dataesr/scientific-paragraphs-categorization huggingface dataset:
For the cluster analysis, we observe the percentage of answers of every modality of the variable. If a variable has no modality with more than 66% of answers we will consider this variable as active variable and use it to build the clusters with SPAD software. We tried the cluster analysis with other choices for active variables (for example with variables from the parts problem solving and computing) but it was difficult for us to interpret the clusters proposed by the software. In this case this active variable divides the population in two comparable blocks. The other variables (where a modality is dominant with more than 66% of answers) will be reintroduced later as illustrative variables to illustrate the clusters. For the cluster analysis we begin with a multiple correspondence analysis (MCA) on the actives variables.
Lipid composition of bovine embryos. Liquid chromatography high-resolution mass spectrometry (LC-HRMS) spectra were obtained for 87 individual Q1 expanded blastocysts using ultra-high pressure liquid chromatography) (UHPLC) and 1686 features were identified. After visual inspection of the data, elimination of ions with coefficient of variation (CV) superior to 30% in the quality control (QC) and isotopes elimination, 496 features were conserved. Among those 496 features, 74 were annotated using the SimLipid Database. Annotated lipids are mostly triglycerides (32/74), diglycerides (12/74), glycerophospholipids and lysophospholipids (12/74) (Supplementary Table  S1 ). Among these 87 individual Q1 blastocysts, 43 were produced by OPU-IVF and 44 by embryo collection. Concerning the 43 in vitro embryos, 22 underwent lipid extraction in a fresh state (13 male and 9 female embryos), while 21 were first frozen before undergoing lipid extraction (8 male and 13 female embryos).
This QC sample was injected once at the beginning of the analysis, then after every 10 sample injections and at the end of the run. LC-HRMS data processing. Galaxy Workflow4metabolomics was used to process the raw data for features detection and retention time correction. Spectra of QC samples was analysed, and each chromatographic peak that differed from the background noise corresponded to a peak. Features with variance intensities greater than 30% in QC samples or with QC variance superior to sample variance were removed as well as those identified as background noise or poorly integrated after visual inspection  62. Lipid annotation was performed on SimLipid, a high throughput lipid identification and quantification software. The peak intensities were normalised by the total area of the spectra for each sample, transformed into a logarithm using the automatic transformation tool of SIMCA software (Umetrics, Umeå, Sweden).
Lipids were annotated (< 0. 01 ppm) according to either the homemade SimLipid (highlighted in yellow, in Supplementary Table  S1 ), database or to the LIPID MAPS Lipid Classification System  63, 64  (not highlighted in Supplementary Table  S1 ). (https:// www. lipid maps. org/ resou rces/ tools/ bulk_ struc ture_ searc hes. php? datab ase= LMSD). Statistical analysis of data on lipid profile. PCAs were performed on the data as exploratory unsupervised analysis representing the distribution of embryos, of the different comparisons, according to their lipid profile. The proportion of explained variance is represented by the sum of the R 2 of the first two components. A higher R 2 indicated a more accurate model. The ellipse represents the 95% confidence interval (Hotelling's T-square). Multivariate analysis was performed with orthogonal partial least square (O-PLS-DA) approaches, which were performed on the data set in the form of supervised analysis to predict groups by maximising the explained variance between groups, using the SIMCA Software  65.
Patient population The present analysis pooled data from 3 large randomized trials of antithrombotic treatment in patients with AF: the Atrial Fibrillation Clopidogrel Trial With Irbesartan for Prevention of Vascular EventsdAspirin (ACTIVE-A),  16  the Randomized Evaluation of Long-term Anticoagulation Therapy (RE-LY),  17  and the Apixaban Versus Acetylsalicylic Acid to Prevent Strokes in Atrial Fibrillation Patients Who Have Failed or Are Unsuitable for Vitamin K Antagonist Treatment (AVERROES)  18  studies. In brief, ACTIVE-A enrolled 14,260 patients, with a mean [standard deviation (SD)] follow-up time of 2. 4 (1. 4) years for the evaluation of clopidogrel plus aspirin for the prevention of stroke and other vascular events in AF patients. Patients were required to have AF at enrollment or at least 2 episodes of AF in the previous 6 months and at least one additional risk factor for stroke (age 75 years; treated hypertension; previous stroke, transient ischemic attack, or nonecentral nervous system systemic embolism; left ventricular ejection fraction (LVEF) < 45%; peripheral vascular disease; age of 55-74 years and diabetes mellitus or coronary artery disease).
Funding Sources P. K. is supported by the  University of Basel , the  Mach-Gaensslen Foundation , and the  Bangerter-Rhyner Foundation. L. J. is supported by governmental funding within the  Swedish National Health Services , the  Swedish Society of Medicine , the  Swedish Heart and Lung Foundation , the  Swedish Heart and Lung Association , the  Swedish Society of Cardiology , and the  Bergqvist Foundation. D. C. holds a  McMaster University Department of Medicine Mid-Career Research Award. W. F. M. is supported by fellowship awards from the  Canadian Stroke Prevention Intervention Network  and the  Canadian Institutes of Health Research. Disclosures J. H. S. reports research grants and speaking fees from  BMS/ Pfizer  and  Servier. The other authors have no conflicts of interest to disclose.
a) Theoretical training (Task 2) We harmonized the training materials between the different pharmacy sectors by developing a common frame with the software Powerpoint ® (Task 2. 1). We added a theoretical training about the declaration of adverse events (introduced in May 2017). To help pharmacy residents to assimilate the trainings' explanations and take notes at the same time, an in-house on-call duty notebook was developed (Task 2. 2). It contents: - Pharmacy residents regularly meet with the residents' coordinator to talk about in-house oncall duties' conduct. We created in June 2017 a dedicated insert in each written sum up (Task 2. 4) that will come back on a difficult situation lived by a resident and how to deal with it.
Another novel finding in the present study is that the type of IFN produced in response to different PRR pathways varies according to cell types. In keeping with ACE2 + cells being the primary cells infected by SARS-CoV-2, we measured a potent immune response in hBECs, but not in cDCs, infected with SARS-CoV-2. Nevertheless, we found that cDCs efficiently express specific members of the IFN-III and IFN-I families when exposed to the supernatant of lung epithelial cells previously infected with SARS-CoV-2 or in response to double-stranded RNA (dsRNA). These data suggest that cDCs, despite not responding directly to SARS-CoV-2 infection, may play fundamental roles in recognizing intermediates of viral replication and/or damage-associated molecular patterns (DAMPs) released by infected cells that are dying.
Nevertheless, additional studies are needed to directly link specific IFNs to particular cell types and, above all, specific protective or detrimental immune cell functions. As an example, our data suggest that cDCs do not directly sense SARS-CoV-2. Intriguingly, a recent report showed that specific cDC subtypes may instead directly respond to SARS-CoV-2  (Marongiu et al. , 2021) , but the capacity of these subtypes to produce specific IFNs remains an open question. Furthermore, understanding the specific contribution of different PRRs to the IFN response elicited in patients infected with SARS-CoV-2 also requires further analyses. (A-C ) Targeted RNA-seq of nasopharyngeal swabs from SARS-CoV-2-positive patients who were ICU inpatients (Swab ICU; 3), hospitalized (Swab HOSP; 6), or home-isolated (Swab HI; 4); SARS-CoV-2-negative (Swab NEG; 2) patients; and BALF from SARS-CoV-2-positive patients (BALF POS, 7) and patients with noninfectious lung pathologies (BALF NEG CTRL; 3) was performed.
Data were deconvoluted based on publicly available single-cell RNA-seq (scRNA-seq) datasets  (Ziegler et al. , 2021)  using CIBERSORTx  (Newman et al. , 2019)  to extrapolate the relative cellular composition of samples. (A and B) Each cell population in swab (A) and BALF (B) samples is depicted as a fraction of total cells. (C) Fraction of epithelial or hematopoietic cells in swab and BALF samples is depicted. Each dot represents a patient. Median with range is depicted. (D) Schematic of experimental setup. hBECs were infected with SARS-CoV-2 for 24 and 48 h. hLECs were infected with SARS-CoV-2 for 72 h. cDCs were treated with supernatants from hLECs, infected or not, for 24 and 48 h. Gene expression was evaluated in hBECs and cDCs (created with BioRender). (E-H) IFNL1 (E), IFNL2,3 (F), IFNB1 (G), and IFNA4 (H) mRNA expression was evaluated in hBECs 24 and 48 h after infection with SARS-CoV-2.
Data and code availability d Targeted transcriptomics data have been deposited at GEO and are publicly available as of the date of publication. Accession numbers are listed in the Key resources table. d Gene expression matrix from targeted transcriptomics, Gene expression matrix from qPCR experiments, cytokine expression matrix from multiplex analysis of BALF, Plasma and supernatants of phagocytes are deposited at Mendeley and are publicly available as of the date of publication. The DOI is listed in the Key resources table. d The code used to analyze the data is available upon request to the corresponding authors.
EXPERIMENTAL MODEL AND SUBJECT DETAILS Clinical samples for gene expression analysis and targeted RNA-sequencing Nasopharyngeal swabs were collected using FLOQSwabsâ (COPAN Cat#306C) in UTMâ Universal Transport Medium (COPAN Cat#306C) from 155 SARS-CoV-2 positive patients and from 28 negative subjects undergoing screening for suspected social contacts with SARS-CoV-2 positive subjects. Nasopharyngeal swabs were collected at San Raffaele Hospital (Milan, Italy) from April to December 2020. BALF was obtained from 26 SARS-CoV-2-positive patients hospitalized at San Raffaele Hospital (Milan, Italy) from Clinical metadata were obtained from the COVID-BioB clinical database of the IRCCS San Raffaele Hospital. The study was approved by the Ethics Committee of San Raffaele Hospital (protocol 34/int/2020).
SARS-CoV-2 propagation and titration For hBECs infection experiments with SARS-CoV-2, the isolate England/02/2020 (GISAID accession ID: EPI_ISL_407073) was propagated and titrated in Vero E6 cells (ATCC Cat# CRL-1586). For cDCs infection experiments with SARS-CoV-2 the isolate hCoV-19/ Italy/UniSR1/2020 (GISAID accession ID: EPI_ISL_413489) was propagated and titrated in Vero E6 cells (ATCC Cat# CRL-1586). All infection experiments were performed in a biosafety level-3 (BSL-3) laboratory.
Targeted Transcriptomics For targeted transcriptome sequencing, RNA (15ng) isolated from clinical samples described in Tables  S4  and S6  was retro-transcribed to cDNA using SuperScript VILO cDNA Synthesis Kit (Invitrogen Cat# 11754-05). Barcoded libraries were prepared using the Ion AmpliSeq Transcriptome Human Gene Expression Kit (Ion Torrent Cat# A26325) as per the manufacturer's protocol and sequenced using an Ion S5 system (Ion Torrent Cat# A27212). Differential gene expression analysis was performed using the Transcriptome Analysis Console (TAC) software with the ampliSeqRNA plugin (ThermoFisher Scientific). We used CIBERSORTx  (Newman et al. , 2019)  to estimate the abundances of epithelial end hematopoietic cell types using using bulk gene expression data as an input and scRNaseq signature matrices from single-cell RNA sequencing data to provide the reference gene expression profiles of pure cell populations.
The scRNaseq signature matrix used to deconvolute RNaseq dataset from swabs or BALFs were derived from  Wauters et al. (2021)  and  Ziegler et al. (2021). Gene set enrichment analysis and enrichment plot were generated in R using the Fast Gene Set Enrichment Analysis package (fGSEA)  (Korotkevich et al. , 2021). Heatmaps were generated in R and visualized with the ComplexHeatmap package  (Gu et al. , 2016). Clustering analysis was performed using Euclidean distances on individual z-scores. Code available upon request. One-way ANOVA with Turkey's post hoc test was used to compare continuous variables among multiple groups. Kruskal-Wallis test with Dunn's post hoc test or Multiple Mann-Whitney tests with Holm-Sı ´dak method were used instead when data did not meet the normality assumption. Fisher's exact test was used to compare categorical variables.
ACKNOWLEDGMENTS We thank the members of the  Zanoni and Mancini laboratories  for thoughtful discussion and comments on the project. I. Z. is supported by  NIH  grants  2R01AI121066 ,  5R01DK115217 , and  NIAID-DAIT-NIHAI201700100  and the  Lloyd J. Old STAR Program  ( CRI3888 ) and holds an Investigators in the  Pathogenesis of Infectious Disease Award  from the  Burroughs Wellcome Fund. N. M. is supported by  IRCSS San Raffaele Hospital Program Project  Covid-19 funds. Research done in the Wack lab was funded in whole, or in part, by the  Wellcome Trust  ( FC001206 ). For the purpose of Open Access , the author has applied a CC BY public copyright license to any author accepted manuscript version arising from this submission. S. C. and A. W. were supported by the  Francis Crick Institute , which receives its core funding from  Cancer Research UK  ( FC001206 ), the  UK Medical Research Council  ( FC001206 ), and the  Wellcome Trust  ( FC001206 ).
| Study species, relative abundance and encounter rates During standardised surveys in January each year over a 17year period, we recorded seven species of sea snakes in Baie des Citrons and Anse Vata (we have also found an eighth species, Hydrophis coggeri, but not during our surveys; Figure  2 ). Table  1  provides the information on relative abundance of these taxa at these beaches, with a brief assessment of snakebite risk for each species based on encounter likelihood, propensity to bite and toxicity. We used survey data collected over the 17-year period to estimate relative abundance and encounter rates of commonly observed species of sea snakes within Baie des Citrons and Anse Vata.
| Spatial and temporal overlap between sea snakes and people We have quantitative data on this topic only for the two telemetered species (A. duboisii and H. major) that were frequently recorded by listening stations adjacent to the beaches for which we quantified human presence. For the other species, we rely upon published reports, our experience during fieldwork and information from colleagues. We assessed the spatial overlap between telemetered snakes and beachgoers during daylight hours and at night. Numbers of residency events of each telemetered snake were summarised for each acoustic receiver for the entire period of the study using the VTrack r package  (Campbell et al. , 2012). Residence events for each snake at each receiver were estimated as the time an individual was continuously detected within the detection range of the receiver.
| Spatial and temporal overlap between sea snakes and people We obtained 37,422 detections from 14 H. major, and 13,619 records from 4 A. duboisii, but only 15 records from one of two telemetered A. laevis. Estimation of residence events resulted in a total of 6,118 residency events for the tracked H. major, 3,456 residence events for A. duboisii and a single residence event for A. laevis. The spatial patterns in residency between the two species for which sufficient data were available revealed interspecific differences in spatial ecology. Residency of all four A. duboisii monitored was restricted to shallow habitats within Baie des Citrons, whereas H. major moved more actively throughout shallow and deeper habitats (Figure  3 ). The use of beaches by people was high in Baie des Citrons during daytime, overlapping with residency patterns of A.
laticaudata and H. coggeri were invariably most often sighted over coralline rather than sandy substrates. F I G U R E 3 Bubble plot highlighting spatial overlap between recreational users of the Noumea bays, and two species of acoustically tracked sea snakes in the same bays. Size of points represent mean numbers of human beach-users recorded across all sites (grey circles), and mean numbers of residence events measured for telemetered Aipysurus duboisii (n = 4 snakes; left-hand panels) and Hydrophis major (n = 14 snakes; right-hand panels). Colour of points for snake residency represent shallow (orange) and deepwater (green) receivers.
, 2020; Nuriel et al. , 2020)  were analyzed in each session to assess accuracy and repeatability. Correction for matrix effects with WC-1 was done by anchoring to a value of 0. 85 common-lead, while samples and secondary reference materials were not anchored. No disequilibrium correction was applied. U-Pb ages were calculated from Tera-Wasserburg concordia lower intercepts using the IsoplotR software package  (Vermeesch, 2018). All uncertainties are reported at the 95% confidence level. A long-term excess variance of 2. 5% relative was propagated by quadratic addition to the uncertainty of the individual, lower intercept dates  (Guillong et al. , 2020). Prior to and after the LA-ICP-MS measurements, cathodoluminescence microscopy was conducted in order to identify potential growth zonings and to identify misplaced or defective ablation spots which were then excluded from the data.
, 2013). Data reduction were carried out with the Easotope software package  (John & Bowen, 2016). Normalization and projection of clumped isotope measurements into the carbon dioxide equilibrium scale (CDES) was done using the carbonate standards ETH-1, ETH-2, and ETH-3 with the values of  (Bernasconi et al. , 2018). Δ 47 temperatures were calculated with the recalculated  Kele et al. (2015)  calibration  (Bernasconi et al. , 2018)  and δ 18 O fluid was calculated using the calibration of  (Kim & O'Neil, 1997). Measurements failing outlier tests and with a deviation from the median Δ 47 value of the sample of ≥0. 090‰ (2% of all measurements) were not considered. Errors in Δ 47 temperatures are reported at the 95% confidence level  (Fernandez et al. , 2017). LOOSER ET AL. 10. 1029/2020TC006439 Tectonics 5.
The slickenfibers from the AU thrust yielded four U-Pb ages between 11. 3 ± 0. 9 and 9. 9 ± 0. 6 Ma. The slickenfibers from the HB thrust plot in two groups with significantly different ages: A first group with four ages ranging from 10. 6 ± 0. 4 to 8. 0 ± 0. 6 Ma and a second group with two ages of 5. 7 ± 0. 7 and 4. 5 ± 1. 5 Ma, respectively. The sample from the AK strike-slip fault yielded an age of 9. 3 ± 1. 1 Ma and the sample from the AA strike-slip fault of 6. 1 ± 0. 5 Ma, respectively. The age data of the AK strike-slip fault is in good agreement with the only other reported calcite slickenfiber U-Pb age of 9. 1 ± 0. 9 Ma, stemming from a similar structural feature in the Jura Mountains ∼25 km west of Schafisheim  (Madritsch, 2015; Rittner, 2013). LOOSER ET AL.
Clumped Isotope Analysis A total of 300 measurements on a subset of 25 samples with reliable age data and covering the entire time span of recorded deformation were considered for the reconstruction of clumped isotope temperatures (Δ 47 ) and the oxygen isotope composition of the precipitating fluids (δ 18 O fluid ). A table with all data can be found as supporting information and the entire data set including the carbonate standards is available as Easotope Database. When plotted as Δ 47 temperature vs. δ 18 O fluid , the data from the different sites and fault types group in fields reflecting three distinct burial settings at the time of faulting (Figure  7 ). For the SHA thrust, the Δ 47 temperatures and δ 18 O fluid compositions of the four vein populations are indistinguishable from each other at the 95% CL (Figure  7 ) and pooled together yielded a Δ 47 temperature of 104 ± 3 °C and a δ 18 O fluid of +9.
3 Ma) and in the Jura Mountains (11. 3 Ma) might indicate a foreland-directed thrust propagation signal (Figure  9 ). However, the U-Pb data need to be interpreted with caution in this regard, because of the spatially LOOSER ET AL. 10. 1029/2020TC006439 10 of 16  limited coverage of the available samples. In other words, potential older deformation in other locations in the Jura Mountains may have been missed. Similarly, the oldest ages from the SHA thrust should be regarded as a minimum age for the onset of tectonic activity along the basal décollement and it is possible that initiated even earlier. Also, it is important to keep in mind that any motion of the thinskinned foreland thrust system more distal than Schafisheim must also occur at the basal décollement of Schafisheim to some extent, even if not recorded by the analyzed veins in the footwall of SHA thrust.
, 2016). The youngest age constraints for thrusting obtained in this study (4. 5 Ma at the HB thrust) are well in line with previous estimates for the termination of thin-skinned deformation  (Madritsch et al. , 2008; Ustaszewski & Schmid, 2007). Combining our data with the existing biostratigraphic age constraints from different locations in the foreland suggests that the decoupling and thrusting along the basal décollement initiated at ∼20-16 Ma close to the Alpine front  (Beck et al. , 1998; Deville et al. , 1994; Pfiffner, 2014)  and was followed by foreland-directed propagation of deformation toward the distal Molasse LOOSER ET AL. Basin at Schafisheim (initiating at 14. 3 Ma at the latest, this study), to the Internal Jura Mountains (initiating at 11. 3 Ma at the latest, this study), and to the frontal thrusts (initiating only after ∼11-9 Ma;  Becker, 2000; Kälin, 1997 and references therein).
Acknowledgments The authors thank the  Swiss National Cooperative for the Disposal of Radioactive Waste (Nagra)  for access to the Schafisheim cores. This study was funded by the  Swiss National Science Foundation  project number  200021_169849. The authors thank the Associate Editor,  Djordje Grujic  and the two reviewers  Perach Nuriel  and  David Hindle  for their constructive comments that helped to improve the manuscript. This work also benefited from comments by  Adrian Pfiffner ,  Christoph von Hagke , and  Uwe Ring  on an earlier manuscript version.
In chronic kidney disease stages 4 and 5, only 34% and 40% of patients had seen a dietitian, and 33% and 54% had received information about treatment options, respectively. The average waiting time for a first appointment with a nephrologist was longer, 60 days and its duration shorter, 30 vs 38 to 40 minutes, in university hospitals compared with non-university hospitals and private clinics. [17] , et les caracteristiques initiales des patients ont eterapportees  [15, 18]. La cohorte CKD-REIN est enregistree dans ClinicalTrials. gov (NCT03381950).
CKD-REIN est financepar l'Agence nationale de la Recherche a travers le programme 2010 « Cohortes-Investissements d'Avenir » (ANR-IA-COH-2012/3731) et par le Programme national hospitalier de Recherche clinique 2010. CKD-REIN est egalement soutenu par un partenariat public-priveavec Amgen, Fresenius Medical Care et GlaxoSmithKline (GSK) depuis 2012, Lilly France depuis 2013, Otsuka Pharmaceutical depuis 2015, Baxter et Merck Sharp & Dohme-Chibret (MSD France) de 2012 a2017, Sanofi-Genzyme de 2012 a2015, Vifor Fresenius et AstraZeneca depuis 2018. Inserm Transfert a mis en place et gere ce partenariat depuis 2011. (CHU, Nantes), Dr A. Testa (Centre de dialyse, Reze), Dr D. Besnier (CH, Saint-Nazaire), Pr G. Choukroun (CHU, Amiens), Dr G. Lambrey (CH, Beauvais), Pr S. Burtey (CHU, Marseille), Dr G.