dataesr/scientific-paragraphs-categorization huggingface dataset:
Consequently, the model of Fig. 21c  is extended to include the complete tree Φ. A model of tree evolution is then added to the picture, symbolized by the relationship P(Φ|Z), where Z denotes the set of parameters of the tree evolution model. This new model is represented in Fig. 25. We distinguish between two cases regarding the form of P(Φ|Z): • P(Φ|Z) is a phenomenological prior for the tree. It reflects prior knowledge about the reconstructed tree that is not derived from an assumed model of tree evolution. Actually, such priors are assigned on the reconstructed rather than the complete tree. These phenomenological tree priors exist in Bayesian implementations of the phylogenetic model because Bayesian inference requires that every free parameter of a model have a prior distribution. For instance, in the program MrBayes  (Huelsenbeck and Ronquist, 2001) , the reconstructed tree topology can receive a uniform prior distribution (every topology is equally likely), and branch lengths may be uniformly or exponentially distributed.
In contrast, the DEC + J model ("J" for jump) allows the colonization of a new region during speciation  (Matzke, 2014). The R package BioGeoBEARS  (Matzke, 2015)  implements many of the existing biogeographic models into a BioGeoBEARS supermodel. The free C-CTMC model, to our knowledge, is implemented only in the program RevBayes  (Höhna et al. , 2016) , where it is up to the user whether to apply constraints on parameters  (Landis, 2017).
For instance, on the left example, n 1 and n 2 are different nucleotides (A and G) but are identical by descent. On the right, n 1 and n 2 are the same nucleotide (G) but are not identical by descent. A gene tree represents such chains of ancestry linking the observed molecules (at tips) to unobserved ancestral molecules, on the principle that two molecules on the same path in the tree are identical by descent. Gene tree models such as the MSC model the evolution of gene trees, without reference to the state of molecules, while a model of molecular evolution can be further included to model the evolution of the state of the molecules (A, C, G or T for single nucleotides) along the gene tree. the tree treated as a parameter. In this case, the collection of data such as DNA, and the use of a character evolution model would be necessary to estimate the trees jointly with the DAISIE parameters.
First, not all the models of one module are jointly implemented in the same program with all the models of another module. For instance, to the best of our knowledge, the diversity-dependent  (Etienne et al. , 2011)  or the multiple-rate MEDUSA  (Alfaro et al. , 2009)  birth-death models of tree evolution are implemented in stand-alone packages that do not include a model of character evolution. Consequently, if an investigator wants to assess whether diversity-dependence or rate heterogeneity has characterized the evolution of a clade, they need to estimate first T with one program, and then estimate the speciation-extinction dynamics with another program. The same typically goes for models of tree and character evolution such as ClaSSE. The current implementation of ClaSSE, and of most SSE models, does not allow the inclusion of characters other than those linked to the speciation-extinction dynamics.
All operations on netcdf files were performed using CDO (Climate Data Operators) (Schulzweida, 215 2019). Maps, plots and analyses were produced using the R free software (R Core Team, 2018) and the libraries ncdf4 (http://dwpierce. com/software), raster  (Hijmans and van Etten, 2012) , FactoMineR  (Lê et al. , 2008) , corrplot  (Wei and Simko, 2021)  and ggplot2  (Wickham, 2015). 3 Results.
1; 2). Previous studies of this area have shown that the Mass Transport Deposits (MTDs) are located along the slope where numerous gas seeps and evidence of gas hydrates have been recorded  (Popescu et al. , 2007; Riboulot et al. , 2017; Hillman et al. , 2018; Ker et al. , 2019). The work presented here is based on a multi-scale seismic database (mainly 2D-high-resolution and nearbottom very high-resolution). The data provide detailed stacking patterns of turbidite systems and MTDs, fault patterns, and their relationship with BSR (Bottom Simulating Reflector) and free gas extents. The main objective is to enhance the identification and definition of the relative importance of factors controlling sediment instability in this particular context of gas/gas-hydrate dynamics, multi-phased tectonics and sea-level fluctuations.
, 1990; Sloan Jr. , 1998; Dickens and Quinby-Hunt, 1997). The BSR was first mapped by  Ion et al. (2001) , then  Popescu et al. (2006). Pockmarks, gas flares, and seismic facies related to the presence of gas have been also reported. The gas flares were generally acoustically detected in the water column upward the landward limit of the GHSZ at 660 m water depth  (Popescu et al. , 2004; Riboulot et al. , 2017). They mainly consist of gas emissions released to the ocean from the seafloor from underlying sources. Finally, the study area has undergone major changes in environmental conditions relative to sea-level changes and induced connection-disconnection of the Marmara-Mediterranean Sea during last interglacial-glacial cycles Fig. 2. Morpho-bathymetric map based on EMODNET2016 and GEBCO2014 bathymetric data with superposed structural map, offshore Romania.
Note the distribution of canyons and paleo-valleys. The distribution of faults is indicated with: in red, compilation from  Diaconu et al. , 2020  from the data of  Dinu et al. , 2005; Morosanu, 2007 and Munteanu et al. , 2011;  in light blue, gravitational faults from  Tambrea et al. , 2002 and Dinu et al. , 2003 ; in dark blue gravitational faults from  Konerding et al. , 2010. Note that the sets of faults of different colors have been mapped from distinct and incomplete grids of seismic profiles thus leading to an incomplete map. In grey dotted line, the border of the Histria Basin (from  Pȃtruț et al. , 1984 and Anton et al. , 2019). The earthquake epicenters (time period 1900-2019) are from the ISC catalog (http://www. isc. ac. uk/iscbulletin/search/c atalogue/). The nearest earthquakes of the study area are presented in Table  1.
Methodology The results presented in this paper originate from the interpretation of several data sets including (Fig. 3B):  (1) Multi-beam echo-sounder data acquired during the GHASS (2015) campaign (Reson SeaBat 7111 for shallow water 5-500 m, and 7150 for deeper water 200-2000 m) with a bathymetric resolution of 20 m (already published). They have provided the geomorphology of the seafloor from a dense grid of profiles. Water column acoustic data processed on board with SonarScope and GLOBE software have provided the distribution of gas flares. These profiles have not been mapped on Fig. 3B. (2) 2D-high and very-high-resolution (VHR) seismic reflection profiles acquired during the 1998 BlaSON surveys of Ifremer and GeoEcoMar. High-resolution seismic profiling was implemented using a mini-GI air-gun seismic source (frequency range 150 Hz and vertical resolution of 2.
5 m) and a 24-channel streamer. Subbottom profiles (Chirp) were acquired simultaneously to investigate surficial sediments. (3) 2D-high-resolution (HR) multi-channel seismic profiles acquired during the GHASS survey using a single 24/24 mini-GI air-gun seismic source (central frequency at 115 Hz and vertical resolution of 3. 2 m) for profiles GAS031, GAS033 to GAS039, two 24/ 24 for profile GAS030, a single 13/13 for profiles GAS040 and  GAS041, and a 96-channel solid streamer (inter-trace of 6. 25 m and maximum source-receiver offset of 650 m). These profiles are named HRxxx in Fig. 3B. The seismic dataset was processed using a conventional post-stack sequence with constant velocity (1500 m/s)  (Ker and Riboulot, 2015). (4) 2D-very high-resolution hull-mounted Sub-Bottom Profiler (SBP) data acquired during the GHASS survey.
The SBP operates at the frequency range 1800-5300 Hz, giving a vertical resolution close to 20 cm. The quality control of SBP data was performed using the Ifremer QC Subop software  (Dupont, 2015; Ker and Riboulot, 2015). (5) 2D-very high-resolution deep-towed seismic profiles were acquired with the Ifremer SYSIF system  (Marsset et al. , 2010; Marsset et al. , 2014; Marsset et al. , 2018)  during the GHASS survey. SYSIF is a deep-towed seismic device hosting a Janus-Helmholtz transducer emitting a linear chirp signal in the frequency bandwidth 220-1050 Hz and a streamer, both towed at 2 knots, 100 m above the seafloor. Processing includes correction of altitude, and seismic signature deconvolution and provides 15-mlateral resolution at the seafloor and 1-m-vertical resolution. All seismic data were integrated into IHS Kingdom software for interpretation.
Measurements in meters were calculated from Two-Way Traveltime (TWT) values using v = 1500 m/s. Seismic interpretation is based on: (1) analysis of the reflectors' lateral terminations (onlap, downlap, erosional truncation) according to the general principles of seismic stratigraphy  (Mitchum et al. , 1977) ; and (2) characterization of seismic facies and correlation of distinctive reflectors between profiles. The cross-correlation between complementary seismic data sets provided mapping of unconformities, sedimentary bodies, faults, and gas systems. SBP profiles are not presented in this paper due to the poor quality of data caused by the presence of shallow gas. Only one Blason profile is presented. SYSIF was mainly used to identify sedimentary discontinuities such as scarps related to MTDs, channel sidewalls, and faults.
Acknowledgments The officers and crew during the GHASS cruise on board R/V Pourquoi Pas? and the Genavir and Ifremer technical staff during and after the cruise are greatly thanked. S. Ker ,  V. Riboulot ,  B. Marsset ,  F. Colin ,  Y. Thomas  are greatly thanked for their scientific and technical contribution. Andrew S. Madof  and an anonymous reviewer are thanked for their comments that helped to improve this manuscript. We also thank the editor  Liviu Matenco  for his general comments. We sincerely thank  Alison Chalm  for revision of the English language.
Significantly, the effectiveness of these seasonal palaeothermometers has also been demonstrated on the European Atlantic façade for Phorcus lineatus (da Costa, 1778)  21, 31, 32  , a topshell species that comprises a significant proportion of Mesolithic shell middens found in the region. The difficult task, until now, however, has been to find a shell midden with sufficient temporal resolution to enable inference of short and abrupt changes in climate conditions and human behaviour  19. Here, we report chronological, archaeomalacological and isotopic data from shellfish remains recovered from the site of El Mazo in northern Spain (Fig. 1 ; Supplementary Text 1; Supplementary Fig. 1 ). We performed a large number of radiocarbon measurements on different materials, including bone from terrestrial animals, microbotanical remains, and marine mollusc shells to generate a high-resolution chronological sequence of the human use of the cave.
e. , difference between winter and summer) (13. 8 °C) were recorded at the bottom of the sequence Satellite map in the upper-left corner of (a) was created by authors using Adobe® Illustrator software. The original base map was extracted from the maps-for-free web site (https:// maps-for-free. com/) (© Collaborators of OpenStreetMap, Open Database License [ODbL]). Map in the upper-right corner of (a) was generated by Alejandro Garcia-Moreno using ArcGIS software. Lower map of (a) was created by Luis C. Teira Mayolini using ArcGIS and Adobe Suite software. (unit 108: 8995-8760 cal BP). Minimum and maximum SST increased at unit 107 (8550-8330 cal BP) by 2. 1 and 1. 4 °C, respectively. Seasonality during this period (13. 1 °C) was lower than in the oldest unit. For both units dating to the 8.
Methods Radiocarbon dating and Bayesian modelling. An outlier Bayesian chronological model for El Mazo was implemented using the OxCal v. 4. 4. 2 software  33, 34. Radiocarbon calibrations relied on the IntCal20 calibration curve for the northern hemisphere  35  and on the marine calibration curve from Heaton et al. 36. Corrections for marine radiocarbon reservoir effects (ΔR) in shell samples from northern Iberia followed the recommendations in García-Escárzaga et al. 28. According to that study, a different ΔR value should be used depending on the mollusc species: -114 ± 170 for P. vulgata and -257 ± 120 for P. lineatus. A stratigraphic model was defined by grouping samples from the same archaeological layer within a phase with start and end boundaries in accordance with OxCal terminology.
These were set in a sequence following the available stratigraphic information. The OxCal model code is given in Supplementary Code 1. The Bayesian model was run 4-5 times and results compared to assess reproducibility, which was observed to be present for scales of ca. 5-10 years and consequently all reported dates here were rounded to the nearest lustrum. The obtained chronological sequence was compared with the Greenland Oxygen Isotopic record (NGRIP)  6, 39. We used the OxCal Date command to provide a reference for an undated object within a phase. This is also used to provide a rough estimate of the chronology of each phase in this study. Estimates of the start, end, and duration of each phase, plus dates for each object within the stratigraphic units, are given in Supplementary Data 1.
To determine the intertidal zone where P. vulgata specimens were collected, length/ height (L/H) ratios were calculated from each limpet. Then the control value obtained by Gutiérrez-Zugasti  71  for northern Iberia was applied to determine whether the specimens were harvested in the lower or higher intertidal zone. In order to establish the occurrence of size selection during collection, a normality test (Shapiro-Wilk) was applied under the assumption that non-normal distributions reflect some kind of shell size selection  71. The statistical tests were performed using the software PAST. Stratigraphic units where the number of measurable specimens was lower than 30 were not considered for the biometric study.
Acknowledgements This research was performed as part of the projects  HAR2016-75605-R  and  HAR2017-86262-P , funded by the  Spanish Ministry of Economy and Competitiveness, MINECO. During the development of this research AGE was funded by the  University of Cantabria  through a predoctoral grant (no code available), by the  Basque Country Postdoctoral Programme  (Grant number  POS_2020_2_0032 ), by the  University of La Rioja  through a posdoctoral grant (no code available) and he is currently supported by the  Catalonia Postdoctoral Programme  through a  Beatriu de Pinós fellowship  (grant number  2020 BP 00240 ). ABMA was funded by the  SUBSILIENCE ERC-CoG project  (Grant agreement No. 818299 ). This study has also been supported by the  Prehistoric Research Consolidated Group of the Basque Country University  ( IT1223-19 ), funded by the  Basque Country Government.
Data availability All of the data reported in this article is provided in the Supplementary Information, Tables, Figures, and Data files. Bayesian modelled results were included in Fig. 2 , as well as in Supplementary Fig. 2  and Supplementary Data 1. All stable oxygen isotope values obtained from Phorcus lineatus (da Costa, 1778) mollusc species, as well as the sea surface temperatures (SST) estimated from these isotopic values, are provided in Supplementary Data 2. Mollusc species representation and shell sizes over time are included in Supplementary Table  3  and Supplementary Fig. 3 , respectively. All other data supporting the findings and interpretations of this study are available in existing publications and the Supplementary Information provided alongside this manuscript. The archaeological remains studied and sampled for oxygen isotope analysis are curated in the Archaeology collection at the University of Cantabria (Santander, Spain).
(2016)  presented a significant negative bias. To better assess the contribution of glaciers to lowland streamflow, the Antisana Glacier 12 (AG12) was monitored since 2004. Over this catchment, discharge modeling has only been done with conceptual and semi-empirical approaches (e. g. ,  Villacís, 2008). The variations of melting with elevation and hence the origin of waters have never been clearly analyzed. This latter scientific concern is analyzed in this paper using a glacier-wide distributed SEB modeling and calculation of the transfer function of flows from each zone of the glacier towards the outlet of the catchment, which may result in more accurate results than statistical approaches  (Veettil et al. , 2017). The distributed SEB has been successfully applied in many areas, but it requires a large amount of data to provide accurate results  (Gerbaux et al.
Meteorological Data The data used in this study were collected by an automatic weather station (AWS) SAMA-1 located at 4,753 m a. s. l. , near the glacier snout. Records extend for 23 months between 07/ 02/2011 and 05/16/2013, referred to as the Study Period (SP) hereafter. The station was equipped with sensors calibrated prior to their installation. The station records the 30-min average of air temperature (T), relative humidity (RH), wind speed (Ws), incoming (SWi) and reflected (SWr) short-wave radiation, and incoming (LWi) and outgoing (LWo) longwave radiation measured every 15 s, except for the wind direction which is measured once every 30 min. Supplementary Table  SA1  summarises the technical specifications of all sensors used. Furthermore, the cloud factor (CF-dimensionless-) was included to relate the cloud cover attenuation to the net radiation  (Favier et al.
A scheme based on temperature ranges was used to estimate the phase of precipitation (see Section 3. 1. 2). Between 29/09/2011 and 30/08/2011 (32 days) and between 31/10/2011 and 29/11/2011 (29 days), a precipitation data gap was filled using measurements from another rain gauge (P-ORE, 4,850 m a. s. l. ) located in the AG15 moraine (Figure  1B ). Correlation between P8 and P-ORE were significant over the study period (r 2 P8-PORE = 0. 63), but not very high because the P-ORE rain gauge was more sheltered from easterly winds by the volcano itself. Nevertheless, P-ORE was located near the ablation zone, making data more relevant for the study of the ablation of the AG12 than other rain gauges around the Antisana volcano. Air temperature variation with elevation was studied using observation data from stations located above SAMA-1.
Glaciological Data Point surface mass balance (SMB) measurements have been performed monthly in the ablation zone of the glacier using stakes, which were distributed between 4,735 and 4,797 m a. s. l. Over the study period, a specific focus was made on data from three periods of short duration, hereafter referred to as MP1, MP2, and MP3 (Table  1 ). These periods were selected due to the available continuous mass balance series. Moreover, we use the 2012 mass balance profile computed by  Basantes-Serrano (2015)  for elevation ranges of 50 m between 4,750 and 5,700 m a. s. l. These values were obtained from direct mass balance measurements on stakes and in snow pits, and from the geodetic approach based on aerial photogrammetry restitutions (for details, refer to  Basantes-Serrano et al. , 2016).
Climatological Data To put in context the meteorological conditions of SP concerning the regional long-term average conditions, we used historical monthly time series of temperature and precipitation. Here we used the 1979-2018 monthly air temperature from ERA-5 single levels reanalysis (https:// www. ecmwf. int/en/forecasts/datasets/reanalysis-datasets/ era5) from the European Centre for Medium-Range Weather Forecasts (ECMWF), available at a 0. 25 °resolution  (Hersbach et al. , 2020). Data were retrieved over the Antisana Massif (0. (Funk et al. , 2015). Data from the 1981-2019 period were considered for the closest cell to the Antisana site (78. 15 °W, 0. 45 °S). 3 DESCRIPTION OF SEB MODEL.
s. l. Above this elevation range, both TLR gives similar mass balance because melt becomes negligible. Therefore, TLR of -5. 9 °C km -1 may be less representative because it was derived from a smaller dataset of air temperature measurements (N = 1,224). Conversely, the TLR of -5. 5 °C km -1 produced fewer deviations since this value was derived with a larger dataset available (N = 54,683, 28,713, and 8,297 for SAMA-1, -2, and -3, respectively), thus allowing a better representation of glacier conditions. Overall, the best fit between simulated and observed MB (RMSE = 0. 55 m w. e. ) is obtained with the value of -5. 5 °C km -1 , and considering that precipitation increases linearly with elevation at a rate of 10% (100 m) -1. This temperature lapse rate is close to the value -5. 1 °C km -1 computed by Erazo (2020) for interpolations above 5,500 m a.
ACKNOWLEDGMENTS The authors thank the  Escuela Politécnica Nacional (EPN)  and  Instituto Nacional de Meteorología e Hidrología (INAMHI)  through the project  SENACYT-EPN PIC-08-506  for the support provided to install and operate the AWS SAMA-1. To the INAMHI research program  Glaciares Del Ecuador  and the  MsC. Bolívar Cáceres  for the glaciological information provided. To the GLACIOCLIM Observation Service for the information on the E-ORE station used, and to  Ruben Basantes  for the glaciological and geographical information provided. J-CR-H thanks to  Secretaría Nacional de Educación Superior, Ciencia ,  Tecnología e Innovación, SENESCYT  for financial support through a PhD scholarship. The authors acknowledge  Juan Carvajal  for the field data acquisition.
Further, we evaluate simulated against observed riverine DOC fluxes, which are obtained from different water quality surveys and scientific publications. Assuming a realistic representation of DOC reactivity in the river network, which is to be evaluated against observations as well, this model-data comparison of riverine DOC fluxes represents a valuable and additional possibility to assess the validity of simulated soil DOC leaching. So far, ORCHILEAK has been successfully tested and applied on large, near-natural river systems such as the Amazon  (Lauerwald et al. , 2017 (Lauerwald et al. , , 2020;; Hastie et al. , 2019) , the Congo  (Hastie et al. 2021 ) and the Lena rivers, with a version also including some specific permafrost-related mechanisms  (Bowring et al. , 2019 (Bowring et al.
, , 2020)). In this study, for the first time, ORCHILEAK is applied to, and evaluated for, the European river network, which is subject to direct impacts of agricultural land use in contrast to more natural river basins. For this reason, we devote special attention to manure application as an anthropogenic non-point source of DOC for the river network, while we assume that for the period of simulation , due to the quality of sewage water treatment, anthropogenic point sources of DOC are now negligible for most parts of Europe. Moreover, as shown for instance by  Meybeck (1986) , DOC from sewage is highly labile and only affects concentration within short distances downstream of water processing plants. Avoiding observational data from sites that are known to be directly impacted by sewage inputs, we are able to evaluate model performance with regard to fluvial transfers of soil-derived DOC, which is the focus of our study.