dataesr/scientific-paragraphs-categorization huggingface dataset:
d XAS spectrum simulation Two types of simulation approaches are used to describe the final state, depending on the orbitals involved in the X-ray absorption process: -When the states probed are d orbitals, a multielectronic approach based on multiplet theory must be used. Iron L2,3edges in ferrocyanide complexes and in analogous Prussian blue 3d compounds  39, 40  have been simulated in this manner. -When the states probed are 2p orbitals, multielectronic effects can be ignored and a monoelectronic approach is used. For the cyano ligand, hybridized 2p orbitals are diffuse and very sensitive to geometry (distances, symmetry) and charge transfer (LMCT or a b MLCT). To simulate the C and N K-edges, partial atomic charges are needed and preliminary DFT calculations are therefore essential. We selected the FDMNES code for K-edge simulations.
This code is described in the literature  41  and the methodology has already been applied to actinide compounds  31, 37, 38. The FDMNES program may be used in two different modes for the calculation of potentials: the Green formalism with a muffin-tin approximation and the Finite Difference Method (FDM). The FDM method avoids spherical muffin-tin shaped atomic potentials. A schematic description of the methodology selected is given in SI. 2. To validate this monoelectronic approach, the carbon K-edge spectrum of K4[Fe(CN)6] was used as a reference to test the different procedures. The first attempt, using muffin-tin potentials (SI. 3) did not give satisfactory agreement with the experimental data. Although more time-consuming, the FDM was therefore employed. Moreover, simulations were systematically performed using 3 different electronic configurations: (i) neutral charges, (ii) Mulliken electronic populations from the DFT, and (iii) NPA electronic population also derived from DFT (Table  2 ).
Acknowledgements This work was supported by  CEA/DEN  under the  RBPCH Program of Basic Research in Chemistry and by the European IRSES program  under the  HEXANE  project (number  2 30807 ). Work at the  Advanced Light Source  is supported by the Director,  Office of Science, Office of Basic Energy Sciences ; the  Molecular Environmental Sciences Beamline 11. 0. 2 is supported by the Director,  Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences , and  Biosciences Condensed Phase and Interfacial Molecular Sciences program ; and DKS is supported by the Director,  Office of Science, Office of Basic Energy Sciences Division of Chemical Sciences, Geosciences , and  Biosciences Heavy Element Chemistry Program ; all of the  U. S. Department of Energy at Lawrence Berkeley National Laboratory  under Contract No.
Acknowledgements We thank the  CNRS , the  University of Bordeaux  and the  Agence Nationale de la Recherche  for financial support. We are also grateful to  Prof. P. Renaud  ( University of Bern ),  Prof. I. Ryu  and  Prof. T. Fukuyama  ( University of Osaka Prefecture ) and  Prof. M. Heinrich  ( University of Erlangen ) for fruit-.
The solid was separated by centrifugation and washed with hot water. It was characterized by X-ray diffraction, infrared spectroscopy and 31 P Magic Angle Solid-state Nuclear Magnetic Resonance (MAS NMR) spectroscopy. Unfortunately, the 31 P MAS NMR spectrum showed the presence of an additional broad signal proving the existence of other species. It is therefore difficult to draw conclusions about whether the polyoxometalate is entirely encapsulated within the zeolite or not, especially as the cesium salt of PMo 12 is insoluble and could be located on the external surface. In addition, X-ray data showed that, at high loadings, the crystallinity of the zeolite was lost, as expected from the works of Mukai et al. who observed the destruction of the framework in the presence of the highly acidic PMo 12.
The polyoxometalate was as a sodium salt (acidic or not, no data were given about this point) and it was deposited on Hβ zeolite by impregnation. Various loadings between 10 and 40 wt % were prepared. The impregnated materials were treated with 10% 0. 1 M HCl and then washed with distilled water. As SiW11 is not stable in these conditions, this treatment has probably transformed part of it into SiW12 and/or has replaced some sodium ions by protons. An interesting point is the presence of mesopores in this zeolite (diameter 2. 48 nm), whose diameter decreases after adsorption of SiW11 (to 1. 71 nm) proving that the polyoxometalate is located inside them. The acidity was determined by n-butylamine titration and the solids were used in the esterification of oleic acid by methanol and the transesterification of soybean oil.
The polyoxometalate was as a sodium salt (acidic or not, no data were given about this point) and it was deposited on Hβ zeolite by impregnation. Various loadings between 10 and 40 wt % were prepared. The impregnated materials were treated with 10% 0. 1 M HCl and then washed with distilled water. As SiW 11 is not stable in these conditions, this treatment has probably transformed part of it into SiW 12 and/or has replaced some sodium ions by protons. An interesting point is the presence of mesopores in this zeolite (diameter 2. 48 nm), whose diameter decreases after adsorption of SiW 11 (to 1. 71 nm) proving that the polyoxometalate is located inside them. The acidity was determined by n-butylamine titration and the solids were used in the esterification of oleic acid by methanol and the transesterification of soybean oil.
03 % and was not significant Fig. 4  PET profiles during 13 C-MRSI ON and OFF. PET line plots of voxels between the black lines of the inserts, through a the largest sphere (single slice) and b background region (10 slices). Conditions of simultaneous 13 C-MRSI ON and OFF are shown as red and blue colors, respectively Fig. 5  PET activity for all NEMA phantom measurements. Measured PET activity in the largest sphere (blue points) and in a background region of the phantom (black points). Error bars are standard deviations on estimates. For odd PET scan numbers, simultaneous 13 C-MRSI was performed, as indicated by the yellow bars (p = 0. 21, CI (-5. 51 to 1. 38 %)) for [1- 13 C]urea and was -2. 28 % and not significant (p = 0. 15, CI (-5. 61 to 0. 98 %)) for [1-13 C]acetate. Further examination of the data revealed that neither noise level nor integrated peak areas were significantly different between PET gantry OFF and ON conditions.
7 and g eff,t ¼ 0. 85 (see ESI †). That this is an impurity signal is conrmed by the fact that these g eff values would give a magnetic moment of ca. 0. 5 cm 3 K mol À1 if they derived from the bulk species. Both 2 and 3 are EPR silent, as expected. Although the magnetic and EPR data for 1 are consistent with only the presence of magnetic impurities, they do not, because of the diamagnetic correction being large compared to the weak paramagnetism, rule out excited state mixing, i. e. a multi-congurational ground state, due to the shallow positive gradient that could be attributed to temperature independent paramagnetism. In order to conclusively show that 1 is cerium(IV), and therefore that comparisons to 2 and 3 are valid, we recorded the XANES spectrum of 1.
Computational details Unrestricted and restricted geometry optimisations were performed as appropriate for full models of 1, 2, and 3 and the components of the exchange reactions using coordinates derived from their X-ray crystal structures. No constraints were imposed on the structures during the geometry optimisations. The calculations were performed using the Amsterdam Density Functional (ADF) suite version 2010. 01. 46, 47 The DFT geometry optimisations employed Slater type orbital (STO) triple-z-plus polarisation all-electron basis sets (from the ZORA/TZP database of the ADF suite). Scalar relativistic approaches were used within the ZORA Hamiltonian for the inclusion of relativistic effects and the local density approximation (LDA) with the correlation potential due to Vosko et al. 48 was used in all of the calculations.
Acknowledgments: This work was partly supported by the  Programme Samuel-De-Champlain  from the  Commission Permanente de Coopération Franco-Québécoise (CPCFQ) , by the  LabEx de Chimie des Architectures Moléculaires Multifonctionnelles et des Matériaux  (CHARM 3 AT), by the  ANR  (project  ANR Blanc Cathymetoxy  ( ANR-11-BS07-024 ) and by a  Natural Sciences and Engineering Research Council of Canada (NSERC)   Discovery Grant   RGPIN 2016-05557  (to N. D. ). D. G. held an  NSERC   Alexander Graham Bell Canada Graduate Scholarship. Author Contributions:  Christian Herrero  and  Rémy Ricoux  conceived and designed the experiments;  Donald Gagné ,  Fabien Hammerer , and  Nhung Nguyen-Thi  performed the experiments and contributed reagents/materials/analysis tools,  Christian Herrero  and  Rémy Ricoux  analyzed the data;  Jean-Pierre Mahy ,  Frédéric Banse ,  Rémy Ricoux , and  Nicolas Doucet  wrote the paper.
Acknowledgements This work was supported by  Grants-in-Aid for Scientic Research  ( Innovative Areas "Element Block," Area 2401 ,  KAKENHI 25102527  and  15H00746 ) from  MEXT  and the  Japan Society for the Promotion of Science (JSPS). A. O. acknowledges support from the  Japan Association of Chemical Innovation (JACI). This program was supported by the  Strategic International Collaborative Research Program (SICORP) ,  JST. This work was also supported by the  JST-ANR program TMOL "Molecular Technology " project  MECANO  ( ANR-14-JTIC-0002-01 ).
This is consistent with POM observations mentioned earlier, where the finger-print texture characteristic of the N* phase develops only after many hours in these highly viscous samples. As a result, orientation of the micelles is preserved in all the three phases during SAXS data collection from freshly prepared samples. This opportune feature makes it possible to probe BO in the plane normal to n even in the chiral system. Diffraction patterns of the N* and chiral 2D-H phases in the parallel geometry (Fig. 4(d, f )) are also identical to those of the achiral system (Fig. 2(d, f )), indicating the absence and presence of long-range BO in these two phases, respectively, as expected. However, SAXS pattern of the chiral N + 6 phase in the parallel geometry is different (Fig. 4(e) ), with the appearance of a ring in the q ⊥ plane, instead of the six spots seen in the achiral system (Fig.
They were then placed inside the temperature-controlled chamber (heating or cooling rate 1 °C/min) and observed between crossed polarizers. The temperature of each sample was varied from 25 to 60 °C. SAXS experiments were carried out using a Hecus SAXS-Eye system, in conjunction with either a CCD detector or a position sensitive detector. Details about the experimental set up and data acquisition have been described quite elaborately elsewhere  32. The instrumental resolution was 0. 06 nm -1. Temperature stability was better than 0. 1 °C. Samples for SAXS studies were taken in sealed glass capillaries. All the samples were initially aligned in the nematic phase and the alignment was found to be retained on heating to the higher temperature phases. Orientation of the average micellar axis, i.
MALDI TOF Mass Spectrometry-Mass spectrometric analysis was performed using a MALDI UltraFlex II time-of-flight (TOF) instrument equipped with a Smartbeam laser (355 nm emission wavelength) having a maximum repetition rate of 200 Hz and controlled by a FlexControl 3. 0 (Build 158) software from Bruker Daltonics, GmbH (Bremen, Germany). The full MS spectra were acquired in positive linear mode with delayed extraction within the 3000 -20,000 m/z range by accumulating 5000 laser shots at a repetition rate of 200 Hz. The laser energy was fixed to be just slightly above the threshold energy for ion detection. Medium deflection of the low mass ions below m/z 3000 was used to enhance the detection of proteins. The MALDI target was always calibrated prior to analysis using Protein Calibration Standard 1 (Bruker Daltonics, GmbH), which contains a mixture of six proteins covering a mass range of m/z 5500 -17,000.
Mass values expressed in the text correspond to the centroid of the m/z values of the [M ϩ H] ϩ ions. The MALDI-TOF raw data of the H/D exchanges have been deposited at the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD004630. Protein Identification by Top-Down Microflow LC-MS-Proteins were extracted from a consecutive 12-m rat brain tissue section. One microliter of the protein extract was suspended in either 10 or 30 l 5:95 ACN/0. 1% FA in H 2 O and 4 l of these samples were injected in a 200 m ϫ 50 cm ProSwift RP-4H monolithic capillary column (Thermo Fisher Scientific, Bremen, Germany). Proteins were eluted using a linear gradient from 3% to 40% ACN for 60 min, then to 95% ACN for 10 min, followed by a wash out until 90 min, at a flow rate of 1.
The exclusion list size was set to 500 and the exclusion duration to 180 s. ϩ1, ϩ2 and ϩ3 charge states were rejected. For top-down analysis, the data were analyzed with ProSightPC 3. 0 (Thermo Fisher Scientific) and Proteome Discoverer 2. 1 (Thermo Fisher Scientific) utilizing the ProSightPD 1. 0 node. Spectra were then searched using a three-tiered search tree. The first search was an Absolute Mass search with MS1 tolerance of 100 Da, MS2 tolerance of 10 ppm, against a Rattus norvegicus UniProt database containing 35,953 canonical and isoform sequences accessed on July 8, 2016, or the ProSightPD 1. 0 database available at their website (ftp://prosightpc. northwestern. edu/). The second search was a ProSight Biomarker search with MS1 tolerance of 10 ppm, MS2 tolerance of 10 ppm, against the same databases.
Finally, a second Absolute Mass search was performed with MS1 tolerance of 1000 Da, MS2 tolerance of 10 ppm, using Delta M mode, against the same databases. Protein assignments can be found in supplemental Data S1. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the same data set identifier (PXD004630). The *. xml Search files for 20160719_TopDown2 correspond to searches done using the UniProt database, whereas those for 20160719_ topDown correspond to searches performed using the ProSightPD database.
3A, top ). Likewise, the full MS spectrum acquired from the tissue section incubated in NH 4 OAc buffer also showed abundant signals (Fig. 3A , bottom), even when no lipid removal steps were incorporated into the protocol to enhance the detection of intact proteins  (22). More importantly, several of the signals from the full MS spectrum of the extracted proteins in solution can be matched with those observed from the direct tissue analysis, as shown in Fig. 3   In order to identify the proteins common to the tissue extracts and in situ on the tissue, proteins were extracted from a consecutive tissue section of same thickness and submitted to Top-Down analysis. Extracted intact proteins were analyzed in LC-MS by separation on a monolithic column and fragmented using the HCD cell of the LTQ-orbitrap instrument before identification by database interrogation.
Protein assignments are given in supplemental Data S1. An example of the monitoring of deuterium uptake in both conditions is shown in Fig. 3B  for Ubiquitin (m/z 8563). Because of experimental limitations such as the time interval between the analyses of two data points, the first data point was monitored only after 10 min of exchange. Nonetheless, results indicate that the deuterium uptake can still be monitored using this approach and H/D exchange could monitored both in solution and from tissue sections up to 43 h. Fig. 4  compares the deuterium uptake of several proteins in solution and on tissue. In the four examples plotted, it can be observed that overall the maximum amount of deuterium uptake for proteins in solution is much higher than when observed on tissue. If the tissue environment does not affect the conformation and in-teraction of proteins, we should expect that the deuterium uptake behavior would be similar.
6A  and 6C, bottom). In this case, the protein microenvironment becomes the major factor in evaluating deuterium uptake evolution and consequently the protein structure. It should be pointed out that with this approach, only the deuterium uptake of abundant proteins was monitored as only they provide traceable signals discernible in MALDI. To summarize, the study showed for the first time the possibility to perform H/D exchange directly at the tissue level. The current evidence thus provides an alternative way to look at protein structure as it occurs in response to variations in its microenvironment. The data showed differences in H/D exchange behavior for the same proteins in solution and on tissue and should be expected to provide a more approximate interpretation of protein structure as it occurs in situ.
We also observed differences for the same proteins in different loca-tions of the tissue. The variations found are not only lying in the global amount of deuterium uptake across the different proteins, but also in the rates observed, which can be interpreted as both a change in the interacting partner environment as well as conformational change. In perspective, the next step will be to carry out local exchange analysis to determine the exact regions in the proteins affected by these interactions. To do so we will have to separate the components using short gradients and initially generate a database of tandem MS spectra from the undeuterated sample and use this to identify the proteins. This would be achieved by aligning the chromatographic traces and matching the undeuterated protein with the deuterated one using the retention times of their peptides.
XRD acquisition X-ray powder diffraction data for all mixed oxalates were obtained with a BRUKER D8 Advanced diffractometer (LynxEye detector) using Cu-Kα radiation (λ = 1. 5418 Å). Each powder pattern was recorded within an angular range of 5°-60°in 2θ, with steps of 0. 02°and a counting time of 0. 5 s per step. The stripping of the Kα2 radiation according to the Rachinger method as well as the baseline and angle shift corrections was done using empirical calculations and DIFFRACplus EVA software. 27 ilicon was added to all samples as an internal standard to calibrate the angular positions of the observed XRD lines. Actinide oxalates were mixed with an epoxy resin to prevent contamination spreading and their diffraction patterns were compared with the recently built M + -U(IV)-Ln(III) oxalate structures database  20, [24] [25] [26]  to detect isomorphic similitude.
Fluorescence spectra were corrected for dead time using a measured relationship between incoming count rate (ICR) and selected channel analyzer (SCA) readings for each channel using the SixPack software package. 30 For plutonium, the Pu-L II edge (22266 eV) was preferred for EXAFS analysis because, as we previously observed,  31  EXAFS oscillations collected at Pu-L III which were distorted due to the U-L III EXAFS signal. Nevertheless, the XANES data collected at Pu-L III could be used as both the white line intensity and the edge jump are much stronger than U-L III EXAFS oscillations. Energy calibrations were performed using a Y foil (17 038 eV) for data at the U-L III edge, a Zr (foil 17 998. 0 eV) for data at the Pu and Am L III edges or a Mo foil (20 000. 0 eV) for data at the Pu-L II edge.
The metallic foils were positioned after the second ionization chamber. The E 0 values were taken as the first inflection point using the first zero-crossing value of the second derivative. The first zero-crossing of the first derivative was used to determine the position of the white line (WL) maximum. A minimum of two spectra were collected per edge and per sample. For each spectrum, XANES spectra of the reference foil detailed previously was systematically collected simultaneously. The acquisition conditions were typically 0. 8 eV steps for XANES (U-L III , Pu-L III and Am-L III ) and 0. 05 Å -1 steps for EXAFS (U-L III , Pu-L II and Am-L III ). Before averaging scans, each scan was aligned using the XANES spectra collected on the reference foils. The ATHENA software  32  was used for XANES spectra normalization using linear functions for both pre-and post-edge regions.
To determine the oxidation states of U, Pu and Am cations, XANES spectra were compared to data collected on several reference compounds at the same beam line (BM20) using the same experimental set-up. The reference compounds were U +IV O 2 for uranium, Am +IV O 2 for americium,  33  Pu +IV O 2 and Pu +III F 3 for plutonium  31  and the data were collected at U-L III , Am-L III and Pu-L III , respectively. The ATHENA software  32  was used for extracting EXAFS oscillations. The experimental EXAFS spectra collected on the (U,Pu) and (U,Am) mixed oxalate samples were Fourier-transformed using a Hanning window over the full k space range available for each edge: 2. 6-13. 5 Å -1 for U and Am L III ; 2. 6-12. 8 Å -1 for Pu-L II. Curve fitting of the EXAFS spectra was performed simultaneously on k 1 , k 2 and k 3 -weighted data in an R-space between 1.
This result is in very good agreement with the structure including five oxalate ions (C 2 O 4 ) around U +IV , Pu +III and Am +III cations in the mixed (U 0. 9 Pu 0. 1 ) and (U 0. 9 Am 0. 1 ) oxalates. The same values of the Debye-Waller factors around both U and Am in the (U,Am) sample compared to values observed in (U,Pu) sample were measured. As the data were collected at 15 K, these similar σ 2 values illustrate that a similar structural disorder is observed in the two mixed oxalates. For each compound, the only significant differences observed between the two actinides are systematically shorter distances around uranium than around Pu or Am. These differences could be explained by the difference in ionic radii between U +IV and trivalent Pu and Am, but these values are unknown for such cations that are ten-coordinated.
w. ), AA(t) is the antioxidant activity (lM TEAC), K 1 is Peleg's maximal rate of extraction (at the studied conditions) and K 2 is Peleg's maximal extraction yield (at the studied conditions). All K i coefficients (K 1(TP) , K 2(TP) , K 1(AA) , K 2(AA) ) were expressed as functions of the three studied parameters, namely temperature (X 1 ), ethanol content in the solvent (X 2 ) and ultrasound power (X 3 ) and all of their interactions: K i ¼ a 0 þ a 1 X 1 þ a 2 X 2 þ a 3 X 3 þ a 11 X 2 1 þ a 22 X 2 2 þ a 33 X 2 3 þ a 12 X 1 X 2 þ a 13 X 1 X 3 þ a 23 X 2 X 3 þ a 123 X 1 X 2 X 3 ð3Þ Experimental data obtained in these 17 experiments were used to build the model. The objective was to determine optimal values of regression coefficients (a 0 , a 1 , a 2 , a 3 , a 11 , a 22 , a 33 , a 12 , a 13 , a 23 and a 123 ) for each coefficient K i , so as to minimize the deviation between experimental and model kinetic curves.
A high-resolution synchrotron-based X-ray tomographic image was obtained from the Diamond-Manchester branchline I13-2 at Diamond Light Source. 19 The samples were kept at 300 K on the beamline using an in-house environmental stage. 20 A polychromatic filtered parallel-beam setup was used with a 0. 81 μm effective pixel size and ∼2 μm spatial resolution. Over the 180°rotation, 3600 projections were collected at 0. 05 s exposure time and tomographically reconstructed into a 3D volume using software developed at Diamond Light Source. 21 Visualization package Avizo was used to produce the 3D images and quantify shrinkage. The gel samples for the μ-CT measurements were prepared from AlCl mg/mL) (the supporting note is in the Supporting Information). The mixtures were placed at 25 °C for 72 h. Supernatants of respective mixtures were collected through a membrane filter (0.