dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments: We thank  A. Richard  and  A. Sauldubois  from the  "Centre de Microscopie Electronique" of University of Orléans  for assistance in SEM and TEM data acquisition. This work was supported by the  Romanian Ministry of Research and Innovation ,  UEFISCDI , through the projects  PN-III-P1-1. 2-PCCDI-2017-0134 ,Contract Nr. 23PCCDI/2018 ,  PN-III-P1-1. 2-PCCDI-2017-0629 ,Contract No. 43PCCDI/2018  and Contract No. T-IS 251801/04. 05. 2018.
The bond valence energy landscape map was then obtained by setting an energy threshold (1 eV in our case). Furthermore, the Maximum Entropy Method (MEM)/Rietveld analysis was carried out using the RIETAN-FP software. 43 ifferential Scanning Calorimetry (DSC). DSC measurements were performed using a Netzsch DSC 204F1 apparatus operating at heating/cooling rates of 10 K min -1 between 238 and 623 K. During the measurement, samples were heated from 298 to 623 K, cooled down to 238 K, heated to 623 K, and then cooled back to 298 K. AC Impedance. The ionic conductivity was measured using pellet samples, which had been sintered in a FCT Spark Plasma Sintering apparatus at 100 K min -1 up to 973 K for 30 min under an applied pressure of 100 MPa and under vacuum. The sintered pellets (of 90% compactness) were polished and then metalized on each face by gold sputtering using a Bal-Tec SCD 050.
45 A one-pulse sequence with high power 0. 75 μs pulses and a recycle delay of 1. 0 s was applied to acquire the spectra. RT  29  Si MAS NMR (14 kHz MAS frequency) measurements were performed at 11. 7 T (Avance III console) using a Bruker triple resonance 4. 0 mm MAS probehead. Signal shifts have been referenced to trimethylsilylpropanoic acid at 0 ppm. 46 The spectra were acquired by applying a one-pulse sequence with the pulse length of 1. 30 μs and a recycle delay of 60 s. NMR data acquisition, processing, and raw data handling were done using the Bruker Topspin 3. 2 package. Activation energies (E a ) were derived by fits of the temperature dependent  23  Na T 1 values applying both a Bloembergen-Purcell-Pound (BPP, 3D diffusion) and a 2D diffusion model  [47] [48] [49] [50]  using in-house Mathematica scripts.
RESULTS AND DISCUSSION 3. 1. Crystal Structures and Local Atomic Environm e n t s. D i ff r a ct io n. T h e c r y s t a l s t r u c t u r e s o f Na 3 Sc x Zr 2-x (SiO 4 ) 2-x (PO 4 ) 1+x and Na 2 Sc y Zr 2-y (SiO 4 ) 1-y -(PO 4 ) 2+y (x, y = 0, 0. 25, 0. 50, 0. 75, and 1) have been investigated first using diffraction techniques. For each composition, the synchrotron X-ray diffraction data have been collected at 295 and 473 K. For N3 compositions (Na 3 Sc x Zr 2-x (SiO 4 ) 2-x (PO 4 ) 1+x ) at 295 K, the diffraction patterns can be indexed using the β-NASICON model (C2/c, Supporting Information Table  S1 ). To illustrate this, Figure  2 , presents a typical synchrotron XRD pattern of Na 3 Sc 0. 25 Zr 1. 75 (SiO 4 ) 1. 75 (PO 4 ) 1. 25 and the Rietveld refinement results. Notably, the pattern cannot be indexed in the higher symmetry γ-NASICON structure (R3̅ c) at 295 K.
Motivation: Detecting protein domains sharing no similarity to known domains, as stored in domain databases, is a challenging problem, particularly for unannotated proteomes, domains emerged recently, fast diverging proteins or domains with intrinsically disordered regions. Results: We developed pyHCA and HCAtk, a python API and standalone tool gathering together improved versions of previously developed methodologies, with new functionalities. The developed tools can be either used from command line or from a python API.
Introduction The annotation of a protein sequence is very often the first step of many bioinformatics analyses, for instance for studying the function of a gene or the evolution of organisms. Protein domain annotation dominates analyses, describing a protein as a list of blocks corresponding to evolutionary and functional conserved segments. Protein domain families have been extensively compiled through sequence or structure similarity searches and stored in several public databases. These domain databases represent 1/16 state of the art of our current knowledge of the protein domain universe  [11, 18]. However, many protein sequences escape, at least partially, domain annotation, particularly in non-model organisms and remain in the so-called dark protein sequence universe  [4]. Classical methodological approaches model protein domain families as Hidden Markov Models (HMMs).
However, to that aim, sequences need to be clustered and aligned based on the identification of sequence similarities. Therefore, proteins from organisms distant from the species considered in the model, fast diverging proteins, recently emerged domains and domains containing disordered regions, are less likely to be annotated using this methodology  [5]. Here, in order to provide a comprehensive view of protein domain architectures, we present a standalone software named HCA toolkit (HCAtk), and its associated python API pyHCA. The package is easily installable and extend our previous developed tools making use of the Hydrophobic Cluster Analysis (HCA) of protein sequences  [6, 8-10, 12, 24] , with new functionalities. The HCA methodology, based on a two-dimensional representation of protein sequences, highlights clusters of hydrophobic amino acids making up globular domains.
Methods Seg-HCA  [10]  was developed to automatically delineate potential "foldable" domains within protein sequences and is the core part of our package. Recently, Piovesan et al. [21]  implemented an in-house version of Seg-HCA in FELLS, which allows to nicely visualize different properties of a protein sequence. Our new version of Seg-HCA was rewritten for speed and a score is now computed, describing the general composition in hydrophobic clusters of the delineated foldable domains. This score is compared to an empirical distribution computed over 734 disordered protein sequences from DisProt v7  [20]  to produce a p-value. Figure  1A  shows the distributions of scores computed using non redundant sequences of the Protein Data Bank for the set of globular domains and the set of DisProt protein sequences.
The resulting p-value can thus be used to evaluate the likelihood of the delineated domains to fold into globular structures. Interestingly, some Seg-HCA domains are reported with a high p-value. A closer inspection revealed these sequences as partially disordered and undergoing possible folding upon binding. A detailed description of scores with some examples is provided in the supplementary material. The second methodology included in the package is our TREMOLO-HCA software (Traveling through REMOte homoLOgy)  [9]. Using as queries domains delineated using Seg-HCA, remote similarity search is performed against protein sequences from the Uniprot database  [29]  using HHBlits  [25]. For each hit, 2/16 Figure  1 : HCA score and HCA plot example. Panel A, left, shows the normalized HCA score distribution calculated for protein sequences from DisProt v7 (left, orange -disordered sequences) and from PDB (right, violet -globular domains).
The HCA p-value assessing the globularity of delineated foldable segment, is computed using the empirical distribution from DisProt sequences. Panel B, right, shows the HCA plots of three BRCT domains from the Pfam family (PF00533). The aligned protein sequences were used as an input and conserved amino acids can be visualized in red (highly conserved) and yellow, in the context of hydrophobic clusters (HC), in order to evaluate the secondary structure conservation, relatively to the HC shapes. domain arrangement of the Uniprot targets is retrieved from the Interpro database  [17]. The final output allows to directly link unknown protein domains, delineated by Seg-HCA, to existing annotations and to analyze these unknown domains in the context of their domain arrangement. The original tool was based on PSI-Blast and the CDD webserver.
The new implementations based on HHBlits and Interpro allows a more sensitive detection of protein sequence remote similarity combined with a larger coverage of the protein domain universe thanks to the multiple sources of annotations integrated in Interpro. Several scripts are also provided to easily parse and query the TREMOLO output and to quickly retrieve protein domains of Interpro overlapping the unknown Seg-HCA domains or to retrieve the whole protein domain architectures associated with the Seg-HCA domains. Finally, two drawing functionalities were developed. The first functionality allows visualization of hydrophobic clusters of protein sequences, whether these are aligned or not. For each protein provided in a fasta file, an HCA plot is drawn, allowing the quick inspection of the hydrophobic cluster content of a protein sequence, which gives information about its composition in regular secondary structures.
A 3/16 detailed description of the drawing methodology is provided in the Supplementary Material. Moreover, another new functionality was implemented to highlight conservation between aligned protein sequences on their HCA plots. Conserved protein sequence positions can therefore be inspected in the context of their hydrophobic cluster organization (Figure  1B ). The second drawing functionality is a new methodology built on the TREMOLO results to easily visualize the known protein domain annotation (from Interpro) and the newly delineated domains in an evolutionary context by using the NCBI taxonomic database. The tree is automatically built by fetching the taxonomic id of the Uniprot target sequences found by TREMOLO thanks to the ete3 python package. The Seg-HCA domains of TREMOLO can then be analyzed in the context of their protein domain arrangement and visualized in terms of taxonomic specificity and domain association (Fig.
S1 ). The HCA toolkit is written in python3 and is provided under the CeCILL-C license agreement. The functions associated with the HCA analyses in the toolkit can also be directly used through a python API and as such can easily be used in other software. correspond to regions where a high density in hydrophobic clusters is detected, have been shown to correspond to domains that have the ability to fold, either in an autonomous way or following contact with partners  [5, 10] ; these segments are later referred to as HCA domains. The advantage of Seg-HCA for the characterization of the dark proteome is to allow the prediction of these foldable domains from the only information of a single amino acid sequence, without the prior knowledge of homologous sequences. Regular secondary structure (RSS) elements can be easily visualized on the 2D plot, mainly corresponding to hydrophobic clusters, which are separated from each other by loops.
This methodological choice is justified as a minimal number of residues is generally necessary for a protein domain to fold into a globular structure. 6/16 has a DNA binding motif  [23] , whose activity requires a high level of intrinsic flexibility. Examples of disordered regions with high HCA scores. (typical of regular secondary structures), as found in globular proteins, but with a slightly lower total content in hydrophobic amino acids (24% for both against 30% expected). The first example concerns a disordered region (amino acids 291 to 352) found in the chicken zing finger FYVE domain-containing protein 9 (UniProt O95405, Fig. S5 ). The 3D structure of only the FYVE domain has been experimentally characterized, corresponding to the FYVE zinc finger domain (PF01363) (amino acids 663 to 751), the second domain corresponds, from amino acids 1048 to 1400, to a Pfam domain of unknown function (PF11979).
Figures S7 and S8 show two examples of HCA plots for sequences extracted from the PDB. Figure  S7  corresponds to the HCA plot of the Archeoglobus fulgidus VapC ribonuclease (Uniprot O28590, amino acids 1 to 156) whose 3D structure has been solved X-ray crystallography (PDB entry 1W8I). This ribonuclease is involved in a toxin-antitoxin module with toxin activity  [1]  and includes one known domain   Examples of PDB sequences with low HCA scores. [16] ). This nucleoprotein has RNA binding activity, packaging the positive strand of the human SARS coronavirus RNA genome into a helical ribonucleocapsid  [27]. The RNA binding activity is mediated by the region encompassing amino acids 45 to 181, such binding activity is usually mediated by a high level of flexibility. The full-length protein is made of one or two protein domains according to the Pfam database (PF00937, from 15 to 378) or the SUPERFAMILY database (SSF110304, from 28 to 181 and SSF103068, from 252 to 365).
The 3D structure of the first SSF domain is made of four β-strands (from amino acids 61 to 59, 84 to 91, 102 to 113, and 130 to 135) and one small α-helix (50 to 57), with a large number of flexible loops around the β-sheet core  (Saikatendu et al. , 2007). According to the coverage of the sequence by large loops, this protein domain has a lower percentage of hydrophobic residues (26%), than the regularly admitted of 30% limit, characteristic of globular domains. (SasG) (Uniprot Q2G2B2 sequence, PDB entry 5DBL). The full-length protein is made of 19 domains. The sequence starts with a signal peptide motif, followed by pairs of G5 domain/E domain (Pfam PF04650, PF17041) and ends by a cell wall anchor domain (PF00746). Amino acids 501 to 548 and 547 to 629 corresponds to a pair of E domain/G5 domain.
The temperature dependence of J th for this laser is shown in red in Fig. 4b. The threshold current density increased slowly with temperature between 80 and 160 K whereas above 180 K its temperature dependence was exponential with a characteristic temperature T 0 = 150 K. Figure  4b  shows also the data for a reference laser (in blue). They demonstrated a similar temperature behavior but J th increased however a little faster in the exponential part of the curve, with a characteristic temperature T 0 = 145 K. We measured a large number of devices with different dimensions. The threshold current density of the wide lasers decreased by about 20% compared with narrow devices when the ridge width varied in the range of 10-20 µm. The higher J th in narrow QCLs is due to a larger overlap of the optical mode with absorbing dielectric on the mesa walls  44.
For example, a scale-up synthesis was carried out in a 250 mL round bottom flask under the same condition results in 30. 4 g of product (94% yield) with a space-time yield of 7296 kg m -3 day -1. Characterization. Powder X-ray diffraction (PXRD) data were recorded on a highthroughput Bruker D8 Advance diffractometer working on transmission mode and equipped with a focusing Göbel mirror producing CuKα radiation (λ = 1. 5418 Å) and a LynxEye detector. Nitrogen porosimetry data were collected on a Micromeritics Tristar instrument at 77 K. SEM-EDX results were recorded with an FEI Magellan 400 scanning electron microscope. TGA data were collected on Mettler Toledo TGA/DSC 2, STAR System apparatus with a heating rate of 2 °C/min under the oxygen flow. Elemental analyses were performed on a Vario EL-III elemental analyzer.
We then assessed the effect of both drugs on amastigotes of L. major and L. tropica strains histologically. Consistent with the transcript results, both drugs had a leishmanicidal effect on both strains (Fig 1E  and 1F ). Whilst Imiquimod displayed similar results against L. major at both time points (Fig  1E ), EAPB0503 was more potent against L. tropica strain (Fig  1F ). Altogether, these data show that EAPB0503 acts at the low dose of 0. 1 μM and as early as 10h, when compared to its parental compound Imiquimod.
QENS experiment. QENS experiments The standard data reduction of the D7 spectra was performed in the LAMP software package  43. The raw data were corrected for empty cell, cryostat and time-independent (ambient neutrons/electronic noise) background contributions, sample geometry dependent self-attenuation and detector efficiency, converted to energy scale and finally binned into several Q-groups with ΔQ = 0. 1 Å -1 to ensure adequate data statistics. After the separation of the coherent and nuclear spin-incoherent scattering  22, 30  , simultaneous fitting in the (E, Q)-domain was performed in a program module  44  based on the MPfit procedure  45.
MD analysis. The details of the MD simulation are presented in our previous publication  28. The comparison of the MD trajectories with respect to the neutron scattering experiment was carried out using the nMoldyn/ MDANSE software  31. In particular, weighted incoherent and coherent intermediate scattering functions were calculated for all the particles in the simulation as well as for selected groups of atoms (bridging methylene groups, terminal methyl groups, N-H proton etc). The weights of the terms are defined from the neutron scattering lengths and proportional to α b ,inc.
Acknowledgements This work was financially supported by the  Swiss National Science Foundation (SNF)  through the project " Influence of H-bonding on dynamical properties of Ionic Liquids " (Project Number  200021_157175 ). The beamtime on D7 at  Institute Laue-Langevin  is greatfully acknowledged. The authors thank  Prof. Dr. R. Hempelmann  for long-lasting collaboration and support,  Dr. P. Ballone  for performing MD simulations, fruitful discussions and valuable comments on the manuscript.
To avoid introduction of dif ferent anions that may potentially influence complexation, we used perchloric acid for protonation of the azadithiacrown ether residue. Addition of Mg(ClO 4 ) 2 to a solution of 1 results in a blue shift (Δλ = 52 nm) of the O chromophore absorption whereas the N chro mophore absorption remains unaffected (Fig. 1A , Table  1 ). Conversely, the introduction of Hg(ClO 4 ) 2 and HClO 4 causes a blue shift of the N chromophore absorption (Hg(ClO 4 ) 2 : Δλ = 124 nm; HClO 4 : Δλ = 148 nm) without significant changes of the O chromophore ab sorption (Fig. 1B  and C , Table  1 ). The stability constants of the com plexes of 1 were obtained from the spectrophotometric titration data (Figs. S1  and S2 , ESI) and are collected in Table  1. According to the classical description of the Förster resonance en ergy transfer (FRET), an efficient energy transfer requires a spectral overlap between the emission of the donor and the absorption of the acceptor chromophores  [24, 25].
66 fs resolution. The solutions were placed in a 2 mm circulating cell. White light signal and reference spectra were recorded using a two channel fibre spec trometer (Avantes Avaspec 2048 2). A home written acquisition and experiment control program in LabVIEW made it possible to record transient spectra with an average error less than 10 -3 of optical density for all wavelengths. The temporal resolution of the set up was better than 50 fs (for more details see ESI, Section 4. 2).
Acknowledgements This work was supported by  RFBR  (project  15 03 04705 ) and the  Russian Science Foundation  (project  16 13 10226 ). The publication was financially supported by the  Ministry of Education and Science of the Russian Federation  (the Agreement number  02. a03. 0008 ). We thank  Prof. Dr. Heiko Ihmels  ( Universität Siegen, Germany ) for his kind assistance with the preparation of the manuscript.
9 To assess the fertilization success (% of fertilized eggs) photographic analyses were realized after 35 minutes of exposure. At last, developmental analysis were done using an automatic biometric data recording procedure. 10 Here, distance between eyes were determined in 6-days old tadpoles exposed from the fertilization. CuSO 4 and Bordeaux mixture solutions were prepared weekly by dilution in ND96 (oocyte maturation) or in dechlorinated tap water (fertilization and development). Concentrations used in the experiments are environmentally relevant and were derived from the environmental quality standards defined in France in the water framework directive context. 3 The following range of concentrations has been tested: 0, 0. 00399, 0. 0399, 0. 399 and 3. 99 µM of Cu 2+ contained in CuSO.
No anomaly of phosphorylation patterns was detected after the exposures, whether the maturation was hormone-dependent or spontaneous (data not shown). These results differ from other studies concerning oocyte maturation of Xenopus laevis. Cadmium was shown to disrupt numerous phosphorylation steps in the MAPK pathway, in the activation of MPF and its activity. In a second set of experiments, in vitro fertilizations were performed in increasing concentrations of CuSO 4 or Bordeaux mixture. After 35 minutes of exposure, the number of fertilized eggs was measured. The data revealed no effect of the both forms of Cu 2+ on fertilization success (data not shown). Similar results have already been observed with lead. Indeed, PbCl 2 did not modify fertilization success. 9 n order to study the effects of CuSO 4 on the tadpoles' growth, after 6 days of exposure from the fertilization, tadpoles were fixed and stained in Alcian blue.
90 mg) sealed in polypropylene bag (size and mass: 3 × 0. 5 × 0. 02 cm; 27. 6 mg). The magnetic data were corrected for the sample holder and intrinsic diamagnetic contributions of the sample. Heat capacity was measured on a manually pressed pellet of Cr(pyrazine)2(OSO2CH3)2 (7. 0 mg) between 298 and 2 K by a thermal relaxation technique with a Quantum Design Physical Property Measurement System (PPMS-9) in zero-dc field. A blank including a small amount of Apiezon N grease (1. 5 mg) used for thermal contact was measured prior to sample mounting and subtracted from the measured total heat capacity.
The acquisition time was 10 hours. Indexing of the X-ray powder diffraction pattern, Pawley refinement, structure solution by the rigid body direct space method using the Cu based isostructural compound as reference  [10] , and final Rietveld refinement were performed with the Materials Studio program  [11]. Crystal data are summarized in Table  S1  and the powder diffractogram can be found in the Supplementary Materials (Figure  S1 ).
Spectroscopic confirmation of the chromium oxidation state In the recently reported coordination polymer Cr(pyrazine)2Cl2  [5] , the pyrazine ligands are partially reduced by the Cr II metal ions, resulting in the oxidation of the chromium centers in the final material. To explore this possible redox phenomenon in Cr(pyrazine)2(OSO2CH3)2, X-ray absorption spectroscopy (XAS) measurements were performed at the Cr K-edge to confirm the +II-oxidation state of the chromium sites suggested by the X-ray structure analysis and DFT calculations (vide supra). XAS data were also collected for two reference compounds, trans-[Cr II Cl2(NCNH2)4] (Cr(II))  [20]  and trans-[Cr III (pyridine)4Cl2](ClO4)•1/4H2O (Cr(III))  [5]  in order to make a direct comparison of the XAS signature for Cr(pyrazine)2(OSO2CH3)2 and chromium-based complexes which have a well-established oxidation state.
Acknowledgements This work was supported by the  University of Bordeaux , the  Région Nouvelle Aquitaine , the  Centre National de la Recherche Scientifique (CNRS)  and the  Marie Sklodowska-Curie  grant  745696   ETSMM  ( Postdoctoral fellowship  for I. O. ). The authors thank the GdR  MCM-2  ( Magnétisme et Commutation Moléculaires ) and the  MOLSPIN COST  action  CA15128. E. A. S. acknowledges financial support from the  Russian Science Foundation  (Project  16-13-10155 ),  EPSRC  ( EP/N006895/1 ), the  Supercomputer Center of Novosibirsk State University  and the  IRIDIS High Performance Computing Facility. X. Ma ,  A. Hen ,  M. Platunov ,  E. Lebraud  and  S. Exiga  are thanked for helpful discussions and experimental assistance.