dataesr/scientific-paragraphs-categorization huggingface dataset:
RESULTS AND DISCUSSION Genomic characterization of the isolates. A total of 79 draft genomes of E. coli ST1250 or ST1250-SLV/DLV, consisting of 54 sequences obtained in this study and 25 retrieved from EnteroBase or GenBank, were analyzed. The majority of isolates belonged to phylogroup B1 (73/79 [92. 4%]), followed by phylogroups A (5/79  [6. 3%] ) and E (1/79 [1. 2%]). Since the collection studied was aimed at E. coli ST1250 and ST1250-SLV/DLV, the majority of the isolates in the collection indeed belonged to ST1250 (60/79 [75. 9%]), followed by ST1250-SLV/DLV: DLV-ST4164 (4/79 [5. 0%]), SLV-ST826 (3/79 [3. 3%]), SLV-ST4527 (2/79 [2. 5%]), SLV-ST1686 (2/79 [2. 5%]), SLV-ST11123 (2/79 [2. 5%]), and SLV-ST2336, SLV-ST4552, SLV-ST7434, DLV-ST11033, SLV-ST11121, and SLV-ST11122 (1/79 [1. 2%] each).
Five plasmids harbored an MDR region of 41,754 bp (p15S04714-1) to 49,700 bp (p15S0829-4) between genes encoding a hypothetical protein of the backbone (Fig. 3, p15S04714-1 ). The very same position of the MDR region is found in pEQ1, of equine origin, and pHCM1 (GenBank accession no. AL513383), of human origin, designated a type 2 IncHI1 plasmid based on integration sites of the MDR region inside the plasmid backbone  (32). The other three plasmids contained an MDR region divided into two parts (14,708 bp and 34,143 bp) by a part of the inverted plasmid backbone of 14,228 bp (Fig. 3, p99063 ). This inversion was presumably mediated by two copies of IS26 flanking the backbone part (14,228 bp) and the larger, 34,143-bp part of the MDR region. This finding points to the existence of two variants of highly conserved epidemic IncHI1/ST9 plasmids differing in genetic structure, length, and the integration site of the MDR region.
coli strains of diverse sequence types have been obtained from five different pig farms from different geographical regions of China  (35). The fos operon is highly diffused among ST1250 strains and is carried by IncHI1/ST9 plasmids. The collection of 79 E. coli ST1250 and ST1250-SLV/DLV isolates was screened in silico for the presence of the 8,896-bp fos operon, which is involved in the metabolism of scFOS. Fifty-eight (58/79 [73. 4%]) isolates harbored the fos operon, while 1 isolate (ESC_ZA2274AA_AS) lacked the fosK gene, suggesting the presence of a nonfunctional operon. The majority (56/58 [96. 6%]) of isolates harboring the fos operon also harbored an IncHI1/ST9 plasmid. A BRIG comparison including all IncHI1/ST9 draft genome assemblies from short-read sequencing data (n = 56) showed that the fos operon is highly conserved and is carried by this plasmid lineage (Fig.
coli ST1250 isolates (99783-3RV and T20) had different genetic contexts. Analysis of the genetic surroundings of the fos operon of the 99783-3RV isolate showed the presence of an IncFIB(K) replicon on the same contig, suggesting the carriage of the fos operon by plasmids other than IncHI1/ST9 plasmids. The limited information provided by the short-read sequencing did not enable us to identify the genetic context of the fos operon within the T20 strain. However, plasmid replicons IncFIB(K) and IncY were identified in T20, suggesting the possibility that the fos operon is either mediated by plasmid types other than IncHI1/ST9, as in the 99783-3RV isolate, or chromosomally encoded, as observed previously for E. coli BEN2908 (GenBank accession no. AY857617)  (36). It has been suggested that a plasmid-mediated sugar metabolic element, such as the fos operon, could play a key role in strain fitness, contributing to the successful dissemination and maintenance of the fos operon-containing MDR IncHI1/ST9 plasmids in the equine intestinal microbiota  (6).
S1 ). Short-read sequencing. All isolates were subjected to whole-genome sequencing (WGS) with at least 50Â expected coverage. Genomic DNA was extracted using the NucleoSpin Tissue kit (Macherey-Nagel, Germany) and was used for DNA library preparation with a Nextera XT Library Preparation kit. Sequencing was performed on a MiSeq system (Illumina) using 2 Â 250-bp paired-end sequencing. Publicly available data. We searched EnteroBase (http://enterobase. warwick. ac. uk/species/index/ ecoli) for sequence data for E. coli ST1250 and ST1250-SLV/DLV, and assemblies along with corresponding metadata were downloaded. Available data sets for ST1250 isolates irrespective of the plasmid content and ST1250-SLV/DLV variants harboring IncHI1 were selected. Thirteen draft genome assemblies originating in Switzerland (n = 7), Germany (n = 2), Canada (n = 1), the United States (n = 1), and unknown origin (n = 2) were retrieved from EnteroBase.
Additional ST1250 and ST1250-SLV/DLV sequences from horses in The Netherlands (n = 11) and Guadeloupe (n = 1) were retrieved from BioProject (record numbers PRJEB34847  [10]  and PRJNA388339  [15] , respectively). In total, 25 draft genome assemblies of E. coli ST1250 and ST1250-SLV/DLV isolates were obtained from the public databases; among these, 22 originated from horses, 2 were of unknown origin, and 1 isolate was of human origin (Fig. S1 ). Long-read sequencing. PacBio sequencing was used to obtain complete high-quality reference chromosomal and plasmid sequences. Subsequently, sequences of randomly selected IncHI1 plasmids were obtained using MinION sequencing. For PacBio sequencing, genomic DNA was extracted using a NucleoSpin Microbial DNA kit (Macherey-Nagel, Germany). Libraries were prepared according to the microbial multiplexing protocol.
Shearing was performed using g-tubes (Covaris, USA), and no size selection was done during library preparation. Sequencing was performed with the Sequel I platform (Pacific Biosciences, Menlo Park, CA, USA). For Oxford Nanopore Technologies (ONT) sequencing, the DNA was extracted using a Gentra Puregene Yeast/Bact. kit and a DNeasy blood and tissue kit (Qiagen, Hilden, Germany). Libraries were prepared using a 1D ligation barcoding kit (catalog no. SQK-LSK109 and EXP-NBD104; ONT, Oxford, UK) and were sequenced in R9. 4. 1 and Flongle flow cells with a MinION Mk1B (ONT). Sequence data analysis. Raw data from short-read sequencing were adaptor and quality (Q # 20) trimmed using Trimmomatic (38), v 0. 36. De novo assembly was performed using SPAdes (39), v3. 13. 1, with the "careful" option. For PacBio data, HGAP4  (40)  in SMRT Link, v.
6, was used to perform the assemblies with a minimum seed coverage of 30. Long reads from MinION were demultiplexed and converted from fast5 to fastq format using Guppy, v3. 2. 1 (ONT). The adaptors and low-quality ends (Q # 8) were trimmed using Porechop, v0. 2. 2 (https://github. com/rrwick/Porechop) and BBDuk (https://sourceforge. net/projects/bbmap/), respectively. De novo hybrid assembly using short reads from Illumina and long reads from MinION was performed with Unicycler (41), v0. 4. 7. The complete chromosomal and plasmid sequences were annotated using RASTtk (42) and were manually curated according to GenBank in Geneious, v9. 0. 5.
Genomic characterization. The draft genome assemblies from WGS and EnteroBase were analyzed for the presence of antibiotic resistance genes (ARGs), virulence genes, plasmid replicons, and serotypes. For this purpose, ABRicate (https://github. com/tseemann/abricate) was used with thresholds set to 90% identity and 95% query coverage against the databases ResFinder (43), VFDB  (44) , PlasmidFinder  (45) , and EcOH  (46) , respectively. Plasmid multilocus sequence typing (pMLST) was performed using pMLST by the Center for Genomic Epidemiology  (45). MLST profiles were verified by mlst (https://github. com/ tseemann/mlst), and the phylogroups were assessed using ClermonTyping  (47). Phylogenetic analysis. The phylogenetic relatedness of isolates was evaluated. The open reading frames were predicted from draft genome assemblies using Prokka  (48) , and GFF3 files were used for core genome alignment in Roary  (49)  with default settings (the percentage of isolates a gene must be in to be considered a core gene is 99%).
The alignment was then used in RAxML  (50)  for calculating the phylogenetic tree under the GTR1GAMMA model supported by 1,000 bootstraps. The tree was visualized in iTOL, v4  (51) , and GrapeTree  (52). The nucleotide similarity between the isolates was determined by assessing the number of single nucleotide polymorphisms using snp-dists (https://github. com/ tseemann/snp-dists) with the core genome alignment as an input. Comparative genomics. Comparison of four high-quality annotated complete chromosomal E. coli ST1250 sequences obtained from PacBio sequencing with E. coli K-12 as a reference (GenBank accession no. U00096) was performed using progressiveMauve  (53). E. coli K-12 was selected especially because of the lack of virulence genes and the high level of characterization its genetic content.
Therefore, the comparison allowed us to see if there are virulence factors or any other genes that could offer an advantage for E. coli ST1250, since E. coli K-12 is a nonpathogenic strain. The complete annotated plasmid sequences were compared with respect to their plasmid replicon and plasmid ST using BLAST Ring Image Generator  (54). The structure of the fos operon (nucleotides 61904 to 70800 of pEQ1 [GenBank accession no. KF362121]) was examined and compared to the sequence within pEQ1. Data availability. The draft genome assemblies, the complete plasmid and chromosomal sequences, and the raw data from short-read sequencing have been deposited in GenBank and SRA, respectively, under BioProject number PRJNA638007. The complete nucleotide sequences of the plasmids have been deposited in GenBank under accession numbers MT586601 to MT586609.
ACKNOWLEDGMENTS We thank  Katerina Rehakova ,  Iva Kutilova  and  Martina Masarikova  for their excellent work in the laboratory. We thank  Alois Cizek , the staff from the  Equine Clinic of the University of Veterinary and Pharmaceutical Sciences Brno , and the terrain veterinarians for collecting and providing the samples or bacterial isolates. We are also grateful to  Stefan Börjesson  for his cooperation. The study was funded mainly by the  Czech Science Foundation  (award  18-23532S  to M. D. ). P. S. received funds from the  Internal Grant Agency of the University of Veterinary and Pharmaceutical Sciences Brno  (award  204/2020/FVHE ). J. H. , I. B. , and PacBio sequencing were funded by the  Charles University Research Fund PROGRES  (project  Q39 ), by  National Sustainability Program I (NPU I)  grant  LO1503 , and by project  CZ.
02. 1. 01/0. 0/0. 0/16_019/0000787 ," Fighting Infectious Diseases ," provided by the  Ministry of Education, Youth, and Sports of the Czech Republic. Isolates from the Czech Republic were collected and partially characterized within the project funded by the  Internal Grant Agency of the University of Veterinary and Pharmaceutical Sciences Brno  (grant  116/2015/FVL ). MinION sequencing was funded by  Horizon 2020  (award  773830 ),  OH-EJP-H2020-JRP-AMR-2-ARDIG , and internal funding from  Utrecht University. We have no potential conflicts of interest to declare.
Anticipated intake of the NF EFSA performed an assessment of the anticipated daily intake of the NF based on the applicant's proposed uses and maximum proposed use levels (Table  4 ), using individual data from the EFSA Comprehensive European Food Consumption Database  (EFSA, 2011). The estimated lowest and highest mean and 95th percentile daily intake of the NF among the EU dietary surveys are presented in Tables  5  and 6 , expressed as mg/kg body weight (bw) per day and mg per day, respectively. The estimated daily intake of the NF for each population group from each EU dietary survey is available in the Excel files annexed to this scientific opinion (under supporting information). As stated in Section 3. 6 on Specifications, the NF contains 580-595 lg vitamin D 2 /gram NF. Therefore, based on the highest (P95) estimated daily intakes of the NF and using a maximum content of 595 lg vitamin D 2 /g NF, the highest P95 estimated daily intakes of vitamin D 2 calculated both in absolute values per day (lg/day) and on a per body weight basis (lg/kg bw per day) are reported in Table  7.
7 lg/day in older children (4-13 years) and 4. 0 lg/day in adolescents (11-18 years). The P95 intakes from the sum of food and supplements were, however, available for children (up to 15 lg/day) and adolescents (up to 8 lg/day) in this previous opinion of the  EFSA NDA Panel (2012)  and were also used in the present calculations, but without considering the intake of vitamin D 2 from the NF as food supplement. Table  8  provides an overview of the exposure to vitamin D from different sources separately and combined, and the tolerable upper intake levels (ULs) established for young children, children, adolescents and adults. For infants  (4-12 months) , data on vitamin D intake were estimated by EFSA using composition data from the EFSA nutrient composition database and individual consumption data from national surveys from six European countries (EFSA NDA Panel, 2018).
Estimated intake of the NF based on its use as an ingredient in the intended food categories at the maximum proposed use levels (mg NF/kg bw per day) Intakes are assessed for all EU dietary surveys available in the food comprehensive database on 04/12/2020. The lowest and the highest mean intake observed among all available EU surveys are reported in these columns. The data relate to a period in which UK was still a Union Member State. (b): Intakes are assessed for all EU dietary surveys available in the food comprehensive database on 4/12/2020. The lowest and the highest P95th intake observed among all EU surveys are reported in these columns (P95th based on less than 60 individuals are not considered). The data relate to a period in which UK was still a Union Member State. (c): Referred as 'toddlers' in the EFSA food consumption comprehensive database (EFSA, 2011).
Estimated intake of the NF based on its use as an ingredient in the intended food categories at the maximum proposed use levels (mg NF/day) Intakes are assessed for all EU dietary surveys available in the food comprehensive database on 4/12/2020. The lowest and the highest P95th observed among all EU surveys are reported in these columns (P95th based on less than 60 individuals are not considered). The data relate to a period in which UK was still a Union Member State. (c): Referred as 'toddlers' in the EFSA food consumption comprehensive database (EFSA, 2011). (d): Includes elderly, very elderly, pregnant and lactating women.
83 14. 52 9. 89 21. 00 Other children 3-< 10 8. 47 17. 60 14. 64 28. 66 Adolescents 10-< 18 8. 12 15. 90 16. 47 34. 45 Adults (d) ≥ 18 12. 58 17. 24 22. 33 34. 45 (a): Intakes are assessed for all EU dietary surveys available in the food comprehensive database on 4/12/2020. The lowest and the highest averages observed among all EU surveys are reported in these columns. The data relate to a period in which UK was still a Union Member State. (b):.
Compression test The test of compression was performed using the HAAKE MARS (Fig. 2a ), Modular Advanced Rheometer System, Thermo Scientific instrument with a parallel geometry of 20 mm of diameter (TiLL11030P20). The measurement steps were managed with the HAAKE RheoWin Job manager software 4. 85. 0002. The zero gap was determined and the temperature was set to 25 °C, then the geometry was raised to 10 mm. A cowpea seed was placed for each measurement between the geometry and the plate then a first step program was run to bring the geometry onto the surface of the seed (Fig. 2b ). The instrument geometry stopped going down when it measured a force of 25 mN. The force was reset to 0 at the current height, geometry position, or before the start of the compression test, the geometry position was taken as the initial height (h0) of the seed.
work was financially supported by the educational ministry of TOGO. The Laboratoire Rhéologie et Procédés (LRP) is part of the LabEx Tec 21 (Investissements d'Avenir -grant agreement n°ANR-11-LABX-0030) and of the PolyNat Carnot Institut Investissements d'Avenir -grant agreement n°ANR-11-CARN-030-01).
MATERIAL AND METHODS: Human study This study is ancillary to a previously published studies  (30)  that included subjects with severe obesity involved in a bariatric surgery program (RYGB) carried out at the Pitié-Salpétrière University Hospital, Nutrition and visceral Surgery Departments (Paris, France). Obese subjects were stratified according to their metabolic status, and two groups were constituted: obese subjects without T2D (Ob, n= 14) and obese subjects with T2D (ObD, n= 13) receiving antidiabetic treatments or yet untreated  (30). Results related to EEC preparation, RNA-sequencing and its subsequent analysis have been already published  (30). The RNA-Seq gene expression data and raw fastq files are available on the GEO repository (www. ncbi. nlm. nih. gov/geo/) under accession number GSE132831.
After sequencing, raw fast5 read files generated by the MinKNOW™ software (ONT) were base called and demultiplexed using Guppy (version 2. 1. 3). Taxonomic binning was performed as follow: sequences were then mapped on an 8,000 reference genomes database using Centrifuge and the assignment was further quality-checked using Minimap2. From this step, species-level abundance tables were built and integrated with taxonomic information and sample metadata in phyloseq objects for subsequent analyses with phyloseq R package. Samples were rarified to 35,000 reads per sample before quantitative analyses. All analyses on abundance data were performed after rarefaction and exclusion of rare taxa (detected in less than 20% of the samples). Relative abundances values were calculated for each sample by dividing the rarefied abundances by the sum of the abundances.
FACS for enriched-EEC preparation in mouse We adapted to mice the FACS method for enriched-EEC preparation in humans described in  (30). Epithelial cells were scrapped and rinsed in FACS buffer (PBS, 3% FCS, 2 mM EDTA), blocked with Fc Receptor Binding Inhibitor Antibody (eBioscience) and stained with the following antibodies: CD45-BV421 (Bio Legend), CD326-APC (Biolegend) and CD24-FITC (Biolegend). Dead cells were excluded with propidium iodure (eBiosciences). During sorting experiments, cells were placed in FACS buffer with RNAse inhibitor (Life Technologies). CD24 marker was used to select enteroendocrine, Paneth and stem differentiated cells, CD45 to get rid of B lymphocytes that also expressed CD24 and CD326-APC to select epithelial cells. CD45-negative, CD326 positive, CD24-positive EEC enriched cell fraction was on a jet-in-air flow cytometer, the MoFlo Astrios with Summit software (Beckman Coulter).
Statistical analysis We used GraphPad Prism and R softwares for all statistical analysis. For human data, details of all analyses and tests are described in Osinski & al  (30). Briefly, to assess differential expression on semi-quantitative techniques such as RNAseq data, EdgeR (Biocomputing) package was used using negative binomial test. P-values were adjusted using the false discovery rate (FDR) method with a threshold of 0. 001. Only genes with count per million (cpm) over 100 for at least 2 individuals were considered. Statistical differences in mice were demonstrated with one-way or two-way ANOVA or t-tests as described in each figure legend after the outliers have been removed with ROUT method (Q=1%) and the sample distribution normality checked with D'Agostino & Pearson omnibus or Shapiro-Wilk tests.
C57BL6J mice received NLs via gavage for 5 days per week for 8 weeks. Weight and food intake were monitored biweekly throughout the study. No significant changes in body mass or food intake were observed during the experimental period (data not shown). Plasma total cholesterol (TC) and triglyceride (TG) levels were determined at T0 and after 8 weeks of NL treatment. TC levels were 100. 80 ± 11. 75 mg/dL and 102. 04 ± 15. 32 mg/dL in the C and NL groups, respectively; plasma TG levels were 28. 17 ± 18. 40 mg/dL and 26. 90 ± 25. 22 mg/dL in the C and NL groups, respectively. There was no statistically significant difference for either parameter, suggesting that NL treatment via gavage did not lead to any effects on plasma lipid levels. Therefore, the small amounts of TG and cholesterol in the NLs did not lead to hyperlipidemia.
Method This exploratory national qualitative study used the inductive process to analyse the structure of lived experience (IPSE) approach  (25) , a qualitative method specifically developed for clinical medical research to reach concrete proposals. This approach relies on an inductive process exploring in-depth the lived experience of patients, their loved ones and healthcare providers as well as the analysis of the structure of lived experience. Five stages structure the entire research process. The report of this study complies with the COREQ guideline  (26). This study was conducted from January 2018 through April 2019 and was approved by the "Comité consultatif de l'Information en matière de recherche dans le domaine de la santé (CCTIRS, ref 15903)", the "Commission Nationale de l'Informatique et des Libertés (CNIL, ref DR-2016-011) and is registered in ClinicalTrials.
Stage 4: Data collection, access to experience From February 2018 through April 2019, two researchers (LB, CS) conducted the interviews. They met each participant, obtained his/her written consent and collected social/demographic data to facilitate the subsequent research interview. A few days later in the participant's workplace, they conducted semi-structured one-on-one interviews using an open-ended approach, structured by areas to explore topics. These areas (table  2 ) were collectively determined by the group based on the assessment of two pilot interviews. The interviewers used an interactive conversational style. In an IPSE study, participants are considered the experts on their own experience and researchers must conduct interviews that offer them the opportunity to recount it. The interviews lasted 60-90 minutes.
These stages are carried out with the help of QSR NVivo 12 software. During the group process, these three researchers and the other group members -familiarized with the data through listening and reading all the interviews as many times as necessary -met nine times, after the analysis of five interviews, for two-hour meetings in order to conduct (i) the structuring phase, that is to regroup the categories into axes of experience; these axes being constructed such that each can be linked to its subjacent categories, and then to determine the structure of lived experience characterized by the central axes; and (ii) the practical phase, a process of triangulation with the data in the literature to identify the original aspects of the results.
Results We included 45 physicians and residents working in 13 departments, including 16 who had experienced burnout and 29 of their colleagues. Every potential participant we reached agreed to participate. For 3 departments, two physicians had experienced burnout. Among the colleagues, some reported being under psychotropic medication or seeing a psychotherapist. More than half of them mentioned feeling at risk of developing a burnout and/or having been "almost in burnout", or in what many called "a pre-burnout". The general characteristics of all participants are described in table  3. The data analysis showed that the structure of experience around workplace environment in this particular situation was common for both the physicians who experienced burnout and their colleagues. All participants reported experiencing a specific atmosphere around burnout in their workplace.
Acknowledgments We thank all the participants and  Jo Ann Cahn  for translating and editing the manuscript. We also want to thank  Maxime Ronot -Professor  of radiology,  Department of Radiology, AP-HP, Hôpital Beaujon , F-92118 Paris, France -and  Philippe Ducrotté  ( †) -Professor of Gastroenterology,  Department of Gastroenterology, CHU Rouen, F-76031 Rouen, France  -for their invaluable help and contribution during the recruitment process.