dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments: This work was funded by the incentive grant,  Inter-Pasteurian Concerted Actions  ( ACIP-06-2016 ). LL and FA were supported by the  European Union 's  Horizon 2020 research and innovation programme under ZikaPLAN  grant agreement no. 734584  and the  French Government 's  Investissement d'Avenir program Laboratoire d ' Excellence Integrative Biology of Emerging Infectious Diseases  (grant  ANR-10-LABX-62-IBEID ). We gratefully thank the  Clinical Research Department of the Center for Translational Research in Paris  for its support in ethics procedures. We thank  Laurent Wantiez  and  Katie Anders  for their helpful discussion on statistical approaches. We also thank  Louis Cognet  for his contribution to samples handling.
Chen et al. (2019)  studied the degradation of atrazine from soil and demonstrated a reduction in stress effects on soybean growth when bioorganic fertilizer was used. This fertilizer was prepared using agricultural waste and organic cattle manure (76. 20%), biochar (4. 46%), and poly-(γ -glutamic acid (8. 63%), as well as one of the atrazine degrading strains (DNS10) belonging to Arthrobacter sp. (0. 91 × 10 8 CFU g -1 ). This strain of bacteria was isolated from atrazine-containing soils. In this study, using Design-Expert software, an optimal formulation was obtained to maximize atrazine degradation for the preparation of BOF, called DNBF10. Using DNBF10, the degradation efficiency of atrazine with an initial concentration of 15. 26 mg kg -1 was 95. 05% after just ten days. In general, the results of soybean planting in soil containing 75% chemical fertilizer and 25% DNBF10 fertilizer showed better growth than soil with 100% chemical fertilizer.
RNA Extraction, Library Preparation, and Sequencing and TE Library Construction RNA extraction, library preparation, and RNA sequencing data were performed as in Banho et al. [30]. The TE library was built based on TE insertions annotated in D. m. wrigleyi and D. arizonae, publically available (https://www. ncbi. nlm. nih. gov/assembly/GCF_ 000005175. 2 and https://www. ncbi. nlm. nih. gov/assembly/GCF_001654025. 1/GCA_00 1654025. 1, accessed on 10 December 2021). The RepeatMasker  [37, 38]  results for such genomes were obtained from NCBI and filtered to remove repeat sequences that are not TEs, classified as Simple repeat, Satellite, Low complexity, tRNA, rRNA, Unknown, and ATCG enriched regions. In addition, we have filtered all TEs insertions shorter than 100 nt. To merge all LTR sequences with their respective LTR element and small fractions of the same DNA element with overlapping positions in the genome, we have used One Code to Find Them All  [39]  (http://doua.
prabi. fr/software/one-code-to-find-them-all, accessed on 10 December 2021). Due to the RepeatMasker misclassification possibility caused by insufficient sequence similarity to define the correct TE family  [40] , we have minimized the super estimation of family numbers by removing the species names from family classification (e. g. , "Gypsy-1-Dmoj" = "Gypsy-1"). From this, we have annotated 41,546 TEs for D. mojavensis and 17,347 for D. arizonae, classified into 276 and 249 families, respectively. These manually curated TE classifications were merged into one file containing 58,893 TE sequences, which were classified in 298 families. As a result, our TE library presents 227 TE families shared between D. arizonae and D. m. wrigleyi, 49 exclusive to D. m. wrigleyi, and 22 exclusives to D. arizonae genome.
Small RNA Extraction, Library Preparation, and Sequencing Small RNAs were extracted from the ovaries (70 pairs) and testes (100 pairs) of D. arizonae, D. m. wrigleyi, and their interspecific hybrids using as described by Grentizinger et al. [41]. Two Illumina libraries were prepared for each sample from 1 to 6 ng of the purified small RNA fraction using the TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA), and sequencing was performed by GenomEast platform, a member of the 'France Génomique' consortium (ANR-10-INBS-0009)", using Illumina HiSeq 4000 instrument (read length 1 × 50 bases) (Illumina Inc, San Diego, CA, USA). Overall, 729 million reads were obtained, and reads from 23 to 30 nt were retained as piRNAs.
TE and Gene Read Mapping and Differential Expression Analysis The sequenced transcriptomes were trimmed using UrQt  [42]  to remove polyA tails (from RNA-Seq reads) and low quality nucleotides, and then the sequence quality was assessed using FastQC software (available at: http://www. bioinformatics. babraham. ac. uk/projects/fastqc, accessed on 10 August 2021). TE expression analyses were performed with the module TEcount from the TEtools pipeline  [37] , available at https://github. com/ l-modolo/TEtools, 10 August 2021. RNA-Seq reads were aligned to our TE library using Bowtie2  [43]. The read count step was computed for each TE family by adding all reads mapped on copies of the same family. In addition, the parental and hybrid transcriptomes were aligned to all annotated (20,110 mRNAs) coding sequences (CDS) of D.
mojavensis r1. 04 public genome [available at http://flybase. org/, accessed on 10 December 2021] using Kallisto  [44]  in order to verify the expression of genes regulating the piRNA pathway, according to the same procedure as described in Banho et al. [30]. We have used these data in the differential expression analyses to identify the genes involved in the piRNA pathway. Differential expression analyses were performed with the R Biocondutor package DE-Seq2  [45, 46]  (available at https://bioconductor. org/packages/release/bioc/html/DESeq2. html, accessed on 10 December 2021) using raw read counts to identify differential expression of TEs and genes in the reproductive tissues from the hybrids compared to the parental species. TE families and genes were classified as differentially expressed (DE) when the adjusted p-value (FDR level) was less than 0.
Small RNAs and Ping-Pong Analyses The small RNA-Seq analyses were performed using the method described by Fablet et al. [52]. The data were initially cleaned using Cutadapt  [53]  to remove the adapter sequences, and PRINSEQ-lite version 0. 20. 4 [54]  was used to filter the reads with a size ranging from 23 to 30 nucleotides to select piRNAs. The TEcount module from TEtools  [37]  was used to map the sense and antisense piRNA reads against our TE library, previously used differential TE expression analysis. Small RNA read counts were normalized using miRNA sequences of D. mojavensis (available at http://52. 23. 126. 124/genomes/ Drosophila_mojavensis/dmoj_r1. 04_FB2015_02/fasta/dmoj-all-miRNA-r1. 04. fasta. gz, accessed on 10 December 2021). For this, miRNA data were aligned, using Bowtie  [55] , against the cleaned small RNA data (before the size filtering).
Funding: This research was funded by the  Agence Nationale de la Recherche  (Grant Number  14-CE19-0016 ); by  Brazilian  agency  FAPESP-Fundação de Amparo à Pesquisa do Estado de São Paulo  (Grant Number  2016/19271-2 ); and  CNPq-Conselho Nacional de Desenvolvimento Científico e Tecnológico  (Grant Numbers  303455/2017-9 ,  141413/2016-6 ); by fellowships from the  Eiffel program ; and  Idex Lyon. Institutional Review Board Statement: Not applicable. Informed Consent Statement: Not applicable.
Study design and population The design and the primary results of the SYNTAX trial have been published previously  [14] [15] [16]. Briefly, the SYN-TAX trial (NCT00114972) was an international, multicentre, randomised controlled trial which randomised allcomers patients with de novo 3VD and/or LMCAD, deemed eligible for both PCI and CABG, in a 1:1 fashion to either CABG (n = 897) or PCI (n = 903) with the TAXUS Express paclitaxel-drug eluting stents (Boston Scientific Corporation, Marlborough, MA, USA). The SYNTAX trial completed patient follow-up at 5 years  [16]. The SYNTAXES study (NCT03417050) was an investigator-driven initiative that extended follow-up and aimed to evaluate vital status up to 10 years  [13] , funded by the German Heart Research Foundation (GHF; Frankfurt am Main, Germany).
The Cox proportional hazards regression model included the following covariates: age, gender, body mass index, medically treated diabetes, hypertension, chronic obstructive pulmonary disease, left ventricular ejection fraction, creatinine clearance (ml/min), disease type (3VD or LMCAD), and the anatomical SYNTAX score, with all these variables selected based on prior knowledge of their association with clinical outcomes  [17]. All analyses were performed using SPSS Statistics, version 25 (IBM Corp. , Armonk, 281 N. Y. , USA) and a p value of < 0. 05 was considered statistically significant.
Baseline and procedural characteristics A total of 1800 patients were randomised in the SYNTAX trial, of which 29 had at least one missing piece of data on the status of co-existing established CVD. The study cohort, therefore, comprised of 1771 (98. 3%) patients, of whom 827 (46. 7%) had documented established CVD (Online Fig. 1 ). The median duration of follow-up was 11. 2 years (IQR 7. 9-12. 1) overall and 11. 8 years (11. 0-12. 3) in survivors. Patients with established CVD were older and had significantly higher rates of insulin treated diabetes, chronic obstructive pulmonary disease, renal impairment, congestive heart failure, and unstable angina. They had higher Euro-SCOREs, Parsonnet scores, anatomical SYNTAX scores, and had more 3VD, lesions, total occlusions, bifurcations, stents, and had a longer total stent length (Online Table  1 ).
These early events may be procedure related, with the reduced hazard over time reflective of the accumulated prognostic benefit of secondary preventative medications. The 10-year follow-up in the present study was much longer than prior studies, unveiling the decline in risk, which may have also potentially contributed to the comparable mortality between patients with only one affected arterial bed and those without. Comparison between PCI and CABG in patients with established CVD has not been fully investigated. Observational data from patients with PVD and multi-vessel CAD showed that revascularization with CABG led to better adjusted 3-year survival than PCI  [30]. In contrast, randomised data from the BARI study showed no difference in 5-year survival between patients with multi-vessel disease and established CVD treated with balloon angioplasty or CABG, however, this study was hampered by limited power to detect a treatment effect due to the small size of the established CVD subgroup (n = 303/1816)  [20].
Acknowledgements Not applicable. Funding The SYNTAX Extended Survival study was supported by the German Foundation of Heart Research (Frankfurt am Main, Germany). The SYNTAX trial, during 0-to 5-year follow-up, was funded by Boston Scientific Corporation (Marlborough, MA, USA). Both sponsors had no role in the study design, data collection, data analyses and interpretation of the study data, nor were involved in the decision to publish the final manuscript. The principal investigators and authors had complete scientific freedom. This work, RW, CG and WW are supported by Science Foundation Research Professorship Award (15/ RP/2765).
The 13 C NMR were acquired at 101 MHz and referenced to 77. 1 ppm for the CDCl 3 solvent. The NMR data was processed with MestReNova11 NMR software. HPLC was performed using a Gilson GX-271 instrument (Middleton, Wisconsin, United States of America) at 254 nm with Trilution LC V3 software. Analytical HPLC was carried out using a 5 µm 250 × 4. 6 mm Phenomenex Lux chiral column (Amylose-2 or Cellulose-2). In analytical HPLC, the normal phase separation method used was: eluent = hexane: ethanol (15:95 to 20:80) with 0. 1% TFA, detection (254 nm), flow rate (0. 5 mL/min), temperature (25 • C), and run time (20 min). Mass spectra were measured by the University of Illinois Mass Spectrometry Laboratory using the electrospray ionization technique (ESI). The optical rotations were measured for purified samples using the digital polarimeter JASCO (model DIP-370).
Population and setting This study was a prospective RCT (1:1) with two parallel arms, blinded evaluation, and a hypothesis of superiority. The protocol was preregistered on https://clinicaltrials. gov/(protocol ID: NCT03375073). Approval was obtained from the ethics committee of the French Society of Anesthesia & Intensive Care Medicine (IRB 00010254-2019-066) on May 19, 2019. The study was conducted at the medical simulation centre of the Grenoble Alpes University Hospital (Alps Research Assessment and Simulation Centre) during the 2017e8 academic year. The study followed the recommendations of the International Committee of Medical Journal Editors and the Consolidated Standards of Reporting Trials guidelines  22  and its extensions for clustered trials, non-pharmacological treatment intervention, and healthcare simulation research.
Baseline data and secondary endpoints The duration of crisis management, from occurrence of laryngospasm to authorisation given to resume the procedure, was measured. The proportion of teams that issued a call for help in a timely manner (i. e. before SpO 2 fell to <80%) was examined. Heart rate variability was recorded to assess physiological stress response in each member of the anaesthesia team. Point-by-point HR was measured and recorded by a pectoral HR monitor (Smart Sensor®; Suunto, Vantaa, Finland) connected to a dedicated mobile software (Car-dioMood®; CardioMood, Moscow, Russia). Sympathetic activation in response to acute stress is associated with a decrease in HR variability, and thus in standard deviation normal to normal (SDNN). 24 The SDNN was calculated for each participant over six relevant consecutive periods: at subjects' arrival (during 5 min), during handover (1 min), during the pre-crisis.
Statistical analysis With the assumption that the mean (standard deviation [SD]) clinical-team-based performance score would increase from 45 (10)/100 points in the control group to 55 (10)/100 points in the intervention group, a 5% a risk, a 10% b risk, and a bilateral test, the total number of teams required was 32 (16 per group). All analyses were intention to treat and all statistical tests were bilateral. Analyses were performed with Stata 15® software (Timberlake, London, UK). A P-value 0. 05 was considered significant. The distribution of quantitative variable was studied by examining graphic representations (frequency histograms and QQ plots) and using ShapiroeWilk's test. Data were then expressed as mean (SD) or median [25th to 75th percentiles], as appropriate. Student's t-test was used to compare team-based clinical performance scores between groups.
Results were expressed in terms of absolute differences in scores and their 95% confidence intervals (95% CIs). Duration of crisis management was compared using Wilcoxon's test because of an extreme variable. Raw data from the pectoral HR monitor were recovered and analysed independently (none of the CardioMood software analyses were used). RR outliers presumed to be attributable to artifact were graphically eliminated blindly from the randomisation group and before any statistical analysis. The effect of intervention on SDNN and PLS over time was analysed using linear mixed-effects regressions.
Acknowledgements The authors thank  P. Lafont  and  P. Romegoux  for precious help in conducting the study, the  Alps Research Assessment and Simulation Centre of the Grenoble Alpes University Hospital , and the  CRNA School of the Grenoble Alpes University Hospital  for their logistical support. The authors also thank the six experts who helped develop the scoring tool:  C. Buleon ,  C. Dadure ,  M. Lilot ,  P. Roulleau ,  G. Savoldelli , and  I. Tanoubi , and the residents and nurses for their participation.
Data are archived in the GEO repository (www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE152576). Quantitative reverse transcription PCR Quantitative reverse transcription PCR (RT-qPCR) was performed in triplicate using SYBR Green PCR Master Mix (Applied Biosystems, Foster City, CA, USA) and primers for mouse C2cd4a and βactin genes. Immunofluorescence and imaging for subcellular localisations Rodent (MIN6  [15] , INS1[832/13] [21]) or human (EndoCβH1  [30] ) beta cell lines (previously confirmed as being mycoplasma free) were cultured for 12 h or 24 h post transfection (with C2CD4A-or C2CD4B-FLAG tagged constructs) and fixed in 4% (wt/vol. ) paraformaldehyde (Sigma-Aldrich, Gillingham, Dorset, UK) before being incubated with anti-FLAG antibodies. Images were collected by a spinning disk microscope and a confocal inverted microscope.
Immunoprecipitation and mass spectrometry Mycoplasmafree MIN6 cells grown in standard culture conditions  [31]  were transfected in duplicate with FLAG-tagged-C2CD4A or -C2CD4B expressing plasmids or with a FLAG tag-only expressing plasmid using Lipofectamine 2000 (Thermo Fisher Scientific). Immunoprecipitation and affinity purification-MS (AP-MS) analysis were performed, as previously described  [32] , with minor modifications. The mass spectrometry proteomics data have been deposited to the ProteomeXchange repository (www. ebi. ac. uk/pride/archive/projects/ PXD021597).
Results C2CD4A and C2CD4B expression in mouse and human islets Human C2CD4A and C2CD4B are 83% homologous. Like their murine homologues, the two human genes are predicted to have evolved from a common ancestor (see phylogenetic tree, ESM Fig. 2a ). Conservation of genomic architecture (synteny) at this locus argues for direct homology between the human and murine forms of each gene. The zebrafish (D. rerio) possesses two C2cd4-like genes homologous to H. sapiens and Mus musculus: C2cd4a and C2cd4c (ESM Fig. 2a ). Scrutiny of gene expression databases (http:// Biogps. org, accessed March 2020), and previous publications  [33, 34] , reveals approximately tenfold higher levels of C2cd4b than C2cd4a mRNA in mouse islets and purified mouse beta cells (ESM Table  1 ). In contrast, roughly equal levels of C2CD4A and C2CD4B mRNA are present in human islets  [35]  and purified beta cells  [36].
Acknowledgements We thank  I. Cebola  ( Division of Systems Medicine, Imperial College London, London, UK ) for her comments and revision of the manuscript. We also thank  S. Rothery  and other members of the  Imperial College Facility  for Imaging by  Light Microscopy  (FILM;  Imperial College London ) for training and use of the wide-field and confocal microscope. We also thank  H. M. Muhitu  and  X. Li  ( Section of Cell Biology and Functional Genomics, Imperial College London ) for quantification of mouse islet beta cell mass and for plasmid cloning, respectively. This work was presented at the Diabetes UK Annual Conference Manchester (2017),  Diabetes UK Annual Professional Conference  ( 2018 ), and the  EASD Annual Conference, Berlin  ( 2018 ).
Data availability The datasets generated and/or analysed during the current study are available in the Biorxiv repository, (www. biorxiv. org/content/10. 1101/2020. 05. 18. 099200v1 ). RNA-Seq ( GSE152576 ) and proteomics (PXD021597) data have been deposited to GEO (www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE152576) and ProteomeXchange (www. ebi. ac. uk/pride/archive/projects/PXD021597) repositories, respectively. Funding GAR was supported by  Wellcome Trust Senior Investigator  ( WT098424AIA ) and Investigator ( WT212625/Z/18/Z ) awards,  MRC Programme grants  ( MR/R022259/1 ,  MR/J0003042/1 ,  MR/L020149/1 ,  MR/R022259/1 ) and  Experimental Challenge Grant  (DIVA,  MR/ L02036X/1 ),  MRC  ( MR/N00275X/1 ),  Diabetes   UK grants  ( BDA/11/ 0004210 ,  BDA/15/0005275 ,  BDA 16/0005485 ) and  Imperial Confidence in Concept (ICiC)  grants.
This project has received funding from the  European Union 's  Horizon 2020 research and innovation programme via the Innovative Medicines Initiative 2 Joint Undertaking  under grant agreement No  115881  (RHAPSODY) to GAR. Work in the DJW laboratory was funded by the  Medical Research Council  ( MC-A654-5QB40 ). SJM was supported by an  Imperial College/Wellcome Trust   ISSF Springboard Fellowship.
The European strong motion database (ref. 3 ) contains only eight recordings (over 23,014) of superficial events recorded <5 km from the rupture plane, all of them being from earthquakes with local magnitude lower than 4. 5. Two cases of superficial events with M w ~5 and causing exceptional ground motions (i. e. , with Peak Ground Acceleration-PGA-exceeding 5 m/s 2 ) were reported in California (ref. 19 ) and in Nevada (ref. 20 ). In the absence of near-fault strong motion recording for the Le Teil earthquake we conduct numerical predictions of the ground acceleration (Fig. 1b ). First we perform a source analysis and generate a suite of rupture models, describing the space-time distribution of slip across the fault. The rupture models are calibrated based on the Interferometric SAR slip model proposed by (ref.
We compiled a database of displaced rocks and a database of funeral slabs displacements. After the Le Teil event, we observed, in specific places, that tens of stones and rocks, which are numerous in this back country of smooth hills and scattered limestone outcrops, had been displaced and sometimes freshly fractured and broken (Fig. 4 , Methods, Table  S2 , Fig. S6 ). Freshness of cuts and fractures and the consistency of several tens of observations indicate that some of these rocks were tossed into the air during the earthquake, with breakage occurring at the time of impact, implying that vertical acceleration exceeded gravity (e. g. , refs. 50, 51 ). All the evidences for upthrown and displaced rocks are located in the vicinity of the SW part of the surface fault trace (Fig. 1a  and S6 ), an area that remarkably coincides with the area where simulated vertical PGA exceeds gravity (Fig.
g. , ref. 61  ). Figure  S3a  shows examples of generated rupture models. Velocity structure and near-fault wave propagation. A representative 1D velocity model was derived from the analysis of 6 days of continuous seismic ambient noise recorded synchronously by 19 temporary seismological stations deployed after the Le Teil earthquake (Fig. 1a , Table  S1 ). Rayleigh and Love wave dispersion curves and signed ellipticity of Rayleigh waves were measured with the 0. 1-4 Hz frequency range using a three-component beamforming method (ref. 43 ) implemented in the open-source Geopsy software (ref. 62 ) (Fig. S5a-c ). Dispersion estimates above 1 Hz are controlled by ambient noise recorded by seismic stations located within 3 km from the epicenter location. Dispersion estimates have been inverted by using the Conditional Neighboorhood Algorithm (ref.
Observations of funeral slab displacement. We inspected five cemeteries located in the fault vicinity (Fig. 1a ). The structure of French tombs is generally simple, composed of a vault covered by a rectangular granite slab backing onto a headstone (Fig. 5a ). We observed that the slabs, which were relying loosely without joints, were displaced during the earthquake. We compile a database of 48 slab displacements from cemetery C1 containing a large majority of the observations and located about 200 m from the northern fault rupture termination (Table  S3 , Fig. S7 ). We reported only a few sparse observations with smaller displacements in cemeteries C2 and C3, while no displacement was seen in cemeteries C4 and C5. 75% of the observations in C1 corresponds with slabs backing onto N70°-oriented headstones.
Acknowledgements We thank  Stéphane Baize ,  Pierre-Yves Bard ,  Michel Bouchon ,  Marc Cushing ,  Isabelle Douste-Bacqué ,  Stéphane Guillot ,  Estelle Hannouz ,  Sébastien Hok ,  Christophe Larroque  and  Jean-François Ritz  for fruitful discussions. We thank  Romain Jolivet  for providing the InSAR slip distribution before publication. This work was partially financed by  SINAPS@ research project  ( ANR-11-RSNR-0022 ) and by the  Ministry of Ecological Transition  ( research program  " Prévention des Risques ",  N°2201198104 ). J. R. G. 's contribution was partially supported by  Fonds européen de développement régional (FEDER)  ( SISM@LP-Swarm research project ,  POAI-PA0014885 ).