dataesr/scientific-paragraphs-categorization huggingface dataset:
py [37]. Clustering was performed using uclust v1. 2. 22q  [38]  in QIIME  [37]. The reads were processed with UCHIME  [39]  to remove chimeric sequences. Assigning Operation Taxonomic Units (OTUs) and taxonomic assignments were performed with an open-reference OTU picking approach against the UNITE database in QIIME  [37]. A similarity threshold of 97% was adopted. Taxonomic assignment of representative OTUs was run at a 0. 97 confidence threshold against the UNITE ITS1 database with UNITE 7. 2 reference OTU database ("UNITE+INSD" dataset) using the assignTaxonomy method  [40]. The raw reads were deposited in the SRA database with the accession number PRJNA574255.
Statistical analysis Rarefaction and extrapolation sampling curves were computed and plotted to estimate sample completeness (sample coverage) in R package iNEXT (iNterpolation/EXTrapolation) with the 95% lower and upper confidence limits for the isolation and metabarcoding data  [41]. Principle component analysis (PCA) was used to analyze trends in fungal species composition (based on OTU and percentage normalization of reads) of the sediments (black or yellow) collected from the three collection spots (vent region, east of Turtle Island, west of vent area, Fig  1 ) between 2015 and 2017 and calculated by R (version 3. 6. 1) using R studio  [42]  using package factoextra  [43]. Alpha (abundance) and beta (Bray-Curtis similarity) diversities were calculated in R package  [42]. To investigate the relationship between species composition and sampling sites, i.
Culturable diversity of fungi A total of 94 isolates was cultured from the crab Xenograpsus testudinatus, sediment, seawater and animal egg samples (S1 Table ). These fungi were identified based on comparisons of their ITS sequences with those in the GenBank database. The identity of the fungi was referred in most cases to a species name and in some cases to a genus, based on the top BLAST results with the highest score, in terms of high query coverage (%) and identity (%). When the top BLAST results were unidentified/uncultured fungi, the next result with a name was used if the % query coverage and % identity were high (�95%); if these figures were low, the identity was only referred to the family, order, class or phylum. and 23 species from the black sediment. Thirteen species were isolated from the crab samples.
Majority of the sequences from these samples was of a fungal origin; a low number of sequences (ranged from 41 to 294 reads) was classified as unassigned in 4 out of the 13 subsamples. The PCA analysis based on operational taxonomic units (OTU) and percentage normalization of reads shows that the first axis (PC1) described 16. 8% of the variation in the species composition between sediment samples while the second axis (PC2) described 13. 7% of the variation, giving a total of 30. 5% of the variation in the dataset (Fig  4 ). From the score plot, sediment samples with a similar species composition clustered together. Generally, there was a gradient of species composition along PC2 axis, decreased from the black sediment samples collected at site W (west of vent area) to site V (vent area), and to site E (further away from vent).
2. 2 (http://bowtie-bio. sourceforge. net/index. shtml) without allowing mismatches but permitting multi-mapped reads (Supplementary Tables  S7  and 8 ). Small RNA counts were extracted using ShortStack v3. 8. 5 (http://sites. psu. edu/axtell/software/shortstack/) and normalized by the total number of mapped reads. Boxplots of 24 nt siRNAs were generated in R, counting reads per kb per million mapped (RPKM) within pol IV differentially methylated regions (DMRs) (loci hypomethylated in nrpd1-51 versus WT SucSul). Wilcoxon rank sum tests were then performed using the ggpubr package (Supplementary Table  S12 ).
Differentially methylated regions Adapter and quality trimming (q > 20) were performed on the WGBS data using TrimGalore (v0. 4. 4). Clean reads were mapped to the Arabidopsis reference genome (TAIR10) using Bismark v0. 18. 1 (https: //www. bioinformatics. babraham. ac. uk/projects/bismark/). Methylation information for each methylcytosine context (CG, CHG and CHH) was extracted (bismark methylation extractor) after de-duplication (deduplicate bismark). DMRs were identified from the Bismark analysis files using the BSseq R package (v1. 10. 0). WT Suc-Sul was used as the reference sample for calling DMRs. These DMRs were called using the BSseq default t-stats quantile cutoff and only including cytosine positions supported by at least four reads in both replicates (Supplementary Tables  S5  and 6 ).
ACKNOWLEDGEMENTS L. F. and T. B. designed the study. L. F. , C. H. , M. B. and T. B. performed all benchtop experimental procedures, except the assays in Figure 2 and Supplementary Figure S2F, which were performed by J. S. , and the retrotransposon heatactivation assays in Figure 6D, which were performed by M. T. D. P. conducted the bioinformatic analyses in Figures 3B-C,  5A ,  5C ,  6A ,  Supplementary Figures S3  and  S5. A. G. and T. B. performed the protein alignments in Supplementary Figures  S2A  and  S4 , as well as contributing to NGS analysis and data display. E. B. and C. S. P. provided critical advice for the study and helped edit the manuscript. L. F. and T. B. mounted the final figures and wrote the manuscript. Bart Rymen provided helpful comments on the Nucleic Acids Research, 2019, Vol.
FUNDING LabEx NetRNA Consortium ,  French Investissements d'Avenir funds  [ ANR-10-LABX-0036 NETRNA  to T. B. ];  French Agence Nationale de la Recherche Grant  [ ANR-17-CE20-0004-01  to T. B. ]; Howard Hughes Medical Institute  funds [to C. S. P. ]; European Commission Grants [PITN-GA-2013-608422-IDP BRIDGES to M. T. , 725701 BUNGEE to E. B. ]. Funding for open access charge:  Agence Nationale de la Recherche Grant  [ ANR-17-CE20-0004-01 ].
The beam was focalized in a 200 µm spot and the fiber, rotated 45 • with respect to the incoming X-ray beam, was oriented with the long axis, i. e. , the c-axis, parallel to the radiation polarization plane, allowing a single fiber embedded in kapton to be probed. A time period of 90 min were necessary to acquire a complete spectrum, with 10 s counting time per point. A good signal-to-noise ratio was obtained up to 10 Å -1 in k, allowing for the resolution of several coordination shells around the Fe atom. The EXAFS data analysis is in progress to better clarify the structural environment of iron. In Figure  3 , we compare the pre-edge of the single fiber with that of a powdered sample of riebeckite. In the fit, we used Gaussian curves for each component, left free to vary the energy position in a range of ±0.
The EXAFS data analysis is in progress to better clarify the structural environment of iron. In Figure  3 , we compare the pre-edge of the single fiber with that of a powdered sample of riebeckite. In the fit, we used Gaussian curves for each component, left free to vary the energy position in a range of ±0. 75 eV from the initial value. Their FWHM was constrained to be constant at ~1. 5 eV (the core-hole of Fe). The incoming energy resolution was ~0. 3 eV  [6, 7]. The spectra show clear differences: for the single fiber oriented parallel to the beam polarization the pre-edge is sharper, and two features are easily visible, while it is broader for the powder sample, where four contributions are needed in the fit, probably due to the multi-orientation of the grains. This evidences the importance of having a small polarized beam in these kinds of experiments.
A selection of Fe K-edge XANES and EXAFS spectra of soil samples is presented in Figure  4 ; the spectra have been collected in fluorescence mode by using the same geometrical configuration described in Section 3. A SDD single channel detector Vortex EM from the ESRF instrument pool and the Si(111) crystal pair were used. Each spectra was acquired in 50 min. (5 s counting time per point) and in some cases for the most diluted samples several spectra were averaged for the final spectrum. In this way, although the statistic was not exactly the same, the noise resulted to be sufficiently low to allow a reliable data analysis. The origin, type, and average Fe concentration of the samples are indicated in Table  1. The spectra show marked differences: sample SPTI shows a more intense pre-edge peak at 7115 eV, a broad hump at 7126 eV, and a less pronounced white line at 7131 eV; sample LHGZ shows two more pronounced features at 7122 eV and 7126 eV, and a sharper white line at 7131 eV, which on the contrary, is broader for the ALS and WNH samples; these last two samples show a broad hump at 7125 eV.
Acknowledgments: We acknowledge  Giancarlo Della Ventura  ( Roma Tre University ) for the fiber sample presented in Section 2,  Federico Galdenzi  ( Roma Tre University ) for Figure 3 and the fit presented in Section 2. We acknowledge  Augusto Marcelli  ( INFN-Laboratori Nazionali di Frascati ),  Giannantonio Cibin  ( Diamond Light Source ),  Giovanni Baccolo  ( Università degli Studi di Milano-Bicocca ),  Valter Maggi  ( Università degli Studi di Milano-Bicocca ), and  Du Zhiheng  ( Chinese Academy of Sciences ), for the data presented in Section 3.
background Performing mechanical thrombectomy (MT) in patients with basilar artery occlusion (BaO) is currently not evidence-based. Objective To compare patients' outcome, relative merits of achieving recanalization, and predictors of futile recanalization (Fr) between BaO and anterior circulation large vessel occlusion (aclVO) MT. Methods in the multicenter BeYOnD-sWiFT registry (ncT03496064), univariate and multivariate (displayed as adjusted Odds ratios, aOr and 95% confidence intervals, 95%-ci) outcome comparisons between BaO (n=165) and aclVO (n=1574) were performed. The primary outcome was favorable outcome at 90 days (modified rankin scale, mrs 0-2). secondary outcome included mortality, symptomatic intracranial hemorrhage (sich) and Fr. The relative merits of achieving successful recanalization between aclVO and BaO were evaluated with interaction terms.
MeThOdS Details of the BEYOND-SWIFT Registry are in the public domain (NCT03496064) and have been published previously. 24 Briefly, the registry is a retrospective, multicenter, non-randomized observational study designed to investigate the safety and efficacy of a Medtronic market-released neurothrombectomy device (applied as the initial device used for interventions) in patients with acute ischemic stroke who do not fulfill treatment eligibility requirements according to the current guidelines. An overview of the patients included in the registry, the follow-up data for each center, and ethical approval procedures can be found in online supplementary table I. Ethical approval was obtained in Bern for pooling and analyses of the registry data (KEK Bern, Bern, Switzerland ID 2018-00766). Most patients included in the registry (n=2046) were treated for large-vessel anterior circulation strokes (n=1832).
Importantly, we could identify interventional predictors of FR, mainly higher maneuver count and intracranial stenting. After adjusting for confounders, only age, baseline NIHSS score, and intracranial stenting remained significant prognostic factors for FR in our dataset. Together with a lower mortality rate in successfully recanalized patients, the observation of increased FR suggests that by MT, death was avoided but long-term dependence created. Those finding should be included in the discussion to treat or withhold treatment according to patient preferences. Corroborating our observations about the beneficial effect of successful recanalization, the meta-analyses by Kumar et al also reported that mortality was bisected in patients in whom successful recanalization (mTICI 2b or mTICI 3) was achieved.
Study population We used data from the NutriNet-Santé study, a large webbased observational cohort launched in France in 2009 with a scheduled follow-up of 10 years. It was implemented in a general population and targeted Internet-using adult volunteers. Briefly, eligible participants were recruited by a variety of means. Initially a vast multimedia campaign called for volunteers, and then campaigns were repeated every 6 months. Further information is maintained on a large number of websites (national institutions, city councils, private firms) and a billboard advertising campaign is regularly updated via professional channels (e. g. , doctors, pharmacists, dentists, business partners, municipalities). The study was designed to investigate the relationship between nutrition and health, as well as determinants of dietary behavior and nutritional status  [16].
This study was conducted according to guidelines laid down in the Declaration of Helsinki, and all procedures were approved by the Institutional Review Board of the French Institute for Health and Medical Research (IRB Inserm no. 0000388FWA00005831) and the "Commission Nationale Informatique et Libertés" (CNIL no. 908450 and no. 909216). Electronic informed consent was obtained from all subjects. This study is registered in EudraCT (no. 2013-000929-31).
Events' ascertainment Participants self-declared health events through the yearly health status questionnaire (in which they can also declare family medical history), using a specific check-up questionnaire for health events (every 3 months) or at any time through a specific interface on the study website. Following this declaration, participants were invited to send their medical records (diagnosis, hospitalization, radiological reports, electrocardiograms, etc. ). If necessary, the study's physicians contacted the participants' treating physician or the medical structures to collect additional information. Then, data were reviewed by an independent physician expert committee, which validated all major health events. The present study focused on cases of hypertension, type 2 diabetes, and cardiovascular events (strokes, transient ischemic attacks, myocardial infarctions, acute coronary syndromes and angioplasties) diagnosed between May 2010 and November 2016.
Foods were classified according to the information provided in the French National Nutrition and Health Program guides  [25]. Food groups (in g/day) considered in the present study were vegetables, fruits, meat, processed meat, fish, starchy foods, whole grain products, milk and yogurt, cheese, butter and other added fats, oil, sugar and sweetened products, sweetened cream desserts, fatty-sweet products, savory sauces, salted snacks and appetizers, sweetened soft drinks and alcoholic beverages. Values for energy were estimated using published nutrient databases  [26]. We used the three closest dietary records to the PrefQuest questionnaire (or two if one was missing).
Statistical analyses The present analysis focused on participants of the NutriNet-Santé cohort, living in metropolitan France, who had completed the PrefQuest and the set of complementary questionnaires, and who had self-reported health information, even no event to declare, over 6 years of follow-up. Liking scores for fat-and-salt, fat-and-sweet, salt and sweet were computed as detailed previously  [18, 28]. Briefly, liking data were linearly transformed to a standardized ten-point scale so one-point change is equivalent to a 10% change in the scale value for liking. Regarding dietary intake, for each participant, daily mean quantities of the food group (in g) and energy intake were calculated from two or three 24 h records, weighted according to the day (week or weekend). Diet-underreporting participants were identified by the method proposed by Black  [32].
Results Among the 65,683 participants in the NutriNet-Santé study in May 2010, 49,066 responded to the PrefQuest (75% participation rate). Among responders, 48,336 had available health information in 2010. Then, we excluded 1902 subjects with a history of CVD or with diabetes at baseline, 3785 who were identified as diet-underreporting participants or who did not answer to 24 h dietary records in 2010 and 1327 women who were pregnant at baseline, which left 41,322 participants available for analysis of cardiovascular diseases and diabetes (32,055 women and 9267 men). Regarding hypertension analysis, starting from the 48,336 participants, 5609 subjects with a history of CVD or hypertension at baseline were excluded, as well as 3469 who did not have dietary intake data and 1322 pregnant women, which left 37,936 participants for analysis of hypertension (29,828 women and 8108 men).
Moreover, incidences of CVD, type 2 diabetes and hypertension in participants were lower than in the general French population  [49]  which might underestimate our association. Caution is therefore needed when interpreting and generalizing the results. In addition, dietary data were collected using 24 h dietary records, which can underestimate energy intake  [50]. Individual characteristics, sensory liking and dietary intake were assessed at baseline only, so cumulative effect of these behaviors on the development of CMDs could not be assessed. Furthermore, residual confounding cannot be excluded because other confounders of sensory liking in CMDs risk such as genetics or psychological factors could not be taken into account in the analysis. Finally, some associations did not succeed to attain the cut-off of 10% for practical significance, thus low effect sizes of some HRs suggest caution when interpreting.
However, the strength of our study is its prospective design with the 6 years of follow-up that allows us to explore the inference of causality between sensory liking and the CMDs risk. Another limitation was that self-reported data could be not accurate as measured data. Compared with liking as assessed by sensory tests, self-reported liking by questionnaire may lead to misreporting. Recalled liking can be influenced by the recalled pleasure arising from the sensory cues, but also by other external cues such dietary habit, dietary restraint, social desirability, health considerations and other variables  [9, 51]. However, this questionnaire was carefully developed through a series of pretests and pilots that demonstrated its repeatability, feasibility and internal validity  [18] , and positive correlations with sensory test measurements have been shown  [20, personal communication].
Acknowledgements We thank the scientists, dieticians, technicians and assistants who helped carry out the  NutriNet-Santé study , and all dedicated and conscientious volunteers. We especially thank  Mohand Aït-Oufella ,  Paul Flanzy ,  Yasmina Chelghoum ,  Véronique Gourlet ,  Nathalie Arnault  and  Laurent Bourhis. We thank Voluntis (a healthcare software company) and MXS (a software company specializing in dietary assessment tools) for developing the NutriNet-Santé web-based interface according to our guidelines.
Participants The methodology was the same as in real-life studies of other cancer treatments:  [13] [14] [15]  in France, cabazitaxel is only available through hospital prescriptions on a named-patient basis. All hospitals dispensing cabazitaxel were identified between September 2013 and December 2014 from sales data provided by the manufacturer. The pharmacists of these centres were invited to participate in the study. Those who accepted provided a list and the contact details of the oncologists who had prescribed cabazitaxel during the study period. These oncologists were invited to participate in the study and if so, include in the study all patients who had received at least one cycle cabazitaxel, irrespective of the number of cycles received, except those who had been enrolled in a clinical trial.
Data collection Clinical and prostate specific antigen (PSA) data were extracted from the hospital records during the eighteen-month period following the first administration of cabazitaxel, or until the patient died and entered into an electronic case report form by a dedicated clinical research assistant. All data collected were validated by the participating physician and included the following: date of first cabazitaxel administration, patient demographics, disease history including prior treatments, cabazitaxel treatment modalities, outcomes (clinical, biological, radiological), date of death, analgesic use and adverse events (AEs) reported during cabazitaxel treatment. Adverse events were coded using the current MedDRA classification and their severity was coded according to the grading system of the National Cancer Institute's Common Terminology for the Classification of Adverse Events (NCI-CTCAE v4.
Statistical analysis The target sample size (400 subjects) was chosen to estimate OS at eighteen months with a precision of 4. 9%, considering a median OS in TROPIC trial of 15. 1 months. 16 OS and PFS were estimated using Kaplan-Meier survival analysis. Cox proportional hazard models over the eighteen-month follow-up period were used to identify risk factors associated with death or progression. The variables entered into the Cox models are listed in supplementary data Table  1 , and pertain to factors occurring before cabazitaxel, to patient status at first cabazitaxel injection and to per-treatment events. Survival estimates were also provided for patients with synchronous or metachronous metastases. All statistical analyses were performed with SAS ® (SAS Institute, version 9. 4, Cary, USA), according to a statistical analysis plan defined prior to data lock.
Ethics The study was conducted in accordance with all relevant national legislation and guidelines for observational studies, with approval from the French national data-protection Agency (CNIL). The study protocol was submitted to and approved by the French health authorities as part of the post-marketing commitments of the manufacturer of cabazitaxel (Sanofi-Aventis). All patient data in the study database were anonymised. The study was registered with the EU PAS registry (ENCEPP/SDPP/10391).
Author's reply: Dear Dr Beltran-Bech and members of the PCI Ecology managing board, Thank you for the positive reply and for carefully checking our latest revisions! We have added a reference to Figure  3  in the text in Methods > Planned Sample: "Females were caught at all but one site, such that comparisons are possible of the genetic relatedness of pairs of females trapped at various distances from each other. Males were not caught at all trap sites, but there are several sites at which multiple males were caught and sufficient sites for comparisons of males that were caught close to each other, at intermediate, and at long distances (Figure  3 ). " As before, the version-tracked version of this preregistration is in rmarkdown at GitHub. In this document, we have now also included the reference to PCI Ecology at the top: https://github.
Dear Dr. 's Beltran-Bech and Durand, Thank you for checking our revised preregistration again in such detail and for providing this helpful feedback! We made these changes to our preregistration and associated files at http://corinalogan. com/Preregistrations/gdispersal. html, and we responded to your comments below. As before, the version-tracked version of this preregistration is in rmarkdown at GitHub: https://github. com/corinalogan/grackles/blob/master/Files/Preregistrations/g dispersal.
Moreover, Legendre and Fortin (2010) conclude that Mantel correlograms are not very powerful and should be avoided when other methods are available. Of course, if the authors find more support for Mantel correlograms and can argue that this method is relevant to detect sex-biased dispersal, I will have no objection to this analysis. I nevertheless suggest to consider a different way to analyse the data. In particular, Legendre and Fortin (2010) mention spatial autocorrelation analyses which are easy to perform using the program Genalex (Peakall and Smouse 2006) and have successfully detected sex-biased dispersal in Maybe the authors should consider the possibility of performing such analyses (and adapt the manuscript in consequence, as the method is based on spatial autocorrelation and not on isolation by distance).