dataesr/scientific-paragraphs-categorization huggingface dataset:
INTRODUCTION The White-Kauffmann-Le Minor (WKL) scheme summarizes antigenic formulae of all known Salmonella serovars, on the basis of antigenic variability in the outer membrane lipopolysaccharides (O antigen), flagellar proteins (H1 and H2 antigens) and capsular polysaccharide (Vi antigen)  (1). The most recent edition of the WKL scheme has identified over 2,500 serovars belonging to the five subspecies of Salmonella enterica  (1, 2). Traditional serotyping of Salmonella based on slide agglutination has been used for decades worldwide (3), and it is still considered the gold standard method for Salmonella serotyping. According to this phenotype-based approach, the surface antigens are detected by agglutination of bacterial cells using specific Salmonella antisera (3). Traditional serotyping is labor intensive, and it requires trained technicians to provide valuable data  (3).
Whole Genome Sequencing and Data Analysis Genomic DNA was extracted using QIAamp DNA Mini Kit (Qiagen, Valencia, CA) and quantified with a Qubit 3. 0 Fluorometer (Life Technologies, Carlsbad, CA). Libraries for sequencing were prepared using Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA). High-throughput sequencing was performed on Illumina MiSeq with 2 × 250 paired-end reads. Raw sequence data were submitted to the European Nucleotide Archive (http://www. ebi. ac. uk/ena) under accession number PRJEB27935. Raw reads were assembled using SPAdes (version 3. 9) (  14 ), available online at the Center for Genomic Epidemiology (CGE) (www. genomicepidemiology. org). The serotyping was performed analyzing contigs with SeqSero (version 1. 2) (15) and raw reads with Salmonella TypeFinder version 1.
Numerical Solutions of the 2D Shallow Water Equations The approximation described in the previous section holds if the error remains small. We now evaluate this error by solving numerically the 2D problem (3. 1)-(3. 3), compute h, u and see how these values agree with the pseudo-conservation laws (4. 6),(4. 9),(4. 11) and (4. 7). We chose the T geometry shown in the right panel of Figure  1  for simplicity and considered symmetric and non symmetric initial conditions. We also increased the wave amplitude to estimate the effect of the non linearity. The Equations (3. 1)-(3. 3) were discretized using as space unit the depth d. The time unit was d g. The variables and fields was rescaled as We solved the nonlinear shallow water equations using a first order finite volume scheme on an unstructured triangular mesh produced with the Gmsh meshing software (see details in  [6] ).
We used the width w = 0. 125 and the typical size of the triangles is 0. 02. The time advance used a variable order Adams-Bashforth-Moulton multistep solver (implemented in Matlab under ode113 subroutine  [18] ). The relative and absolute tolerances were set to 10 -5. x = x d , t = t g d , h = x d , u = u √ gd. ( 5 The initial condition is taken as a travelling solitary wave of velocity c. This is an exact solution for the mass conservation law. We used a solitary wave inspired by the Serre Table  1. The two different dynamic problems for the T-branch.
Acknowledgments The authors thank  Tim Minzoni  and  Nick Ercolani  for useful discussions. We also thank the  Centre Régional Informatique et d'Applications Numériques de Normandie  for the use of its computers. J. -G. Caputo  was partially supported by  ANR  grant " Fractal grid ". D. Dutykh  acknowledges the support of  CNRS  through the project  PEPS InPhyNiTi "FARA ".
OCT proved to be a precise and reproducible method for non-invasive visualization and quantification of retinal layers and plays a crucial role in analyzing retinal changes in various neuroinflammatory disorders  [17] [18] [19] [20]. In a cross-sectional study, MOG-IgG-related OCT features indicated subclinical pathology in eyes without a history of ON (Eye ON-)  [16]. However, no longitudinal OCT data is reported in MOG-IgG-associated diseases so far and the pattern of longitudinal retinal damage still remains elusive. Using OCT, we assessed retinal layer thinning as a marker of neuro-axonal damage in a cohort of MOG-IgGseropositive patients without ON during follow-up (F/U). We aimed to investigate at baseline and longitudinally microstructural changes in MOG-IgG-seropositive patients, extending previous work in AQP4-IgG-seropositive NMOSD  [21, 22].
All patients were matched by age (W = 370, p = 0. 542) and sex (χ 2 = 0,937, p = 0. 333) to 56 eyes of 28 healthy controls (HC; F/U) [years; median (IQR)] 1. 9 (1. 9-2. 3) from the NeuroCure Clinical Research Center, Charité -Universitätsmedizin Berlin, Germany. Inclusion criteria were the detection of MOG-IgG, complete longitudinal clinical and OCT imaging data with minimum F/U of 8 months and age between 15 and 75 years at baseline. Only eyes without concomitant potentially confounding diseases (glaucoma, diabetes mellitus, retinal surgery, retinal disease, ametropia > 6 diopters) were included. Eyes with a history of ON ≤ 5 months before baseline were excluded. Clinical data (diagnosis, disease onset, number of ON, date last ON, brain attacks, myelitis, EDSS, relapses, treatment history) were collected for all patients.
For two patients (8. 3%), the ring scan protocol changed during the acquisition period (ring scan to inner ring of a star-and-ring scan). Segmentation of all layers was performed semi-automatically using software provided by the OCT manufacturer (Eye Explorer 1. 9. 10. 0 with viewing module 6. 3. 4. 0, Heidelberg Engineering, Heidelberg, Germany). Experienced raters (BK for TU Munich data, JH for all other data) carefully checked all scans for sufficient quality and segmentation errors and corrected if necessary. OCT data in this study is reported and analyzed according to the APOSTEL and OSCAR-IB recommendations  [24, 25]. Macular microcysts were defined as the presence of cystic lesions on at least one scan detected by experienced raters (BK for TU Munich scans, JH for all other scans). Additionally, we collected habitually corrected monocular high-contrast visual acuity (VA) using ETDRS (Early Treatment Diabetic Retinopathy Study) charts at baseline in 20 ft distance for a subset of patients (N = 15).
Acknowledgements We acknowledge support from the  German Research Foundation (DFG)  and the  Open Access Publication Funds of Charité-Universitätsmedizin Berlin. JH and FCO like to thank  Charlotte Bereuter ,  Angelika Bamberger ,  Luise Böhm , and  Ivonne Hinz  for their excellent technical support. SJ would like to thank  Mrs. Anna Eschlbeck  and the  Nikon Imaging Center at the University of Heidelberg  for excellent technical assistance. MR would like to thank  Mrs. Kathrin Schanda  for excellent technical assistance. Nocturne UG, unrelated to this work. OO reports grant for research from  Novartis-Pharma  and grants and personal fees from  Biogen ,  Genzyme ,  Merck ,  Novartis-Pharma , and  Teva-Pharma , outside the submitted work. BK reports grants from the  Bundesministerium für Bildung und Forschung (Kompetenznetz Multiple Sklerose KKNMS) , intramural funding from the  Technical University of Munich  ( KKF program ) and a grant from  Novartis  unrelated to this study.
HZ reports a research grant from  Novartis  related to this study and speaking fees from  Teva  unrelated to this study. LB has nothing to disclose. JBS has received travel grants and speaking fees from  Bayer Healthcare, Biogen Idec ,  Merck Serono, Sanofi-Aventis/ Genzyme ,  Teva Pharmaceuticals  unrelated to this study. SJ has nothing to disclose. The  Neurological Research Laboratory (Medical University of Innsbruck  and  Tirol Kliniken , MR) receives payments for antibody assays (AQP4-and anti-neuronal antibodies) and for AQP4-and MOG-antibody validation experiments organized by  Euroimmun (Germany). KR was supported by the  German Ministry of Education and Research (BMBF/KKNMS ,  Competence Network Multiple Sclerosis ) and has received research support from  Novartis  and  Merck Serono  as well as speaking fees and travel grants from  Guthy Jackson Charitable Foundation ,  Bayer Healthcare, Biogen Idec ,  Merck Serono, Sanofi-Aventis/Genzyme ,  Teva Pharmaceuticals ,  Roche  and  Novartis.
Acknowledgements H. R. acknowledges the funding support from the  Victoria  Fellowship as well as the  Humboldt Research Fellowship  from the  Alexander von Humboldt Foundation. P. G. , G. B. , P. N. , S. H. , S. C. , and V. B. acknowledge funding from the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation programme  (Grant agreement no. 639109 ).
Ethical considerations Participation in this questionnaire was voluntary. Informed consent was obtained from each respondent on the first electronic page of the questionnaire. Furthermore, blinded processing of information was used to insure the anonymity of participation. Participants' privacy and voluntary participation were guaranteed and rigorously considered throughout the study course. According to these conditions, responses from participants who refused to participate in data analysis -even after completing the questionnaire-or withdrew at any stage of the study were excluded. All included participants were 18 years or older.
Paragraph 3 (English): Question 1 (in Arabic): 411 (27. 3%) answers were correct. Question 2 (in English): 1260 (84%) answers were correct. These two questions were answered correctly by 346 (23%) participants. The estimated time was less than 1. 5 min for 1117 (74. 3%) participants. Results from the three paragraphs are summarized in (Figs. 1and 2 and Additional file 1: Table  S1 ). The previous data underwent statistical analysis in a three-step process. In order to homogenize the analyzed data, a cohort of 44 (2. 97%) responses from preparatory year students and 20 responses with missing data were excluded (Additional file 1: Figure  S1 ). Step 1: At this stage, only Syrian Universities students' responses only were included. The total number of valid responses was 1193. Each response with two right answers for one    24]  point.
However, an Egyptian one-university study had shown that 31. 5% of students were opposed to the idea of mother tongue curricula, and about 44% of them mentioned that learning in a foreign language posed a problem in understanding the scientific information, while nearly half of students translated most of the words in medical books to their mother language to facilitate studying  [5]. The results of the aforementioned study may be discussed in light of the implicit all-or-none strategy proposed in their questionnaire. In comparison to this study; the evaluation in our study was focused solely on the written texts as a part of the educational process instead of doing an overall evaluation of the educational methods. As aforementioned, the sample size was calculated on the basis of the last published data released by Syrian Ministry of Higher Education at the time of study design, the additional number (254) of Arabic-speaking participants from different Arabic and foreign universities represents an added value, in our opinion, as it allowed us to enlarge our sample size and evaluate potential differences in the preferable and most comprehensive written linguistic method between students from Syrian and non-Syrian Universities.
Acknowledgements The authors would like to thank the participants. Authors would like also to thank the Syrian Researchers and its collaborated platforms for their help in launching the survey online. The authors are grateful for  Cham Said from Las Positas College, USA ,  Danah El-Refaie  from  University of Houston, USA , and  Dr. Hasan Iessa, PhD. , UK, for proof reading of this manuscript. And for  Amer Hatem  for the historical and linguistic information critical review. The authors highly appreciate the efforts made by  Fatima Aysha  and Gheith Alabdallah in Data Analysis. Authors would like also to thank  Mouhannad Malek  and the medical team of Syrian Researchers for their scientific support of this work.
For this purpose, miRs mimics were used, and their increased expression was confirmed by RTqPCR (Supplementary Figure  S3 ). Tumor nodules were observed in two out of the four mice with subcutaneous injection of glyphosate-exposed MCF10A overexpressing miR-182-5p, whereas none of the other five miRs were associated with tumor formation (Figure  2B ). Moreover, no tumor nodules were observed with subcutaneous injection of glyphosate/miR-182-5p/siRNA-TET3-exposed MCF10A, confirming that TET3 is implicated in glyphosate-mediated tumorigenic pathway (Figure  2C ). The use of the Pan-cancer RNA-seq data available from the KM plotter database revealed that although TET3 overexpression is associated with a favorable overall survival in head and neck squamous cell carcinoma, thymoma, and thyroid carcinoma, it is associated with an unfavorable overall survival in breast cancer, as well as cervical squamous cell carcinoma, kidney renal papillary cell carcinoma, liver hepatocellular carcinoma, pheochromocytoma, paraganglioma, and uterine corpus endometrial carcinoma (Supplementary File F1).
Glyphosate Exposure Induces Sustained TET3-Mediated Gene Demethylation The hypomethylation induced by glyphosate treatment is sufficient for tumor onset when using a two-factor hit model with induced overexpression of miR-182-5p. Therefore, we investigated the possibility that an epimark of hypomethylation might be imprinted in the DNA. We postulated that the putative epimark induced by glyphosate might be the hypomethylation of TET3-targeted genes because TET3 mediates glyphosate-induced DNA hypomethylation. The chromatin immunoprecipitation (ChIP) atlas database identifies MTRNR2L2, COL23A1, MSH3, DHFR, and DUX4 as the most frequently present in TET3-ChIP hits. According to this predictive finding, ChIP experiments using anti-TET3 antibody were performed for chromatin obtained from MCF10A cells treated or not with glyphosate for 21 days, such as described in Figure  1A.
Interestingly, only MTRNRL2 and DUX4 genes were immunoprecipitated by TET3 in MCF10A cells treated with glyphosate. COL23A1, MSH3, and DHFR genes were not immunoprecipitated in both untreated and treated MCF10A cells. Thus, the prediction made by the ChIP atlas database was validated for MTRNRL2 and DUX4 genes and not for the COL23A1, MSH3, and DHFR genes, suggesting a context-dependent accessibility for this set of TET3-controled genes. Accordingly, quantitative methylation-sensitive restriction enzyme (qMSRE) revealed that MTRNRL2 and DUX4 genes were strongly methylated in control cells and became hypomethylated in MCF10A cells exposed to glyphosate (Figure  5A ). The involvement of TET3 in the glyphosate-induced hypomethylation of DUX4 and MTRNR2L2 was confirmed by the abrogation with siRNA-TET3 of the glyphosate-induced hypomethylation of these genes (Figure  5B ).
, 2017). But our analysis with KM plotter database revealed a potentially unfavorable outcome for breast cancers when TET3 is overexpressed (Supplementary File F1). Our work shows that two epigenetic events (global DNA hypomethylation and overexpression of a miR) cooperate to promote breast cancer. Other epigenetic events described to be involved in breast cancer development include the reduction of H3K9 acetylation via TIP60 downregulation that promotes ER-negative tumors  (Bassi et al. , 2017; Judes et al. , 2018). Histone acetyltransferase p300 activity and BIM1mediated histone H2A ubiquitination that remodel chromatin are also two epigenetic events described as promoters for the development of aggressive breast tumors. A body of literature reports that miRs also play a crucial role in mammary tumorigenesis.
Results with KM plotter and bc-GenExMiner indicate that DUX4 level is negatively associated with breast cancer prognosis. No data seems available on MTRN2L2 in these databases. Based on the literature, DUX4 could act as an oncogene in various sarcomas and hematological malignancies  (Dib et al. , 2019) , while we could not find information in the literature revealing a putative oncogenic role for MTRNR2L2. These TET3-controlled genes are worth further investigation to establish their causal effect in mammary tumorigenesis in future work. Knowing the epigenetic pathway involved in glyphosatemediated risk increase might lead to prevention strategies to follow detection of the epigenetic risk. Our findings suggest that TET-specific inhibitor DMOG might be a plausible therapeutic intervention since it gave a satisfactory response on both DNA methylation and tumor incidence.
Migration Assay Cells (3 × 10 5 ) were seeded in six-well plates, cultured until they reached 80-90% confluence, and treated with 10 μg/ ml of mitomycin C (Sigma, France) for 2 h (to prevent cell proliferation). The monolayer of cells was scratched using a two-well silicone insert (Ibidi, Germany). Cell migration was monitored by microscopy (Incellis Cell Imager, Bertin, France). The images acquired at different time points  (0, 4, 8, 24, 28, 32, and 48 h)  for each sample were analyzed quantitatively. For each image, distances between one side of the wound and the other side were measured with ImageJ software; the mean value of 10 measurements all along the wound was recorded. The average migration speed was obtained by calculating the ratio distance/ time along the time course.
In-Cell ELISA In-cell ELISA was performed using the In-Cell ELISA Kit (Abcam, France) according to the manufacturer's instructions and after a fixation step performed with 4% of paraformaldehyde solution (10 min at room temperature). Primary antibodies were incubated overnight at 4°C. Adequate HRP-conjugated secondary antibodies were incubated for 1 h at room temperature. Detection was performed at 450 nm. After the washes, cells in each well were incubated with 1X Janus Green Stain for 5 min at room temperature, according to the manufacturer's instructions. Data were expressed in normalized unit, according to the following calculation: (HRPsignal 'minus' HRPsignal in absence of primary antibody)/(Janus Green signal 'minus' Janus Green signal in absence of cells). Antibodies used were anti-TET1 (sc163446, Santa Cruz, France), anti-TET2 (sc398535, Santa Cruz), anti-TET3 (sc139186, Santa Cruz), anti-ERα (sc8002, Santa Cruz), anti-PR (sc130071, Santa Cruz), and anti-HER2 (sc-393712, Santa Cruz).
Statistics Statistical analyses were performed using GraphPad PRISM (GraphPad Software, Inc. , CA, USA) statistical software. Descriptive statistics included numbers (%) for categorical variables and, for quantitative variables, median (IQT 25;75). We used the Fisher exact test to compare categorical variables and the non-parametric Mann Whitney U test to compare quantitative variables. Correlations of different measures of metabolic parameters with type of lipodystrophy or adherence or TSQM®-vII were evaluated using Spearman's rank correlation test or linear regression analysis. P values < 0. 05 were considered significant.
Funding Funding sources from  DHOS-INSERM  ( Translational Clinical Research Program 2010 ),  ICAN Foundation  (grant  ANR-10-IAHU ), the  National Program for Diabetes Research (PNRD/ARD ) and PhD grant from the  Conseil Régional d'Ile de France  ( Cardiovasculaire-Obésité-Diabète Domaine d'Intérêt Majeur ).
The Institutional Review Board and the Committee for Ethical Research (CEI) of the Instituto de Salud Carlos III (ISCIII) also approved the study. Clinical data. The information of each patient was collected from medical records, as we have previously described  15. All information was recorded using an online form in a shared database, which included all demographic, clinical, virological and laboratory data. A liver stiffness measurement (LSM) was performed by transient elastography (FibroScan ® , Echosens, Paris, France), as we have previously described  15. Patients were stratified according to the following LSM cutoffs: <7. 1 kPa (F0-F1), 7. 1-9. 4 kPa (F2; significant fibrosis), 9. 5-12. 4 kPa (F3; advanced fibrosis), 12. 5 to 25 kPa (non-risk of bleeding varices), 25 to 40 kPa (risk of bleeding varices), and >40 kPa (risk of hepatic decompensation).
Clinical outcomes. The clinical interpretation of HEV screening was as follows: i) acute hepatitis E: a patient had acute hepatitis E when positive for anti-HEV IgM antibodies or both IgM and IgG, and/or HEV-RNA was detected; ii) resolved hepatitis E: a patient had resolved hepatitis E when only anti-HEV IgG antibodies were detected; and iii) exposure to HEV: a patient was exposed to HEV when acute or resolved hepatitis E was detected. This interpretation was made based on data confirmed by immunoblot since all patients positive for IgM came out negative for viral detection.
Statistical analysis. Analyses were performed using IBM SPSS Statistics for Windows, Version 21. 0 (IBM Corp, Armonk, NY, USA) and OpenEpi (http://www. openepi. com/Menu/OE_Menu. htm)  30. All p-values were two-tailed and statistical significance was defined as p < 0. 05. For the descriptive study, values were expressed as absolute number (percentage) and median (25th; 75th percentile). Categorical data and proportions were analyzed using the chi-squared test or Fisher's exact test. Mann-Whitney test was used to compare data among independent groups. The inter-rater agreement or concordance between serological techniques was measured by Cohen's kappa coefficient.
Acknowledgements We want to acknowledge the patients in this study for their participation particularly, and to the  Spanish HIV HGM BioBank  integrated into the  Spanish AIDS Research Network (RIS)  and collaborating centers for the generous gifts of clinical samples used in this work. The  HIV BioBank , integrated in the  Spanish AIDS Research Network , is supported by the  Institute of Health Carlos III, ISCIII ,  Spanish Health Ministry  (Grant n°  RD06/0006/0035  and  RD12/0017/0037 ) as part of the  State Plan for Scientific and Technical Research and Innovation  and co-financed by  ISCIII-Sub-Directorate General for Research Assessment and Promotion  and  European Regional Development Fund (ERDF) and Foundation for Research and Prevention of AIDS in Spain (FIPSE). This study would not have been possible without the collaboration of all the patients, medical and nursing staff and data managers who have taken part in the project ( See Text, Supplemental Digital Content 1 , which show all collaborators).
The  RIS Cohort (CoRIS)  is funded by the  ISCIII  through the  Spanish AIDS Research Network  ( RIS C03/173  and  RD12/0017/0018 ) as part of the  State Plan for Scientific and Technical Research and Innovation  and co-financed by  ISCIII-Sub-Directorate General for Research Assessment and Promotion  and  European Regional Development Fund (ERDF). This study was supported by grants from  Instituto de Salud Carlos III  (ISCII; grant numbers grant numbers  PI14/01094  and  PI17/00657  to JB,  PI14/01581 , and  PI17/00903to  JGG,  PI14CIII/00011 , and  PI17CIII/00003  to SR),  Ministerio de Sanidad, Servicios Sociales e Igualdad  (grant number  EC11-241 ). The  RD16CIII/0002/0002 ,  RD16/0025/0017 , and  RD16/0025/0018  projects also funded the study as part of the Plan Nacional R + D + I and co-funded by  ISCIII-Subdirección General de Evaluación  and the  Fondo Europeo de Desarrollo Regional (FEDER).
Gateway LR cloning between pDONR2017-U3gRNA1-U6gRNA2 vector and pDE-CAS9Kr vector was then performed to create CRISPR-PDS or CRISPR-TFL1. 1. Sequences are given in Supplementary File S1. Primers used to verify the cloning at each step (primers 7 and 8: BP cloning and gRNAs addition, primers 9 and 10: LR cloning) are indicated in Table  1. MdU3 or MdU6 promoters driving gRNAs were, respectively, found upstream MD10G1073100 and MD07G1138500 genes 2  by BLAST with AtU3 and AtU6 sequences (respectively, found upstream X52629 and X52528;  Marshallsay et al. , 1990). Sequences are given in Supplementary File S1. Target sequences in gRNA were chosen with CRISPOR software 3   (Haeussler et al. , 2016)  using the Malus domestica INRA GGDH13 Version 1. 1 genome. Sequences are given in Supplementary File S1.