ice flux in the polar regions in our simulations, in the range that has been indirectly deduced from observations. In the mesosphere, notable amounts of CO ice clouds form only when water ice crystals are used as condensation nuclei in addition to dust particles, and their spatial distribution is in agreement with observations. The mesospheric temperature structure, dominated by tides, dictates the longitudinal and seasonal distribution of these clouds. The seasonal and local time variations of the clouds are not fully reproduced by the model. There is a long pause in CO ice cloud formation in the model around the aphelion season, but clouds have been observed during this period, although with a lower apparition frequency. Modeled mesospheric clouds form mainly during the night and in the morning, whereas during the daytime, when most of the cloud observations have been made, the model rarely predicts clouds. These discrepancies could be explained by the strong dependence of the cloud formation process on mesospheric temperatures that are themselves challenging to reproduce and sensitive to the MGCM processes and parameters. The rare possibilities for nighttime observations might also bias the observational climatologies towards daytime detections. Future developments of the model consist in the inclusion of a possible exogenous condensation nucleus source in the mesosphere and the radiative effect of CO ice clouds. © 2022 Elsevier Inc. All rights reserved.This paper presents the results of ten years of development that has been supported by funding from several sources. We thank the Agence National de la Recherche for funding (project MECCOM, ANR-18-CE31-0013). We are also grateful for the financial support by the LabEx (Laboratoire d’Excellence) ESEP, by the French space agency CNES and the European Space Agency ESA. We acknowledge the support of the French national planetology programme (PNP) as well. F.G.-G. is funded by the Spanish Ministerio de Ciencia, Innovación y Universidades, the Agencia Estatal de Investigación and EC FEDER funds under project RTI2018-100920-J-I00, and acknowledges financial support from the State Agency for Research of the Spanish MCIU through the Center of Excellence Severo Ochoa” award to the Instituto de Astrofísica de Andalucía (SEV-2017-0709). This work was performed using HPC computing resources from GENCI-CINES (Grant 2021-A0100110391), and resources at the ESPRI mesocentre of the IPSL institute .Peer reviewe

Identification of protein-coding sequences using the hybridization of 18S rRNA and mRNA during translation

We introduce a new approach in this article to distinguish protein-coding sequences from non-coding sequences utilizing a period-3, free energy signal that arises from the interactions of the 3′-terminal nucleotides of the 18S rRNA with mRNA. We extracted the special features of the amplitude and the phase of the period-3 signal in protein-coding regions, which is not found in non-coding regions, and used them to distinguish protein-coding sequences from non-coding sequences. We tested on all the experimental genes from Saccharomyces cerevisiae and Schizosaccharomyces pombe. The identification was consistent with the corresponding information from GenBank, and produced better performance compared to existing methods that use a period-3 signal. The primary tests on some fly, mouse and human genes suggests that our method is applicable to higher eukaryotic genes. The tests on pseudogenes indicated that most pseudogenes have no period-3 signal. Some exploration of the 3′-tail of 18S rRNA and pattern analysis of protein-coding sequences supported further our assumption that the 3′-tail of 18S rRNA has a role of synchronization throughout translation elongation process. This, in turn, can be utilized for the identification of protein-coding sequences

Expression Profiling of a Genetic Animal Model of Depression Reveals Novel Molecular Pathways Underlying Depressive-Like Behaviours

The Flinders model is a validated genetic rat model of depression that exhibits a number of behavioural, neurochemical and pharmacological features consistent with those observed in human depression.In this study we have used genome-wide microarray expression profiling of the hippocampus and prefrontal/frontal cortex of Flinders Depression Sensitive (FSL) and control Flinders Depression Resistant (FRL) lines to understand molecular basis for the differences between the two lines. We profiled two independent cohorts of Flinders animals derived from the same colony six months apart, each cohort statistically powered to allow independent as well as combined analysis. Using this approach, we were able to validate using real-time-PCR a core set of gene expression differences that showed statistical significance in each of the temporally distinct cohorts, representing consistently maintained features of the model. Small but statistically significant increases were confirmed for cholinergic (chrm2, chrna7) and serotonergic receptors (Htr1a, Htr2a) in FSL rats consistent with known neurochemical changes in the model. Much larger gene changes were validated in a number of novel genes as exemplified by TMEM176A, which showed 35-fold enrichment in the cortex and 30-fold enrichment in hippocampus of FRL animals relative to FSL.These data provide significant insights into the molecular differences underlying the Flinders model, and have potential relevance to broader depression research