dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments We particularly thank  Cl ementine Vitte  ( CNRS, GQE-Le Moulon, Gif-sur-Yvette, France ),  J erome Gouzy  ( INRA, UMR LIPM, Toulouse, France ), and  Mark Tepfer  ( INRA, IJPB, Versailles, France ) for valuable discussions. We thank  Pierre Montalent  ( INRA, GQE-Le Moulon, Gif-sur-Yvette, France ) for technical assistance with Galaxy. Three anonymous reviewers are also acknowledged for their helpful comments on the manuscript. P. M. P. was supported by a PhD fellowship from the  French Ministere de l'Enseignement Sup erieur et de la Recherche (MESR). Experiments dedicated to sRNA library construction and sequencing were funded by the  Institut F ed eratif de Recherche   87  " La plante et son environnement" (Gif-sur-Yvette, France ) and the  Direction Scientifique of AgroParisTech (Paris, France).
Cryo-electron microscopy imaging and cryo-ET data acquisition Minicell solution was supplemented with 10 nm colloidal protein A-gold particles (Cell Microscopy Core, University Medical Center, Utrecht, The Netherlands). R 2/1 or R 3. 5/1 on 300 mesh Cu/Rh grids (QUANTIFOIL) were glow discharged for 45 s at 25 mA. 3 μL of the sample was applied to grids and plunge frozen in liquid ethane using a Vitrobot Mark IV (Thermo-Fisher Scientific). Grids were stored under liquid nitrogen until imaging. Screening of the grids was performed on an FEI F20 microscope at 200 keV. Tilt-series acquisition was performed on a Titan Krios transmission electron microscope operated at 300 keV, through a Gatan Quantum energy filter and Volta phase plate onto a K2 Summit direct electron detector, using SerialEM software.
45 For both search and navigational purposes, low-magnification montages were acquired. For tilt-series acquisition, a magnification which produced a calibrated pixel size of 2. 24 Å was selected. Data were collected at tilt-angles between -60° and +60° in 2° increments in a grouped dose-symmetric tilt scheme (0, +2, +4, +6, +8, +10, -2, -4, -6, -8, -10, 12, 14, 16, 18, 20, -12, -14, -16, -18, -20 etc). 46 Images at each tilt-angle were acquired as movies comprising 5 frames. Target total dose for tilt-series acquisition was 60 e - Å -2 s -1.
Tomographic Reconstruction. CC-BY-ND 4. 0 International license available under a not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint (which was this version posted August 5, 2019. ; https://doi. org/10. 1101/723692 doi: bioRxiv preprint Tilt-series were aligned, binned by two and tomograms were reconstructed by weighted backprojection using the IMOD software package. 48 Six tomograms of WM4196 minicells were selected for further processing.
Acknowledgements This work has received funding from a  European Union 's  Horizon 2020 research and innovation programme  under grant agreement No  647784  to IG. Research in the JSP and WM labs was supported by grants  GM19559  and  GM131705 , respectively, from the  U. S. National Institute of General Medical Sciences. This work was also supported by the  U. S. National Institutes of Health  grant  P41GM104601  to CKC and ZL-S, the  U. S. National Science Foundation  grant  PHY1430124  to CKC and ZL-S, and the  U. K. Biotechnology and Biological Sciences Research Council  grant  BB/S003339/1  to CKC and PJS. We acknowledge  Diamond Light Source  for access and support of the cryo-EM facilities at the  UK's national Electron Bio-imaging Centre (eBIC) , funded by the  Wellcome Trust ,  MRC  and BBRSC.
Cryo-ET data acquisition has been supported by iNEXT, grant number  653706  (PID: 2626  to IG), funded by the  EU   Horizon 2020 programme. For initial minicell characterisation and grid screening, we used the platforms of the Grenoble Instruct-ERIC Center (ISBG:  UMS 3518 CNRS-CEA-UGA-EMBL ) with support from  FRISBI  ( ANR-10-INSB-05-02 ) and GRAL, a project of the  University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS  ( ANR-17-EURE-0003 ). IBS acknowledges integration into the  Interdisciplinary Research Institute of Grenoble (IRIG, CEA ). The IBS electron microscope facility is supported by the  Rhône-Alpes Region , the  Fondation pour la Recherche Médicale (FRM) , the fonds  FEDER , the  Centre National de la Recherche Scientifique (CNRS) , the  Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) , the  University of Grenoble Alpes ,  EMBL , and the  GIS-Infrastructures en Biologie Santé et Agronomie (IBISA).
Study population The EPIC study is an ongoing multicenter prospective cohort study aimed at investigating the association between diet, lifestyle, genetic and environmental factors and the development of cancer and other chronic diseases. The methodological details and rationale of the EPIC study have been described previously. 30, 31 In brief, the cohort comprises of 521,448 men and women, aged 25-70 years, recruited between 1992 and 2000 from 23 centers located in 10 European countries including Denmark, France, Germany, Greece, Italy, Norway, Spain, Sweden, the Netherlands and the United Kingdom. Participants were mostly recruited from the general population with some exceptions: French participants were recruited via health insurance databases; some participants of the Italian and Spanish cohorts were recruited through local blood donor registries; participants of the Utrecht (the Netherlands) and Florence (Italy) cohorts were recruited via breast cancer screening programs; the Oxford (United Kingdom) cohort included a large proportion of vegetarians.
Assessment of anthropometric and reproductive data Anthropometric measurements including height, weight, waist circumference (WC) and hip circumference (HC) were taken at recruitment by trained health professionals in most EPIC centers, except for most of the Oxford cohort, the Norwegian cohort and approximately two-thirds of the French cohort, in which height and weight were self-reported. BMI was computed as weight in kilograms divided by height in meters squared, waist-to-hip ratio (WHR) was computed as WC (cm) divided by HC (cm) and waist-to-height ratio (WHtR) was computed as WC (cm) divided by height (cm). Information on reproductive history was collected at recruitment. The following reproductive characteristics were assessed: age at menarche, duration of menstrual cycle, ever been pregnant, age at first pregnancy, number of full-term pregnancies (parity), number of live-born children, breastfeeding, menopausal status, age at menopause, menopausal hormone use, oral contraceptive (OC) pill use and ovariectomy.
More details on questionnaires can be found elsewhere. 30, 31 llow-up and identification of cancer cases Participants were followed-up from study entry until cancer diagnosis, death or end of follow-up, which is currently up to 2015, whichever came first. Population-based cancer registries, as well as postal follow-up questionnaires, are used in most of the countries to identify incident cancer cases. In France, Germany, Greece and Naples (Italy) cancer cases are additionally identified through active follow-up. Data on mortality and movement of participants are obtained through periodic linkage to regional and national mortality registries. First primary incident esophageal and gastric cancers were coded according to the 10th revision of the International Classification of Diseases (ICD-10).
54, 95% CI: 0. 32-0. 91). In addition, compared to women who had not undergone ovariectomy, women who had a bilateral ovariectomy had a higher risk of GNC (HR 1. 87, 95% CI: 1. 04-3. 36), although there were only 13 cases in this group. We excluded underweight group from the analysis due to few number of cases. Exclusion of esophageal and gastric cancer cases diagnosed in the first 2 years of follow-up did not substantially change the associations observed for anthropometric or reproductive factors (data not shown). In addition, analyses restricted to measured anthropometric factors yielded similar results to those when participants with self-reported data were included (data not shown). Finally, comparing the baseline characteristics of included participants to those excluded from the analysis because they lacked dietary or lifestyle information, revealed no substantial differences between the two groups, except participants excluded were very slightly older than the included participants.
Our study has some limitations. We used a single assessment of anthropometric and reproductive factors collected at baseline as data during follow-up was not available; if anthropometric and reproductive factors changed during follow-up, this could lead to some misclassification and possibly bias the results toward null. Although we adjusted for several potential confounders, we lacked information on GERD and Helicobacter pylori infection, which have been associated with EA and GC, respectively; therefore, residual confounding cannot be excluded. We also lacked data on the reason for ovariectomy in the women who underwent this procedure. In addition, EPIC cohort participants are of European descent, which limits the generalizability of our findings to other ethnicities. Finally, as we analyzed anthropometric and reproductive factors in relation to both esophageal and gastric cancer by subtype and subsite, some of our associations may have arisen by chance as a result of multiple comparisons.
Acknowledgements This research was funded by the  Stand Up to Cancer campaign for Cancer Research UK. The coordination of EPIC is financially supported by the  European Commission (DG-SANCO)  and the  International Agency for Research on Cancer. The national cohorts are supported by  Danish Cancer Society (Denmark) ;  Ligue Contre le Cancer ,  Institut Gustave Roussy, Mutuelle Générale de l'Education Nationale ,  Institut National de la Santé et de la Recherche Médicale (INSERM, France) ;  German Cancer Aid ,  German Cancer Research Centre (DKFZ) ,  Federal Ministry of Education and Research (BMBF) ,  Deutsche Krebshilfe, Deutsches Krebsforschungszentrum and Federal Ministry of Education and Research (Germany) ; the  Hellenic Health Foundation (Greece) ;  Associazione Italiana per la Ricerca  sul.
The measurements were carried out at 23 • C and a relative humidity of 85%, according to the standard ASTM F 1249. The standard deviations of all measured water vapor transmission rate (WVTR) values were <5%. The surface morphology was characterized using a Nanoscope V multimode atomic force microscope (AFM) (Digital Instruments, Bresso, Italy), and the root-mean-square roughness (Rq) values were calculated on scan areas of 5 µm × 5 µm with the Software Nanoscope Analysis of Bruker (version 1. 40). Dynamic mechanical analyses (DMA) were carried out using a Q800 analyzer (TA Instruments, New Castle, DE, USA). The tests were performed in tensile mode, at a frequency of 1 Hz, in the temperature range of 30-190 • C, under a heating rate of 3 • C/min. Transparency measurements were performed on the film samples using a Lambda 800 UV-VIS Spectrophotometer (Perkin-Elmer Inc.
MALDI-TOF Mass Spectrometry MALDI-TOF spectra were analyzed in reflectron positive mode using a 4800 TOF/TOF spectrometer (Applied Biosystems, Framingham, MA, USA) equipped with a pulsed nitrogen laser (337 nm and frequency of 200 Hz). An average of 5,000 shots per spot was used for MS data acquisition. Samples were prepared by mixing directly on the target 0. 5 µl of oligosaccharide solution in water (10-50 pmol) with 0. 5 µl of 2,5-dihydroxybenzoic acid matrix solution (10 mg/ml in CH 3 OH/H 2 O, 50:50, V/V). The samples were dried at room temperature.
STATISTICAL ANALYSIS All experiments were performed with at least five different batches of GAG and oligosaccharides and a minimum of four blood donors. All statistics of in vitro experiments were carried out with a two-tailed unpaired Wilcoxon-Mann-Whitney Test by the free-of-charge software EDISON-WMW  (Marx et al. , 2016). Statistical analyses from in vivo experiments (Figure  5 ) were performed with one-or two-way ANOVA. Data, from one experiment using 10 mice/group, were expressed as mean ± SD and were analyzed in triplicate using GraphPad Prism Software. P values are indicated by asterisk as follows: * p < 0. 05; * * p < 0. 01; * * * p < 0. 001.
FUNDING This research was funded by the  Aviesan project Aspergillus , the  French Government 's  Investissement d'Avenir program ,  Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases  (Grant No  ANR-10-LABX-62-IBEID ), la  Fondation pour la Recherche Médicale  ( DEQ20150331722 LATGE Equipe FRM 2015 ). RS thanks Fundação para a Ciência e  Tecnologia (FCT)  contract  IF/00021/2014.
" Using data from the Earth Microbiome Project and SRA databases, we also demonstrate that members of "Ca. Aquarickettsia" are found globally in dozens of invertebrate lineages. The coral-associated "Candidatus A. rohweri" is the first finished genome in this new clade. "Ca. A. rohweri" lacks genes to synthesize most sugars and amino acids but possesses several genes linked to pathogenicity including Tlc, an antiporter that exchanges host ATP for ADP, and a complete Type IV secretion system. Despite its inability to metabolize nitrogen, "Ca. A. rohweri" possesses the NtrY-NtrX two-component system involved in sensing and responding to extracellular nitrogen. Given these data, along with visualization of the parasite in host tissues, we hypothesize that "Ca. A. rohweri" reduces coral health by consuming host nutrients and energy, thus weakening and eventually killing host cells.
Inquiry on ProbeMatch (RDP; http://rdp. cme. msu. edu/probematch/search. jsp) using 100% sequence match suggests that the probe only matches 16S sequences previously assigned to Rickettsia species or unclassified alphaproteobacteria in the database. A single-mismatch probe, RICKNEG (5′-CCTCCAA-TACTCCATTGG-3′), was designed as a negative control to confirm probe specificity and matches 0 bacterial sequences in the RDP database. Optimal formamide concentration (40%) for the specific probe was empirically determined by using the highest formamide concentration that simultaneously exhibited presence of mixed EUB338 binding and RICK binding, and absence of RICKNEG binding.
Metagenome preparation, sequencing, and sequence quality control pipeline An Acropora cervicornis fragment from ref. [3]  with a relative abundance of 87. 9% for one Rickettsiales OTU was selected for genome assembly. DNA extraction was performed using EZNA Tissue DNA Kit (Omega Bio-Tek), and DNA yield was quantified using the Qubit dsDNA HS Assay and analyzed on a Qubit 3. 0 Fluorometer. A barcoded DNA fragment library was prepared using the Nextera XT (Illumina) sample preparation kit (Supplementary Table  S1A ). This sample was shotgun sequenced on an Illumina Miseq with a v3 reagent kit at OSU's Center for Genome Research and Biotechnology (CGRB). A total of 13,785,074 metagenomic reads were sequenced with an average sequence length of 301 bp and a mean phred score of  36. Further details about the sample used for genome assembly are accessible as National Center for Biotechnology Information (NCBI) BioSample SAMN10490412.
Genome assembly and quality assessment The filtering and trimming of low-quality sequences and removal of adaptor sequences were conducted with FQtrim (Supplementary Table  S2 ). The program PEAR  [32]  was used with default settings to merge high-quality paired-end sequences. The contaminating reads were filtered out by mapping to the human genome  [33] , and genomes of Acropora digitifera  [34]  (as there was no genome available for A. cervicornis), and the algal symbiont Symbiodiniaceae spp  [35]. , using Bowtie2  [36]  (Supplementary Table  S3 ). The remaining 13,688,870 reads (99. 46%) were assembled with the de novo meta-assembler IDBA-UD, a de novo assembler  [37] , and SPAdes  [38]  were subsequently used to improve assembly. Unsupervised binning of contigs was performed with MaxBin v.
2. 2. 1  [39]  using default parameters, and VizBin was implemented to visually bin contigs further. Sequence bins were analyzed by BLAST searches  [40]  to the NCBI nonredundant database (NR) and to all complete bacterial genomes in RefSeq  [41]. Bins with sequences identified as Trichoplax adhaerens were retained due to previous observations that genomic scaffolds of this organism contained sequences from Rickettsial endosymbionts that may have been horizontally transferred to the placozoan host  [42]. We used SSPACE  [43]  to merge contigs and create scaffolds, and MaxBin was re-run (with minimum contig length 500) to confirm that all sequences belonged to a single bin. We conducted manual quality control on contigs in this final bin using BLAST, and removed contigs with identity to Symbiodiniaceae spp.
that had erroneously been retained. CheckM  [44]  was used to assess assembly quality and contamination (Supplementary Table  S4 , Fig. S1 ) using marker genes that are ubiquitous and single copy within a given lineage. We elected to use marker genes from all of Alphaproteobacteria rather than exclusively Rickettsiales due to the large amount of divergence between the three families of Rickettsiales and an overrepresentation of the comparatively well-studied Rickettsiaceae in the marker gene database. The program Pseudo-Finder  [45]  was used to identify potential pseudogenes, which were left in the genome assembly but removed from calculations of coding density (see below).
Genome annotation and comparative genomics Prokka  [46]  was used to annotate the genome, and annotations were uploaded to the KAAS  [47]  server. KEGG orthology (KO) identifiers were assigned using BLAST+ against the KEGG GENES  [48]  database with the BBH (bidirectional best hit) method to assign orthologs and enable the reconstruction of KEGG pathways and BRITE hierarchies (Supplementary Table  S5 ). KO numbers linked to the KEGG pathway maps and BRITE functional hierarchies were used to group genes into modules and assess the metabolic pathway completion. OrthoFinder 2. 2. 3  [49]  was used to identify orthologous clusters of genes that were compared between species (listed in Supplementary Table  S6 ) to assess shared and unique gene clusters. CGView  [50]  was used to generate a circular representation of the genome by providing the program with a Mauve  [51]  alignment of the draft genome to a reference genome ("Ca.
Phylogenetic analysis of coral-associated Rickettsiales The full-length 16S rRNA region of the genome was identified using BLASTn searches against 16S rRNA regions from other Rickettsiales species from Greengenes (Version 13. 8)  [59]  as a partial 16S rRNA sequence from this OTU already existed in the Greengenes database  [3]. The trimmed sequence was aligned to 16S rRNA sequences from 79 members of Rickettsiales and 11 Alphaproteobacteria outgroups (Supplementary Table  S9 ) using cmalign (part of the INFERNAL 1. 1. 1 package)  [60]  with a covariance model built using the Rfam seed alignment for bacterial small subunit ribosomal RNA. PhyML  [61]  was used for phylogenetic analysis, with 1000 bootstrap replicates and parameters selected using jModelTest  [62]  (Supplementary Table  S10 ).
These replicates were summarized using the Geneious 11. 1. 4 Consensus Tree Builder command  [63]. Sequences were manually BLASTed to the NCBI RefSeq database  [41] , and metazoan hosts were identified from 100% identical sequences in the database with reported hosts from NCBI sequence description information. Pairwise BLAST was performed between the 16S rRNA sequence of "Ca. A. rohweri" and closely related sequences from "Ca. Midichloriaceae. " A concatenated marker protein-based phylogeny was generated using a previously curated set of 92 orthologous, single-copy marker genes present in all bacteria  [64]  (Supplementary Table  S11 ). Hmmsearch 3. 1b2  [65]  was used to identify these marker genes in 20 genomes within Rickettsiales and four outgroups. Sequences were aligned using MAFFT 7.
The appropriate number of samples to discard as "burnin" was independently determined first by visual inspection of parameter trace plots, and then by optimizing convergence criteria. For amino acid analyses, the maxdiff statistic was 0, while for Dayhoff6 recoded data the statistic was 0. 046. The minimum effective sample size was >50 (>100 for Dayhoff6) and the maximum rel_diff statistic was <0. 3 (0. 1 for Dayhoff6). Node support was evaluated using posterior probabilities.
Redbiom search for presence of "Ca. A. rohweri" The Earth Microbiome Project (EMP) tool Redbiom  [72]  was used to search for the presence of "Ca. A. rohweri" and other OTUs within the genus "Ca. Aquarickettsia" in the Qiita database. The Rickettsiales OTU from the sample selected for "Ca. A. rohweri" genome assembly was determined by Shaver et al. [3]  to match most closely to Greengenes  [59]  OTU 150441, so this and the five most closely related Greengenes OTUs (as determined using the Greengenes reference phylogeny and confirmed by BLAST to NR) were considered members of the genus. The command "redbiom search features" was used to search 173,714 16S rRNA libraries from the EMP sequencing context "Pick_closed-reference_OTUs-Greengenes-illumina-16S-v4-100nt". This context provides the most resolution of the 16S rRNA sequence without losing samples that were not sequenced to 150 bp.
Biogeography analysis confirms the association of "Ca. Aquarickettsia" with non-bilaterian metazoans worldwide To survey the global prevalence of this genus and identify new hosts, we used Redbiom to query the publicly available Earth Microbiome Project (EMP) database; in all, our Redbiom analysis represents an evaluation of a total of 173,714 16S V4 Greengenes Illumina 100 nt samples (Fig. 6 ). "Ca. A. rohweri" was prevalent in marine sediments (rocks and sand), seawater, and freshwater, and marine organisms such as corals, sponges, the ctenophore Mnemiopsis, and kelp (Fig. 6 ). The presence of "Ca. A. rohweri" in marine sand and sediments suggests either that these habitats provide a potential vector for transmission, represent "Ca. A. rohweri" hosted by interstitial organisms, or contain marine invertebrate eDNA  [98].
"Ca. J. acanthamoeba" is horizontally transferred in aquatic environments  [75] ; both freshwater and seawater may thus play a role in transmission of "Ca. Aquarickettsia. " "Ca. A. rohweri" was absent in terrestrial samples, such as dust, groundwater, and "mammal-associated" data sets, including those from human medical samples (Fig. 6  gray bars). This analysis was repeated for OTUs within "Ca. Aquarickettsia" and compared to other OTUs from "Ca. Midichloriaceae" that were not part of the proposed genus (Supplementary Table  S13 ). Out of the 1401 total coral samples in the EMP database, 457 (32. 62%) had OTUs identified as "Ca. A. rohweri" (i. e. , >97% identity), whereas 494 (38. 2%) had OTUs within "Ca. Aquarickettsia. " As metadata for coral samples in the EMP database included sampling coordinates and host identity, we had the capability to determine how "Ca.
A. rohweri" was distributed globally and in which coral species it was identified (Fig. 7 ). We found that this OTU is present in the Pacific, Atlantic, and Indian Oceans in 51 scleractinian genera, 11 cnidarian outgroups, and a ctenophore, Mnemiopsis. When we mapped the distribution of EMP sponge samples (primarily from the Sponge Microbiome Project  [99] ) in which "Ca. A. rohweri" was identified (Fig. S12 ), we found an even more global distribution, with samples spanning 76 sponge genera. "Ca. A. rohweri" was identified in sponge samples across the world, and is widespread throughout Europe (North Sea, Northern Atlantic, Mediterranean Sea), the Red Sea, the Caribbean, and Australia. To supplement results from analysis of the EMP database, we queried the SRA database with the full-length 16S rRNA sequence of "Ca.