AndreaBozzo/ceres-open-data-index huggingface dataset:
1986-2018 near-surface sea temperature registered daily at the pumping station of the Nuclear Power Station of Flamanville (25 km south west of Cherbourg, Northwest Cotentin, sea Channel)

[Lien vers la fiche source] During 33 years, from January 1986 to December 2018, seawater temperature has then been registered daily at 4pm in the pumping station[1] of the Nuclear Power Station of Flamanville located 25 km south west of Cherbourg. In order to cool their condensers, seawater has been drawn off with a water flows of 45 m3s-1. The monthly average seawater temperature minimum has been registered in February (8,90°C), with extremes values in 1986 (6,80°C) and 2016 (10,33°C). The maximum of the seawater temperature has been registered in august (17, 81°C), varying from 16,28°C in 1986 to 18,60°C in 2014. The annual average seawater temperature is 13,09°C when using monthly average values and 13,13°C using all 12053 individuals values. Mean annual values differ from 11,37 °C in 1986 to 14,18 °C in 2014. Before this time-series of 33 years, the only dataset available had been registered between 1904 and 1923 and had been published in 35 by J. R. Lumby[2], from the Ministry of agriculture and fisheries of London (627 values during 20 years at the point R 26[3] , the closest from the head of Flamanville. In order to complete the time-series, EDF, in collaboration with the National Laboratory of Hydraulic (LNH[4]), uses the two sensors Fertex and Aanderaa[5] at 12 meter depth to get an additional time-series of 999 seawater temperatures recorded from September 1976 to May 1980, in a discontinuous way. An increase of 1,2 °C in the annual mean seawater temperature is observed between the first and the third time-series. A key point when analysing those three time-series is to keep in mind the difference in the location, depth and in the sensor. Conclusions from comparisons of those three time series need to be done carefully. Those data are now updated each year before being published in an annual report for Ifremer and EDF[6] about the ecological and fishery monitoring of Flamanville Nuclear Power Station location. [1] Geographical coordinates of the pumping station : 49,53 N – 1,88 W [2] LUMBY, J.R. 1935.- « Salinity and temperature of the English Channel ». Fishery Investigations, series II, vol. XIV, n°3 [3] Coordonnées géographiques du R 26 : 49° 37’ N – 02° 14’ W [4] Today Laboratoire National d'Hydraulique et Environnement (LNHE) [5] Geographical coordinates of Fertex and Aanderaa : 49° 32’ 29’’N - 001° 53’ 49’’W [6] ROPERT M., E. ANTAJAN, G. COURTAY, L. DREVES, A. FOVEAU, T. HERNÀNDEZ FARIÑAS, C. LOOTS, I. SCHLAICH , B. SIMON. (2019). Surveillance écologique et halieutique du site électronucléaire de Flamanville : Année 2018. RST/ODE/UL/LERN-19.001. Conv. EDF C4493C0850. 217 p.
Oxygen optode, data from EMSO-Molène Observatory, 2017-01-01 to 2017-05-04

[Lien vers la fiche source] This dataset contains the data acquired using the oxygen optode on EMSO-Molène observatory. The sensor was protected against the fouling by a micro-chlorination device. The sensor is set on the instrument module, oposite the camera, next to the CTD.
Data from: Connectivities with shellfish farms and channel rivers are associated with mortality risk in oysters

[Lien vers la fiche source] Two age-classes of Pacific oysters (Crassostrea gigas), i.e. young and adult, were used as sentinels to monitor mortality in the Baie des Veys (Normandy, France) from mid-April to October 2014. Oysters were deployed at 39 sites spread over a 37 km2 surface area inside and outside of the shellfish farms. Each site was visited 9 times (12-15 May, 13-16 June, 26-30 June, 12-18 July, 27-29 July, 11-14 August, 25-27 August, 9-12 September, 16 October 2014) during spring tides. For young oysters, cumulative mortality obtained in September is provided. For adult oysters, cumulative mortality is provided for 2 periods: from mid-April to mid-July (Period 1) and from mid-July to October (Period 2). A validated 3-D hydrodynamic Model for Applications at Regional Scale (MARS-3D) coupled with a biogeochemical model (ECOMARS-3D) was used to generate high frequency data of seawater temperature, salinity, chlorophyll a concentration (derived from phytoplankton) and hydrodynamic connectivity to oyster farms and to the mouths of the channel rivers at the 39 sites. For seawater temperature, salinity and chlorophyll a, the minimum, maximum and mean values of hourly data are provided for the whole study period as well as the mean of daily mean or median of daily median for Periods 1, 2 (used for adult oysters) and the period from mid-April to September (used for young oysters). Hydrodynamic connectivities to river channels (Carentan and Isigny) and shellfish areas (Grandcamp and Utah Beach) were estimated in February, May and August 2014. This database is part of the ANR GIGASSAT project No. ANR-12-AGRO-0001.
EMSO-Azores observatory real-time data 2015 deployment

[Lien vers la fiche source] This dataset contains the real-time data acquired from the EMSO-Azores observatory between April 2015 and September 2015. It was daily updated. Data are from 11 types of instruments: Geodesic GPS, Iridium GPS modem, Meteorological station, Ocean Bottom Seismometer, Optode oxygen sensor, Pressure gauges (JP), Turbidity sensor, Connected in-Situ Instrumented Colonization System (CISICS) and Communication and Storage Front-end (COSTOF).
Offshore oil and gas services: estimated business data; world exploration and production investments and fuel prices

[Lien vers la fiche source] Offshore oil and gas services are not identified as a sector in the French classification of economic activities (NAF). They include a range of high value added segments among engineering services but also maritime works and manufacturing activities, some of which are included in other maritime activities analysed in the present report, e.g. maritime works (for offshore oil rig construction), LNG carrier building and cable and pipe making and laying. Turnover is analysed using a rough breakdown per main activity segment as proposed by the industry association. Value added and employment are estimated using INSEE data on larger business sectors. Exploration and production investment and fuel prices data are sourced from the oil and gas extraction industry and IMF, and supplement the description as key drivers of the activity.
Alpage, bâti (Vasserot)

Zones bâties et non bâties identifiées par des couleurs différentes sur les plans Vasserot. Chaque bâtiment est individualisé et informé en correspondance avec le plan Vasserot. La couverture n'est pas exhaustive et la vectorisation est en cours : elle a été commencée par A.-L. Bethe (2010-2009).
Alpage, parcelles (Vasserot)

Limites parcellaires correspondant aux parcelles colorées sur les plans d’îlots Vasserot (parcelles foncières et non morphologiques). Cet état du parcellaire de 1810-1836 résulte d’une vectorisation manuelle réalisée par A.-L. Bethe entre 2007 et 2010, à partir du géoréférencement des plans d’îlots Vasserot.
Alpage, quartiers (Vasserot)

Quartiers au début du 19e s., en usage au moment du dessin des plans d’îlots Vasserot (1810- 1836). Pour le Paris antérieur à 1860, on compte 4 quartiers pour chacun des 12 arrondissements, soit un total de 48 quartiers. Ils sont issus des sections révolutionnaires.
Alpage, îlots (Vasserot)

Limites d’îlots des plans Vasserot (1810-1836). Cette couche des îlots du début du 19e s. a été vectorisée manuellement par A.-L. Bethe à partir du géoréférencement des plans Vasserot entre 2007 et 2010. Les limites d’îlots ne sont pas optimales car le géoréférencement choisi ne visait pas à avoir des limites d’îlots parfaites, respectant les largeurs des rues, mais qui auraient induit des grosses déformations à l’intérieur de l’îlot, dans le parcellaire. Il a été décidé de répartir la déformation sur tout l’îlot pour exploiter le parcellaire. Pour une utilisation couplée des îlots et du parcellaire, il faut donc utiliser cette version 1 des îlots. Pour une utilisation des seuls îlots, sans le parcellaire (par exemple pour un fond de plan), il faut utiliser la version optimale des contours d’îlots (qui respectent les largeurs de voies), soit la version n°2 de cette même donnée.
Aides audiovisuelles 2020

Aides audiovisuelles attribuées par la Région Réunion en 2020 Dans le cadre de son partenariat avec le Centre National du Cinéma et de l’image animée et l’État (DAC de La Réunion), la Région Réunion a mis en place un fonds de soutien en faveur de la filière cinématographique, audiovisuelle et multimédia. Les mesures d’aides sont multiples : elles s’adressent à des projets à valeur patrimoniale pour la télévision, le cinéma et les nouveaux médias. Les projets doivent valoriser La Réunion à travers ses décors naturels et ses ressources humaines et techniques
Vitesse de circulation sur Rennes Métropole

Cette couche indique les limitations de vitesse sur les voiries métropolitaines (dont les zones de circulation apaisée, zones de rencontre, zone 30, zone piétonne...). Sur la Ville de Rennes, la base de données a été initiée dès 2010 par le Service Patrimoine de la Direction de la Voirie. Elle a vocation à être consolidée sur la Ville de Rennes et étendue aux 42 autres communes de la Métropole à partir des arrêtés permanents communiqués par les services détenteurs du pouvoir de police de la circulation et du stationnement (communes en agglomération et plateformes de voirie hors agglomération) et des informations relatives à la signalisations verticale et horizontale mises en œuvre. Cette donnée est en cours de consolidation et n'est donc pas exhaustive. Toute anomalie constatée doit être signalée au gestionnaire des données à l'adresse dvpat@rennesmetropole.fr.
MassJ : Julia package for mass spectrometry data treatment and analysis

[Lien vers la fiche source] MassJ is a package for loading, processing and plotting mass spectrometry data. It provides a range of functionalities such as: * Getting information on the file * Load a file * Averaging mass spectra based on various criteria that may be combined * Chromatogram * Processing the data - smoothing - baseline correction - peak-picking * Calculation of isotopic distribution
Zona T centro storico

La cosiddetta "T" è situata nel cuore del centro storico di Bologna, in una zona di grande interesse turistico e monumentale che costituisce anche una delle zone commerciali più vivaci della città. La sua denominazione nasce proprio dalla sua conformazione geografica, in quanto le tre strade rappresentano, viste in planimetria, una T capovolta. La zona "T" comprende: 1. via Rizzoli (tranne la semicarreggiata che da via Calzolerie porta verso piazza della Mercanzia) 2. via Ugo Bassi (tranne la semicarreggiata che da piazza Malpighi porta a via Testoni e quella che da via Nazario Sauro porta a via Marconi) 3. via Indipendenza (dall’intersezione con Ugo Bassi e Rizzoli fino all’intersezione con Righi e Falegnami) La "T" è controllata, 24 ore su 24, dal sistema di telecontrollo RITA.
Water use-related traits in a bi-parental population of grapevine (cv Syrah X cv Grenache)

[Lien vers la fiche source] This dataset comes from a pseudo-F1 progeny of 186 two year-old genotypes obtained as the first generation from a reciprocal cross between the grapevine (Vitis vinifera L.) cultivars Syrah and Grenache (Adam-Blondon et al., 2004; Fournier-Level et al., 2009). In 2012 and 2013, six and five clones, respectively, of each genotype (all offsprings and the two parents) were phenotyped as replicates in randomized blocks into the PHENOARCH high-throughput phenotyping platform (https://www6.montpellier.inrae.fr/lepse_eng/M3P). Two watering scenarios were imposed by maintaining soil water content in pots at target values using watering stations coupled to weighing terminals. Daily water loss by transpiration was recorded for each potted plant using variation in weigh after correction for soil evaporation determined on empty pots. Individual plant dry weight was calculated daily using image taken in the platform and processed for conversion into biomass. Total water loss by transpiration and increase in dry biomass per plant were calculated over a period of 10–15 days when soil water content had stabilized. Whole plant transpiration efficiency was determined as the ratio between biomass increase and the total amount of transpired water over the same period. Nighttime transpiration, daytime transpiration and midday leaf water potential were measured on a specific day when the plants were taken off the platform and placed into a chamber to ensure stable and repeatable climatic conditions. Soil-to-leaf hydraulic conductance was then deduced from daytime transpiration and leaf water potential using the conventional, evaporative flux method for the whole path from soil to transpiring leaves. This work was supported by funding from the project Long Term Impacts and Adaptations to Climate Change in Viticulture and Oenology (LACCAVE) of the French National Institute for Agricultural Research (INRA) and by Grant ANR-09-GENM-024-002 from the French National Research Agency. Aude Coupel-Ledru received a PhD grant from the French government. Along with genotypic data (Huang et al., 2012) for QTL detection, this dataset was used to explore: (i) The genetic and physiological origins of iso vs anisohydric behaviours (Coupel-Ledru et al., 2014 J Exp Bot), (ii) The role of abscisic acid in the control of isohydry through the regulation of hydraulic conductance (Coupel-Ledru et al., 2017 Plant Phy) (iii) The genetic architecture of nighttime transpiration and its impact on water-use efficiency (Coupel-Ledru et al., 2016 PNAS) This dataset was also re-analysed using univariate and multivariate methods for genomic prediction and QTL detection with denser genotyping data (Brault et al., 2021).
M. incognita protein-coding genes expression patterns

[Lien vers la fiche source] M. incognita protein-coding genes expression values across 4 life stages in triplicates. Life stages are as follows: - W: eggs - J2: pre-parasitic infective juveniles - J3: infective juveniles (mic of late J2, J3 and J4) - Fem: adult female Two tables are given, one with the raw FPKM values for each replicate produced by RSEM, another with the median log10(FPKM+1) value over 3 replicates.
PPN-specific candidate effectors expressed in endophytic phases of M. incognita parasitic life cycle

[Lien vers la fiche source] Annotated list of M. incognita candidate effector proteins that fulfil these criteria: - the proteins are PPN-specific according to orhtofinder and return no significant hit over than in other PPN against the NCBI's nr. - the protein does not belong to a multigene family - the corresponding gene shows substantial and higher expression in endophytic phases - the protein is present in at least two other Meloidogyne species The annotated table in XLSX format shows the following informations in columns: 1. Protein / Gene acessions number 2. Presence of at least one effector-enriched MERCI motif in the 100 first amino acids 3. Gene expression values across four different life stages 4. Comparison of average expression in endophytic vs. exophytic stages. 5. Orthogroup of origin and distribution in other PPN species. A text version with tab-separated values is also available.
Horizontal gene transfer candidates in M. incognita

[Lien vers la fiche source] Analysis of horizontal gene transfer (HGT) candidates on the M. incognita predicted proteins from (Blanc-Mathieu et al. 2017), using Alienness (Rancurel et al. 2017) on a Diamond search against the NCBI's nr library. The following parameters were used in Alienness Taxonomic group of interest: 33208 (Metazoa; HGT of non metazoan origin in a metazoan species) Taxonomic group to exclude: 33283 (Tylenchomorpha; to ignore self hits to plant-parasitic nematodes in Clade 12) Additional taxonomic groups to classify potential donors: 3041 (Chlorophyta); 35493 (Streptophyta) M. incognita proteins with an AI>0 have a better hit to non-metazoa than metazoa and this can include possible HGT M. incognita proteins with an AI>14 have a better hit to non-metazoa than metazoa, with a magnitude of difference >1E6 and this can be considered likely HGT
Experimental validations of TE-impacted coding or regulatory loci

[Lien vers la fiche source] Contains experimental validations results. The sup_mat_2.pptx file summarize: i) Characteristics of the tested loci: position in the genome, inserted TE, the region surrounding the insertion point, TE frequency values per isolate, experimental design (primers sequences, Tm), ii) PCR results (gel), iii) Sequencing results. All the other files are the original result pictures from the PCR experiments testing the insertion of TEs in 12 isolates of M. incognita.
Genes differentially expressed across four life stages in M. incognita and GO enrichments

[Lien vers la fiche source] Meloidogyne incognita protein-coding genes differentially expressed at four stages during the parasitic life cycle: - eggs - pre-parasitic second stage juvenile (J2) - mix of parasitic second, third and fourth stage juveniles (J3) - adult females The genes show significantly differential expression between the stages according to three methods EBseq + EdgeR + DEseq2. The following thresholds were used to consider differential expression as significant: - Log2 fold change >2 - false discovery rate (fdr) <0.05 The six first files correspond to the six comparisons between the four developmental life stages as follows: eggs--(1)-->J2--(2)-->J3--(3)-->female--(4)-->eggs With the two remaining comparisons being: J2--(5)-->female eggs--(6)-->J3 Each of these files are in tab-separated values format (tsv) and present expression values and statistics of DEseq2, EdgeR and EBseq (from Rsem). A seventh file in XLSX Excel format groups all the above information and adds some statistics on genes known to be specifically expressed in dorsal gland (DG) or subventral gland (SvG) cells. Finally, the last files provide a graphical representation of the genes differentially expressed during the M. incognita developmental life cycle as well the gene ontology (GO) 'Molecular Function' terms overrepresented at the different transitions.
Enriched gene ontology terms in upregulated genes at the transition from J2 to J3-J4 larval stages

[Lien vers la fiche source] Analysis of differentially represented (over and under) Gene Ontology (GO) terms in the genes showing significant up-regulation at the transition between the the pre-parasitic J2 and J3-J4 stage. GO over and under representation of terms are according to the hypergeometric test as implemented in the GofuncR Bioconductor package (https://www.bioconductor.org/packages/release/bioc/html/GOfuncR.html). Results are separated by: - Molecular Function - Biological Process - Cellular Component And, in each ontology, under, over and all differentially expressed GO terms are given. All the files are in table separated values format, with the last common providing the accession numbers of proteins annotated with the GO term under consideration.
Enriched GO terms in the eight clusters of differentially expressed genes

[Lien vers la fiche source] Enriched gene ontology terms in each of the eight clusters of differentially-expressed M. incognita genes. For each cluster (A-H), enriched GO terms, as compared to the whole set of differentially expressed genes, were identified using a hypergeometric test as implemented in the GofuncR Bioconductor package (https://www.bioconductor.org/packages/release/bioc/html/GOfuncR.html). To eliminate redundancy between GO terms and only keep representative ones, the option '-refine' was used in GOfuncR. Because we made 8 comparisons (8 clusters) we considered as significant GO terms that returned a corrected p-value of 0.05/8 = 0.00625.
Mapping of known effector genes on five Meloidogyne genomes

[Lien vers la fiche source] Based on the literature, we established a manually curated list of M. incognita genes specifically expressed in sub-ventral or dorsal secretory gland cells. We started from the list published in (Truong, Nguyen, Abad, Quentin, & Favery, 2015) and manually checked the figures associated with the cited references to only keep genes with evidence for specific expression via in-situ hybridization. We completed this list with the Mi-PNF3 gene published more recently (Leelarasamee, Zhang, & Gleason, 2018) and eliminated redundancy between the sequences at the protein level. We retrieved the corresponding CDS sequences and aligned them to the M. incognita, M. arenaria, M. javanica, M. enterolobii and M. hapla genome sequences (Blanc-Mathieu et al., 2017; Koutsovoulos et al., 2020, Opperman et al. 2008) using the splice aware aligner SPALN (Iwata & Gotoh, 2012) with the following parameters. 'spaln -Q7 -O4 -M -d Mi.mfa CDS > input.gff -M = report multiple hits and only the best -Q4= DP mode, 5-7 = maximum number of reported hsp -O4= megablast-like format We performed this operation for the subventral (SvG) and (DG) subsets, separtely and provide a summary of the results in MS Word and PDF Format.
Ancestral reconstruction of the origin of M. incognita effectors in the Meloidogyne genus

[Lien vers la fiche source] Based on the mapping of non-redundant known M. incognita subventral (SvG) and dorsal (DG) gland effectors on the genomes of five Meloidogyne species ancestral numbers were deduced across their phylogeny using parsimony inference with Mesquite (Maddison & Maddison, 2014). In the genomes of M. incognita, M. arenaria, M. javanica and M. entetolobii, only genes mapping with >90% identity on >66% of their length were considered unambiguously present (character state ‘1’ in Mesquite). Genes with a significant spaln mapping but that did not meet the % identity and % coverage thresholds were considered as unsure to be present (character state ‘?’ in Mesquite). Because M. hapla is phylogenetically much more distant, only a length coverage threshold was used to infer unambiguous presence following a significant spaln mapping from the ATG position. Genes that returned no significant spaln mapping were considered absent from the genomes under consideration (character state ‘0’ in Mesquite). The tree topology of the five Meloidogyne species used for ancestral states reconstruction was taken from (Álvarez-Ortega, Brito, & Subbotin, 2019). We used the analysis ‘Trace all Characters’ to reconstruct characters (presence / absence of each effector) at each ancestral branch. To infer the minimal unambiguous number of effectors at each ancestral branch the sum of 1’s at this branch was calculated while equi-parsimonious 0/1’s ancestral state were considered an absence in a conservative scenario.
Enriched gene ontology terms in upregulated genes at the transition from eggs to J2

[Lien vers la fiche source] Analysis of differentially represented (over and under) Gene Ontology (GO) terms in the genes showing significant up-regulation at the transition between the eggs and the pre-parasitic J2 stage. GO over and under representation of terms are according to the hypergeometric test as implemented in the GofuncR Bioconductor package (https://www.bioconductor.org/packages/release/bioc/html/GOfuncR.html). Results are separated by: - Molecular Function - Biological Process - Cellular Component And, in each ontology, under, over and all differentially expressed GO terms are given. All the files are in table separated values format, with the last common providing the accession numbers of proteins annotated with the GO term under consideration.