dataesr/scientific-paragraphs-categorization huggingface dataset:
Funding L. W and P. J. K. L. acknowledge support from the Research Foundation Flanders (FWO, fwo. be) (postdoctoral fellowships 1234620N and 1242021N). C. M. received funding from the "Fondation Léon Fredericq" and the "Fond d'investissement de recherche scientifique" from the CHU of Liège. G. D. received "Post-doctorate Clinical Master Specialists" funding from the Fund for Scientific Research (F. R. S. -FNRS, frs-fnrs. be). We used computational resources and services provided by the Flemish Supercomputer Centre (VSC), funded by the FWO and the Flemish Government. The funding agencies had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Shorter connecting lines signify closer structural similarity. Cry11Aa and Cry11Ba are structurally similar to each other, but distant from the other 13 delta-endotoxins. The closest structural homolog of Cry11Aa and Cry11Ba is Cry2Aa. The PDB ID codes are reported next to the toxin name. Species of origin are annotated in parentheses. Bta, Bti, Btj, Btk, Btm and Btt abbreviate insectidal Bacillus thuringiensis subspecies aizawai, israelensis, jegathesan, kurstaki, medellin and tenebrionis, respectively. Bt-YBT1518 is a strain displaying nematocidal activity.
We sought to characterize the conformational changes that ensue pH elevation, preceding dissolution of the crystals in the mosquito larvae gut  28. As the crystals are naturally labile at pH 11, we aimed at collecting data from crystals soaked at slightly lower pH than 11, hypothesizing that early conformational changes would show but the crystal packing still hold. In the case of Cry11Aa crystals, diffraction quality was decreased dramatically at pH values of 9. 5 (CAPS buffer, glycerol 30%) and above, preventing collection of a sufficiently large number of diffraction patterns to produce a high-pH dataset. Hence, large conformational changes occur in Cry11Aa at pH as low as 9. 5, opposing diffraction quality, despite crystals dissolving as of pH 11 only (Fig. 4a ). In the case of Cry11Ba, 2.
65 Å diffraction was preserved up to pH 10. 4 (Table  1 ). Comparison between the refined 'pH10. 4' and "pH6. 5" structures points to large interdomain rearrangements induced by pH increase. Detailed analysis of structural changes at the side chain level was yet prevented by the non-isomorphism of the "pH6. 5" and "pH10. 4" datasets. A 1 % unit-cell contraction, and hence tighter crystal packing, was observed in the "pH10. 4" crystals in comparison to the "pH6. 5" crystals. However, because a higher glycerol concentration was used for injection of Cry11Ba crystals at pH 10. 4, we cannot exclude that unit cell contraction might be caused by crystal dehydration. Crystals are made of full-sized monomers of Cry11 protoxins. In both Cry11Aa and Cry11Ba toxins, the β pin (residues E339-Q350 and I341-Y350, respectively) is a ~10-residue long β-strand that hydrogen-bonds with a twofold related symmetry mate, contributing the interface that assembles dimers (AC and BD) into tetramers.
6 ) resulted in a major band ~70 kDa, in line with previous reports  [31] [32] [33]. As the denaturing treatment would have broken any disulfide-bridge or noncovalent interactions that could maintain cleaved fragments together, this result suggests that Cry11Aa occurs in crystals as a full monomer. We further verified this hypothesis by use of MALDI TOF mass spectrometry. In MALDI mass spectra collected after direct solubilization of the natural crystals in sinapinic acid matrix in presence or absence of DTT, we observed main peaks at m/z of 72246 and 72235 (mass error: ± 100 Da) and 36154 and 36129 Da, respectively, in agreement with expected molecular masses for singly-and doubly-charged ions of a fullsize monomer (expected mass: 72. 349 kDa) (Uniprot accession number: P21256; Supplementary Fig.
For negative staining TEM, samples were prepared by adding 5 µL of pure crystal fractions in 10 µL ultrapure H 2 O. In total, 2. 5 µL of this sample was added to 300 mesh Cu F/C grids that were positively glow discharged. These samples were then wicked away using Whatman 1 filter paper; washed with 2. 5 µL ultrapure H 2 O, wicked; and negatively stained with 2. 5 µL 2% uranyl acetate, wicked. These were allowed to dry overnight to ensure all moisture had evaporated and imaged at 120 keV. Images were recorded on a Gatan 2 K x 2 K CCD. Crystal characterization by atomic force microscopy (AFM). Crystals of Cry11Aa were visualized by AFM as previously described  12. Briefly, 5 µL of crystals suspended in ultrapure water were deposited on freshly cleaved mica. After 30 min in a desiccation cabinet (Superdry cabinet, 4% relative humidity), crystals were imaged on a Multimode 8, Nanoscope V (Bruker) controlled by the NanoScope software (Bruker, Santa Barbara, CA).
During our first LCLS-SC3 beamtime (cxi04616), we collected data from native Cry11Ba (2. 3 Å resolution), and in our second beamtime (LO91), we collected data from native Cry11Aa (2. 8 Å resolution). Nanocrystals grown by recombinant expression in the modified acrystalliferous 4Q7 strain of Bti were injected by a microfluidic electrokinetic sample holder (MESH) device  22  in the microfocus chamber of LCLS-SC3  21. After data reduction using cctbx. xfel and dials (hit-finding through merging)  [71] [72] [73] [74]  , we attempted phasing of both datasets by molecular replacement (MR), using sequencealignment based multi-model approaches implemented in Mr Bump (based on MR by Molrep  75  ) as well as custom-scripts testing models produced by Rosetta  24  (using the Robetta server; http://robetta.
Hence, we shifted focus to Cry11Aa crystals soaked with a recently introduced cagedterbium compound, Tb-Xo4  16, 17  (P125 experiment). Crystals were injected using a GDVN  23  liquid microjet in the microfocus chamber of LCLS-SC3  21. Online data processing was performed using NanoPeakCell  77  and CASS  78. Offline data processing with NanoPeakCell 77 (hit finding) and CrystFEL  57  (indexing and merging) revealed a strong anomalous signal that enabled determination of the substructure and phasing of the SFX data, using Crank2  79  and its dependencies in the CCP4 suite  80  (see below for more details). The Cry11Aa structure was thereafter used to phase the Cry11Ba datasets by molecular replacement. A posteriori, we discovered that two of the heavy atom compounds that we used for soaking actually did bind Cry11Ba (Supplementary Fig.
Indeed, the use of a GDVN device, compatible with injection of a colloidal suspension of crystals in pure water, enables constant background in the diffraction patterns. This is less straightforward to achieve using a MESH device as the smaller size of the jet (reducing sample consumption by 5-10 fold) results in decreased stability (requiring to reposition the jet more often) and in the necessity to add highly viscous solvents to the crystal slurry (to avoid freezing in the vacuum chamber). To conclude on this point, a systematic study would be needed, whereby datasets assembled from the same number of images collected with either type of injector would be compared. Data collection and processing, and structure refinement. During the P125 beamtime at LCLS, where the SAD data used for the phasing of the Cry11Aa structure were collected, the X-ray beam was tuned to an energy of 9800 eV (i.
e. , a wavelength of 1. 27 Å), a pulse duration of 50 fs, a repetition rate of 120 Hz, and a focal size of 5 μm. SAD data were collected from nanocrystals soaked for 30 h with Tb-Xo4 at 10 mM in water, prior to GDVN injection  23. Of 558747 images collected using the 5 µm beam available at LCLS-SCC, 76687, 292, 217 and 177 were indexed (i. e. , a total of 77373 images) using Xgandalf 56 , Dirax 81 , taketwo  82  and Mosflm  83  , respectively, in CrystFEL v. 0. 8. 0  57. Post-refinement was not attempted, but images were scaled one to another using the 'unity' model in CrystFEL partialator, yielding a derivative dataset extending to 2. 55 Å resolution. A posteriori, we found that simple Monte Carlo averaging using the 'second-pass' option in CrystFEL pro-cess_hkl would have yielded data of similar quality, most probably because of the large number of indexed images.
A native dataset was also collected and processed in the same fashion yielding, from 792,623 collected patterns of which 48,652 were indexed, a dataset extending to 2. 60 Å resolution. The substructure of the derivative dataset was easily determined by ShelxD (figure of merit (FOM): 0. 22), prompting us to try automatic methods for structure determination. Using Crank2  79  and its dependencies (ShelxC, ShelxD, Solomon, Bucanneer, Refmac5, Parrot) in CCP4 Online  84  , the FOM was 0. 52 after density modification, and rose to 0. 88 upon building of 613 residues. This first model was characterized by R work /R free of 27. 7/ 32. 1% and was further improved by automatic and manual model building in phenix. autobuild  85 and Coot 86 until 630 residues were correctly built. This model was then used to phase the native data.
2] [73] [74]  and PRIME  88  , yielding a dataset extending to 2. 4 Å resolution. The Cry11Aa structure was used as a starting model to phase the Cry11Ba pH 6. 5 dataset by molecular replacement using Phaser  76  with initial R work /R free being 34. 4/40. 4 %. Manual model building (using Coot  86  ) and refinement (using Refmac5 61 , phenix. refine  87 nd Buster 89 ) afforded a model characterized by R work /R free of 18. 7/23. 1 % (Table  1 ). We used the refined Cry11Ba pH 6. 5 structure as the starting model for the Cry11Ba pH 10. 4 structure. We used Refmac5 61 to perform rigid body refinement and then Refmac5 61 , phenix. refine  87 , and Buster 89 to perform individual atomic refinement at a resolution of 2. 65 Å. We performed manual model building with Coot  86. The R work /R free of the final model was 23.
refine  87 and Coot  86  , with final R work /R free values of 21. 2/25. 1 % for Cry11Aa-F17Y, 22. 4/25. 1 % for Cry11Aa-Y449F and 21. 5/25. 4 % for Cry11Aa-E583Q (Table  2 ). Structure analysis. Figures were prepared using PyMOL v. 2. 5  90  (Figs. 2, 3  and Supplementary Fig. 4, 5, 10, 14, 15, 16, 17) and aline (Supplementary Fig. 3 )  91. Radii of gyration were predicted using the PyMOL script rgyrate (https:// pymolwiki. org/index. php/Radius_of_gyration). Interfaces were analyzed with PISA  27  and root mean square deviations (r. m. s. d. ) among structures were calculated using PyMOL using the 'super' algorithm. Sequence based alignment-performed using EBI laglign and ClustalW  92  -was challenged by the large gaps between Bti Cry11Aa, Btj Cry11Ba, Btk Cry2Aa and Btt Cry3Aa, while structurebased alignment-performed using SSM  93  -was blurred by the varying size of secondary structure elements in the three domains of the various toxins.
Hence, for Supplementary Fig. 1, 3 , the alignment of Bti Cry11Aa, Btj Cry11Ba, Btk Cry2Aa and Btt Cry3Aa was performed using strap  94  which takes into account both sequence and structural information. Specifically, the online version of the program was used (http://www. bioinformatics. org/strap/)  95. To generate the phylogenetic tree in Fig. 1 , We used the CCP4 program lsqkab to compute all pairwise superpositions of the 15 delta-endotoxins, and the r. m. s. d. of aligned alpha carbons. We uploaded a 15 × 15 matrix of r. m. s. d. values to the T-REX phylogenetic tree plot server www. trex. uqam. ca  96. Structure prediction using AlphaFold2 and RosettaFold. RosettaFold 58 predictions were obtained by submitting the sequence to the Rosetta structure-prediction server (https://robetta.
The concentration of soluble toxin in the supernatant was quantified using a Nanodrop 2000 (Thermo Fisher Scientist) by measuring the OD at 280 nm and by using the molar extinction coefficient and toxin size (102,930 M -1 cm -1 and 72. 349 kDa, respectively, as calculated with the ProtParam tool of ExPASy (https://www. expasy. org) using the Cry11Aa protein sequence available under accession number "P21256"). Solubility was measured in triplicate for each toxin (Cry11Aa WT and mutants) and each pH. Data are normalized and represented as percentage of solubilization by dividing the concentration measured at a given pH by the maximum measured concentration. For Cry11Ba and its mutants, the crystal suspensions were centrifuged at 13,300 × g for 3 min and ultrapure H 2 O was removed from crystals.
They were then resuspended in one of 18 buffers ranging from pH 7 to 14. These crystals were incubated for 1 h, afterwards the solution was centrifuged at 13,300 × g and the supernatant was separated from the crystal pellet. The concentration of the supernatant was then quantified by a ThermoFisher Nanodrop One (Thermo) by measuring the OD at 280 nm and using the molar extinction coefficient and toxin size (114600 M -1. cm -  and 81. 344 kDa respectively) that were calculated with Expasy ProtParam using the Cry11Ba sequence available at Uniprot. org under accession number Q45730. Solubility was measured in triplicate for each toxin at each pH measured. Data are normalized and represented as percentage of solubilization by dividing the concentration measured at a given pH by the maximum measured concentration.
For Cry11Ba WT, this was then further tested by conducting a turbidity assay by resuspending the crystal pellet in 150 µL ultrapure H 2 O and placed in a 96-well plate to be read on a NEPHELOstar Plus (BMG Labtech) nephelometer. These counts were normalized by subtracting the background signal and conducted in triplicate. Solubility of Cry11Aa WT, Cry11Ba WT and their mutants was compared by calculating SP 50 (pH leading to solubilization of 50% of crystals) as previously described  12  , by globally fitting the data using a logistic regression model for binomial distribution using a script modified from Ref. 101. Differences in SP 50 between mutants were considered significant when 95% confidence intervals (CI), calculated using a Pearson's chi square goodness-of-fit test, did not overlap  102  , and was confirmed by the individual fits of each of the triplicate measurement (Supplementary Fig.
19 ). All statistics were conducted using the software R 3. 5. 2  103. Proteomic characterization. For SDS-PAGE experiments, samples heated to 95 °C were migrated on 12 % SDS-PAGE gels (1 h, 140 V) after addition of Laemmli buffer devoid of DTT. After staining by overnight incubation in InstantBlue (Sigma Aldrich, France), gels were washed twice in ultrapure water and migration results were digitalized using a ChemiDoc XRS + imaging system controlled by Image Lab software version 6. 0. 0 (BioRad, France). MALDI TOF mass spectrometry. MALDI TOF mass spectra on Cry11Aa were acquired on an Autoflex mass spectrometer (Bruker Daltonics, Bremen, Germany) operated in linear positive ion mode. External mass calibration of the instrument, for the m/z range of interest, was carried out using as calibrants the monomeric (66.
The mass spectrometer was calibrated for high-mass range using Protein A and Trypsinogen standards under Linear Mode. Data were analyzed using FlexAnalysis software and plotted using Graphpad Prism. In-gel digestion and peptide mass fingerprinting of Cry11Aa using MALDI. Selected bands were in-gel digested with trypsin as previously described  104. MALDI mass spectra of the tryptic peptides were recorded on an Autoflex mass spectrometer (Bruker Daltonics, Bremen, Germany) in the reflectron positive ion mode. Before analysis samples were desalted and concentrated on RP-C18 tips (Millipore) and eluted directly with 2 µL of α-cyano-4-hydroxy cinnamic acid matrix (10 mg/ mL in water/acetonitrile/trifluoroacetic acid: 50/50/0. 1, v/v/v) on the target. In-gel digestion and peptide mass fingerprinting of Cry11Ba using GeLC-MS/ MS.
Tandem mass spectra were acquired in a data-dependent manner with a quadrupole orbitrap mass spectrometer (Q-Exactive Plus Thermo Fisher Scientific) interfaced to a nanoelectrospray ionization source. The raw MS/MS data were converted into MGF format by Thermo Proteome Discoverer (VER. 1. 4, Thermo Scientific). The MGF files were then analyzed by a MASCOT sequence database search. Native mass spectrometry. Crystals of Cry11Aa were centrifuged for 5 min at 5000 × g during the buffer wash and washed twice with ammonium acetate buffer (pH adjusted to 6. 4 with acetic acid). Pelleted crystals were then dissolved in ammonium acetate buffer (pH adjusted to 11. 5 using ammonium hydroxide). Gold-coated capillary emitters were prepared as previously described and used to load the protein sample  105.
The sample was analyzed on a Synapt G1 mass spectrometer (Waters Corporation). The instrument was tuned to preserve noncovalent interactions. Briefly, the capillary voltage was set to 1. 60 kV, the sampling cone voltage was 20 V, the extraction cone voltage was 5 V, the source temperature was 80 °C, the trap transfer collision energy was 10 V, and the trap collision energy (CE) was set at 30 V. For MS/MS characterization, a particular charge state was isolated in the quadrupole and the complex was dissociated by application of 200 V of CE. The data collected were deconvoluted and analyzed using UniDec  106. Heat stability and aggregation propensity. The thermal unfolding of Cry11Aa WT and mutants was measured by following changes as a function of temperature (15-95 °C) in tryptophan fluorescence leading to an increase of the F350/F330 ratio.
Acknowledgements We thank  Aline LeRoy  for help during experiments with the Nanotemper apparatus and  Dr. Guy Schoehn  for his support. We thank  Dr. Filipe Maia  for deposition of the raw diffraction data on CXIDB. We thank  Sarah Rudd  for assistance with the Cry11Ba mutagenesis. IBS acknowledges integration into the  Interdisciplinary Research Institute of Grenoble (IRIG, CEA). We thank the  LCLS  for beamtime allocation under proposals cxi0416,  L091 ,  P127 ,  P125  and  P141 , and the EuXFEL for beamtime allocation under proposals  P2156  and  P2545. This work was supported by the  Agence Nationale de la Recherche  (grants  ANR-17-CE11-0018-01  and  ANR-2018-CE11-0005-02  to J. -P. C. ), the  CNRS (PEPS SASLELX  grant to M. W. ) and used the atomic force microscopy (AFM) platform at the  IBS  and the electron microscopy (EM) platform of the Grenoble Instruct-ERIC center (ISBG;  UAR 3518 CNRS-CEA-UGA-EMBL ) within the  Grenoble Partnership for Structural Biology  (PSB).
Platform access was supported by  FRISBI  ( ANR-10-INBS-05-02 ) and GRAL, a project of the  University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS  ( ANR-17-EURE-0003 ). The EM facility is supported by the  Auvergne-Rhône-Alpes Region , the  Fondation Recherche Medicale (FRM) , the fonds  FEDER  and the  GIS-Infrastructures en Biologie Sante et Agronomie (IBiSA). Use of the LCLS at the  Stanford Linear Accelerator Center (SLAC) National Laboratory , is supported by the  US Department of Energy, Office of Science, and Office of Basic Energy Sciences  under contract no. DE-AC02-76SF00515. The CXI instrument was funded by the  Linac Coherent Light Source Ultrafast Science Instruments  project, itself funded by the  DOE Office of Basic Energy Sciences. Parts of the sample injector used at LCLS for this research were funded by the  National Institute of Health ,  P41GM103393 , formerly  P41RR001209.
Data processing was supported by  National Institutes of Health  grant  GM117126  to  N. K. S. N. A. S. 's contributions reported in this publication were supported by the  Ruth L. Kirschstein National Research Service Award of the National Institutes of Health  under award number  GM007185. B. F. acknowledges funding support from the  Pacific Southwest Regional Center of Excellence for Vector-Borne Diseases  funded by the  U. S. Centers for Disease Control and Prevention (Cooperative Agreement   1U01CK000516 ).
Data availability The data that support this study are available from the corresponding author upon reasonable request. Structures and structure factor amplitudes are available in the PDB databank under accession codes 7QX4 (Cry11Aa WT, pH 7. 0), 7QX5 (Cry11Aa Y449F, pH 7. 0), 7QX6 (Cry11Aa E583Q, pH 7. 0), 7QX7 (Cry11Aa F17Y, pH 7. 0), 7QYD (Cry11Ba WT, pH 6. 5), 7R1E (Cry11Ba WT, pH 10. 4). Raw image files are deposited in the Coherent X-ray Imaging Data Bank (CXIDB) under accession number 190 [https:// doi. org/10. 11577/1873154]. The source data for Fig. 4 and for Supplementary Figs. 6, 7, 8, 9, 12 and 13, as well as uncropped blot scans for Supplementary Figs. 6, 9 and 11 are provided in a combined Source Data file. Source data are provided with this paper.
, 2017)  for a similar procedure). At the end of each block, upon completion of the 80 keypresses, the color of the green-colored imperative stimulus turned red, and participants were then required to look at the fixation cross during the 30-s rest period. This protocol controlled for the number of movements executed per block to ensure that the same amount of practice with the task was afforded across participants during a particular session. Stimuli presentation and response registration were controlled using the MATLAB R2016b software from The MathWorks (Natick, MA) and the Psychophysics Toolbox extensions  (Kleiner et al. , 2007). The study started at 1. 00 pm to minimize the putative impact of both circadian and homeostatic factors on individual performance levels and sleep characteristics  (Dijk et al.
Participants in the PP group were asked to physically execute the sequence task with their left-hand fingers, as previously described. Participants in the AO group were instructed to keep their fingers on the corresponding response keys. Following the imperative green-cross stimulus and audio cue, a video of a model performing the motor task was displayed on the screen. The model was depicted so that the observers could see both the finger movements of the model and the green cross appearance on the screen. This viewing angle was adopted in order to closely match the perspective view of the AO participants. An  EEG-EMG data acquisition and pre-processing for details). Based on previous motor sequence learning findings  (Boutin et al. , 2018) , performance improvements of the model across training blocks followed the power-law of practice (mean response time (RT) between consecutive keypresses ranging from RTBlock1 = 616 ms to RTBlock14 = 223 ms).
Motor skill consolidation was assessed by analyzing the post-nap retention performance gains, and indexed by the percentage of RT changes from the post-test to the retention test. Finally, inter-manual skill transfer capacity was assessed by computing the difference (in percentages) between RT performance on the retention and transfer test blocks. Note that negative values reflect impairments in skill transfer. EEG-EMG data acquisition and pre-processing EMG recordings. Two bipolar Ag-AgCl electrodes with 10 kΩ safety resistor were placed at a distance of 3 cm from each other along the belly of the left flexor digitorum superficialis. During training, the EMG signal was monitored and controlled online to ensure the absence of micro finger movements for the MI and AO groups. If the experimenter detected any muscle activity, participants were instructed to immediately relax their hand.
EEG recordings. EEG was acquired using a 64-channel EEG cap (actiCAP snap BrainProducts Inc. ). The EEG cap included slim-type electrodes (5kΩ safety resistor) suitable for sleep recordings, with FCz and AFz being, respectively, the reference and ground electrodes. For reliable sleep stage scoring, we also added electrooculography (EOG) and EMG recordings using bipolar Ag-AgCl electrodes. We recorded the vertical EOG component by placing pairs of electrodes above and below the left eye. EMG bipolar electrodes were placed over the chin. All EEG, EMG and EOG data were recorded using two battery-powered 32channel amplifiers and a 16-channel bipolar amplifier (respectively, BrainAmp and BrainAmp ExG, Brain Products Inc. ). All signals were recorded at a 5-kHz sampling rate with a 100-nV resolution.