Gene Similarity-based Approaches for Determining Core-Genes of Chloroplasts

In computational biology and bioinformatics, the manner to understand evolution processes within various related organisms paid a lot of attention these last decades. However, accurate methodologies are still needed to discover genes content evolution. In a previous work, two novel approaches based on sequence similarities and genes features have been proposed. More precisely, we proposed to use genes names, sequence similarities, or both, insured either from NCBI or from DOGMA annotation tools. Dogma has the advantage to be an up-to-date accurate automatic tool specifically designed for chloroplasts, whereas NCBI possesses high quality human curated genes (together with wrongly annotated ones). The key idea of the former proposal was to take the best from these two tools. However, the first proposal was limited by name variations and spelling errors on the NCBI side, leading to core trees of low quality. In this paper, these flaws are fixed by improving the comparison of NCBI and DOGMA results, and by relaxing constraints on gene names while adding a stage of post-validation on gene sequences. The two stages of similarity measures, on names and sequences, are thus proposed for sequence clustering. This improves results that can be obtained using either NCBI or DOGMA alone. Results obtained with this quality control test are further investigated and compared with previously released ones, on both computational and biological aspects, considering a set of 99 chloroplastic genomes.Comment: 4 pages, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2014

Finding the Core-Genes of Chloroplasts

Due to the recent evolution of sequencing techniques, the number of available genomes is rising steadily, leading to the possibility to make large scale genomic comparison between sets of close species. An interesting question to answer is: what is the common functionality genes of a collection of species, or conversely, to determine what is specific to a given species when compared to other ones belonging in the same genus, family, etc. Investigating such problem means to find both core and pan genomes of a collection of species, \textit{i.e.}, genes in common to all the species vs. the set of all genes in all species under consideration. However, obtaining trustworthy core and pan genomes is not an easy task, leading to a large amount of computation, and requiring a rigorous methodology. Surprisingly, as far as we know, this methodology in finding core and pan genomes has not really been deeply investigated. This research work tries to fill this gap by focusing only on chloroplastic genomes, whose reasonable sizes allow a deep study. To achieve this goal, a collection of 99 chloroplasts are considered in this article. Two methodologies have been investigated, respectively based on sequence similarities and genes names taken from annotation tools. The obtained results will finally be evaluated in terms of biological relevance

Building a Chaotic Proven Neural Network

International audienceChaotic neural networks have received a great deal of attention these last years. In this paper we establish a precise correspondence between the so-called chaotic iterations and a particular class of artificial neural networks: global recurrent multi-layer perceptrons. We show formally that it is possible to make these iterations behave chaotically, as defined by Devaney, and thus we obtain the first neural networks proven chaotic. Several neural networks with different architectures are trained to exhibit a chaotical behavior

Data Processing using Artificial Neural Networks to Improve the Simulation of Lung Motion

International audienceTo optimize the delivery in lung radiation therapy, a better understanding of the tumor motion is required. On the one hand to have a better tumor-targeting efficiency, and on the other hand to avoid as much as possible normal tissues. The 4D-CT allows to quantify tumor motion, but due to artifacts it introduces biases and errors in tumor localization. Despite of this disadvantage, we propose a method to simulate lung motion based on data provided by the 4D-CT for several patients. To reduce uncertainties introduced by the 4D-CT scan, we conveniently treated data using artificial neural networks. More precisely, our approach consists in a data augmentation technique. The data resulting from this processing step are then used to build a training set for another artificial neural network that learns the lung motion. To improve the learning accuracy, we have studied the number of phases required to precisely describe the displacement of each point. Thus, from 1118 points scattered across 5 patients and defined over 8 or 10 phases, we obtained 5800 points of 50 phases. After training, the network is used to compute the positions of 40 points from five other patients on 10 phases. These points allow to quantify the prediction performance. In comparison with the original data, the ones issued from our treatment process provide a significant increase of the prediction accuracy: an average improvement of 16% can be observed. The motion computed for several points by the neural network that has learnt the lung one exhibits an hysteresis near the one given by the 4D-CT, with an error smaller than 1 mm in the cranio-caudal axis

Essaie de Description du Système Foncier Congolais d’avant Le Contact Formel Avec La Civilisation Occidentale

The present study focuses on the description of the Congolese land system prior to formal contact with Western civilization. Contrary to what has been imagined, the natives of Congo have understood the notion behind landed property. This property is rather peculiar in that it does not fulfill all the criteria imposed by modern law. A few elements have enabled us to describe it. The notion of landed property has been made known to the natives. This property is established at the moment the pacific takes possession of it or by conquest of the soil. It is essentially influenced by the beliefs that characterize traditional Africa. However, the beliefs in the existence and interaction of the world of the dead with that of the living, and the beliefs in the divinity of the soil, makes it possible to specially guide the perception of landed property. Moreover, the community character directs land ownership towards collective ownership rather than individual ownership