dataesr/scientific-paragraphs-categorization huggingface dataset:
Values for binding constant (K), molar fluorescence intensity of the complex (f ), and the stoichiometric coefficient (n) were estimated by fitting the F vs. Lt curves against Equations (1) and (2) using a least-square regression program Scientist (MicroMath, Salt Lake City, UT, USA), where F is fluorescence intensity, [L] the free ligand concentration, [L t ] the total ligand concentration, and c the total albumin concentration. Since all values of n were close to 1, a simple 1:1 binding model was used. In all cases, the inner filter effect was taken into account by using absorption of free ligands at excitation and emission wavelengths (ε ex and ε em , respectively) (Equation (  3 )), where F corr is the fluorescence corrected for the inner filter effect, F 0 is the measured fluorescence, ε is the sum of ε ex and ε em , l = 0.
[35]  Additionally, docking of (R)-and (S)-warfarin was also performed in presence of crystallized (R)-warfarin to locate a putative secondary binding site located in Sudlow's site I. The three-dimensional forms of the ligands were drawn and their initial geometries were optimized in HyperChem 8. 0 (Hypercube, Inc. , Gainesville, FL, USA), and their charge was set to represent the most abundant species at pH 7. 4, calculated according to Rimac et al. [48] , as well as verified at chemicalize. com. For (R)-and (S)-warfarin, anionic species were docked, while for quercetin and quercetin-3-O-glucuronide, two most prevalent anionic and fluorescent species  [49]  were docked. Afterward, ligands were read in the AutoDock software in a compatible file format and partial charges were set according to Ionescu et al.
Acknowledgments: We would like to thank  Professor Valerije Vrček  ( University of Zagreb, Faculty of Pharmacy and Biochemistry ) for a very productive discussion and  Professor Marica Medić-Šarić  for setting the ground work for this research. This work was supported by the  Croatian Science Foundation  under the project  UIP-2014-09-5704  and  INRA, Avignon, France. H. R. acknowledges a travel grant from the  French Embassy.
PfCRT transports iron indicated, the specific PfCRT-mediated uptake was determined by subtracting the corresponding background uptake measured in water-injected oocytes from that of PfCRT-expressing oocytes. Uptake was performed at 25 °C for 60 min, if not indicated otherwise. In the case of iron uptake, the raw data were not normally distributed. The raw data did, however, follow a log-normal distribution, and we could therefore compute a mean of the logarithms of the individual measurements. We report the data as the antilogarithms of these means of logarithms. In all cases, at least three separate experiments were performed (on oocytes from different frogs), and in each experiment, measurements were made from 8 -10 oocytes/treatment.
Edited by Ruma Banerjee This work was supported by the joint  French-German Research Initiative  sponsored by the  Agence Nationale de la Recherche (ANR)  and the  Deutsche Forschungsgemeinschaft (DFG)  Grants  EVOTRANSPORT/ANR-14-CE35-0012-01  and  LA 941/11-1  and  PHC PROCOPE  Grants  30995WE  and  ID 57051467. The authors declare that they have no conflicts of interest with the contents of this article. This article contains supplemental Table S1 and Figs. S1-S6. 1 Both authors should be considered senior authors. 2 Supported by  INSERM ,  CNRS , and the  Université Paris-Descartes.
TOF-SIMS images represent the spatial localization of linoleic acid, oleic acid, palmitoleic acid, palmitic acid and stearic acid [M -H] -carboxylate ions corresponding to the optical image obtained from the same skin sample. The integrity of epidermal layer in all samples was confirmed by hematoxylin and eosin stained histological sections and cholesteryl sulfate ion distribution, which is mainly localized in the upper part of epidermis (for all TOF-SIMS images, see supplementary materials). Samples treated with natural oils were compared to the control skin samples-skin without treatment. All skin samples were obtained from the same patient to avoid inter-individual variability. The control sample data was taken from our previously published research, since the skin samples were obtained from the same patient and skin area  [19].
Control sample data was reprocessed along with the data of skin samples treated with natural oils. All experimental procedures for the samples treated with natural oils were performed in the same manner as for the control samples. Notable increase of FAs content was determined in TOF-SIMS images of skin samples treated with natural oils compared to the untreated skin samples. Particularly, increased ion intensities of all selected FAs were determined in the samples treated with sea-buckthorn pulp oil (Figure  2 ). Increase of linoleic and oleic acids was clearly identified in the skin samples subjected to soybean, olive, avocado and raspberry seed oils. It must be noted that in the samples treated with olive oil (Figure  3 ) higher intensity regions of co-localized linoleic, oleic, palmitic and palmitoleic acids were determined in dermis layer.
The cutting direction was parallel to the epidermis, which was selected to avoid sample contamination with stratum corneum lipids. The samples were dried under vacuum at a pressure of a few hectopascals for 15 min before the TOF-SIMS analysis. A subsequent skin section of each sample was cut and deposited on a glass slide to measure the thickness of epidermis. A standard histological hematoxylin and eosin (HE) staining method was performed. Optical images of samples for TOF-SIMS analysis and images of HE stained sections were recorded with Olympus BX51 microscope (Olympus, Rungis, France) equipped with lenses ×1. 25 to ×50, SC30 color camera, monitored by Olympus Stream Motion 1. 9 software and a motorized scanning stage (Marzhauser Wetzlar GmbH, Wetzlar, Germany). Olympus Stream Motion software was used to measure the thickness of epidermis in images of H&E stained samples.
Mass calibrations were conducted internally, and the signals used for initial calibration were H -, C -, CH -, CH 2 -, C 2 -, C 3 -and C 4 H -. The intensities of linoleic, palmitoleic, palmitic, oleic and stearic acids as well as cholesteryl sulfate were measured using the conditions described above in negative ionization mode and expressed as ion intensity images. TOF-SIMS analysis was repeated in triplicate for each natural oil exposed tissue to confirm analytical repeatability and biological reproducibility. The data was acquired and processed using SurfaceLab Version 6. 2 (ION-TOF GmbH, Münster, Germany) software. Further analysis and manipulation of acquired data was carried out using Origin Version 9. 0 (OriginLab, Northampton, MA, USA, 2012) software.
Statistical Analysis of Data The non-parametric Mann-Whitney test was applied to determine the significance of FA content differences determined in the skin by TOF-SIMS analysis. One-way ANOVA (LSD honestly significant difference criterion) test was used to compare DHQ flux values into the skin from control formulations and formulations containing natural oils. The level of significance was determined as p < 0. 05. Statistical analysis of experimental data was performed using IBM ® SPSS ® Statisticsfor Windows, Version 21. 0 (Armonk, New York, USA: IBM Corp. 2012).
The objective of the present study was to compare the prevalence of Pfcrt, Pfmdr1, Pfdhfr, and Pfdhps mutations and the copy number of Pfmdr1 gene in P. falciparum isolates collected in two areas with different malaria endemicity in Hodh Elgharbi region after the introduction of artemisinin-based combination therapy (ACT) in 2006, in order to establish a baseline database for monitoring drug-resistant P. falciparum in the malaria hotspot in the Malian-Mauritanian border area.
Statistical analysis Based on similar epidemiological and ecological characteristics in the study sites of Aioun and Tintane  [16] , data from these two districts were pooled and compared to those from Kobeni. The frequency of a particular mutant allele was calculated as the proportion of the specific mutant samples among the total number of samples successfully analysed for this mutation. Similarly, the frequencies of double, triple, quadruple, and quintuple mutants were determined as the proportion of subjects with two, three, four, or five mutations among the total numbers of samples tested. Pairwise comparison of mutation frequencies between the northern (Aioun and Tintane) and southern (Kobeni) sites was performed using the Chi square test. The distribution of Pfmdr1 and Pfcrt SNPs in relation to Pfmdr1 copy number was compared using Fisher's exact test.
Funding This work was partly supported by the  Mauritanian Programme National de Lutte contre le Paludisme, Délégation Générale pour l'Armement  (grant  10 CO 404 ),  Direction Centrale du Service de Santé des Armées, Service de Coopération et d'Action Culturelle of the French Embassy in Nouakchott ,  French Agence Nationale de la Recherche  (project  RES-ATQ , Grant  ANR-08-MIE-024 ), and  Expertise France  ( 5%   Initiative  Project).
Acknowledgements The authors thank  Eli Lilly  (P. R. ), the  Royal Thai Government  and  SCI (T. K. ) , and the  EU  ( FP7-PEOPLE-2012-ITN-RADIOMI-316882  to L. P. ) for generous funding. V. G. thanks the  Royal Society  for a  Wolfson Research Merit Award , and  Prof. S. Zard  ( Ecole Polytechnique, France ) and  Prof. J. Burton  ( University of Oxford, UK ) for very helpful discussions.
Acknowledgements We thank  Patricia Beaunier  from the  Transmission Electron Microscopy imaging platform Institut des Matériaux de Paris-Centre  (IMPC) -FR 2482 and  Céline Berjaud  from  NANOBIOTIX  who have acquired the images. We thank  Charles River , in particular  Dick Schoutsen , who have contributed to the LC/MS/MS analysis. The authors also wish to thank  Professor Mike Eaton  who assisted in the proof-reading of the manuscript.
Equal amounts of proteins were separated using SDS-PAGE and transferred onto nitrocellulose membranes. The membranes were blocked and incubated with the appropriate primary antibodies at a final dilution of 1:1000. After washing steps, the membranes were incubated for 2 h at room temperature with a horseradish peroxidaseconjugated secondary antibody (final dilution 1:10,000), and the proteins were detected by enhanced chemiluminescence (Western Lightning Plus-ECL, Perkin Elmer, Courtaboeuf, France) using a Syngene G:Box system (Ozyme, Saint-Quentin-en-Yvelines, France) with the GeneSnap software (Syngene UK, Cambridge, UK, release 7. 09. 17). The detected signals were quantified with the GeneTools software (Syngene UK, release 4. 01. 02), and the results were expressed as the signal intensity in arbitrary units after normalization as indicated in the figure legends.
Statistical analysis The data for the comparison of differences in mRNA expression and protein production between treated and untreated cells were expressed as relative values. The data are expressed as the mean value of triplicates ± SEM. Because the data are independent and non-normally distributed, they were analysed using the Kruskal-Wallis test followed by Bonferroni-Dunn post-test group comparison tests of means using GraphPad (GraphPad Prism version 4. 00 for Windows; GraphPad Software, San Diego, CA, USA). The statistical differences between the various treatments were considered significant either when the P-values were < 0. 05 (*) or < 0. 01 (**).
Acknowledgements This work was financed by a grant from the  BPI-France/ISI   Ulvans  project (n°:  I1110001W ) to  Amadéite company, Bréhan (France). The authors wish to thank  Christelle Gouin  ( Amadeite ) for the production of the demineralized algal extracts and for her contribution to the proximate analyses and  Dr. Nathalie Guriec  ( CHU Brest ) for the LPS analysis. We also gratefully acknowledge  Dr. Isabelle Oswald  ( Toxalim Unit, INRA center of Toulouse, France ) for kindly providing the IPEC-1 cell line.
In addition, the bioguided purification process is laborious, time-consuming and costly, and often leads to reisolation of known structures. The problem of reisolation of known structures is now being addressed by a number of novel bioinformatics tools that efficiently process and analyze mass spectrometry (MS) and nuclear magnetic resonance (NMR) data acquired from complex extracts and assist the process of dereplication. 5  These tools, combined to ad hoc databases, provide structural information on known compounds prior to their isolation and may even allow the annotation of previously unreported metabolites by in silico prediction. 6, 7 Possessing such data at the early stages of investigations allows targeting the isolation of novel or desired scaffolds only. Nevertheless, if current dereplication tools can identify NPs upstream of the isolation process, effective strategies for the early detection of bioactive NPs within crude extracts are still crucially lacking.
There are still no approved therapies focusing on this pathway, making it a promising target for drug discovery. 25 All extracts were screened in a CHIKV replication inhibition assay affording EC 50 ranging from 0. 02 to 100 μg mL -1. For the Wnt bioassay, IC 50 values were determined from two replicates of five concentrations: 100, 33, 10, 3, and 0. 3 μg mL -1. During bioassays, some extracts showed strong cytotoxicity, which prevented determination of their IC 50. Organization and Annotation of Chemical Data. All extracts were profiled by UHPLC-HRMS using a generic linear chromatographic gradient. In parallel, automated data-dependent fragmentation data were acquired using an Orbitrap MS analyzer. The LC-MS 2 data were organized as MN to map the chemical space of the Euphorbiaceae extracts library.
More than 1. 8 million spectra were organized as 88 687 nodes, themselves grouped in 7840 clusters (Figure  1A ). Additionally, MS 2 spectra constituting the whole MN were annotated against an in silico fragmented database of all NP structures previously reported to occur in Euphorbiaceae (subset of the Dictionary of Natural Products). 26 The spectral comparison was made using parent mass as a filter for a direct match or using the variable dereplication mode to link experimental spectra to possible structural analogues according to a previously described workflow. 27 eneration of the Multi-informational Molecular Map. All data acquired at the chemical, biological, and taxonomical levels were then merged as a multi-informative molecular map constituting the core of the strategy. Bioassay Results Mapping.
6 μg mL -1 , was selected for further chemical investigation, and only ions from MN 1 were targeted. To provide insight into the structural characteristics of compounds of MN 1-4 , MS 2 spectra of previously isolated Euphorbiaceae diterpenoids were uploaded in the massive molecular network. A standard analogue matching with ions from MN 2 (see Supporting Information S48)  28  suggested that molecules from this cluster potentially shared the 12deoxyphorbol scaffold. The crude extract was subjected to normal-phase flash chromatography to yield 25 fractions of increasing polarity. The LC-MS 2 profiles of all fractions were combined with data from the initial massive MN, and mapping was done according to fraction numbers (Figure  1D ). Ions from MN 1 were distributed in fractions F11-F19. Based on peak intensities (Supporting Information Figures  S44-S47 ), the four major compounds were selected for a targeted isolation.
In addition, it should be noted that good compatibility between data sets obtained from different instruments was observed. Even though the crude extract collection on one hand and Bocquillonia fractions on the other hand were analyzed on an Orbitrap and a Q-ToF instrument, respectively, no complications hampered the generation and analysis of the merged MN. This overall compatibility between experimental data acquired using different MS systems implies that these massive MNs can serve as a common base for interlaboratory collaborative projects. Using a reporter gene methodology, compounds 1-6 were evaluated for their capacity to inhibit the Wnt signaling pathway in HTB-19 cells (Table  1 ). When compared to the IC 50 values of known natural inhibitors,  29  compound 2, and to a lesser extent 1 and 4, proved to be highly potent inhibitors as evidenced by their IC 50 values (0.
■ MATERIALS AND METHODS Data Dependent LC-HRMS 2 Analysis. Chromatographic separation was performed on an Acquity UHPLC system interfaced to a Q-Exactive Plus mass spectrometer (Thermo Scientific, Bremen, Germany), using a heated electrospray ionization (HESI-II) source. The LC conditions were as follows: column, Waters BEH C18 100 × 2. 1 mm, 1. 7 μm; mobile phase, (A) water with 0. 1% formic acid; (B) acetonitrile with 0. 1% formic acid; flow rate, 600 μL min -1 ; injection volume, 1 μL; gradient, linear gradient of 5-100% B over 8 min and isocratic at 100% B for 3 min. In positive ion mode, the di-isooctyl phthalate C 24 H 38 O 4 [M + H] + ion (m/z 391. 28429) was used as an internal lock mass. The optimized HESI-II parameters were as follows: source voltage, 3. 5 kV (pos); sheath gas flow rate (N 2 ), 48 units; auxiliary gas flow rate, 11 units; spare gas flow rate, 2.
0 s. Data Dependent LC-HRMS 2 Analysis (Fractions of B. nervosa). LC-UV analyses were performed with a Dionex Ultimate 3000 RSLC system with an Accucore C18 column (2. 1 × 100 mm; 2. 6 μm ThermoScientific). The mobile phase consisted of wateracetonitrile (MeCN) with 0. 1% formic acid 80:20 over 5 min, then a gradient from 80:20 to 0:100 over 20 min, at a flow rate of 350 μL min -1. A 2 min isopropanol-MeCN 50:50 washout was applied after each run. The separation temperature was maintained at 30 °C during the analysis. LC-MS analyses were achieved by coupling the LC-UV system to a quadrupole time-of-flight mass spectrometer 6540 Agilent (Agilent Technologies, Massy, France) equipped with an ESI dual source, operating in positive-ion mode. ESI conditions were set with the capillary temperature at 325 °C, source voltage at 5 kV, and a sheath gas flow rate of 69 L min -1.
The mass spectrometer was operated in full-scan mode. Mass spectra were recorded from m/z 50 to m/z 1000 at 2 GHz, leading to a mass resolution of 20 000 at m/z 922. A MS 1 scan was followed by MS/MS scans of the three most intense ions above an absolute threshold of 3000 counts (2 m/z isolation width, a collision energy of 35 eV and an active exclusion of 30 s after three consecutive scans on a same parent ion). Calibration solution, containing two internal reference masses (purine, C 5 H 4 N 4 , m/z = 121. 0509, and HP-921 [hexakis-(1H,1H,3H-tetrafluoropentoxy)phosphazene], C 18 H 18 O 6 N 3 P 3 F 24 , m/z = 922. 0098), routinely led to mass accuracy below 2 ppm. LC-UV data were analyzed with Chromeleon software (Dionex), and MS data were analyzed with MassHunter software (Agilent). Molecular Network Analysis.
The MS 2 data were converted from the. RAW (Thermo) or. d (Agilent) standard data format to. mzXML format using the MSConvert software, part of the ProteoWizard package. 34 The molecular networks were created using the online workflow at Global Natural Products Social molecular networking (GNPS; http://gnps. ucsd. edu). MS 2 spectra were window filtered by choosing only the top six peaks in the ±50 Da window throughout the spectrum. The data were clustered with MS-Cluster with a parent mass tolerance of 0. 1 Da and a MS 2 fragment ion tolerance of 0. 5 Da to create consensus spectra. 35 Further, consensus spectra that contained less than two spectra were discarded. A network was then created where edges were filtered to have a cosine score above 0. 7 and more than six matched peaks. Further edges between two nodes were kept in the network if and only if each of the nodes appeared in each other's respective top 10 most similar nodes.
The library spectra were filtered in the same manner as the input data. All matches kept between network spectra and library spectra were required to have a score above 0. 7 and at least six matched peaks. The full MS data set is uploaded and accessible on the GNPS servers as Massive Data sets nos. MSV000079034 (GNPS_New_Ca-ledonian_Euphorbiaceae_part1) and MSV000079069 (GNPS_New_-Caledonian_Euphorbiaceae_part2). ■ ASSOCIATED CONTENT * S Supporting Information The Supporting Information is available free of charge on the ACS Publications website at DOI: 10. 1021/acschembio. 7b00413. Plant extraction and isolation processes, bioassay procedures, supporting networks, structures and NMR spectra for compounds 1-7, structural elucidation and NMR data for compounds 1-3 and 7, anti-HIV-I and anti-HIV-II activities of compounds 1-6 (PDF).
■ ACKNOWLEDGMENTS The authors are very grateful to South and North Provinces of New Caledonia that have facilitated our field investigation. This work has benefited from an " Investissement d'Avenir " grant managed by  Agence Nationale de la Recherche  ( CEBA ,  ANR-10-LABX-25-01 ). The authors are grateful to  V. Dumontet  ( ICSN ) for his contribution to plant materials collection and identification and to  C. Collard ,  N. Verstraeten ,  K. Erven , and  C. Vanderheydt  from the  "Laboratory for Virology and Experimental Chemotherapy" at the "Rega Institute for Medical Research" in Leuven , for the evaluation of antiviral activity. J. L. W. is thankful to the  Swiss National Science Foundation  for the support of metabolomics projects (SNF grants  310030E-164289  and  316030-164095 ). TOC contains modified icons by  Gan Khoon Lay ,  Fredrik Edfors ,  Edward Battistini ,  Nimal Raj ,  Sergey Demushkin ,  Jakob Vogel  and  Michael Wohlwend  from thenounproject.
Discussion Plants have been used throughout history to cure human diseases. Worldwide, people still use medicinal plants for healing and relieving physical suffering. Many modern medicines have been derived either directly or indirectly from medicinal plants  [30]. Many studies still focus on identifying new medicinal plants. In this study, we identified the chemical content of Crataegus azarolus L leaf extracts and assessed their therapeutic value. Interestingly, our phytochemical analysis showed the presence of various important medicinal components in the tested plant, including alkaloids, resins, phenol, quinones, diterpenes, lignin, sterols/steroids, flavonoids, carbohydrates, cardiac glycosides, reducing sugars, phlobatannins, and flavones. In agreement with previous observations  [31] [32] [33] , our data showed that the alcoholic solvents (ethanol and methanol) were more efficient than the aqueous one in extracting those bioactive compounds.
Data Analysis IC 50 data analyses were performed using the GraphPad Prism 5. 0 by Graphpad Software, Inc. (La Jolla, CA, USA). The log inhibitor concentration versus normalized response calculation was used to determine IC 50 values for each trapping agent against each major CYP isoform, with two significant figures. Each trapping agent was assessed in triplicate and average IC 50 values plus 95% confidence intervals were calculated and reported in Table  1. Potential activation, where metabolite formation increased with increasing concentrations of agent, was noted as an underlined IC 50 value.
This type of analysis requires laborious sample preparation and complex analytical methods. 23 These analyses also lack sufficient data regarding how deep the components penetrate and possible effects of CPEs on epidermis and dermis barrier function. Bioimaging mass spectrometry techniques provide simpler and more informative ways to analyze biological samples. ] [26]  TOF-SIMS is particularly suitable for analyzing lipid components. 27 The applicability of the method has been confirmed by recently published results on visualization and analysis of skin penetration by drug substances roflumilast, tofacitinib, and ruxolitinib,  28  conventional antimicrobial component chlorhexidine digluconate,  29  and ZnO and TiO 2 nanoparticles. 30 The TOF-SIMS method was also applied to evaluate the penetration of tolnaftate into human skin ex vivo in the presence of individual FAs.