dataesr/scientific-paragraphs-categorization huggingface dataset:
If AA is a cause of RCC, public awareness of AA will have implications for RCC prevention in other parts of the world where herbal remedies containing AA is prevalent. to observed data for the two renal parenchyma samples where glomeruli were not present (when removed from the analysis: P ¼ 0. 0560). Levels of dA-AL-I were set to zero when below the detection threshold of 0. 3 adducts per 10 8 DNA bases. For Romanian subjects, dA-AL-I levels measured in DNA samples isolated using a phenol/chloroform extraction protocol were used for this analysis. Similar results were obtained using levels measured in DNA extracted using a standard Autopure (Qiagen) protocol.
ACKNOWLEDGEMENTS We thank  David Zaridze  and  Anush Moukeria  ( Russian NN Blokhin Cancer Research Centre, Moscow, Russian Federation ),  Ivana Holcatova  ( First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic ) and  Antonin Brisuda  ( University Hospital Motol, Prague, Czech Republic ),  Lenka Foretova  and  Marie Navratilova  ( Masaryk Memorial Cancer Institute and MF MU, Brno, Czech Republic ) for the collection of biospecimens and data from the  Russian Federation  and the  Czech Republic ;  Christine Carreira  ( International Agency for Research on Cancer, Lyon, France ) for processing renal biosamples in preparation for pathological review and DNA extractions;  Cyrille Cuenin  ( International Agency for Research on Cancer, Lyon, France ) for his technical support in DNA extractions;  David Muller  ( International Agency for Research on Cancer, Lyon, France)  for statistical support; Members of the CAGEKID consortium (http:// www.
Crystal Structure Determination Diffraction data were collected on a Nonius Kappa CCD diffractometer equipped with an Oxford Cryosystems low-temperature apparatus operating at T = 115 K. Data were measured using ϕ and ω scans using MoK α radiation (λ = 0. 71073 Å, X-ray tube, 50 kV, 32 mA). The total number of runs and images was based on the strategy calculation the program Collect. 41 Cell parameters were retrieved using the SCALEPACK software and refined using DENZO. 42 Data reduction was performed using the DENZO  42  software which corrects for Lorentz polarisation. The structure was solved by Direct Methods using the SIR92  43  program structure solution program and refined by Least Squares using version of the ShelXL  44, 45   (Sheldrick, 2008). All nonhydrogen atoms were refined anisotropically.
Acknowledgements The authors are grateful for the financial support provided by  CNRS  ( Centre National de la Recherche Scientifique ), the  "Ministère de l'Education Nationale et de la Recherche" , the  "Conseil Regional de Bourgogne " (grant Pari  II-smt8 ), and the  Agence Nationale pour la Recherche  (grant  07BLAN292-01  MetChirPhos). It is a pleasure for us to acknowledge for helpful discussion and technical assistance of  J. Bayardon ,  M. J. Eymin ,  M. J. Penouilh ,  F. & M. Picquet  and  B. Rugeri  from the  Institut de Chimie moléculaire de l'Université de Bourgogne and Welience.
Electrochemical, spectral and microscopic analysis Electrochemical experiments were performed with an Autolab PGSTAT100 potentiostat (Metrohm/Eco Chemie Netherlands) equipped with Nova 1. 10. 4 software using an electrochemical cell with three electrodes: a glassy carbon working electrode, an Ag/AgCl reference electrode and a counter electrode of platinum. In the case of square wave voltammetry (SWV) experiments, the established parameters are: initial potential -0. 3 V, end potential 1 V, amplitude 25 mV and a frequency of 25 Hz. The amperometric determinations were made at -0. 2 V in solution kept under stirring (200 rpm). An Alpha 300R (WiTec) confocal Raman microscope was used for the Raman spectroscopy determinations performed on the modified electrodes at 532 nm for laser and 60 seconds time accumulation, while the WiTec Control software was used for data analysis.
ACKNOWLEDGEMENTS Special thanks to  Cosmin Farcău, PhD ,  Prof. Iuliu Marian, PhD ,  Tamara Liana Topală, PhD  for spectral analysis and to  Karine Gorgy, PhD  and  Alan Le Goff, PhD  for their kind revision. This paper was published under the frame of  European Social Found, Human Resources Development Operational Programme 2007-2013 , project no. POSDRU/159/1. 5/S/136893. This paper was published under the frame of  European Social Found, Human Resources Development Operational Programme 2007-2013 , project no. POSDRU/159/1. 5/S/138776. This work was financially supported by  UEFISCDI , through the project number  PN-II-ID-PCE-2011-3-0355.
4b. x N also decreases with 0. 46 mol kg À1 NaClO 4. However, no significant change is observed regarding the ethanol-rich contrast for Cl À and ClO 4 À. All correlation lengths, sizes, and other useful data can be found in the ESI, † Section B and Table  S1. DLS was also measured for the composition a with increasing salt concentrations. The autocorrelation functions for each salt can be found in the ESI, † Section C. The characteristic dynamic sizes x D as obtained from DLS are plotted against the anion concentrations, see Fig. 3b. x D increases and diverges at a.
Acknowledgements Authors want to thank the  Labex Chemisyst  for providing invited Professorship. Prof. Thomas Zemb  acknowledges the  ERC  for the support of project '' REE-CYCLE '' for rare earth separation and the  COST Network   CM1011. All authors acknowledge very helpful discussions with  Prof. Dominik Horinek. We also thank  Isabelle Grillo  and  Bruno Deme  ´from the  Institut Laue Langevin (Grenoble, France)  for their help during the SANS experiments for the proposal 9-10-1395, and  Bruno Corso  for the in-house SAXS bench alignment and calibration.
The solution of polymer was lyophilized to yield a light pink solid. The conversion was 94% as determined by 1 H NMR spectroscopy. The dithiobenzoic ω-end group was removed by the method introduced by Perrier 42 using V-501 and the polymer isolated by dialysis and lyophilization to obtain a white solid. The obtained polymer was characterised by SEC M n = 26 200 g mol -1 , Đ = 1. 29. The synthetic parameters and molecular weight data of polymers prepared via RAFT polymerization are described in Table  TS1  (ESI †).
Scattering techniques The dynamic light scattering (DLS) measurements were performed using an ALV CGE laser goniometer consisting of a 22 mW He-Ne linear polarized laser operating at a wavelength (λ = 632. 8 nm), an ALV 6010 correlator, and a pair of avalanche photodiodes operating in the pseudo cross-correlation mode. The samples were loaded into 10 mm diameter glass cells and maintained at 25 ± 1 °C. The data were collected using the ALV Correlator Control software and the counting time was 30 s. The measured intensity correlation functions g 2 (t ) were analysed using the algorithm REPES (incorporated in the GENDIST program)  43  resulting in the distributions of relaxation times shown in equal area representation as τA(τ). The mean relaxation time or relaxation frequency (Γ = τ -1 ) is related to the diffusion coefficient (D) of the nanoparticles as: D ¼ Γ q 2 where q ¼ 4πn sin θ 2 λ is the scattering vector, n is the refractive index of the solvent and θ is the scattering angle.
The solvent scattering was measured before and after the sample scattering to control for possible sample holder contamination. Eight consecutive frames comprising the measurement of the solvent, sample, and solvent were performed. No measurable radiation damage was detected by the comparison of eight successive time frames with 15 s exposures. The final scattering curve was obtained using the PRIMUS program by averaging the scattering data collected from the different frames. The automatic sample changer for sample volume 15 µL and filling cycle of 20 s was used.
Acknowledgements This research was supported by the Norwegian Financial Mechanism 2009-2014 under Project contract no  7F14009. C. R. -E. acknowledges the  Grant Agency of the Czech Republic (GACR)  under contract no. 15-09368Y  and the project " BIOCEV -Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University " ( CZ. 1. 05/1. 1. 00/02. 0109 ),from the  European Regional Development Fund. M. D. acknowledges  BIMF (Bayreuth Institute of Macromolecular Research)  and  BZKG (Bayreuth Center for Colloids and Interfaces)  for financial support. F. N. acknowledges support through the  CNRS  project  PICS  no. 06130.
These calculations were performed with the program package ADF. 2013  [87]. The bonding situation of the donor-acceptor bonds was investigated by an energy decomposition analysis (EDA) which was developed by Morokuma  [88]  and by Ziegler and Rauk  [89, 90]. The bonding analysis focuses on the instantaneous interaction energy ∆E int of a bond A-B between two fragments A and B in the particular electronic reference state and in the frozen geometry AB. This energy is divided into three main components (Equation  1 ). (1) The term ∆E elstat corresponds to the classical electrostatic interaction between the unperturbed charge distributions of the prepared atoms (or fragments) and it is usually attractive. The Pauli repulsion ∆E Pauli is the energy change associated with the transformation from the superposition of the unperturbed wave functions of the isolated fragments to the wave function Ψ 0 = NÂ[Ψ A Ψ B ] , which properly obeys the Pauli principle through explicit antisymmetrization (Â operator) and renormalization (N = constant) of the product wave function.
Grazing incidence small angle X-ray scattering (GISAXS) experiments were conducted using a Rigaku Smartlab thin film diffractometer with a 9 kW Cu-K a source, parallel line beam optics, in-plane arm and a DTex250 1D detector. The incident beam was a 0. 1 Â 5 mm line fixed at 0. 251 incidence angle, and data were collected from 1-101 2y in in-plane and out-of-plane modes. For in-plane scans 0. 51 Soller slits were used on the incident side and a 0. 2281 in-plane analyser on the detector side. Scanning electron microscopy (SEM) used a Jeol JSM-6500F or a Zeiss Supra 55-VP FEGSEM microscope operating at 10-20 kV. Energy dispersive X-ray analyses (EDX) were carried out with a Thermofisher Ultradry detector with NS7 analysis platform on a Philips XL30-ESEM. Transmission electron microscopy (TEM) was conducted in a JEOL 2100 LaB 6 instrument operating at 200 kV and an aberration corrected JEOL ARM200F operating at 200 kV.
Acknowledgements The authors thank  EPSRC  for funding under the  Supercritical Fluids Electrodeposition project  ( SCFED ,  EP/I033394/1 ) and for funding the Smartlab diffractometer ( EP/K00509X/1  and  EP/ K009877/1 ). Mahboba Hasan  is thanked for collecting the EDX data and  Veronika Urbanova  for assisting with initial EASA depositions.
Acknowledgments We thank the  Ministère de l'Education Nationale, de la Recherche et de la Technologie , the  CNRS , the  ANR  ( 10-BLAN-724-1-NCPCHEM  and  12-BS07-0004-METALHEL-01 ) and the  LIA Rennes-Durham  for financial support. J. A. acknowledges the  UB Center for Computational Research  and thanks the  National Science Foundation  ( CHE 1265833 ) for financial support. M. S. thanks the  Foundation for Polish Science Homing Plus program  co-financed by the  European Regional Development Fund  and the  Ministry of Science and Higher Education in Poland scholarship. G. M. thanks  NIH MBRS  ( 1 SC3 GM089589-05  and  3 S06 GM008192-27S1 ) and the  Henry Dreyfus Teacher-Scholar Award  for financial support.
A. Experimental methods Magnetization M(H) and specific heat C(H) measurements have been performed in house by means of a cryomagnetic system with  3  He insert that allows to reach temperatures as low as 0. 3 K and a superconducting coil operating up to µ 0 H = 7 T. All measurements have been done on Cr 8 Zn single crystals. Magnetization was measured by Hall probes made of 2DEG semiconducting heterojunctions. 23 We have collected specific heat data in a commercial calorimeter, using a thermal relaxation method under quasi-adiabatic conditions. The single-crystal sample of Cr 8 Zn was thermalized by Apiezon N grease, whose contribution was subtracted by means of a phenomenological expression. High field torque and heat capacity measurements have been performed at LNCMI laboratory in Grenoble (F).
ACKNOWLEDGMENTS This work was financially supported by the Italian FIRB Project No. RBFR12RPD1 of the Italian MIUR "New Challenges in Molecular Nanomagnetism: From Spin Dynamics to Quantum-Information Processing. " Very useful discussions with P. Santini, G. Amoretti, G. Allodi, and R. De Renzi are gratefully acknowledged. L. Bordonali and M. Mariani are acknowledged for help in some experimental measurements.
A. 0. 45. Quantification analysis was performed with the NIS-Elements software. The average cell migration speed was obtained for a minimum of hundred cells in at least 3 sets of experiments for each condition. Actual numbers of analyzed cells are designated in Table  1  as degrees of freedom (DF). Unpaired two-tailed Student's t test was used for the statistical evaluation of differences between control and treated cells. Probability (p) values are also shown.
Acknowledgements We are very grateful  L. Alvarez-Montes  and to  J. Díaz-Gómez  for their help and to the  Nikon A1R Laser Microscopy Unit of the IDIVAL Institute. We also thank  Dr. Baylo  and  Dr. Toporski  of the  WITec Company  for their help with the confocal Raman imaging. This work has been supported by the  Spanish ISCIII-MINECO  under Projects ref. PI13/01074 ,  AES 2013 ;  MAT2012-38664-C02-01 ;  MALTA Consolider-Ingenio ref. CSD2007-00045 ,  PI10/02002 ,  AES 2010 , and the  Spanish ISCIII  programs RTICC refs. RD06/0020/0074  and  RD12/0036/0022. We especially thank  Fundación Eugenio Rodríguez Pascual  ("ayudas de investigación" 2014, ref. 02-H048-64003 ) to MLF. Received: ((will be filled in by the editorial staff)) Revised: ((will be filled in by the editorial staff)) Published online: ((will be filled in by the editorial staff)).
Experimental principles and interpretation of neutron reflection data Neutron reflectometry is widely used to study adsorption on flat solid substrates and at air-liquid interfaces  [23, 24]. The measured signal depends on the variation of the refractive index, n, in the direction perpendicular to the surface. The experiment involves determination of the reflectivity of an interface as a function of the wavelength or angle. The data allows quantitative, structural, and compositional information about the adsorbed material to be obtained at molecular length scales. In specular neutron reflection, the ratio of the intensity of the reflected beam to that of the incident beam is measured as a function of the momentum transfer, Q normal to the reflecting surface. The specular condition occurs when the angle of the incident beam is equal to the angle of the reflected beam and Q is given by Q ¼ ð4p=kÞ sin h ð1Þ where k is the incident neutron wavelength and h is the angle of incidence.
Characterization of the substrate Experiments were carried out to check the substrate cleanliness and to characterize the interface before further studies of adsorption were made of the protein and protein-surfactant mixtures. To characterize the sapphire surface, reflectivity profiles were first measured in pure water with different isotopic contrasts 50% D 2 O, H 2 O and D 2 O in this order, a typical data set is shown in Fig. 1. A model was found in a combined fit of the three contrasts for reflection data in the range of Q from 0. 008 to 0. 15 Å À1 for 50% D 2 O and H 2 O contrasts and only up to Q equal to 0. 032 Å À1 for D 2 O due to the low signal seen at larger Q. A summary of the densities and scattering lengths of the materials is provided in Table  1. The sapphire substrate was found to have a surface layer with about 15% reduced density over a thickness 15 ± 2 Å with a solvent fraction of about 20% in the outer 5 Å of this layer.
Crystallography Single crystals were mounted on the top of a thin glass fiber. Data were collected either on a Stoe-IPDS at room temperature or on a Nonius KappaCCD diffractometer at 150 K, both equipped with graphite-monochromated Mo Kα radiation (λ = 0. 71073 Å). Structures were solved by direct methods (SHELXS-97) and refined (SHELXL-97)  [48]  by full-matrix least-squares methods, as implemented in the WinGX software package  [49]. Absorption corrections were applied. Hydrogen atoms were introduced at calculated positions (riding model), included in structure factor calculations, and not refined. Crystallographic data are summarized in Table  6.
Computational details DFT  [50, 51]  calculations were performed with the hybrid Becke-3 parameter exchange functional  [52] [53] [54]  and the Lee-Yang-Parr nonlocal correlation functional  [55]  (B3LYP) implemented in the Gaussian 03 (revision D. 02) program suite  [56] , using the 6-31G(d) basis set and a quadratically convergent self-consistent field procedure with the default convergence criteria implemented in the program. The X-ray diffraction data of model compounds were used as a starting point for initial geometry optimization calculations. Final geometries are given in Supporting Information File 1. Representation of frontier orbitals included in Figure  2  were generated with Molekel 4. 3  [57]. TD-DFT calculations were performed at the B3LYP/6-311G** level of theory, on the previously converged geometries.
EMITTER TUNABILITY AND PULSE ENERGY PERFORMANCES The pulse energies, spatial beam-quality and spectral performances are measured at the output of the amplification stages. First, we investigate the tuning capability of the emitter. Figure  2  presents the spectral coverage of this optical source, by temperature tuning, for two different quasi-phase matching (QPM) grating periods of the NesCOPO type II PPLN ω s ω i M2 M1 M3 ω p crystal. We also display the absorption lines of different gas species, calculated using Hitran 2012 database, to show how this emitter can target i) different species of interest, ii) different absorption lines for each species. Indeed, with the QPM period of 14. 369 µm, the CO 2 (2. 051 µm), and H 2 O (2. 056 µm) absorption lines can be targeted, with a temperature variation of only 6 °C.
8 ), with low dissociation rates (k 5 , k 6 ). Structural snapshots of these very subtle and local conformational transitions have been obtained by X-ray crystallography for rational PDF1B mutants, allowing the sequence of events triggered by ligand binding to be reconstructed (see Movies S1 and S2 in ref 42). First, actinonin binds to the enzyme by aligning its long aliphatic chain in the hydrophobic S1′ pocket of PDF1B, triggering a conformation change as key sidechains adjust and reshape the pocket. This local rearrangement is followed by a global closure of the enzyme and the formation of a crucial hydrogen bond. The present paper investigates the putative benefits of native MS and IM-MS in understanding the response of PDFs to ligand binding. Indeed, although enzymatic data suggest that other classes of PDFs bind ligands through induced-fit, the transient nature of the encounter complex means that PDF1B is the only system for which this mechanism has been evidenced at the atomic-scale.
However, an overall comparison of the X-ray structures of PDF1B bound to either actinonin (PDB code: 3M6P) or 6b (PDB: 3O3J) highlight other subtle conformational changes away from the active site. The structures of apoPDF1B and PDF1B : actinonin differ mainly in the vicinity of the active site (Fig. S5  in the ESI, † pairwise alpha carbon deviations of up to 1. 2 Å), but also along the adjacent secondary structure elements ( pairwise deviations ranging from 0. 6 to 1 Å). The latter reflects the slight global extension of PDF1B when actinonin binds. This example illustrates the complementarity of high-and low-resolution biophysical techniques-in this case X-ray diffraction and IM-MS-to decipher global and local conformational changes. In conclusion, this combination of native and IM-MS offers direct evidence that the inhibition of PDF1B occurs through STB mediated by an induced-fit process.
Conformational studies of crystallographic structures The crystallographic structures of apoPDF1B (PDB code: 3PN2), PDF1B : actinonin (3M6P) and PDF1B : 6b (3O3J) were visualized using Pymol (DeLano Scientific, San Carlos, CA, USA). The alpha carbons of the apoPDF1B and PDF1B : actinonin structures were aligned using the software Visual Molecular Dynamics. 63 The theoretical CCS values reported above were obtained from the same three structures using Mobcal,  64, 65  ignoring solvent and metal atoms and altering the starting coordinates using random seed numbers. The uncertainties quoted correspond to the standard deviations of six Mobcal replicates.
Acknowledgements The authors would like to thank  Julien Marcoux  for fruitful discussions and  Matteo Degiacomi  for the sequence alignments. This work was supported by the  French National Research Agency  ( ANR-10-BLANC-1510 ), the  Centre National de la Recherche Scientifique , the  University of Strasbourg (UdS) , the  "Fondation pour la Recherche Médicale" , the  Alsace Region , and the  GIS IBiSA  (funding for a Synapt G2 HDMS mass spectrometer). S. P. -B. was supported by a studentship from the  CNRS  and NovAliX; J. S. acknowledges the  Institut de Recherches Servier  for supporting his doctoral fellowship.
Molecular Modeling of the h␤4GalT7 Active Site in the Presence of 4-MUX and UDP-Gal-The crystal structure of h␤4GalT7 bound to UDP and to the manganese ion (PDB code 4IRQ) was used as template  (34). The crystal structure of d␤4GalT7 (PDB code 4M4K), an inactive mutant (D211N) of d␤4GalT7 in complex with UDP-Gal, and xylobiose was superposed to the human enzyme structure, which was straightfor-ward considering their strong sequence similarity (58% overall identity). Due to crystallization conditions, a Tris molecule is bound within the active site of the h␤4GalT7. When retrieved, it frees space within the cavity that can thus accommodate the Gal moiety. The coordinates of the Gal molecule from the d␤4GalT7 complex were merged to the UDP moiety of h␤4GalT7. This did not generate any steric clash within the active site.
The resulting complex was then prepared using the Protein Preparation Wizard tool of the Schrödinger Suite (Schrödinger LLC, New York), with default settings  (36). All water molecules were retrieved, except the one that coordinates the manganese ion. The hydrogen atoms were added to the protein and the ligand, ascribing a pH of 7. 0. The histidine residues were treated as neutral. The selection of histidine enantiomers and the orientation of the asparagine and glutamine side chains were performed so as to maximize the hydrogen bond network. The partial atomic charges derived from the OPLS-2005 force field (37) were assigned to all ligand and protein atoms. Finally, an all-atom energy minimization with a 0. 3 Å heavy-atom root mean square deviation criteria for termination was performed using the Impref module of Impact and OPLS-2005  (38).
EXPERIMENTAL PROCEDURES Expression Vector Construction-The h␤4GalT7 sequence (GenBank nucleotide sequence accession number NM_007255) was cloned by PCR amplification from a placenta cDNA library (Clontech), as previously described  (41). For bacterial expression, a truncated form of h␤4GalT7 was expressed as a fusion protein with glutathione S-transferase (GST). The sequence lacking the codons of the first 60 N-terminal amino acids was amplified from the full-length cDNA and subcloned into NcoI and NotI sites of pET-41a(ϩ) to produce plasmid pET-␤4GalT7  (31). For the heterologous expression of h␤4GalT7 in mammalian cell lines, the full-length cDNA sequence was modified by PCR at the 5Ј end to include a KpnI site and a Kozak consensus sequence, and at the 3Ј end to include a sequence encoding a Myc tag and an XbaI site to be then subcloned into the KpnI-XbaI sites of the eukaryotic expression vector pcDNA3.