dataesr/scientific-paragraphs-categorization huggingface dataset:
New shoreline 14 C ages from Incahuasi Island Our new 14 C ages (Table  2 ) and all previously published radiocarbon ages were calibrated relative to 2010 using OxCal 4. 2  (Ramsey, 2009)  and the IntCal13 calibration curve  (Reimer, 2013). This updated dataset was used to refine our knowledge of the evolution of the lake level through time (Fig. 11 ). Our four new calibrated ages span the Tauca and Coipasa lake cycles, with sample INC-13-2 (15. 97 ± 0. 11 cal kyr BP) belonging to the transgressive or deep part of the Lake Tauca cycle. Both replicates of INC-13-3 (INC-13-3A and INC-13-3B) yield ages of 12. 75 ± 0. 03 and 12. 09 ± 0. 13 cal kyr BP, respectively, precisely coeval with the Lake Coipasa highstand. However, sample INC-13-1 does not fit the lake level curve established by  Blard et al.
(2011a) ; its age of 13. 44 ± 0. 05 cal kyr BP is 1 kyr too young to belong to the Tauca highstand and 1 kyr too old for the Coipasa highstand. This single sample is at odds with the complete dataset, which supports the near-complete evaporation of the lake between 14 and 13 ka BP (see summary in  Blard et al. , 2011a). Thus, we consider sample INC-13-1 to be partially contaminated by modern or dead carbon and exclude it from further discussion. Table  2. Radiocarbon results for lacustrine bioherms of Incahuasi Island. The most important update from this new dataset is that the two 14 C ages of bioherms INC-13-3A and B belong to the Lake Coipasa (Younger Dryas) event (Fig. 11 ). These samples stand at 3,720 m asl, indicating that the Coipasa highstand was probably 15-20 m higher than previously reported  (Blard et al.
Nevado Sajama Smith et al. (2009) used 36 Cl cosmogenic data to establish the first glacial chronology for Nevado Sajama. In agreement with their results, our 3 He dataset confirms the presence of late-glacial moraines on Nevado Sajama. However, the important scatter of their 36 Cl ages (possibly due to intersample variability in Cl content;  Schimmelpfennig et al. , 2009)  precludes a more detailed comparison with our results. Nevado Sajama records a major glacial advance around 16 ka BP, coeval with the end of the transgression and the beginning of the Lake Tauca highstand. The ELA shift between 16 and 15 ka BP is less than 60 m (2 km of horizontal retreat), suggesting that climatic conditions remained relatively stable during this period. The age of moraine M4 is coeval with the end of the Coipasa highstand, and its corresponding ELA (4,871 m asl) is not significantly higher than that at the end of the Tauca highstand as observed on moraine M3 (ELA = 4,800 m asl).
Regional and global paleoclimatic implications Our reconstruction of both absolute precipitation and temperature during the last deglaciation represents a unique dataset documenting the regional and global paleoclimatic mechanisms affecting the southern Tropical Andes. Our new reconstructions reveal that (i) precipitation variability over the Altiplano reacted synchronously with the Greenland-Atlantic dynamic during the deglaciation  (Andersen et al. , 2004; McManus et al. , 2004) , whereas (ii) temperatures were in phase with Antarctic temperature fluctuations  (Jouzel et al. , 2007). These new observations are key in deciphering the paleoclimatic connections between the Northern and Southern Hemispheres and the Tropics.
Only a few empirical studies have suggested common Antarctic and Tropical atmospheric temperature patterns. The meta-analysis of Tropical Andean moraine ages by Jomelli et al. (2014)  showed that most Tropical Andean glaciers had a greater extent during the ACR than during the Younger Dryas. They also used a transient general circulation model (GCM) simulation to show that the connection between Southern Hemispheric and Tropical temperatures results from a combination of several atmospheric mechanisms, including AMOC modulation, CO 2 level, precipitation, vegetation, and local heat budgets. However, Groot et al. (2011)  presented a contradictory paleotemperature dataset; based on a continuous 284-kyr-long pollinic record from a core drilled in Lake Fúquene, Columbia (5°N, 2,540 m asl), they asserted that temperature fluctuations in Columbia follow North Atlantic-Greenland fluctuations on glacial-interglacial time scales.
Acknowledgments This work was funded by the  INSU EVE-LEFE program  and the  ANR Jeunes Chercheurs   GALAC  project ( ANR-11-JS56-011-01 ). We greatly appreciated the logistical support of the  Institut de Recherche pour le Développement (IRD)  of  La Paz  (Bolivia) during our field trips between 2010 and 2013. The  ASTER French national AMS  facility (CEREGE, Aix-en-Provence) is supported by  INSU/CNRS , the  ANR  through the  "Equipements d'Excellence" program ,  IRD , and  CEA. Field measurements of mass balance and ELA on Bolivian and Ecuadorian glaciers were provided by the Andean part of the  Service National d'Observation GLACIOCLIM , funded by the  French IRD , the  Universidad Mayor de San Andres (IGEMA, IHH) in Bolivia  and the  Insituto Nacional de Meteorologia e Hidrologiain Ecuador.
In contrast with our aforementioned structures, the majority of the 20 nonredundant complex structures of PXR in the Protein Data Bank (PDB) show ligands with a more central position in the LBP, mainly extending from subpocket 1 to subpocket 4 (e. g. , SR12813, SI Appendix, Fig. S8A ; garcinoic acid, SI Appendix, Fig. S8B ). Besides, rifampicin is the only one ligand which occupies almost all of the LBP (SI Appendix, Fig. S8C ), thus covering the four groups defined in this study. However, few ligands are more specifically bound to one of the four subsites (e. g. , a benzothiazine in 3, SI Appendix, Fig. S8D ; the HIV-1 integrase and S1P 1 inhibitors in 1, SI Appendix, Fig. S8 E  and F ; the P2X4 and HIV reverse-transcriptase inhibitors in 2, SI Appendix, Fig. S8 G  and H ). Finally, all ligands except estrogens of group 4 established contacts with the aromatic cage of subpocket 1 through π-stacking or C-H/π interactions, and half of them occupy at least subpocket 2 also.
3 mM luciferin. Luciferase activity was measured for 2 s in intact living cells using a plate reader (PerkinElmer Luminometer). EC 50 values were measured using GraphPad Prism (GraphPad Software). PXR Crystal Structures. The human PXR LBD (residues 130 to 434) was coproduced with a fragment of the steroid receptor coactivator-1 (SRC-1, 623-710) to enhance PXR stability and purified as previously described  (8). Crystals of the PXR LBD complexes were obtained by mixing 1 μL of protein (4 mg/mL) preincubated (1 h) with ligand (3 molar equivalents with 1 ligand or 1. 5 each for 2 ligands) and 1 μL of precipitant [50 to 100 mM imidazole, pH 7. 0 to 7. 4, 8 to 14% (vol/vol) isopropanol] and equilibrated against a reservoir of 500 μL of precipitant. Crystals appeared in 24 to 48 h. Diffraction data were collected on the ID23-1, ID23-2, ID29, ID30A-1, or ID30B beamlines at the European Synchrotron Radiation Facilities (Grenoble, France) and on the PX1 beamline at the Swiss Light Source (Villigen, Switzerland).
Data were processed and scaled with XDS and XSCALE  (26). Crystals belong to space group P4 3 2 1 2. The structure was solved and refined using Phenix  (13)  and COOT  (27). Data collection and refinement statistics are summarized in SI Appendix, Table  S1. Figures were prepared with PyMOL (https://pymol. org/2/). ESI-MS Analyses. Denaturing MS experiments were carried out on an electrospray time-of-flight mass spectrometer (LCT; Waters) coupled to an automated chip-based nanoelectrospray source (Triversa Nanomate; Advion Biosciences) operating in the positive ion mode. First, purified PXR LBD was buffer-exchanged against 150 mM, pH 8. 0, ammonium acetate buffer (Sigma) using 0. 5-mL Zeba Spin desalting columns (Thermo Fisher Scientific). Then, protein concentration was determined using a Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific).
PXR LBD was then incubated with a 10-molar excess of TBT or PRE ligands during 5 min at 20 °C at a final concentration of 20 μM (and 200 μM for each ligand, keeping 1% amount of DMSO). Prior to MS analyses, an external calibration was performed using the multiply charged ions produced by 2 mM horse heart myoglobin solution (Sigma) diluted in water/acetonitrile/formic acid (50/50/1, vol/vol) over the m/z range of 500 to 5,000. Samples were analyzed to a final concentration of 2 μM of PXR LBD diluted in the water/acetonitrile/formic acid solution using tuning parameters of the mass spectrometer as follows: backing pressure and cone voltage were set to 2. 1 mbar and 40 V respectively, while raw data were acquired with MassLynx 4. 1 (Waters). Native MS experiments were performed on a hybrid electrospray quadrupole time-of-flight mass spectrometer (Synapt G2 HDMS; Waters) coupled to an automated chip-based nanoelectrospray source (Triversa Nanomate; Advion Biosciences) operating in the positive ion mode.
Binding data were fitted using a sigmoidal dose-response model using GraphPad Prism (GraphPad Software). RT-PCR and Real-Time qPCR. Total RNA was isolated with EXTRACTME Total RNA Kit (Blirt; cat. no. EMO9. 1). One microgram of total RNA was reversetranscribed to cDNA using the 5× All-In-One RT Master mix (Abm; cat. no. G490). qPCRs were performed using SYBR green (Qiagen) and specific primers with the LightCycler-480 real-time PCR system (Roche Diagnostics). Sequences of each primer were as follows: Cyp3a4, forward, 5′-GCCTGGTGC-TCCTCTATCTA-3′; and reverse, 5′-GGCTGTTGACCATCATAAAAG-3′; Actb, forward, 5′-AGGCACCAGGGCGTGAT-3′; and reverse, 5′-GCCCACATAGGA-ATCCTTCTGAC-3′. The relative amount of RNA was calculated with the 2 ΔΔCT method, and gene expression was normalized using β-actin. the skeletal-dorsal muscle as previously described  (29, 30).
Imaging and Fluorescence Quantification. Tadpoles were placed in MS222 0. 1% until immobility, washed in clean water, and placed into a wet chamber. Images were acquired using a Leica MZ16F fluorescence stereo microscope (MZ16F) equipped with a Q. imaging retiga camera, driven by QCapture Pro-6. 0 software, and an eGFP filter bandpass. All pictures were taken with the same parameters (40× objective and 600-ms exposure time, gain 4). The quantification of fluorescence was measured only in a region of interest delimited to the transfected muscle fibers using ImageJ software. Statistical Analysis of Results. Experiments were reproduced three times following the same protocol with three different batches of animals. For each independent experiment, data from all groups were normalized to the control group (to 100 value).
Then, a pool of all data was made. Graphs and statistical analysis were done using GraphPad Prism (GraphPad Software). When two groups are presented on a graph, nonparametric Mann-Whitney tests are used; for three or more groups, we used nonparametric Kruskal-Wallis tests with Dunn's multiple comparison posttest. Data Availability. The atomic coordinates and structure factors have been deposited in the PDB under accession codes 7AX8 (apo), 7AX9 (CC), 7AXA (CLO), 7AXB (END), 7AXC (FER), 7AXD (FIP), 7AXE (OXA), 7AXF (PRE), 7AXG (TBT), 7AXH (ZEA), 7AXI (CC/E2), 7AXJ (CLO/E2), 7AXK (END/E2), and 7AXL (HEP/E2).
ACKNOWLEDGMENTS. We acknowledge experimental assistance from the staff of the  European Synchrotron Radiation Facility (Grenoble, France ) during data collection. We acknowledge financial support from the  Agence Nationale de la Recherche (ANR) , projects SYNERACT (to  P. Balaguer  and W. B. ) and TOXSYN (to B. D. , J. -B. F. ,  P. Balaguer , and W. B. ),  Plan Cancer INSERM  project  SYNERPXR 2. 0  (to  P. Balaguer  and W. B. ), and the  French Agency for Food, Environmental and Occupational Health & Safety projects XENOMIX  (to  P. Balaguer  and W. B. ) and TOXCHEM (to  P. Balaguer  and W. B. ). This project has received funding from the  European Union 's  Horizon 2020 research and innovation program  under Grant Agreements No. 825489  (to  P. Balaguer  and W. B. ), No. 825759 , and No.
825161  (to J. -B. F. and B. D. ). Centre de Biologie Structurale  is a member of  France-BioImaging  and the  French Infrastructure for Integrated Structural Biology. Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO)  is part of the  French Proteomic Infrastructure , three national infrastructures supported by the  French National Research Agency  ( ANR-10-INBS-04-01 ,  ANR-10-INBS-05 , and  ANR-10-INBS-08-03 , respectively). The LSMBO would like to thank  Groupement d'Intérêt Scientifique Infrastrutures en Biologie Sante et Agronomie  and  Reǵion Alsace  for financial support in purchasing a Synapt  G2 HDMS instrument.
e. food resources and temperature). DEB models can be built with data coming from experiments and/or literature, to quantify age, length, weight of the different life stages and provide information on reproduction, growth and metabolic rates to calibrate the model  (van der Meer 2006 , Marques et al. 2014). Application of DEB models to Antarctic species is increasing. They can be easily extracted from the AmP collection, using the software AmPtool. The Matlab command "select_eco('ecozone', {'MS'})" presently gives a list of 37 species, where MS stands for "Marine, Southern Ocean". Command "select_eco('ecozone', {'TS'})" gives another 3 species for the terrestrial Antarctic environment, among which the mite Alaskozetes antarcticus. Among the most common and well studied Southern Ocean benthic invertebrates are the sea star Odontaster validus  (Agüera et al.
The energy is allocated within and in between these branches by the establishment of some priorities, where somatic maintenance (p M ) has priority over growth and maturity maintenance (p J ) has priority over maturity and reproduction. During its lifetime, the organism allocates energy to maturity which symbolizes its complexity and reaches some life stages at some defined thresholds (, birth, when the organism is capable to feed; E H j , metamorphosis; E H p , puberty, when it can reproduce). After reaching sexual maturity, the energy that was formerly allocated to maturity is attributed to the reproduction buffer and the available energy is allocated to the development of gametes. Different types of DEB models have been developed and coded for parameter estimation, see frequently updated https://github.
Data collection and DEB calibration DEB models were calibrated using zero-variate data (single data points at defined life stages, such as length or weight at sexual maturity, number of eggs produced per female) and uni-variate data (relationships between two variables such as oxygen consumption and temperature, length~weight , weight or size~time relationships)  (van der Meer 2006 , Guillaumot 2019b). Data that were collected from the literature (Table  2 ), paying attention to the different taxonomic names adopted for the species through time (see http://www. marinespecies. org/aphia. php?p=taxdetails&id=197296, accessed December 2018); to the sampling area to enable the two morphotypes to be distinguished (intertidal/subtidal) and to the environmental conditions under which each dataset was recorded (available food resources and temperature).
Data from the literature were supplemented by experiments led by S. Morley at Rothera Station (Adelaïde Island, Western Antarctic Peninsula) in January-February 2018 (details in Appendix A). Individual shells were brought back to Europe and processed with imagery to collect growth ring data (Appendix B). Some data are shared between the intertidal and subtidal morphotypes due to a lack of information on the morphotypes physiology in the literature (Table  2 ). The characteristics of the first developmental life stage, when the larvae become able to feed (i. e. age, length and weight at birth) and the pace of development (i. e. age at puberty, maximal observed age) are assumed to be identical. Each data set was characterised by the corresponding temperature and food resources present in the field.
1), using the Nelder-Mead simplex method, updated and explained in  Marques et al. (2018 Marques et al. ( , 2019)). The loss function that is minimized is + = = w n d p d p ( )2 i n j n ij j ij ij i i 1 1 2 2 i ( 1 ) where i scans datasets and j points in this dataset. d ij and p ij are respectively the data and the predictions and d ¯i and p ¯i their average values in set i. w ij are the attributed coefficients, n is the number of data sets, n i denotes the data in a dataset, n j the data in data-points. The value of the loss function is evaluated for each parameter trial. The goodness of fit of each prediction was quantified by the relative error (RE). The mean relative error (MRE) quantifies the overall model performance. RE corresponds to the sum of the absolute differences between observed and predicted values, divided by the predicted values.
Parameters of DEB models DEB predictions for the separate intertidal and subtidal models are accurate, with MRE values lower than 0. 2 (Table  3 ). Average MRE value of the AmP collection is close to 0. 06. Relative Errors are quite low, with the highest values obtained for length~GSI data (RE= 0. 6089 and 0. 8702 for intertidal and subtidal models respectively) and time~length relationships, obtained from the sclerochronology measurements, that are highly variable between each measured shell (respectively RE= 0. 3645 and 0. 5924 for intertidal and subtidal models) (Fig. 3 , Table  3 , Appendix B). In view of the substantial morphological difference between the populations, we expected to see a clear difference in the shape coefficient δ M. We found a slightly larger value of δ M for the intertidal morphotype, meaning that for the same shell length, it has slightly more structure, compared to the subtidal one.
Comparison between morphotypes In a second step, we evaluated if known contrasts in physiological traits between the morphotypes could be highlighted by the modelling approach. By simply comparing the two single models, we observed minimal energetic contrasts between the intertidal and subtidal morphotypes (small differences in assimilation rate and ability to store reserves, Table  3 , Fig. 3 ). By using the augmented-loss-function method, we tried to merge the models into a single one, parameter by parameter, to evaluate the contrasts in parameters between the types  (Lika et al. 2020). Results show that models were merged without generating significant changes in MRE and loss function values (Fig. 4, Appendix D ). Predictions of the uni-variate data are really similar between the three models (Fig.
3 ), with only minor differences in temperature-corrected parameter values between both populations, meaning that the observed differences are best explained by differences in environmental conditions (temperature and food availability). Despite the known physiological contrasts in the field, the available data did not allow the models to capture these physiological differences between the morphotypes, using only the available data. Scatter distribution of the data used to calibrate the model (Fig. 3 ) can hide metabolic differences, which calls for more experiments to describe the physiology of the different morphotypes. Using more complete datasets, for which all parameters are independent between intertidal and subtidal morphotypes, may also help to further constrain the differences. In our case study, several zero-variate data are shared between the intertidal and subtidal models, among which age, length and weight at birth, that control the very beginning of the development.
Acknowledgements We are thankful to  Philippe Pernet  for N. concinna pictures, and  Jonathan Flye-Sainte-Marie ,  Jean-François Cudennec  for sclerochronology protocol advices,  Eric Dabas ,  Rémi Laffont  for sclerochronology lab trials. This work was supported by a " Fonds pour la formation à la Recherche dans l'Industrie et l'Agriculture" (FRIA)  and " Bourse fondation de la mer " grants to  C. Guillaumot. SMOR was supported by  Natural Environment Research Council  core funding to the  British Antarctic Survey. This is contribution no. 40  to the vERSO project (www. versoproject. be), funded by the  Belgian Science Policy Office (BELSPO , contract  n°BR/132/A1/vERSO ). Research was also financed by the " Refugia and Ecosystem Tolerance in the Southern Ocean " project (RECTO;  BR/154/ A1/RECTO ) funded by the  Belgian Science Policy Office (BELSPO) , this study being contribution number  14.
Daily T B observations at H polarization are processed according to  Picard and Fily (2006) ;  Picard et al. (2007)  to derive daily surface melt from 1979 to 2018 (data available from http://gp. snow-physics. science/melting). This data set provides daily melt status, i. e. presence or absence of liquid water, for every grid point on the Southern stereographic polar grid with a grid spacing of 25 km 2. The effective resolution of the product is coarser, of the order of 40 km, close to that provided by SMOS.
The difference observed between 19 GHz and 1. 4 GHz could be exploited to determine if the melt event was limited to the few first centimeters of snowpack or if the event was produce a lot of water that percolated over a sufficient thickness to be detected by SMOS. Figure  7  maps the mean number of melting days detected at 1. 4 GHz without concurrent detection at 19 GHz during summer season over our dataset. It shows that the geographical distribution is related to the total number of melt event (Figure  3 ), meaning that all the areas are concerned by the differential detection at both frequencies. On average, 10±8 days are detected only by SMOS. Moreover, over a total of about 117,000 melting days taking all pixels and summer seasons together detected at 1. 4 GHz, 28% are not concurrently detected at 19 GHz.
Animal activity The animal activity procedure was performed as in Rivera-Ingraham et al  [22]. Briefly, 5 animals that had previously been exposure to different conditions were stained with Mitotracker Deep Red 633 (Ex: 633nm; Em: 660 nm) at a concentration of 0. 33 μM for at least 1 h before the analysis and were kept in this medium until the end of the experiment. Animals were observed individually in a ≈ 200 μm-deep slide and 3 μl medium, all covered by a coverslip. This ensured that animals could only move in the X-Y axis while staying under focus and permanently in the field of vision of the microscope objective. Animals were scanned for 2 min with at least 1800 frames at a frequency of 67 msec using an Olympus SZX microscope coupled with a CellSens camera. Pictures were stacked using ImageJ (NIH, Rasband WS) and then imported into Imaris, with which behavioral parameters were analyzed using the "Imaris Track" module (Bitplane).
Fluorescence intensity For monitoring the heavy metal response, treated animals were incubated for 1-0. 5 hour with different types of fluorescence probes (Table  2 ) and then imaged using a Zeiss Axio Imager Z1 microscope equipped with an apotome (Zeiss Oberkochem, Germany). The pictures were analyzed using ImageJ software. Images were converted to 8-bits, and to standardize all measurements only the head region of each worm was considered for analysis, following Rivera-Ingraham et al. [29]. In the present study, all experiments were carried out using 10 animals per treatment with 3 replicates each, resulting in 27-30 animals in total. In order to avoid inevitable interferences with and among dyes, exposure times were kept as brief as possible and all dyes we used separately. The median and maximum value of the signal was analyzed using ImageJ software.