Prediction of super-secondary structure in α-helical and β-barrel transmembrane proteins

International audienceA dynamic programming algorithm is proposed to predict the structure of different families of proteins and is tested with the b-barrel transmembrane proteins.Un algorithme est proposé qui permet, par programmation dynamique, de prédire la strucutre de différentes familles de protéines. Il est testé sur les proteeines transmembranaires (beta)

Altimetry for the future: Building on 25 years of progress

In 2018 we celebrated 25 years of development of radar altimetry, and the progress achieved by this methodology in the fields of global and coastal oceanography, hydrology, geodesy and cryospheric sciences. Many symbolic major events have celebrated these developments, e.g., in Venice, Italy, the 15th (2006) and 20th (2012) years of progress and more recently, in 2018, in Ponta Delgada, Portugal, 25 Years of Progress in Radar Altimetry. On this latter occasion it was decided to collect contributions of scientists, engineers and managers involved in the worldwide altimetry community to depict the state of altimetry and propose recommendations for the altimetry of the future. This paper summarizes contributions and recommendations that were collected and provides guidance for future mission design, research activities, and sustainable operational radar altimetry data exploitation. Recommendations provided are fundamental for optimizing further scientific and operational advances of oceanographic observations by altimetry, including requirements for spatial and temporal resolution of altimetric measurements, their accuracy and continuity. There are also new challenges and new openings mentioned in the paper that are particularly crucial for observations at higher latitudes, for coastal oceanography, for cryospheric studies and for hydrology. The paper starts with a general introduction followed by a section on Earth System Science including Ocean Dynamics, Sea Level, the Coastal Ocean, Hydrology, the Cryosphere and Polar Oceans and the ‘‘Green” Ocean, extending the frontier from biogeochemistry to marine ecology. Applications are described in a subsequent section, which covers Operational Oceanography, Weather, Hurricane Wave and Wind Forecasting, Climate projection. Instruments’ development and satellite missions’ evolutions are described in a fourth section. A fifth section covers the key observations that altimeters provide and their potential complements, from other Earth observation measurements to in situ data. Section 6 identifies the data and methods and provides some accuracy and resolution requirements for the wet tropospheric correction, the orbit and other geodetic requirements, the Mean Sea Surface, Geoid and Mean Dynamic Topography, Calibration and Validation, data accuracy, data access and handling (including the DUACS system). Section 7 brings a transversal view on scales, integration, artificial intelligence, and capacity building (education and training). Section 8 reviews the programmatic issues followed by a conclusion

Altimetry for the future: building on 25 years of progress

In 2018 we celebrated 25 years of development of radar altimetry, and the progress achieved by this methodology in the fields of global and coastal oceanography, hydrology, geodesy and cryospheric sciences. Many symbolic major events have celebrated these developments, e.g., in Venice, Italy, the 15th (2006) and 20th (2012) years of progress and more recently, in 2018, in Ponta Delgada, Portugal, 25 Years of Progress in Radar Altimetry. On this latter occasion it was decided to collect contributions of scientists, engineers and managers involved in the worldwide altimetry community to depict the state of altimetry and propose recommendations for the altimetry of the future. This paper summarizes contributions and recommendations that were collected and provides guidance for future mission design, research activities, and sustainable operational radar altimetry data exploitation. Recommendations provided are fundamental for optimizing further scientific and operational advances of oceanographic observations by altimetry, including requirements for spatial and temporal resolution of altimetric measurements, their accuracy and continuity. There are also new challenges and new openings mentioned in the paper that are particularly crucial for observations at higher latitudes, for coastal oceanography, for cryospheric studies and for hydrology. The paper starts with a general introduction followed by a section on Earth System Science including Ocean Dynamics, Sea Level, the Coastal Ocean, Hydrology, the Cryosphere and Polar Oceans and the “Green” Ocean, extending the frontier from biogeochemistry to marine ecology. Applications are described in a subsequent section, which covers Operational Oceanography, Weather, Hurricane Wave and Wind Forecasting, Climate projection. Instruments’ development and satellite missions’ evolutions are described in a fourth section. A fifth section covers the key observations that altimeters provide and their potential complements, from other Earth observation measurements to in situ data. Section 6 identifies the data and methods and provides some accuracy and resolution requirements for the wet tropospheric correction, the orbit and other geodetic requirements, the Mean Sea Surface, Geoid and Mean Dynamic Topography, Calibration and Validation, data accuracy, data access and handling (including the DUACS system). Section 7 brings a transversal view on scales, integration, artificial intelligence, and capacity building (education and training). Section 8 reviews the programmatic issues followed by a conclusion

Sur l'utilisation d'un SGBD relationnel pour la gestion d'une base de données image

Dans cette note nous présentons un projet original pour la réalisation d'une base de données orientée vers la synthèse d'images et d'animations. L'intérêt de ce système est de permettre la gestion conjointe de données iconographiques et sémantiques et donc d'associer finement la forme et le fond. Pour des raisons de performance ce système est réalisé par la connexion de deux machines spécialisées: - une Machine Iconographique chargée de la génération et de la gestion physique des images; - un Système de Gestion de Base de Données Relationnel permettant: I) de mémoriser des programmes de synthèse en relation avec d'autres informations, ii) d'y accéder par des requêtes variées. Une interface utilisateur met la souplesse inhérente au SGBDR au service d'une large interactivité. Une interface de connexion génère, à partir des données extraites du SGBDR, les commandes pour piloter la MI. Enfin, ce schéma peut être étendu pour conférer au système: - des aptitudes à une synthèse automatique et - la possibilité de piloter une machine iconographique à architecture parallèle fonctionnant selon un principe '«image Flow'

Investigation of the dynamics of the Agulhas Current System in a numerical model

A one-layer model demonstration shows that both inertia and internal friction may account for a partial retroflection where a linear, weakly viscous system has none. When stratification is introduced and baroclinicity increased, the stretching term exerts an increasing influence. With 40 km resolution, terms included so that the numerical model conserves potential vorticity become important as well. When grid resolution is halved, the importance of the extra conserving terms diminishes and the stretching term exerts an even greater influence. The importance of a substantial viscous stress curl along the coast of Africa, as provided by the no-slip condition, is illustrated through comparison with a slippery Africa experiment. Finally, an experiment with a more realistic South African coastal geometry, giving a more realistic order of importance to the planetary vorticity advection in the separating Agulhas is described.Experiments in which rings form exhibit considerably larger values of mean to eddy kinetic energy transfer than those in which no rings form. In a low Rossby number experiment with a rectangular Africa, rings are formed almost continuously, and basin mode resonance plays a significant role in ring formation. Whether a form of instability (barotropic or baroclinic) plays an important role as well is unclear. In two high Rossby number experiments, one with rectangular and the other with triangular African geometry, basin mode resonance is not a factor, and, it appears that ring formation is associated with release of mixed barotropic-baroclinic instability.It is found that, as the ring rounds the tip of Africa, there is only a small influence of the large scale flows on the ring propagation. On the other hand, the presence of the African continent provides an additional westward movement in addition to the one due to $\beta$. As soon as the ring drifts into the South Atlantic subtropical gyre, advection by the large scale flows dominates the ring motion. Furthermore, the model rings have a coherent structure all the way to the bottom and the barotropic component of the flow enhances the westward propagation due to $\beta$ through vertical coupling. (Abstract shortened with permission of author.

Rendre visible la face cachée de l’iceberg. Explorer les documents manuscrits à l’aide de l’intelligence artificielle

Archéorient - Le BlogCompte rendu de la 3e conférence des utilisateurs de Transkribus (Transkribus User Conference 2020) qui s'est tenue les 6 et 7 février 2020 à l’université d’Innsbruck (Autriche). Fondée sur l'intelligence artificielle, la plateforme Transkribus permet la reconnaissance des écritures manuscrites et des imprimés anciens après une phase d’apprentissage supervisé.Le billet est publié sur le carnet de recherche du laboratoire Archéorient : https://archeorient.hypotheses.org/14807

Extraire et structurer des informations géographiques sur les lieux de fouille archéologiques : l’exemple du référentiel du site de Bibracte

Le point de départ de ce travail en cours sur les toponymes du site de Bibracte est le projet « Bulliot, Bibracte et moi », lauréat de l’appel 2019 Services numériques innovants du ministère de la Culture. Ce projet forme le WP 6 du projet HyperThesau et vise la transcription collaborative et l’édition numérique des carnets de fouille manuscrits de Jacques-Gabriel Bulliot (1817-1902), qui a fouillé le site de Bibracte entre 1867 et 1895. Ce travail éditorial suppose une indexation fine des noms de lieux de fouille afin de naviguer dans le corpus qui doit être publié dans une perséïde sur la plateforme Persée. Cette présentation est organisée en 3 parties : un rappel des principes du web sémantique et de ce qu’ils impliquent pour la publication des données de la recherche, le travail d'inventaire des toponymes du mont Beuvray s et la structuration des données géographiques dans un thésaurus.Ce document de travail a été présenté lors d'un séminaire du projet HyperThesau le 8 juillet 202

Extraire et structurer des informations géographiques sur les lieux de fouille archéologiques : le référentiel du site de Bibracte (mont Beuvray, Morvan)

International audienceOur proposal will present a case study on modelling archaeological places as part of research project “Bulliot, Bibracte et moi”, with a thesaurus of mount Beuvray’s field names in connection to excavation sites. Bibracte, a Gaulish oppidum, capital of the Aedui, was situated on top of this mount, near modern-day Autun in Burgundy. Archaeological research took place in two periods. From 1864 to 1907, excavations were carried out under the direction of Xavier Garenne, Jacques-Gabriel Bulliot and Joseph Déchelette. Then in 1984, research started again with the creation of European Archaeological Center, combining a research center and a museum. The thesaurus of mount Beuvray in addition to linking place names and excavation sites aims to retrieve data and information in legacy systems, to map relations between the 19th century archives and contemporary documentation, that is to say heterogeneous and dynamic archaeological data from distributed sources. We use Opentheso, a web-based thesaurus management tool dedicated to the management of vocabularies, developed by the CNRS. This software makes it possible to export data in SKOS format, a standard way to represent knowledge organization systems using the Resource Description Framework (RDF). According to authority repositories such as Rameau or IdRef, geographical names are divided into several categories: human geography which consists of administrative divisions and human constructions, ancient geographical names and physical geography including geographical features and natural regions.It appears necessary to combine controlled vocabulary and data model in order to finely describe the concept of place – as geographical space - and concept of place name – how we name this space. But modelling archaeological places provides challenges to semantic web ontology research. Field names are not stable or reliable identifiers. Place name’s spelling is not fixed (Côme-Chaudron, Comme Chaudron, Caume Chaudron, CC, Come Chaudron). Different names are used from different times and authorities. Geographical boundaries may vary. As an example, Parc aux Chevaux area increases as archaeological discoveries progress and this term was not used as a toponym before the Bulliot excavations. The meaning of the place name may change although the name remains the same: start from original field name then change in cadastral plot, excavation site and finally with archaeological structures (e.g. hydraulic structures, religious institutions, dwellings or workshops) from different periods. So, we process two kinds of multilayered data : geographical areas and archaeological structures.Before the Napoleonic cadastre, the section state in 1792 of the village of Glux (Current Territory of Bibracte) uses place names to locate properties and calculate taxes. Without maps, the areas delimited by these toponyms have become approximate or even impossible to identify today because it only made sense if accompanied by a local oral tradition contemporary to the register.By mapping land use from 1811, the Napoleonic cadastre resolved this problem of transmitting the location of properties. But the new criteria of taxation due to the empire, by modifying and multiplying the boundaries of plots, forced expert surveyors to adapt old toponyms to new surfaces. In consultation with the local authorities, only the most representative toponyms have been selected and allocated to the modified area. During the cadastral regrouping from the 1960s, the place names suffered new cuts on the maps of the territory around mount Beuvray.Moreover toponymy was early associated with archaeology, particularly for prospecting and etymology of place names. Handle with care, recent studies show that etymology is not a science in archaeology but only a question. In Bibracte from the first excavations, the old names of place names and the new names were mixed without distinction as archeologic and spatial indicators of the excavated structures (e.g., Champlain, Les Barlots, Côme-Chaudron). The old toponyms have been often diverted from their original meaning and today it is difficult to differentiate the true from the false (how delimit Place de la foire between La Terrasse or La Chaume ?). Modelling archaeological places is also modelling change in scientific knowledge. We need to express hierarchical link between two place names and the change in hierarchy (e.g. Is monastery part of “Patûre du Couvent”? if so, which is broader?) Information may be uncertain or conflicting, for instance, “Fontaine aux Larmes » and « Pierre de la Wivre » overlap according to some authors, some others distinguish between them. Bulliot and Déchelette named PC 33 (Parc aux Chevaux 33) two different structures located in two different places. We don’t know today where was the “Oval House” discovered in 1864. Each concept of place must be connected into temporal and geographical boundaries and with a bibliographical reference. This is the same approach when different structures have occupied the same place with different names. It’s the case of a domus built on a basilica and a forum (Pâture du couvent); or Saint-Martin chapel built on a temple and Saint-Pierre fountain built on a thermal bath.To model the excavated areas and establish a spatial chronology, a part of our job is to differentiate the old toponyms from the toponyms invented since the beginning of the excavations by studying how the localities are formalized on the maps, in particular the old cadastres. Places and place names are central resources for indexing, aggregating and finding information. But toponyms are not stable and reliable identifiers. We should document each concept with machine readable and transparently modelling archaeological place definition related to a scholar and his works. The inventory of places and place names of mount Beuvray and their chronological, orthographic and spatial variables should enable us to standardize the scientific references necessary today for data retrieval and reuse

Accurate prediction of the statistics of repetitions in random sequences: a case study in Archaea genomes

International audienc