AndreaBozzo/ceres-open-data-index huggingface dataset:
Phytoplankton pigment data collected during the ABRACOS 1 and 2 surveys performed along the northeast Brazilian continental shelf, slope and open ocean

[Lien vers la fiche source] Samples were collected during the “Acoustics along the BRAzilian COaSt (ABRACOS)” oceanographic campaigns, carried out in Austral spring (30 August - 20 September of 2015 - ABRAÇOS1; Bertrand, 2015) and fall (9 April - 9 May of 2017 - ABRAÇOS 2; Bertrand, 2017) on board the French R/V ANTEA. Spring 2015 and fall 2017 are representative of canonical spring and fall conditions in terms of thermohaline structure and currents dynamics (Assunção et al., 2020; Dossa et al., 2021). Water sampling for pigments was carried out using a rosette at four depths defined by CTD profiles: Surface, Mixed Layer, Deep Chlorophyll Maximum (DCM) (which showed a mean depth of 100 m in spring and 80 m in fall) and at 200 m. In shelf shallow stations (< 50 m depth), where no peak of fluorescence was observed, the DCM and 200 m samplings were replaced by a sampling depth at ~10 m above the bottom. For each station and sampled depth, 500 mL of water were filtered in Whatman GF/F glass fiber for the estimation of pigment concentrations of the total phytoplankton community. Size fractionation of water samples was done using 20 μm filter meshes to distinguish the pico- and nanophytoplankton from total phytoplankton pigments. Microphytoplankton fraction (> 20 μm), was estimated by the difference between total and < 20 μm fractions. Filters were stored at 80 ◦C for subsequent HPLC pigment analysis. Chemotaxonomic analysis was carried out on an Agilent Technology 1200 series HPLC following the LOV Method described in Hooker et al. (2000), to assess phytoplankton biomass and diversity. Pigments were extracted in 100% methanol in the dark for 5 min at 4◦C. Samples were then sonicated and filtered on cellulose acetate filters to remove cell debris. A 600 μl aliquot was diluted with 150 μl Milli-Q water. For the analysis, 125 μl of this solution was taken and diluted in an injection loop with 125 μl of a 28 mM solution of Tetrabutyl ammonium acetate. The pigments were then separated on a ZORBAXEclipse XDB-C8 column from Agilent Technology, with 3 mm in diameter,150 mm in length and 3.5 μm in porosity. The column temperature was maintained at 60 ◦C and the flow rate at 0.55 ml min 1. The separation was based on a linear gradient between a solution of methanol/Tetrabutyl ammonium acetate 28 mM, 70:30 (v/v), and a 100% solution of methanol. Chlorophyll-a + Divinyl Chlorophyll-a were used to determine total phytoplankton biomass (TChl-a), while all other pigment markers allowed identifying major algal groups (Table 1). The HPLC system was calibrated with external standards (DHI Water and Environment, Horsholm, Denmark).
Data from: "Impact of environmental conditions on the protein content of Staphylococcus aureus and its derived extracellular vesicles"

[Lien vers la fiche source] Proteomics data generated after in-gel trypstic digestion of whole cell or extracellular vesicle proteins. Mass spetrometer used was a Thermo Scientific Quadrupole-orbitrap Qexactive coupled to a NanoLC reverse phase separation via electrospray ionisation. We used a proteomic approach to provide a complete protein characterization of S. aureus HG003 and its derived EVs under four growth conditions: early- and late-stationaty growth phases, in the absence and presence of a sublethal concentration of vancomycin.
GHRSST Level 3C 4-hour Australasian region skin Sea Surface Temperature Reanalysis (fv02) from Advanced Himawari Imager on Himawari-8 produced by Bureau of Meteorology

[Lien vers la fiche source] This is a regional GHRSST level 3 collated (L3C) dataset on a 0.02-degree rectangular grid over the Australasian domain (70E to 190E, 70S to 20N) based on retrievals from the AHI imager on board Himawari-8 satellite. The Bureau of Meteorology (Bureau) produces Integrated Marine Observing System (IMOS) satellite SST products in the International Group for High Resolution SST (GHRSST) GDS2 file formats for Himawari-8 in real time and delayed mode. This product is composed of reprocessed multi-swath SSTskin retrievals obtained from compositing IMOS Himawari-8 hourly L3C files for previous four hours. Every 10 minutes, the Himawari-8 full disk is processed to retrieve SSTs by using the Radiative Transfer Model (RTTOV12.3) and Bayesian cloud clearing method based on the ESA CCI SST code developed at the University of Reading. The hourly product on the native grid is then produced by compositing over multiple swaths for the previous 1 hour by selecting the highest quality data with priority given to the value closest in time to the product nominal hour. L3C-04hour SSTs are the latest 4-hour pixels with the highest quality taken from the hourly SST product. The L3C-04hour product on native grid is then remapped over the 0.02-degree IMOS grid to compose the IMOS L3C-04hour product. The product format is compliant with the GHRSST Data Specification (GDS) version 2.
GHRSST Level 3C 1-hour Australasian region skin Sea Surface Temperature Reanalysis (fv02) from Advanced Himawari Imager on Himawari-8 produced by Bureau of Meteorology

[Lien vers la fiche source] This is a regional GHRSST level 3 collated (L3C) dataset on 0.02-degree rectangular grid over the Australasian domain (70E to 190E, 70S to 20N) based on retrievals from the AHI imager on board Himawari-8 satellite. The Bureau of Meteorology (Bureau) produces Integrated Marine Observing System (IMOS) satellite SST products in the International Group for High Resolution SST (GHRSST) GDS2 file formats for Himawari-8 in real time and delayed mode. This product is composed of reprocessed multi-swath SSTskin retrievals obtained from compositing IMOS Himawari-8 10-minutes L2P files for previous one hour. Every 10 minutes, the Himawari-8 full disk is processed to retrieve SSTs by using the Radiative Transfer Model (RTTOV12.3) and Bayesian cloud clearing method based on the ESA CCI SST code developed at the University of Reading. The hourly product on native grid is then produced by compositing over multiple swaths for the previous 1 hour by selecting the highest quality data with priority being given to the value the closest in time to the product nominal hour. The L3C-01hour product on native grid is then remapped over the 0.02-degree IMOS grid to compose IMOS L3C-01hour product. The product format is compliant with the GHRSST Data Specification (GDS) version 2.
Curated sequences of cytochrome P450 from Spodoptera frugiperda rice strain

[Lien vers la fiche source] The project contains fasta files of cytochrome P450 genes and proteins corresponding to the sequences curated on the Spodoptera frugiperda whole genome shotgun from the project accession JACWZX, bioproject PRJNA663441, Biosample SAMN16132681; the genomic DNA was obtained from sfR_20170901_p. The sequences are cytochrome P450 manually curated by Frederique Hilliou and officially named by Dr David Nelson
Curated sequences of cytochrome P450 from Spodoptera frugiperda corn strain

[Lien vers la fiche source] The project contains fasta files of cytochrome P450 genes, CDS and proteins corresponding to the sequences curated on the Spodoptera frugiperda whole genome shotgun fropm the project acccession JACWZW01, Bioproject PRJNA662887, Biosample SAMN16099978. the genomic DNA was obtained from the isolate sfC_20170901_p. The sequences are cytochrome P450 manually curated by Frederique Hilliou and officially named by Dr David Nelson
GHRSST GeoPolar MultiSensor Level 3S night Australasian region skin Sea Surface Temperature Reanalysis (fv02) produced by Bureau of Meteorology

[Lien vers la fiche source] This is a regional GHRSST level 3 supercollated (L3S) GeoPolar Multi-sensor SSTskin product on a 0.02-degree rectangular grid over the Australasian domain (70E to 190E, 70S to 20N) for a single night-time period. The Bureau of Meteorology (Bureau) produces Integrated Marine Observing System (IMOS) satellite SST products in the International Group for High Resolution SST (GHRSST) GDS2 file formats for different satellites in real time and delayed mode. This product is derived using sea surface temperature retrievals from the AHI sensor on the Himawari-8, the VIIRS sensor on the Suomi-NPP satellite and JPSS series of satellites, and AVHRR sensor on the NOAA and Metop series of Polar-orbiting satellites. The sensors and satellite platforms contributing to each file are listed in the sensor and platform global attributes in the file header. The quality level for each pixel was remapped using the original ACSPO VIIRS L3U, IMOS AVHRR and AHI L3C-01day quality levels and Sensor Specific Error Statistics (SSES), before compositing single swaths from the sensors. Each grid cell contains the 1-night average of all the highest available quality SSTs that overlap with that cell, weighted by the area of overlap.
OntoBiotope-BioNLP-OST

[Lien vers la fiche source] This version OntoBiotope-BioNLP-OST is a subset of the OntoBiotope ontology. created for the Bacteria Biotope task of BioNLP-OST 2019 competition. OntoBiotope is an ontology of microorganism habitats. Its modeling principle and its lexicon reflect the biotope and the phenotype classification used by biologists to describe microorganism isolation sites (e.g. GenBank, GOLD, ATCC). OntoBiotope is developed and maintained by the Meta-omics of Microbial Ecosystems (MEM) network in which 30 microbiologists from INRA (French National Institute for Agricultural Research) from all fields of applied microbiology participate. The relevance of OntoBiotope terms is evaluated through the PubMedBiotope semantic search engine. It identifies and categorizes microbial biotopes in all PubMed abstracts by applying the ToMap method (Text to Ontology Mapping) to the OntoBiotope ontology. It also indexes 3,35 millions relations between taxa and their habitats.
BRDF (BIDIRECTIONAL REFLECTANCE DISTRIBUTION FUNCTION) DATABASE OF URBAN MATERIALS

[Lien vers la fiche source] Urban Vision was a collaborative project (2019-2022) aiming at developing an image pipeline from video acquisitions to virtual reality applications. The project was sponsored by the FUTURE i-site and involved Université Gustave Eiffel, Institut Géographique National, and Ecole des Ponts ParisTech. One of the goals of this project was to develop a database of the optical reflection properties of urban materials, in order to be able to render these materials in virtual urban environments. This database is made publicly available by the University Gustave Eiffel; it is presented here.
R script and replication data for - The paradox of plant preference: the malaria vectors Anopheles gambiae and Anopheles coluzzii select suboptimal food sources for their survival and reproduction

[Lien vers la fiche source] Anopheles gambiae s.l. mosquitoes, the primary malaria vectors in sub-Saharan Africa, exhibit selectivity among plant species as potential food sources. However, it remains unclear if their preference aligns with optimal nutrient intake and survival. Following an extensive screening of the effects of 31 plant species on An. coluzzii in Burkina Faso, we selected three species for their contrasting effects on mosquito survival, namely Ixora coccinea, Caesalpinia pulcherrima and Combretum indicum. We assessed the sugar content of these plants and their impact on mosquito fructose-positivity, survival, and insemination rate, using Anopheles coluzzii and Anopheles gambiae, and with glucose 5% and water as controls. This is an R script to replicate the analyses from the article entitled "The paradox of plant preference: the malaria vectors Anopheles gambiae and Anopheles coluzzii select suboptimal food sources for their survival and reproduction" by Prisca S. L. Paré, Domonbabele F. D. S. Hien, Mariam Youba, Rakiswendé S. Yerbanga, Anna Cohuet, Louis-Clément Gouagna, Abdoulaye Diabaté, Rickard Ignell, Roch K. Dabiré, Olivier Gnankiné, Thierry Lefèvre (2023) Code developed by Prisca Paré and Thierry Lefevre: prislaure_pare@yahoo.fr; thierry.lefevre@ird.fr
Interactive dashboard (R Shiny) and simulated dataset of "Towards intercrop ideotypes: non-random trait assembly can promote overyielding and stability of species proportion in simulated legume-based mixtures"

[Lien vers la fiche source] Simulated dataset and R Shiny dashborad for visualising data from the article "Towards intercrop ideotypes: non-random trait assembly can promote overyielding and stability of species proportion in simulated legume-based mixtures". The dashboard can can be used to teach basic principles of plant-plant interactions, including competition for light and nutrients and N facilitation related to legumes in intercrops.
Predicted Genes Overlapping Minc Telomeres

[Lien vers la fiche source] Twelve predicted genes in M. incognita overlap Minc telomeric repeat arrays at contig extremities. For each gene we provide a screenshot of the corresponding region in JBrowse and the magnification was set to show the entire gene. From top to bottom: - First track: predicted gene by EuGene - Second track: predicted repeat by EDTA - Last track: coverage by RNA-seq data For the RNA-seq data, we have used a mapping strategy that allows representation of highly multi-mapped reads to be able to visualize transcribed telomeric repeats. The regularly repeated arrays of RNA-seq peaks correspond to the telomeric repeat which is found in the Illumina data.
16S-ITS-23S-DB database

[Lien vers la fiche source] Extraction of 16S-ITS-23S sequences: All GenBank and RefSeq genomes of Archaea and Bacteria from GTDB v214 [1] were downloaded using genome_updater v0.6.2. A total of 402,695 assemblies were downloaded, excluding 4 assemblies with missing fna files and 77,032 assemblies with missing annotation files. These incomplete genomes were ignored, leaving 402,691 assemblies with sequences. The annotation file (GFF) was parsed to identify the 16S and 23S genes. Identification was performed by applying regex patterns to the product or gene attributes of the rRNA annotations. Pairs of 16S and 23S genes were generated under the following conditions: (i) Both 16S and 23S genes must be on the same strand, (ii) the extracted portion must be between 3000 and 7000 nucleotides in length and (iii) the region must begin with 16S and end with 23S. Genomic regions meeting these criteria have been extracted. A total of 358,166 16S-ITS-23S regions were found in 142,377 out of the 402,691 assemblies. Preprocessing of the 16S-ITS-23S sequences Since 358,166 16S-ITS-23S regions, for removing redundant information, identical sequences with the exact same taxonomy were dereplicated, resulting in a total of 199,690 unique sequences. To identify and remove potential eukaryotic contamination, the sequences were blasted against a S. cerevisae 35S sequence. Sequences with a query identity at 70% minimum and a coverage greater than 40% were removed e.g. 283 sequences. 1. Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil PA, Hugenholtz P. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res. 2022;50(D1):D785-D94.
Concentrations of fructose of the G and G+L model cakes

[Lien vers la fiche source] The concentrations of fructose at different times during baking of the G and G+L model cakes at 140°C/25 Hz, 140°C/50 Hz, 170°C/25 Hz, 170°C/50 Hz, 200°C/25 Hz and 200°C/50 Hz were determined after sampling, extraction and analysis by UHPLC-CAD.
Minimal dataset for SQuIRE usage on Prunus Marouch

[Lien vers la fiche source] This dataset is composed of 3 files: (1) the sequence genome of Marouch (.fasta) (2) the annotation of Marouch genome (.gff3) (3) the rmsk informations from RepeatMasker software for Marouch genome. These three files are the minimal input to use SQuIRE as explain here: https://github.com/Elie-Bordron/SQuIRE_usage
Is ecology different when studied with citizen scientists? A bibliometric analysis

[Lien vers la fiche source] Files: * Castagneyrol-Bedessem-Julliard.Rproj -- The RProject, to be opened first * Castagneyrol-Bedessem-Julliard_MS.html -- The manuscript, generated with the .Rmd file open in the R project * Rcodes_Castagneyrol-Bedessem-Julliard_2022-12-07.Rmd -- The Codes Folders: * figures: figures generated by RCodes, or drawn manually * data: |_ table_synonyms_cleaned.csv -- list of synonyms used in the analyses: Ord - a unique number for each keyword; Original_kw - keyword extracted from source articles; N_occurences: number of occurences of Original_kw; Cleaned_kw - the synonym as used in the analyses |_ Wos full records 2011-2021: a folder containing raw data |_ data_wos_complete.csv: raw data as extracted from the web of science database, column names are explicited in the Rcodes_Castagneyrol-Bedessem-Julliard_2022-12-07.Rmd file |_ data_wos_filtered_CitSci_issues.csv: as subset of data_wos_complete.csv containing only journal issues with at least one CitSci article (see manuscript). This file can actually be generated from the codes. It is exported for convenience. |_ number_citsci_journals_wos.txt: number (count) and percentage (%) of articles published in the selected journals (Publication Titles Records)
Original data -- Following the track: accuracy and reproducibility of predation assessment on artificial caterpillars

[Lien vers la fiche source] Original data analysed in the article entitled "Following the track: accuracy and reproducibility of predation assessment on artificial caterpillars" Variable description: * Response_ID: a single ID for each response to any of the online quizes * Respondant: was the respondant a professional scientist, a teacher, a student * Expertise: Self declared previous expertise in predation rate assessments wioth artificial larvae * Quizz: Quiz ID (1, 2, 3) * Language: quiz language (french, English, Spanish, german) * Picture: Picture ID (1 to 20, in each quiz) * Answer: respondant's identification of marks on caterpillar surface * ID: Picture ID, combining columns 'Quizz' and 'Picture' * Expert_answer: Correct predation mark idenitficatiàon as made by an expert, to be compared with respondant's identification ('Answer')
Resilience of helminth - gut microbiota interactions in a large mammal

[Lien vers la fiche source] We used the horse–cyathostomin system to quantify the resilience of the nematode-bacteria interactions following an anthelmintic treatment. This matched case-control study enrolled 20 healthy and 20 naturally infected horses, whereby half received an anthelmintic drug to remove adult worms from the gut lumen without hampering the development of larval stages. Metabarcoding approaches were implemented to track faecal microbiota and cyathostomin community compositions over a 42-day time-course.
Quality trimmed dsRNA and VANA data for synthetic viral communities of varying complexity (5-, 10-, 20- and 60-viruses)

[Lien vers la fiche source] HTS data for synthetic viral communities of varying complexity (5-, 10-, 20- and 60-viruses). This dataset is composed of 47 fasta files: - 22 VANA - 22 dsRNA - 3 controls VANA and dsRNA files are named according to the following convention Method-P[community complexity]-[community number].
Panorama of the nutritional composition of follow-on infant formula commercialized worlwide in 2021

[Lien vers la fiche source] The main objective of infant follow-on formulas, consumed from the age of 6 to 12 months, is to mimic the composition of breast milk in order to meet the nutritional needs of infant. In this context, their composition is governed in Europe by a strict regulation that has evolved in 2020 to force manufacturers to improve the nutritional profile of the formulas. The objective of this dataset was to collect the ingredient lists and nutritional values of infant follow-on formulas present on the world market with a focus on the lipid fraction. The data collection was carried out from December 2020 to April 2021 directly on the product packaging or on the websites of the different brands. Only "classic" infant follow-on formulas that are widely consumed were listed. Thus, the ingredient lists and nutritional values of 91 infant formulas were collected. The nutritional values are systematically presented for 100g of powder, for 100 Kcal and for 100mL of formula. The sources of fats, emulsifiers and vitamins A and E were also extracted from the ingredient lists. This dataset can be used as a tool for the formulation of infant follow-on formulas or to situate the positioning of products in relation to the market.
Overview of the nutritional composition of infant flours commercialized worldwide in 2021

[Lien vers la fiche source] Infancy is a key window of development during which diet plays an essential role. From the age of 4/6 months, breast milk and/or infant formulas are no longer sufficient to cover all of infants nutritional needs. This period is therefore marked by the gradual introduction of complementary foods such as processed cereal-based foods (namely infant flours) to begin the dietary diversification. Infant flours are a commonly consumed food globally, especially in southern regions. The aim of this dataset was to collect lists of ingredients and nutritional values of infant flours on the world market. Data collection took place from December 2020 to April 2021, involving direct information extraction from product packaging, brand websites, and research articles. The dataset specifically focuses on processed cereal-based products composed of simple or mixed cereals that must be reconstituted with milk or other appropriate liquids, and cereals with added protein-rich foods that must be reconstituted with water or protein-free liquids. A total of 96 infant flours were collected for their ingredient lists and nutritional values. The nutritional values are systematically presented for 100g of powder or for 100 kcal. The main sources of the raw materials used in these flours were also identified from the ingredient lists. This dataset serves as an invaluable tool for the development of infant flours, offering insights into the composition and nutritional values of these products.
RPG complété 2021 Région Champagne-Ardenne

[Lien vers la fiche source] RPG complété 2021. Complète le RPG campagne 2021 pour les départements de la région (ancienne région) Champagne-Ardenne (08, 10, 51, 52). (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2023.
Data relative to the article : Influence of two agroforestry systems on the nitrification potential in temperate pastures in Brittany, France" (Mettauer et al., accepted)

[Lien vers la fiche source] This database is composed by the data mobilized within the article "Influence of two agroforestry systems on the nitrification potential in temperate pastures in Brittany, France" by Mettauer et al. (accepted by Plant and Soil 2023). It is composed of data on soil and vegetation properties, as well as on nitrification potential (PNR), nitrifying bacteria (AOB), Ascomycota and Basidiomycota. The data was collected within two adjacent agroforestry plot associated with temporary grassland of the Britany region, France: one planted with a hedgerow system and one planted with an alleycropping system.