dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements The first author is funded by the  British Academy  and the  Royal Society  as a  Newton International Fellow  in the United-Kingdom and is very grateful for the strong support of these two organizations. We thank the  Egyptian authorities  for their support. We also thank all parents and individuals who have agreed to take part in the morphometric data collection. We are grateful to  Dr S. Amblard-Pison ,  Dr A. Person ,  Dr S. Bouquillon-Delerive ,  Prof P. Thomas ,  Dr P. S. Randolph-Quinney ,  Prof. F. Thackeray ,  Prof. J. Robb ,  Dr J. Etling  and  L. Watrin  for discussion and advice, to  Dr S. Meiri  and  E. Maza  from the  Department of Zoology of Tel Aviv University , and  S. Kudryavtsev  from the  Moscow Zoo  for the pictures of.
Acknowledgements We would like to warmly thank  Ana Soto ,  Carlos Sonnenschein ,  Cheryl Schaeberle ,  Paul-Antoine Miquel ,  Charles Wolfe  and  Leonardo Bich  for their careful reading and useful remarks on previous versions of this paper. This work was conducted as part of the research project " Addressing biological organization in the post-genomic era " which is supported by the  International Blaise Pascal Chairs, Region Ile de France. Maël Montévil  was supported by  Labex "Who am I?", Laboratory of Excellence  No. ANR-11-LABX-0071.
Release kinetics of Bovine Serum Albumin (BSA) from the films Release experiments of fluorescently labelled BSA (BSA-FITC) were carried out with a SAFAS Genius XC spectrofluorimeter (Monaco). PLL/HA films were incubated with BSA-FITC solution (1 mg. mL -1 ) for 1 hour and then rinsed 3 times with PBS during 5 minutes. The release experiments were performed in PBS solution and the data were monitored every 5 minutes during 24 hours. The measurement parameters were  ex / em = 495nm/520nm. Before monitoring the release, the quantification of BSA-FITC loaded on the films was done by confocal analysis. The method consisted in using a calibration curve by plotting the fluorescence intensities of BSA-FITC solutions (image sections) as a function of their known concentrations. Then, fluorescence intensities of the image sections of the loaded film were measured and thanks to the calibration curve the concentration of BSA-FITC was determined.
15 nN were the maximal loading force. Elasticity maps were calculated based on Dimitriadis model:  43      4 3 2 2 / 3 2 / 1 2 0975 , 0 769 , 0 283 , 1 133 , 1 1 1 3 4             R E F where δ is the indentation depth, ν the Poisson coefficient, R is the colloids radius and h the sample thickness. The Dimitriadis correction for finite thickness is defined by χ parameter: h R   All the curves were analyzed by mean of an automatic Matlab algorithm described elsewhere. 44 ntrary to the classical Hertz model, Dimitradis model was used in order to take into account the mechanical contribution of both the finite thickness of the soft polyelectrolyte film and the influence of the supporting hard substrate (glass). Furthermore, Dimitriadis model described the mechanical behavior of a finite elastic sample under sphere/plane contact.
This suggests that a change in morphology from a well oriented NHSK crystalline structure to a less well oriented crystalline structure occurs as the crystallization temperature is reduced. To investigate the morphology that emerges during isothermal crystallization and associated crystallization kinetics, 1D meridional SAXS profiles I(q, q) (see Figure  2A ), were computed from the 2D time-resolved SAXS data throughout the crystallization process. From the 1D meridional profiles the normalized scattering invariant, Qs, was obtained allowing the development of the isothermal crystallization process to be followed. From this data the crystallization half-time, t1/2, was determined. Avrami plots,  20  were generated for the isothermal crystallizations process, allowing the rate constant, k, and Avrami exponent, n, to be extracted.
The combined use of SAXS/WAXS and thermal techniques have allowed us to unequivocally show the contrasting morphology in a set of PET-MWCNT nanocomposites compared with neat PET. The data revealed that a NHSK structure predominates in the PET-MWCNT composites, with crystallization being controlled by the residual orientation of the MWCNT matrix. Whereas, an unoriented lamellar structure is observed in the neat PET. This was verified by examining the crystallization kinetics and growth geometry in the samples under hot isothermal crystallization conditions. This is in contrast to observations that a shish-kebab structure will only prevail after an external shear field is applied to the polymer composite (e. g. uniaxial deformation  6. 7  or fiber spinning  15  ). The results here provide a valuable insight into the role of MWCNTs not only in their reinforcing properties, but also in the distinctive modification of the crystalline morphology of a polymer matrix.
1 eV for the acquisition of narrow windows. Charge compensation was done by means of a "dual beam" flood gun. Prior to their introduction in the ultrahigh vacuum chamber, the specimens were ultrasonically cleaned using acetone, then ethanol baths. Ar + ions sputtering at 500 eV and 6 × 10 -8 mbar was used to remove the surface contamination layer in cycles alternating sputtering and data acquisition. Following each sputtering, survey spectra and C1s and O1s windows were recorded. The recorded spectra were processed by means of the Avantage software (purchased from Thermo Fisher Scientific), using a peak-fitting routine with Shirley background and symmetrical 70-30% mixed Gaussian-Lorentzian peak shapes. The C/O ratio was evaluated following normalizations of the peak areas with the Scofield sensitivity factors.
Acknowledgements We acknowledge the financial support of  BASG  during his PhD by  Conselho Nacional de Pesquisa (CNPq) ,  Brazil. The support of  OGRAMAC Ltd  ( Santo Antonio da Posse/SP ) on HVOF experiments is acknowledged. Thanks are also due to S. Migot during EDX experiments,  R. Peignet  during scratch and pin-on-disk tests and S. M. Torres during XRD analysis. One of us (JMD) is grateful to  CNPq  for subsidising his stay at  Rapid Solidification Laboratory ,  Joao Pessoa ,  Federal University of Paraiba, Brazil.
Fluorescence microscopy. Immunofluorescent staining was performed to visualize the HUVECs on the different surfaces. After cell culture, cells were fixed by 4% (v/v) paraformaldehyde, permeabilized with 0. 5% Triton-X 100, blocked with 1% bovine serum albumin (BSA) in PBS solution. The actin cytoskeleton was stained with Alexa Fluor1 488 phalloidin (Invitrogen, France). Nuclei were stained by mounting the samples with ProLong1 Gold antifade reagent containing DAPI (Invitrogen, France). Cell adhesion was imaged using a Leica DM5500B epifluorescence microscope and quantified using the ImageJ software (NIH, http:// rsb. info. nih. gov/ij/). Cell nuclei were counted for evaluation of adherent cell numbers. At least 10 fields at low magnification (10 X) on each surface were analyzed for this study.
Acknowledgments This work has benefited from a  French State grant  (reference  ANR-10-LABX-0042-AMA-DEus ) managed by the  French National Research Agency  under the  initiative of excellence IdEx Bordeaux program  (reference n°ANR- 10-IDEX-0003-02 ). Authors would like to thank  Dr. C. Labrugère  ( PLACAMAT, Université de Bordeaux ) for her contribution in XPS data acquisition and analysis as well as  A. Tanga  ( INSERM U1026 ) for participating in the scientific discussions. JR acknowledges the  Association pour la Recherche en Néphrologie  for support.
Next, the kinetics and dynamics of the paCD : DNA interactions involved in CDplex formation and dissociation in aqueous media were scrutinized for each library member individually. Finally, the pDNA-transfecting capabilities in cellulo have been assessed and critically correlated with the molecular and supramolecular features. Collectively the data point out that, despite all cationic CDs efficiently complexing DNA, gene transfer capabilities critically depend on a delicate balance between the factors influencing reversible CDplex assembly-disassembly among which the HLB plays a central role.
Cell transfection capabilities of CDplexes Gene carrier capabilities were assessed on African green monkey fibroblast-like COS-7 cells using a luciferase-encoding gene ( pTG11236, pCMV-SV40-luciferase-SV40pA). Naked pDNA and JetPEI polyplexes were used as negative and positive controls, respectively. The assays were run with CDplexes formulated at N/P 2, 5 and 10 in 10% serum-containing medium. The level of exogenous luciferase expression (relative to the total amount of proteins) and the cell viability (relative to untreated controls) were measured for each CDplex formulation (Fig. 7 ; data at N/P 10 omitted for clarity; the full data set is collected in ESI, Fig. S36 † ). The non-amphiphilic CDs 7 H and 21 H featured negligible gene transfer abilities under these experimental conditions,  regardless the N/P ratio (Fig.
Acknowledgements This work was supported by the  Spanish Ministerio de Economia y Competitividad (MinECo , contract no. SAF2013-44021-R) , the  Junta de Andalucía  (contract no. FQM2012-1467 ), the  European Union (FEDER and FSE) , the  CSIC , the  CNRS , and  FUSINT  ( CNR  project). We also thank the  CITIUS  for technical support. I. P. is grateful to  CSIC (JAE-PreDoc program ) for a predoctoral fellowship.
In situ X-Ray Diffraction Angle-dispersive XRD spectra were collected in situ at high pressure and high-temperature at beamline 12. 2. 2 of the Advanced Light Source (ALS), Lawrence Berkeley National Laboratory (LBNL), and beamline ID27 of the European Synchrotron Radiation Facility (ESRF) using a monochromatic incident X-ray beam with a wavelength of 0. 4959 or 0. 6199 Å at ALS and 0. 3738 Å at ESRF. The monochromatic X-ray beam was focused to a smaller size than the laser heating spot in order to reduce both the radial and axial temperature gradients, typically: 3 × 3 µm at ID27 beamline and 10 × 10 µm at 12. 2. 2 beamline. The diffraction images were integrated with the Fit2d software  (Hammersley et al. , 1996) , and the one-dimensional diffraction patterns were treated with the General Structure Analysis System (GSAS) software package  (Larson and Von Dreele, 2004)  using the LeBail method to identify the different phases and refine their lattice parameters.
ACKNOWLEDGMENTS EB and WM acknowledge support from the  Deep Carbon Observatory. WM is supported by  NSF -EAR-1055454. Portion of the XRD work was performed at the high-pressure beamline 12. 2. 2,ALS which is supported by the  DOE-BES  under contract  DE-AC02-05CH11231. We thank  J. Yan ,  J. Knight , and  A. MacDowell  for their assistance with XRD experiments at  ALS. We also thank  M. Scott  for providing the rhodochrosite sample.
Acknowledgements The authors thank the  EC Erasmus program  for the stay of GN in Lille and the  Portuguese Foundation for Science and Technology (FCT)  within the scope of the project  UID/QUI/ 00100/2013. Chevreul Institute in Lille (FR 2638 ),  Ministère de l'Enseignement Supérieur et de la Recherche ,  Région Nord -Pas de Calais  and  FEDER  are also acknowledged for supporting and partially funding this work. AV acknowledges the  COST action   CM1302  (SIPs) and the Investigator  FCT2013   Initiative  for the project  IF/01302/2013 , as well as the  FCT, POPH  and  FSE -European Social Fund. Aurélie Malfait  and  Johan Hachani  are gratefully acknowledged for their help with GPC and MALDI ToF measurements, respectively.
13 Measurements were performed on the quenched samples at different temperatures during the whole day or overnight in order to obtain reflections with exploitable intensities. 2. 2. 2 DSC analyses. Two types of DSC were used: A heat flux DSC that served to determine the melting points and the enthalpy of fusion of Form I and Form II. The thermal analyses were performed using a DSC 214 Polyma (Netzsch). Samples were weighed in 25 μL aluminum pans and a heating rate of 5 K min 1 was applied, under nitrogen atmosphere. Data treatment was performed using Netzsch Proteus® software v6. 1. A power-compensated DSC was also used in order to reach low temperatures down to 150 °C. The thermal analyses were conducted in a powercompensated Perkin Elmer Pyris Diamond DSC equipped with a liquid nitrogen cooling system.
Stability relationship between the three forms of NMU X-Ray results were completed by thermal analysis measurements. Thus, the stability behavior and the thermodynamic relationships between Forms I, II and III were investigated. The melt quenching process was reproduced inside the crucible as follows: starting from the commercial batch of Form I, the sample was heated until melting at 5 K min  1. The liquid melt was then rapidly cooled down to 50 °C or to 150 °C with a cooling rate of 20 K min 1 (fastest cooling rate accessible by the DSC apparatus). The sample was heated again at 5 K min 1 up to 130 °C. Data obtained from the quenching experiment at 50 °C. During the first heating of the commercial batch, the DSC    thermogram shows an endothermic peak at 98 °C (ΔH I F = 188. 5 J g 1 ) that was assigned to the fusion of Form I.
Excess solvent was instantly absorbed by a filter paper. For selective staining of PB, the TEM specimens were exposed to OsO 4 vapour for 3 h. Cryogenic transmission electron microscopy. Cryo-TEM imaging was carried out using a JEM 3200FSC field emission microscope (Jeol) operated at 300 kV in bright-field mode with an Omega-type zero-loss energy filter. The images were acquired with an Ultrascan 4000 charge-coupled device camera (Gatan) and with Gatan Digital Micrograph software (version 1. 83. 842), while the specimen temperature was maintained at À 187 °C. Vitrified samples were prepared using a FEI Vitribot placing 3 ml of sample solution on 200-mesh holey carbon copper grids under 100% humidity, then blotted with filter paper for 0. 5-1. 5 s, and immediately plunged into a À 170 °C ethane/propane mixture and cryotransfered to the microscope.
Electron tomography. Electron tomography was performed using the Fei Tecnai 12 electron microscope recording a series of projection images at various tilt angles between ± f max with typical values of ± 60°in 2°increments. Cryogenic electron tomography. Cryogenic electron tomography was performed with the same transmission electron microscope that was used for cryo-TEM imaging. Electron tomographic tilt series were acquired with the SerialEM software package (version 3. 2. 2). Samples were tilted between 69°angles with 3°i ncrement steps. Alignment and reconstruction. The TEM grids were dipped in gold nanoparticle solution before sample deposition (d ¼ 3-10 nm, stabilized by 11-mercapto-1undecanol ligand) to ensure proper alignment of captured images with IMOD  52, 53. The fine alignment and cropping was conducted with custom-made Silicon Graphics JPEGANIM-software package  54.
The images were binned twice to reduce noise and computation time and maximum entropy method reconstruction scheme was carried out with custom-made programme on Mac or Linux cluster with regularization parameter value of l ¼ 1. 0E À 3 (ref. 54). Visualization of 3D reconstruction. Volumetric graphics and analyses were performed with the UCSF Chimera package  55  and volume segmentation was carried out using trainable weka segmentation  56.
Acknowledgements We thank  Dr Holger Schmalz  for helpful discussions about polymer synthesis and  Dr Andreas Hanisch  for the synthesis of four SBT terpolymers. We thank  Adjunct Professor in Molecular Genetics Peter Engelhardt  for help with transmission electron tomography. We acknowledge the  Deutsche Forschungsgemeinschaft (DFG)  for supporting this work within  DFG Mu896/40-1. This work was carried out under the  Academy of Finland's Centre of Excellence Programme  ( 2014-2019 ) and supported by  ERC-2011-AdG  ( 291364-MIMEFUN ). This work was partially supported by  Russian Science Foundation  grant # 14-33-00003. We further made use of the  Aalto University Nanomicroscopy Center (Aalto-NMC ) premises.
Introduction The molten salt fast reactor (MSFR) is an innovating concept of the molten salt reactor (MSR) developed by CNRS (France) since 2004  [1] [2] [3] [4]. This reactor is a nuclear concept of Generation IV, currently in a developing phase (particularly in the frame of the European project SAMOFAR supported by HORIZON H2020), and derived from other concept described in the reference  [5]. This concept is designed for the use of a liquid nuclear fuel composed of a mixture of fluoride salts (liquid in the reactor operation temperature range, 650-850 C), which circulates from the reactor core to the heat exchangers. This reactor is adapted to work under thorium fuel cycle (Th 232 -U 233 ). The nuclear fuel retained for the MSFR is constituted of the fluoride salts, LiF-ThF 4 -(UF 4 -UF 3 ) (77-19-4 mol%).
Prion protein is involved in deadly neurodegenerative diseases. Its pathogenicity is linked to its structural conversion (α-helix to β-strand transition). However, recent studies suggest that prion protein can follow a plurality of conversion pathways, which hints towards different conformers that might coexist in solution. To gain insights on the plasticity of the ovine prion protein (PrP) monomer, wild type (A136, R154, Q171), mutants and deletions of ARQ were studied by traveling wave ion mobility experiments coupled to mass spectrometry. In order to perform the analysis of a large body of data sets, we designed and evaluated the performance of a processing pipeline based on Driftscope peak detection and a homemade script for automated peak assignment, annotation, and quantification on specific multiply charged protein data.
Cross-Section Calibration of the Ion Mobilities Since it was shown by the seminal work of Shvartsburg and Smith  [28]  that the drift time in TWIMS cannot be directly correlated to absolute collisional cross-sections, we processed data according to the protocol referring to CCS (Ω) calibration in TWIMS defined by Ruotolo et al. [29]  in order to obtain an estimate of the absolute collisional cross section. To calibrate CCS denatured myoglobin was used since the charge state distribution (CSD) of this latter globally covers the CSD of the PrP and that both proteins have roughly similar masses (16. 9 kDa for myoglobin and 23 kDa for PrP). This calibration was performed with mobility parameters strictly identical to those used for measuring PrP. It should be pointed out that this calibration procedure is only meant to give an estimate of the absolute cross-section values, since we are aware that the reference values only partially cover those measured on our system and that we had to resort to using a denatured protein and not a native protein.
Ion Mobility Data Processing Data analysis of ion mobility experiments was performed as follows. First, ion mobility spectra were opened in the Driftscope software. Then we performed a peak detection using a resolution of 2000 and a signal threshold detection of 2000 counts. At this stage, an Apex3D ion file (. csv) is created. A home-made Python/Matplotlib/PyQt program allows the extraction of data from the CSV file (m/z, intensities, drift time), selects data points that belong to a charge state of the protein under study, performs CCS calibration using the procedure and parameters described in the previous section, and plots the CCS as a function of charge state with intensities indicated by a color map. This program allows data manipulation (assignment to conformer families, calculation of total and relative intensities, …) and interaction with the plotted data.
Data Processing and Interpretation First authenticity and purity of PrPs were determined by recording their mass spectra under denaturing conditions. These experiments allowed assessing the correct expression and the good purity of all PrPs as well as the presence of an oxidation of the disulfide bond linking α-helices H2 and H3. The mass spectra of the PrPs were then recorded under Bnondenaturingŝ olution conditions. CSD were similar to those observed in denaturing condition. This result was attributed to the relatively unfolded nature of the PrPs  [36]. All prion proteins were shown to be represented by a CSD spanning +12 to +33, in average (an illustration is given in Fig. 1a  for I208M mutant). After recording the ion mobility data, we specifically extracted ion mobility data of the protein under study following the procedure described in the Material and Methods section.
Our script automatically computes CCS values with user provided parameters (X, a, b, and C factors, mass of the drift gas). Ω = f (z) graphs are plotted with this script using a color scale on points to reflect absolute intensities. This is exemplified on Fig. 1b. This led to efficient processing of the data. One should mention here that it is possible that the responses vary for the different conformational ensembles. Hence, what is reported in Figures (signal relative abundances) could not necessarily reflect the molar fractions in solution. However, when looking at changes in abundances between different conditions, or between CSD, these should be representative of changes occurring in solution. Calibration of TWIMS-based systems to provide absolute collision cross-section for proteins is still an issue  [30] [31] [32]  and this article does not aim to resolve it.
The occurrence of different structures is also observed with broad arrival time distributions on some of the charge states. Thus, an interrogation remains: since our data relies on the Driftscope and its ApeX3D peak detection software, is the detection of peaks that are not baseline resolved accurate? Thus, we attempted to check how reliable the detection, annotation, and quantification of the peaks was when mobility profiles contain satellite peaks. To this purpose, we compared the peak fitting procedure of Driftscope, which processes peaks in a three dimension space (drift time, m/z, intensities) with a more standard Gaussian fitting of a two-dimension (drift time, intensity) extracted ion drift plot  [34]. For two selected charge states of the I208M mutant (13+ and 23+) an extracted drift plot encompassing, the entire mass peak width was extracted using MassLynx, exported as CSV file, loaded in GNU Octave, and processed with the peakfit.
1d ). Peak width was determined at 1. 7 ms for the 13+ charge state and 0. 7 ms for the 23+ charge state, which is also in good agreement with peak widths observed for single conformation proteins such as myoglobin. Thus, the results provided by the Driftscope extraction seem to be as reliable as an equal width Gaussian fitting. Processing of the ion mobility data and, more specifically, automated data extraction for specific charge states with our program allowed detecting low intensity conformer families that are hardly accessible when manually extracted in the Driftscope software. In order to further compare conformer families, their relative intensities were calculated by summing the raw intensities (counts) of the various charge states of each conformer family. From these calculations, it appears that relative intensities of the conformer families could differ by 30% (especially on low intensity families) from one experiment to another.
This buffer does not lead to the formation of oligomers: oligomer formation is achieved by thermal unfolding for 2 h at 50 °C to 65 °C in sodium citrate at pH 3. 35  [22]. Mobility data were recorded and compared with those obtained at room temperature. From these experiments, it appears that significant differences are observed in mobility plots when samples were heated. Thus, we observed the reduction of the CSD of conformer families, the appearance of additional conformer families (e. g. , conformer families 0, 0′, and 1′), the modification of ratio intensities of conformational ensembles such as for G3, which was shown to increase in intensity compared with G2 for both I208M and K188A mutants at pH 6. 3 (see Fig. 5 ). To annotate the conformer families observed after thermal unfolding, we used the Ω (av) values of conformer families reported in Table  2.