dataesr/scientific-paragraphs-categorization huggingface dataset:
MS/MS elemental formula and compound class predictions with Sirius Sirius (version 4. 8. 2) was used to predict elemental formulas for MS/MS precursors and for the deep neural network-based compound class prediction as part of the CANOPUS pipeline  (20, 21). Sirius commands are summarized as part of script S13 (see "Code availability" section). Elemental formulas by Sirius were further processed with scripts S14 and S15 (see "Code availability" section) to restore feature IDs and calculate the degree of unsaturation of these formulas. A main strength of CANOPUS-based class prediction is that it does not involve the interrogations of spectral libraries with fragmentation spectra, thereby allowing class prediction of MS/MS features for which no database hit is retrieved and circumventing the possible issue of error propagation when false class prediction is obtained by FBMN network-level propagation from feature-derived database hits.
Mass motif inference by MS2LDA Mass motifs were inferred using standard settings of MS2LDA (version release_23. 1)  (22) , submitted through the GNPS workflow (available at https://gnps. ucsd. edu/ProteoSAFe/status. jsp?task= 6f325f462e1145bfb465c679c2ee17d6). A total of 609 motifs were assigned including already existing motifs from motifdb. To explore mass motifs assignments on a species level, a binary mass motif matrix for all tissues was created by setting features above peak area of 10,000 to the value of 1 and those below to 0 (script S17). The resulting matrix was combined, and presence was summed per tissue and then set again into a binary matrix. Following this binary transposition of motif distributions, feature presence per motif was determined per species, resulting in a motif count table (script S18).
MS/MS annotation based on spectral database interrogations We implemented a three-pronged approach to annotating MS/MS from the interrogation of experimental and in silico fragmentation databases, similar as proposed in Sumner et al. (41). Level 1 in our priority assignment of annotations corresponded to hits retrieved from experimental spectral databases and/or NMR structural confirmation. Highest priority within level 1 of annotated spectra (level 1a) was given to hits confirmed by NMR in this work. Level 1b annotations correspond to hits from spectral alignments (and correspondence of precursor m/z values) using a local MatchMS (score above 0. 65 and >6 matching peaks) implementation (script S8, see "Code availability" section) with the modified cosine score, from an in house high-resolution experimental MS/MS spectra database of N.
attenuata SMs and/or manual inspection of spectra. Level 2 corresponded in our annotation approach to hits retrieved, with the cosine score from high-resolution MS/MS spectra of the GNPS database. Level 3 annotations were considered for hits from alignments with in silico MS/MS spectra or in the case of network propagation of hits from the experimental databases, both after manual inspection. Jobs for the recently developed molDiscovery approach (version 1. 0. 0)  (24)  were submitted through GNPS with both the molDiscovery built-in library and the Jassbi compound database created as part of this study. The Jassbi compound database (429 structures) was compiled from structures extracted from a recent Nicotiana phytochemistry review  (32). In silico MS/MS spectra for the Jassbi compound database were also produced with the fragmentation tool CFM-predict 4.
Consensus substructure and molecular network chemical classes We implemented an algorithmic approach to deal with the high number of annotations retrieved from the various in silico MS/ MS spectral databases. To this end, we used annotations retrieved form Sirius (confidence score above 0. 65), 1M-DB searched with modified cosine (score above 0. 5 and 5 matching peaks), 1M-DB searched with spec2vec (score above 0. 5), Jassbi-CFM (score above 0. 5 and 5 matching peaks), and Jassbi-molDiscovery. These annotations were retrieved at the molecular network or at the MS2LDA mass motif level to calculate consensus substructures for a given network (NCS) or mass motif (MCS). Main steps involved in consensus substructure calculations involved the following commands (scripts S16 and S19, see "Code availability" section): (i) fragment structures, (ii) get the most common fragments, (iii) select the top 50 and only keep the ones with >12 atoms, (iv) cluster by structural similarity, (v) sort by cluster size, (vi) calculate the maximum common substructure within the cluster, and (vii) retrieve the top 4 results.
To harness the vast amount of structural information classified by molecular networking, we selected the top 252 networks sorted by only picking networks containing >10 nodes. The peak areas within these networks were summed with script S24. Peak areas were normalized (Excel's STANDARDIZE function) by cluster ID, and the maximum on tissue level per species was kept. The propagated CANOPUS classes were grouped their peak areas summed (script S28), and the resulting data were used to create per species treemaps in Excel. A summary of the top 252 molecular networks, their calculated consensus substructures, and their propagated CANOPUS classes can be found in data S3. In addition, data S4 and S7 allow the navigation of this multilevel information at mass motif and network levels.
Computing MS/MS-informed phylometabolomics species trees To create MS/MS similarity-based species, referred to in Results as phylometabolomic trees, we used the data compiled as mentioned above (script S24) (Fig. 2A ) or the data from the motif count (script S18) (fig. S9 ) to calculate the Euclidean pairwise distances between species' metabolomes (script S20). The resulting matrix was then used to plot trees in R with the APE package using the neighborjoining algorithm and bootstrapping 999 with iterations (script S21).
The species tree was constructed using NGPhylogeny. fr  (75)  with default one click options and the PhyML maximum likelihood method. For ASR, feature intensities accounting for the species and tissue-wide NANN diversity were retrieved using the above-described mass motif characterization approach. ASR was performed with the MBASR package (76) (script S25) on peak areas of the root that have been transformed into an ordered trait of five categories (Fig. 9  and fig. S1 ).
α-Diversity analysis and CANOPUS class distance computation The α-diversity was calculated for each species based on Shannon entropy (script S29) using the scikit-bio package and sample features as operational taxonomical units. The top 252 networks as mentioned previously were selected their raw peak areas summed on the basis of propagated CANOPUS classes (script S28) and then converted to integers; networks without class annotations were discarded. The vegan package was used to perform NMDS, followed by the calculation of intrinsic variables (CANOPUS classes) with 999 permutations (script S30). The resulting vectors were used to calculate the per species cosine distances (script S31).
Experimental Design The development of DSM-loaded NEs was carried out utilizing a three-level Box-Behnken experimental design (BBD) with three independent factors using Design Expert software (version 13. 0 Stat-Ease, Inc. , Minneapolis, MN, USA). The Box-Behnken design model for response surface approach is useful because it enables: (i) evaluation of the quadratic model parameters; (ii) creation of following designs; (iii) identification of model's lack of fit; (iv) utilization of blocks; (v) the avoidance of severe experimenting because it could lead to disappointing results. In addition, it performs fewer runs of experiments with three factors. The concentration of oil (LG ® 90; X1), concentration of surfactant (tween 80; X2), and concentration of co-surfactant (THP; X3) were the three parameters chosen for this investigation.
Acknowledgements The EXTRIP workgroup includes:  Badria Alhatali ,  Kurt Anseeuw ,  Ingrid Berling ,  Josée Bouchard ,  Timothy E Bunchman Diane P Calello ,  Paul K Chin ,  Kent Doi ,  Tais Galvao ,  David S Goldfarb ,  Lotte CG Hoegberg ,  Sofia Kebede ,  Jan T Kielstein ,  Andrew Lewington ,  Yi Li ,  Etienne M Macedo ,  Rob MacLaren ,  James B Mowry ,  Thomas D Nolin ,  Marlies Ostermann ,  Ai Peng ,  Jean-Philippe Roy ,  Greene Shepherd ,  Anitha Vijayan ,  Steven J Walsh ,  Anselm Wong , and  Christopher Yates. We would like to acknowledge the valuable help of our dedicated translators, librarian, data extractors, and meeting secretary. Official translators were  Mrs. Alexandra Angulo ,  Mrs. Alla Abbott ,  Mr. Anant Vipat ,  Mr. Andreas Betz ,  Mrs. Angelina Kovaleva ,  Mrs. Denise Gemmellaro ,  Mrs.
Emulate mathematical model for understanding and personalize endodontic hydrogels ( Figure 2) In the past decade, there has been a remarkable surge in the generation of experimental and clinical data in biology and dental medicine. However, due to the wide diversity of models used, it has become challenging to compare and extrapolate findings. The future advancements in Artificial Intelligence and 3D imaging of endodontic spaces hold the potential to address this issue by designing virtual models based on scientific databases, such as those produced by omics for high throughput screening and predicting pathological biomarkers  [83, 84]. Similarly, such approaches could be efficiently used to anticipate the bioactivity of these hydrogels based on galenic properties of endodontic hydrogels  [81, 82].
Funding: This work was supported by the  French National Association of Research (ANR   JCJC ENDONANOBIOTIC  ( ANR-21-CE19-0001 ) and  ANR   JCJC TRIDENTOMIC  ( ANR-21 CE44-0015 )), the  Fondation de l'Avenir  ( AP-RM-21-030 ), the  French National Centre for Scientific Research (CNRS)  and the  French Institute for Odontological Research (IFRO). ML is a recipient of a PhD grant from the  French National Association of Research (ANR JCJC ENDONANOBIOTIC).
Phenolamides 4. 3. 1. General Information CP and Kuk_A were purchased from TransMIT PlantMetaChem (Giessen, Germany). TDHCS synthesis was performed under argon atmosphere. Melting points were measured on a Kofler bench and were uncorrected. 1 H and 13 C NMR spectroscopic data were recorded on a Bruker Advance III 400 (400 and 100. 6 MHz, respectively). Chemical shifts were reported in ppm (δ) and were measured related to the signals for the residual solvent  [64]. High resolution mass spectra (HRMS) were recorded on a Bruker MicrOTOFq ESI/QqTOF apparatus. Reaction completion was checked by TLC (Thin layer chromatography) using 60 F254 (Merck) plates and were revealed with UV light (254 nm). Flash column chromatography were achieved on a Reveleris ® Grace equipped with 40 µm silica cartridges.
Acknowledgments: The authors warmly thank  Arnaud Risler ,  Aude Fauvet ,  François Dupire ,  Pascale Lemière  and  Claude Gallois  for their precious help regarding different aspects of the project, including antibacterial and cytotoxic assays, plant culture and sampling together with synthesis of pure phenolamide. Plants were grown on the  Plant Experimental Platform in Lorraine (PEPLor, Université de Lorraine ), metabolomic analyses were conducted on the Metabolomic and  Structural Analytic Platform (PASM, Université de Lorraine ), and antibacterial assays were made on the  ABC Platform ® (Université de Lorraine ).
Polymer characterization 2. 3. 1. 1 H NMR spectroscopy The synthesized polymers were characterized with 1 H NMR spectroscopy using a Bruker 600 Hz MR-NMR spectrometer (Bruker BioSpin GmbH). Data analysis was performed using MestReNova Software. The chemical shifts are referred to the residual solvent peak (δ = 7. 26 ppm for CDCl 3 and δ = 4. 80 ppm for D 2 O).
Cloud point determination Samples of the thermosensitive polymers were dissolved in PBS at a concentration of 3 mg/mL. The cloud point (CP) was measured using a Jasco FP-8300 spectrophotometer (JASCO, Easton, MD) with a watercooled Peltier thermostatted 4-position automatic cell changer. The Spectra Manager program was used for measuring scattering at a wavelength of 650 nm while the temperature was raised from 4 to 40 • C at a rate of 1 • C. min -1. The onset point of increased scattering intensity is reported as CP  [53].
Rheological characterization The rheological properties of the formulations were studied using a Discovery HR-2 Rheometer (TA Instruments Inc. , Etten-Leur, the Netherland) with a Peltier Plate for temperature control and solvent trap to prevent evaporation of the solvent. Empty and drug loaded PNF-PNM hydrogel formulations with different polymer concentrations (5, 10, 15 wt%) were prepared as described in section 2. 4. , after mixing the polymer/drug solutions, the resulting solution was placed under the geometry and measured using a plate-plate geometry (aluminum, 20 mm diameter, initial gap was 200 μm). Normal force was controlled during the experiments to enable measurements of samples while volume changes occur. Data were processed using TRIOS Software version 5. 0. The storage (G') and loss (G") moduli were measured during a temperature ramp ranging from 4 up to 37 • C at a rate of 0.
Gel permeation chromatography Polymer samples were dissolved in the eluent, 10 mM LiCl in DMF, at a concentration of 3 mg/mL. The number average molecular weight (M n ) and polydispersity index (PDI) were determined through gel permeation chromatography (GPC), using a Waters 2695 Alliance (Waters Corporation, Milford, MA) with refraction Index detector and with a PLgel 5 μm Mixed-D column. The analysis was performed with the column set at 65 • C and 1 mL/min flow rate. Empower software was used for data analysis. A calibration curve was obtained by measuring PEG standards of narrow molecular weight (Polymer Standard Service GmbH, Mainz, Germany).
DMA characterization DMA 2980 Dynamic Mechanical Analyzer (TA-Instruments, Etten-Leur, the Netherlands) was used to determine Young's modulus of the hydrogels as previously reported  [38]  Thermosensitive DA hydrogel samples were prepared as described in section 2. 4. 1. The gels (diameter 2. 6 mm, 5. 2 mm height) were placed between the parallel plates, and a force ramp was applied at a rate of 0. 5 N/min up to a total force of 8 N at room temperature. The obtained data were analysed using TA Universal Analysis software and the Young's modulus (E) was calculated from the slope of the linear section of the stress-strain curve. Data are reported as mean ± standard deviation (n = 3).
Acknowledgements We thank  Annemijn de Kleer  for her contribution to this project. We also thank  Dr. Achim Sauer  for his kind advice and  Boehringer Ingelheim  for supplying the FAB antibody used in this study. This research was supported by funding from the  European Union 's  Horizon 2020 research and innovation programme  under the  Marie Skłodowska-Curie  grant agreement No  722717.
#8 Set up an open call for individual patients or patient organisations to register for involvement into HTA. Have and implement a clear policy on conflict of interests Patient involvement should be open to all and non-discriminative on the grounds of previous experience and presumed support time needed. There are multiple initiatives locally and internationally aiming to ease patient recruitment with education, coordination and/or databases. We recommend organisations leading these initiatives to come together and join forces on the base of commonly agreed principles. We also recommend local HTA/payer organisations to set up their open call for local patients, carers, patient advocates, patient experts and patient organisation representatives to be able to express interest. We suggest to actively promote this opportunity to harder to reach patient communities and a periodical revision of the registry.
Transporter mRNA expression in cultures of cryopreserved HepaSH cells Transporter mRNA levels were analyzed in cryopreserved HepaSH cells and primary human hepatocytes cultured for 24 h, 72 h and 120 h under a monolayer configuration. Contaminating mouse cells represented <0. 1% of cultured cells, for both 24 h-old and 120 h-old cultured HepaSH cells (Table  S3 ), thus ruling out any proliferation of mouse cells during the period of HepaSH cell culture, in agreement with previous data (Bachour-El  Azzi et al. , 2022). Examination of cell cultures by phase contrast light microscopy indicated that cultured HepaSH cells exhibited a flattened morphology, rather distinct from the cobblestone-like hepatocyte morphology shown by primary human hepatocytes, especially after 120 h of culture (Fig. S2 ); moreover, cultured HepaSH cells displayed no or only few refractive bile canaliculi-like structures, which were, by contrast, clearly observed in 120 h-cultured human hepatocytes (Fig.
2. ABC transporter mRNA expression in suspended HepaSH cells and primary human hepatocytes. Cryopreserved HepaSH cells and primary human hepatocytes were thawed and put in suspension, before RNA extraction and analysis by RT-qPCR for determining ABC transporter mRNA expression. Data are expressed in arbitrary units (a. u. ). Black bars on the graphs represents the expression mean of 7-9 batches (HepaSH cells) or 11-13 batches (primary human hepatocytes). **, p < 0. 01; ***, p < 0. 001; ns, not statistically significant. HepaSH cells displayed a mRNA expression pattern for SLC and ABC transporters well correlated to those found in cryopreserved primary human hepatocytes and human livers. They additionally exhibited notable activities of main sinusoidal uptake transporters, similar (for NTCP, OCT1 and OATPs) or even higher (for OAT2) than those observed in suspended cryopreserved primary human hepatocytes.
In addition, the miscommunication between human hepatocytes, mouse liver stromal cells and mouse intestinal cells in chimeric mice with humanized livers is likely to cause dysregulation of bile acid homeostasis, as demonstrated in FRG mice  (Chow et al. , 2017). The resulting enhanced levels of circulating bile acids may activate the farnesoid X receptor (FXR) and subsequently the targets of this receptor, including Fig. 3. Rank correlation analysis of transporter mRNA expression in HepaSH cells, primary human hepatocytes and human livers. Drug transporters were ranked according to their mRNA expression mean, with data from Figs. 1 and 2 (for HepaSH cells and primary human hepatocytes) or from the Human Protein Atlas website (for human livers), from the most to the less expressed one. Correlations were analyzed using the Spearman's rank correlation method.
, 2013). In this context, it is noteworthy that various culture conditions have been proposed for Fig. 5. SLC mRNA expression in cultured HepaSH cells and primary human hepatocytes. Cryopreserved HepaSH cells and primary human hepatocytes were thawed and put in monolayer culture for 24-120 h, before RNA extraction and analysis by RT-qPCR for determining SLC mRNA expression. Data are expressed as percentages of transporter expression found in thawed cells before plating. They are the means ± SEM of 5-6 batches (for HepaSH cells) or 8-10 batches (for primary human hepatocytes). *, p < 0. 05, **, p < 0. 01 and ***, p < 0. 001 when compared to expression levels in thawed cells before plating. keeping a high level of differentiation/polarity in cultured human hepatocytes  (Ruoß et al. , 2020) , including the use of improved culture media for monolayer 2-D hepatocyte cultures  (Chen et al.
AUTH O R CO NTR I B UTI O N S F. B. , L. L. , and C. B. provided data and drafted the manuscript; A. O. B. and J. H. S. established the study concept and design and drafted the manuscript; A. S. managed the study and drafted the manuscript. ACK N OWLED G M ENTSWe thank the patients included in this manuscript who have given written informed consent to the publication of their case details. We thank Drs C. Zimmer, E. Pilling, and M. Romet (Synergy Pharm -Santé Active Edition) who provided medical writing and language editing services. FU N D I N G I N FO R M ATI O N This study was funded by Pierre Fabre Dermo-Cosmétique. DATA AVA I L A B I L I T Y S TAT E M E N T The datasets generated and/or analyzed during the current study are not publicly available because the study product is under a European patent.
Materials and methods This study is a retrospective ethnobotanical survey nested in the ANRS 12345 TA PROHM study (ClinicalTrials. gov identifier: NCT02937779). The ANRS TA PROHM study is a multicenter observational and interventional prospective study conducted in five maternities in Cambodia from October 2017 to October 2019 aiming to assess the effectiveness of a HBIg -free strategy to prevent HBV MTCT based on 1/ the use of HBsAg and HBeAg rapid diagnostics tests (RDTs) and ALT level serial algorithm to identify women at risk of HBV MTCT 2/ a preventive treatment by tenofovir disoproxil fumarate (TDF) from 24 weeks of pregnancy for eligible pregnant women 3/ an early vaccination at birth (< 2 hours of life) for all newborns. Eligibility criteria for ANRS 12345 TA PROHM study were pregnant women aged 18 or over accordance with French and European legislation on clinical research and personal health data.
Nevertheless, the research dataset that underlie the results reported in this Article including deidentified participant data and data dictionary can be made available through a request to the Scientific Advisory Board of the TA PROHM study and to the French National Agency for Research on AIDS and Viral Hepatitis. The access request, if validated, will be framed by an agreement between the sponsor and the applicant. Additional documents, including the questionnaires and the informed consent forms can also be made available. The dataset and the additional documents will be available immediately after publication and could be shared with researchers who provide a methodologically sound proposal and after agreement from the Scientific Advisory Board and the French National Agency for Research on AIDS and Viral Hepatitis.
Study population Two groups of women (with and without post-partum hepatocellular injury) were selected from the ANRS 12345 TA PROHM study's database. Hepatocellular injury was defined by having Alanine Aminotransferase (ALT) > 2. 5 times the Upper Limit of Normal (ULN = 40 U/L). The first group consisted of women included in the ANRS 12345 TA PROHM study with normal ALT at inclusion visit but with ALT > 2. 5 times the Upper Limit of Normal (ULN = 40 U/L) at the 6 th week postpartum visit without common risk factors of hepatotoxicity (chronic alcohol consumption, use of drugs with known hepatotoxicity potential, HIV, HCV, HAV and HEV infections). The other group (control group) consisted of women with normal ALT both at inclusion visit in the ANRS 12345 TA PROHM study and at the 6 th week postpartum visit.
Acknowledgments The authors would like to thank all pregnant women and their families for their participation in the study;  Ms SOENG Chivly  for her help in samples storage at laboratory, the traditional healers for identification of the plants, namely  Mr. KY Bouhaing ,  Mr. HUON Chhom  and  Mr. THAY Savy ; the laboratory staff of  Institut Pasteur du Cambodge  for liver function test realization; all the members of the Scientific Committee of the TA PROHM study;  Claire Rekacewicz ,  Isabelle Fournier-Nicolle ,  Nicolas Rouveau ,  Maria-Camila Calvo Cortes  and  Laura Fernandez  for their support.
Objective Healthcare websites allow patients to share their experiences with their treatments. Drug testimonials provide useful information for real-world evidence, particularly on the occurrence of side effects that may be underreported. We investigated the potential of large language models (LLMs) for detecting signals of body weight change as under-reported side effect of antidepressants in user-generated online content. Materials and Methods A database of 8,000 user-generated comments about the 32 FDA-approved antidepressants was collected from healthcare social websites. These comments were manually annotated under the supervision of drug experts. Several pre-trained LLMs derived from BERT were fine-tuned to automatically classify comments describing weight gain, weight loss, or the absence of reference to a weight change.