dataesr/scientific-paragraphs-categorization huggingface dataset:
AutoSol (phenix. autosol) is a comprehensive, automatic tool that performs experimental phasing with the MAD, MIR, SIR or SAD methods 3   (Terwilliger et al. , 2009). The program locates the substructure, estimates phases, performs density modification, identifies noncrystallographic symmetry (NCS), and builds and refines a preliminary model. To carry out the tasks, AutoSol uses the Phenix tools HySS (Hybrid Substruc-  The primary tools for cryo-EM in Phenix. ture Search; Grosse-Kunstleve  & Adams, 2003; Bunkoczi et al. , 2013) , SOLVE  (Terwilliger & Berendzen, 1999 ), Phaser (McCoy et al. , 2007) , RESOLVE  (Terwilliger, 2002) , Xtriage and phenix. refine (Afonine et al. , 2012). 4. 1. 2. Molecular replacement. Molecular replacement (MR) is used to solve structures when a structurally similar model (homologue) is available  (Hoppe, 1957; Rossmann, 1972; Blow et al.
As there are several hundred parameters, the protocols can be customized for specific needs. The phenix. refine graphical user interface (GUI) is integrated with Coot  (Emsley et al. , 2010)  and  PyMOL (DeLano, 2002) , so that refined models and associated maps can be readily displayed and analyzed. While phenix. refine is the main crystallographic refinement program of Phenix, the following integrated alternatives exist. (i) A recent addition integrates the Amber molecularmechanics force field  (Case et al. , 2018)  for restraints with the feature articles functionality of phenix. refine. Amber uses energy-based geometry terms and adds electrostatics and van der Waals attractive/dispersive interactions. Amber refinement in Phenix has been shown to improve model quality, especially sterics and hydrogen bonding at lower resolutions, and to reduce overfitting  (Moriarty et al.
This strategy, called joint X-ray and neutron refinement (joint XN refinement), ameliorates the data-to-parameters ratio by increasing the amount of experimental data used in refinement, leading to more complete and accurate models  (Coppens, 1967; Orpen et al. , 1978; Wlodawer, 1980; Wlodawer & Hendrickson, 1982). Macromolecular models can be refined with phenix. refine using neutron data or X-ray and neutron data simultaneously  (Adams, Mustyakimov et al. , 2009; Afonine et al. , 2010). The program automatically detects exchangeable H/D sites in the model and ensures that the sum of occupancies is equal to one. The position of H (or D) atoms can be refined with a 'riding model'  (Busing & Levy, 1964; Sheldrick & Schneider, 1997)  or individually. All standard tools available for X-ray refinement (Section 6.
Using other programs within Phenix Several programs from external developers can be executed in Phenix. Most require separate installation. feature articles (i) MR-Rosetta (phenix. mr_rosetta) uses homology modeling in the Rosetta program to improve a model before and/or after  MR (DiMaio et al. , 2011; Terwilliger et al. , 2012). Once a potential solution is obtained, Rosetta fills in missing sections and rebuilds the model to improve the fit to the electron-density map and the phases for map interpretation or automated model building. This approach is helpful in cases where the MR model differs greatly from the target. (ii) ERRASER  (Chou et al. , 2013)  improves RNA backbone conformations by combining MolProbity clash analysis, Phenix refinement and a pruned enumeration and optimization in Rosetta.
, 2017). The Q|R source code (https://github. com/qrefine/qr-core) uses cctbx (Section 9. 1) to construct a refinement protocol resembling phenix. refine. (vi) ISOLDE  (Croll, 2018 ) is a plugin to UCSF ChimeraX  (Goddard et al. , 2018)  for improving low-resolution cryo-EM or crystal structures. It performs interactively guided simulation with molecular-dynamics flexible fitting against a map and real-time validation; it will soon be possible to launch it from the Phenix GUI. (vii) Cryo-EM model building with Pathwalker  (Baker et al. , 2012; Chen et al. , 2016)  will soon be available within Phenix. Pathwalker can construct protein backbone models directly from near-atomic resolution cryo-EM density maps using a modified approach to traveling salesman problem solvers. When coupled with Phenix tools, such as phenix.
Architecture Phenix is built on the Computational Crystallography Toolbox (cctbx), which is an open-source library (https:// github. com/cctbx/cctbx_project) of reusable software components for macromolecular structure determination  (Grosse-Kunstleve et al. , 2002). The cctbx components are written both in a compiled language (C++) and a flexible scripting language (Python;  Lutz & Ascher, 1999). This approach is very efficient because high-level algorithms (such as refinement protocols) can be rapidly developed in the scripting language, while computationally intensive algorithms can be implemented in the compiled language. The Boost. Python Library (http:// www. boost. org/) is used to expose the C++ interfaces, classes and functions to Python  (Abrahams & Grosse-Kunstleve, 2003). The GUI is scripted through Python and produces a 'native' look 5  on each operating system.
Documentation The Phenix GUI provides more than 175 tools, with even more programs available on the command line ($500). The extensive online manual covers about 180 separate HTML pages, describes GUI and command-line versions of individual programs and includes tutorials and FAQs. The Phenix Tutorials YouTube channel (https://www. youtube. com/c/ phenixtutorials; Fig. 10 ) currently provides 29 tutorial videos. Each video introduces a Phenix tool, summarizes the input files and parameters, explains how to run the program and discusses the results.
Powders Fieen powders produced at the industrial scale were selected for this study. Table  1  describes their manufacturing processes, their main application elds, and available physico-chemical properties, based the safety or commercial product data sheets. These materials were chosen due to their representativeness of the most handled powders in the workplaces, the variety of applications they integrate and their wide range of properties. In particular, the total surface area values A t (including A Ex and porosity) cover almost 1. 4 orders of magnitude. More details about the powder manufacturing processes and applications for TiO 3. 2 Nitrogen (N 2 ) adsorption N 2 adsorption experiments were carried out in two public research laboratories (Lab A and Lab C) to conduct a comparison of the method and therefore strengthen the data.
General procedures The polymer composition was determined by 1 H NMR spectroscopy recorded on a Bruker AVANCE DRX400 MHz spectrometer. The samples were prepared at 60 mg/mL in CDCl 3 and the spectra recorded at 25 °C with a minimum of 64 transients. DOSY NMR experiments were recorded in DMSO-d 6 at 300 K on a Bruker Advance III spectrometer. The DOSY spectra were acquired with the dstebpgp3s pulse program from the Bruker topspin software, with 32 K time domain data points in the t2 dimension and 32 t1 increments. NMR data was processed using Bruker topspin software version 3. 5. GPC was used to characterize the polymer molar mass, molar mass dispersity (Ð) and BGE content on an Agilent Technologies 1260 Infinity unit comprising a solvent degasser, isocratic pump, an Agilent 1260 Infinity UV detector (G1314F, detection wavelength 254 nm) and a differential refractive index detector (G1362A RID at 35 °C) in series, a Varian PLgel 5 μm MiniMix-D 50 × 4.
Batch dynamic light scattering (DLS) and zeta potential analyses by electrophoretic light scattering were performed on a Zetasizer Nano ZS (Malvern Instrument, UK) instrument with a 633 nm He-Ne Laser. The polymeric NS suspensions (20 μL) were diluted in 1 mM aqueous NaCl (980 μL) and the Z-average hydrodynamic diameter (D h ) was determined from the 173°backscattered light intensity fluctuations via cumulant analysis with the Zetasizer 7. 11 software (Malvern) using the Stokes-Einstein equation and values of 0. 8872 cP (water viscosity) and 1. 330 (water refractive index). AF4 fractionation of the polymeric NS was performed on a Postnova analytics (Landsberg, Germany) AF2000 MT system comprising two PN1130 HPLC pumps (tip and focus pumps) and AF2000 module (crossflow pump), a PN5300 autosampler, PN4020 channel oven, and a separation channel fitted with a Postnova AF2000 MT Series NovaRC AQU 5 kDa cut-off regenerated cellulose membrane and a 350 μm spacer all under controlled temperature (25 or 37 °C).
An initial crossflow of 2. 0 mL/min was applied during injection, maintained for 3 min, was set to decrease exponentially to 0. 05 mL/min over a period of 15 min, maintained at 0. 05 mL/min for 25 min, and kept at 0 mL/min for 8 min allowing complete elution of the sample. The gyration diameters (D g ) were determined for each fraction at 3. 8 s time intervals using the angular variation of the scattered light intensity at angles 20°-164°(19 angles) recorded on the MALS detector using the Postnova AF2000 software calculation for spherical shape model, and D h at 5. 0 s intervals. For AFM analysis a 10 μL sample of the NS suspension was deposited on freshly cleaved mica, dried under a flow of argon and the AFM images were acquired in air at room temperature on a Dimension 3000 equipment monitored by a Nanoscope IIIa controller (Digital Instruments, Santa Barbara, CA, USA).
Acknowledgment The authors thank  Dr Ivana Lula  and  Prof Jarbas Magalhães  at  Laboratório de Ressonância Magnética Multi-Usuário ,  Universidade Federal de Minas Gerais  for 1 H NMR spectroscopy,  Prof J. de Souza  for access to UV-Vis spectroscopy and  Sabrina E. Silva  for assistance with NS preparation.
Funding sources This study is part of the  National Institute of Science and Technology in Pharmaceutical Nanotechnology : a transdisciplinary approach INCT-NANOFARMA, which is supported by  São Paulo Research Foundation  ( FAPESP, Brazil)  Grant # 2014/50928-2 , and by '' Conselho Nacional de Desenvolvimento Científico e Tecnológico'' (CNPq, Brazil)  Grant #  465687/2014-8. The authors also acknowledge financial support from  CNPq , Grants #  BJT 400889/2014-5 , # 310463/ 2015-7  and # 481872/2013-2 ),  Fundação de Amparo a Pesquisa do Estado de Minas Gerais  ( FAPEMIG APQ-02864-16 ),  Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)  and  NANOBI-OMG Network  ( RED-00007-14 )  Minas Gerais.
For a typical biological system, in which the total radiation background (including elastic and inelastic scattering) is substantially more intense than the fluorescence line of interest, the advantage of background removal associated to the HERFD-XAS data acquisition scheme outweighs the disadvantage of having a lower total signal intensity with respect to a standard XAS measuring apparatus, such as a solid-state detector. XAS measurements of samples as diluted as those of interest here are made possible thanks to the use of this set-up that, significantly improve the signal-to-noise ratio, thus allowing nearly background-free measurements. Data acquisition was performed using a liquid helium cryostat in order to limit sample evolution due to radiation damage under the beam. Condens. Matter 2018, 3, x FOR PEER REVIEW 4 of 8 crystal analyser spectrometer and monochromator contributions) was established to be 0.
7 eV by measuring the full width at half maximum of the elastic peak (measured by scanning the incident photon energy, with the monochromator, across the fluorescence photon energy, selected by the spectrometer). All the photons scattered by the crystals were collected using an energy-resolved silicon-drift detector, which allows discriminating the diffracted photons of interest from the other scattered ones. For a typical biological system, in which the total radiation background (including elastic and inelastic scattering) is substantially more intense than the fluorescence line of interest, the advantage of background removal associated to the HERFD-XAS data acquisition scheme outweighs the disadvantage of having a lower total signal intensity with respect to a standard XAS measuring apparatus, such as a solid-state detector.
To determine pharmacokinetic profile of AuNPd in blood, seven groups of five athymic nude female mice were treated with AuNPd at a unique dose of 1 mg/kg by IV injection. Gold concentration was determined by inductively coupled plasma mass spectrometry (ICP-MS) 5 min, 15 min, 30 min, 45 min, 60 min, 4 h and 24 h after AuNPd injection. To prevent underestimation of gold concentration that could be due to an incomplete mineralization of nanoparticulate gold, solutions were dosed with calibration curves carried out with ionic gold standard solutions and gold nanoparticles standard solutions. No significant differences were noted whatever the standard solutions used, confirming validity of the measurement (data not shown). AuNPd blood concentration-time curve with a semilogarithmic scale evidenced a rapid drop in initial concentration, followed by more gradual decline fitting into a classical bi-compartmental pharmacokinetic model characterized by a fast initial distribution phase followed by a terminal elimination phase with slower rate (Fig.
No evidence of atrophy, hyperplasia, necrosis or inflammation was observed. To further explore for abnormalities, histological examination of tissues was performed using hematoxylin-eosin staining. Liver examination did not evidence any negative effects in animals injected with AuNPd compared to control group. The microscopic parenchymal architecture evidenced normal hepatocytes without any signs of steatosis, inflammation nor fibrosis. Similarly, microscopic observation of kidney, spleen and heart did not reveal any sign of inflammation or fibrosis (Fig. 5 ). Uptake and subcellular localization of Aunpd in hepatic and splenic tissues. Biodistribution data have shown that AuNPd preferentially accumulated in liver and spleen. Therefore, we decided to assess subcellular localization of AuNPd in these organs by TEM at 24 h, 7 and 14 days after injection.
Since plasma ALAT, ASAT activities and creatinine level remained almost unchanged and comparable to the parameters of the control mice group, one can conclude that the accumulation of AuNPd did not provoke any hepatic or renal toxicity. Furthermore, we detect no sign of histological damage such as fibrosis or inflammation in tissue. Lastly, the absence of chronic inflammation was supported by plasma IL-6 level that remains normal for 14 days after the AuNPd administration. Since non-specific uptake of nanoparticles can occur in populations of phagocytic cells and dense capillary beds present in non-target organs, we also quantified gold in cardiac and pulmonary tissues. Very low concentrations of gold were observed in these organs, thus confirming a good tolerability of AuNPd. In accordance with previous data  26  , less than 1% of gold was detectable in brain.
After rising in tap water for 10 min, slides were stained with Gründwald Hematoxylin for 30 s. After washing, slides were stained with eosin for 15 s and rapidly rinsed in tap water. Three baths of 100% ethanol were realized, and slides were stained in alcoholic safran solution for 30 seconds. Slides were then cleared in xylene three times and mounted with Eukitt medium. The stained slides were scanned on a whole slide scanner (Nanozoomer 2. 0-HT, Hamamatsu, Japan) at × 40 magnification, obtained images were opened using NP-Viewer software. transmission electron microscopy studies of biological samples. For TEM, samples were processed as followed. Three mice per group were perfused with 2. 0% paraformaldehyde, 2. 5% EM grade glutaraldehyde in PBS (pH 7. 4). Organs were then carefully collected and cut into 1 mm 3 cubes in perfusion solution under binocular loupe.
Acknowledgements The authors thank  Dr. Raphael Berges  for technical help in animal experiments, the animal facility " Centre d'Exploration Fonctionnelle Scientifique" (CEFOS)  agreement  E 13-055-5 , campus  Timone Aix-Marseille University , the PICsL-FBI core electron microscopy facility ( Aïcha Aouane ,  Fabrice Richard  and  Nicolas Brouilly , IBDM,  AMU-Marseille UMR 7288 ), member of the national infrastructure  France-BioImaging  supported by the  French National Research Agency  ( ANR-10-INBS-0004 ). The authors acknowledge the contribution from ITMO cancer  AVIESAN (National Alliance  for the  Life Sciences & Health)  within the framework of the  Cancer Plan  ( GRAVITY  Project  PC201613 ). A. P. and A. V. K. acknowledge support from the  MEPhI Academic Excellence Project  (Contract No.
Given the influence of the different monomers contents, the HT° mechanism can be ascribed to the vinyl isomers whereas the LT° one could be due to the movements of the cis and/or the trans units, whose respective contribution is impossible to distinguish from mechanical spectroscopy. The HT° and LT° contributions are difficult to characterize from the isothermal curves , as the frequency range over which the isothermal are performed are short, and as they seem to overlap over large temperature and frequency domains. To solve this problem, we have chosen to deconvolute the G'' contributions of the mechanical β relaxation. This deconvolution was performed thanks to PeakFit software ©. The isochronal curves at 0. 1Hz of the different materials have been analyzed following the same method  [7] : two peaks are defined with independent parameters, i.
Characterization of samples Samples were characterized before and after acid-etching and cell-mediated resorption. X-Ray Diffraction (XRD) analyses were performed using a D8-Advance diffractometer (Bruker, Germany) with a Lynx-Eye Position Sensitive Detector, using Cu Ka radiation, from 10°to 90°(2h) with a 0. 03°(2h) step size and 2. 4 s/step counting time. The obtained diffractograms were analyzed using the EVA software (Bruker) and phases were identified by comparing the peaks present to PDF files (mainly, files #09-0432 for hydroxyapatite, 09-0348 for a-TCP and 09-0169 for b-TCP). The data were further exploited by Rietveld refinements using the Topas 4 software (Bruker), with a fundamental parameters approach and refining only the scale factor, lattice parameters, crystallite size (parameter Cry Size L) and strain (parameter Strain G).
A fundamental part of the characterization was performed by Scanning Electron Microscopy (SEM) and Electron BackScatter Diffraction (EBSD). SEM images and EBSD maps were obtained with a Zeiss Supra 55VP SEM (Carl Zeiss Microscopy GmbH, Oberkochen, Germany) equipped with a Gemini I SEM column. b-TCP being an insulating material, a low vacuum configuration (10 Pa of gaseous nitrogen) was adopted, in order to avoid any deleterious charge effect without needing to carbon-coat the samples. For EBSD maps, the accelerating voltage was set to 10 kV, samples were tilted to the standard 70°angle and the objective lens aperture was of 120 mm. The so-called High Current Mode was activated and an optimum working distance of 12 mm with respect to the pattern center was used. EBSD maps were acquired with a Nordlys S camera and data were post-processed with HKL Chan-nel5 software (Oxford Instruments, Abingdon, UK), to suppress the non-indexed points without affecting the orientation of their neighbors.
Acknowledgments The authors would like to acknowledge  Mirja Olsson  for the synthesis of the powders,  Nazim Boucida  and  Florian Mercier  for their technical helps. This work was partly supported by the  European Commission  funding of the 7 th  Framework Program (Marie Curie Initial Training Networks ; grant number:  289958 ,  Bioceramics  for bone repair). This study was partly supported by the  Swiss National Science Foundation  (SNSF; 200021_169027).
Data were searched against S. aureus HG001 database using Mascot algorithm (version 2. 5, Matrix Science, London, UK) through ProlineStudio 1. 4 package (http://proline. profiproteomic. fr/). Peptides were validated on Mascot pretty rank equal to 1, an ion score cut-off equal to 25, and 1% FDR on both peptide spectrum matches (PSM) and protein sets (false discovery rate-based ion score). The total number of spectra was recorded for all the proteins, allowing to quantify these proteins across all the samples (quantification by spectral count). Data were submitted to a negative-binomial test using an edgeR GLM regression through R (R v3. 5. 0), normalized according to a median-to-ratio method to calculate fold changes (FC) and P-values. The mass spectrometric data that support our findings are available via ProteomeXchange with identifier PXD013225.
RNAs The structure of RsaC (from HG001 strain) was mapped using selective 2 -hydroxyl acylation by benzol cyanide and the reactivity was analyzed by primer extension (SHAPE). Data were analyzed, and each modification was quantified using QuSHAPE software. The secondary structure was drawn using RNA structure and VARNA considering the reactivity of each ribose. The regions, which were not mapped, are shown in blue. The color code for each reactivity is given on the right side of the secondary structure model, red is for the highest reactivity while green is for the lowest reactivity. A black arrow indicates the +1 of RsaC 544. were then purified using a 6% polyacrylamide-8 M urea gel electrophoresis. After overnight elution in Elution Buffer (0. 5 M ammonium acetate pH 6. 5, 1 mM EDTA and 0.
Gel retardation assays 5 -radiolabeled RsaC 544 (15000 cpm/sample, concentration <1 pM) and cold mRNAs were renaturated separately by incubation at 90 • C for 1 min in Buffer GR-(20 mM Tris-HCl pH 7. 5, 60 mM KCl, 40 mM NH 4 Cl, 3 mM DTT), cooled 1 min on ice, and incubated 15 min at RT in presence of 10 mM MgCl 2. For each experiment, increasing concentrations of cold mRNA were added to the 5 end labelled RsaC 544 in a total volume of 10 l containing Buffer GR+ (20 mM Tris-HCl pH 7. 5, 60 mM KCl, 40 mM NH 4 Cl, 3 mM DTT, 10 mM MgCl 2 ). Complex formation was performed at 37 • C during 15 min. After incubation, 10 l of glycerol blue was added and samples were loaded on a 6% polyacrylamide gel containing 10 mM MgCl 2 under non-denaturing conditions (8 h, 300 V, 4 • C). Quantification of data corresponding to RsaC 544 and to RsaC 544 /mRNA complex was done with ImageQuant TL software (GE Healthcare Life Sciences).
Footprinting assays RsaC 544 -sodA mRNA complex formation was carried out at 37   S2 ). In parallel, ddGTP sequencing of 1 pmole RNA was made with the same oligonucleotide labelled with NED fluorophore. cDNA samples were analysed by capillary electrophoresis and data processed by QuSHAPE software  (34). SHAPE data (Supplementary Table  S6 ) were used to constrain structure prediction by RNAstructure  (35). The secondary structure of RsaC was finally visualized using VARNA (36) (Figure  1B ).
A truncated repeat of 58 nt marks the end of the 5 part of RsaC. Therefore, RsaC is 850 nt-long (2 repeats) in Newman, 984 nt-long (3 repeats) in MW2 and 1116 nt-long (longest form; four repeats) in HG001. We expanded our analysis to all bacterial genomes using a sequence similarity search program (BLASTn; Supplementary Table  S7 ) and observed that RsaC is restricted to S. aureus and the closely related S. argenteus species. The length of RsaC sRNA is ranging from 584 nt (a single truncated repeat) to 1116 nt (four repeats and a truncated repeat). This highlights the wide variability in length and composition of the 5 part of RsaC. We probed the secondary structure of RsaC (from HG001 strain) using selective 2 -hydroxyl acylation of riboses with benzoyl cyanide (BzCN)  (33). Resulting 2 -Oadducts were detected by primer extension and data were analysed and quantified using QuSHAPE software  (34).
Using gel retardation assays, we observed that RsaC binds to every member of znuB-znuC-zur operon and sarA mRNAs, but not with rex mRNA (Figure  6 ). Using IntaRNA software  (41) , pairing sites were predicted between RsaC and each targeted mRNAs validated by gel retardation assays (Supplementary Figure  S13 ). RsaC potentially binds to the ribosome binding site of sufC, ldh1, znuC, znuB, zur and sarA mRNAs, using several exposed C/U-rich sequences located in its 3 part. Conse-quently, RsaC could repress the translation of additional targets, mainly involved in oxidative stress response and metal homeostasis.