AndreaBozzo/ceres-open-data-index huggingface dataset:
Newborn piglets. A dataset to study the associations between the physiological traits of piglets and colostrum intake, neonatal survival and preweaning growth"

[Lien vers la fiche source] Colostrum intake, mortality within 3 days of birth and preweaning growth rate were recorded on 504 piglets, together with piglet characteristics at birth. A subset of 203 piglets was submitted to blood sampling at birth for physiological analyses. The dataset shows sow traits (parity, litter size…), farrowing traits (piglet birth order…) and piglet morphological and physiological traits, including plasma concentrations of hormones and metabolites. Used in the study by Quesnel et al (submitted)
Zone limitazione velocità (30, 20, 10, 5 km/h)

Isole ambientali in cui, in accordo con i Quartieri, si realizzano interventi finalizzati alla moderazione del traffico (ad esempio la limitazione della velocità massima a 30 km orari e il contenimento dei flussi di attraversamento) allo scopo di proteggere l’utenza debole (pedoni e ciclisti), di migliorare la funzionalità e la sicurezza della strada, di ridurre l'inquinamento atmosferico, acustico e visivo. Legenda per la colonna TIPO T=Area T-DAYS ZTLS=Zone a traffico limitato speciali (S. Francesco, Pratello, Università) APU=Aree pedonali urbane ZTLS-ZR=Zone a traffico limitato speciali e Zone residenziali (Molino-Capo di Lucca) ZVL=Zone a velocità limitata (le zone 30) ZR=Zone residenziali EX=Aree non più vigenti
Intervention reducing malaria parasite load in vector mosquitoes: no impact on Plasmodium falciparum extrinsic incubation period and the survival of Anopheles gambiae: analysis data and code

[Lien vers la fiche source] In the fight against malaria, transmission blocking interventions (TBIs) such as transmission blocking vaccines or drugs, are promising approaches to complement conventional tools. They aim to prevent the infection of vectors and thereby reduce the subsequent exposure of a human population to infectious mosquitoes. The effectiveness of these approaches has been shown to depend on the initial intensity of infection in mosquitoes, often measured as the mean number of oocysts resulting from an infectious blood meal in absence of intervention. In mosquitoes exposed to a high intensity of infection, current TBI candidates are expected to be ineffective at completely blocking infection but will decrease parasite load and therefore, potentially also affect key parameters of vector transmission. The present study investigated the consequences of changes in oocyst intensity on subsequent parasite development and mosquito survival. To address this, we experimentally produced different intensities of infection for Anopheles gambiae females from Burkina Faso by diluting gametocytes from three natural Plasmodium falciparum local isolates and used a newly developed non-destructive method based on the exploitation of mosquito sugar feeding to track parasite and mosquito life history traits throughout sporogonic development. This dataset provides the code (for R software) and R data used for statistical analysis to estimate: * the effect of parasite density on parasite extrinsic incubation period ; * the effect of parasite density on mosquito survival ; * the infection prevalence and intensity in mosquito gut at 7 days post blood meal (dpbm) ; * the infection prevalence and intensity in mosquito head/thoraces upon death.
Transcripts containing Minc telomeric repeats and their matches on the genome

[Lien vers la fiche source] We assembled the transcriptomes of four M. incognita developmental life stages RNA-seq datasets using TRINITY. W= egg, J2= pre-parasitic second stage juveniles, J3= a mix of J3 and J4 endophytic staged, F= adult female. We searched for the presence of the motifs constituting the Minc telomeric repeat. Transcripts that contained at least one of the 3 Minc telomeric motifs were mapped to the genome using GMAP.
Phenotype of Atlantic salmon returning to river Scorff, Oir, Bresle, Frome and Tamar over the period 1969-2017 (smolt year)

[Lien vers la fiche source] This data includes individual records of body length (fork length, in mm), sea age at return (is1SW=1 for 1SW, is1SW=0 for 2SW), retrospective growth measurements performed on scales (in mm) and genetic sex, for a sample of adult Atlantic salmon returning to river Scorff, Oir, Bresle, Frome and Tamar. This data was produced,compiled and analysed as part of the Interreg project SAMARCH, to investigate long-term change in the marine growth of salmon originating from the Channel region, Southern Europe. Please refer to the associated paper for further details.
ISO-seq Minc transcripts containing the repeat and matching the genome

[Lien vers la fiche source] We used the publicly available data of IsoSeq sequencing of Meloidogyne incognita (available under NCBI accessions PRJNA787737, SRP350177. The data were obtained using a mix of M. incognita developmental stages of. We searched for presence of telomeric motifs in the ISO-seq reads. We mapped the motif-containing ISO-seq reads to the reference genome of M. incognita using GMAP with default parameters. A summary of the mapping results is provided here.
M. incognita assembled transcriptomes

[Lien vers la fiche source] Assemblies of M. incognita transcriptomes from four developmental life stages. We retrieved Minc RNA-seq Illumina data of four developmental life stages (eggs, pre-parasitic J2, J3-J4 and adult female) from a previous publication (Blanc-Mathieu et al. PLoS Genetics, 2017). For each developmental life stage, we pooled the triplicates and performed a de novo transcriptome assembly using Trinity v2.4.062. The assembled tanscriptomes are available in FASTA format.
Meloidogyne luci gene predictions

[Lien vers la fiche source] Results of EuGene annotation on the M. luci genome. Predictions of gene models in M. incognita, M. javanica, M. arenaria and M. luci genomes were done with the fully automated pipeline EuGene-EP version 1.6.5 (Sallet et al., 2019). EuGene has been configured to integrate similarities with known proteins of Caenorhabditis elegans (PRJNA13758) downloaded from Wormbase ParaSite (Howe et al., 2017) as well as the “nematoda” section of UniProtKB/Swiss-Prot library (UniProt Consortium, 2018), with the prior exclusion of proteins that were similar to those present in RepBase (Bao et al., 2015). We used as transcriptional evidence, transcriptome data for M. incognita, as it is the Meloidogyne species with the most comprehensive expression data available. RNA-seq data from pre-parasitic J2, J2-J3 and adult female stages (Blanc-Mathieu et al., 2017) were assembled de novo using Trinity (Haas et al., 2013) followed by a cleanup that retains for each trinity locus only the transcript that gives the longest ORF. The dataset of M. incognita assembled transcriptome was aligned on the genomes of the four Meloidogyne species using Gmap (Wu and Watanabe, 2005) and except for M. incognita the option "cross-species" was used. Only alignments spanning 30% of the transcript length with at least 97% identity were retained. The EuGene default configuration was edited to set the “preserve” parameter to 1 for all datasets, the “gmap_intron_filter” parameter to 1, the minimum intron length to 35 bp, and to allow the non-canonical donor splice site “GC”. Finally, the Nematode specific Weight Array Method matrices were used to score the splice sites (available at this URL: http://eugene.toulouse.inra.fr/Downloads/WAM_nematodes_20171017.tar.gz).
Meloidogyne arenaria gene prediction

[Lien vers la fiche source] Results of EuGene annotation on the M. arenaria genome. Predictions of gene models in M. arenaria were done with the fully automated pipeline EuGene-EP version 1.6.5 (Sallet et al., 2019). EuGene has been configured to integrate similarities with known proteins of Caenorhabditis elegans (PRJNA13758) downloaded from Wormbase ParaSite (Howe et al., 2017) as well as the “nematoda” section of UniProtKB/Swiss-Prot library (UniProt Consortium, 2018), with the prior exclusion of proteins that were similar to those present in RepBase (Bao et al., 2015). We used as transcriptional evidence, transcriptome data for M. incognita, as it is the Meloidogyne species with the most comprehensive expression data available. RNA-seq data from pre-parasitic J2, J2-J3 and adult female stages (Blanc-Mathieu et al., 2017) were assembled de novo using Trinity (Haas et al., 2013) followed by a cleanup that retains for each trinity locus only the transcript that gives the longest ORF. The dataset of M. incognita assembled transcriptome was aligned on the genomes of the four Meloidogyne species using Gmap (Wu and Watanabe, 2005) and except for M. incognita the option "cross-species" was used. Only alignments spanning 30% of the transcript length with at least 97% identity were retained. The EuGene default configuration was edited to set the “preserve” parameter to 1 for all datasets, the “gmap_intron_filter” parameter to 1, the minimum intron length to 35 bp, and to allow the non-canonical donor splice site “GC”. Finally, the Nematode specific Weight Array Method matrices were used to score the splice sites (available at this URL: http://eugene.toulouse.inra.fr/Downloads/WAM_nematodes_20171017.tar.gz).
Meloidogyne javanica gene predictions

[Lien vers la fiche source] Results of EuGene annotation on the M. javanica genome. Predictions of gene models in M. javanica genome were done with the fully automated pipeline EuGene-EP version 1.6.5 (Sallet et al., 2019). EuGene has been configured to integrate similarities with known proteins of Caenorhabditis elegans (PRJNA13758) downloaded from Wormbase ParaSite (Howe et al., 2017) as well as the “nematoda” section of UniProtKB/Swiss-Prot library (UniProt Consortium, 2018), with the prior exclusion of proteins that were similar to those present in RepBase (Bao et al., 2015). We used as transcriptional evidence, transcriptome data for M. incognita, as it is the Meloidogyne species with the most comprehensive expression data available. RNA-seq data from pre-parasitic J2, J2-J3 and adult female stages (Blanc-Mathieu et al., 2017) were assembled de novo using Trinity (Haas et al., 2013) followed by a cleanup that retains for each trinity locus only the transcript that gives the longest ORF. The dataset of M. incognita assembled transcriptome was aligned on the genomes of the four Meloidogyne species using Gmap (Wu and Watanabe, 2005) and except for M. incognita the option "cross-species" was used. Only alignments spanning 30% of the transcript length with at least 97% identity were retained. The EuGene default configuration was edited to set the “preserve” parameter to 1 for all datasets, the “gmap_intron_filter” parameter to 1, the minimum intron length to 35 bp, and to allow the non-canonical donor splice site “GC”. Finally, the Nematode specific Weight Array Method matrices were used to score the splice sites (available at this URL: http://eugene.toulouse.inra.fr/Downloads/WAM_nematodes_20171017.tar.gz).
Meloidogyne incognita gene predictions

[Lien vers la fiche source] Results of EuGene annotation on the M. incognita nuclear genome contigs. Predictions of gene models in M. incognita, M. javanica, M. arenaria and M. luci genomes were done with the fully automated pipeline EuGene-EP version 1.6.5 (Sallet et al., 2019). EuGene has been configured to integrate similarities with known proteins of Caenorhabditis elegans (PRJNA13758) downloaded from Wormbase ParaSite (Howe et al., 2017) as well as the “nematoda” section of UniProtKB/Swiss-Prot library (UniProt Consortium, 2018), with the prior exclusion of proteins that were similar to those present in RepBase (Bao et al., 2015). We used as transcriptional evidence, transcriptome data for M. incognita, as it is the Meloidogyne species with the most comprehensive expression data available. RNA-seq data from pre-parasitic J2, J2-J3 and adult female stages (Blanc-Mathieu et al., 2017) were assembled de novo using Trinity (Haas et al., 2013) followed by a cleanup that retains for each trinity locus only the transcript that gives the longest ORF. The dataset of M. incognita assembled transcriptome was aligned on the genomes of the four Meloidogyne species using Gmap (Wu and Watanabe, 2005) and except for M. incognita the option "cross-species" was used. Only alignments spanning 30% of the transcript length with at least 97% identity were retained. The EuGene default configuration was edited to set the “preserve” parameter to 1 for all datasets, the “gmap_intron_filter” parameter to 1, the minimum intron length to 35 bp, and to allow the non-canonical donor splice site “GC”. Finally, the Nematode specific Weight Array Method matrices were used to score the splice sites (available at this URL: http://eugene.toulouse.inra.fr/Downloads/WAM_nematodes_20171017.tar.gz).
Meloidogyne arenaria genome assembly

[Lien vers la fiche source] We first used guppy-v6.0.6 in super high-accuracy mode with a minimal quality score of 7 (--min_qscore 7) to base-call reads from the raw sequencing signal. Following QC, we used nanofilt (De Coster et al., 2018) to crop the 50 first and the 30 last nucleotides as these regions showed reduced per-base quality. We then selected reads that were at least 2kb long and had a quality score Q > 12. This returned 10,506,836 cleaned reads for M. javanica. We assembled the genomes from ONT cleaned data using NECAT (Chen et al., 2021) with default parameters and an input genome size of 310Mb. We obtained 398 contigs with an assembly size of 305,105,593 bp and a N50 of 2,046,842. After the removal of the mitochondrial genome, we had a final assembly with 377 contigs
Meloidogyne javanica genome assembly

[Lien vers la fiche source] We first used guppy-v6.0.6 in super high-accuracy mode with a minimal quality score of 7 (--min_qscore 7) to base-call reads from the raw sequencing signal. Following QC, we used nanofilt (De Coster et al., 2018) to crop the 50 first and the 30 last nucleotides as these regions showed reduced per-base quality. We then selected reads that were at least 2kb long and had a quality score Q > 12. This returned 11,506,089 cleaned reads for M. javanica. We assembled the genomes from ONT cleaned data using NECAT (Chen et al., 2021) with default parameters and an input genome size of 300Mb. We obtained 365 contigs with an assembly size of 298,215,187 bp and a N50 of 2,079,353. After the removal of the mitochondrial genome, we had a final assembly with 364 contigs
Meloidogyne incognita genome assembly

[Lien vers la fiche source] We first used guppy-v6.0.6 in super high-accuracy mode with a minimal quality score of 7 (--min_qscore 7) to base-call reads from the raw sequencing signal. Following QC, we used nanofilt (De Coster et al., 2018) to crop the 50 first and the 30 last nucleotides as these regions showed reduced per-base quality. We then selected reads that were at least 2kb long and had a quality score Q > 12. This returned 1,709,063 cleaned reads for M. incognita. We assembled the genomes from ONT cleaned data using NECAT (Chen et al., 2021) with default parameters and an input genome size of 200Mb. After M. incognita assembly and bridging, NECAT formed 298 contigs for a genome size of 199,975,050 bp and a N50 length of 1,856,931 (longest contig = 4,672,579 bp, L50#= 37). We further removed the contigs corresponding to the mitochondrial genome of M. incognita. The final number of contigs is 291.
Taux d'impayés mensuels - entreprises de 10 salariés ou plus, à La Réunion

Séries mensuelles des taux d'impayés (restes à recouvrer : RAR) des entreprises privées à La Réunion de 10 salariés ou plus hors taxations d'office. Les données sont corrigées des variations saisonnières. Profondeur : depuis janvier 2004. Source : Urssaf Le taux d’impayés est calculé comme le rapport entre les cotisations restant à recouvrer (somme des cotisations dues par les entreprises – sommes des cotisations effectivement recouvrées par les Urssaf) et le montant des cotisations dues. Il est calculé hors taxations d’office (taxation provisoire forfaitaire en cas de non transmission de la déclaration dans les délais prescrits). Le taux d’impayés « fin de mois » est calculé comme le rapport entre le montant des cotisations restant à recouvrer exigibles au mois M, vue à la fin du mois M et le montant des cotisations dues exigibles au mois M, vues également à la fin du mois M. Cet indicateur, disponible très tôt, permet d'obtenir une information précoce sur le recouvrement. Néanmoins, un reliquat d’anomalies dans les déclarations subsiste en fin de mois, ce qui conduit à de légères fluctuations additionnelles. Les taux d’impayés « à échéance + 30 jours » et « 90 jours » sont calculés de manière analogue, mais avec des reculs respectifs de 30 et 90 jours après l’échéance. Leurs séries sont donc plus lisses.
Masse salariale et assiette chômage partiel mensuelles du secteur privé à la Réunion

Masse salariale et assiette chômage partiel mensuelles du secteur privé à La Réunion. Profondeur : depuis janvier 2018. Source : Urssaf Précisions méthodologiques - la masse salariale correspond à l'assiette déplafonnée des cotisations sociales. - la part de l'assiette chômage partiel est égale au rapport entre l'assiette chômage partiel et la somme de l'assiette déplafonnée et de l'assiette chômage partiel. [Pour approfondir notre méthodologie]
ÉTUDE BIBLIOGRAPHIQUE D’ESPÈCES VÉGÉTALES RÉSISTANTES À LA SÉCHERESSE ET UTILES POUR LA PLANTATION SUR LES TALUS RATP DANS LE BASSIN PARISIEN

[Lien vers la fiche source] Cette étude décrit une étude visant à établir une liste d'espèces végétales utiles pour la plantation sur les talus des voies ferrées légères à Paris et en région parisienne. L'étude s'articule en trois phases : la première phase de travail consiste à décrire le climat, des sols, des stress biotiques et abiotiques auxquels sont soumises les espèces végétales sur les talus de la RATP. La seconde, à récolter toutes les données possibles pour établir une liste d'espèces végétales adaptées aux périodes prolongées de chaleur et de sécheresse, avec un accent particulier sur les espèces pérennes et indigènes (pour éviter la possibilité que les espèces soient envahissantes). La troisième phase consiste à établir une liste d'espèces végétales avec les mêmes caractéristiques que celles décrites auparavant, mais à horizon 2100.
L'UTILISATION DE LA VÉGÉTATION POUR PROTÉGER LE SOL CONTRE L'ÉROSION, LES GLISSEMENTS DE TERRAIN ET LES TEMPÊTES

[Lien vers la fiche source] Rapport décrivant l'utilisation de la végétation pour fixer le sol sur les pentes et aider à protéger le sol contre les glissements de terrain peu profonds, l'érosion et les tempêtes
Four HMM models for basidiomycete sesquiterpene cyclases

[Lien vers la fiche source] Sesquiterpene cyclases (STC) catalyze the removal of inorganic diphosphate (PPi) from farnesyl diphosphate, and the cyclization of the resulting carbocation. In fungi, STC that share a common ancestor catalyze a same cyclization mechanism: • clade 1 STC catalyze the 1,10-cyclization of (2E,6E)-FPP carbocation; • clade 2 STC catalyze the 1,10-cyclization of the (3R)-NPP carbocation; • clade 3 STC catalyze the 1,11 cyclization of (2E,6E)-FPP carbocation (trans-humulyl-type cyclases); • clade 4 STC catalyze the 1,6 or 1,7 cyclization of the (3R)-NPP carbocation. Here, we provide robust HMM models for the identification of STC genes in basidiomycete genomes. Their classification into one of the four clades will give indication for the prediction of their cyclisation mechanism.
Procesos DecidimVLC - Votos de Participantes

El conjunto de datos incluye información sobre la participación ciudadana en las siete ediciones de los presupuestos participativos DecidimVLC (2015/2016–2022/2023), un proceso que ha tenido como objetivo implicar a los residentes de València en la toma de decisiones mediante fases de propuestas, apoyos, análisis de viabilidad y votación de proyectos de inversión.
URSSAF Effectif par Métier

Ce jeu de données permet d'avoir la répartition du nombre de collaborateurs en CDI (Contrat à durée indéterminé) par métier et famille professionnelle (répertoire des métiers de la Sécurité Sociale). Les données sont regroupées par organisme, nature de contrat, famille professionnelle et métier. Compte tenu des obligations d’anonymisation liées à la diffusion de données en ligne, les libellés métiers sont remplacés par "autre métier" et les libellés famille professionnelle par "autre famille professionnelle" quand l’effectif total est inférieur ou égale à 5 individus.
INRAE's Walnut Genotyping Resources

[Lien vers la fiche source] Persian or English walnut (Juglans regia L.), the walnut species cultivated for nut production, is one of the oldest food sources known and is grown worldwide in temperate areas. In this work, genotyping resources have been developed for two works. Firstly, SSR genotyping has been done using 13 SSR markers, for 253 accessions of the INRAE's Walnut Genetic Resources. These data have been processed in order to assess genetic diversity and structure of the collection. The raw SSR genotyping datafile is in "tab" format and the informations related to the SSR loci are in "txt" format. Secondly, SNP genotyping has been done using the Axiom 700K J. regia SNP array, for 170 accessions of the INRAE's Walnut Genetic Resources. These data have been processed in order to do Genome-Wide Association Study. Moreover, a F1 progeny of 78 individuals from a cross between 'Franquette' and 'UK 6.2' was also genotyped with the array, in order to do QTL mapping. The two raw SNP genotyping "txt" datafiles are in "hapmap" format. A "csv" file is also added to make the link between the ID of Axiom array and the IDs of the INRA's Walnut Genetic Resources (https://doi.org/10.15454/58SYJV).
Camadas Finas III - BR cruise: S-ADCP data

[Lien vers la fiche source] Camadas Finas cruises are part of Brazilian programs whose objective is to study the influence of the Amazon River on the surrounding areas as far as the open ocean. Camadas Finas III carried out in 2012 with R/V Nho Cruzeiro do Sul, which was equipped on-board with an Acoustic Doppler Current Profilers (S-ADCP) to collect the two horizontal components of the current along the ship route (for more information, see Araujo et al., 2017). The 2 min Short Term Averaged (STA) files collected were processed with CASCADE (Chaîne Automatisée de Suivi des Courantomètres Acoustiques Doppler Embarqués) software (Kermabon et al., 2018) and made available.