dataesr/scientific-paragraphs-categorization huggingface dataset:
The sample temperature can be varied between 3. 0 and 300 K. X-Ray crystallography: Data were measured on Stoe IPDS II (1) or IPDS I (2) image plate diffractometers using graphitemonochromated Mo Kα radiation, and were corrected for polarisation and absorption. Structure solution (direct methods) and full-matrix least-squares refinement against F 2 (all data) was carried out by using the SHELXTL software package  [27]. All ordered non-H atoms were refined anisotropically; disordered atoms were refined with partial occupancy and geometrical restraints, either anisotropically with rigid-bond restraints or isotropically. Organic H atoms were placed in calculated positions; the positions of H atoms bonded to O were refined with O-H restrained to 0. 92(4) Å. Crystal data for 1: C 68 H 133 Dy 2 Fe 4 N 13 O 22 , 2033.
5 Å. The size distributions were determined through a manual analysis of 200 NPs of enlarged micrographs with the ImageTool software to obtain a statistical size distribution and a mean diameter. All chemical shifts for 1 H and 13 C are relative to Me 4 Si (TMS). 1D and 2D 1 H-1 H correlated spectroscopy (COSY), 1 H- 13 C heteronuclear single quantum coherence (HSQC), and heteronuclear multiple bond correlation (HMBC). NMR experiments in the liquid state were recorded on a Bruker Avance 500 spectrometer equipped with a 5-mm triple resonance inverse Z-gradient probe (TBI 1 H, 31 P, BB). 2D nuclear overhauser effect spectroscopy (NOESY) measurements were done with a mixing time of 100 ms. Diffusion measurements were made using the stimulated echo pulse sequence. The recycle delay was adjusted to 3 s.
The data of the different syntheses of AuNPs obtained by the decomposition of AuCl(THT) in the THF under gas reduction in the presence of alkylamine ligands are summarized in Table  S1  (ESM Table  S1 ). In summary, it is clearly seen that the use of DDA or HDA as stabilizing agent in THF at 70 °C in CO (1 bar) overnight leads to stable and well defined AuNPs with a narrow size distribution (<1. 0 nm). NMR characterization was performed to understand the stabilization of the AuNPs.
Acknowledgment This work was part of a project financially supported by the  Fondation (Sciences et Technologies pour l'Aéronautique et l'Espace ) the acronym " MAISOE" (Microlaboratoires d'Analyses In Situ pour des Observatoires Environnementaux ) and  ANR  ( ANR  project  MOCANANO ). Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.
g. salts). After a first, quick evaluation by MALDI-MS, a sample can be further analysed by ESI-TOF to determine its mass with higher accuracy. Furthermore, MALDI generates ions containing fewer charges than ESI and therefore acquiring and interpreting MALDI data is more straightforward. This allows students working in structural biology to analyse their recombinant proteins just after a brief training. Two key factors influence the quality of the MALDI spectra: the matrix and the technique used for the matrix deposition (e. g. dried droplet 8 and thin layer  [12] [13] [14] [15] [16] 17, 18  ). A single organic matrix [e. g. sinapinic acid (SA) 19-21 or α-cyano-4-hydroxycinnamic acid (α-CHCA)  14, 22, 23  ] is often used for the MS examination of intact proteins and cross-linked protein complexes.
Acknowledgements We thank  Dr. Christophe Masselon  ( iRTV, CEA, Grenoble ) and members of the Viral Infection and Cancer Group at the  IBS , for their critical evaluation of the manuscript and for useful discussions. We are grateful to  Cyril Dian  for the kind gift of the protein Crm1. This scientific work took place in the mass spectrometry facility of Grenoble Instruct Centre (ISBG;  UMS 3518 CNRS-CEA-UJF-EMBL ). It was financially supported by the  French Infrastructure for Integrated Structural Biology Initiative  ( FRISBI ,  ANR-10-INSB-05-02 ),  GRAL  ( ANR-10-LABX-49-01 ) [within the  Grenoble Partnership for Structural Biology ] and by the  French National Centre for Scientific Research (CNRS).
■ ACKNOWLEDGMENTS Funding for this project was provided in part by the Seventh Framework Program (CP-FP 211468-2-EUMET). This work was supported by the CNRS and the Ministere de la Recherche et de la Technologie. M. M. and F. C. thank the Region Bretagne for its financial support (Fonds de Maturation Feder No. 09005612). J. M. P. thanks AstraZeneca (Industrial CASE studentship to D. J. N. ) and the EPSRC Initiative in Physical Organic Chemistry 2 (EP/G013160/1) for funding.
Thus, the structure of the intermediate phase II of Cl 3 C-CCl 3 was studied only by X ray diffraction experiments. Patterns of the condensed ClF 2 C-CF 2 Cl compound were collected at 10, 120, and 155 K using the high resolution D2B instrument at ILL (Grenoble, France). 44 High resolution data from the equatorial detector bank were obtained by using a wavelength of λ = 2. 398 Å in a 2θ range from 20°to 160°with a step size of 0. 05°. Because of the aforemen tioned problems concerning the incomplete II to III transformation, the pattern at 10 K could not be indexed, and thus the structure of phase III remains unknown. Even the collected pattern at 120 K (phase II) showed three Bragg peaks of the high temperature cubic phase I. Nevertheless, because of the high symmetry of phase I the pattern collected at 120 K was indexed once the 2 theta regions containing the Bragg peaks of phase I were excluded.
RESULTS AND DATA ANALYSIS 3. 1. Structure Determination of the Low-Temperature Phases of Cl 3 C-CCl 3. Phase III. Neutron and X ray patterns of the low temperature orthorhombic phase III were indexed according to the Pnma space group reported by Sasada et al. 34  A Rietveld profile refinement  47  by means of the Materials Studio software  48  was conducted by using the atomic coordinates of the molecule in the asymmetric unit given by Sasada and Atoji  34  as starting parameters (see Figure  1 ). A glance to Figure  1  shows that in spite of the efforts to correct the preferred orientation of the sample, some Bragg peaks with high intensity give rise to a relative noticeable difference between calculated and exper imental patterns. The parameters refined in the procedure both for neutron and X ray measurements are gathered in Table  2.
In both CCl 3 -CF 2 Cl and Cl 3 C-CCl 3 cases the C-C bonds lie in the (0k0) plane, the molecules being alternatively tilted with respect to the [00l] direction by an angle of 7. 0°(at 125 K) and 6. 7°(at 5 K) in CCl 3 -CF 2 Cl and 13. 2°in C 2 Cl 6 (at 10 K). Phase II. We have built up a rigid body molecule by means of the software Forcite from Materials Studio package together with the Compass forcefield. The minimization energy process converged to an almost perfect tetrahedral molecular symmetry (C-C = 1. 586 Å; C-C1 = 1. 776 Å; C-C-Cl = 110. 48°; Cl-C-Cl = 108. 45°). These values are very close to those determined by the final energy minimization of the structure of phase III. The potential solutions of the cell parameters and space groups were obtained using X Cell software  49  available in the module Powder Indexing of Materials Studio applied to the X ray powder diffraction at 323 K.
The parameters refined in the procedure are collected in Table  2 , and the coordinates of the atoms of the asymmetric unit are given in Table  3. Because of the disorder we did not undertake a minimization of energy of the structure, so molecular bond length and angles were kept according to the initial molecular minimization. The software Forcite from Materials Studio package and the Compass forcefield were used to build up a rigid body molecule with trans and gauche conformations. The intramolecular angles so obtained by this minimization process for both isomers are very close for both conformations, and thus, due to the intriguing disordered structure which prevents a final minimization process of the characteristic intramolecular distances, we average them according to the number of Cl and F atoms (as far as angles are concerned) to get the initial molecular unit in the structure.
ACKNOWLEDGMENTS This work was supported by the  Spanish Ministry of Science and Innovation  (Grant  FIS2011 24439 ) and the  Catalan Govern ment  (Grant  2009SGR 1251 ). We thank  FRM II  and  ILL  for providing beam time on the high resolution powder diffraction beams SPODI and D2b, respectively, and  C. Cabrillo  for supplying us the experimental setup for in situ gas condensation of ClF 2 C-CF 2 Cl on the D2B sample holder.
pK a DETERMINATION OF THE CATALYTIC CYSTEINE The pK a measurements of N-terminal active site cysteines (Cys A ) have been performed with WT Grx isoforms following a procedure described in  (Gallogly et al. , 2008). Briefly, 3 μM reduced Grx was incubated with or without 300 μM iodoacetamide (IAM) in 100 mM sodium citrate or phosphate buffers ranging from pH 2. 0 to 7. 0. Following this pre-incubation step, Grx activity was determined by adding an aliquot of the pre-incubation mixture to the HED assay described above. The percentages of remaining activity at each pH were determined by comparing the activity of the enzyme incubated with and without IAM and an adaptation of the Henderson-Hasselbach equation  (Gallogly et al. , 2008)  was used for pK a value determination using the program GraphPad Prism 4.
OXIDATIVE MODIFICATIONS OF CYSTEINE RESIDUES Several observations prompted us to analyze the sensitivity of all dithiol class I Grxs to oxidizing treatments and the resulting changes in their redox state. First, the mutation of Cys B increased the catalytic efficiency of GrxC1 and C2 but not of GrxC3 and C4 suggesting possible difference in the reaction mechanisms. Second, although Cys C does not influence their catalytic activity, the migration of the purified proteins in non-reducing SDS PAGE gels indicated the formation of covalent linkages for GrxC1 and C2 that are not visible for GrxC3 and C4 (data not shown). For this purpose, reduced proteins have been treated for 2 h with a 10 fold excess of GSSG or H 2 O 2 , or a 5 fold excess of GSNO. The resulting redox state was analyzed by mass spectrometry and by protein migration on non-reducing SDS PAGE with or without thiol alkylation by 2 kDa mPEG maleimide, which allows distinguishing reduced and oxidized forms of Grxs.
02°for 2 s per point. The data are collected at room temperature. The unit cell parameters calculated by using the patterns matching the routine of the FULPROOF program  [28]  are a =7. 45 Å and b =6. 974 Å. Figure  2  shows the X-ray diffraction (XRD) pattern of Cu-KDP  (5). All the reflection peaks of the XRD pattern of the sample are indexed in a single-phase tetragonal KDP structure with I 4 2d space group  [29]. Thermogravimetric (TGA) and differential thermal analysis (DTA) are performed on polycrystalline with a TGA/DTA Q600 STD TA Instruments apparatus (sample with Pt crucibles, The infrared absorption spectrum was recorded using a pellet of sample, which was prepared by mixing 1 mg sample in a total weight (samples+KBr) of 200 mg. A Perkin-Elmer FT-IR - - ν O-H (band B) 2,293vw 2,288vw 2,285vw - - - 2,343vw 2,339vw 2,337vw - - - 2,386vw 2,376vw 2,373vw 2,381m 2,383m 2,379m - - - 2,398m 2,394m 2,394m 3,268s 3,264s 3,261s - - - γ (O-H) - - - 3,430w 3,428w 3,428w 3,435w 3,430w 3,425w - - - - - - 3,483w 3,480w 3,483w 3,516w 3,512w 3,513w - - - - - - 3,565w 3,565w 3,565w 3,600m 3,593m 3,592m - - - vs very strong, s strong, m medium, w weak Fig.
Figures  4  and 5  show the infrared and Raman spectra of pure KDP, Cu-KDP (1), Cu-KDP (2), Cu-KDP (3), Cu-KDP (4) and Cu-KDP  (5). Spectral data and proposed assignment are listed in Tables  2  and 3. The analysis is based on the classical identification of external modes implying the whole lattice network, internal modes of the (H 2 PO 4 ) -tetrahedra and stretching and bending modes of OH bonds. The attribution is done with respect to the KDP attribution taken from  [4, 31, 32]  and calculated frequencies of free (H 2 PO 4 ) -ions. II I(a) I(b) Assignment T=303 K T=453 K T=473 K - 61w 64w Lattice vibrations - 73w - - 94w - - - - - - 106w 118m - - - 154m 155m 152m - - 182m - - ν (O-H-O) 193m - - Cu-O 235m 229m 230w 253m - - 286m δ s [ To calculate the frequencies of the vibrational modes of the H 2 PO 4 entity, ab initio RHF/MP2 and DFT/B3LYP electronic structure calculations were carried out using the TZV standard basis set augmented by one diffuse and one polarization functions implemented in the GAMESS program  [33].
To identify different vibrational modes, the MOLDEN package  [34]  was used. Vibrational levels obtained by RHF/MP2 and DFT/B3LYP calculation on free (H 2 PO 4 ) -and in the experimental result are compared with those measured  [32]  in aqueous solution. Figure  6  shows the correlation of the free (H 2 PO 4 ) -group vibrations in C 2v internal vibrations in C 2 factor group symmetry through the D 2d one in the crystal. The spectroscopic characteristics of the free H 2 PO 4 ion with pseudo-symmetry C 2v can be deduced from the free tetrahedral PO 4 entity. The two stretching modes v 1 (~938 cm -1 ) and ν 3 (~1,017 cm -1 ) lead to four stretching modes (two modes ν(PO 2 ), one antisymmetrical (B 1 ) at about 1,033 cm -1 and one symmetrical (A 1 ) at 1,060 cm -1 , and two ν(P (OH) 2 ) around 732 and 759 cm -1 with symmetry A 1 and B 2 , respectively) (Fig.
Acknowledgments Many thanks to  Unité de sepectroscopie Raman FSS Sfax  for the measurements of Raman spectra. The authors wish to express their gratitude to  Prof. Mohamed Bahri  from the  Faculty of Science, Sfax, Tunisia , for the calculation of the frequencies of the ( H 2 PO 4  ) -group. Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.
Paw circumference duplicate measures per time point was done just above the pad using a measuring tape (DMC, Colmar, France). Skin plantar temperature was measured (in degrees Celsius) using an infrared thermometer (Raynger M. Raytek, Fisher Bioblock Scientific -Illkirch -France) at a reference site on the plantar face of the paw, at six different times for each day and measures were performed in triplicate. Data used was the average of the three measurements performed at each time point. Creeping time was measured (in seconds) in a tunnel 6. 38 m long, using a stopwatch (digital stopwatch) in triplicate for each time point and creeping speed (m/s) was used as the final measurement for this endpoint. Lameness score was assessed using a numerical rating scale as developed by Giraudel et al.
[35]. Vertical normalized force i. e. the maximal vertical force applied on the ground by a hind limb was measured with force plates (SATEL Veto; Patrick Savet, Blagnac, France); for each measurement time, three measures were recorded, the mean values were normalized to the dog's body weight (Fmax/b. wt. , kg/kg) and used in the data analyses. Pain was assessed using a hind paw thermal escape model. The model consisted of exposing the hind limb to a light beam delivered by a Hargreaves apparatus (model 390; IITC Inc. , Woodlands Hills, CA)  [13, 36]. A heat intensity  corresponding to 15% of the peak heating value of 150 W was selected. The paw withdrawal time (in seconds) was measured. For each trial, three measures were recorded per measurement time, and the mean of the three measures was used in the data analysis.
Data analysis and modeling Study 1 Pharmacokinetic and PK/PD modeling were performed by least-squares regression analysis using WinNonlin Professional software (WinNonlin® software, version 4. 0. 1, Pharsight Corporation, Mountain View, Ca, USA). For PK analysis, individual plasma cimicoxib concentrations were fitted to polyexponential equations. The data points were weighted by the inverse of the squared-fitted value. The number of exponential (2 or 3) terms needed to obtain the best fit for each data set was determined by the Akaike's information criteria  [37]  and by inspecting the plot of residuals. A biexponential equation corresponding to a mono-compartmental model for extravascular administration with a lag-time was selected (Equation  1 ). C t ð Þ ¼ FDk 01 V k 01 -k 10 ð Þ exp -k 10 Â t-t lag À Á À Á -exp -k 01 Â t-t lag À Á À Â ð1Þ where C(t) is the cimicoxib plasma concentration (μg/L) at time t (h), V/F (L/kg) is the apparent volume of distribution, k01 (1/h) is the rate constant of the initial ascending phase, k10 (1/h) the rate constant of the terminal phase, tlag is the lag time and D is the cimicoxib dose (mg/kg).
No alterations in the expression levels of these genes were found in serum-deprived MDA-MB-231 cells treated with hGX for 96 h (data not shown). However, there were significant changes in the expression of several genes (Figure  7A ) when MDA-MB-231 cells were treated with hGX for 48 h in the presence of serum to induce maximal LD biogenesis (Figure  2C ), then serum-deprived for 24 h in the absence of hGX to allow high levels of LD lipolysis (Figure  3A ). Eight time-points were analyzed to search for possible correlations between the time-course of net LD accumulation in proliferating cells and LD consumption in starved cells with changes in gene expression. A significant decrease was detected in the expression of genes for the lipogenic transcription factor sterol regulatory element-binding protein 1 (SREBP-1) and the key FA synthesis enzymes ACC1, FAS and stearoyl-CoA desaturase 1 (SCD-1) [2,4,29] (Figure  7A ).
Samples were analyzed on a FACSCalibur flow cytometer equipped with a 488-nm Ar-ion laser using the CellQuest software (Becton Dickinson, USA). The logarithmic Alexa 488 fluorescence signal was collected using the FL-1 filter (530/30) and linear 7-AAD fluorescence signal was collected using the FL-3 filter (650LP). Samples were prepared in duplicate with analysis on 2 × 10 4 events per sample.
After a 1 h-blocking step in 5% BSA in TBS or in 1% Western Blocking Reagent in TBS (Roche Applied Science, Germany), the membrane was incubated overnight at 4°C with gentle shaking in a solution of appropriately diluted primary antibody in 2. 5% or 5% BSA in TBS/0. 1% Tween-20 (TBST) or in 0. 5% Western Blocking Reagent in TBS. After three washing steps in TBST, membranes were incubated with horseradish peroxidase (HRP)-conjugated secondary antibodies (Cell Signaling Technology or Jackson ImmunoResearch Laboratories, USA). After three additional washing steps, the proteins bands were visualized using Lumi-Light Western Blotting Substrate (Roche Applied Science, Germany) and Amersham Hyperfilm ECL films (GE Healthcare, UK). Band density was quantified by densitometric analysis using ImageJ software (National Institute of Health, USA).
Acknowledgements We are grateful to  Dr. Roger H. Pain  for critical reading of the manuscript,  Dr. Borut Jerman  for preparation of recombinant hGX,  Franja Božič  for preparation of recombinant hGIIA,  Prof. Michael H. Gelb  for kindly providing the inhibitor AZ-1 and  Dr. Jasmina Kožar Logar  for scintillation counter measurements of oleic acid release. We thank  Minca Ferlin ,  Veronika Ramovš ,  Maruša Rajh  and  Monika Biasizzo  for their technical help. This work was supported by grants  P1-0207  and  J3-0386  from the  Slovenian Research Agency , by the French-Slovene partnership project  BI-FR/12-13-PROTEUS-006 , by a short-term  French Government Scholarship  to A. P. and by  CNRS , the  Association for International Cancer Research  and the  Fondation ARC  pour la recherche sur le cancer to G.
Materials Ultrahigh quality water (resistivity 18. 2 MU cm) from a Millipore Milli-Q system was used in all experiments. D 2 O (99. 9% deuteration) was either purchased from Sigma-Aldrich (Gillingham, UK) or provided by the Institut Laue-Langevin, Grenoble. The phospholipid L-a-distearoylphosphatidylcholine (DSPC) was purchased from Avanti Polar Lipids (Alabaster, USA) in three forms: fully deuterated (d 83 -DSPC), chain deuterated (d 70 -DSPC) and fully hydrogenous (h-DSPC). Before use, the isotopic purity of the various forms of DSPC was conrmed by determining their surface-pressure:area isothermsno difference in the isotherm was observed for any of the isotopic forms of DSPC which all agreed with isotherms previously reported for DSPC. 17 Similarly no difference was seen in the behaviour of the isotherm if measured in D 2 O as opposed to H 2 O (data not shown).
The diffuse scattering component was then subtracted. The custom built in-house Langmuir trough was used in the same manner as described for the neutron reectivity experiments. The Langmuir trough was sealed in a water-saturated helium lled chamber to reduce sub-phase evaporation and parasitic background scattering from air. X-ray reectivity experiments were performed at 295 AE 2 K on h-DSPC monolayers spread either on H 2 O or D 2 O containing 20 mM CaCl 2 with and without 0. 067 mg mL À1 ctDNA and compressed (at a speed of 20 cm 2 min À1 ) to the nal maintained surface pressures of 5, 20, 30 and 40 mN m À1. The monolayers lms were stable at each of the surface pressures examined for the period of the X-ray reectivity experiment, typically 30 minutes. The presence of 20 mM calcium chloride in the sub-phase was denoted by the subscript CaCl 2.
c Calculated as described by Armen. 19 d The volume of the PC head group was calculated as the sum of the volumes of phosphate, glycerol, carbonyl and choline. 19 e The volume of H 2 O/D 2 O was assumed to be 30 Å3 from reported simulation data  20  where water was calculated to have a volume of 30. 4 Å3. f The SLD of the calf thymus DNA (DNA) was calculated assuming a composition of 41. 9% G-C and 58. 1% A-T content (as determined by the manufacturer). Note that when modelling the SNR data, the SLD of the ctDNA was calculated taking into account the differential exchange of its labile protons (Jacrot 1972) and was therefore dependent on whether the sub-phase was air-contrast matched water or D 2 O. Exchange of labile H's in nucleotides in D 2 O were as reported by Jacrot. 21 N/D ¼ not determined.
V 0. 95 (cm 3 g -1 ) is the volume of liquid nitrogen corresponding to the amount adsorbed at a relative pressure P/P 0 = 0. 95  [46]. Pore-size distributions were calculated using the method of Barret, Joyner and Halenda (BJH)  [47]  applied to the desorption branch of the isotherms, using the software supplied with the ASAP 2020 automatic adsorption apparatus.
During experiments, fluorescence images of each well were obtained twice: once before and once after the application of a sodium iodide solution (140 mM NaI, 5 mM KCl, 2 mM CaCl 2 , 1 mM MgCl 2 , 10 mM HEPES, and 10 mM glucose, pH 7. 4) containing defined concentrations of glycine. Mean percentage quench values represent data averaged from four experiments carried out on different plates. Each experimental value was an average of the percentage quench of all fluorescent cells in three wells on the same plate, with each well containing Ͼ200 cells. To determine the glycine dose-response curve from these data, an empirical three-parameter Hill equation was fitted by a nonlinear least squares algorithm using SigmaPlot 12. 0 software. Electrophysiology-Glycine-gated currents were measured in HEK AD293 cells transfected as described above.