AndreaBozzo/ceres-open-data-index huggingface dataset:
Microbial remineralisation of the downward particle flux measured in the upper mesopelagic with the C-RESPIRE dual particle interceptor/incubator

[Lien vers la fiche source] The oceans’ biological pump plays a major role in the carbon cycle by transferring 5-10 Pg carbon annually out of the upper ocean. A relationship formulated >30 years ago – the ‘Martin curve’ – continues to be used to parameterize particle flux attenuation for the global ocean in models. Despite the almost universal adoption of this empirically-derived relationship, we have made little progress in understanding the drivers of C flux attenuation in over three decades. The fundamental problem with obtaining a mechanistic understanding of the C flux attenuation curve is that it represents multiple processes that concurrently attenuate particle flux (zooplankton flux feeding, diurnal vertical migration, and microbial remineralization of settling particles). Disentangling these processes is further confounded by the likelihood that each process will have different patterns with depth, that may also vary regionally. Hence the way ahead to “deconstructing the Martin curve” is to separate these processes and their drivers. We present a novel in situ approach (called C-RESPIRE) that first intercepts sinking particles (covered in attached microbes) in the upper Twilight Zone (~100-300 m depth), immediately isolates the particles from grazers, and then incubates them at depth during the same deployment. This approach, across multiple deployment depths, provides vertical profiles of rates of microbial remineralization of particle flux.
Dataset of near-infrared spectroscopy measurements of rapeseed ground organs to predict nitrogen and carbon content

[Lien vers la fiche source] A total of 2427 samples consisted of various tissues (roots, leaves, stems, flowers and pods) were collected at different developmental stages on 62 genotypes of winter oilseed rape grown under a wide range of environments including three crop seasons (2014–2015, 2015–2016 and 2016–2017), two growth conditions (tunnel or field) and several crop management strategies (limiting (N-) vs. optimal (N+) N fertilization or water supply (W- vs. W+). Elementary analysis allowed to determine carbon (C) and nitrogen (N) content. In parallel, near infrared spectra were measured from 4000 to 12000 cm-1 on MPA (Bruker) FT-NIR spectrometer.
Salles de cinéma associatives en Loire-Atlantique

Liste des Salles de Cinéma Associatives de Loire-Atlantique ([SCALA]) SCALA est une mission confiée au Cinématographe par le Département de Loire-Atlantique concernant les 35 salles associatives du territoire avec comme axes principaux la formation et la professionnalisation des équipes, la mise en réseau et la diversité de la programmation sur le territoire.
Unidades de Acompañamiento y Orientación Personal y Familiar del alumnado educativamente vulnerable en Castilla y León

En el marco del componente C21.I3 del Plan de Recuperación, Transformación y Resiliencia del Gobierno de España, financiado por la Unión Europea, la Consejería de Educación desarrolla el programa de cooperación territorial de Unidades de Acompañamiento y Orientación personal y familiar del alumnado educativamente vulnerable, durante el periodo 2021-2024, como complemento a los Servicios de Orientación existentes
Données de réplication pour : "Solving morphological analogies: from retrieval to generation"

[Lien vers la fiche source] This repository contains the models trained for the article "Solving morphological analogies: from retrieval to generation". The data is split in 3 folders: "models", "results", and "logs". * The folders "models" and "result", respectively found as "model.zip" and "results.zip", contain the path structure "[model]/[dataset]/[langage]/[random_initialization_id]", where "[dataset]" follows the Siganalogies labels: "2016" for Sigmorphon2016 and JBATS; "2019" for Sigmorphon2019. The data contained is as follows: * "models/[...]/model.pkl": PyTorch model file; * "models/[...]/summary.csv": file containing the evaluation results and other metadata about the training and the structure of the model, as well as the timestamp at which the model finished training; * "models/[...]/version_1.0/": PyTorch-Lightning training logs viewable by Tensorboard; * "models/[...]/fails.csv": enumeration of all the test analogies that the model did not manage to predict correctly, in an extensive format (for most purposes, it is not necessary to consult Siganalogies to analyse the results). The two folders cover the following models: * "clf": CNN+ANNc for classification; * "ret": CNN+ANNr for retrieval; * "3cosmul": CNN+3CosMul for retrieval, only contains "summary.csv" and reuses the embedding model of "clf"; * "ret-annc": CNN+ANNc for retrieval, only contains "summary.csv" and reuses the embedding model of "clf". * The folder "logs" has been unpacked in Dorel, and each file can be found separately. The path structure used follows "ae_annr/[dataset]/[langage]/model[random_initialization_id]-data[random_data_split_id]". The data contained is as follows: * "logs/ae_annr/[...]/debug/checkpoints/[...].pkl": PyTorch-Lightning model file; * "logs/ae_annr/[...]/summary.csv": file containing the evaluation results and other metadata about the training and the structure of the model, as well as the timestamp at which the model finished training; * "logs/ae_annr/[...]/debug/": PyTorch-Lightning training logs viewable by Tensorboard; * "logs/ae_annr/[...]/fails.csv": enumeration of all the test analogies that the model did not manage to predict correctly, in an extensive format (for most purposes, it is not necessary to consult Siganalogies to analyse the results). This folder only covers the AE+ANNr model.
SNP Genotyping data for Guadeloupean and Haitian coffee trees

[Lien vers la fiche source] The West Indies, particularly former French colonies like Haiti and Guadeloupe, were central to the spread of coffee in the Americas. The histories of these Islands are shared until the XIXth century, where they diverged significantly. Still, both Islands experienced a strong decline in their coffee sector. Characterizing the genetic and varietal diversity of their coffee resources and understanding historical factors shaping them can help support revitalization efforts. To that end, we performed KASP-genotyping of 80 informative SNP markers on field samples from across main coffee-growing region of Guadeloupe, and two historically important ones in Haiti, as well as 146 reference accessions from international collections, and acquired data from published sources. While most samples are Coffea arabica, other species are represented, namely C. canephora, C. liberia, and C. congensis
Supporting information for: Cordiosides A and B, two new 19-hydroxy-29-norlanostane glycosides isolated from the flowers of Cordia lutea

[Lien vers la fiche source] This set of data is supporting research on a widely used peruvian medicinal plant, Cordia lutea. Two new compounds, Cordiosides A-B were isolated. Their structural assignment is based on NMR, MS analysis and X-Ray crystallographic data. Antibacterial activity was evaluated for Cordioside A. This set of data contains 1D and 2D NMR spectra for Cordiosides A-B.
Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins

[Lien vers la fiche source] Data from Louis M., Galimberti M, Archer F., Berrow S., Brownlow A., Fallon R., O'Brien J., Robertson K., Rosel P. E., Simon-Bouhet B., Wegmann D., Fontaine M. C. *, Foote A. D.*, Gaggiotti O. E.*. 2021. Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins. (*these authors contributed equally). See materials and methods and supplementary material for details on data generation. This data archive includes 4 main files : 1. The VCF file (called genotypes) 1_TtmappednewTtvar_biallelic.vcf.gz: Variant calling format (VCF) file including the biallelic single nucleotide variants (SNVs or SNPs) used in Louis et al. The sample names are in the vcf file header. See the materials and methods and supplementary material of the manuscript for details on data generation. 2. Genotype likelihood Linkage-disequilibrium pruned input file 2_Tursiops_unlinkedSNPs.beagle.gz: Note that the sample order (Ind0 to Ind55) is given in the file Tursiops_samples_no7Tt182.bamlist. Sample 7Tt182 is not included in the beagle file due to its low coverage but clusters with the other NWAp. See materials and methods and supplementary material for details on data generation. 3. haplo file (pseudo-haploid random call) 3_Tursiops_ALL.haplo: Individual order is given in Tursiops_samples_ALL.bamlist. Note that 7Tt182 is included there but was not included in the analyses, which are based on a subset of individuals (one coastal individual and all allopatric pelagic individuals except from 7Tt192).See materials and methods and supplementary material for details on data generation. 4. GhostAncestry-master compressed folder (4_GhostAncestry-master.tar.gz) contains the codes written by Benoit Simon-Bouhet to generate the input files for the ghost ancestry analyses - also available at https://github.com/besibo/GhostAncestry ## The folder 1_One Scaffold contains the code to test the script on one scaffold only ## The folder 2_All scaffolds contains the code to run the script on all scaffolds # R code is FileMaker.R, note that you will need the script Custom_functions.R as well # Example input files are in _infiles # Example output files are in _outfiles - the input files for the ghost ancestry analyses from Skov et al. 2018. See materials and methods and supplementary material for details on data generation.
Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

[Lien vers la fiche source] These data and scripts are accompanying the manuscript "Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum" by Ben Chehida Y., Thumloup J., Schumacher C., Harkins T., Aguilar A., Borrell A., Ferreira M., Rojas-Bracho L., Robertson K.M., Taylor B.L., Vikingsson G.A., Weyna A., Romiguier J., Morin P.A., & Fontaine M.C. The archive here includes the final alignment of complete mitogenome sequences (16,302 bp) from 71 cetaceans (63 from the different porpoise species and 7 outgroup sequences) and various scripts used for the bioinformatics and data analyses.
Surface water quality (2013-2017) - Curuai floodplain, Brazil, Pará

[Lien vers la fiche source] This dataset was acquired within the framework of several successive French-Brazilian projects with the objective of characterizing the spatio-temporal variations of water quality in the Curuai floodplain. It includes data that were acquired between March 2013 and September 2017 during 9 field campaigns conducted at different hydrological periods. In each campaign we visited at least 25 fixed stations distributed in the different lakes that compose the floodplain. The positions of these stations are distributed along north-south transects in order to evaluate the potential variations according to the distance to the upland and the degree of connection with the river. The campaigns were organized at contrasting hydrological periods, making it possible to cover a relatively broad spectrum of water levels (and thus of flood extent and stored water volume) in the floodplain. The dataset contains physico-chemical data (T, conductivity, pH, dissolved oxygen, chlorophyll-a, inorganic suspended solids, nutrients (nitrogen, phosphorus), dissolved and particulate organic carbon) acquired at the surface at different stations (25 at least) and for some of the stations, at several depths. It also contains vertical profiles acquired with a multi-parameter probe (T, conductivity, pH, dissolved oxygen, chlorophyll-a and/or turbidity). It is an interesting water quality benchmark for this type of environments for which water quality data are scarce.
Replication Data for Distribution of Quercus ilex subsp. rotundifolia in Tunisia and intraspecific variation of seed morphophysiological traits along climatic gradients

[Lien vers la fiche source] This dataset gathers geographical information for the distribution sites of Quercus ilex subsp. rotundifolia in Tunisia in 2020, as well as climatic data and seed morpho-physiological traits associated with the 18 main populations identified. In order to identify adaptations to local environments that may reflect ecological strategies for stress avoidance and seed survival, we tested whether seed functional traits vary, in Quercus ilex subsp. rotundifolia, along climatic gradient within its southern range of distribution, at the edge of arid areas, in Tunisia. An updated survey on the distribution of Q. ilex in Tunisia allowed to characterize the bioclimates of the main populations. We have measured variations for seed morphological traits, desiccation sensitivity level, germination and shoot emergence rates under controlled conditions, among 18 populations of Q. ilex sampled over the entire Tunisian distribution of the species. We have explored the relationships between observed variations in seed traits and climate factors. Contents * The Excel file "Data_Quercus_ilex_Tunisia_2020.xls" used in Amimi et al. includes 5 sheets: Sheet 1 ("Info_legend"): description of the variables used; sheet 2 ("Quercus ilex coordinates"): geographical coordinates, elevation of Quercus ilex subsp. rotundifolia distribution sites in Tunisia; sheet 3 ("Measured_data"): Locations of the 18 source populations for Quercus ilex in Northern Tunisia, and their main associated climate characteristics, as well as variation in morphological and physiological traits of seeds and acorns among the 18 Tunisian Holm oak populations studied ; sheet 4 ("Analyzed_data1"): Cross-correlation matrix between seed morphophysiological traits; sheet 5 ("Analyzed_data2"): Correlation matrix between seed morphophysiological traits and climatic variables at the site of harvest. * The file "Quercus_ilex_Tunisia_Info_legend.tsv" (text format, tabulated data) describes the variables used. * The file "Quercus_ilex_Tunisia_Quercus_ilex_coordinates.tsv" includes geographical coordinates, elevation of Quercus ilex subsp. rotundifolia distribution sites in Tunisia. * The file "Quercus_ilex_Tunisia_Measured_data.tsv" includes locations of the 18 source populations for Quercus ilex in Northern Tunisia, and their main associated climate characteristics, as well as variation in morphological and physiological traits of seeds and acorns among the 18 Tunisian Holm oak populations studied. * The file "Quercus_ilex_Tunisia_Analyzed_data1.tsv" includes correlation matrix between seed morphophysiological traits and climatic variables at the site of harvest. * The file "Quercus_ilex_Tunisia_Analyzed_data2.tsv" includes Cross-correlation matrix between seed morphophysiological traits.
Replication data and scripts for - Mitochondrial variation in Anopheles gambiae and Anopheles coluzzii: phylogeographic legacy and mito-nuclear associations with metabolic resistance to pathogens and insecticides

[Lien vers la fiche source] Supporting data and scripts related to the study: Romero, J. E. A., Chenal, C., Chehida, Y. B., Miles, A., Clarkson, C. S., Pedergnana, V., Wertheim, B., & Fontaine, M. C. (2024). Mitochondrial variation in Anopheles gambiae and Anopheles coluzzii: phylogeographic legacy and mito-nuclear associations with metabolic resistance to pathogens and insecticides. Accepted in the journal Genome Biology & Evolution (Oxford University Press). (biorXiv preprint: [https://doi.org/10.1101/2023.07.18.549472]) Content summary - Multiple alignments of DNA sequences of mitogenomes generated in the present study. - Input data, scripts, and metadata required to replicate the Analysis of Molecular Variance (AMOVA). - Codes and scripts are available via GitHub ([https://github.com/jorgeamaya/automatic_genome_assembly] and [https://github.com/jorgeamaya/malaria_mitogenome]). Research abstract Mitochondrial DNA (mtDNA) has been a popular marker in phylogeography, phylogeny, and molecular ecology, but its complex evolution is increasingly recognized. Here, we investigated mtDNA variation in Anopheles gambiae and Anopheles coluzzii, in relation with other species in the Anopheles gambiae complex (AGC), by assembling the mitogenomes of 1219 mosquitoes across Africa. The mtDNA phylogeny of the AGC was consistent with previously reported highly reticulated evolutionary history, revealing important discordances with the species tree. The three most widespread species (An. gambiae, An. coluzzii, Anopheles arabiensis), known for extensive historical introgression, could not be discriminated based on mitogenomes. Furthermore, a monophyletic clustering of the three salt-water tolerant species (Anopheles merus, Anopheles melas, Anopheles bwambae) in the AGC also suggested that introgression and possibly selection shaped mtDNA evolution. MtDNA variation in An. gambiae and An. coluzzii across Africa revealed significant partitioning among populations and species. A peculiar mtDNA lineage found predominantly in An. coluzzii and in the hybrid taxon of the African “far-west” exhibited divergence comparable to the inter-species divergence in the AGC, with a geographic distribution matching closely An. coluzzii's geographic range. This phylogeographic relict of the An. coluzzii and An. gambiae split was associated with population and species structure, but not with the rare Wolbachia occurrence. The lineage was significantly associated with SNPs in the nuclear genome, particularly in genes associated with pathogen and insecticide resistance. These findings underline potential mito-nuclear coevolution history and the role played by mitochondria in shaping metabolic responses to pathogens and insecticides in Anopheles.
Raw datas Minimal effective dose of bedaquiline administered orally and activity of a long acting formulation of bedaquiline in the murine model of leprosy

[Lien vers la fiche source] Raw datas of the manuscript "Minimal effective dose of bedaquiline administered orally and activity of a long acting formulation of bedaquiline in the murine model of leprosy" published in Plos Neglected Tropical Disease in 2023. The current multidrug therapy is effective against leprosy but remains long and difficult to observe for patients supporting the need of monthly -based treatment. Bedaquiline (BDQ), a diarylquinoline with a long half-life, is a candidate drug to shorten leprosy treatment by targeting the electron transport chain and inhibiting the ATP synthesis. In this work, we determined the minimal effective dose of BDQ administered orally against M. leprae and the activity of a BDQ long acting formulation in a murine model of leprosy
Pôle Attractivité - Patrimoine architectural du territoire de la CC Autour de Chenonceaux Bléré-Val de Cher

Ce jeu de données réunit les données des jeux [Monuments sites et musées en Région Centre-Val de Loire], [Inventaire du patrimoine culturel en Région Centre-Val de Loire], ainsi que les [monuments historiques.] Il est utilisé dans la visualisation [Patrimoine architectural en Région Centre-Val de Loire].
Surplus de phosphore départementaux (1920-2020) - résultats du modèle CASSIS-P

[Lien vers la fiche source] Ce jeu de données est le résultat de modélisation (CASSIS-P) de la quantification des surplus de phosphore annualisés à l'échelle départementale entre 1920 et 2020. Le surplus de phosphore est calculé en faisant la différence entre les apports (engrais minéraux, lisiers, dépôts atmosphériques) et les exports qui correspondent aux récoltes. Le modèle utilise la base de données [ SAGRIDA ] comme données d'entrées. La description du modèle est disponible sur https://cassis.univ-tours.fr/CassisP.html et dans les publications associées. Le jeu de données permet de comparer les imports, exports et surplus de phosphore à l'échelle départementale mais aussi leurs évolutions à l'échelle européenne avec d'autres jeux de données comparable.
Early detection of septoria infection on wheat leaves using hyperspectral imaging data

[Lien vers la fiche source] The present hyperspectral imaging (HSI) database is composed of healthy leaves and leaves infected with Zymoseptoria tritici fungal pathogen responsible for Septoria tritici blotch (STB). Leaves of two durum wheat genotypes were studied under controlled conditions to track the evolution of STB disease and capture significant spectral and spatial differences until the onset of symptoms. Hyperspectral image acquisitions were purchased with two cameras in visible-near infrared (VNIR) and short-wave infrared (SWIR) spectral ranges on eighteen dates between one day before inoculation and twenty days after inoculation. For each wavelength range studied, a total of 1175 images provided information on 3326 leaves measured throughout the experiment.
Replication Data for: Invert emulsions alleviate biotic interactions in bacterial mixed culture

[Lien vers la fiche source] The large application potential of microbiotas has led to a great need for mixed culture methods. However, microbial interactions can compromise the maintenance of biodiversity during cultivation in a reactor. In particular, competition among species can lead to a strong disequilibrium in favor of the fittest microorganism. In this study, an invert emulsion system was designed by dispersing culture medium in a mixture of sunflower oil and the surfactant PGPR. Granulomorphometric analysis was performed to investigate the effect of incubation and of the introduction of bacteria on the particle size distribution of invert emulsions. Selected bacteria were propagated as single-strain cultures in order to assess the effect of invert emulsion on bacterial growth upon 24 h and 72 h timescales. A two-strain antagonistic model was co-cultivated on a range of inoculum levels in order to inquire into the bacterial interaction alleviation properties of invert emulsions. Finally, the effect of this cultivation system on the structure of bacterial communities was assessed by propagating a bacterial consortium consisting of six bacterial species. Metabarcoding analysis was then conducted by Illumina sequencing of 16S rRNA (v4) gene amplimers.
Data for: Maize-cowpea intercropping as an ecological intensification option for low input systems in sub-humid Zimbabwe: productivity, biological N2-fixation and grain mineral content

[Lien vers la fiche source] This dataset comprises data from on farm trials conducted in sub-humid Zimbabwe during two cropping seasons (2017/18-2018/19). The study investigated the effect of maize-cowpea intercropping on productivity, biological N2-fixation and grain mineral content compared to sole crops. The effect of soil characteristics (homefield vs outfield) and of cowpea varieties (improved vs landrace) was also studied
Energiförbrukning i Geografiska området 154110 (Obbola)

Anonymiserad förbrukningsdata från Umeå Energi per nyckelkodsområde i Umeå Kommun. Detta data bör inte ses som exakta och kompletta förbrukningsvärden utan mer som en kvalificerad uppskattning av förbrukningen i syfte att se trender och indikationer. Datafilerna kommer endast innehålla värden för fastigheter i Umeå kommun där Umeå Energi är nätägare och informationen inte anses vara olämplig för distribution. Uppdateras normalt en gång varje månad med nytillkomna värden. Frågor kring detta förbrukningsdata hänvisas till matdata.datalager@umeaenergi.se
Energy consumption in the Geographical area 2001 (part of I20-området)

Anonymiserad förbrukningsdata från Umeå Energi per nyckelkodsområde i Umeå Kommun. Detta data bör inte ses som exakta och kompletta förbrukningsvärden utan mer som en kvalificerad uppskattning av förbrukningen i syfte att se trender och indikationer. Datafilerna kommer endast innehålla värden för fastigheter i Umeå kommun där Umeå Energi är nätägare och informationen inte anses vara olämplig för distribution. Uppdateras normalt en gång varje månad med nytillkomna värden. Frågor kring detta förbrukningsdata hänvisas till matdata.datalager@umeaenergi.se