dataesr/scientific-paragraphs-categorization huggingface dataset:
Isothermal titration calorimetry The affinity of SFTSV CBD to m 7 GTP and GTP was measured by isothermal titration calorimetry (ITC) using a Mi-croCal PEAQ-ITC instrument (Malvern Panalytical). Proteins were dialyzed overnight at 4 • C against 50 mM Naphosphate pH 6. 5, 150 mM NaCl, 10% (w/v) glycerol. The ligand m 7 GTP was dissolved and GTP was diluted in the exact same dialysis buffer. Titrations were done with 150 M CBD in the cell and 5. 0-6. 5 mM m 7 GTP or GTP in the syringe at 25 • C with 19 injections of 2 l (first injection 0. 5 l). Spacing between injections was constant with 150 s for all measurements. Data were analyzed and fitted with the respective PEAQ ITC evaluation software (Malvern) applying a single side binding model and fixing the stoichiometry value to 1.
Crystallisation and crystallography SFTSV CBD crystals grew within 14 days after mixing of one part SFTSV CBD at 18. 6 mg/ml protein concentration supplemented with 4 mM m 7 GTP in 50 mM Na-phosphate pH 6. 5, 150 mM NaCl, 10% (w/v) glycerol with two parts of 7% (v/v) 2-Butanol, 150 mM MES pH 6. 0 and 27. 4% PEG 4000 in a sitting drop vapor diffusion setup at 20 • C. Crystals were flash frozen in liquid nitrogen without cryo protectants and datasets were obtained at beamline P14 of PETRA III at Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany. Datasets were processed with XDS  (27)  and the SFTSV CBD structure was solved by molecular replacement using Phaser  (28)  and the RVFV CBD (PDB: 6QHG) monomer without the ␤-hairpin and loops as an input model. The structure was refined by iterative cycles of manual model building in Coot (  29 ) and computational optimization with PHENIX  (30).
Electron cryo-microscopy Aliquots of 3 l of SFTSV L protein diluted to 0. 6 M in buffer (20 mM HEPES pH 7. 0, 500 mM NaCl, 20 mM MgCl 2 ) were applied to glow-discharged Quantifoil R 2/1 Au G200F4 grids, immediately blotted for 2 s using an FEI Vitrobot Mk IV (4 • C, 100% humidity, blotting force -10) and plunge frozen in liquid ethane/propane cooled to liquid nitrogen temperature. The grids were loaded into a 300-keV Titan Krios transmission electron cryo-microscope (Thermo Scientific) equipped with a K3 direct electron detector and a GIF BioQuantum energy filter (Gatan). A total of 2626 movie frames were collected using the EPU software (Thermo Scientific) at a nominal magnification of ×105 000 with a pixel size of 0. 87 Å and a defocus range of -1 to -3 m. Each movie fractionated into 60 frames, was collected for a total exposure time of 3 s with a flux of 15 electrons per physical pixel per second and a total exposure of 59.
7 • angular sampling. One major class was identified as the most populated (223 604 particles) and better defined class, and was selected for auto-refinement and post-processing in Relion resulting in a 3D electron density map (SFTSV map A) with an estimated resolution of 3. 8 Å using gold standard Fourier Shell Correlation (0. 143 cut-off). The globally refined volume was then used as a template to sort particles again into 10 new 3D classes. This time a distinct class was visible containing additional volume for the C-terminal region (73 357 particles). This class submitted to auto-refine and post-processing and yielded a 3D EM map of 4. 3 Å estimated resolution. The model was built de novo into SFTSV map A by the Map-to-model program included in Phenix (37) using the core domain of LACV L protein structure (PDB: 5AMQ) as a starting model.
Small angle X-ray scattering Small angle X-ray scattering (SAXS) of SFTSV L protein was performed with an in-line size exclusion chromatography on a Superdex 200 Increase 5/150 GL column (GE Healthcare) with a buffer containing 50 mM HEPES(NaOH) pH 7, 500 mM NaCl, 5% (w/v) glycerol and 2 mM dithiothreitol. Data was collected at the SAXS beamline P12 of PETRA III storage ring of the DESY, Hamburg, Germany (38) using a PILATUS 2M pixel detector at 3. 0 m sample distance and 10 keV energy ( = 1. 24 Å), a momentum transfer range of 0. 01 Å-1 < s < 0. 45 Å-1 was covered (s = 4 sin /, where 2 is the scattering angle). Data were analyzed using the ATSAS 2. 8 package  (39). The SEC-SAXS data were analyzed with CHROMIXS and the forward scattering I(0) and the radius of gyration R g were extracted from the Guinier approximation calculated with the AutoRG function within PRIMUS  (40).
Structure determination of SFTSV L protein by cryo-EM We used a full-length construct of SFTSV L gene (strain AH12, GenBank accession HQ116417) for baculovirusdriven protein expression in insect cells. The L protein was either expressed as wild-type protein or as single-site mutants D112A (endonuclease inactive) or D1126A (RdRp inactive). The protein was purified to homogeneity, with a final yield of up to 11 mg pure SFTSV L protein per litre of cell culture, and used for cryo-EM experiments. Based on map A, derived from the single particle 3D reconstruction and with a resolution of 3. 8 Å (Supplementary Figure  S1 , Supplementary Table  S2 ), the apo-SFTSV L protein (apo-L) structure was determined for ∼1100 residues mainly belonging to the RdRp core region (Figure  1 ). Density for the endonuclease domain was visible but the resolution was insufficient for de novo model building indicating mobility of this domain in the apo-conformation of the L protein.
The 5 hook RNA binding site in LACV is formed by the PA-C like and the fingers domains. We identified potential 5 RNA-binding residues in SFTSV that closely match in location and number with the residues detected for 5 hook binding in LACV (Figure  2D , Supplementary Figure  S7B , Supplementary Alignment File). Similar to LACV we observe clustering of positively charged residues in this pocket that, in terms of size, allows to accommodate the 5 RNA of LACV (Figure  2D , Supplementary Figures  S7B  and S8B ). However, the exact residues interacting with the 5 RNA cannot be predicted, as the 3D structure of the SFTSV hook remains unclear. In an attempt to characterize the possible conformations of the SFTSV 5 RNA, we used the RNA secondary structure prediction program Mfold  (48). This resulted in several possible hook structures but without consistency between the S, M and L segment promoters.
Where indicated, radioactively labeled primers were used instead of [␣] 32 P-GTP. (B) The intensity profiles of the gel lanes from (A) were analyzed using ImageJ software  (26)  and illustrate the size differences between the product bands shown in (A). Sizes were determined by linear regression using the RNA marker (lower X-axis). (C) The table summarizes the RNA oligonucleotides used as primers in this experiment and the possible products with and without realignment. In brackets the length of the product RNA, relative to the de novo product is given. (D) Schematic representation of the possible priming scenarios. Scenario 1 depicts terminal initiation: ATP primes the reaction by binding to the first nucleotide (position +1) of the template and is further elongated without realignment, resulting in a product with the same length as the de novo reaction product (+/-0).
ACKNOWLEDGEMENTS The synchrotron MX data were collected at beamline  P14  operated by  EMBL Hamburg  at the  PETRA III storage ring  ( DESY, Hamburg, Germany ). We would like to thank  Thomas Schneider  and  Isabel Bento  for the assistance in using the beamline and  Isabel Bento  additionally for helpful advice. The synchrotron SAXS data were collected at beamline  P12  operated by  EMBL Hamburg  at the  PETRA III storage ring  ( DESY, Hamburg, Germany ). We would like to thank  Tobias Graewert ,  Haydyn Mertens  and  Cy Jeffries  for the assistance in using the beamline. We also thank.
FUNDING Leibniz Association, Leibniz competition programme [ K72/2017 ]; Wilhelm und  Maria Kirmser-Stiftung ; Part of this work was performed at the  Cryo-EM Facility at CSSB , supported by the  UHH  and  DFG [INST 152/772-1|152/774-1|152/775-1|152/776-1|152/777-1 FUGG] ;  Individual fellowship  from the  Alexander von Humboldt foundation  (to E. Q. ); T. K. holds a fellowship from the  EMBL Interdisciplinary Postdocs  ( EI3POD ) initiative co-funded by  Marie Skłodowska-Curie  [664726]; iNEXT [653706] funded by the  Horizon 2020 programme of the European Union. Funding for open access charge: Leibniz Association.
The identification of minerals is achieved using the crystal-chemical database from the Mineralogical Society of America and the Crystallography Open Database (COD). A thermobarometric reconstruction of the diagenetic history was carried out by the study of fluid inclusions in the different generations of cements filling veins (including calcite and quartz) to define the composition and temperature-pressure conditions of the fluid having circulated in the Parras Basin since the end of the Cretaceous. This study attended to characterize the physical conditions of the different fluids that participated in the mineralization of diagenetic phases and to better understand the interactions between deformation processes, fluid migration and diagenesis  (Roedder, 1984; Shepherd et al. , 1985; Goldstein, 2001).
This method was initially developed in the range 300-700°C by  Beyssac et al. (2002). The method has been then expanded to be used for lower thermal conditions in the range 150-300°C  (Lahfid et al. , 2010). RSCM method allowed completing Rock-Eval results for high maturity values. Temperatures defined by microthermometry and Raman spectroscopy were finally used to reconstruct the burial history of the Parras Basin by 1D modeling performed with the GENEX-GENTECT software®. The location of the 1D model has been chosen at the place where samples 64A and 68A were collected (Fig. 6B ). The data used for the modeling include lithostratigraphic descriptions of each formation, their thickness and the estimated erosion as summarized in Fig. 6B. Thermal parameters of these formations were chosen taking into account their lithology from the default data base of the GENEX software.
Acknowledgements Thanks are due to TOTAL SA ( DBR  project) for financial support. Thanks are also due to  Nicole Guihlaumou  for her help in the work of Clement Dutranoy concerning the fluid inclusions study and to  Emily Albouy ,  Stéphane Raillard  and  Nadine Ellouz  who took part in field-trips in the Parras Basin. Thanks are also due to  Michael Joachimski  from the  University of Erlangen  for carbonate isotopic analyses. We thank also the reviewers for their constructive contributions to improve the form of the initial manuscript. This paper is dedicated to the memory of  Marc Tardy.
In this chapter an experimental investigation is carried out on high strength concrete beams without transverse reinforcement and with transverse reinforcement. The beams were tested in bending under two concentrated loads using the technique of digital image correlation. In the test setup, the shear zone which is defined by the area of beam between the support point and the loading point was studied by the camera of high resolution. The Gom-Aramis software was used to record and analyse the numerical images by determination of the deformation of concrete in the compressed zone of the beam, to calculate the opening, the spacing and the length of the diagonal cracks. The experimental shear strength of the beams was compared with the theoretical values predicted by the different design codes, such as the American ACI 318, the British Standard BS 8110, the European Eurocode 2, the New Zealand NZS 3101 and the Indian Standard IS456.
Mechanical properties of concrete The compressive strengths of HSC used in making the beams without transverse reinforcement and with transverse reinforcement were measured through the crushing tests of cylindrical concrete specimens of 80 mm diameter by 160 mm in height, using a press with capacity of 500 kN. Measurements of the longitudinal compressive strains were carried out with the help of an extensometer (Figure  2 ) and enabled the modulus of elasticity of the HSC. The results were recorded in a data acquisition system (Figure  3 ) for the complete stress-strain curve of HSC (Figure  4 ). The tensile strength was also evaluated for the HSC by splitting tests of concrete cylinders, 80 mm in diameter and 160 mm in height. Figure  4  shows that the pre-peak behaviour is quasi-linear with greater rigidity, and the average ultimate deformation (ε cu = 2%) decreases with the increase in the compressive strength, which is below the ultimate deformation required by the different universal design codes (ε cu = 3.
Steel reinforcement The longitudinal reinforcement composed of two high yield bars of 10 mm diameters in the top zone of the beam (compression), two high yield bars of 8 mm diameters in the bottom zone of the beam (tension) and 6 mm for the transverse reinforcement in the form of stirrups, as shown in Figures  6(a  tested under direct tension using a machine with capacity of 500 kN to determine the Young's modulus and the elastic limit. Measurement of the current deformations is carried out by Gom-Aramis software [11] using Digital Image Correlation (DIC) technique (Figure  5 ). The test results give a Young's modulus of 204 GPa and an elastic limit of 500 MPa.
Statistical Analyses Statistical analyses were performed using the GraphPad Prism 6 software (GraphPad Software, La Jolla, CA, USA) via one-way ANOVA (with Holm-Sidak's post-test correction for multiple comparisons). All data are expressed as means ± SEM of at least three independent experiments, * p < 0. 05, ** p < 0. 01, *** p < 0. 001.
Acknowledgments: The authors are grateful to  Ron (Institute of Metabolic Science, Cambridge, UK), Moon (University of Washington, Seattle, WA USA) and Gazarian (Burke Medical Research Institute)  for sharing respectively the  Fv2E-PERK , the  Flag-NRF2  and the Neh2-luc reporter plasmids. We thank  L. Du Fraysseix  for technical assistance. The authors declare that they have no competing financial interests.
Statistical analysis Data are presented with descriptive statistic as mean (range, standard deviation [SD]). Pre-operative blood examinations were analysed and compared among groups. The Kruskal-Wallis and Wilcoxon Mann-Whitney rank-sum tests were used for comparison among groups. To evaluate the diagnostic accuracy of the different parameters, multiple logistic regression models were fitted, and the receiver operator characteristic (ROC) curves were derived. Statistical analysis was performed using the software Stata (version 13, TStat S. r. l, Sulmona, Italy).
41. In brief, the analyses were conducted with a SEM (JSM-6480LV, JEOL) equipped with an EDX spectrometer (X-Max n , Oxford Instrument) and an EBSD system (NordlysMax 2 ) operated at Moscow State University, Russia. Polished cut samples were coated with 35 nm of carbon. Analyses were conducted at 20 kV accelerating voltage, 0. 7 nA probe current and count rate about 17 kcps (with dead time about 22-25%) during 100 s live time. Program INCA (version 21b, "Oxford Instruments") with XPP-correction model was used for processing of EDX spectra. Identification of the space group of carbonates was conducted using EBSD. For the analysis of the diffraction patterns and processing the results, software HKL (Oxford Instruments) and Inorganic Crystal Structure Database (ICSD) were used. The elementary compositions of four shells of borers Lignopholas fluminalis and four shells of non-borers Scaphula deltae from the same Kaladan River were compared after acid digestion of organic-free carbonate component of the shells following Bolotov et al.
Acknowledgements The  Ministry of Science and Higher Education of Russia , the  Ministry of Europe and Foreign Affairs of France (MEAE) , and the  Ministry of Higher Education, Research and Innovation of France (MESRI)  supported I. N. B. , I. V. V. , A. V. K. , and  O. S. P. under project No. 05. 616. 21. 0114  (unique identification code  RFMEFI61619X0114 ) of the  Hubert Curien Partnership  ( PHC ) for the  Franco-Russian Cooperation for Science and Technology (PHC Kolmogorov 2019 ). The collecting of freshwater bivalves and host rocks was performed under the survey permission No. 5/6000/LFR(210/2018 ) issued by the  Ministry of Agriculture, Livestock and Irrigation of Myanmar  and the export permission No. NWCD/CITES/9/5666/2018  issued by the  Forest Department of the Ministry of Environmental Conservation and Forestry of Myanmar.
As workpackage 5 of the PaNOSC project, the VIrtual Neutron and x-raY Laboratory (VINYL) is designed to be a virtual facility providing a simulation capability from the source to the detector representing all major components of real photon and neutron RIs. By harmonizing existing "state-of-the-art" simulation tools, VINYL should ultimately provide the functionality to simulate whole experiments with various parameters at each part of the experimental instrument. The simulations can help estimate the most optimal experimental environment based on the final simulated data quality for a particular experiment. Ultimately, the simulation results are expected to be stored and shared in a open science database to benefit the broader scientific community. In this paper, we will first describe the architecture of the VINYL simulation platform, and then we will introduce the simulation examples of the X-ray Gaussian source simulation, serial crystallography simulation, and polychromatic diffraction simulation, showing the potential of the VINYL project.
THE ARCHITECTURE OF VINYL The elements of VINYL are schematically shown in the block diagram Fig. 1. On the top is the simulation platform providing the user interface connecting users' commands and the computing resources. The user can choose to either use a Jupyter Notebook 2 through a JupyterHub service or use a remote desktop service. The simulation platform will provide a harmonized Application Program Interface (API) where three different existing simulation APIs for different scenarios can be called in a uniform way. A virtual photon or neutron facility experiment consists of a sequence of simulations describing the physical and conceptual entities of the experiment. In the framework of VINYL, the simulation starts from the source followed by the propagation of the beam through the beamline optics, then considers the complex process of the interaction of the beam with the sample, such as radiation damage, and eventually ends at the simulation of the scattered intensities.
Interfacing data format Standards drafted for VINYL There are various simulation codes involved in the simulation pipeline. These codes are developed in different groups with different input/output data format definitions. In order to achieve seamless exchange of data between simulation software in simulation pipelines, a standardized formatting and hierarchical organization of simulation data is needed. At the same time, this kind of format standard can also benefit from 3rd party data visualization and analysis software that support these formats. We choose openPMD 4 meta data standard as the interfacing data format, therefore our workflows and results become accessible, inter-operable, and reusable to stay in line with the core concepts of FAIR Data Principles. 5 penPMD stands for open particle and mesh data.
It was initially developed as a metadata and data hierarchy standard for particle-in-cell (PIC) simulations of high-power laser-matter interaction at the Helmholtz-Zentrum Dresden-Rossendorf. It is currently not only limited to define PIC simulation data, but, thanks to its flexibility, also widely adopted in numerous simulation codes, visualization codes, and simulation workflow platforms by defining the domain extension in addition to the base standard. The data conforming openPMD standard can be naturally written in hierarchical file formats, such as HDF5, ADIOS1, ADIOS2  6  and JSON. It is noteworthy that the streaming function provided by ADIOS2 is promising to speed up the computing in the workflow where a large amount of data needs to be passed from one program to another. In VINYL, we have defined the domain extensions for coherent wavefront propagation, photon raytracing, neutron raytracing and molecular dynamics simulations to support the data exchange between the simulation modules.
Simulation backends In VINYL, three existed simulation applications are considered as the backends of the API: SimEx, OASYS and McStas. SimEx 7 is the API of the SIMEX platform for simulation of experiments at advanced laser and X-ray light sources. It brings all aspects of typical experiments at light source infrastructures into a streamline of simulation. The simulations of photon source, light transport through optics elements in the beamline, interaction with a target or sample, scattering from the latter, photon detection, and data analysis can be done with various modules within the framework. The simulation framework has been actively used for single particle imaging studies. 8, 9   YS (OrAnge SYnchrotron Suite) is a versatile and user-friendly container of APIs dedicated to optical simulations.
X-ray Gaussian source and its propagation This example is a quickstart example for users to get familiar with the usage of the SimEx API. An X-ray source with Gaussian distribution, both temporal and spatial, is the simplest description for starting a wavefront propagation simulation. The source is defined by its photon energy, pulse energy and photon energy relative bandwidth as shown in Fig. 2  in one jupyter notebook cell. SimEx also provides analysis functions to visualize the temporal and spectral profiles (Fig. 3 ) and wavefront intensity map of a 2D slice (Fig. 4 ). After saving the source file in HDF5 format, the output can then be input into wave propagation modules, such as WPG  14  to continue the start-to-end simulation by, for eaxmple, simulating the propagation and focusing of the X-ray beam for specific X-ray optics and geometries.
By collecting a large dataset of diffraction patterns from nano/micrometer sized crystals, which are delivered by liquid jets, a number of experimental results  [19] [20] [21] [22] [23] [24]  have shown the prospects of this method and make it a class of experiments where simulation may also help provide insight and direction. The 1 megapixel Adaptive Gain Integrating Pixel Detector (AGIPD)  25  is the most commonly used diffraction detector in the SPB/SFX instrument of the European XFEL. As shown in the schematic in Fig. 5  generated by EXtra-geom,  26  this 1M AGIPD detector consists of 4 movable quadrants, each having 4 detector tiles with ADU noise, non-functional pixels and diffraction from the medium in which crystals are suspended will all add complications to extracting the exact structure information from diffraction patterns.
Polychromatic diffraction simulation using OASYS and SimEx As an exercise to bring the SimEx photon simulation framework and OASYS optical simulation environment together, several demo jupyter notebooks are created to show how SimEx takes the output data of OASYS complying with the openPMD wavefront domain extension defined in https://github. com/PaNOSC-ViNYL/op enPMD-standard/blob/upcoming-2. 0. 0/EXT PRAYTRACE. md and generates the diffraction patterns using the GAPD 28 diffraction calculator integrated in SimEx with the wavefront data. In this application case, we simulate the X-ray wavefront using OASYS. Beamline ID23 at ESRF 29 has been used as an example. It consists of a slit, Si-111 monochromator (E = 14. 2 keV) and a KB-focusing mirror system. A ray-tracing simulation using ShadowOui package has been performed.