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DNA metabarcoding is a widespread approach for the molecular identification of organisms. While the associated wet-lab and data processing procedures are well established and highly efficient, the reference databases for taxonomic assignment can be implemented to improve the accuracy of identifications. Insects are among the organisms for which DNA-based identification is most commonly used; yet, a DNA-metabarcoding reference database specifically curated for their species identification using software requiring local databases is lacking. Here, we present COins, a database of 5' region cytochrome c oxidase subunit I sequences (COI-5P) of insects that includes over 532 000 representative sequences of >106 000 species specifically formatted for the QIIME2 software platform. Through a combination of automated and manually curated steps, we developed this database starting from all COI sequences available in the Barcode of Life Data System for insects, focusing on sequences that comply with several standards, including a species-level identification. COins was validated on previously published DNA-metabarcoding sequences data (bulk samples from Malaise traps) and its efficiency compared with other publicly available reference databases (not specific for insects). COins can allow an increase of up to 30% of species-level identifications and thus can represent a valuable resource for the taxonomic assignment of insects' DNA-metabarcoding data, especially when species-level identification is needed https://doi.org/10.6084/m9.figshare.19130465.v1.

International audience; A large number of advanced finite element shell formulations have been developed, but their adoption is hindered by complexities of transforming mathematical formulations into computer code. Furthermore, it is often not straightforward to adapt existing implementations to emerging frontier problems in thin structural mechanics including nonlinear material behaviour, complex microstructures, multi-physical couplings, or active materials. We show that by using a high-level mathematical modelling strategy and automatic code generation tools, a wide range of advanced plate and shell finite element models can be generated easily and efficiently, including: the linear and non-linear geometrically exact Naghdi shell models, the Marguerre-von Karman shallow shell model, and the Reissner-Mindlin plate model. To solve shear and membrane-locking issues, we use: a novel re-interpretation of the Mixed Interpolation of Tensorial Component (MITC) procedure as a mixed-hybridisable finite element method, and a high polynomial order Partial Selective Reduced Integration (PSRI) method. The effectiveness of these approaches and the ease of writing solvers is illustrated through a large set of verification tests and demo codes, collected in an open-source library, FEniCS-Shells, that extends the FEniCS Project finite element problem solving environment.

International audience; Multi-stable shells have been recently proposed as an effective solution to design morphing structures. We describe a class of shallow shells which are bistable after one of their sides is completely clamped. Employing the polar method, we investigate the influence of the constitutive properties of the laminate on its multistability.

Shell, plate and beam (thin) structures are widely used in civil, mechanical and aeronautical engineering because they are capable of carrying high loads with a minimal amount of structural mass. Because the out-of-plane dimension is usually much smaller than the two in-plane dimensions, it is possible to asymptotically reduce the full 3D equations of elasticity to a whole variety of equivalent 2D models posed on a manifold embedded in 3D space. This reduction results in massively reduced computational expense and remains a necessity for practical large-scale computation of structures of real engineering interest such as the fuselage of an aircraft. The numerical solution of such mathematical models is a challenging task, especially for very thin shells when shear and membrane locking effects require special attention. As originally noted by [Hale and Baiz, 2013], the high-level form language UFL provides an excellent framework for writing extensible, reusable and pedagogical numerical models of thin structures. To our knowledge fenics-shells represents the first unified open-source implementation of a wide range of thin structural models, including Reissner-Mindlin, Kirchhoff-Love, Von Karman and hierarchical (higher-order) plates, and Madare-Naghdi and Madare-Koiter shell models. Because of the broad scope of fenics-shells, in this talk we will focus on how to cure numerical locking by applying the Mixed Interpolation of Tensorial Components (MITC) approach of [Dvorkin and Bathe, 1986] and [Lee and Bathe, 2010] to a shell with an initially flat reference configuration. The MITC approach consists of an element-by-element interpolation of the degrees of freedom of the rotations onto the degrees of freedom of a reduced rotation space, the latter typically constructed using H(curl) conforming finite elements such as the rotated Raviart-Thomas-Nédélec elements. Then, the bilinear form is constructed on the underlying H(curl) space. Because of the interpolation operator, the original problem is expressed in terms of the degrees of freedom for the rotations only. Within DOLFIN we have implemented this projection operation using two UFL forms within a custom assembler compiled just-in-time using Instant. We show numerical convergence studies that match the apriori bounds available in the literature. E. N. Dvorkin and K.-J. Bathe, “A continuum mechanics based four-node shell element for general non-linear analysis,” Engineering Computations, vol. 1, no. 1, pp. 77–88, 1984. P. S. Lee and K. J. Bathe, “The quadratic MITC plate and MITC shell elements in plate bending,” Advances in Engineering Software, vol. 41, no. 5, pp. 712–728, 2010. J. S. Hale and P. M. Baiz, “Towards effective shell modelling with the FEniCS project” presented at the FEniCS Conference 2013, Jesus College, Cambridge, 19-Mar-2013.

Soil is a fundamental component of the biosphere, whose properties and quality are affected by human activities, such as agriculture. Soil health is fundamental for different ecosystem services and soil biota has a crucial role in maintaining it. Elucidating how different crops and agricultural practices affect soil invertebrates communities is of relevance. In the present study, a DNA metabarcoding approach was adopted to evaluate the effects of different biotic and abiotic factors, including agricultural practices, on the composition and diversity of soil invertebrate communities of different agro-ecosystems (Po Plain-Italy). At this aim, the DNA markers and the more effective primers in retrieving soil metazoan communities were established. Bulk soil samples from different agro-ecosystems (i.e., cornfield, alfalfa, paddy fields, vineyard, stable meadow, woodland) were collected and, processed for obtaining 18S rRNA and coi sequences (raw reads analyzed using QIIME2 and R). Soil physical and chemical parameters were measured for each soil sample (e.g., pH, carbon-nitrogen ratio, texture, porosity) and metadata on farms management were retrieved. The most efficient primer pairs in recovering soil metazoans were M620F/M1260R for 18S rRNA, and mlCOIintF/jgHCO2198R for coi gene. Soil communities resulted dominated by Nematoda, Arthropoda, Annelida, Rotifera and Tardigrada. The most diverse invertebrate communities have been found in the soil of stable meadows and woodlands, while cornfields showed the lowest level of diversity. The diversity of soil invertebrate communities (Hill numbers) was positively correlated with the level of porosity and carbon-nitrogen ratio, while it was negatively correlated with the phosphate abundance. This pattern probably reflects the negative effect of excessive fertilization with phosphates on soil fauna, while the abundance of organic matter and microhabitats were found to enhance the presence of more complex communities. Other soil properties were correlated only with specific taxa (e.g., pH was negatively correlated with the diversity of Annelida and Rotifera).

In Southern Italy, since 2013, there has been an ongoing Olive Quick Decline Syndrome (OQDS) outbreak, due to the bacterium Xylella fastidiosa, which has caused a dramatic impact from both socio-economic and environmental points of view. The main players involved in OQDS are represented by the insect vector, Philaenus spumarius, its host plants (olive trees and weeds) and the bacterium, X. fastidiosa. Current agronomic practices are mainly based on uprooting the sick olive trees and their surrounding ones, with later installment of olive cultivars more resistant to the bacterium infection. Unfortunately, both of these practices are having an undesirable impact on the environment (most of these olive trees were monumental ones) and on the economy. Based on a mathematical model expressed in terms of a nontrivial system of ordinary differential equations, our analysis has provided a clear picture of all possible steady states (feasible equilibria) and their stability properties, corresponding to a variety of different parameter scenarios; all of this has been illustrated by a set of computational experiments. A significant original contribution of this paper is the proof of the global asymptotic stability of each of the feasible equilibria under its existence assumptions, a fact that excludes multiple equilibria under the given conditions. It has emerged that the removal of a suitable amount of weed biomass (host plants of the juvenile stages of the insect vector of X. fastidiosa) from olive orchards and surrounding areas leads to the eradication of the epidemic, without requiring neither the removal nor the substitution of the existing olive trees.