dataesr/scientific-paragraphs-categorization huggingface dataset:
Clearly, the main part of the present dataset is not devoted to tracking any climatic change in water mass properties; the SeaSoar, the MVP and the rapidCAST are rapidly moving platforms, leading to acquiring less-precise temperature, conductivity and above all deduced salinity data than the standardized CTD protocol. MVP and rapidCAST are equipped with unpumped sensors, and the three tools reach high ascending or descending velocity (above 2 m s -1 ) that leads to inescapable thermal-lag issues across sharp fronts. Readers interested in this topic should only use the classical CTD station data. Four cruises were conducted between 2015 and 2018 by the "Service Hydrographique et Océanographique de la Marine" (SHOM) in the Western Mediterranean basin, during winter or early spring, managing mainly the towed undulating vehicle SeaSoar to investigate the subsurface (0-400 m) layer.
When the deployment of this vehicle was either unsafe (over shallow water) or even impossible (due to rough meteorological conditions, breakdown of the winch or vehicle) or when complementary observations were requested (e. g. , to go below 400 m or collect water samples for biochemical analysis), CTD casts were performed instead. On-board routinely acquired data (vessel-mounted acoustic Doppler current profiler -VMADCP -and thermosalinograph -TSG) were also included in this database. We present here, in a synthetic dataset, all data recorded during the cruises (Fig. 2 ; Table  1 ). Complementary data used to design the cruise, to adapt the strategy on field or to interpret results (altimetric tracks, remotely sensed sea surface temperature or chlorophyll a) are available on CMEMS servers (http://marine.
copernicus. eu, last access: 19 February 2020). An eddy detection tool called AMEDA (Le  Vu et al. , 2017)  was also used to detect and track structures during the cruises. Surface and Argo drifters were also dropped during the cruises, and data are available on companion datasets (Table  2 ). The first cruise, called PROTEVS-MED 2015_leg1, took place from 7 to 24 January 2015 aboard the R/V Pourquoi Pas?. Its main objective was to observe the dynamics of the NC from the Ligurian Sea to the Gulf of Lions and the associated mesoscale and submesoscale processes. Attention was paid to cross-slope transects in the Gulf of Lions in order to examine the behavior of the Northern Current and the exchanges across the shelf break. An intensive survey of the Northern Current between Toulon and Nice was performed.
The first leg (leg1) gave a general overview of the oceanic situation, followed by a more intensive survey (leg2) planned on the basis of daily release of near-real-time satellite imagery, altimetry and lagrangian analyses, performed on land by using a dedicated package (http://www. mio. univ-amu. fr/SPASSO/ last access: 19 February 2020, as in  Nencioli et al. , 2011; de Verneil et al. , 2017). Satellite data of altimetry, sea surface temperature and ocean color revealed ubiquity throughout the cruise period of very fine oceanic structures such as dipolar structures or tenuous fronts. A special focus was on the region south of Mallorca, where fronts were detected by altimetryderived currents and diagnosis (e. g. , Finite Singular Lyapunov Exponents; d  'Ovidio et al. , 2004)  and by contrasting surface chlorophyll a concentrations and confirmed by highfrequency flow cytometry analyses of phytoplankton performed onboard (data not included in the present dataset).
A Lagrangian strategy was specifically set up in order to study the structure and growth rate (at 24 h timescale) of the various phytoplankton groups as defined by flow cytometry measurements as in  Marrec et al. (2018). Lastly, it is noticeable that a companion campaign (PRE-SWOT) managed by IMEDEA-SOCIB was conducted in the same area and during the same period aboard the R/V García del Cid (not included in the present dataset; see  Barceló-Lull et al. , 2018).
CTD casts and LADCP The CTD casts were performed with the Sea-Bird SBE-9 instrument mounted in a General Oceanics 12-place rosette frame fitted with 12 Niskin bottles. Sometimes a RDI 150 kHz current profiler was also implemented on the rosette, and then the LADCP (lower acoustic Doppler current profiler) performed measurements during the cast. Standard hydrographic procedures for CTD casts were applied. When available, LADCP recorded data were processed following the inversion method of  Visbeck (2002).
TSG During the cruises, a Seabird SBE-21 thermosalinograph recorded the sea surface temperature and conductivity. The inlet was equipped with an SBE-38 thermometer. The recorded sea surface temperature and salinity contributed to the Global Ocean Surface Underway Data (GOSUD) program (Gosud, 2016). The metrological traceability and the data treatment are insured according to the procedures described in  Gaillard et al. (2015) , which explains the delayed mode processing of datasets and presents an overview of the resulting quality. The calibrations are complemented with rigorous adjustments on water samples, leading to a salinity accuracy of about 0. 01 or less.
VMADCP The hardware used, its configurations and the way it is used are similar on the R/V Pourquoi Pas?, R/V L'Atalante and R/V Beautemps Beaupré. The VMADCPs are the 150 and 38 kHz Ocean Surveyor by Teledyne RDI. They are both monobloc antennas using the beam-forming process to form four beams oriented towards 30 • from the vertical. Nominally, they emitted a ping per second, which allows the ensemble to have less-noisy profiles. Two ensembles are routinely processed: a short-term average (hereafter STA) which gathers and averages the pings of a 2 min window and makes an ensemble of at least 120 pings, a long-term average (hereafter LTA) made of 600 pings or averaged over 10 min. The series of geometric transformations necessary to pass from beam coordinates along beam data to absolute geographic coordinate and geophysical velocity are performed thanks to VMDAS software from Teledyne RDI.
It combines the position (latitude and longitude) from the DGPS (Differential Global Positioning System) Aquarius and Octans central system with the PHINS inertial navigation system from IXSEA (that provides vessel attitude data: pitch, roll, heaving) to provide synchronized single-ping Earth coordinate data (file. ENX) and short-and long-term ensembles (STA and LTA). This native format (. STA and. LTA) was also processed with WinADCP in order to extract and provide only signif-icant (i. e. , with a satisfactory signal-to-noise ratio) data that are additionally formatted to a text file. Note that data processed by CASCADE software can be requested from the SISMER repository, collecting and processing progressively all VMADCPs from French research vessels (https://sextant. ifremer. fr/record/ 60ad1de2-c3e1-4d33-9468-c7f28d200305/en/index.
Data metrological traceability and calibration SBE-9 temperature and conductivity sensors deployed on all CTD sensors were calibrated before and after each campaign or at least once a year in the SHOM's thermo-regulated baths, whose temperature can be stabilized to less than 1 mK (peak to peak) during control and calibration operation. Such a procedure allows the monitoring of sensors drifts between calibrations and the detection of anomalies. In the cases in which sensors kept a good linearity, which is the most common, data are corrected with offset-slope coefficients. Figure  3a  shows a review of the corrections applied on data at 15 • C, after the calibrations of SBE-3 sensors used for PROTEVS-MED campaigns. Figure  3b  shows a review of corrections applied at 40 mS cm -1 after the calibrations of SBE-4 sensors.
The temperature of the thermo-regulated bath is monitored with SBE-35, which is used as a laboratory reference temperature sensor. It is linked to the International Temperature Scale of 1990 (ITS-90), thanks to calibrations performed once a year in a triple-point-of-water cell and at the melting point of gallium. These reference cells are regularly calibrated by the French National Metrology Institute (NMI) LNE-CNAM. The calibration expanded uncertainty of SBE-3 sensors is between 1. 8 and 2. 3 mK, according to the residual linearity errors of SBE-3 sensors. The conductivity calibration of SBE-4 sensors is made in the same bath during the temperature calibration. Seawater samples are taken into the bath and tested against Autosal and Portasal salinometers. The calibration procedure and the propagation of uncertainties to the calculated salinities from SBE-9 data are described in Le Menn (2011).
www. earth-syst-sci-data. net/12/441/2020/ Earth Syst. Sci. Data, 12, 441-456, 2020 ) by entering the WMO numbers in the field "Platform codes", adjusting the time period of interest (e. g. , 1 January 2018 to 30 June 2019) and clicking on "refresh". The web interface displays the trajectories of the buoys, profilers or TSG and can be used to find additional opportunity data. The data can then be downloaded in NetCDF format.
Data processing levels Three levels of processing are available for each dataset: -Level 0 (L0) consists of the direct output of sensors at full temporal resolution. -Level 1 (L1) displayed data in ASCII (. csv) or netCDF (. nc) files are only processed from the software of the constructor, keeping the full resolution and computing the derived variables into standard units. A recent instrumental system (AML and Valeport probes) directly provides L1 files. L1 files are corrected for eventual drift of sensors. -Level 2 (L2) is proposed as gridded, controlled and resampled data in netCDF files (. nc). Gridded datasets for salinity and temperature were resampled vertically every meter, removing spikes, spurious values and density inversions when they persist after the first process supplied by the sensor manufacturer.
They are then posi-tioned as vertical profiles at the mean geographical position of the ascending or descending record. Temperature and salinity data were also compared to the historical data in the neighborhood of the profiles or transects using the validated CORA database distributed by the Copernicus Marine and Environment Service  (Cabanes et al. , 2013; Szekely et al. , 2019). PROTEVS-MED data are not yet included in this database but will be transmitted for a future release. All gridded profiles or transects were plotted for a visual quality check and are available as "quick looks" on the repository. The L1 and/or L2 dataset is released in the present database. L0 data remain available in constructor format upon request to the data-providing institution (SHOM; data-support@shom. fr).
Companion datasets During the field experiments, surface drifters with holey socks located at 100, 75, 50 or 15 m depth were deployed, www. earth-syst-sci-data. net/12/441/2020/ Earth Syst. Sci. Data, 12, 441-456, 2020 given the opportunity at the beginning of their track to perform a Lagrangian survey of observed structures. A few Argo floats were also dropped and experienced the first PROTEVS-MED dedicated mission with high temporal resolution (daily cycle) and parking depths adjusted to the observations to maintain the drifters as long as possible within the targeted structures (typically 100 m deep). After the drifter left the structure, it used the usual Argo standard procedure in the Mediterranean (i. e. , a 5 d cycle and a parking depth of 350 m). Already stored in dedicated and accessible stable repositories, they can be found using their WMO (World Meteorological Organization) identifiers (see Table  2 ).
Data availability Data are freely available on the SEANOE repository (https://doi. org/10. 17882/62352; Dumas et al. , 2018). Some of the data are already being investigated or are in publications; the authors would appreciate collaboration proposals. For an initial overview, quick looks of all SeaSoar, MVP or rapidCAST transects and XBT and CTD profiles are available in catalogues on the repository. SeaSoar, MVP, rapidCAST, CTD, LADCP and XBT data are stored in both CSV (ASCII) and netCDF files for L1 (directly extracted from the instrument or constructor software) and in netCDF for L2 (resampled every meter) files. For TSG, the present database provides only L1 files; L2 (validated and resampled data) data are available from the dedicated repository (see Table  2 ). For the sake of simplicity, VMADCP files were concatenated over each cruise duration to provide a single file per cruise; for a given cruise, the data are a function of time and depth within the single file dedicated to the cruise.
Data are displayed by cruises and instruments, and the syntax is instrument_data-type_cruises_starting-date-of-record_index. file-type, where instruments = ctd,seasoar,ladcp,xbt,rapidcast,mvp, vmadcp_xxx data-type = "L1" or "L2" cruises = cruise and leg name date = the date of the first record in the file index = sequential index of this kind of profile recorded during the cruise file-type = csv(. csv) or netcdf(. nc). Additionally, data extracted from onboard automatic acquisition are provided in netCDF files for the ship navigation. Future PROTEVS-MED experiments are scheduled, and results will be added to the repository.
Conclusions The PROTEVS-MED dataset available through an unrestricted unique repository is an unprecedented opportunity for the community to approach the fine-scale dynamics in the Western Mediterranean Sea and more largely the submesoscale dynamics associated with strong mesoscale dynamics. In the framework of the high-resolution altimetry this dataset can help to characterize the scales of fine-scale structures in the Western Mediterranean Sea and to design combined experiments using high-resolution in situ measurements (SeaSoar or MVP) and altimetry with the future SWOT satellite (d  'Ovidio et al. , 2019). It also complements the repeated glider lines maintained in the framework of the MOOSE observatory  (Coppola et al. , 2019)  and is useful for designing future combined multi-platform experiments.
In situ observations of ageostrophic dynamics remain rare, and the synergy between these observations and theory, and then between these observations and modeling, should be very fruitful. These data should contribute to the knowledge of small scales and fill some of the gaps in observing systems in the Mediterranean Sea  (Tintore et al. , 2019). As numerical modeling resolution becomes higher (on the order of few hundred meters), the simulation of submesoscale processes (layering, subduction, stirring, vertical velocities) is therefore expected, and this dataset, providing data at similar scales, is an opportunity to validate the secondary simulated circulation. Author contributions. SL, SC, PG and FD designed and conducted the field experiments as principal investigators. ML managed the calibration and the metrological traceability of SBE sensors.
VG carefully checked the dataset. All co-authors carried out the experiments, participated in the cruise or processed the data. PG and FD prepared the paper and the data, with contributions from all co-authors. Competing interests. The authors declare that they have no conflict of interest. Acknowledgements. The authors acknowledge that the French government defense procurement and technology agency (Délégation Générale de l'Armement) funded all the campaigns reported here extensively through Protevs and Protevs II "programme d'étude amont". They thank the technical team at the French Naval Hydrologic and Oceanographic Service (SHOM) and the crews of the French navy ship Beautemps-Beaupré, the R/V Pourquoi Pas ? and the R/V L'Atalante for their contribution to the field experiments. Financial support.
Methods The study was reported according to the STROBE guideline  [18]. A protocol was registered at Clinical-Trials. gov (ID NCT02995096). The study was approved by the Danish Data Protection Agency (RH-2018-70, I-Suite number 6610). This study is a register-based observational study with prospectively recorded data from the ELTR. The ELTR is a pan-European database including pretransplant and follow-up data from 172 liver transplantation centres. Patients are treated and followed up locally at each centre. The database comprises information on donor, recipient, locoregional treatments, immunosuppression, pathology from explanted liver (tumour size, tumour number, and vascular invasion), underlying liver disease, cirrhosis, time of death, and cause of death. We included all patients in the ELTR undergoing liver transplantation due to HCC from 1990 to November 2016.
The criteria for cirrhosis and selection for transplantation were not dictated by the ELTR and may vary between centres. Outcomes were overall mortality, HCC-specific mortality (death due to HCC recurrence), and non-HCC-specific mortality (death due to other causes than HCC recurrence). As confounder variables, we included number of HCC tumours, year of transplantation, size of largest tumour, vascular invasion (micro-or macrovascular), time on waiting list, centre volume, age, sex, locoregional treatment before transplantation, and MELD score  [8, 22]. We estimated the association between cirrhosis and mortality using a Cox regression model. We estimated an unadjusted model, an age-and sex-adjusted model, and a model adjusted for variables in the large dataset without any missing data (age, sex, year of surgery, and size of centre).
We performed PS calibration to adjust hazard ratios (HRs) from the model adjusted for variables in the large dataset by including additional information from a subset of the dataset with complete data on other confounding variables (time on waiting list, number of HCC tumours, vascular invasion, size of largest tumour, locoregional treatment before transplantation, and MELD score). We calculated two PS in the subset with complete information. The first PS was the error-prone PS (X EP ), where we estimated the probability of cirrhosis conditional on confounders measured in the whole dataset. The second PS was the corrected PS (X corr ), where we estimated the probability of cirrhosis conditional on all confounders measured in the subset with complete information. Both PS models were estimated using multivariable logistic regression.
The %blinplus macro provided the adjusted HR estimates, including 95% confidence intervals (CIs) adjusted for additional uncertainty from the estimation of the measurement error model in the subset data. Mortality was illustrated using Kaplan-Meier plots with 95% CIs including numbers at risk. The analyses were performed using SAS version 9. 4 (SAS Institute, Cary, North Carolina, USA) and R version 3. 5. 1 (R Core Team, Vienna, Austria).
Results We included 22,787 patients, of whom 21,995 (96. 5%) had cirrhosis. Among the patients with cirrhotic livers, 41. 2% had hepatitis C-related cirrhosis, 23. 9% had alcoholic cirrhosis, and 14. 4% had hepatitis B-related cirrhosis. Among the patients without cirrhosis, 23. 4% had hepatitis C virus, 11. 7% had hepatitis B virus, 9. 4% had other hepatitis viruses, and 7% had hemochromatosis. The subset of patients with data on all variables included 2,528, of whom 2,425 (95. 9%) had cirrhosis. These patients were comparable to those of the whole dataset regarding baseline characteristics (Table  1 ). However, the subset patients were more likely to be transplanted in the later part of the period. Patient characteristics were largely comparable between cirrhotic and non-cirrhotic patients except for age and locoregional treatment while on the waiting list.
The present study is the largest to date to investigate transplantation in non-cirrhotic patients with HCC. Moreover, the study is the first of its kind to use PS calibration to adjust for unmeasured confounding, which may be a major issue in database studies  [11, 12]. Included patients were comparable with respect to background liver disease and accompanying comorbidity, which strongly affects outcome. However, non-cirrhotic patients are generally younger and may be treated differently. Closer follow-up and more focus on recurrence may lead to bias in reporting of HCC-specific mortality. The present study was based on a pretransplant diagnosis of non-cirrhosis, which may be inaccurate. However, it represents the scenario on which the clinical decision to select patients for transplantation is taken.
Furthermore, studies have indicated that immunosuppression with the mammalian target of rapamycin inhibitor sirolimus improved prognosis in patients transplanted for HCC  [26, 27]. Variables regarding immunosuppression are included in the ELTR database. However, due to the quality and structure of available data, meaningful analyses were not possible. Thus, we could not account for the fact that some patients were treated with sirolimus. Lastly, additional confounding from variables not available in the ELTR database could not be corrected for. Among these, pretransplant alpha-fetoprotein is considered an important prognostic variable [28-30], and sarcopenia has been associated with lower survival after living donor liver transplantation for any indication [31, 32] and higher recurrence risk after living donor liver transplantation for HCC  [33].
The implication of the present study may be more strict transplantation selection criteria for non-cirrhotic patients in the future. Promising new methods to include alpha-fetoprotein  [28] [29] [30]  in transplantation criteria need to be validated for non-cirrhotic patients. Positron emission tomography/computed tomography may be used for staging of non-cirrhotic patients as it provides accuracy superior to that of conventional imaging  [34]. Locoregional treatment before transplantation may be considered standard regardless of tumour characteristics. Thus, response to such treatment could be used to select patients with acceptable prognosis  [35]. In conclusion, using a method to account for unmeasured confounding in the large ELTR database, this study showed that HCC in non-cirrhotic livers may represent a more aggressive cancer form with different tumour biology.
Acknowledgements Thanks to all the centres that contribute to the  ELTR. The Organ Sharing Organizations the French ABM (Sami Djabbour and Alain Jolly) , the  Dutch NTS (Cynthia Konijn) , the  Eurotransplant Foundation  ( Undine Samuel  and  Marieke Van Meel ), the  Spanish ONT  ( Gloria de la Rosa ), and the  UK-Ireland NHSBT  ( Mike Chilton  and  Julia Micciche ) are acknowledged for data cross-check and sharing with the ELTR.
Statistical Analyses For the in vivo study, the data were expressed as mean ± SD. The normality of distributions was verified by means of the Lilliefors-corrected Kolmogorov-Smirnov test. The data were analyzed using a one-way analysis of variance (ANOVA) followed by a Tukey's tests to assess specific differences among groups or conditions using GraphPad Software Inc. For animal studies, the sample size calculation software G Power (http://www. gpower. hhu. de/, last access date: 1st February 2020) was used. The sample size of each experiment was determined by power analyses based on data from previous studies and preliminary experiments with alpha of 0. 05 and 85% power. For the in vitro experiments, data were expressed as mean ± SD. The normality of distributions was verified by means of the Lilliefors-corrected Kolmogorov-Smirnov test.
Funding: This work was supported by:  Miguel Servet  contract  CP13/00221  from the  "Instituto de Salud Carlos III-FEDER", Fondo de Investigaciones Sanitarias  [ PI18/01875 ], the  Agence Nationale de la Recherche  ( ANR-16-CE14-0021-01 ), the  Fight-HF Avenir Investment Program  ( ANR-15-RHUS-0004 ), and the  FP7 -funded  COST ADMIRE network  ( BM1301 ). BB was supported by a PhD grant from the  Region Ile de France ARDoc. LM was supported by a PhD grant from the  "Instituto de Salud Carlos III-FEDER ". EJ supported by a  Sara Borrell Contract  from the  "Instituto de Salud Carlos III-FEDER ". Acknowledgments:  Elisa Reta Zubiri. Communication and Design Unit. Navarrabiomed 2020.