dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments: The authors would like to sincerely acknowledge F Raucoules with Captec (SARL) for their numerous fruitful discussions about comparison between standard commercialized heat flux transducers and the prototypes developed in our laboratory. E Gaviot thanks  MD J Y Pello  with the " Sarthe Departmental Council " for contributing valuable experiments with food colouring agents and for his advices regarding prospective biomedical applications. The authors are also grateful to  Dr. G Failleau  at  LNE-CNAM  for his valuable advice and suggestions for this paper. T. Mhammedi  thanks  Professor P Thery  for his keen interest and the advice given during the 2018 Eurosensors conference.
The rise of intact protein analysis by mass spectrometry (MS) was accompanied by an increasing need for flexible tools allowing data visualization and analysis. These include inspection of the deconvoluted molecular weights of the proteoforms eluted alongside liquid chromatography (LC) through their representation in three-dimensional (3D) liquid chromatography coupled to mass spectrometry (LC-MS) maps (plots of deconvoluted molecular weights, retention times, and intensity of the MS signal). With this aim, we developed a free and open-source web application named VisioProt-MS (https://masstools. ipbs. fr/mstools/visioprot-ms/). VisioProt-MS is highly compatible with many algorithms and software developed by the community to integrate and deconvolute top-down and intact protein MS data. Its dynamic and userfriendly features greatly facilitate analysis through several graphical representations dedicated to MS and tandem mass spectrometry (MS/MS) analysis of proteoforms in complex samples.
Introduction Top-down proteomics consists in the analysis of intact proteins using liquid chromatography coupled to mass spectrometry (LC-MS), followed by their identification by tandem mass spectrometry (MS/MS). This informs on the protein composition of the analyzed sample, and their potential combinations of post-translational modifications, splicing events, and/or mutations. Intact protein mass spectrometry (MS) recently increased in throughput  1  and became quantitative,  2, 3  thereby allowing the in-depth characterization of proteoforms 4 in complex samples. 5 Such development was associated with the establishment of a specific lexicon,  6, 7  dedicated databases (repository. topdownproteomics. org), [10] [11]  Typically, top-down and intact protein MS analysis relies on the measurement of the deconvoluted molecular weights (MWs) of proteoforms after separation by liquid chromatography (LC).
Data analysis and visualization For MS traces, raw files were automatically deconvoluted with the rolling window deconvolution software RoWinPro  8  and the proteoform footprints were visualized with VisioProt-MS v2. 0. 17 Top-down raw data were analyzed with Proteome Discoverer v2. 2 (Thermo Scientific) using the ProSight PD Top-Down Low/High node. Briefly, intact protein spectra were deconvoluted with ReSpect (precursor mass between 20 000 and 30 000 Da and 100 ppm mass tolerance, charge state range between 15 and 35). Tandem mass spectrometry spectra were deconvoluted with Xtract (S/N threshold = 3, m/z range between 200 and 2000 Da, 60 000 resolution) and searched against a custom database including all human 20S subunits (generated in ProSight PC v4. 0, Thermo Scientific). The search was performed in absolute mass mode with a fragment mass tolerance of 15 ppm and a precursor mass tolerance of 200 Da.
Comparison of the std20S and i20S To demonstrate the advantages of VisioProt-MS in the context of comparative sample analysis, we chose the commercial samples of std20S and i20S. Their LC-MS maps are presented in Figure  2 , first alone with color-coded intensities (Figure  2A  and B ) and together for their direct comparison (Figure  2C ). These graphical representations indicate the unexpected presence of the subunits β1, β2, and β5 among the i20S-specific subunits of the i20S sample, thereby highlighting a contamination by the std20S (Figure  2B ). ] [25]  Besides zooming and dynamic labeling of the data points, VisioProt-MS allows the user to hide experiment-dependent background noise with the "Threshold" option of the sidebar menu. This defines the percentage of high-intensity MS signal that is visualized on the LC-MS map.
The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This work was supported by the  Novo Nordisk Foundation  ( NNF14CC0001 ), the  French Ministry of Research  ( Investissements d'Avenir Program ,  Proteomics French Infrastructure ,  ANR-10-INBS-08 ) and the  Fonds Européens de Développement Régional Toulouse Métropôle  and the  Région Midi-Pyrénées. DeClARATIon oF ConFlICTIng InTeReSTS: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.
Data Availability Raw files corresponding to the analysis of the commercial std20S (OFJMX180306_15. raw) and i20S (OFJMX180306 _18. raw) as well as immunopurified std20S in MS (OFJMX160905_42. raw) and MS/MS (OFJMX160905_30. raw) have been deposited to the MassIVE repository with the dataset identifier MSV000084069 (ftp://massive. ucsd. edu/ MSV000084069).
05% aqueous KMnO 4 ; Ninhydrin: 0. 2 g of ninhydrin were dissolved in 100 mL of ethanol. Macherey-Nagel silica gel (40-63 lm) was used for flash chromatography, and the elution was generally performed with a mixture of cyclohexane/ethyl acetate or dichloromethane/ethyl acetate systems. Infrared (IR) spectra were performed as neat on Perkin Elmer FT-IR spectrophotometer. For the cited compounds, only broad and strong signals are reported (wavenumbers, cm -1 ). 1 H and 13 C NMR spectroscopic data were recorded on a Bruker Avance 300 spectrometer at room temperature at 300 MHz and 75 MHz respectively by using broadband proton decoupling for 13 C NMR. All spectra were calibrated using the residual solvent peaks as references: 7. 26 and respectively 77. 00 ppm for CDCl 3 or 2. 50 and 39. 50 respectively for DMSO-d 6.
General Procedure for Batch Photochemical Transformation of 1a to 2a With the quartz tubes (QT2, QT4, QT6) in the support, an aqueous solution of 1a with potassium carbonate (1. 2 mol equiv. ) in a specific concentration (20, 40, 60, or 80 mM) was added. The support was placed inside the photochemical home-made UV reactor and was irradiated up to 10 h at room temperature (the measured temperature inside the top of the reactor was below 34 ºC). At selected times, samples were collected from the reaction mixture, concentrated under vacuum and analyzed by 1 H NMR (D2O). All data are available in the Supporting Information.
General Procedure for Batch Photochemical Transformation of 1a to 2a With the quartz tubes (QT2, QT4, QT6) in the support, an aqueous solution of 1a with potassium carbonate (1. 2 mol equiv. ) in a specific concentration (20, 40, 60, or 80 mM) was added. The support was placed inside the photochemical home-made UV reactor and was irradiated up to 10 h at room temperature (the measured temperature inside the top of the reactor was below 34 ºC). At selected times, samples were collected from the reaction mixture, concentrated under vacuum and analyzed by 1 H NMR (D 2 O). All data are available in the Supporting Information. In addition, 1 QT was removed from PQT6 reactor, cleaned and placed back in the support. This clean QT was used under continuous-flow conditions and allowed determination of the reaction conversion by 1 H NMR.
Computational details All complexes were optimized at the DFT level with the hybrid wB97XD functional, a LANL2DZ effective core potential for Ru ion, and a 6-311G(d) basis set for all other atoms, without symmetry constraints. The same level was used for the frequency calculations and confirmation that optimized geometry has only real frequencies. The gas phase structures of 1 and 3 were re-optimized in DMSO, simulated by the universal solvation model (SMD)  [17]. Calculated electronic transitions were carried out within the time dependent density functional theory (TD-DFT) approach, using the same functional, the basis sets and the solvent. The quantum chemical calculations were done with Gaussian09 software  [18]. The condensed Fukui function is calculated from eqns. 1-3, where q N , q N-1 and q N+1 are the partial charge of the atom A in neutral, anionic and cationic forms, respectively.
Molecular docking with DNA In order to explore the most feasible binding sites, interaction modes, and binding affinities docking studies have been performed on the Ru(II) complexes (1-3) with B-DNA (PDB ID: 1BNA). The docked model (figure  3 ) revealed that 1 and 2 were tailored tightly into the curved contour of the targeted DNA minor groove within A-T rich region, in such a way that planar part of the aromatic rings made favorable electrostatic (π-anion) and hydrophobic (π-sigma) contacts with the DNA functional groups. Complex 3 interacts with DNA through electrostatic (π-anion) and hydrophobic (π-sigma) interactions at the minor groove with an affinity to both A-T and G-C region. The resulting binding energies of docked structures were -8. 50, -8. 52 and -10. 09 kcal/mol for 1-3, respectively, indicating the higher binding affinity between DNA and 3 as compared to 1 and 2.
Data collection Twenty-seven healthy males (25. 9 ± 4. 5 years; 1. 8 ± 0. 1 m; 75 ± 11. 6 kg) gave their consent for the study (CPP SOOM I, France no. 2018-A00484-51). Participants seated with their dominant leg alongside a Con-Trex MJ® isokinetic dynamometer (CMV AG, Dübendorf, Switzerland). The dynamometer axis was aligned with the knee epicondyles in flexion at 90°. Tight straps immobilized the thigh and the shank. Range of motion was adjusted to the subject. Goniometric measurements were used to calibrate angular values. After a warm-up, five maximal voluntary knee flexions and extensions hold for four seconds at angles equally spaced through the range of motion were recorded as isometric trials. Then, three repetitions of concentric isokinetic trials were recorded at 60°. s -1 , 120°.
Computational Solubility Assessment The solubility of (i) β-carotene from carrots, (ii) S-carvone and d-limonene aromas from caraway seeds, and (iii) model triglycerides (glyceryltrilinolein, LLL; glyceryloleoyl-dilinoleoyl, OLL; and glyceryllinoleoyl-oleoyl-palmitoyl, LOP) from rapeseeds was evaluated for both p-menthane and n-hexane using the theoretical prediction model COSMO-RS (COSMO software). Computation methods consider the technical properties of the solvents to assay and examine the solutes. The chemical structures of the solvents and solutes were transformed by JChemPaint version 3. 3 (GitHub Pages, San Francisco, CA, USA), while for the entry syntax, (SMILES) notation was followed. They were then used for the solubility parameters calculation of solvents and targeted compounds.
32 mm × 0. 25 µm), as well as an FID and an auto-sampler. The carrier gas was helium at 33 mL/s. The sample injection volume was 2 µL, while the split ratio was set at 1:20 at 250 • C. The oven initial temperature was set at 50 • C for 1 min, and then increased to 20 • C/min until it reached 180 • C, then a rate of 2 • C/ min until 230 • C, and was then held isothermally at 230 • C for 10 min. Data collection was carried out by Agilent EZChrom Elite software. Identification of FAMEs was performed in comparison with purified FAME standards (Sigma Co. , St Louis, MO, USA), while the quantification was achieved using internal calibration. The internal standard used was glyceryl triheptadecanoate (Sigma Co. , Cleveland, OH, USA).
Conclusions In this work, the potential of p-menthane as a green alternative to petroleum solvents such as n-hexane and toluene was investigated. This bio-based solvent was prepared by hydrogenation of Dlimonene, a by-product of deterpenation of essential oils obtained from orange peels. The solubility of certain bioactive compounds in p-menthane was experimentally and theoretically compared with n-hexane using a simulation software COSMO-RS. It was found that both solvents have relatively similar solvation efficacy. Experimentally, it was observed that a slightly higher extraction yield can be obtained on carrots using the alternative solvent, while for caraway aromas and rapeseed oils, similar extraction potential was recorded for both solvents. p-Menthane was also used for water determination using Dean-Stark apparatus.
IC 50 values were calculated after the logit-logtransformation of relative growth and subsequent regression analysis by the corresponding software tool contained in the Excel software package (Microsoft, Seattle, WA). For long term treatment assays, N. caninum infected HFF grown in T25 culture flasks were exposed to 250 nM of complexes 1, 2 or 9 for a period of 15 days, with medium changes and addition of fresh compounds every 3 days. At the end, the cultures were washed with medium and were further maintained in medium devoid of drugs. Regrowth of parasites was monitored on a daily basis by light microscopy.
Acknowledgements This study was financially supported by the  Swiss National Science Foundation  (SNSF professorships PP00P2_133568 and This journal is © The Royal Society of Chemistry 2018 Metallomics  PP00P2_157545  [to G. G. ],  SNSF  grants  310030_165782  [to A. H. ] and  CRSII5_173718  [to J. F. , A. H. , and G. G. ]), the  University of Bern (UniBe-ID ; to J. F. and A. H. ), the  University of Zurich  (to G. G. ), the  Stiftung fu ¨r wissenschaftliche Forschung of the University of Zurich  (to G. G. ), the  UBS Promedica Stiftung  (to R. R. and G. G. ), the  Forschungskredit of the University of Zurich  (to R. R. ), and the  Novartis Jubilee Foundation  (to R. R. and G. G. ). This work has received support under the program Investissements d'Avenir, launched by the  French government  and implemented by the  ANR , with the reference  ANR-10-IDEX-0001-02 PSL  (to G.
The authors acknowledge financial support from the  Austrian Science Fund FWF (DK CoQuS   W1210 ,  DK Solids4Fun W1243 , and DiPQCL  P30709-N27 ) and the  ERA. NET RUS   PLUS  project  COMTERA  ( FFG 849614 ). H. D. acknowledges funding through an  APART Fellowship  of the  Austrian Academy of Sciences  and funding through the  ESF  under the Project No. CZ. 02. 2. 69/0. 0/0. 0/16_027/0008371.
7 s. 66] The full structural formation and ordering mechanism of the PDMSB-b-PMMA copolymer during spin coating can thus be inferred by considering the simultaneous laser interferometry and the GISAXS results. The laser is incident along the y-z plane at a 45° angle with respect to the x-y plane on the spinning substrate. The specularly reflected laser signal is recorded using a photodiode. X-rays are incident along the x-direction at an angle of α i = 0. 12° and the sample-to-detector distance is 3200 mm. B) Evolution of the drying wet layer thickness retrieved from the laser interferometry data as a function of time during spin coating at 1000 rpm. C-E) Representative GISAXS patterns of the BCP thin film at 5, 13. 4, and 19. 5 s, respectively. F,G) Evolution of the horizontal, I(q y ), and vertical, I(q z ), time-lapse GISAXS intensity cuts taken at q z = 0.
Acknowledgements The  ESRF  and  NWO  are acknowledged for allocating beam time at the  Dutch-Belgian beamline (DUBBLE)  for the GISAXS experiments. A. Legrain  and  M. Zelsmann  are acknowledged for STEM imaging. J. J. van Franeker  is acknowledged for useful discussions around the laser interferometry. The authors acknowledge financial support from the  Industrial Chair (Arkema/ANR)  within the grant agreement no. AC-2013-365. This work was performed within the framework of the  EquipEx  ELORPrintTec  ANR-10-EQPX-28-01  and the  LabEx AMADEus   ANR-10-LABEX-0042-AMADEUS  with the help of the  French state Initiative d'Excellence IdEx   ANR-10-IDEX-003-02. G. P. acknowledges the  Zernike Institute for Advanced Materials  for the startup funds and the  LabEx AMADEus  visiting professor grant received from the  University of Bordeaux.
Magnetic susceptibility measurements. Temperature dependence of molar susceptibility was obtained by SQUID based magnetometer MPMS 5XL (Quantum Design) in the temperature range 1. 8-300 K on three samples MOF-76(Gd)-DMF, MOF-76(Gd) and MOF-76(Gd)-H 2 O in both regimes ZFC/FC (zero field cooled and field cooled regimes) in magnetic field 100 mT. The powder specimens (20. 6 mg for MOF-76(Gd)-DMF, 20. 2 mg for MOF-76(Gd), and 17. 8 mg for MOF-76(Gd)-H 2 O) were fixed in a gelatine capsule and the capsule was held by a straw. The signal contribution of empty gel cap and the straw was subtracted from the total signal. Also, the obtained data were corrected for the diamagnetic contribution using Pascal's constants.
29 , which for an isothermal-isobaric process after integration yields Eq. 1  30, 31  expressed as: As it is known, the magnetic entropy change -ΔS M can be obtained from the experimental magnetization data at various magnetic fields and temperatures from the Maxwell equation, Eq. 1. The results of -ΔS M calculated from experimental data at different magnetic fields and temperatures are given in Fig. 3. With the aim to estimate the magnetocaloric properties of studied samples 1-3 via magnetic entropy change, the isothermal magnetization data recorded by standard measurement protocol was applied. The details of standard protocol are described in ESI. ∫ Δ =      ∂ ∂     . S M T dH (1) M H The -ΔS M (T) value shows a gradual increase with increasing ΔH and decreasing temperature, giving -ΔS Mpk (T) = 31 J kg -1 K -1 for MOF-76(Gd)-DMF, -ΔS Mpk (T) = 42 J kg -1 K -1 for MOF-76(Gd) and -ΔS Mpk (T) = 38 J kg -1 K -1 for MOF-76(Gd)-H 2 O at an applied field change of 5 T (-ΔS Mpk = peak of magnetic entropy change).
We report a series of Pd K-edge and Pt L 3 -edge X-ray absorption spectra (XAS) collected in situ during thermal treatment of functionalized UiO-67-Pd and UiO-67-Pt metal-organic frameworks in inert and reducing atmospheres. We present raw synchrotron data from three subsequent experiments at different beamlines, normalized XAS spectra and k 2 -weighted oscillatory c(k) functions extracted from one of the datasets. Pd K-edge spectra were collected for the samples in 5% H 2 /He, 3% H 2 /He and pure He in the temperature range from room temperature (RT) to 450 C. Pt L 3edge were collected for the samples in 3% H 2 /He, 10% H 2 /He and pure He in the temperature range from RT to 300 C. All spectra are reported together with the used atmosphere and temperature. For the analysis of all reported datasets, please see "Evolution of Pt and Pd species in functionalized UiO-67 metal-organic frameworks".
Data The dataset contains 77 Pt L 3 -edge XAS spectra and 72 Pd K-edge XAS spectra collected during thermal treatment of UiO-67 samples functionalized by Pt  [1]  and Pd  [1, 2] , respectively, in inert (He) and reducing (H 2 /He) atmospheres with different H 2 /He content. The raw data is presented in the form of unnormalized X-ray absorption coefficient m(E) (see files with extension *. mu in the Supporting materials) together with the normalized ones (see Figs. 1e6 and files with extension *. norm in the Supporting materials). For 10 extended X-ray absorption fine structure (EXAFS) spectra collected at Pd K-edge, extracted k 2 -weighted oscillatory c(k) functions are also reported in Fig. 6b  and file "11_Pd_5H2_ramp. chik2" of the Supporting materials. The experimental conditions under which the spectra were collected are reported in Tables  1  and 2  for Pt L 3 -edge and, respectively, Pd K-edge data.
Subject area Physics, chemistry More specific subject area In situ spectroscopy of functionalized metal-organic frameworks Type of data Value of the data Extensive datasets of X-ray absorption spectra collected at Pd K-and Pt L 3 -edges under various external conditions for functionalized UiO-67 metal-organic frameworks. EXAFS data can be used for single-and multiple-shell Fourier analysis. XANES data can be used to characterize the local atomic and electronic state of Pd and Pt atoms in the as synthesized functionalized UiO-67 and during treatment in inert and reducing atmospheres. XANES spectra of the initial structures and intermediates can be utilized for databases, e. g. for implementation of machine learning approaches. Pt L 3 -edge XAS spectra for UiO-67-Pt samples (Figs. 1e3) were collected at BM01B beamline  [7]  (now moved to BM31 port) of ESRF.
5 ). The samples were first heated stepwise until no spectral changes were observed and were then kept at 300 and 215 C in inert and reducing flux, respectively, and the spectra were measured continuously. The photon energy was scanned from 24. 0 to 25. 4 keV using Si(111) double crystal monochromator operated in continuous scanning mode. In such mode, one full spectrum was collected in 11 minutes. The rejection of higher harmonics was achieved by detuning of the second crystal until 80% of the maximal intensity (when both crystals are perfectly tuned) was observed. Additional measurements were performed at BM23 beamline of ESRF using the sample in a pelletized form to optimize the absorption step and collect also high-quality EXAFS data (Fig. 6 ). A pelletized sample was held in a microtomo cell  [8]  and was activated in a flow of 5% H 2 /He (50 mL/min).
A double-crystal fixed-exit Si(111) monochromator was employed. Harmonic rejection was done by two flat Pt-coated mirrors positioned at 2 mrad angle. The spectra were collected in the energy range from 24. 1 to 25. 1 eV, which correspond to k max of about 14 Å À1. The energy step in the pre-edge region was set to 5 eV with acquisition time of 1 s per point. In XANES region, 1 eV step was used with 1 s/ point. In the EXAFS region, the step of 0. 04 Å À1 in the k-space was used, with the time per point increasing linearly from 1 to 4 s. All spectra were collected in transmission mode, and Pt and Pd foils were measured simultaneously with third ionization chamber for energy calibration. Demeter software  [9]  was used to normalize the data and to obtain oscillatory c(k) functions reported in Fig.
Database searches The Mascot ® probability based search engine (Matrix Science, London, version 2. 4. 0) was used to interrogate the SwissProt 2019_03 primary database. LC-MS. wiff files of each sample were searched for protein identification and oxidative post-translational modifications (oxPTMs). For protein identification, variable modifications of methionine oxidation and carbamidomethyl cysteine were used. For the analysis of the lipoxidation products, the initial searches additionally used a variable modification list including reduced and unreduced ACR (mass changes of  56.
Identification and mapping of lipoxidation on pyruvate kinase following 10 min treatments The modification of pyruvate kinase by acrolein, MDA and HHE was investigated using LC-MS/MS to map the sites of modification following treatment in vitro at 37 °C for 10 min. Initially the MASCOT ® software was used to identify modified peptides, and then each potential modification was confirmed by de novo sequencing of the MS/MS spectrum including detection of diagnostic ions as reported previously  [46] ; examples of modification by each aldehyde are shown in Suppl. Figures  1  and 2. This approach allowed the identification of 11 peptides modified by acrolein, 10 peptides modified by HHE and 9 peptides modified by MDA based on peptide molecular weight, mass/charge ratio and charge of the peptide ion, MS/MS ion score and LC retention time (Table  1 ).