dataesr/scientific-paragraphs-categorization huggingface dataset:
Flow cytometry After 96 h of incubation HL60 cells were washed in PBS/0. 1% BSA, incubated for 1 h on ice with 1 µl CD14-PE (ImmunoTools, Friesoythe, Germany). Cells were washed and suspended in 350 µl of PBS/0. 1%BSA prior to analysis on the Accuri C6 (Becton Dickinson, San Jose, CA). Data analysis was performed using Becton Dickinson Accuri C6 software. The assay was repeated 3-5 times. Percentages of positive cells were plotted to the graphs and EC 50 values were calculated using GraphPad Prism 7 software (GraphPad Software, San Diego, CA).
Crystallization and structure determination Expression of zebrafish VDR LBD (residues 156-453) and the following purification were done by the procedure reported previously  [40]. The protein was concentrated using Amicon ultra-30 (Millipore) to 3-7 mg/ml and incubated with a two-fold excess of ligand and a threefold excess of the coactivator SRC-1 NR2 (686-RHKILHRLLQEGSPS-700) peptide (IGBMC peptide synthesis common facility). Crystals were obtained in 50 mM Bis-Tris pH 6. 5, 1. 6 M lithium sulfate and 50 mM magnesium sulfate. Protein crystals were mounted in a fiber loop and flash-cooled under a nitrogen flux after cryo-protection with 20% glycerol. Data collection from a single frozen crystal was performed at 100 K on the PX2A beamline at SOLEIL (France). The raw data were processed with XDS  [51]  and scaled with AIMLESS  [52]  programs.
Acknowledgement We thank  Xunta de Galicia, Spain  ( GRC/ED431B/ 2018/13 ) for financial support. We also thank institutional funds from  Instruct-ERIC  for support and use of resources of the  French Infrastructure for Integrated Structural Biology  ( ANR-10-LABX-0030-INRT  and  ANR-10-IDEX-0002-02 ). We thank  Prof. M. A. Maestro  for the X-ray studies, Dishman-Netherlands B. V. for the gift of vitamin D 2 ,  P. Eberling  for peptide synthesis,  A. McEwen  for help in X-ray data collection and the staff of PX2 beamline of SOLEIL synchrotron for assistance during X-ray data collection. S. G. thanks the  European Union  for an  Erasmus Mundus Euphrates  scholarship (Project  2013-250/001-001-EMA2 ). K. B. and E. M. were supported by the  Leading National Research Center Poland (KNOW).
Transmission electron microscopy measurements: Transmission electron microscopy (TEM) images were recorded using a JEOL 2100F microscope equipped with a high-resolution objective lens pole piece at 200 kV. The tomography series were acquired between tilting angles of ±70° with a 2° Saxton scheme, and the subsequent series alignments were performed with the IMOD software using Au nanoparticles (5-7 nm) as fiducial markers. To resolve details at maximum resolution we used the SIRT algorithm implemented in fast software running on multicore computers, Tomo3D. The size of the TEM projections used for the reconstruction was 2k x 2k pixels.
Density functional theory calculations: The periodic density functional theory (DFT) calculations were performed using the Vienna Ab initio Simulation Package (VASP). [29, 30]    Perdew Burke Ernzerhof (PBE) exchange-correlation functional in the generalized gradient approximation (GGA) proposed by Perdew et al. [31]  was employed. The electron-ion interactions were described using the projector augmented plane wave (PAW) method of Blöchl  [32]  as adapted by Kresse and Joubert. [33] A planewave cutoff energy of 400 eV was used in all calculations. The Kohn-Sham equations were solved self-consistently until the energy difference between cycles becomes lower than 10 -6 eV. A primitive rhombohedral cell of FAU with two supercages containing total of 144 atoms was used for the calculations (Figure  S8 ).
Acknowledgements The authors acknowledge funding from the  Sino-French joint LIA laboratory "Zeolites". This work was supported by the  National Natural Science Foundation of China  ( 21706285 ,  21972142 ,  21991090 ,  21991091 ,  21991092 ,  21975285 ,  22022202 ),  LiaoNing Revitalization Talents Program  ( XLYC1807227 ),  International Partnership Program of Chinese Academy of Sciences  ( 121421KYSB20180007 ),  Qingdao Applied Basic Research Project  ( 19-6-2-70-cg ), the  Fundamental Research Funds for the Central Universities  ( 18CX02013A );  Thousand Talents Program for Foreign Experts  ( WQ20152100316 ). †Zhengxing Qin and  Shu Zeng  contributed equally to this work.
Besides, A549 and Calu-3 cells are epithelial cells representative of the two main regions of NP deposition in the airways, namely the alveoli and the bronchi, respectively. They are also among the most commonly used lung epithelial cell lines in nanotoxicology studies  [49]. Our data show that although exhibiting similar ζ-potential, not all cationic NPs of our library were internalized and triggered viability loss and/or NP-associated cell responses including oxidative stress, cytokine secretion, mitochondrial perturbation and lysosome integrity changes. Consistent data among the different toxicity endpoints we measured were obtained for all NPs. Thus, we confirmed our previous observation made in macrophages that cytotoxicity of cationic carbon NPs is not necessarily linked to the absolute value of their ζ-potential  [33]  and extended this observation to airway epithelial cells.
Characterization of NPs The elemental composition of the NPs was determined by analysis on a Vario EL III instrument (Elementar) and expressed as carbon (C), hydrogen (H), and nitrogen (N) mass content (%). The size of the NPs was determined by transmission electron microscopy (TEM). CD samples (0. 5 µL, 1. 0 mg/mL in 1. 5 mM NaCl pH 7. 4) were deposited on glow-discharged (90 V and 2 mA for 15 s) carboncoated grids (Cu-300HD, Pacific Grid Tech). After at least 2-hour drying at rt, the grids were observed using a bench top LVEM5 microscope (Delong Instrument) operating at 5 kV. The average size of the NPs was determined by image analysis using the ImageJ software (v 1. 50i, NIH), from a set of 300-1000 particles. The hydrodynamic diameter and ζ-potential value of NPs were measured by dynamic light scattering (DLS) on a Zetasizer NanoZS apparatus (Malvern Instruments).
Measurements were performed in triplicate on fresh samples (1. 0 mg/mL in 1. 5 mM NaCl pH 7. 4) at 25 °C. Data were analyzed using the multimodal number distribution software supplied with the instrument and expressed as mean (± SD). DLS was also used to assess the aggregation of NPs in culture medium. NP dispersions were prepared at 1. 0 mg/mL in complete RPMI-1640 or DMEM-F12 containing 10% fetal serum, and measurements were performed extemporaneously without sonication of the dispersions. The surface charge density of NPs was determined by means of polyelectrolyte titration  [69, 70] , monitoring ζ-potential variation of CDs (1. 0 mg/ mL, NaCl 1. 5 mM pH 7. 4) along spiking with a solution of poly(acrylic acid) (PAA, MW ± 1,800 Da, NaCl 1. 5 mM pH 7. 4). The amount of PAA required to reverse the sign of ζ-potential was approximated by linear interpolation of the titration curve at the isoelectric point.
To perform PALS on thin films, a setup that converts a continuous positron beam into a pulsed monoenergetic positron beam of low energy (<20 keV) is required. [29] Such setups allow depth profiling through a precise variation of the positron implantation energy. The beam intensity and time resolution depend on the positron source and instrument characteristics. The highest time resolution is currently obtained with the Pulsed Low Energy Positron System (PLEPS) at the NEPOMUC facility of the research nuclear reactor FRM-II in Munich (DE), where the data for this study were acquired. [30] he positron mean implantation depth  [31] ρ = • 1/2 z A E n (1) with E = implantation energy (keV), sample density ρ (g cm -3 ), A = 2. 81 µg cm -2 keV -n and n = 1. 71 for polymers. So far, this value has only been determined for polymers, and is assumed to hold for MOFs.
PALS spectra are analyzed through fitting a continuous range of lifetimes (e. g. , with the software packages MELT,  [32]  LT,  [33]  or CONTIN  [34]  ), or a set of discrete lifetimes (e. g. , with POSWIN,  [35]  PALSfit3  [36]  ). The average pore size is obtained from discrete fitting and ideally coincides with the peak of the distribution obtained from a continuous fit. In general, the spectra of porous materials are resolved into 3 or more lifetimes (τ ): the p-Ps (τ 1 , ≈125 ps), the free e + (τ 2 , ≈400 ps) and one or more o-Ps (τ 3,4,… < 142 ns), with respective intensities I 1 , I 2 , and I 3,4,…. The quality and uniqueness of the fit determine how accurately lifetimes can be resolved. Especially for fitting a continuum of lifetimes, the uniqueness is a well-known problem and the resulting pore size distributions are therefore referred to as "plausible".
Because of improved diffusion kinetics in comparison to thicker films on a flat substrate, equilibration takes minutes instead of hours (Figure  S5. 1, Supporting Information). To measure large flat wafers directly, dedicated large-volume measurement tubes are necessary. Another way to reduce the required substrate size is to deposit thicker films. QCM and EP measurements were performed with MeOH as a probe molecule. Adsorption isotherms were measured at room temperature in the range 0 ≤ P P 0 -1 ≤ 0. 8. The normalized data are plotted in Figure  8  (-Δv and Δ at 633 nm for QCM and EP, respectively), while the non-normalized data can be found in the Supporting Information (Figures S3. 1 and S4. 1, Supporting Information). The sigmoidal shape of the isotherms is in perfect agreement with that of a reference MeOH isotherm measured volumetrically on ZIF-8 powder, and stems from adsorption at different sites: clustering near the window followed by cage filling.
Acknowledgements T. S. , R. V. , and I. S. thank the  Research Foundation Flanders (FWO)  for SB-Ph. D. and postdoctoral fellowships ( 1S53316N ,  1S00917N , and  12L5417N ). R. A. thanks the  European Union  for the  Horizon 2020 FETOPEN-1-2016-2017 research and innovation program  (grant agreement No  801464 , acronym: SPRINT), the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation program  (grant agreement No  716472 , acronym: VAPORE), the  Research Foundation Flanders (FWO)  for research projects and grants  G85720N ,  G0E6319N ,  G0H0716N ,  G083016N , and  1501618N , and  KU Leuven  for research project  C32/18/056. Nathalie Wauteraerts  is thanked for her kind help with KrP measurements. Max Tietze  and  Dmitry Kravchenko  extensively assisted with the assembly and operation of the adsorptive dosing setup.
Characterization techniques Transmission Electron Microscopy (TEM) was performed on a Tecnai microscope (200 kV). A drop of the colloidal suspension was deposited onto a carbon coated copper grid. Metal particle size distributions have been determined from the measurement of around 200 particles found in arbitrarily chosen area of the images using ImageJ software. NMR spectra were recorded at 298 K on a Bruker Avance III HD 300 NanoBay spectrometer equipped with a 5 mm broadband probe BBFO with Z-gradients, operating at 7. 05 T field strength at 300 MHz for 1 H nuclei. DMSO-D6 (99. 80 %isotopic purity) and D2O (99. 92 % isotopic purity) were purchased from Euriso-Top. Mass spectra were recorded on a MALDI-TOF/TOF Bruker Daltonics Ultraflex II in positive reflectron mode with 2,5-DHB as matrix.
Acknowledgements The  TEM facility in Lille (France)  is supported by the  Conseil Regional des Hauts de France , and the  European Regional Development Fund (ERDF). The authors are grateful to  Dr. Ahmed Addad  ( UMET, University of Lille 1 ) for technical assistance in TEM measurements. We thank  Dr. Nicolas Kania  and  D. Prévost  for the technical assistance and  Dr. Jérémy Ternel  for NMR spectroscopy experiments. We also thank  Johan Hachani  ( Plateau technique de protéomique et de spectrométrie de masse de l'Université d'Artois ) for his help with mass spectrometry analysis.
SEM Imaging and EDX Analysis We investigated the morphology of the tested membranes using SEM with a field emission gun (FEG) electron source Tescan Lyra dual beam microscope. The elemental composition of the modified membranes was analyzed using an EDX analyzer and detected by XMaxN with a 20 mm 2 Silicon drift detector (SDD) (Oxford Instruments). AZtecEnergy software monitored the measurements and gathered results. The samples were placed on conductive carbon tape, and samples analysis was carried out using 15 kV electron beam analysis.
Acknowledgements We thank the CCSM, CRMN and CCRMN for assistance on Mass Spectrometry, DOSY, High field liquid and solid-state NMR analyses respectively. We acknowledge the contribution of  SFR Biosciences  ( UMS3444/CNRS ,  US8/Inserm ,  ENS de Lyon, UCBL)  facilities:  Protein Science Facility -Frédéric DELOLME  for performing MALDI-TOF-MS analysis. We are grateful to  S. Vidal  for providing access to his  UPLC facility  ( ANR-17-CE07-0054 ). Financial support from the  Chinese Scholarship council (Y. Z scholarship ) and  UCB Biopharma (P. T. S and B. O scholarships)  and the  IR-RMN-THC Fr3050 CNRS  is gratefully acknowledged. This work was supported by the  LABEX iMUST  ( ANR-10-LABX-0064 ) of  Université de Lyon , within the program " Investissements d'Avenir " operated by the  French National Research Agency (ANR).
The proton-gated cation channel GLIC, from the prokaryote Gloeobacter violaceus, has been a popular model system for structure-function studies in this superfamily  (3) ; it accounts for 40% of all pLGIC structures in the Protein Data Bank (PDB). This channel is pH gated, and its structure has been solved at both high and low pH in apparent closed and open states, respectively  (4) (5) (6) (7). A static structural state is considered functionally open if the pore of the structure could conduct relevant ions; otherwise, it is considered a functionally closed state. These, however, are not necessarily the major physiological open and closed states. A further complication is that generally in pLGICs there are at least two closed physiological states-the resting state and the desensitized state-and a nonconducting conformation of the pore could indicate either of these states.
However, the scattering curves exhibited slight differences at Q-values around 0. 10-0. 12 Å-1 -the region where differences are expected based on theoretical scattering curves calculated from crystal structures. A summary of the structural parameters calculated from the experimental curves is available in SI Appendix, Table  S1. Concerning GLIC measured at pH 7. 5, the paused-flow SEC-SANS arrangement-which enabled measurement of the same fraction at two detector distances-was compared with the classical cuvette-SANS configuration, and the continuous-flow SEC-SANS arrangement. Coupling inline size exclusion immediately prior to scattering measurements (SEC-SANS) eliminated the accumulation of low-order aggregates evident in the cuvette measurement. This is obvious in the pairwise distance distribution where there was close agreement between both SEC-SANS datasets and the distribution expected from the closed atomic model, while the cuvette measurement displayed a low amount of interatomic distances up to 150 Å (Fig.
2B ). Solution Scattering Corresponds to Resting X-ray Structures. To assess how the shape of solution-phase GLIC matches putative three-dimensional (3D) structures, we first compared our SANS data to scattering curves calculated from atomic models derived from previously reported X-ray structures: GLIC crystallized at pH 7. 0 (closed, PDB ID 4NPQ) and 4. 0 (open, PDB ID 4HFI), ELIC in the absence of agonist (tightly closed pore, PDB ID 3RQU), and sTeLIC in the presence of agonist (wide pore, PDB ID 6FL9). For the latter two comparisons, to ensure that model fits represented differences in large-scale conformation rather than local sequence differences between channels, we constructed homology models of GLIC based on template structures of ELIC and sTeLIC, respectively. Fitting of these theoretical spectra to the experimental measurements showed that the closed-state GLIC structure exhibited the best fit to the scattering curves under both resting and activating conditions (χ 2 goodness of fit of 2.
Contribution from this or another desensitized form, either within or beyond regions sampled in our MD simulations, may prove a productive area of future investigation. In conclusion, paused-flow SEC-SANS proved effective in determining distinct room temperature solution structures of a key model pentameric ligand-gated ion channel under resting versus activating conditions. These solution structures, deposited in the Small-Angle Scattering Biological Database (SASBDB)  (45) , should prove valuable as reference points for the aver-age conformation of GLIC in solution, and as models that can be used in future studies, e. g. , as launching points for MD simulations. Furthermore, our results from pH 3 represent an independent experimental technique pointing to a closed majority population under activating as well as resting conditions.
Lycksell et al. Probing solution structure of the pentameric ligand-gated ion channel GLIC by small-angle neutron scattering PNAS | 7 of 9 https://doi. org/10. 1073/pnas. 2108006118 and the extinction coefficient calculated from the amino acid sequence using ProtParam  (50). In merging data from the two detector distances, data from the detector distance covering low Q (11. 2 m for continuous-flow and cuvette-mode, 8 m for paused-flow) were used up to 0. 070 Å-1 continuousflow and cuvette-mode, and up to 0. 095 Å-1 for paused-flow. Above this, data from 2 m (continuous-flow and cuvette-mode) and 2. 8 m (paused-flow) were used. A small additional constant was subtracted as a final adjustment to the background. Model Preparation. Models based on X-ray crystal structures were constructed using PDB entries 4NPQ (GLIC, closed conformation) (6), 4HFI (GLIC, open conformation) (51), 3RQU (ELIC)  (52) , and 6FL9 (sTeLIC)  (22).
ACKNOWLEDGMENTS. We acknowledge the  Institut Laue-Langevin  and  European Synchrotron Radiation Facility for developments in SEC-SANS  and allocated beam time at the D22 instrument. This work was supported by grants from  SwedNess , the  Knut and Alice Wallenberg Foundation, Swedish Research Council  ( 2017-04641 ,  2018-06479 , and  2019-02433 ),  Swedish e-Science Research Centre, BioExcel Center of Excellence  ( EU 823830 ), and the  Lundbeck Foundation  through the  Brainstruc grant. Computational resources were provided by the  Swedish National Infrastructure for Computing.
Data Availability. The raw experimental data have been deposited at https://doi. org/10. 17605/OSF. IO/TDZX4 for cuvette-SANS and continuousflow SEC-SANS  (47, 67) , and at https://doi. ill. fr/10. 5291/ILL-DATA. 8-03-1002 for paused-flow SEC-SANS  (48). Processed SANS data and representative models have been deposited in the Small-Angle Scattering Biological Data Bank (SASBDB), https://www. sasbdb. org/project/1317/ (paused-flow SEC-SANS at pH 7. 5 [SASDL33], paused-flow SEC-SANS at pH 3 [SASDL43], continuous-flow SEC-SANS at pH 7. 5 [SASDL53], and cuvette-SANS at pH 7. 5 [SASDL63]) (68).
226 Ra concentration was measured by Thermal Ionization Mass Spectrometry (TIMS) using a Thermo-Scientific Triton mass spectrometer. Uranium and thorium concentrations were calculated from the measured 235 U/ 233 U and 232 Th/ 229 Th ratios, respectively. A standard-sample-standard bracketing method was applied to correct raw data for instrumental mass bias using the IRMM-184 standard solution for U measurements and a mixture of IRMM-035 standard solution and 229 Th spike for Th measurements (see  Pelt et al. , 2008 or Jeambrun et al. , 2012 for details). The 232 Th/ 230 Th isotopic ratio proposed by  Sims et al. (2008)  for the IRMM-035 standard was used (87,873 ± 738 2SD) rather than the original certified value. The 232 Th tailing over the 230 Th was corrected by an exponential law fitted on the signals measured in 229.
Except otherwise specified, analytical uncertainties (2SD) are based on the external reproducibility of rock standards. a Analytical uncertainties (2SD) rising from the counting statistics of the samples. b Reported uncertainties were estimated by summing the internal and external error during 230 Th and/or 226 Ra analysis because internal error exceeded usual internal error of rock standard measurements. c Data calculated from mass balance (see section 3. 3. 2 for explanation). Uncertainties were estimated using a Monte Carlo simulation. No ( 210 Pb/ 226 Ra) and ( 228 Ra/ 232 Th) ratios were reported because propagated uncertainties reached more than 100% for these ratios. activity ratios in the bulk soil samples decrease with depth, from radioactive equilibrium at the surface to 0. 954 in the deepest layer, except in two layers (50-70 cm and 110-130 cm), where the ( 234 U/ 238 U) ratio remains close to radioactive equilibrium (Fig.
In addition it is assumed that the leaching and gain remain constant with time. The evolution of each nuclide activity ( 238 U, 234 U, 230 d 238 U dt = -(λ 238 + k 238 ) × 238 U + f 238 × 238 U 0 (4) d n N dt = λ n-1 × n-1 N -(λ n + k n ) × n N + f n. n N O where n N stands for the number of 234 U, 230 Th or 226 Ra atoms, n N 0 is the corresponding initial abundance at t = 0 and f n , k n and λ n (y -1 ) are the gain, leaching and decay constants of the nuclide n N, respectively. An unsuccessful attempt to solve Eqs. 4 was performed using the differential equation solver (ode45) proposed by the Matlab® commercial software with a Monte Carlo random trial of the unknown gain and leaching constants to try to reproduce bulk soil U-series disequilibria. 10 7 sets of k n and f n values were tested over 1.
Conclusion U-and Th-series disequilibria were measured in bulk samples and in separated fractions of a forested soil profile to evaluate the meaning of bulk soil data to probe weathering. This study assesses the redistribution of U, Th and Ra nuclides between mineral fractions and thus identifies the mechanisms and the timescales of the mobilization and/or retention of these nuclides. The study soil profile evolved from acidic Valanginian heterogeneous sediments that were mainly composed of goethite, clay minerals, quartz and minor amount of feldspar. Our results precise the respective roles of the fine <2 μm fraction and Fe-oxides in the U-and Th-series signature of the bulk soil. Hence, the affinity of the nuclides for Fe-oxide decreases in the order Th > U > Ra, while the affinity for the <2 μm fraction decreases as Ra > Th > U.
Acknowledgements The authors acknowledge the  INRAE-BEF (Biogéochimie des Ecosystèmes Forestiers ) team and  ANDRA  for the charge of the Montiers site,  Thierry Perrone  for Sr isotopic analyses,  René Boutin  for major elements analyses and  Amélie Aubert  for XRD analyses. This work was financially supported by an  ANDRA  and  IRSN  fellowship to EL and the  CNRS-ANDRA-EDF-IRSN NEEDS Environnement program. The constructive comments of  A. Dosseto , one anonymous reviewer and  C. France-Lanord  helped to improve the manuscript. This research is an EOST-IRSN-ANDRA contribution.
Furthermore, the selectivity obtained for 2-methylpentylamine 3 l was low, also probably because of racemization of intermediate 2 l in the reaction mixture. No formation of the unsaturated amines 4 was observed in these cascade reactions, which confirms the high chemoselectivity of AmDHs toward saturated carbonyl substrates 2 versus unsaturated carbonyl substrates 1, while benefiting from the much higher activity of OYEs compared with AmDHs toward enones and enones/enals 1. Thus, the EREDs/AmDHs combination can be run in one pot cascade reactions without requiring a sequential procedure. Interestingly, presence of small amount of alcohol in reactions with substrates 1 d, 1 e, 1 i and 1 k, was observed (data not shown). Formation of alcohol 5 d was quantified by GC-MS to facilitate peak attribution due to partial co-elution.
Acknowledgements C. E. P. acknowledges an  NWO   Veni grant  (no  722. 015. 011 ). R. J. C. Oosten ,  L. Koekkoek-van der Weel  and  M. J. F. Strampraad  are gratefully acknowledged for their technical assistance. C. V. V acknowledges  Rudy Bayakimissa  for initial experiments on this project.