dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements The authors would like to express their gratitude to all people, local dyers and small cosmetics manufacturers who have participated in this screening of La Réunion Island dye plant species diversity, and  Prof. Dominique Cardon  for his helpful discussion about the project  PLANTIN  investigated here. We gratefully acknowledge  Aurélia Wolff  who provided technical supports for wool and cotton dyeing with the dye plants collected in this study. We are grateful to the  Réunion National Park  ( Parc National de la Réunion ) and the  National Forestry Office (Office national des Forêts-ONF ) who authorized the collection of all protected plant materials.
Electron Microscopy From Malfait et al. [14] , the porosity size of the SBA powder specimen does not change with the milling process (an example of a TEM micrograph of un-milled particles is visible in Figure  8d ). However, milling modifies the particle sizes. The low accelerating voltage used for SEM analyses does not allow the application of an automatic method for the measurement of the particle sizes. Consequently, they were measured with a manual tracing method. This methodology is described in Figure  8  (example of an un-milled SBA powder specimen): particles are traced by hand (Figure  8b ), then isolated from each other (Figure  8c ) to estimate their proportion and size distribution (Figure  8d ) using the ImageJ software. Another example of a bimodal size distribution measurement is described in Figure  9.
The physicochemical and pharmacokinetic properties of lamotrigine The molecular descriptors and other physicochemical properties of lamotrigine like the experimentally determined water solubility and the n-octanol/water partition coefficient (LogP) were obtained from the DrugBank database  [47]. Additionally, ALOGPS v. 2. 1 (The Virtual Computational Chemistry Laboratory, VCCLAB, Germany) and ChemAxon (ChemAxon, Budapest, Hungary) were used to calculate the computational n-octanol/ water partition coefficient (cLogP). A correlation plot was created between LogP and cLogP for a set of 35 drug molecules including metoprolol that was used as a benchmark for high/low benchmark of paracellular intestinal permeability from  [6, 9, 19, 21, 23, [48] [49] [50]. The correlation plot is shown in Supplementary Figure  S1.
PATIENTS AND METHODS The CANONIC and PREDICT cohorts The study was based on data from the CANONIC and PREDICT study cohorts. The CANONIC study, performed on 1343 consecutive patients from February to September 2011, aimed to assess prevalence, diagnostic criteria, mechanisms, clinical course and outcome of ACLF. 3  The PREDICT study, performed from March 2017 to July 2018 in 1271 patients, was initially designed to explore precipitating events and early (3-month) clinical course of AD only in patients hospitalised without ACLF. However, a few months after study onset, we also recruited 202 consecutive patients hospitalised with ACLF as controls. 1 6 linical and standard laboratory data and biobanking material were obtained in both cohorts at hospital admission and sequentially during hospitalisation in the CANONIC cohort, and at admission and during 3 months after admission in the PREDICT cohort.
Follow-up liver transplantation and mortality were recorded in both studies. The current article includes 1682 patients explored by untargeted metabolomics of serum samples obtained at enrolment (831 and 851 patients from the CANONIC and PREDICT studies, respectively). The identification of the death-related metabolomic fingerprint was obtained by using both cohorts and clustering prognostic results hierarchically. The design of the metabolomic models was performed in the CANONIC cohort and validated in the PREDICT cohort. The PREDICT study has been registered in ClinicalTrials. gov as NCT03056612.
Quality control (QC) samples were obtained by pooling aliquots of each sample and were injected every 10 samples throughout the experiments for further data normalisation/standardisation. In addition, a cocktail of standards, carefully chosen not to interfere with endogenous metabolites, was added to every analysed sample to monitor performances of chromatographic separation and mass spectrometry detection. 24 25 Data processing was performed using the Workflow4Metabolomics (W4M) platform. 26 Annotation of metabolite features was first performed by comparison of accurate measured masses, chromatographic retention times and MS/MS spectra to an in-house library made from ~1200 authentic pure standards analysed under identical conditions. To ensure accurate and consistent metabolite quantification, chromatographic peaks of the annotated metabolites were integrated for subject, patient and QC samples by using the Trace Finder software (Thermo Fisher Scientific).
Peak integrations were then manually reviewed for each sample and the resulting peak areas were normalised with respect to QC samples with the LOESS algorithm to correct for variation resulting from batch-to-batch signal differences. 27   2 ) repeatability (the coefficient of variation obtained on chromatographic peak areas of QC samples should be below 30%); and (iii) ratio of chromatographic peak areas of biological to blank samples above a value of 3. The resulting dataset was expressed in arbitrary units, representing the area of the chromatographic peak for each metabolite. We did not apply batch effect correction between cohorts.
Analysis of data Variables are described by their absolute value and relative percentage or by their median and IQR and compared between study cohorts through χ 2 or Kruskal-Wallis' hypothesis testing, as appropriate. A log2 transformation of the metabolite levels has been carried out before computing the fold change and corresponding p value when comparing survivors and non-survivors at 28 days in each study cohort. These comparisons have been represented using volcano and Cleveland plots. P values offered in the volcano plots were adjusted by Benjamini & Hochberg methods to control the false discovery rate. How mortality is distributed along time has been evaluated through the estimation of the cumulative incidence function and compared with Gray's test. Ability to predict the risk of death has been computed using Harrell's concordance index (C-index).
This approach reduced the dimension of the dataset from hundreds of metabolic features ('peaks') into a manageable number of ca. 130 metabolites with interpretable biological and pathophysiological significance in a complex context of severe SI and multiorgan dysfunction/failure. This pragmatic strategy, which in the end led to the identification of a death-related metabolomic fingerprint and specifically three highly sensitive prognostic metabolites closely related to new pathophysiological mechanisms of AD (alarm response and mitochondrial dysfunction associated with SI), paves the way for future implementation of metabolomics in routine clinical practice, as previously described. 28 29 inally, in our study, the metabolomic assessment was performed shortly after the onset of AD in all our patients, when SI and metabolic dysregulation were maximal, as suggested before.
Acknowledgements The study was supported by the  European Foundation for the Study of Chronic Liver Failure (EF CLIF ). EF CLIF is a non-profit private organisation. EF CLIF receives unrestricted donations from  Cellex Foundation  and  Grifols  and is partner or contributor in several  EU Horizon 2020 program projects MICROB-PREDICT  (project  ID   825694 ),  DECISION  (project  ID   847949 ) and  IHMCSA  (project  ID   964590 ). The funders had no influence on study design, data collection and analysis, decision to publish or preparation of the manuscript. on March 10, 2023 at  KU Leuven Libraries. Protected by copyright. http://gut. bmj. com/Gut: first published as 10. 1136/gutjnl-2022-328708 on 14 February 2023. Downloaded from.
O. maingayi is a commercial timber that is mostly distributed in Peninsular Malaysia, Borneo, Sumatra, and Thailand  [8, 9]. The bark root of O. missionis, which is typically discovered in India, has been used to treat ulcers, fever, rheumatism, jaundice, edema, hepatitis, and haemophilia  [6, 7]. Prior phytochemical studies of the leaves of O. maingayi  [10]  revealed that indole alkaloids are the predominant compounds and are active towards vasorelaxant activities. In this study, we report the chemical constituents, particularly indole alkaloids, in the bark from this plant. First, the LC-MS/MS data of crude and fractions were acquired, then the. RAW data from LC-MS/MS were converted to. mzXML format using MSConvert (http:// proteowizard. sourceforge. net, accessed on 4 March 2021). Every.
mzXML file was processed using MZmine 2 v53 to produce the. mgf data  [11]. The. mgf preclustered spectral data file and its corresponding. csv metadata file (for RT and integration) were exported and submitted to GNPS (Global Natural Product Social Molecular Networking). Next, a molecular network was constructed using a minimum cosine score value of 0. 6 and a network topK of 10 with six match fragment ions, which indicated similarity in the MS/MS spectra. The generated molecular network can be viewed and analyzed using Cytoscape (ver 3. 8. 2). To further prove this analysis, MS2LDA decomposes the fragmentation spectra into blocks of co-occurring fragments and losses, referred to as "Mass2Motifs"  [12].
9% water/0. 1% formic acid (LC/MS grade) and mobile phase B containing 100% MeOH (LC/MS grade), which were pumped at a rate 0. 250 mL/min. According to the following gradient sequence of percentage Solvent B increment: maintained at 5% from 0 to 2 min, increased from 5 to 100% from 2 to 30 min, maintained at 100% until 40min. MS/MS analysis was performed in positive mode, with the following optimized operating conditions: spray voltage, 3. 5 (+) and 2. 5 (-) kV; column temperature 40 • C; capillary temperature 325 • C; sheath gas flow rate (Arb): 50, auxiliary gas flow rate (Arb): 10; Sweep gas (Arb): 1; RF lens (%): 60; Scan range (m/z): 100-1000; Collision-induced dissociation (CID) energy was adjusted to 30%. All data were recorded and processed using Themo Xcalibur software version 4. 3.
Feature-Based Molecular Networking The MS2 data files were converted from the. raw (Orbitrap) standard data format to. mzXML format using MSConvert Software, which is part of the ProteoWizard package  [13]. All. mzXML files were then processed using  MZmine 2 v53 [11]. The mass detection was realized by keeping the noise level at 5. 0E5 at MS1 and at 5. 0E4 at MS2. The ADAP chromatogram builder was used with a minimum group size of scan of 5, a group intensity threshold of 3. 0E5, a minimum highest intensity of 3. 0E5, and m/z tolerance of 0. 001 Da (or 5ppm). The ADAP wavelet deconvolution algorithm was used with the following standard setting: a chromatographic threshold =1%, a search minimum in RT range min = 0. 30, a minimum relative height = 1%, a minimum absolute height = 5. 0E5, a minimum ratio peak top/edge = 2, and a peak duration range (min) = 0 to 2 min.
The isotopologues were grouped using the isotopic peak grouper algorithm with a m/z tolerance of 0. 006 Da (20 ppm) and a RT tolerance of 0. 5 min. Peak alignment was performed using the join aligner module (m/z tolerance of 0. 001 Da (or 5 ppm), weight for RT = 2. 0, and absolute RT tolerance 0. 3 min). The feature list row filler peak mz was 100 to 1000, which kept the MS2 scan and reset the ID. The peak list was gap filled with the same RT and m/z range gap filler module (m/z tolerance 0. 001 or 5ppm). Eventually, the. mgf preclustered spectral data file and its corresponding. csv metadata file (for RT and integration) were exported using the dedicated "Export/Submit for GNPS/FBMN" option.
Molecular Networking Parameters A molecular network was created using the online workflow (https://ccms-ucsd. github. io/GNPSDocumentation/, accessed on 16 August 2021) on the GNPS  [14]  website (http://gnps. ucsd. edu, accessed on 16 August 2021). The data were filtered by removing all MS/MS fragment ions within +/-17 Da of the precursor m/z. The MS/MS spectra were window filtered by choosing only the top 6 fragment ions in the +/-50Da window throughout the spectrum. The precursor ion mass tolerance was set to 0. 02 Da with a MS/MS fragment ion tolerance of 0. 03 Da. A network was then created where the edges were filtered to have a cosine score above 0. 6 and more than 6 matched peaks. Furthermore, the edges between two nodes were kept in the network if and only if each of the nodes appeared in the other's respective top 10 most similar nodes.
Finally, the maximum size of a molecular family was set to 100, and the lowest scoring edges were removed from the molecular families until the molecular family size was below this threshold. All matches kept between the network spectra and the library spectra were required to have a score above 0. 7 and at least 6 matched peaks. The spectra in the network were then searched against the GNPS spectral libraries. The molecular networking data were analysed and visualized using Cytoscape (ver 3. 8. 2)  [15].
177 Da) from the loss of hexose sugar at C-21 and a double bond at C16-C17, which has a similar pattern of fragmentation pathway as seen in cadambine 9 (Figure  4 ). Peak numbers correspond to the numbering of peaks that appear in the total ion chromatogram (TICs). a Structural hit obtained from GNPS spectral library matching. b Compounds have been elucidated from fractions (Figure  3 ). c Compounds previously reported in the leaves of O. maingayi  [10]. d MS/MS spectra matched with published literature  [22]. 16 ), and naulafine  (19). Next, to further prove our elucidation on 7, we utilized the web-based MS2LDA  [12, 16]  to process our MS/MS data and explore the results through interactive visualizations. This process indicated that Cluster A exhibits a Mass2motif (motif_370) shared by 16 parent masses that possess IA scaffold.
Results For the ten selected NCAs, the retrieved information is detailed in Tables 1, 2, 3 (for ECHA and EFSA, see Additional file 2). The overall data collection was carried out between February and December 2022; the collection period specific to each NCA is mentioned with each set of results. EFSA and five NCAs replied to the cnDAspe letter: Anses (France), BfR (Germany), Ctgb (Netherlands), KEMI (Sweden), and Nébih (Hungary). None of these NCAs called into question the approach and the method used by the cnDAspe. Needs for corrections or additions        The BfR considers that EFSA's DoIs good practice is not relevant for its agents, mostly civil servants, who are subject to specific German legal obligations (not detailed in the BfR response), a stand that may be challenged, EU-level requirements being considered as minimum requirements to be applied in each Member State.
However, this method has several advantages: it is easily reproducible; it gives a general picture of the information that is readily available to the public who understands the language in which NCAs' websites are written (or in English, when NCAs have English version of their websites). In addition, mail exchanges, with the support of an official public body (cnDAspe), gave the NCAs the opportunity to provide complements and corrections to the data retrieved from their website, leading, if necessary, to more accurate characterization of the LoIs management rules. We cannot rule out the hypothesis that some NCAs might have in-depth but non-open access LoIs management rules. Yet, none of the response messages contested or challenged the method adopted by the cnDAspe and the way it had converted the information it could retrieve.
On the other hand, formal procedures for managing LoIs are sometimes unclear or difficult to interpret. As a result, some of the criteria used were sometimes difficult to include in the analysis and in the comparison tables, e. g. , in case of incomplete data with an unspecified scope. However, most of the criteria were clear and the uncertainties do not question the main conclusions of the study. Overall, our work may be viewed as an indirect and approximate analysis, yet informative, of the existing LoIs management rules in each NCA taking part to the EU MA process for PPPs. It could be completed subsequently, taking into account the other NCAs involved in the PPP regulatory processes and additional relevant criteria. Improving the management of LoIs in EU expertise agencies is just one of many actions  [51] [52] [53] [54]  (e.
Rheology measurements Continuous and oscillatory measurements were performed using a rotational rheometer Kinexus PRO + (Netzsch-Gäretebau GmbH), equipped with a parallel plate geometry (PU40, roughened), with a diameter of 40 mm. All the experiments were carried out at 25 ± 0. 1°C. A fixed gap between the geometries was pre-set to 0. 1 mm and the sample's excess was removed. The software rSpace was used to process the data. To obtain the flow properties of the emulsions, continuous ramp testing was performed by recording shear stress and viscosity at increasing shear rates, ranging from 0. 01 to 10. 000 s -1 (logarithmic mode) for 860 s. Viscoelastic behaviour of the samples was studied using oscillatory measurements. To determine the linear viscoelastic region, the amplitude sweep test was performed at a constant frequency of 1 Hz with an increasing strain from 0.
Human skin permeation experiments The permeation test was conducted using static vertical glass Franz diffusion cells (nine-cell setup) with a diffusion area of 0. 64 cm 2 and a receptor volume of 5. 0 mL (Permagear Inc. ). All formulations were tested in three replicates, and the data were reported as mean ± S. D. Experimental setup: Human skin biopsies were taken out of the freezers, on the evening proceeding the day of the experiments and thawed overnight in a cold room (4°C). On the experiment day, biopsies were then mounted on the Franz diffusion cells. The receptor compartment of each cell was filled with degassed PBS (pH 7. 4) and was maintained at 37°C. The receptor medium was kept under continuous synchronous stirring using a magnetic stirrer. Before applying the formulations, the skins were placed in contact with the receptor medium (PBS) for 30 min to reach equilibrium hydration.
HPLC analysis HPLC analyses were performed using an Ultimate 3000 (Thermo Fisher Scientific, Voisins-le-Bretonneux) piloted with Chromeleon 7. 1 software. A C18 column with a particle size of 5 μm and length of 4. 6 × 150 mm (Interchim) was used and adjusted at 25°C. The software used was Chromeleon 7. 1 (Thermo Scientific, chromatography data system software).
Genes All biosynthetic genes used in the current study are listed in Supplementary Table  3. Genes were synthesized by either Integrated DNA Technologies or Twist Bioscience and optimized for expression in S. cerevisiae unless stated otherwise (_nat). The new candidates of AS (RteAS1-RteAS5) were predicted by using the RNA-sequencing reads from project PRJEB39488, downloaded from NCBI. This project contains libraries prepared from young developing leaves and mature and immature leaves and roots. Reads were trimmed with fastp v0. 22  (ref. 48) and first merged into super reads following the procedure described in the StringTie v2. 0 manual using the super-read module from MaSuRCA  49. Paired reads were then de novo assembled with Trinity v2. 8 (ref. 50) using the merged super reads as long-read data.
9 was comparatively higher for serpentine than alstonine (Extended Data Fig. 6 ). The analysis of halogenated MIAs was performed on a Vanquish Duo UHPLC binary system (Thermo Fisher Scientific) coupled to an Orbitrap ID-X mass spectrometer (Thermo Fisher Scientific). The data were acquired in positive mode with a voltage of 3,500 V, and the rest of the parameters were as described previously by Kildegaard et al. 58. For detection of halogenated compounds, LC-MS/MS analysis was performed using a Vanquish Duo UHPLC binary system (Thermo Fisher Scientific) coupled to an Orbitrap ID-X Tribrid mass spectrometer (Thermo Fisher Scientific). Chromatographic separation was achieved under reverse-phase conditions as previously described  58. The MS measurements were performed in positive-heated electrospray ionization mode with a voltage of 3,500 V acquiring the full MS/MS spectra (data-dependent acquisition-driven MS/MS) in the mass range of 70-100 Da.
Glucose, ethanol and organic acids Glucose, ethanol and organic acids were analyzed using a Rezex ROA-Organic Acid H + (8%; 150 × 7. 8 mm) column on a Vanquish dual-system HPLC coupled with a refractive index (IDEX RefractoMax 521) and diode array detector. The HPLC was run with a flow rate of 0. 7 ml min -1 (isocratic) using 9 mM sulfuric acid at a column temperature of 60 °C. The injection loop volume was kept to 5 µl for all samples and standards. For diode array detection, a 210-nm wavelength was used for detection and confirmation of organic acids. Peak identification was based on the relative retention times determined by injection of standard solutions. Quantification of compounds was performed using calibration curves on Chromeleon software, version 7. 2. 8.
Acknowledgements This work was supported by the  Novo Nordisk Foundation Copenhagen Bioscience PhD Programme  (grant number  NNF19SA0035438  to S. A. B. ), the  Danish National Research Foundation  (grant number  DNRF137  (CeMIST) to L. D. and Y. Q. ), the  US Department of Energy  (grant number  DE-SC0018368  to R. T. G. ), the  Agence Nationale de la Recherche  (grant number  ANR-20-CE43-0010  (MIACYC) to V. C. ) and the  Novo Nordisk Foundation Center for Biosustainability  (grant number  NNF20CC0035580 ) and  European Union   Horizon 2020 research and innovation program  (grant number  814645  (MIAMi) to M. K. J. ). We would like to thank  T. Wulff  and  L. Guillonneau  for analytical support.
Thus, enones 2a and 2e were not transformed into the corresponding indanones 3 in neat sulfuric acid (H 2 SO 4 ) at room temperature for 3 days. That is in accord with literature data  [19] , where H 2 SO 4 was used for dehydration of hydroxy ketones 1 into enones 2, and no cyclization into indanones was detected in this acid. However, in the current study, we carried out the reaction of electron-donating naphthyl-substituted enone 2n in H 2 SO 4 at room temperature, which resulted in the quantitative formation of indanone 3n after 3 days. The reactions of enones 2a,e,n with an excess (5 equiv) of AlBr 3 or AlCl 3 in CH 2 Cl 2 solution at room temperature for 3 days afforded complex mixtures of compounds. Then, the protonation of compounds 1 and 2 in TfOH was investigated by means of NMR spectroscopy.
Acknowledgements Financial support from the  Agence Nationale de la Recherche  ( ANR-19-CE07-0008-01 -HYPE4ALL ), the  Ministère de la Recherche , and the  CNRS , including doctoral & post-doctoral research assistantships for R. S. and R. N. , is gratefully acknowledged. This work has benefited from the analytical facilities and expertise of the CESAMO platform at the  University of Bordeaux. The  Centre de Calcul Intensif d'Aix-Marseille  is also acknowledged for granting access to its high performance computing resources.
Ziziphus lotus (L. ) Lam. (Rhamnaceae) is a plant species found across the Mediterranean area. This comprehensive overview aims to summarize the botanical description and ethnobotanical uses of Z. lotus and its phytochemical compounds derived with recent updates on its pharmacological and toxicological properties. The data were collected from electronic databases including the Web of Science, PubMed, ScienceDirect, Scopus, SpringerLink, and Google Scholars. It can be seen from the literature that Z. lotus is traditionally used to treat and prevent several diseases including diabetes, digestive problems, urinary tract problems, infectious diseases, cardiovascular disorders, neurological diseases, and dermal problems. The extracts of Z. lotus demonstrated several pharmacological properties in vitro and in vivo such as antidiabetic, anticancer, anti-oxidant, antimicrobials, antiinflammatory, immunomodulatory, analgesic, anti-proliferative, anti-spasmodic, hepatoprotective, and nephroprotective effects.