dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements. We thank  Y. Hoshina  and  A. Ekaykin  for sharing their data and  J. Freitag  and  A. M. Dolman  for discussions and detailed editing. We are grateful to the reviewers  B. Markle  and the two anonymous reviewers, for their detailed comments on the manuscript. T. Laepple  and  T. Münch  were supported by the  Initiative and Networking Fund of the Helmholtz Association  grant  VG-NH900. M. Casado  and  A. Landais  have received funding from the  European Research Council (ERC)  under the European Union's  Seventh Framework Programme  ( FP7/2007-2013)/RC  grant agreement number  306045  and  T. Laepple  has received funding from the  ERC  under the European Union's  Horizon 2020 research and innovation programme  (grant agreement no. 716092 ). The article processing charges for this open-access publication were covered by a  Research Centre of the Helmholtz Association.
Background: Viral metagenomic studies have suggested a role for bacteriophages in intestinal dysbiosis associated with several human diseases. However, interpretation of viral metagenomic studies is limited by the lack of knowledge of phages infecting major human gut commensal bacteria, such as Faecalibacterium prausnitzii, a bacterial symbiont repeatedly found depleted in inflammatory bowel disease (IBD) patients. In particular, no complete genomes of phages infecting F. prausnitzii are present in viral databases. Methods: We identified 18 prophages in 15 genomes of F. prausnitzii, used comparative genomics to define eight phage clades, and annotated the genome of the type phage of each clade. For two of the phages, we studied prophage induction in vitro and in vivo in mice. Finally, we aligned reads from already published viral metagenomic data onto the newly identified phages.
Indeed, annotation of viral sequences, and in particular the prediction of the bacterial host, is mainly based on alignment to reference viral sequences in databases  [19] , and limitations in the viral databases render annotation of most viral sequences difficult if not impossible. Limitations are particularly flagrant concerning phages infecting important groups such as Ruminococcaceae, previously known as Clostridium cluster IV. There is, to our knowledge, no phage infecting members of this family whose complete genome has been deposited in viral databases. Isolating and describing phages infecting Clostridiaceae species such as F. prausnitzii is thus a prerequisite for investigation of their potential role in dysbiosis. In this study, we characterize for the first time complete F. prausnitzii temperate phages and show that they belong to eight new proposed viral genera.
The 23 retained prophages were compared pairwise at the nucleotide level, allowing the definition of six phylogenetic clades (Fig. 1 ), within which gene synteny was well conserved, and two singletons. The clusters/singletons are well separated from each other, mostly with no gene shared between clusters. None of the predicted prophages had significant nucleotide similarity with a viral genome of the NCBI RefSeq genome database on more than 5% of its genome, indicating they all correspond to new viruses. According to current taxonomic metrics whereby phages within a genus share at least 40% of their proteins, and phages of the same species have more than 95% identity on the whole genome  [24, 25] , the 23 prophages correspond to 18 species and 8 genera (Additional file 2), for which we propose names (Table  1  and Fig.
1 ). Of note, Taranis and Toutatis belong to related genera since they share 26% of their proteome, with an overall 39% amino acid identity. Given the ubiquity of F. prausnitzii in human gut microbiota, we investigated whether similar phage sequences had been found in other studies. To this end, we compared the prophage genomes against the NCBI nr database. Prophages Lagaffe, Mushu, and Touta-tisSL3/3 have homology to four large contigs assembled from reads obtained by sequencing DNA from virus-like particles (VLPs) isolated from human fecal samples  [26]  (Fig. 1 ). In addition, ToutatisL2/6 is homologous to a 9kb contig assembled from reads of the VLPs of a human fecal sample. This contig had been predicted to correspond to a F. prausnitzii prophage  [10]. This provides further support for the proposition that these prophage regions are of viral nature.
We then looked for CRISPR spacers matching the prophages in the 15 F. prausnitzii genomes, and found spacers for eight prophages (Table  1 ), which is indicative of recent infection of these strains by the respective phages  [27]. Overall, indications of activity were obtained for at least one prophage of each proposed genus, as summarized in Table  1. For six of the eight prophage groups, the host range seemed to be restricted to F. prausnitzii, since no similar prophage could be detected by BLASTn in other genomes of the NCBI RefSeq database. On the other hand, prophages with 65% overall sequence identity to Mushu prophage were found in the unclassified Ruminococcaceae bacterium D16 (Fig. 1  and Additional file 3) and in the unclassified bacterium SS3/4 (Genbank sequence FP929062. 1). Even more striking was the detection of a prophage almost identical to Lagaffe (98% nucleotide identity) in the genome of Blautia hansenii DSM 20583 (Fig.
Functional annotation of prophage genes reveals a high prevalence of diversity-generating retroelements Within each proposed genus, we chose one representative prophage, which we subsequently refer to as the "type phage" for the group. Each type phage was annotated by using the Phagonaute webserver (genome. jouy. inra. fr/phagonaute), which uses remote homology searches and gene synteny information  [28, 31]. We improved the functional predictions as compared to the previous automatic annotation using RAST server by 2. 5-to 5-fold (Fig. 2 ). All phage functional modules were detected in each prophage, providing further indication that these prophages correspond to complete phage genomes. A remarkable feature of these genomes is the high prevalence of diversity-generating retroelements (DGRs).
Analysis of reads also revealed the Mushu and Lagaffe precise integration sites in the A2-165 chromosome (Fig. 3b ). Mushu integration site presents the typical 5 bp direct repeat of some Mu-like phages  [37]. More surprisingly, Lagaffe is also flanked by direct repeats, whereas a sequence composed of inverted repeats is expected to form the integration site of IS30 transposases  [23]. Analysis of Lagaffe reads with the PhageTerm tool  [38] , dedicated to the detection of the strategy used by phages to package their genome into capsids, identified the cos region of Lagaffe, upstream of the terminase gene termS. For both phages, reads spanning the VR region of the DGR are more variable than the rest of the genome, an evidence of DGR activity (Additional file 5C). The level of variability observed in Mushu is however remarkable, since the phage genomes sequenced result in theory from a single cycle of multiplication (they are produced following induction in lysogenic cells), and suggests a very high efficacy of TR-to-VR transfer in this DGR.
Alignment by BLASTn of reads from this dataset to 17 of the identified prophages retrieved a large number of hits (ToutatisL2/6 being very close to Toutatis, 96% identical over 80% of its length; it was not included in this analysis). Altogether, virome reads mapping to at least one of the eight type phages represented 0. 02% of all reads in healthy samples and 0. 30% in IBD samples (mean of the proportion of reads matching on F. prausnitzii type phages over total number of reads). Remarkably, reads mapping to phage Oengus represented 22% of reads in one sample (Fig. 4 , sample ERR843984). In that sample, we could assemble the matching reads into a contig covering 93% of Oengus genome with 99% identity. Yet matching read coverage was not always even on the prophages (Fig. 4 ), suggesting the presence of phages only sharing genome fragments with the phages of this study.
05). Since F. prausnitzii populations are generally less abundant in IBD patients than in healthy controls  [7] , the higher occurrence and proportion of some F. prausnitzii temperate phages suggest that they are more active in the microbiota of IBD patients and that this activity is related to the depletion of F. prausnitzii. Fig. 4  F. prausnitzii phages are present in intestinal viromes. Read coverage for six type phages in samples with the best abundance and coverage from the datasets of Norman et al. [18]  and Reyes et al. [52]. Number of aligned reads (ordinate) is represented as a function of position in the phage genome (abscissa). Phage name, virome name, total number of aligned reads, and ratio of aligned to total reads are shown for each panel Discussion F. prausnitzii genomes are particularly rich in prophages: in this study, we found that 85% of them harbor at least one complete prophage, as opposed to only 46% of all completely sequenced bacterial genomes  [47].
The 23 identified complete prophages in this study correspond to 18 different phages, which can be grouped into eight new viral genera. Thanks to experimental and in silico investigations, we found evidence of activity for at least one member of each proposed genus. Their novelty and diversity are striking and greatly enrich the viral databases, which are at present highly skewed towards phages infecting proteobacteria or other pathogens, which together account for more than 75% of phages in the NCBI viral genome database (as of December 2017). The novelty of the viral proteins coded by F. prausnitzii phages should not only improve the analysis of viral metagenomic sequences but might also lead to biotechnology applications, such as genetic engineering of F. prausnitzii. A very high proportion F.
prausnitzii phages possesses DGRs: these diversification systems are present in 10 out of the 18 phages. By comparison, only 0. 05% of the 876 phages present in the Phagonaute database (comprising all fully sequenced phage genomes available at the NCBI as of May 2014) possess DGRs. This high prevalence in F. prausnitzii phages might explain the previously observed high frequency of DGRs in intestinal viromes  [26]. By generating variants of target genes, DGRs presumably confer selective advantages to the phages, such as the ability to infect bacteria with different variants of the surface component used as receptor by the phage, as has been shown in the case of B. pertussis phage BPP1. In this phage, the DGR-mediated diversification of the MTD protein generates at low-frequency phage variants able to infect bacteria with receptors different from those of the original host  [33].
We found that the F. prausnitzii temperate phages described here are present in 5 to 40% of the human fecal samples from the study of Norman and colleagues  [18]. Despite their relatively low abundance in most samples of this dataset, they can represent up to 22% of total viral reads (Additional file 10). Most importantly, some of them are either more prevalent or more abundant in samples from IBD patients compared to that of healthy controls. This result is striking since IBD patients have generally a lower abundance of F. prausnitzii in their microbiota  [6, 7]. This suggests that this higher prevalence or abundance is not just the consequence of a higher abundance of their bacterial host but rather that these F. prausnitzii prophages are more active in the microbiota of IBD patients as compared to healthy controls.
Conclusion Here, we describe for the first time complete F. prausnitzii temperate phage genomes. These phages belong to the new viral genera, and most of their proteins have only remote homology with previously described viral proteins. The novelty of F. prausnitzii phages warrants great enrichment of databases, which should in turn significantly improve annotation of viral gut metagenomic sequences. In addition, we show that some of these F. prausnitzii phages are either more prevalent or more abundant in the fecal samples of IBD patients compared to that of healthy controls, suggesting that these phages might play a role in the disease. Future mechanistic exploration of the nature of phage-bacteria interactions is now necessary to elucidate the role of temperate phages in dysbiosis.
Prophage detection and comparison F. prausnitzii genomes listed in Additional file 1 were analyzed with PHASTER (http://phaster. ca). "Intact" and "questionable" regions were then validated by manual inspection. We retained regions with genes in each of the following modules: replication, capsid, lysis, and lysogeny, and no genes specific of integrative plasmids or insertion sequences. Of note, several prophage regions were on borders of contigs, suggesting that some complete prophages could have been missed because of splitting between two contigs and that some of the retained prophages might lack some genes. Prophage borders were refined by searching for phage integrase and phage-specific genes by BLASTp against the nr NCBI database. In several cases, the ORF corresponding to the integrase had not been detected automatically and was added manually.
For type prophages, few other ORFs were also added. In addition, repeats on both sides (attL and attR sites) were searched for. They could be identified only in prophages encoding a tyrosine integrase, which is not surprising since tyrosine integrases generally use longer identical repeat than serine integrases. A multi-fasta file containing all prophage nucleotide sequences is available in the Additional file 11. The type phage genomes were deposited in the NCBI viral database (accession numbers in Additional file 1) and are consultable on the Phagonaute webserver (genome. jouy. inra. fr/phagonaute). Genomic regions homologous to the 18 prophages were searched for in the nr/nt nucleotide collection of the NCBI by BLASTn, with the discontinuous megaBLAST default parameters. Sequences producing alignments covering more than 5% of the query were retained.
Shared proteins between prophage pairs For each prophage pair to be compared, all proteins of the first phage were compared to the proteins of the second one (BLASTp, E value < 10 -3 ), and best hits were considered shared proteins. The proportion of shared proteins was then calculated by dividing the number of shared proteins by the total protein number (minimal value of the pair), and the average identity percent of the shared proteins was computed. To select an outgroup phage for each proposed genus, all proteins of the type phage were compared to the viral protein database subset of the NCBI. The most frequent subject phage among the top 10 results for each protein was selected as the outgroup phage.
Gene product prediction Gene function prediction for type prophages was achieved by combining Virfam  [28]  and Phagonaute  [31]  web tools. Concerning Virfam, default homology thresholds were used for recombinase and connector proteins. In Phagonaute, the proteins having a HHsearch hit against Pfam (P > 95%) were annotated with the Pfam information. Otherwise, the protein was searched against all other phage proteins (probability threshold of 95% and two iterations of HHsearch) and annotated using the most prevalent annotation. If no homolog with experimentally validated function was retrieved by the second iteration, the word "putative" was indicated in the Genbank file.
Virome read treatments Reads from 171 viromes extracted from feces of healthy subjects and patients with inflammatory bowel diseases  [18]  were downloaded from the EBI (fastq files, accession numbers ESR698653-ESR699023). Paired-end reads were treated with trimmomatic  [51]  to remove low-quality reads and unclip primer sequences present at the 3′ ends of reads, using the following command ILLUMINACLIP: TruSeq3-PE. fa:2:30:10 SLIDINGWINDOW:4:15 MIN-LEN:36. Reads were then dereplicated with fastx uniques from the usearch9 suite. Since ~30% of reads were no longer paired after the trimmomatic treatment, only one read from each pair was used for mapping analyses, to remain quantitative and avoid over-representation of some phage sequences compared to others. Average read length was 250 bp. To complement this analysis, we also analyzed the viral contigs generated in the Reyes et al.
Two additional specific controls of F. prausnitzii DNA presence were included for the mapping analysis: a 50-kb segment corresponding to the beginning of the F. prausnitzii A2-165 Genbank file and a 50-kb segment encoding mainly metabolic genes (coordinates 1,451,689-1,501,688). Samples were classified as phage-positive for a given phage when the proportion of reads homologous to that phage was significantly higher than the proportion of reads homologous to these two bacterial regions (one tailed two-proportion z test, p < 0. 05). As a control of the method, we included the highly prevalent crAssphage in the analysis and found that it is more prevalent in healthy controls than in IBD patients (Fig. 5a , two-tailed two-proportion z test, p < 0. 01), in agreement with previously published results  [17].
Acknowledgements We are very grateful to  Chantal Bridonneau  for her expertise in anaerobic culture; to  Anne Foussier ,  Fatima Joly , and  Aurélie Balvay  from the  Anaxem facility  for their help with the animal handlings; to  Christine Longin  from the MIMA2 facilities ( UMR 1313 GABI ,  INRA ) for the TEM observations; to the  Migale platform (INRA)  for the bio-informatics environment; and to  Colin Tinsley  for his careful reading of the manuscript.
Instrument For the purpose of the study, a self-reported questionnaire was developed, entailing the following sections: Respondents' characteristics Data were collected on participants' sociodemographic characteristics (gender, age, educational attainment, self-reported economic status) and their involvement in the CPO. In particular, participants had to rate their degree of familiarity with cancer and their knowledge about its treatment/their country's healthcare system/ their country's reimbursement process (rating options: very low to low moderate to high-to very high). Moreover, they had to rate their degree of involvement in the organisation (rating options: absent-very low to low moderate to high to very high). Data were also gleaned with regard to their position in the organisation (president/or other board members-employed by the organisation-voting member-non-voting but active member-non-active member) and the duration of their membership.
20 rticipants and procedures Potential participants were identified through various channels (eg, internet search, on line databases of European cancer patients' associations, registries of the ministry of health, etc). CPO was considered any non-profit organisation with a legal entity. In addition, the CPO should have been cancer specific, be primarily composed of patients and their caregivers and representing and/or supporting their needs. To be recruited for the study, a CPO should have had an active representation of patients with cancer at a national level and a valid and accessible website. CPOs from EU-28 member states were included in the study. In order to be eligible for participation, an individual should have been a member of a CPO and older than 18. An email was sent to CPO board members informing them about the study and inviting them to participate.
The Tropospheric Ozone Assessment Report (TOAR) is an activity of the International Global Atmospheric Chemistry Project. This paper is a component of the report, focusing on the present-day distribution and trends of tropospheric ozone relevant to climate and global atmospheric chemistry model evaluation. Utilizing the TOAR surface ozone database, several figures present the global distribution and trends of daytime average ozone at 2702 non-urban monitoring sites, highlighting the regions and seasons of the world with the greatest ozone levels. Similarly, ozonesonde and commercial aircraft observations reveal ozone's distribution throughout the depth of the free troposphere. Long-term surface observations are limited in their global spatial coverage, but data from remote locations indicate that ozone in the 21 st century is greater than during the 1970s and 1980s.
igacproject. org/activities/TOAR). Initiated in 2014, TOAR's mission is to provide the research community with an up-to-date scientific assessment of tropospheric ozone's global distribution and trends from the surface to the tropopause. TOAR's primary goals are, 1) Produce the first tropospheric ozone assessment report based on all available surface observations, the peer-reviewed literature and new analyses, and 2) Generate easily accessible and documented ozone exposure metrics at thousands of measurement sites around the world. Through the TOAR-Surface Ozone Database (https://join. fz-juelich. de, Schultz et al. , 2017)  these ozone metrics are freely accessible for research on the global-scale impact of ozone on climate, human health and crop/ecosystem productivity (TOAR-Surface Ozone Database,  Schultz et al.
, 2017). The assessment report is organized as a series of papers in a Special Feature of Elementa: Science of the Anthropocene. Three of the papers focus on the global distribution and trends of ozone relevant to different aspects of tropospheric ozone impacts, utilizing a range of ozone metrics described in the companion paper, TOAR-Metrics  (Lefohn et al. , 2018). TOAR-Health  (Fleming et al. , 2018)  and TOAR-Vegetation  (Mills et al. , 2018)  rely on ozone metrics drawn exclusively from the TOAR-Surface Ozone Database  (Schultz et al. , 2017). These metrics are of interest to scientists and policy-makers who wish to explore the impacts of ozone on human health and vegetation, impacts which typically occur during the warm spring and summer months. In contrast, this paper (hereinafter referred to as TOAR-Climate) presents seasonal surface ozone metrics that are designed to understand mean changes of ozone around the world, and that are appropriate for evaluating the global atmospheric chemistry models that calculate ozone's radiative forcing  (Stevenson et al.
Finally, Section 5 discusses ozone trends or distributions in several regions of the world and describes how the datasets used in TOAR-Climate can be accessed. (Lefohn et al. , 2018)  describes all of the ozone metrics in the TOAR database. The metrics relevant to climate and global atmospheric chemistry model evaluation that were selected for TOAR-Climate are: 1) the seasonal daytime average (8:00 to 20:00 local time) for surface observations, 2) seasonal nighttime averages (20:00 to 8:00 local time) at mountaintop sites, 3) monthly and seasonal means for free tropospheric observations from commercial aircraft (IAGOS), ozonesondes and lidars, as well as for TCO retrievals from space and ground-based remote sensing instruments. In some instances 5 th , 50 th , 95 th and 98 th percentiles are also shown.
Regionally representative surface sites The TOAR-Surface Ozone Database  (Schultz et al. , 2017)  contains climate-relevant ozone metrics at hundreds of surface sites around the world, both urban and rural. For this analysis a subset of non-urban surface sites has been selected for the purposes of illustrating the spatial and temporal variability of regionally representative ozone around the globe and for straightforward comparison to global atmospheric chemistry models. Urban sites were not considered because in spatial terms they are not regionally representative and because the local emissions and photochemical and deposition processes are too small-scale to be resolved by global atmospheric chemistry models, as described by TOAR-Model Performance  (Young et al. , 2018). Sites were classified as urban if they exceeded thresholds for human population and satellitedetected nighttime lights intensity (see TOAR-Surface Ozone Database for a detailed description of the site classification algorithm,  Schultz et al.