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The dramatic increase in the number of microbe descriptions in databases, reports, and papers presents a two-fold challenge for accessing the information: integration of heterogeneous data in a standard ontology-based representation and normalization of the textual descriptions by semantic analysis. Recent text mining methods offer powerful ways to extract textual information and generate ontology-based representation. This paper describes the design of the Omnicrobe application that gathers comprehensive information on habitats, phenotypes, and usages of microbes from scientific sources of high interest to the microbiology community. The Omnicrobe database contains around 1 million descriptions of microbe properties. These descriptions are created by analyzing and combining six information sources of various kinds, i.e. biological resource catalogs, sequence databases and scientific literature. The microbe properties are indexed by the Ontobiotope ontology and their taxa are indexed by an extended version of the taxonomy maintained by the National Center for Biotechnology Information. The Omnicrobe application covers all domains of microbiology. With simple or rich ontology-based queries, it provides easy-to-use support in the resolution of scientific questions related to the habitats, phenotypes, and uses of microbes. We illustrate the potential of Omnicrobe with a use case from the food innovation domain.

Brevetoxins (BTXs) are marine biotoxins responsible for neurotoxic shellfish poisoning (NSP) after ingestion of contaminated shellfish. NSP is characterized by neurological, gastrointestinal and/or cardiovascular symptoms. The main known producer of BTXs is the dinoflagellate Karenia brevis, but other microalgae are also suspected to synthesize BTX-like compounds. BTXs are currently not regulated in France and in Europe. In November 2018, they have been detected for the first time in France in mussels from a lagoon in the Corsica Island (Mediterranean Sea), as part of the network for monitoring the emergence of marine biotoxins in shellfish. To prevent health risks associated with the consumption of shellfish contaminated with BTXs in France, a working group was set up by the French Agency for Food, Environmental and Occupational Health & Safety (Anses). One of the aims of this working group was to propose a guidance level for the presence of BTXs in shellfish. Toxicological data were too limited to derive an acute oral reference dose (ARfD). Based on human case reports, we identified two lowest-observed-adverse-effect levels (LOAELs). A guidance level of 180 µg BTX-3 eq./kg shellfish meat is proposed, considering a protective default portion size of 400 g shellfish meat.

SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2), a virus causing severe acute respiratory disease in humans, emerged in late 2019. This respiratory virus can spread via aerosols, fomites, contaminated hands or surfaces as for other coronaviruses. Studying their persistence under different environmental conditions represents a key step for better understanding the virus transmission. This work aimed to present a reproducible procedure for collecting data of stability and inactivation kinetics from the scientific literature. The aim was to identify data useful for characterizing the persistence of viruses in the food production plants. As a result, a large dataset related to persistence on matrices or in liquid media under different environmental conditions is presented. This procedure, combining bibliographic survey, data digitalization techniques and predictive microbiological modelling, identified 65 research articles providing 455 coronaviruses kinetics. A ranking step as well as a technical validation with a Gage Repeatability & Reproducibility process were performed to check the quality of the kinetics. All data were deposited in public repositories for future uses by other researchers.Measurement(s)Decimal reduction timeTechnology Type(s)Modelling of kineticsFactor Type(s)Temperature • Relative humidity • Genus • StrainSample Characteristic - OrganismCoronaviridae

The dramatic increase in the amount of microbe descriptions in databases, reports and papers presents a two-fold challenge for accessing the information: integration of heterogeneous data in a standard ontology-based representation and normalization of the textual descriptions by semantic analysis. Recent text mining methods offer powerful ways to extract textual information and generate ontology-based representation. This paper describes the design of the Omnicrobe application that gathers comprehensive information on habitats, phenotypes and usages of microbes from scientific sources of high interest to the microbiology community. The Omnicrobe database contains around 1 million descriptions of microbe properties that are created by analyzing and combining six information sources of various kinds, i.e. biological resource catalogues, sequence database and scientific literature. The microbe properties are indexed by the Ontobiotope ontology and their taxa are indexed by an extended version of the taxonomy maintained by the National Center for Biotechnology Information. The Omnicrobe application covers all domains of microbiology. It provides an easy-to-use support in the resolution of scientific questions related to the habitats, phenotypes and uses of microbes through simple and complex ontology-based queries. We illustrate the potential of Omnicrobe with a use case from the food innovation domain. Competing Interest Statement The authors have declared no competing interest. Footnotes * Supplemental files updated

Microbiology research has access to a very large amount of public information on the habitats of microorganisms. Many areas of microbiology research uses this information, primarily in biodiversity studies. However the habitat information is expressed in unstructured natural language form, which hinders its exploitation at large-scale. It is very common for similar habitats to be described by different terms, which makes them hard to compare automatically, e.g. intestine and gut. The use of a common reference to standardize these habitat descriptions as claimed by (Ivana et al., 2010) is a necessity. We propose the ontology called OntoBiotope that we have been developing since 2010. The OntoBiotope ontology is in a formal machine-readable representation that enables indexing of information as well as conceptualization and reasoning.

Polydiacetylene (PDA) inserted in films or in vesicles has received increasing attention due to its property to undergo a blue-to-red colorimetric transition along with a change from non-fluorescent to fluorescent upon application of various stimuli. In this review paper, the principle for the detection of various microorganisms (bacteria, directly detected or detected through the emitted toxins or through their DNA, and viruses) and of antibacterial and antiviral peptides based on these responsive PDA vesicles are detailed. The analytical performances obtained, when vesicles are in suspension or immobilized, are given and compared to those of the responsive vesicles mainly based on the vesicle encapsulation method. Many future challenges are then discussed.

Extremely thin absorber (ETA) solar cells made of ZnO/TiO2/Sb2S3 core–shell nanowire heterostructures, using P3HT as the hole-transporting material (HTM), are of high interest to surpass solar cell efficiencies of their planar counterpart at lower material cost. However, no dimensional optimization has been addressed in detail, as it raises material and technological critical issues. In this study, the thickness of the Sb2S3 shell grown by chemical spray pyrolysis is tuned from a couple of nanometers to several tens of nanometers, while switching from a partially to a fully crystallized shell. The Sb2S3 shell is highly pure, and the unwanted Sb2O3 phase was not formed. The low end of the thickness is limited by challenges in the crystallization of the Sb2S3 shell, as it is amorphous at nanoscale dimensions, resulting in the low optical absorption of visible photons. In contrast, the high end of the thickness is limited by the increased density of defects in the bulk of the Sb2S3 shell, degrading charge carrier dynamics, and by the incomplete immersion of the P3HT in the structure, resulting in the poor hole collection. The best ETA solar cell with a short-circuit current density of 12.1 mA/cm2, an open-circuit voltage of 502 mV, and a photovoltaic conversion efficiency of 2.83% is obtained for an intermediate thickness of the Sb2S3 shell. These findings highlight that the incorporation of both the absorber shell and HTM in the core–shell heterostructures relies on the spacing between individual nanowires. They further elaborate the intricate nature of the dimensional optimization of an ETA cell, as it requires a fine-balanced holistic approach to correlate all the dimensions of all the components in the heterostructures.

Extremely thin absorber (ETA) solar cells made of ZnO/TiO /Sb S core-shell nanowire heterostructures, using P3HT as the hole-transporting material (HTM), are of high interest to surpass solar cell efficiencies of their planar counterpart at lower material cost. However, no dimensional optimization has been addressed in detail, as it raises material and technological critical issues. In this study, the thickness of the Sb S shell grown by chemical spray pyrolysis is tuned from a couple of nanometers to several tens of nanometers, while switching from a partially to a fully crystallized shell. The Sb S shell is highly pure, and the unwanted Sb O phase was not formed. The low end of the thickness is limited by challenges in the crystallization of the Sb S shell, as it is amorphous at nanoscale dimensions, resulting in the low optical absorption of visible photons. In contrast, the high end of the thickness is limited by the increased density of defects in the bulk of the Sb S shell, degrading charge carrier dynamics, and by the incomplete immersion of the P3HT in the structure, resulting in the poor hole collection. The best ETA solar cell with a short-circuit current density of 12.1 mA/cm , an open-circuit voltage of 502 mV, and a photovoltaic conversion efficiency of 2.83% is obtained for an intermediate thickness of the Sb S shell. These findings highlight that the incorporation of both the absorber shell and HTM in the core-shell heterostructures relies on the spacing between individual nanowires. They further elaborate the intricate nature of the dimensional optimization of an ETA cell, as it requires a fine-balanced holistic approach to correlate all the dimensions of all the components in the heterostructures.

Chaix Louis. Meso 2000. 6th international Conférence on the Mesolithic in Europe. Nynäshamn (Suède), 4-8 septembre 2000. In: Bulletin de la Société préhistorique française, tome 98, n°1, 2001. pp. 154-157.