dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements L. G. acknowledges an Erasmus traineeship. D. J. A. thanks the  EPSRC for a Fellowship  ( EP/L021978/1 ), which also funded B. D. E. R. D. thanks the  Leverhulme Trust  for an  Early Career Fellowship  ( ECF-2017-223 ) and the  University of Glasgow  for an  LKAS leadership fellowship. This work benefitted from SasView software, originally developed by the  DANSE  project under  NSF  award  DMR-0520547. SasView also contains code developed with funding from the  EU   Horizon 2020 programme  under the  SINE2020  project Grant No. 654000. The SANS data was collected on D33 at the ILL, experiment number  9-10-1523. We thank  Dr. Giovanni Rossi  ( University of Glasgow ) for help with collecting the FTIR data.
Data availability The data sets generated during this study (CV data, UV-Vis absorption spectra and spectroelectrochemical data) are available from the corresponding author upon reasonable request. All analysed data collected is contained within the Supplementary Information that supports this work. The SANS data sets collected on D33 from the ILL are freely available here, DOI: 10. 5291/ILL-DATA. 9-10-1523 from experiment number 9-10-1523.
X-ray diffraction: The definition of phase composition and type of crystal structure has been performed on the conventional X-ray diffractometer EMPYREAN (firm PANalytical) in Cu-Kα radiation with Ni filter in the room temperature (25 o C). The operation mode of the device was 40 kV voltage and 30 mA current. The scanning has been done with a step of 0. 026 o and 2 s per step for 2θ. Analysis of phase composition and type of crystal structure of composite material has been performed using ICDD database. RAMAN spectroscopy: Raman spectroscopic analyses can be applied for various materials, such as nanoparticles and polymer composites. This method is an important analytical and research tool which provides key information about polymer nanocomposites and material structure. Raman spectra were collected on a Horiba Lab RAM HR evolution spectrometer.
Spectra were obtained in the wavelength range 3500-50 cm -1. The instrument has two lasers: a HeNe laser with the emission lines at 633 nm and 325 nm from He-Cd. The HeNe laser was focused on the sample with a 100× objective in the experiment. Filter was not used during the measurements. HORIBA Scientific's Lab Spec 6 software was used for complete instrument control and data processing. FTIR Spectroscopy: To study structural changes in the samples, was used the technique of IR spectroscopy based on the measurement of transmission spectra of semi-transparent films. Spectra were obtained by the FTIR spectrometer of Shimadzu FT-IR in the wavelength range 4000-750 cm -1. Samples for study were obtained in the form of thin films with a thickness of 80-100 microns size 8x30 mm 2 stage-by-stage pressing at a pressure of 6x10 4 N/m 2 at room temperature using a special mold of Shimadzu.
SANS analysis The small-angle neutron scattering curves of HDPE+ZrO2 (1, 3, 10 and 20%) and the pair distribution functions P(R)obtained from program GNOM (inset) are shown in Figure  2. It can be seen that P(r) does not change much as the ZrO2 volume fraction increases. Total excluded volume Vp (the aggregation volume), maximal length of nanocluster, number of aggregation (Nagg) were obtained using the data analysis software ATSAS 2. 8. 2 software program DAMMİF and Gnom  [25, 26, 27]. The results are shown in Table  1. The average distance D between ZrO2 aggregates in the polymer matrix (1-20%) was obtained from eq. 1, using the approximation of a primitive cubic lattice: 3 p DV   (1) Where, D is the mean distance between nanoclusters, φ is the volume fraction of the filler and Vp is the average volume of the nanocluster (see tab.
We study the avalanche and extreme statistics of the global velocity of a crack front, propagating slowly along a weak heterogeneous interface of a transparent polymethyl methacrylate block. The different loading conditions used (imposed constant velocity or creep relaxation) lead to a broad range of average crack front velocities. Our high-resolution and large dataset allows one to characterize in detail the observed intermittent crackling dynamics. We specifically measure the size S, the duration D, as well as the maximum amplitude V max of the global avalanches, defined as bursts in the interfacial crack global velocity time series. Those quantities characterizing the crackling dynamics follow robust power-law distributions, with scaling exponents in agreement with the values predicted and obtained in numerical simulations of the critical depinning of a long-range elastic string, slowly driven in a random medium.
g. clusters of high local crack front velocity  [12] [13] [14]. Moreover, in contrast with the more recent works reported in  [15, 16]  (that focused on the avalanche shape and on the waiting time between subsequent avalanches, respectively), different loading conditions were used here. We thus could obtain a very highresolution large dataset, with in particular a broad range of average crack front velocities, spanning close to five decades, allowing us to characterize in detail the crackling dynamics. Indeed, we quantify the avalanche crack front dynamics by measuring the size and duration of global bursts in this crackling noise signal, e. g. the global crack front velocity. We show that our results are in quantitative agreement with previous theoretical and numerical results  [15, 46, 48] , with power-law exponents characterizing the size S, as P(S) ∼ S -τ , with τ = 1.
Therefore, this discrepancy might simply arise from the fact that the quasi-static assumption of the depinning model is not satisfied in those experiments. To further characterize the statistics of these avalanches, we also examine their maximum amplitudes measured by V max , where we have renormalized the crackling noise signal by the average crack front velocity value, i. e. V l (t)/ v , to compare experiments performed at very different average velocities. Figure  6  shows the distributions of the maximum amplitudes of avalanches measured for the same dataset analysed previously (figure  5 ), e. Strikingly, we observe that the distributions follow a power-law behaviour with an exponential cut-off, independent of the threshold C, P(V max ) ∼ V - max , with = 1. 34 ± 0. 15. (3. 4) Moreover, in the inset of figure  6 , we also show that the avalanche maximum velocity scales in average with the avalanche duration as V max | D ∼ D β , with β = 0.
034 for Berkovich indenter, E and ν are Young's modulus and Poisson's ratio of the sample, and E i and ν i are the same quantities for the Berkovich indenter (for diamond: E i = 1141 GPa and ν i = 0. 07). materials mechanical behaviour, including work of elastic and plastic deformation, elasto-viscoplastic behaviour, time-dependent behaviour, and creep behaviour. Methods are even currently being developed to enable the determination of stress-strain curves as well. In the present paper, experimental nanoindentation data were used as input to the commercial ABAQUS software using a macroscopic elasto-plastic model. Simulating the mechanical behaviour of nanoindentation tests is much more challenging than FE modelling of classical indentation tests (see for instance  [54] ). The main objectives for the present work were to characterise binderless flexible graphite response by nanoindentation simulations through comparisons with experimental data, and to show that a numerical procedure can be developed for characterising a porous material based on nanoindentation tests.
Flux variables : 2 || || p H n σ ε λ λ σ = =    Plastic strain rate tensor (6) (1 ) r br λ = --  Isotropic hardening rate  (7)  with: :H: σ σ σ = (8) G H H G 0 0 0 H H F F 0 0 0 G F F G 0 0 0 H 2N 0 0 2M 0 2L + - -     - + -     - - + =           (9) and where λ  is the plastic multiplier, H is the fourth order operator reflecting Hill anisotropy, n is the normal to the loading surface f (see below), and b is the non-linear isotropic hardening coefficient. The Hill criterion f is given as follows, which is a function of six parameters, F, G, H, L, M and N  [61, 62] : || || 0 yield f R σ σ = -- ≤ (10) where yield σ is the limit yield stress. These equations give the classical elasto-plastic constitutive equations and were implemented into the ABAQUS/Explicit FE software  4.
Contact force computation and Coulomb friction model In nanoindentation tests, contact and friction play a central role at the interfaces between the Berkovich indenter and the sample. Coulomb friction model is used for most contact problems with friction, and reads: || || || || T N F F µ =   ( 27 ) where µ is the friction coefficient, and T F  is the tangential force to the normal force N F  at any point of the contact interface  [68, 69]. In ABAQUS software, the contact interface conditions were taken into account using the penalty method based on the master/slave surfaces approach. The friction constitutive equation was modelled by the well-known Coulomb model characterised by the single friction parameter µ such that 0 0 5. µ ≤ ≤.
Conclusions The objective of this work was to propose a simple numerical methodology for determining the mechanical properties of binderless flexible graphite from nanoindentation tests. We believe that such numerical procedure can be extended to other porous materials characterised by nanoindentation. The model took into account the main mechanical phenomena involved, such as orthotropic elastic behaviour, anisotropic plastic with nonlinear isotropic hardening, large plastic deformations occurring during nanoindentation tests, and contact and friction between the rigid indenter and the comparatively soft sample. This model, which was presented here from both theoretical and numerical aspects, was implemented in ABAQUS/ Explicit software using the Vumat user's subroutine. The quality of the results obtained in terms of distribution of mechanical stresses, as well as of prediction of the experimental nanoindentation curves obtained under different peak loads ranging from 100 µN to 1 mN, was very satisfactory.
Acknowledgements The authors are indebted to  Guillaume Berthout  ( CSM Instruments, Switzerland ) for providing experimental nanoindentation data. The authors also gratefully acknowledge the financial support of the CPER 2007-2013 " Structuration du Pôle de Compétitivité Fibres Grand'Est" (Competitiveness Fibre Cluster ), through local ( Conseil Général des Vosges ), regional ( Région Lorraine ), national (DRRT and FNADT) and  European (FEDER)  funds.
Acknowledgments We thank  A Browaeys  and  P Grangier  for fruitful discussions. The research was supported by a  DGA-MRIS  ( Direction Générale de l'Armement Mission Recherche et Innovation Scientifique ) scholarship, by the SAFRAN-IOGS chair on Ultimate Photonics and by a public grant overseen by the  French National Research Agency (ANR)  as part of the  Investissements d'Avenir Programme  (reference:  ANR-10-LABX-0035 ,  Labex NanoSaclay). J-JG  acknowledges the support of  Institut Universitaire de France.
4 to -0. 8 kcal mol -1 for these mono-mutants, but lower than that (-0. 9 kcal mol -1 ) for the V115A:Q119S: E434V triple mutant (Table  2 ). The side-chain conformation of Glu119 present at a central position in a 24-residue helix is notably distorted in the salt-bridge interaction with the (L)aspartate substrate α-amino group in the R-state of the ternary complex with the Mg-ADP reaction co-product. [24]  The χ1 dihedral angle value is close to zero (-8˚), compared to a value of -75˚in the crystallographic structure of LysC in the apo T-state (PDB code 2j0x). [24]  The shift in Glu119 sidechain orientation, brought about through the adoption of an energetically less favourable rotomeric conformer induced by binding of the cognate (L)-aspartate substrate, is overlain on a modelled complex of the LysC V115A:E119S double mutant with (L)-malate in Fig 5.
Carbon atoms in (thin) stick side-chains representations in an overlay of the X-ray structure of the R-state holo complex of the wild-type enzyme with (L)aspartate and Mg-ADP (PDB code 2j0w) are shown in green. For comparison an alternative E119 side-chain conformation observed in the inactive T-state apo form of the wild type enzyme (PDB code 2j0x), re-constructed on the 2j0w backbone, is depicted in (thin) stick representation with yellow-coloured carbon atoms. https://doi. org/10. 1371/journal. pone. 0193036. g005.
Acknowledgments This work was supported by the  French National Research Agency  ( ANR   programme d'Investissement d'Avenir , Project  SYNTHACS ,  ANR-10-BTBR-05-01 ) and by the  Adisseo Company. The authors are grateful to  Sophie Bozonnet  and  Sandrine Pizzut-Serin  for assistance in using the ICEO high-throughput facility at the LISBP, devoted to the engineering and screening of new and original enzymes. This work was granted access to the  HPC resources of the Computing Center of Region Midi-Pyrenees (CALMIP, Toulouse, France ).
This work was supported by the  French National Research Agency  ( ANR   programme d'Investissement d'Avenir , Project  SYNTHACS ,  ANR-10-BTBR-05-01 ) and by the  Adisseo Company. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the 'author contributions' section.
Water H atom positions were calculated (on the O11⋯ -O 2 C lines at the distances 0. 8 Å from water oxygen) and refined using a riding model. In [NFX + Fum + H 2 O] (1 : 1 : 2) all "active" (amino and hydroxy) hydrogen atoms were found from the difference Fourier map and refined isotropically. All other H atoms (carbon) were placed in calculated positions and refined using a riding model. The crystallographic data for anhydrous ciprofloxacin hemifumarate, monohydrate and dihydrate of norfloxacin hemifumarate have been deposited with the Cambridge Crystallographic Data Centre as supplementary publications under the CCDC numbers 1567143-1567145. Single-crystal X-ray diffraction data for [NFX + Fum + H 2 O] (1 : 1 : 1) were collected on a Bruker AXS Kappa APEX II diffractometer at 100 K. The structure was solved and refined using Olex2 software  30  and deposited under the CCDC number 1567678.
Expression and purification of the TmTsaBDE subunits We prepared the TmTsaBD binary complex and the TmTsaE protein individually. A bicistronic expression vector (named BC14) aimed to co-express TmTsaD and TmTsaB-His was designed as described  (33). All synthetic gene constructs were optimized according to E. coli codon usage using the EuGene software (34) (Supplementary Table  S2 ) and obtained from Genscript (Piscataway, USA). The DNA sequences coding for TmTsaD and TmTsaB containing a 6His-tag at the C-terminus have been cloned into a pET21a backbone using the NdeI and XhoI restriction sites. The second vector (named BC15) aimed to express TmTsaE-Nt-his was cloned into a pET24d backbone between NcoI and XhoI restriction sites. This plasmid, was used to express TmTsaE with a N-terminal 6His-tag followed by a TEV proteolytic recognition site to remove the 6his-tag if necessary.
Crystal structure determination Purified TmTsaBD and TmTsaE were mixed at a 1:1:1 ratio of the three subunits up to a final concentration of 12 mg. ml -  (0. 148 mM) in HEPES buffer 20 mM pH 7. 5, 200 mM NaCl, 5 mM 2-mercaptoethanol supplemented with 3 mM AMPCPP and 6 mM MgCl 2. Crystals of TmTsaBDE were obtained at 293 K using the sitting-drop vapour diffusion method by mixing 100 nL of a protein solution with 100 nl of 13% PEG 8000, 0. 1 M Imidazole pH 7. 35. Crystals were cryoprotected with reservoir solution supplemented with 30% glycerol and 3mM AMPCPP, flash-frozen and stored in liquid nitrogen for data collection. X-ray diffraction data collection was carried out on beamline Prox-ima2 at the SOLEIL Synchrotron (Saint-Aubin, France) at 100K. Data were processed, integrated and scaled with the XDS program package  (35).
TmTsaBDE crystals belonged to space group P2 1 2 1 2 1 with unit cell parameters of a = 84. 31 Å, b = 113. 94 Å, c = 177. 62 Å. The structure of TmTsaBDE was solved by molecular replacement using the PHASER module  (36)  implemented in the CCP4 software package  (37). Search models for TmTsaB and TmTsaD were obtained by the MODELLER program (38) using the crystal structure of the EcTsaBD heterodimer (PDB ID: 4YDU) and TmTsaE was modelled from the HiTsaE structure (PDB ID: 1FL9). The initial structure was refined using the PHENIX program  (39)  and completed by interactive and manual model building using COOT  (40). Two copies of the TmTsaBDE trimer were present in the asymmetric unit. AMP-CPP molecules and MgCl 2 ions could be modeled into the residual Fo-Fc electron density contoured at 3.
Sequence alignment and structure comparison The sequence conservation was analysed using the program CONSURF  (43)  with TmTsaBDE as the query. The frequency of the occurrence of amino acids on the consensus sequence was produced by WebLogo  (44). Structural comparison was performed with the PDBeFold web server  (45). All graphic structure representations were produced with PYMOL  (46). The electrostatic potential representation were rendered and produced by PDB2PQR  (47)  and APBS in the Chimera visualization system  (48).
We modeled a complex of a rigid tRNA substrate with EcTsaBD using the HADDOCK software  (41). The tRNA in the HADDOCK model extensively interacts with the positive surface patch present on TsaBD (Figure  4B ) and most importantly sterically overlaps with TmTsaE in the TmTsaBDE complex. Electrostatic surface calculation of TmTsaE reveals a negatively charged surface patch centered on the ␣3 helix that is positioned onto a positively charged patch at the TmTsaBD interface. Although the residues at the interface are not completely conserved, the electronegative character of this region is maintained in the Ec-, Bs-and TmTsaE homologues (Supplementary Figure  S6 ). TsaE can be considered as an electrostatic competitor of the tRNA substrate. The competition between tRNA and TsaE also explains why the strong ATPase activity upon binding of TsaE to TsaBD is observed independently of tRNA  (22, 23).
Our HADDOCK model of the tRNA-TsaBD complex positions the N 6 -amino group of the A37 anticodon base close to the carbamoyl group of TC-AMP and is well positioned for a nucleophilic attack of the TC-AMP carbonyl (Figure  4b ). We hypothesize that the altered conformation of TsaD induced by TsaE could still allow binding of TC-AMP but not its chemical conversion. Superposition of TobZ onto TsaBDE, shows that the TsaC-like module of TobZ is bound to the TsaD-like module at the opposite side of TsaD compared with TsaE. TobZ contains a large central cavity that connects the active sites of the TsaC-and TsaD-like modules. This tunnel prevents diffusion of the unstable carbamoyl-phosphate intermediate into the bulk solution and channels it directly to the active site of the TsaD-like module  (53).
ACKNOWLEDGEMENTS Sophia Missoury received a scholarship from the  'Fondation de la Recherche Médicale '. We thank the staff of the Proxima1 and 2 beamlines at the SOLEIL synchrotron for Nucleic Acids Research, 2018, Vol. 46, No. 11 5859  assistance during the diffraction data collections. We are grateful to  Marc Graille  ( Ecole Polytechnique, Palaiseau ) and  Tamara Basta  ( I2BC, Gif s/Yvette ) for critical reading of the manuscript. Authors Contributions: S. M. , S. P. , I. G. , D. D. , B. C. , D. L. , R. D. and W. Z. did the experimental work. S. M. , B. C. and H. v. T. wrote the paper.
Acknowledgments We gratefully acknowledge  E. Eyraud ,  D. Lepoittevin , and  C. Hoarau  for their technical contributions and motivating discussions. We thank  J. F. Motte ,  T. Crozes ,  B. Fernandez ,  S. Dufresnes  and  G. Julie  for Nano-fabrication development,  S. Thiele  and  C. Thirion  for help with development of the experiment. Samples were fabricated in the NANOFAB facility of the  Néel Institute. This work is partially supported by the  French National Agency of Research  through the  ANR-13-BS10-0001  MolQuSpin, by the  German Research Foundation (DFG)  through the  Transregio  Project No. TR88  " 3MET " and by the  Alexander von Humboldt Foundation. Correspondence and requests for materials should be addressed to: wolfgang. wernsdorfer@neel. cnrs. frand franck. balestro@grenoble.
Plant Material Complete leaves of 20 Pteridaceae species were collected from habitats ranging from aquatic to xeric, and included both terrestrial and epiphytic taxa (Table  1 ; Figure  2 ). The tropical, terrestrial Dennstaedtia cicutaria was chosen as the outgroup because it belongs to the Dennstaedtiaceae, an earlier-branching sister clade to the Pteridaceae. D. cicutaria thus represents the nearest relative outside of the clade of interest  (Schuettpelz and Pryer, 2007). The Pteridaceae Phylogeny A two-gene (plastid atpA and rbcL) dataset was assembled in order to resolve relationships among the focal taxa (Figure  2 ). For each taxon, previously published sequences were obtained from GenBank; accession numbers are provided in Supplementary Data Sheet 1. In five instances, due to the unavailability of suitable sequences from the focal species, it was necessary to use sequences from a closely-related species in the same genus Supplementary Data Sheet 1.
Anatomical data were collected from n = 3 leaves belonging to separate individuals from each species, except in D. cicutaria and P. pungens, for which only two individuals were available. Mid-stipe cross sections were excised by hand, stained with phloroglucinol to highlight lignified tissues, and mounted in glycerin. The sections were then photographed with a Moticam 2,300 digital camera attached to a Motic BA400 compound microscope (www. motic. com) at magnifications ranging from 20× to 400×. ImageJ software  (Schindelin et al. , 2012)  was used to measure morphological and anatomical attributes. No discernible differences were evident in the sterome structure within a cross section, so sterome attributes were measured from three regions that included the adaxial, abaxial and lateral sides.
Petiole tissue outlines were orientated in the natural dorsal-ventral orientation, and crosssectional area and axial second moment of area of each tissue surface was calculated using the commercial image analysis software Optimas (Media Cybernetics, MA, USA), and a specially written macro for calculating axial second moments of area of complex structures (Tancrède Almeras; CNRS, Montpellier, France). The macro establishes the center of mass for the entire cross sectional area and then calculates I (mm 4 ) of each tissue area with reference to a theoretical neutral line (neutral plane of bending) that passes through the center of mass for the two orthogonal directions relative to the x (horizontal) and y (vertical) planes of bending. The macro thus computed I for all four tissue types and the entire I for both the vertical and horizontal directions.
, 1999). Hence, PIC analyses were performed with the "ape" package in R using the Pteridaceae topology (Figure  2 ; Table  2 ;  Paradis et al. , 2004). The tree was pruned using the "drop. tip" function as necessary to account for missing I and EI data for Acrostichum aureum. Petioles in this species were too large and brittle to generate a stitched, composite photograph of the entire petiole cross-section with any confidence. Lastly, the simple leaf area reconstruction in Figure  2  was generated using the 'Parsimony Ancestral States' function in Mesquite 3. 04  (Maddison and Maddison, 2015).
ACKNOWLEDGMENTS This project was funded by the  National Science Foundation  ( IOS-1258186 ). We thank  Rehman Mohmin  for assistance in the field, and Felipe and  Marino Chacón  for facilitating our work at  San Gerardo de Dota , as well as the staff at the  Organization for Tropical Studies  for their support. We are very grateful to  Tancrède Almeras  for allowing us to apply his t-inertie programme to our petioles. Lastly, we thank three reviewers for their helpful comments and suggestions.