Group design in group testing for COVID-19 : A French case-study

Group testing is a screening strategy that involves dividing a population into several disjointed groups of subjects. In its simplest implementation, each group is tested with a single test in the first phase, while in the second phase only subjects in positive groups, if any, need to be tested again individually. In this paper, we address the problem of group testing design, which aims to determine a partition into groups of a finite population in such a way that cardinality constraints on the size of each group and a constraint on the expected total number of tests are satisfied while minimizing a linear combination of the expected number of false negative and false positive classifications. First, we show that the properties and model introduced by Aprahmian et al. can be extended to the group test design problem, which is then modeled as a constrained shortest path problem on a specific graph. We design and implement an ad hoc algorithm to solve this problem. On instances based on Santé Publique France data on Covid-19 screening tests, the results of the computational experiments are very promising

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

La Theotokos dans l'art byzantin (recherche sur l'iconographie des origines jusques après l'iconoclasme)

LYON3-Bibliothèques (693872102) / SudocSudocFranceF

A New Member of the Growing Family of Contact-Dependent Growth Inhibition Systems in Xenorhabdus doucetiae

Xenorhabdus is a bacterial symbiont of entomopathogenic Steinernema nematodes and is pathogenic for insects. Its life cycle involves a stage inside the insect cadaver, in which it competes for environmental resources with microorganisms from soil and the insect gut. Xenorhabdus is, thus, a useful model for identifying new interbacterial competition systems. For the first time, in an entomopathogenic bacterium, Xenorhabdus doucetiae strain FRM16, we identified a cdi-like locus. The cdi loci encode contact-dependent inhibition (CDI) systems composed of proteins from the two-partner secretion (TPS) family. CdiB is the outer membrane protein and CdiA is the toxic exoprotein. An immunity protein, CdiI, protects bacteria against inhibition. We describe here the growth inhibition effect of the toxic C-terminus of CdiA from X. doucetiae FRM16, CdiA-CTFRM16, following its production in closely and distantly related enterobacterial species. CdiA-CTFRM16 displayed Mg2+-dependent DNase activity, in vitro. CdiA-CT (FRM16)-mediated growth inhibition was specifically neutralized by CdiI(FRM16). Moreover, the cdi(FRM16) locus encodes an ortholog of toxin-activating proteins C that we named CdiC(FRM16). In addition to E. coli, the cdiBCAI-type locus was found to be widespread in environmental bacteria interacting with insects, plants, rhizospheres and soils. Phylogenetic tree comparisons for CdiB, CdiA and CdiC suggested that the genes encoding these proteins had co-evolved. By contrast, the considerable variability of CdiI protein sequences suggests that the cdiI gene is an independent evolutionary unit. These findings further characterize the sparsely described cdiBCAI-type locus

Quelle image la matière organique sédimentaire est elle susceptible de conserver de son environnement originel? L'exemple d'un lac eutrophe : Aydat (Puy de Dôme, France).

National audienceLa démarche mise en œuvre vise essentiellement à tester les possibilités de reconstitutions paléoenvironnementales via l'identification des marqueurs moléculaires, dans les sédiments. A cette fin, nous avons étudié la distribution de divers constituants biologiques (sucres, lignine, lipides) au long d'une carotte de 44 cm de sédiments superficiels du Lac d'Aydat couvrant environ 100 ans. La lignine, bien que peu abondante, marque une relative constance de la contribution des végétaux du bassin versant aux apports sédimentaires, avec une composition apparemment héritée de tissus mous d'Angiospermes. Inversement, les monosaccharides spécifiques des végétaux supérieurs (xylose, glucose cellulosique) qui ne se trouvent que dans quelques rares niveaux, y témoignent alors d'une préservation accidentelle. Les acides gras libres, ceux libérés par hydrolyse acide et par saponification, proviennent de stocks biogéochimiques différents et apportent donc des informations complémentaires. Seuls ceux libérés par saponification se montrent relativement stables dans le sédiment. A l'information sur les sources végétales primaires (lacustre/ terrestre) apportée par les acides linéaires saturés s'ajoute celle de divers marqueurs bactériens fonctionnalisés. Avec la profondeur, cette diversité moléculaire s'atténue, la signature des microorganismes méthanotrophes devenant dominante au détriment de celle des organismes qui les ont précédés durant la diagenèse. Au total, malgré de très importantes distorsions du signal biologique originel, certaines informations fondamentales apparaissent effectivement bien préservées. Cette préservation reste cependant le fait de combinaisons chimiques particulières (e.g. lignine, lipides) plutôt que de composés simples (e.g. acides gras). Les causes de la préservation de certains constituants demeurant malgré tout conjecturales, comme les polysaccharides pourtant réputés labile