dataesr/scientific-paragraphs-categorization huggingface dataset:
Currents The currents are monitored by acoustic Doppler current, single point current meters (Aquadopp) and profiler current meters (AquaPro and AWAC). These sensors record the speeds in the axis of their three beams. The raw binary data file was directly processed by the TDB software. First, the velocity data are reprojected in a terrestrial landmark, on the north-east-vertical axes. Then, measurements close to the surface and polluted by the secondary lobes of the acoustic beams are suppressed. The processed data was subjected to final validation by a qualified hydrographer. Prior to their deployment, the magnetic compasses of these current meters were previously calibrated on a dedicated Shom platform. The calibration procedure and the uncertainty of current data are described in  Menn and Morvan (2020).
Sea States The sea states are monitored by three different sensor types, directional wave buoy, wave pressure gauge, and acoustic wave and current profiler. Each sensor type requires specific processing. The directional wave buoys recorded wave motion in three directions. The raw displacement datas were computed directly aboard the buoys. First, the buoy's displacement measurements were low-pass and high-pass filtered to give the threedimensional buoy motion in the frequency range of 0. 01-0. 64 Hz. Then, the spectral data were computed from heaven-northwest displacements. Finally, the statistical wave parameters were computed using spectral data. A quality control based on skewness and kurtosis of vertical displacement were carried out. A 30-minutes data burst with |Skewness|>0. 3 and Kurtosis>5 have been marked with a quality control flag (QC=0).
On this dataset, we use three different reconstruction methods : hydrostatic method, linear method and non linear weakly dispersive method (e. g Supplementary materials A. 1). The pressure records were separated in a 20-min burst, each burst was linearly detrended to suppress tidal motion. The reconstruction methods were applied to reconstruct the surface elevation. Statistical wave parameters were computed by spectral analysis and wave-by-wave analysis (e. g Supplementary materials A. 2). The acoustic waves and currents profiler record surface elevation from Acoustic Surface Tracking (AST) and current in wave cells at high frequency. The raw data is directly processed using the Quickwave manufacturer software. High-frequency surface elevation combined with current measurements allow the reconstruction of a directional wave spectrum using SUV method  (Pedersen et al.
Acknowledgements. The authors would like to thank the  Shom GHOA ,  IES  and Altimétrie littorale teams and all those who participated in the measurement campaign. This research is supported by  Shom ,  Saint-Malo ,  SMA ,  Departmental Council of Ille et Vilaine (CD35) ,  Brittany region  and the  French State. This research is also supported by  PROTEVS research program  funded by  DGA  and conducted by  Shom. The.
Mass spectrometry analysis of protein interacting with 2ccPA beads Nano LC-MS/MS analysis was conducted by JPROteomics (Sendai, Japan) using the LTQ Orbitrap XL Mass Spectrometer (Thermo Fisher Scientific). Nano LC-MS/MS analysis was then conducted, and the MS/ MS data obtained were searched using Mascot (Matrix-Science, London, UK) for protein identification  [23]. Briefly, the data generated using the MALDI-TOF/TOF procedure were searched using the Mascot algorithm (http://www. matrixscience. com). Protein identification was carried out using the UniProtKB protein sequence database. The following parameters were used when performing the search using Mascot: up to two maximum trypsin missed cleavages, mass tolerance of 50 ppm, cysteine carbamidomethylation (fixed modification), methionine oxidation (variable modification), and a charge state of +1.
Apoptosis assay Cells were harvested and washed twice with ice-cold phosphatebuffered saline (PBS). Subsequently, the cells were labeled with Annexin V & Dead Cell Assay kit according to the manufacturer's instructions (Merck Millipore, Darmstadt, Germany). This assay is based on the detection of phosphatidylserine on the apoptotic cells surface using fluorescently labeled Annexin V in combination with the dead cell marker, 7-aminoactinomycin D (7-AAD). The samples were counted by using the Muse Cell Analyzer (Merck Millipore) and analyzed using a software provided by Merck Millipore. n = 3 independent biological replicates; data were presented as mean ± SEM. **, P < 0. 01 versus PAO alone. We used Student's t-test for pairwise comparison.
Caspase-3 colorimetric assay Colorimetric assays were performed to measure the amount of active caspase-3 in the supernatant using the APOPCYTO Caspase-3 Colorimetric Assay Kit (Medical and Biological Laboratories, Nagoya, Japan), according to the manufacturer's protocol. Briefly, total cell protein was extracted using ice-cold cell lysis buffer. Following that, 100-200 μg of total protein was diluted in 50 μL of lysis buffer and 50 μL of 2× reaction   containing 10 mM DTT. Next, 5 μL of caspase-3 substrate was added to each well of a 96-well microplate. After incubation at 37 • C for 3 h, the absorbance was measured at 405 nm. n = 3 independent biological replicates; data were presented as mean ± SEM. **, P < 0. 01 versus PAO alone. We used Student's t-test for pairwise comparison.
ROS measurement using dihydroethidium Intracellular ROS levels were analyzed using the Muse Oxidative Stress Kit (Merck Millipore, Germany), according to the manufacturer's instructions. Cells were seeded into 6-well plates (Corning, NY, USA) at a density of 5 × 10 5 cells/mL. After serum starvation for 12 h, the cells were treated with various concentrations of BK with or without 2ccPA for 12 h. Cells were then harvested and incubated with DHE (Merck Millipore) for 30 min in the dark. The assay provides the relative percentage of cells that are ROS negative/positive upon carrying out flow cytometry (Muse Cell Analyzer) to measure the fluorescence of DHE. n = 3 independent biological replicates; data were presented as mean ± SEM. **, P < 0. 01 versus PAO alone. We used Student's t-test for pairwise comparison.
Calcium measurement Cells were grown on poly D-lysine-coated glass bottom culture dishes (D11141H, Matsunami). Changes in free intracellular Ca 2+ concentrations were monitored using the fluorescent Ca 2+ indicator dye Fluo-4 AM (Dojindo, Japan). Live cell fluorescence microscopy of Fluo-4 AM (Ex/Em: 495/518 nm) was performed. Images of Fluo-4 AM-loaded cells were collected using an inverted fluorescence microscope (BZ-X710, KEYENCE, Japan). n = 3 independent biological replicates; data were presented as mean ± SEM. **, P < 0. 01 versus PAO alone (0. 5 μM). We used Student's t-test for pairwise comparison.
Acknowledgments This work was supported by grants from the  Grants-in-Aid for Scientific Research (C)  (to Tamotsu Tsukahara),  19K07098  (to  Mari Gotoh ) from the  Japan Society for the Promotion of Science. Kimiko Murakami-Murofushi  acknowledges the financial support from  Japan Science and Technology Agency  ( PROJECT-07050777 ). This work was the result of using research equipment shared in the  MEXT Project for the promotion of public utilization of advanced research infrastructure  (Program for supporting the introduction of the new sharing system) Grant Number  JPMXS0422500320. Mari Gotoh  acknowledges support from the inter-university exchange agreement between  Ochanomizu University and Strasbourg University  for a long-term stay at Strasbourg University; she thanks  Dr. Laurent D ÉSAUBRY  and his laboratory members.
| Setting COHERE in EuroCoord was a collaborative group of adult, pediatric, and mother/child HIV cohorts across Europe. The collaboration allows comparisons across age categories and provides a mechanism to rapidly compile datasets to address novel research questions that cannot be studied adequately in individual cohorts (www. eurocoord. net, www. cohere. org) [24]. Data were extracted from the 2015 merger of COHERE that included 23 European cohorts, with information on patient characteristics (age, sex and transmission category), use of ART (type of regimen and dates of start and discontinuation), CD4 cell counts and plasma HIV-RNA over time and their dates, AIDS-defining conditions and indicator variables for drop-out or death.
HIV replication has been shown to be an important, and CD4 count an independent, factor interfering with immunocompetence. It has also been associated with a higher risk of tuberculosis  [28] , and with a lower response to vaccination against yellow fever  [29] , influenza  [30]  and hepatitis B  [31]. Taking an upper 95% confidence limit for the incidence of PjP to be less than 10/1000 py as a threshold to safely withholding prophylaxis is somewhat arbitrary. However, in many of the pivotal studies defining the safety of discontinuation of PjP prophylaxis, the upper 95% confidence level of incidence was in this range, or even slightly higher  [9] [10] [11] [12] [13] [14] [15]. Showing the smoothed effect of current CD4 count on incidence of PjP by fitting the spline models (Figure  1b ) allows the treating physicians to define the safety margin themselves, based on our  large observational database.
7 ). In contrast, the CBD-like domain has considerable rotational freedom, with a difference of ~84°in its orientation with respect to the mid-link domain in the MID-LINK and ELONGATION structures, respectively (Supplementary Fig. 7 ). The C-terminal region was previously visualised in a dimeric form of MACV L protein (PDB:6KLH), but at an insufficient resolution to build a correct model  9. The MACV cryo-EM density (EMD-0710) for the C-terminal region is fully compatible with the LASV C-terminal model and shows an extended configuration similar to that observed in the MID-LINK Fig. 4  Elongation state of the L protein. a Schematic presentation of the primed reaction was carried out to obtain the ELONGATION structure with the L protein stalled in an early elongation state. Nucleotides that are not visible or not clearly assignable from the experimental map are shown in grey italics.
A severe, general loss of 90% of activity was observed for L protein mutant P109G (Supplementary Fig. 10 ). The EN active site itself is exposed to the outside, but access is blocked by residues 1092-1105 from the PB1-like region, which we refer to as the 'inhibitory peptide' (Fig. 5a, b ). The arena-conserved 1096-LCFYS motif (Supplementary Data 1) is intimately bound in the EN active site pocket (Fig. 5b  and Supplementary Figs. 10, 11) and would thus prevent any substrate RNA binding there (e. g. superposition of LCMV EN structure with bound inhibitor shows overlap  28  ) (Supplementary Fig. 11 ). A similar interaction with the EN is observed in the apo-MACV structure (PDB:6KLD) (Supplementary Fig. 4 ). In the MID-LINK and DISTAL-PROMOTER structures, the EN has flipped by ~160°around a hinge between G195-G199.
Even though mutation of W1390 to alanine in a previous study did not impair overall L protein activity  36  , from the structure we would not expect a small hydrophobic alanine residue to disturb the remaining contacts between these domains. Additionally, residues G1391 and D1392 were shown to be selectively important for viral transcription  36  , further emphasising the importance of this interaction site. Residue Y2176, also identified as being selectively important for viral transcription  24  interacts with the thumb-ring residue F1715 (Supplementary Fig. 9 ). These data suggest that the configuration of the C-terminal region and its interaction with the core, as observed in the ELONGATION structure is critical for transcription.
Electron microscopy APO-, DISTAL-PROMOTER, MID-LINK, PRE-INITIATION and ELONGATION structures. The grids were loaded into an FEI Tecnai Krios electron microscope at the Centre for Structural Systems Biology (CSSB) Cryo-EM facility, operated at an accelerating voltage of 300 kV and equipped with K3 direct electron counting camera (Gatan) positioned after a GIF BioQuantum energy filter (Gatan). Cryo-EM data were acquired using EPU software (FEI) at a nominal magnification of x105,000, with a pixel size of 0. 85 or 0. 87 Å per pixel. Movies of a total fluence of ~50 electrons per Å 2 were collected at ~1 e-/Å 2 per frame. A total number of 15,488 (APO-); 13,462 (DISTAL-PROMOTER and MID-LINK); 13,204 (PRE-INITIA-TION); 10,368 (ELONGATION) movies were acquired at a defocus range from -0. 4 to -3.
1 μm (Supplementary Table  2 ). 3′ END-structures. The grids were loaded into an FEI Tecnai Krios electron microscope at European Synchrotron Radiation Facility (ESRF) beamline CM01  49  , operated at an accelerating voltage of 300 kV and equipped with K2 Summit direct electron counting camera (Gatan) positioned after a GIF Quantum energy filter (Gatan). Cryo-EM data were acquired using EPU software (FEI) at a nominal magnification of x165,000, with a pixel size of 0. 827 Å per pixel. Movies of a total fluence of ~50 electrons per Å 2 were collected at ~1 e-/Å 2 per frame. A total were set up in binding buffer (100 mM HEPES(NaOH), pH 7. 0, 100 mM NaCl, 50 mM KCl, 2 mM MnCl 2 , 2 mM dithiothreitol, 0. 1 μg/μL Poly(C) RNA (Sigma), 0. 1 µg/µL bovine serum albumin and 0. 5 U/μl RNasin (Promega)) and incubated on ice for 30 min.
Products were separated by native gel electrophoresis using 25% polyacrylamide 0. 5-fold Tris-borate-EDTA gels and 0. 5-fold Tris-borate running buffer. Signals were visualised by phosphor screen autoradiography using a Typhoon FLA-7000 phosphorimager (Fujifilm) and the respective FLA-7000 software. Uncropped images are provided as Source Data. Primer-dependent polymerase assay. Primer GCG, C1, St1 and C8 (Supplementary Table  1 ) were chemically synthesised with 5′-hydroxy ends (Biomers), primer C8ppp (Supplementary Table  1 ) with 5′ Triphosphate modification (Chemgenes). An N 7 -MeGppp (Cap0) was introduced at the 5′ terminus of C8ppp using the ScriptCap m7G Capping System (CELLSCRIPT) with 1 nmol C8ppp oligo using the manufacturer's standard protocol. After the addition of Ammonium acetate (2.
Data were evaluated using Prism 7. 0d and are always presented as the mean of a given amount (n) of biological replicates as well as the respective standard deviation (SD). For Northern blot analysis, 750 ng of total cellular RNA was separated in a 1. 5% agarose-formaldehyde gel and transferred onto a Roti ® -Nylon plus membrane (pore size 0. 45 μm, Carl Roth). After UV cross-linking and methylene blue staining to visualise 28 S rRNA the blots were hybridised with a 32 P-labelled riboprobe targeting the Ren-Luc gene. Transcripts of Ren-Luc genes and complementary replication intermediate RNA of the minigenome were visualised by autoradiography using a Typhoon FLA-7000 phosphorimager (Fujifilm) and the respective FLA-7000 software. Quantification of signals for antigenomic RNA and mRNA was done in ImageJ 2.
All uncropped images are provided as Source Data. Statistics and reproducibility. Unless stated otherwise in the figure legends all in vitro assays (electrophoretic mobility shift assay, polymerase assay, endonuclease assay), as well as Coomassie-stained SDS gels, have been repeated with similar results at least twice. The total number of micrographs included in each cryo-EM dataset is given in Supplementary Table  2 , representative micrographs are shown in Supplementary Fig. 24, 26, 28, 30 and 32.
1-D CNN A CNN regression model was implemented to estimate subjects' BP. CNNs learn the BCG signal patterns by utilizing the instantaneous phase, calculated from the two-channel BCG, as an input. Our previous study performed a regression analysis with an artificial neural network (ANN) using the IPD calculated from the differences in the two-channel BCG phase. However, in this study, the CNN model learned the pattern of the two-channel BCG phase and hence did not require IPD features. The CNN model was implemented using Python 3. 7. 1 and Tensorflow 2. 3. 1. A single CNN model was implemented to estimate the systolic and diastolic blood pressures (SBP and DBP) in both the rest and recovery sessions. The architecture of the proposed CNN model is presented in Figure  4. is. This value is directly connected to BP.
In our previous study, BP was estimated using data from a rest session. As a result, the standard deviation was 6. 74 in SBP and 5. 83 in DBP. However, in the CNN model, the standard deviation was 6. 24 in SBP and 5. 42 in DBP. The standard deviation difference in SBP was about 0. 5, and the CNN regression model result was better than that of the IPD based ANN model. The standard deviation difference in DBP was about 0. 41, and the CNN model showed better results than IPD. The IPD feature is calculated when the difference between BCG 2-channel phases becomes constant. It could not be used in the recovery session due to the noise caused by the breathing and movements of subjects when they exercised. Therefore, we could not compare the IPD and the CNN regression model in the recovery session dataset.
However, the CNN model learns the relationship between BCG 2-channel phases without calculating IPD. Moreover, it can predict BP in a recovery session with similar performance to a rest session. While measuring the BP, many factors (gender, age, disease, BP measurement time, etc. ) have a significant influence on the BP estimation. Therefore, by increasing the BP of the subjects through exercise, we tried to exclude the factors that interfere with BP measurement. Despite the noise in the recovery session dataset the CNN regression model exhibited good BP estimation performance. When we attempted to train the CNN model with the rest and recovery sessions together, the model exhibited overfitting. Therefore, the CNN regression model was trained separately for each session. As a result, it was possible to estimate the BP in the recovery session.
Late Eocene vegetation composition in the CMB Based on the sporomorph types recorded during this study, the vegetation in the late Eocene CMB is thought to have included perhumid/moist, evergreen, seasonally dry forests; swamp forests along rivers, with herbaceous swamps and marshes, possibly associated with floodplain lakes; coastal vegetation including mangroves, and montane forests. The ecological attribution of pollen types which grew in these different vegetation types, and their absence-presence data are listed in Table  S4. The main vegetation types based on the evaluation of the botanical affinities of the pollen and spore flora recovered from the CMB are detailed below.
Acknowledgements We thank members of the  Myanmar Paleoclimate and Geodynamics Research Group (MyaPGR)  for sample collection;  Malcolm Jones  for processing pollen samples;  Edwin Scholl  for guidance on the SEM microphotography of Sapotaceae;  Henry Hooghiemstra  and  Keith Richards  for help on pollen identification;  Nicolas Gentis  for his designing concept on Fig. 3;  Friðgeir Grímsson  and  Reinhard Zetter  for their great assistance on microphotography of pollen micrographs. We also thank  Limi Mao  and  Carlos Jaramillo  for their constructive comments that help us improve the manuscript. H. H. is supported by the  China Scholarship Council  ( CSC grant   201604910677 ) and the  University of Amsterdam ; D. P. -P. acknowledges the  Treub Maatschappij (Society for the Advancement of Research in the Tropics)  for its support on the fieldwork in Myanmar; G.
Study design and patients For this study, the recruited individuals represented a subset from a study approved by the ethics committees of the Centre Hospitalier Universitaire Brugmann (CHU Brugmann, Bruxelles) and the Hôpital Universitaire Des Enfants Reine Fabiola (HUDERF, Bruxelles) in Belgium (the number "CHUB-BDS-Covid19 ClinicalTrials. gov: NCT04462627"). The study was carried out in accordance with the principles of the Declaration of Helsinki. The authors assume responsibility for the accuracy and completeness of the data and analyses. Briefly, the study carried out between 11 March 2020 and 16 June 2020 in Brussels, Belgium, at the Brugmann University Hospital and the HUDERF, enabled the recruitment of 290 patients with or without symptoms of COVID 19, and with a positive RT-PCR test for SARS-CoV-2 on nasal and pharyngeal swab specimens.
Acknowledgements The authors are grateful to  Dr. D. Blanchard  ( Etablissement Français du Sang, Pays de la Loire, Nantes ) for his kind gift of the monoclonal anti-Tn antibody and to  Drs O. Schwartz  and T. Bruel ( Pasteur Institute, Paris ) for their gift of S protein stably expressing and control HEK-293T cells. We also thank the  Cytometry Facility Cytocell (SFR Sante Francois Bonamy, Nantes)  for expert technical assistance. The work was supported by  Inserm , the  University of Nantes , the  University Hospital of Nantes. N. Bovin  was supported by grant # 20-04-60335  of the  Russian Foundation for Basic Research.
Biological invasions, as a result of human intervention through trade and mobility, are the second biggest cause of biodiversity loss. The impacts of invasive alien species (IAS) on the environment are well known, however, economic impacts are poorly estimated, especially in mega-diverse countries where both economic and ecological consequences of these effects can be catastrophic. Ecuador, one of the smallest mega-diverse countries, lacks a comprehensive description of the economic costs of IAS within its territory. Here, using "InvaCost", a public database that compiles all recorded monetary costs associated with IAS from English and Non-English sources, we investigated the economic costs of biological invasions. We found that between 1983 and 2017, the reported costs associated with biological invasions ranged between US$86.
Abstract in French Coûts économiques des invasions biologiques en Équateur : l'importance des îles Galapagos. Les invasions biologiques, résultant de l'intervention humaine par le commerce et la mobilité internationaux, sont la deuxième cause de perte de biodiversité. Les impacts des espèces exotiques envahissantes (EEE) sur l'environnement sont bien connus, mais les impacts économiques sont mal estimés, en particulier dans les pays à biodiversité méga-diverse où les conséquences économiques et écologiques de ces effets peuvent être catastrophiques. L'Équateur, l'un des plus petits pays méga-divers, ne bénéficie toujours pas de description complète des coûts économiques des espèces exotiques envahissantes pour son territoire. Ici, nous avons étudié les coûts économiques des invasions biologiques en utilisant "InvaCost", une base de données publique qui compile tous les coûts monétaires associés a ces invasions, provenant de sources en langues anglaise et non-anglaise.
e. Andean region), representing serious agricultural problems in the poorest regions of Central Ecuador where monitoring programs are most needed  (Dangles et al. 2010 ). Yet, these costs are generally unknown, very case-specific and/or difficult to contextualize. So far, there has been no national assessment of all the economic costs incurred by IAS in Ecuador, although such cost assessments are of strong interest for both research and management purposes  (Dana et al. 2013; Diagne et al. 2020a ). Using the "Inva-Cost" database, we addressed this knowledge gap. Our aims were to (i) quantify all the reported economic costs of IAS in Ecuador, (ii) evaluate the distribution of such costs across space, taxonomic groups, impacted sectors and over time, and (iii) assess the highest types of costs incurred, whether damage costs or management expenditures.