dataesr/scientific-paragraphs-categorization huggingface dataset:
ACKNOWLEDGMENTS Diffraction data of the A. aeolicus LpxC/LPC-069 complex were collected at the  Southeast Regional Collaborative Access Team (SER-CAT ) 22-ID beamline at the  Advanced Photon Source, Argonne National Laboratory , supported by the  U. S. Department of Energy, Office of Science and the Office of Basic Energy Sciences  under contract number  W-31-109-Eng-38. This work was funded in part by  National Institutes of Health  grants  AI094475  and  GM115355  awarded to P. Z.
High-resolution mass spectra (HRMS) were recorded on Q-TOF Micro WATERS. Infrared spectra were recorded on a PerkinElmer Spectrum One Spectrophotometer. The wave numbers (n) of recorded IR signals are quoted in cm À1. Analytical thin layer chromatography was performed on precoated 200 mm layer thickness silica gel 60 Alumigram Xtra SIL G/UV254. Visualization was accomplished with short wave UV light, potassium permanganate, or phosphomolybdic acid staining solution followed by heating. Flash chromatography was performed on Merck silica gel (40e63 mesh, solid deposit) by a standard technique. Yields refer to chromatographically and spectroscopically pure compounds. The products 1aed  [20, 23] , 3  [21] , 4  [24] , 5  [12] , 9  [12] , and  10 [12]  have previously been described and were identified by comparison of their physical and spectroscopic data ( 1 H, 19 F, and 13 C NMR) with those in the cited references.
Acknowledgments This work was promoted by the  Interregional Norman Chemistry Network (CRUNCh). The " Re ́gions Basse et HauteÀNormandie " are gratefully thanked for their financial support. ENSICAEN and  University of Caen, INSA Rouen, Rouen University, CNRS , and  Labex SynOrg  ( ANR-11-LABX-0029 ) are also thanked for their support.
However, the enzymes responsible for the synthesis of preakuammicine, or any preakuammicinederived product from strictosidine aglycone remain unknown. While the enzymatic reactions remain cryptic, extensive isolation of reaction intermediates as well as model chemical studies suggest a sequence of reactions: 4,21-dehydrogeissoschizine (strictosidine aglycone isomer) is reduced to geissoschizine, which is followed by oxidative rearrangement and reduction to preakuammicine  [4] [5] [6] [7] [8] [9] [10]. Preakuammicine can non-enzymatically deformylate to produce the alkaloid akuammicine  8, [10] [11] [12]  or serve as a precursor for additional alkaloid scaffolds  8. Here we use a transcriptomic database for the medicinal plant Catharanthus roseus to identify two enzymes, an alcohol dehydrogenase (GS) and a cytochrome P450 (GO), that act in tandem on 4,21-dehydrogeissoschizine (strictosidine aglycone) to yield akuammicine, a Strychnos alkaloid.
Results Identification of gene candidates. To identify genes responsible for generating Strychnos scaffolds such as preakuammicine and akuammicine (Fig. 1a ), we mined a transcriptomic database of C. roseus tissues  13, 14  , which also included data from plants with increased alkaloid levels due to folivory  15. Gene candidates identified were initially screened in C. roseus by virus-induced gene silencing (VIGS), a transient silencing system in which qualitative perturbations in the metabolic profile between silenced and control tissue provide clues to the metabolic function of the gene of interest. Transformation into preakuammicine requires both reduction and oxidation steps (Fig. 1b , Supplementary Fig. 1 )  [4] [5] [6] [7] [8] [9] [10]. Therefore, we focused on alcohol dehydrogenases (reductase) and cytochromes P450 (oxidase); alcohol dehydrogenases have been implicated in other monoterpene indole alkaloid biosynthetic steps  [16] [17] [18]  , and cytochromes P450 are well known to play important roles in oxidative transformations in plant metabolism  16, 19.
Unit resolution was applied to each quadrupole. Targeted methods for each compound were developed using either commercial standards (caffeine, ajmalicine, serpentine, catharanthine, vindoline, vindorosine, loganic acid, tetrahydroalstonine, and yohimbine were purchased from Sigma-Aldrich and tabersonine from Avachem Scientific) or enzymatically produced compounds isolated as described here or as previously reported (strictosidine  17  and isositsirikine, this work). Akuammicine was synthesized and provided as a gift  26. Flow injections of each individual compound were used to optimize the MRM conditions. This was done automatically using the Waters Intellistart software. A minimum dwell time of 25  The apparent rate under saturating substrate concentrations (observed k cat ) for GS1 was measured using NADPH absorbance using strictosidine (100 µM), NADPH (100 µM) and GS1 (0.
83 µM) in an assay previously reported  17. The apparent k cat was 0. 04 ± 0. 007 s -1. Initial rates for GO can be calculated from the data presented in Fig. 3a: 9. 73 nmol l -1 s -1 (100 µM concentration of strictosidine, 5 μM GS1, 5 mM NADPH) and 7. 99 nmol l -1 s -1 (300 µM strictosidine, 5 μM GS1, 5 mM NADPH). The specific activity for GO was not calculated since it was used as a crude microsomal preparation (as is standard for microsomal cytochrome P450s). Chiral column liquid chromatography. Synthetic akuammicine and enzymatically produced akuammicine were subjected to chiral resolution analysis by LCMS. Chromatography was performed on a Lux i-Cellulose 5 (150 × 3. 0 mm, 3 μm) column (Phenomenex) under isocratic conditions using 60% 10 mM ammonium acetate and 40% acetonitrile for 10 min with a flow rate of 0.
Peak areas were calculated using the Waters MassLynx software and normalized. Large-scale enzyme assay. For full characterization of GS1 and GO (CYP71D1V1) products, two large-scale enzyme assays were performed. For the characterization of the compounds (16R)-E-isositsirikine (  1 ) and (16R)-Z-isositsirikine (2) produced by GS1, 9. 2 mg of strictosidine prepared as described previously  17  were dissolved in 50 mL of 50 mM phosphate buffer (pH = 7. 0). To generate strictosidine aglycone as substrate, 5 nM of SGD enzyme was added and incubated at 37 ˚C for 20 min. The consumption of strictosidine was monitored by flow injection MS performed on an Advion express-ion Compact Mass Spectrometer. NADPH (25 mg) and aliquots of GS1 to final concentration 5 µM were added to the reaction mixture. A NADPH-generation/regeneration system consisting of glucose, glucose dehydrogenase (Sigma-Aldrich) was used additionally.
Compound characterization. High-resolution electrospray ionization mass spectrometry spectra and UV-Vis spectra were measured with a Shimadzu IT-TOF mass spectrometer as described above. NMR spectra ( 1 H NMR,  13  C NMR) were acquired using a Bruker Avance III 400 NMR spectrometer equipped with a BBFO plus 5 mm probe, operating at 400 MHz for 1 H and 100 MHz for  13  C. The residual 1 H-and  13  C NMR signals of CD 3 Cl (δ 7. 26 for 1 H and δ 77. 36 for 13 C) were used as internal chemical shift references. The number of scans depended on the concentration of the sample. The 1 H NMR spectra were compared with those of standards and literature data  24, 26. For NMR, mass spectrometry and spectroscopic data, see Supplementary Figs  5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23. (16R)-E-isositsirikine (1).
5 min and brought back to 10% Solvent B5. Peak areas were calculated using the Shimadzu Profiling Solution software and normalized by leaf mass (fresh weight). Analysis revealed that the only significant metabolic change with the GS1 silencing fragment was the accumulation of heteroyohimbines. The diastereomers tetrahydroalstonine and ajmalicine, which are both naturally present in C. roseus seedlings, do not separate under these chromatographic conditions. For targeted metabolomic analysis, the secondary metabolite content of GS silenced leaves was determined by a different chromatographic method. Leaf powder was weighed (1-6 mg), extracted with methanol (2 ml) and vortexed for 1 min. After a 10-min centrifugation step at 17,000 g, an aliquot of the supernatant (200 µl) was filtered through 0.
01 min) and m/z 375 for loganic acid ([M-H] -, RT = 4. 94 min). The acquired data was processed by the QuanLynx™ software (Waters, UK). Relative quantification was performed by correcting peak areas by sample masses. Gene silencing was confirmed by qRT-PCR. For GS1-silenced plants, RNA extraction was performed using the RNeasy Plant Mini Kit (Qiagen). RNA (1 µg) was used to synthesize cDNA in 20 µl reactions using the iScript cDNA Synthesis Kit (Bio-Rad). The cDNA served as template for quantitative PCR performed using the CFX96 Real-Time PCR Detection System (Bio-Rad) using the SSO Advanced SYBR Green Supermix (Bio-Rad). Each reaction was performed in a total reaction volume of 20 µl containing an equal amount of cDNA, 0. 25 mM forward and reverse primers, and 1x SsoAdvanced SYBRGreen Supermix (Bio-Rad).
Transitions m/z 355. 3 > 117. 1 (Cone 48, Collision 42), m/z 355. 3 > 144. 1 (Cone 48, Collision 26), m/z 355. 3 > 212. 2 (Cone 48, Collision 18) and m/z 355. 3 > 224. 2 (Cone 48, Collision 18) were used for detection of isositsirikine, yohimbine. Transitions m/z 323. 2 > 182. 0 (Cone 50, Collision 36), m/z 323. 2 > 234. 1 (Cone 50, Collision 34), m/z 323. 2 > 291. 3 (Cone 50, Collision 22) were used for detection of akuammicine. Peak areas were calculated using the Waters MassLynx software and normalized.
Acknowledgements This work was supported by grants from the  European Research Council  ( 311363 ),  BBSRC  ( BB/J004561/1 ) (S. E. O. ) and from the  Région Centre-Val de Loire, France  ( ABISAL grant  and  BioPROPHARM  project  -ARD2020 ) (V. C. ). J. F. gratefully acknowledges DFG postdoctoral funding ( FR 3720/1-1 ) and T. T. -T. D. an  EMBO   Long trem Fellowship  ( ALTF 239-2015 ). We gratefully acknowledge the generous gift of akuammicine from  Chris Vanderwal  ( UC Irvine ).
Data availability. Sequence data for GS1 (KF302079. 1), GS2 (KF302078. 1). and GO (JN613015) have been deposited in GenBank as described in the manuscript. Transcriptome data used in this study has already been published as referenced in the manuscript (see also, http://medicinalplantgenomics. msu. edu/). Data supporting the findings of this study are available within the article and its supplementary information files and from the corresponding author upon reasonable request.
Measurement of Intracellular ROS ROS production was assessed by using the fluorescent probe 2', 7' dichlorodihydro fluorescein diacetate (H 2 DCFDA) according to the method previously described  (Chang et al 2013). SK-N-SH cells were cultured in 6-well plates at a density of 3 x 10 5 cells/2ml and incubated in a CO 2 incubator overnight at 37°C for 24h. The medium was aspirated and cells were washed with 1ml of PBS. Cells were then pre-treated with 100 µg/ml of CtEA, CtME or with 10 µM of resveratrol for 24h at 37 0 C in 5% CO 2 /95% air and then incubated with 14µM of paraquat for 4-6h to induce ROS production. Cells were subsequently treated with 10µM of H 2 DCF-DA for 30min at 37 0 C. Fluorescence was finally measured (using a flow cytometer BD FACS Calibur and the CellQuest Pro software), at an excitation wavelength of 488 nm and an emission wavelength of 535 nm.
Determination of total polyphenols The total amount of polyphenols present in the C. tora extracts were determined by the Folin-Ciocalteu method  (Singleton et al. 1999). Extracts of different volumes were mixed with aqueous Na 2 CO 3 (1. 5 ml) and vortexed before the addition of 500 μl of folin-ciocalteu reagent and incubation for 5 min at room temperature. Then, the solutions were incubated in dark for 2h and the absorbance was measured at 734 nm using UV/visible spectrophotometer. The results were converted to gallic acid equivalent (GAE) using a 0 to100 µg/ml standard curve. Data of total.
Type of data Figures and table How data was acquired The Raman spectroscopy (RS) data were obtained on a MultiRAM FT spectrometer, Bruker, equipped with a Nd:YAG laser. The Fourier transformed infrared spectroscopy (FTIR) data was acquired on an ATR Crystal spectrometer, Bruker. The X-ray diffraction (XRD) data was collected on a D8 -Discover diffractometer, Bruker.
Raman Scattering (RS) RS between 200 and 3500 cm -1 were collected at room temperature using a MultiRAM FT-Raman spectrometer from Bruker equipped with a Nd:YAG laser. An incident wavelength of 1064 nm was used to measure the powder samples that were carefully mounted inside of glass vials. The powder samples were put in small glasses and a laser power of 250 mW was used to measure the HP-β-CD and the LA samples. Due to the lower density of the complex BVC-HP-β-CD, very thin pellets were made with the encapsulated drugs powders and a laser power of 500 mW was used. The data analysis was only qualitative in this experiment.
Acknowledgements Work by MLM was financed by the  Science without Borders Program  (Grant number  205609/ 2014-7 ) and HJ partially funded by an internship grant offered by the  Institute Laue-von-Langevin  (ILL). ECS work was financed by the  Norwegian Research Council  ( RCN) SYNKØYT Program  (project number  228551 ). The work of RI was part of a student project and supported by collaboration between HNB and AM. EP acknowledges  FAPESP  (# 14/1447-5 ) grant. We acknowledge the support of the ILL in providing the neutron research facilities used in this work. This was financed by  NMI3 , CoNext and Danscatt. The thermoanalysis apparatus used in the work were financed by Carlsbergfondets (grants  2013_01_0589  and  CF14-0230 ). This research also used resources of the  National Energy Research Scientific Computing Center , a  DOE Office of Science User Facility  supported by the  Office of Science of the U.
Piperlongumine is a natural amide alkaloid isolated from several species of Piper and is described in the literature as selectively cytotoxic to several cancer cell lines. Inhibiting cell migration has gained considerable interest as an approach for discovering antimetastatic agents because this process is fundamental to metastasis. Piperlongumine, selected from cell-based assay screening of NuBBE Database, inhibited the migration of MDA-MB-231 breast cancer cells with an EC 50 of 3. 0 ± 1. 0 µM by the Boyden chamber assay. A series of five analogous compounds based on the structure of piperlongumine were designed, synthesized and evaluated in cell migration and cytotoxicity assays. The analogue designed by molecular simplification ((E)-N-acryloyl-3-(3,4,5-trimethoxyphenyl)acrylamide) was the most active of the series, with an EC 50 of 1.
14 Within this context, we selected the natural product piperlongumine (1), also known as piplartine, from cell-based assay screening of NuBBE Database (NuBBE DB )  15  and evaluated its ability to inhibit cancer cell migration using biological and target-based experiments. Piperlongumine (1, Figure  1 ) is an alkamide isolated from several species of Piper (Piperaceae). 16 It is described as possessing antifungal properties,  17  cytotoxicity toward several cancer cell lines,  18, 19  and trypanocidal effects,  20  as well as other biological activities. 21 Furthermore, piperlongumine selectively induces cell death in cancer cells but does not reduce viability in normal cells. 22 his natural compound also demonstrates an interesting capacity to reduce angiogenesis and inhibit the formation of blood vessels in tumor xenografts in mice.
This system was incubated for 6 h at 37 °C and 5% CO 2. After incubation, the medium in the insert was removed along with the cells that had not migrated to the bottom of the membrane. The cells that had migrated to the lower portion of the membrane were fixed and stained with 1% aqueous toluidine blue in borax for 5 min. The membranes were cut using a surgical lancet and placed on a slide, and the migrated cells were counted using a Nikon Eclipse E600 optical microscope (Nikon Instruments Inc. , Melville, NY, USA) and NIS-Elements Image processing software. The assays were performed in duplicate using colchicine as a positive control and DMSO as a negative control. The EC 50 was determined from the curve of the log concentration versus the percent inhibition. The curves were plotted using data obtained for six different concentrations of the compounds tested in duplicate.
Acknowledgments This work was supported by the  State of São Paulo Research Foundation  ( FAPESP, Fundação de Amparo à Pesquisa do Estado de São Paulo) , grant No. 2013/07600-3 ;  Biota-FAPESP , grant No. 2003/02176-7 ;  SISBIOTA-CNPq-FAPESP , grant No. 2010/52327-5 ;  Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)  and  Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). The researchers also acknowledge scholarships, grant No. 2010/17329-7 , No. 2010/06741-4  and No. 2007/56140-4  from the  São Paulo Research Foundation (FAPESP).
Synthesis of Clx-BPA as Potential Endocrine Disruptor and Their Glucorono, Sulfo Analogues Manon Doumas 1,2,3 , Antoine Dupuis 1,3,4 , Sylvie Rabouan 1,3 , Nicolas Venisse 3,5 ,  Marion Albouy -Llaty 1,3,6 , Claire Grignon 1,3,4 , Pascale Pierre Eugene 1,3 , Virginie Migeot 1,3,6 andPascal Carato 1,3, * Acknowledgments: We thank  Prostate Cancer UK  for financial support.
Synthesis of Clx-BPA as Potential Endocrine Disruptor and Their Glucorono, Sulfo Analogues Manon Doumas 1,2,3 , Antoine Dupuis 1,3,4 , Sylvie Rabouan 1,3 , Nicolas Venisse 3,5 ,  Marion Albouy - Llaty 1,3,6 , Claire Grignon 1,3,4 , Pascale Pierre Eugene 1,3 , Virginie Migeot 1,3,6 andPascal Carato 1,3, * Acknowledgments: We thank  Prostate Cancer UK  for financial support.
Synthesis of Clx-BPA as Potential Endocrine Disruptor and Their Glucorono, Sulfo Analogues Manon Doumas 1,2,3 , Antoine Dupuis 1,3,4 , Sylvie Rabouan 1,3 , Nicolas Venisse 3,5 ,  Marion Albouy -Llaty 1,3,6 , Claire Grignon 1,3,4 , Pascale Pierre Eugene 1,3 , Virginie Migeot 1,3,6 and Pascal Carato 1,3, * Acknowledgments:  Delphine Parrot  is acknowledged for bacterial isolation and preliminary assays. The Acknowledgments:  Delphine Parrot  is acknowledged for bacterial isolation and preliminary assays. The "Ligue contre le cancer" is also acknowledged for financial support for the BioFlo ® 115 bioreactor.
Design, Synthesis, and Evaluation of the Cytotoxic Activity of New 3-{4-[(4-(Substituted)piperidin-1-yl)benzyl]}-2-Phenylindoles in Myeloid and Lymphoid Leukemia Cell Lines Jean Guillon 1, *,  Marian Vincenzi  1,2 , Noël Pinaud 3 ,  Luisa Ronga 1  ,  Filomena Rossi 2  ,  Solène Savrimoutou 1  ,  Stéphane Moreau 1  ,  Mathieu Marchivie  4 and  Vanessa Desplat  5 Acknowledgments: The members of the scientific committee would like to thank the local organizing committee and all the staff who collaborated in the organization of the conference and made this event possible. The local organizing committee warmly thanks the  University of Angers, Angers Loire Metropole, Ville d'Angers ,  Bruker Optics , JEOL,  Laboratoire Servier  for their financial support and also the other partners ( Giffard, Grosseron and Fisher Scientific ) for providing their deeply appreciated material support.
Acknowledgements The authors thank  Laura Smales  ( BioMedEditing, Toronto, Canada ) for language revision of this protocol, and the members of  New York University's Science, Health and Environmental eporting Program  for their assistance rewriting some of the news items used in this work. contributors RH: Helped with conception of study design, selecting news items, rewriting news items and wrote the draft of the protocol. AY: Helped with validation of rewritten news items and French translation of selected news items. PR: Conception of study design. GB: Helped in writing the statistical analysis. IO: Helped with survey questionnaire and validation of rewritten news items. GS: Helped with survey questionnaire. IB: Conception of study design, validating rewritten news items and helped writing the draft of the protocol.
Simultaneous Binding of Warfarin and Flavonoid Glycosides Additional measurements were performed under the assumption that warfarin would obstruct binding of flavonoid glycosides more easily. Flavonoid glycosides have lower binding constants and are bulkier so they are expected to interact with warfarin more easily than their aglycon counterparts. As with aglycons, two different behaviors were observed: (a) quercetin derivatives (all substituted at position 3) experience a slight decrease in F max with little or no impact on the c max , except with HSA being 92% saturated (Figure  2C , data for the other quercetin derivatives are not shown due to similarity) and (b) luteolin derivatives (substituted at positions 6 and 7) experience no decrease in F max nor c max , again with the exception of the HSA being 92% saturated (Figure  2D , data for isoorientin are not shown due to similarity).
Molecular Modeling of the Quercetin-HSA and Quercetin-3-O-glucuronide-HSA Complexes The comparison of docked (R)-and (S)-warfarin with the crystallographic structure of (R)-warfarin bound to HSA (Protein Data Bank (PDB) entry 2BXD) showed high similarity of ligands' positions (Figure  4 ) and validating the appropriateness of this approach. In warfarin vicinity, there are four positively charged residues, Lys-199, Arg-222, His-242, and Arg-257, and three residues that are not charged, Tyr-150, Leu-238, and Leu-260. Warfarin also forms three hydrogen bonds, with Tyr-150, Arg-222, and His-242. Molecules 2017, 22, 1153 6 of 14 warfarin does influence the distance between quercetin and HSA, but the results do not explicitly show displacement. They can also suggest conformational changes.
Simultaneous Binding of Warfarin and Flavonoid Glycosides Additional measurements were performed under the assumption that warfarin would obstruct binding of flavonoid glycosides more easily. Flavonoid glycosides have lower binding constants and are bulkier so they are expected to interact with warfarin more easily than their aglycon counterparts. As with aglycons, two different behaviors were observed: (a) quercetin derivatives (all substituted at position 3) experience a slight decrease in Fmax with little or no impact on the cmax, except with HSA being 92% saturated (Figure  2C , data for the other quercetin derivatives are not shown due to similarity) and (b) luteolin derivatives (substituted at positions 6 and 7) experience no decrease in Fmax nor cmax, again with the exception of the HSA being 92% saturated (Figure  2D , data for isoorientin are not shown due to similarity).
Molecular Modeling of the Quercetin-HSA and Quercetin-3-O-glucuronide-HSA Complexes The comparison of docked (R)-and (S)-warfarin with the crystallographic structure of (R)warfarin bound to HSA (Protein Data Bank (PDB) entry 2BXD) showed high similarity of ligands' positions (Figure  4 ) and validating the appropriateness of this approach. In warfarin vicinity, there are four positively charged residues, Lys-199, Arg-222, His-242, and Arg-257, and three residues that are not charged, Tyr-150, Leu-238, and Leu-260. Warfarin also forms three hydrogen bonds, with Tyr-150, Arg-222, and His-242. A docking summary for quercetin species can be found in Table  2. From all the shown clusters, only clusters number 1 and 3 of both 7-and 4 -quercetin anions and cluster 4 from 3,4 -fluorescent quercetin anion show overlap in binding positions with warfarin, but these clusters are formed from a very low number of runs (3 and 2 for quercetin anion at position 7, 1 and 1 for quercetin anion at position 4 , and 3 for fluorescent quercetin anion at positions 3 and 4 , respectively) and thus are unlikely.