dataesr/scientific-paragraphs-categorization huggingface dataset:
Contents lists available at ScienceDirect Genomics Data j o u r n a l h o m e p a g e : h t t p : / / w w w. j o u r n a l s. e l s e v i e r. c o m / g e n o m i c s -d a t a / to 1 week. bTCs, bXECs, and bXMCs were isolated as previously described for human trophoblast cells  [3]. Briefly, the extra-embryonic tissues were digested with a sterile 0. 05% (w/v) collagenase/trypsin solution (Gibco Life Sciences) at 37 °C. The digested tissues were centrifuged and the supernatant was discarded. The pelleted cells were resuspended in DMEM and filtered through a sterile 70-μm filter (BD Biosciences) prior to separation on a 55%-20% Percoll density gradient. All fractions were collected and cell viability was determined with Trypan blue dye (Invitrogen). bTCs were grown either on collagen IV-or Matrigel-coated culture dishes, whereas bXECs and bXMCs were grown directly on plastic culture dishes in DMEM (supplemented with 10% FCS, 2 mM glutamine, 100 IU/ml penicillin, and 100 μg/ml streptomycin).
Array hybridization, image acquisition and quantification Array hybridization was also described in  [5, 7]. Briefly, 500 ng of amplified RNA (aRNA) was labeled with [α 33 P] dATP by reversetranscription and hybridized to an INRA bovine 10K array (GPL7417) using ExpressHyb™ Hybridization Solution (Clontech) at 68 °C overnight. Arrays were washed four times in 2 × SSC, 1% SDS and once in 0. 1× SSC, 0. 5% SDS at 68 °C for 30 min each. They were then exposed to phosphor-screens for 7 days. The hybridization signals were quantified with Imagene 5. 5 software (BioDiscovery) on the PICT/ICE platform. These datasets are available in the Gene Expression Omnibus database (http://www. ncbi. nlm. nih. gov/geo, GSE52967). Data were log-transformed and mean-centered.
Acknowledgments This work was supported by the  PremUp foundation (S. A. D. postdoctoral fellowship) ;  INRA   Department programs   ACI PHASE 2008 , 2009, and  AIP AGROBI. The author is grateful to  I. Hue  ( INRA ,  UMR1198 ),  D. Evain-Brion & T. Fournier  ( INSERM UMR-S1139 ) who have contributed to the original work [1] as well as  C. Richard  ( INRA ,  UE1298 ),  D. Krauss  ( INRA ,  UE0332 ), and their teams for their contributions in collecting D18 bovine embryos, and  P. Bardou  ( SIGENAE team, INRA, Toulouse, France ) for the submission of the array dataset to the  GEO database.
The Tara Oceans expedition (2009-2013) sampled contrasting ecosystems of the world oceans, collecting environmental data and plankton, from viruses to metazoans, for later analysis using modern sequencing and state-of-the-art imaging technologies. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. The interpretation of such an extensive collection of samples in their ecological context requires means to explore, assess and access raw and validated data sets. To address this challenge, the Tara Oceans Consortium offers open science resources, including the use of open access archives for nucleotides (ENA) and for environmental, biogeochemical, taxonomic and morphological data (PANGAEA), and the development of on line discovery tools and collaborative annotation tools for sequences and images.
Overall, Tara Oceans surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. Organising such a knowledge base is essential to safeguard, discover and share Tara Oceans data. To address this challenge, Tara Oceans offers open science resources, including the use of open access data archives and the development of online tools for the collaborative annotation of sequences and images, and the discovery of Tara Oceans data. Tara Oceans adopts the principle of open access and early release of raw and validated data sets. In the case of molecular data, raw short sequence reads are archived at the European Bioinformatics Institute short read archive (http://www. ebi. ac. uk/ena/) and made available immediately after manual curation of metadata.
More advanced data (assemblies, annotations, etc. ) will be released immediately after validation and before publication, and other versions will be released when available. In the case of environmental, biogeochemical, taxonomic and morphological measurements, data are published at PANGAEA, Data Publisher for Earth and Environmental Science (http://www. pangaea. de) and made available immediately after manual curation of metadata. By combining modern sequencing and state-of-the-art imaging technologies, Tara Oceans is at the cutting edge of marine science  3. The amount of data generated by these technologies is unprecedented in the field of plankton ecology and requires adapted storage infrastructures and collaborative platforms to carry out manual and automated annotation of sequences and high throughput images.
These open science resources are currently being developed by Tara Oceans. A first series of publications has demonstrated the potential of Tara Oceans data to study the ecology of plankton and the structural and functional diversity of viruses, prokaryotes and eukaryotes in the global ocean  [4] [5] [6] [7] [8] [9] [10] [11]. These publications are based on a fraction of the samples analysed so far and thus represent only the tip of the iceberg. The exploration of Tara Oceans data by the scientific community will undoubtedly lead to new hypotheses and emerging concepts in domains unforeseen by the Tara Oceans Consortium. The current discovery portal of Tara Oceans offers a simple map interface that links each sampling location to available environmental and molecular data (http://www. taraoceansdataportal.
org/). It will however evolve to offer advanced search functionalities based on geospatial, methodological, environmental, morphological, taxonomic, phylogenetic and ecological criteria. Here, we present an overview of the sampling strategy and size-fractionation approach of the Tara Oceans Expedition (Methods Section) and we explain the rationale behind the choice of sampling devices (Technical Validation Section). Most importantly, we provide registries (data sets) describing all campaigns (from port-to-port), stations and sampling events (Data Records Section). These registries contain geospatial, temporal and methodological information that will be essential for researchers to explore and assess the quality of Tara Oceans data. Environmental data sets are already available openly, in whole or in part, and additional data sets will be progressively released to the community.
Meteorological forecast services, satellite observations (Chlorophyll a, sea surface temperature (SST) and altimetry) and real-time ocean model outputs (Mercator Ocean) were also used on a daily basis to revise sampling positions with respect to the selected oceanographic features. Mapped altimetry from AVISO (Archiving Validation and Interpretation of Satellite Data in Oceanography), mapped operational SST (OSTIA), and satellite ocean colour (ACRI-ST GlobColour service) were used to describe the spatial and temporal variability of key environmental parameters at each sampling station. In addition, Temperature-Salinity profiles available around sampling stations were compiled from the Argo autonomous network array. Finally, a [BATOS] meteorological station mounted on-board Tara continuously measured wind speed and direction, and air temperature, pressure and humidity, which helped determine the variability of atmospheric conditions and vertical mixing of surface waters.
For topical experiments, oceanographic context was sometimes enriched by using automated underwater vehicles (e. g. , gliders  12  , ProvBio  13  ), surface-tethered Argo drifters, lowered ADCP mounted on the rosette, basin scale eddy-field simulations and climatologies, and state-of-the-art physical models of global ocean circulation with biogeochemistry and genome-informed models of microbial processes  14. The specific sampling strategy of each topical experiment is available in the respective campaign summary reports (see Data Records Section). Tara Oceans data corresponding to methods described in this section are in part already open to the public at PANGAEA (Data Citation 1). [2] Properties of seawater and particulate matter from physical, optical and imaging sensors mounted on the continuous surface water sampling system Continuous measurements of surface water physical, chemical and biological properties serve the dual purpose of a) assessing the boundaries and the homogeneity/heterogeneity of an ecosystem studied during a station, and b) assessing the connectivity between stations.
Underway measurements were often used to fine tune the location of sampling stations that were initially selected based on satellite images. The in-line, Continuous Surface Sampling System [CSSS] installed on SV Tara (15,000 miles long track) comprised a SeaBird [TSG] temperature and conductivity sensor, a WETLabs [AC-S] spectrophotometer, a WETLabs chlorophyll [Fluorometer], and a Fast Repetition Rate Fluorometer [FRRF] to assess photosynthetic efficiency. All data were recorded simultaneously and archived daily in a single file, including navigation, date/time and GPS position. Water was pumped at the front of the vessel from ~2 m depth, then de-bubbled and circulated through the [AC-S], [TSG], [Fluorometer], and [FRRF]. An automated switching system provided periodic 0. 2 μm filtered samples to the [AC-S], such that its particulate optical properties were not affected by instrument drift  15.
Systems maintenance (instrument cleaning, flushing) was done approximately once a week and in port between successive campaigns. In the Arctic Ocean and Arctic Seas (2013 campaigns), additional sensors for pH, PCO 2 , optical backscattering (3 wavelengths), fluorescence emission [ALFA] and surface Photosynthetically Active Radiation [PAR] were added to the in-line system. A [FlowCytobot] also recorded images of microplankton every 20 min. Using daily discrete measurements of CDOM absorption with an [UltraPath] system, we calibrated the [AC-S] to also provide hourly CDOM absorption (besides particulate absorption and attenuation). Data were processed, quality-controlled, and are consistent with remote sensing. A total of 60 tracks of continuous measurements corresponding to methods described in this section are in large part already open to the public at PANGAEA (Data Citation 2 and Data Citation 3).
5-20 μm (WETLabs), a one-wavelength backscatter meter for particles 0. 5-20 μm (WETLabs), and a Underwater Vision Profiler  16  for particles >100 μm and zooplankton >600 μm (Hydroptic). A sbe43 oxygen sensor (Sea-Bird) and an In Situ Ultraviolet Spectrophotometer (ISUS) nitrate sensor (SATLANTIC) were also mounted on the Rosette. In the Arctic Ocean and Arctic Seas (2013 campaigns), a second sbe43 oxygen sensor (Sea-Bird) and a four frequency acoustic profiler (Aquascat) were added. Each component was powered on specific Li-Ion batteries and CTD data were self-recorded at 24 Hz. All sensors were calibrated in factory before, during and after the four year programme. Oxygen data were validated using climatologies. Nitrate and Fluorescence data were adjusted with discrete measurements from Niskin bottles mounted on the Rosette, and dark calibrations of the optical sensors were performed monthly on-board.
A total of 837 vertical profiles were made during the Expedition. Additional stand-alone Sea-Bird components [sbe19] and [sbe9S] were exceptionally mounted directly on the oceanographic cable during harsh sea conditions, when the deployment of the rosette was not safe. In addition, apparent optical properties of sea water were measured using a surface tethered [RADIOMETRE-TSRB] in 2009-2012 and a profiling [RADIOMETRE-COPS] in 2013. Finally, a total of 101 deployments of the Secchi disk [SECCHI] provide a valuable, world-wide contribution to historical records of this very simple and yet fundamental sampling device. Tara Oceans data corresponding to methods described in this section are already open to the public at PANGAEA (Data Citation 4). [4] Properties of seawater and particulate & dissolved matter from discrete water samples In addition to sensors mounted on the Rosette Vertical Sampling System [RVSS], seawater was collected using Niskin bottles [NISKIN] (6 × 8-L Niskins and 4 × 12-L Niskins) in order to further characterise environmental conditions in the ecosystem under study.
Measurements include pigment concentrations from HPLC analysis (10 depths per vertical profile; 25 pigments per depth), the carbonate system (Surface and 400 m; pHT, CO 2 , pCO 2 , fCO 2 , HCO 3 , CO 3 , Total alkalinity, Total carbon, OmegaAragonite, OmegaCalcite, and quality Flag), nutrients (10 depths per vertical profile; NO 2 , PO 4 , N0 2 /NO 3 , SI, quality Flags), DOC, CDOM, and dissolved oxygen isotopes. More than 200 vertical profiles of these properties were made across the world ocean. DOC, CDOM and dissolved oxygen isotopes are available only for the Arctic Ocean and Arctic Seas (2013 campaigns). Tara Oceans data corresponding to methods described in this section are already open to the public at PANGAEA (Data Citation 5).
[5] Environmental features and sampling stations During the Tara Oceans Expedition (2009-2013), plankton were sampled from 5-10-m thick layers in the water column, corresponding to specific environmental features that were characterised on-board from sensor measurements. Environmental features are defined by controlled vocabularies in the environmental ontology (EnvO; http://environmentontology. org/)  17. The surface water layer (ENVO:00002042), sometimes labelled in the literature and databases as "surface", "SRF", "SUR", "SURF" or "S", was simply defined as a layer between 3 and 7 m below the sea surface. The deep chlorophyll maximum layer (ENVO:01000326), often labelled in the literature and databases as "DCM" or "D", was determined from the chlorophyll fluorometer (WETLabs optical sensors) mounted on the Rosette Vertical Sampling System [RVSS].
The presence of a DCM may indicate a maximum in the abundance of plankton bearing chlorophyll pigments, or it may result from the higher chlorophyll content of plankton living in a darker environment  18. This can be assessed a posteriori using water samples analysed for pigments by HPLC methods and from plankton counts. The mesopelagic zone (ENVO:00000213), also labelled in the literature and databases as "MESO" or "M", corresponds to the layer between 200 and 1000 m depths. The sampling depth within the mesopelagic zone was selected based on vertical profiles of temperature, salinity, fluorescence, nutrients, oxygen, and particulate matter. The selected depth varied from station to station, targeting for example a nutricline, a minimum concentration of oxygen, a maximum concentration of particulate matter, or a fixed depth of ca.
400 m when no particular feature could be identified. Other environmental features of special scientific interest include the oxygen minimum zone (ENVO:01000065), often labelled in the literature and data sets as "OMZ" or "O", and the epipelagic mixing layer (ENVO:01000061), also labelled in the literature and data sets as "ML", "MIX" or "X". A complete sampling station consisted of collecting plankton from three distinct environmental features, typically the surface water layer, deep chlorophyll maximum layer, and mesopelagic zone (Fig. 4 ). Such a station lasted typically 24-48 h and special care was taken to reposition SV Tara in order to remain within a radius of 10 km and sample a homogeneous ecosystem as much as possible (see previous two sub-sections). The sequence of sampling deployments varied but generally followed the order illustrated in Fig.
4, i  Plankton were sampled from a total of 210 stations, of which: 51 stations did not target a specific environmental feature and conducted classical vertical profiles of physical and optical sensors and depth integrated net tows; 57 stations sampled only the surface water layer; 62 stations sampled the surface water layer and a second depth-specific feature; and 40 stations sampled the surface water layer, the deep chlorophyll maximum layer and a third depth-specific feature. Tara Oceans data corresponding to methods described in this section are already open to the public at PANGAEA (Data Citations 6-8) and are described in the Data Records Section of the present paper. [6] Marine plankton Plankton sampled during the Tara Oceans Expedition cover six orders of magnitude in size (10 -2 -10 5 μm) and correspond to viruses, giant viruses (giruses), prokaryotes (bacteria and archaea), unicellular eukaryotes (protists), and multicellular eukaryotes (metazoans).
Detailed protocols concerning the filtration, preservation and storage of plankton samples will be described in detail as a separate publication. Morphological data will be openly released at PANGAEA (http://www. pangaea. de) and nucleotides data will be openly released as they become available at the European Nucleotide Archive (http://www. ebi. ac. uk/ena/). [6a] Sampling planktonic viruses, prokaryotes and unicellular eukaryotes. Sampling devices used to collect small size organisms ( o20 μm size fractions) include Niskin bottles [NISKIN] mounted on the rosette [RVSS] or occasionally attached individually on the oceanographic cable, a High Volume Peristaltic Pump [HVP-PUMP], and exceptionally a 10-L plastic bucket [BUCKET] (Table  1  (available online only)). Waste waters from Tara were not released automatically at sea and were not purged during stations.
Registries The Tara Oceans Expedition (2009-2013) comprised 60 campaigns (from port-to-port), 210 stations and over 3200 sampling events. Three registries listing the campaigns, stations and events are published at PANGAEA, Data Publisher for Earth and Environmental Science: Campaigns registry (Data Citation 6): http://doi. pangaea. de/10. 1594/PANGAEA. 842191 Stations registry (Data Citation 7): http://doi. pangaea. de/10. 1594/PANGAEA. 842237 Events registry (Data Citation 8): http://doi. pangaea. de/10. 1594/PANGAEA. 842227 The campaigns registry provides details about the scientific interest of each campaign, a list of scientists on board, and URLs for the corresponding campaign summary report (pdf), environmental data sets and nucleotides data sets. The stations registry provides details about the geographic context of each station, including mean and maximum bathymetric depth (extracted from the General Bathymetric Chart of the Oceans; GEBCO), minimum distance from the coast, the corresponding marine biomes and biogeographical provinces defined by Longhurst  34  , and when applicable information about the corresponding exclusive economic zone and related legal aspects.
All available metadata information about a single campaign/station/event can be extracted from the respective registries using a web service (description: https://ws. pangaea. de/dds-fdp/). Here we provide an example for each registry: Campaign-specific metadata query: https://ws. pangaea. de/dds-fdp/rest/panquery?datasetDOI=doi. pangaea. de/10. 1594/PANGAEA. 842191&filterParameter=Campaign&filterValue=TARA_20110401Z Station-specific metadata query: https://ws. pangaea. de/dds-fdp/rest/panquery?datasetDOI=doi. pangaea. de/10. 1594/PANGAEA. 842237&filterParameter=Station&filterValue=TARA_100 Event-specific metadata query: https://ws. pangaea. de/dds-fdp/rest/panquery?datasetDOI=doi. pangaea. de/10. 1594/PANGAEA. 842227&filterParameter=Event&filterValue=TARA_20110416T1306Z_100_ EVENT_CAST Additionally, the same web service can be used to extract information about all stations from a campaign, all events from a campaign, or all events from a station as shown in these examples: Stations-from-a-campaign metadata query: https://ws.
pangaea. de/dds-fdp/rest/panquery?datasetDOI= doi. pangaea. de/10. 1594/PANGAEA. 842237&filterParameter=Campaign&filterValue=TARA_20110401Z Events-from-a-campaign metadata query: https://ws. pangaea. de/dds-fdp/rest/panquery?datasetDOI= doi. pangaea. de/10. 1594/PANGAEA. 842227&filterParameter=Campaign&filterValue=TARA_20110401Z Events-from-a-station metadata query: https://ws. pangaea. de/dds-fdp/rest/panquery?datasetDOI= doi. pangaea. de/10. 1594/PANGAEA. 842227&filterParameter=Station&filterValue=TARA_100.
pdf). Most of the information found in reports and log sheets was extracted manually, quality checked using controlled vocabularies, and archived in the campaigns, stations and events registries. Nevertheless, these narrative documents remain a valuable and complementary source of information. The three registries contain universal resource locators (URLs) pointing to the reports and log sheets of each campaign/station/event. Reports and log sheets can also be browsed directly in the PANGAEA store: Campaign reports: http://store. pangaea. de/Projects/TARA-OCEANS/Campaign_Reports/ Station reports: http://store. pangaea. de/Projects/TARA-OCEANS/Station_Reports/ Event log sheets: http://store. pangaea. de/Projects/TARA-OCEANS/Logsheets_Event/ Up-to-date lists of available nucleotides and environmental data sets Tara Oceans data will progressively be released openly following their analysis and validation.
Up-to-date lists of nucleotides and environmental data sets can be obtained from universal resource locator (URL) queries that are made specific to any campaign/station/event by using labels from the campaigns, stations and events registries. A list of environmental data sets published at PANGAEA can be obtained by combining the following base URL: http://www. pangaea. de/search?q= with a search term. The URL query is made specific to any Tara Oceans campaign, station or event by adding the corresponding label as the search term, see examples below. Already-built URL queries for each campaign, station or event are provided in the three respective registries (Data Citations 6-8). Campaign-specific environmental data query: http://www. pangaea. de/search?q=TARA_20110401Z Station-specific environmental data query: http://www.
pangaea. de/search?q=TARA_100 Event-specific environmental data query: http://www. pangaea. de/search?q=TARA_20110416T1306Z_ 100_EVENT_CAST A list of nucleotides data published at ENA can be obtained by combining the following base URL: http://www. ebi. ac. uk/ena/data/search?query= with a search term. The URL query is made specific to any Tara Oceans campaign, station or event by adding the corresponding label as the search term. Alreadybuilt URL queries for each campaign, station or event are provided in the three respective registries (Data Citations 6-8). 2 ) for viruses (including giant viruses), prokaryotes, protists and metazoans (coloured boxes). The sampling devices used to collect plankton o 5 μm in size (i. e. , high volume peristaltic pump and rosette with Niskin bottles) and >5 μm in size (i.
Based on this assessment, it appears that our sampling strategy would capture o50% of total richness for viruses and small size protists (0. 8-5 μm). Accordingly, one would need to filter thousands of litres of seawater in order to capture 75% of total richness for these groups. This is both impractical for most field campaigns and dependent on how one defines the currency of richness for these groups, i. e. , the concept of species. In all other groups and size fractions, our sampling strategy appears to capture >75% of species richness, and 100% in the case of large size protists and metazoans. It is important to note that data about plankton richness is very scarce in the literature, so that this assessment is only a first approximation. Tara Oceans data will undoubtedly contribute to fill this knowledge gap and improve the sampling design of future ocean biodiversity surveys.