LibSBGN: current status and future plans

LibSBGN is a community project started in 2009: it aims at facilitating the development of SBGN-compliant tools, and improving interoperability between these tools.
These goals will be achieved by defining a standardized electronic implementation of the Systems Biology Graphical Notation: an XML-based file format (SBGN-ML), complemented by a software library (LibSBGN).
The project is organized around a number of online tools, which allow the community to discuss problems, share ideas, and formalize solutions.
Current versions of SBGN-ML and LibSBGN have already been adopted by three different SBGN-compliant tools. The first official release of SBGN-ML is imminent.

For more information:
http://libsbgn.sourceforge.ne

Systems Biology Graphical Notation: Entity Relationship language Level 1 (Version 1.2)

Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Descriptions, the Entity Relationships and the Activity Flows. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The current document presents version 1.2 of the first level of the SBGN Entity Relationship language. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signaling pathways, metabolic networks and gene regulatory maps

Couple’s Entrepreneurship: Who Loves me Follows me

By mobilizing the theoretical field of decision-making and the empirical study of 15 cases, this article highlights and analyzes the recurrence of conjugal interactions leading to the decision to undertake as a couple. The results show that the spouse who initiates the project becomes the ‘leader’, while the other positions himself, more or less voluntarily, as a ‘follower’. This decision-making configuration induces a renunciation on the part of the follower, a follower who remains, still today, overwhelmingly the woman. The discussion considers the potential impact of this specific decision-making process on the future governance of the company, in terms of the distribution of roles and powers, the satisfaction of spouses, but also the choice of partner. The movement of the reflexive cursor in a period prior to the copreneurial installation enriches the field of research, almost unexplored, of the decision to undertake as a couple, opens the way to the study of problems of copreneurship through the innovative prism of events that have occurred before its implementation and offers practitioners new keys to understanding the complex dynamics within which they evolve. © 2023 Villéger

Restitution d'énergie élastique et locomotion (REEL) : une approche adimensionnelle

L'objectif de ce travail est de développer une approche adimensionnelle de la locomotion humaine, et plus précisément de la marche et de la course. En d'autres termes, le principal enjeu de cette thèse est d'induire des similitudes locomotrices entre des hommes de tailles différentes. Ces similitudes locomotrices attendues entre des individus de différentes tailles sont les mêmes que celles que les physiciens recherchent lors de l'élaboration de prototype à partir de maquette. Dans l'approche que nous tentons de développer tout au long de ce document, nous considérons qu'un individu petit est le modèle réduit d'un plus grand. Notre approche est au croisement des champs de la physique, de la modélisation et de la biomécanique. L'application de l'analyse dimensionnelle aux modèles simples de locomotion permet de mettre en avant l'intérêt des nombres adimensionnels de Froude (vitesse adimensionnelle) et Strouhal (fréquence adimensionnelle) pour étudier la locomotion humaine. Ces modèles simples de locomotion simplifient le corps humain à la masse du corps concentrée au centre de gravité oscillant à l'extrémité d'un ressort. Ils prennent en compte une composante élastique et mettent en avant des transferts se réalisant au centre de gravité entre les énergies cinétique, potentielle de pesanteur et potentielle élastique. Le rapport de ces énergies est appelé Modela. Modela possède deux variantes, une pour la marche et l'autre pour la course, et est dépendant de Froude et Strouhal. Dans un premier temps, les conditions expérimentales de vitesse de déplacement (à partir de Froude) et de fréquence de pas (à partir de Strouhal), toutes deux relatives à l'anthropométrie des individus, ont permis d'engendrer des similitudes locomotrices pour la marche et la course chez des individus de tailles différentes. Ces résultats révèlent tout l'intérêt d'une approche adimensionnelle de la locomotion en montrant qu'exprimés indépendamment de l'anthropométrie des individus, leurs comportements adimensionnels est le même. Utiliser cette approche pour comparer des locomotions au sein même de l'espèce humaine a un grand intérêt pour étudier des comportements déviants d'un comportement standard. Aussi, cette approche peut être un moyen de mettre en avant des organisations du mouvement communes à différentes espèces. Dans un second temps, l'accent est mis sur la comparaison entre le modèle simple et le modèle complexe du corps humain. D'un coté, le modèle simple du corps humain prend en compte une composante élastique et ne s'intéresse qu'au centre de gravité. De l'autre coté, le corps humain peut être modélisé comme un ensemble de segments corporels articulés entre eux. Ici, un lien est fait entre le mouvement global du centre de gravité et les coordinations des segments poly-articulés, lors du mouvement, et tout ce que cela engendre en termes de transfert d'énergie. Le rapprochement des deux modèles explique comment un individu peut se comporter comme une masse bondissante lors de la marche et la course ou comment les expérimentations futures pourront investir le champ de l'élasticité humaine et de l'économie d'énergie.The aim of this paper is to develop a dimensionless approach of the human locomotion, and more specifically of walking and running gaits. In other terms, the main goal of this PhD thesis is to induce locomotor similarity between different-sized humans. These similarities are the same that the physicians look for when they design a prototype from a scale model. Throughout the thesis paper, this approach allows the consideration that a small human is a reduced model of a tall one. Our approach is cross-fielded like Physics, Modelization, and Biomechanics. The dimensional analysis application to the common locomotion models allows to highlight the interest of using the dimensionless numbers of Froude (dimensionless speed) and Strouhal (dimensionless frequency) to study human locomotion. These locomotion models are reduced to the body mass represented at its center of mass oscillating at the end of a massless spring. They take into account an elastic component and enlighten transfers occurring at the center of mass between the kinetic, potential and elastic energies. The ratio of these energies is called Modela. A Modela corresponds to both walking and running, and depends on Froude and Strouhal. First, the experimental conditions such as speed displacement relative to anthropometry (from Froude) and step frequency relative to anthropometry (from Strouhal) allow us to generate locomotor similarity between different-sized subjects for walking and running. These results reveal the interest of the dimensionless approach of the locomotion by showing that the dimensionless behaviors are the same when they are expressed independently of the subject anthropometry. The use of this approach to compare human locomotions is interesting to study behavior different to the gold dimensionless standard. Also, this approach may be a means to highlight a global organization of the movement which is common to many species. Then, the comparison between the simple model and the complex model is investigated. In one hand, the model takes into account an elastic component and only describe the center of mass movement. In the other hand, the human body is represented as a whole of body segment poly-articulated. A link is done between the global movement of the center of mass and the movement of the poly-articular model, and especially regarding for the energy transfers. The link between the models explain how a subject has the same behavior of a spring mass, and how the future works will be able to investigate the fields of the human elasticity and the saving energy mechanisms

Active species in N2 and N2-O2 afterglows for surface treatments

Production of active species is studied in N2 and in N2-O2 afterglows of electrical discharges at low and atmospheric gas pressures. They are produced in microwave discharges in a large range of gas pressures from a few Torr to 100 Torr and in corona discharges at atmospheric gas pressure. The active species in N2 afterglows are the N-atoms which are in the range of a few percents in the afterglows. The effect of O2 molecules in low percentages in low pressure N2 microwave plasmas and as impurity in corona N2 discharges is specially analysed. The interaction of N and O-atoms with surfaces is studied for bacteria decontamination and for transmission of N-atoms though porous membranes. The processes of bacteria decontamination in N2-O2 afterglows are described for low pressure microwave and atmospheric pressure corona discharges. Transmission of N-atoms through porous membranes is studied at medium pressure (10100 Torr) microwave afterglows.Postprint (published version

Refractory Hard Alloys Elaborated by Casting of Ternary (Co, Ni Fe)-30Cr-2.5 to 5 wt% C Compositions

International audienceThree series of ternary alloys of the {M-30Cr-xC}-type with M = Co, Ni or Fe and x ranging from 2.5 to 5 wt% were elaborated by casting. Their microstructure characterizations by XRD and SEM show that very high volume fractions in chromium carbides (even more than 50%) may be obtained in a metallic matrix by this way. However graphite may also appear in very low quantities in the carbon-richest alloys. The hardness increases with the carbon content (up to 1000 Hv30kg) but it may be a little lowered when graphite is also present. The results show that very hard alloys may be simply obtained by casting of rather cheap elements

Functional over-redundancy and high functional vulnerability in global fish faunas on tropical reefs

When tropical systems lose species, they are often assumed to be buffered against declines in functional diversity by the ability of the species-rich biota to display high functional redundancy: i.e., a high number of species performing similar functions. We tested this hypothesis using a ninefold richness gradient in global fish faunas on tropical reefs encompassing 6,316 species distributed among 646 functional entities (FEs): i.e., unique combinations of functional traits. We found that the highest functional redundancy is located in the Central Indo-Pacific with a mean of 7.9 species per FE. However, this overall level of redundancy is disproportionately packed into few FEs, a pattern termed functional over-redundancy (FOR). For instance, the most speciose FE in the Central Indo-Pacific contains 222 species (out of 3,689) whereas 38% of FEs (180 out of 468) have no functional insurance with only one species. Surprisingly, the level of FOR is consistent across the six fish faunas, meaning that, whatever the richness, over a third of the species may still be in overrepresented FEs whereas more than one third of the FEs are left without insurance, these levels all being significantly higher than expected by chance. Thus, our study shows that, even in high-diversity systems, such as tropical reefs, functional diversity remains highly vulnerable to species loss. Although further investigations are needed to specifically address the influence of redundant vs. vulnerable FEs on ecosystem functioning, our results suggest that the promised benefits from tropical biodiversity may not be as strong as previously thought

A global database for metacommunity ecology, integrating species, traits, environment and space

The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology

The Use of Thermal Techniques for the Characterization and Selection of Natural Biomaterials.

In this paper we explore the ability of thermal analysis to check elastin and collagen integrity in different biomaterial applications. Differential Scanning Calorimetry (DSC) has been used to analyze the first and second order transitions of the biological macromolecules in the hydrated and dehydrated state. First, we report the characterization of control cardiovascular tissues such as pericardium, aortic wall and valvular leaflet. Their thermal properties are compared to pure elastin and pure collagen. Second, we present results obtained on two collagen rich tissues: pericardia with different chemical treatments and collagen with physical treatments. Finally, more complex cardiovascular tissues composed of elastin and collagen are analyzed and the effect of detergent treatment on the physical structure of collagen and elastin is brought to the fore

Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet

Background The surface of marine animals is covered by abundant and diversified microbial communities, which have major roles for the health of their host. While such microbiomes have been deeply examined in marine invertebrates such as corals and sponges, the microbiomes living on marine vertebrates have received less attention. Specifically, the diversity of these microbiomes, their variability among species, and their drivers are still mostly unknown, especially among the fish species living on coral reefs that contribute to key ecosystem services while they are increasingly affected by human activities. Here, we investigated these knowledge gaps analyzing the skin microbiome of 138 fish individuals belonging to 44 coral reef fish species living in the same area. Results Prokaryotic communities living on the skin of coral reef fishes are highly diverse, with on average more than 600 OTUs per fish, and differ from planktonic microbes. Skin microbiomes varied between fish individual and species, and interspecific differences were slightly coupled to the phylogenetic affiliation of the host and its ecological traits. Conclusions These results highlight that coral reef biodiversity is greater than previously appreciated, since the high diversity of macro-organisms supports a highly diversified microbial community. This suggest that beyond the loss of coral reefs-associated macroscopic species, anthropic activities on coral reefs could also lead to a loss of still unexplored host-associated microbial diversity, which urgently needs to be assessed