dataesr/scientific-paragraphs-categorization huggingface dataset:
Genomic Characterization The genome of phage Idefix is a double stranded linear DNA, consisting of 18,168 bp with inverted terminal repeats 61 bp long and an average GC content of 33. 2%. It is highly homologous to Enterococcus phages vB_EfaP_IME195 (95% coverage and 92% nt identity) and vB_Efae230P-4 (75% coverage and 85% identity) (Figure  2 ). These genomes belong to virulent podophages, which were isolated from sewage samples in China and Poland, respectively  [13, 44]. A close relative phage, vB_EfaP_IME199, infecting an E. faecium strain has also been described  [14]. Genbank accession numbers of these genomes are listed in Table  S3. Viruses 2019,  11  9 Comparative genomic analyses clearly show that Idefix and the other homologous Enterococcus phages belong to the Picovirinae subfamily  [78]  composed of small virulent podophages infecting Gram-positive bacteria and encoding a phi29-like DNA polymerase.
Abiα nevertheless constitutes a PFAM domain referred to as DUF4393 (158 sequences, 140 species, both Gram + and Gram -), suggesting already its broad distribution (see below). Abiα also shares similarity with Pfam entry PF10987 and PDB entry 3H35 without providing any substantial information about Abiα function. To characterize the Abiα mode of action, lysis curves were conducted and indicated that strain pp -containing plasmid pJL3 lyses ~10 min earlier than its isogenic strain devoid of abiα after infection by Idefix (MOI 10) (Figure  5A ). The same results were obtained when comparing lysis curves of the prophage positive and prophageless strains pp6 + and pp -, respectively (Figure  5B ). We concluded that Abiα provokes a lysis asynchrony. from abiA to abiZ have been used once to designate over 20 L.
lactis Abi systems  [18, 81] , we renamed ef2833 as "abiα". The corresponding encoded protein contains 272 residues, and does not exhibit similarity with any domain or protein of known function. Abiα nevertheless constitutes a PFAM domain referred to as DUF4393 (158 sequences, 140 species, both Gram + and Gram -), suggesting already its broad distribution (see below). Abiα also shares similarity with Pfam entry PF10987 and PDB entry 3H35 without providing any substantial information about Abiα function. To characterize the Abiα mode of action, lysis curves were conducted and indicated that strain pp -containing plasmid pJL3 lyses ~10 min earlier than its isogenic strain devoid of abiα after infection by Idefix (MOI 10) (Figure  5A ). The same results were obtained when comparing lysis curves of the prophage positive and prophageless strains pp6 + and pp -, respectively (Figure  5B ).
We concluded that Abiα provokes a lysis asynchrony. To evaluate the prevalence of abiα and its genetic context, the protein sequence was searched in the JGI database with the IMG interface (  [82] ; BLASTP, E-value < 3. 10 -8 , Identity ≥ 25%). Homologs of Abiα were found mostly on prophages, with some of them shown in Figure  S6 : the closer relatives (61-59% sequence identity) came from various enterococci, such as E. faecium and Enterococcus villorum isolates, and subsequent analyses with the NCBI nt database also revealed a homolog in an Enterococcus hirae prophage (not shown in Figure  S6 ). Other Abiα were found in about 50 Lactobacillus strains (27-42% sequence identity). Roughly, half of these genes are encoded on prophages (as in L. johnsonii, L. salivarius or L. plantarum isolates) whereas the other half are located on the chromosomes (as in L.
lindneri and L. helveticus isolates). Interestingly, in L. helveticus, and in two Oenococcus species (O. kitaharae and O. oeni), the abiα gene is close to other putative Abi systems, and may belong to a phage resistance island. Sporadic occurrences (31-37% sequence identity) were also found in three Streptococcus species (S. suis, S. bovis, and S. parasanguinis), and one Carnobacterium isolate. A prophage context was detectable in this latter and in S. parasanguinis. Additional prophage-encoded To evaluate the prevalence of abiα and its genetic context, the protein sequence was searched in the JGI database with the IMG interface (  [82] ; BLASTP, E-value < 3. 10 -8 , Identity ≥ 25%). Homologs of Abiα were found mostly on prophages, with some of them shown in Figure  S6 : the closer relatives (61-59% sequence identity) came from various enterococci, such as E.
faecium and Enterococcus villorum isolates, and subsequent analyses with the NCBI nt database also revealed a homolog in an Enterococcus hirae prophage (not shown in Figure  S6 ). Other Abiα were found in about 50 Lactobacillus strains (27-42% sequence identity). Roughly, half of these genes are encoded on prophages (as in L. johnsonii, L. salivarius or L. plantarum isolates) whereas the other half are located on the chromosomes (as in L. lindneri and L. helveticus isolates). Interestingly, in L. helveticus, and in two Oenococcus species (O. kitaharae and O. oeni), the abiα gene is close to other putative Abi systems, and may belong to a phage resistance island. Sporadic occurrences (31-37% sequence identity) were also found in three Streptococcus species (S. suis, S. bovis, and S. parasanguinis), and one Carnobacterium isolate.
Supplementary Materials: The following are available online at http://www. mdpi. com/1999-4915/11/1/48/s1, Figure  S1 : Structural and functional map of family of B phage DNA polymerases belonging to the "protein priming" subfamily. S1 : Bacterial strains, plasmids, and oligonucleotide primers used. Table  S2 : Description of Enterococcus isolates tested as potential Idefix hosts. Table  S3 : Respective genome accession numbers of the Enterococcus Picovirinae phages. Table  S4 : Features of Idefix ORFs and predicted functions of their products. Table  S5 : Spontaneous mutation in epaX (ef2170) or ef2169 in pp6 -and resistance to Idefix infection.
Acknowledgments: We thank  Marianne De Paepe  and  Lionel Rigottier-Gois  for their help during this study;  Christine Longin  from the MIMA2 facilities ( UMR 1313 GABI ,  INRA ) for the TEM observations;  Laurent Debarbieux  and  Sylwia Bloch ,  Alicja Węgrzyn  as well as Vincent Cattoir who respectively provided sewage water samples and enterococci isolates.
Models were fitted with package "lmer4"  (Bates, Mächler, Bolker, & Walker, 2014) , setting a binomial distribution and a logit link function, with region and stakeholder as fixed effects, and inquiry ID as a random effect. Model building started with both region and stakeholder, followed by backward elimination using the drop1 function (applying likelihood ratio chi-square tests). All analyses were performed using R for Windows (R Core Team 2016). Data are available as a CSV file in the Supporting Information S1-S3. Previous similar initiatives often used final workshops with subgroups and consensus-based discussions to identify the more important questions within topics  (Sutherland et al. , 2011). In our case, this would have been hard to achieve given the logistic constraints caused by the wide diversity of regions and stakeholders included.
Dataset Among the 61 organizations that returned the questionnaire indicating that they have germplasm collections, 42 gene banks from 15 European countries (Austria, Belgium, France, Germany, Hungary, Iceland, Italy, Latvia, Poland, Slovenia, Spain, Sweden, The Netherlands, United Kingdom, Ukraine) and 2 non-European countries (Kenya, Tunisia) provided information about their cryopreserved material. In most countries, data were provided by a single gene bank, with the significant exception of Spain, where 22 (regional) gene banks provided answers. We restricted the data analysis to 11 livestock species (excluding fish, wild species and companion animals). The dataset included the information about 667 NBP representing 373 local breeds and 226 transboundary breeds) (see Supplementary Box 1 for definitions).
For each breed, the survey requested the number of donor animals and samples for the following types of reproductive biological material: semen, embryos, oocytes, ovarian tissue and somatic cells (males and females). The material stored is mostly semen (94. 9% of NBP with material reported) followed by embryos (8. 2% NBP with material reported). Less than 1% of the NBP have other types of material stored. For preliminary comparative analysis, we extracted the numbers of NBP with cryopreserved material for the 17 countries from three different datasets, namely: (i) the country reports for the SoW2  [2] ; (ii) information on cryopreserved materials per NBP in DAD-IS system; and (iii) the responses to the IMAGE survey. Note some that national coordinators, which were the data providers for DAD-IS and SoW2 country reports, were also involved in the IMAGE project.
Then, the list of all NBP from the corresponding species and countries were extracted from DAD-IS, for a total of 3949 NBP (2377 local and 572 transboundary breeds) and merged with the results of the IMAGE survey to identify the NBP with cryoconserved material. We created a second dataset for comparison of local versus transboundary breeds. This was accomplished by merging together (i. e. , across countries) the information from NBPs representing the same regional or international transboundary breed. For example, we combined data from all NBPs of Holstein cattle across the 17 countries to form a single "breed". In this study, the methodology chosen (and in SDG Indicator 2. 5. 1b) to define "sufficient" quantities of semen doses and donors for breed reconstitution is based on a 150% breed replacement plan  [9].
To perform our analysis, we created different categories. The first category, called the cryoconservation status, had three groups: (i) populations (NBP or breeds depending on the dataset) with no material reported, i. e. , breed reported in DAD-IS but with no material reported in the survey (no material reported); (ii) populations with some material stored, but in quantities insufficient to allow restoration of the population (material); and (iii) populations with sufficient material stored for breed reconstitution (sufficient material). Since most of the material stored was semen and no information was given about the genetic background of the donors of the stored embryos, which is needed to assess sufficiency for breed reconstruction,  [2] , we used only the information about semen to perform our classification.
Results When comparing the three original sources of data for the 17 countries, the IMAGE survey indicated a number of NBP with material collected (657) similar to that from the SoW2 country reports (688), whereas this number was much smaller in DAD-IS (381). Among the three data sources, the number of NBP per country with material was the largest for the IMAGE survey, with the exception of Italy and France (see Figure  S1 ). The SoW2 country reports did not provide detailed information about the NBP with stored material, so only the IMAGE survey data were used for further analysis. As indicated previously, for the 17 countries that were represented in the IMAGE survey, response data from 3949 NBP and 2949 breeds were extracted from DAD-IS. Among these 3949 and 2949 NBP, 657 (12. 9%) and 596 (15.
All of these factors may help explain the low percentages of breeds that have material or sufficient material stored. This survey was the first to allow a gap analysis at the population scale, taking into consideration the endangerment level of breeds, as well as the cryoconservation status of transboundary breeds, either at national level (i. e. , NBP level) or by merging information on material across countries (i. e. , breed level). The comparison between the survey and other datasets, i. e. , the SoW2 country reports and DAD-IS data relating to cryopreserved material, demonstrated that, despite being the official structure for the computation of SDG indicators related to livestock biodiversity, DAD-IS continues to have substantial gaps in the reporting of data regarding cryopreserved material.
Reads were demultiplexed, then merged using PEAR  (Zhang, Kobert, Flouri, & Stamatakis, 2013) , with a minimum overlap of 50 bp and minimum quality of Q20. Assembled reads were then quality filtered and converted to FASTA format using FastX Toolkit  (Gordon & Hannon, 2010)  with the threshold of at least 90% of sequences having at least Q30 quality. Sequences were clustered into OTUs (operational taxonomic units) at 97% similarity, and chimeras were removed, using USearch  (Edgar, 2010). Prey OTUs were identified to the lowest possible taxonomic level using a blast search   (Altschul, Gish, Miller, Myers, & Lipman, 1990)  against the National Center for Biotechnology Information (NCBI) database. OTU tables showing the number of sequence reads of each prey OTU for each specimen were built using USearch.
All OTUs that matched family Tetragnathidae were discarded as likely belonging to the Tetragnatha spiders rather than the prey. Prey read counts of each specimen were then rarefied to equal coverage (500 reads per specimen) using the GUniFrac package  (Chen, 2012 ) in r. To allow for more accurate comparisons of dietary diversity, each Tetragnatha species was randomly subsampled using a random number generator so that species were represented by equal numbers of individuals within each clade (n = 5 for web-building species, n = 6 for Spiny Leg species; Table  S1 ). CTL = ∑ T l + T s ∕2 × x i , MW = 0. 5 × D u ∕(R u -1) + D l ∕(R l -1) , TA B L E.
| Data analysis All statistical analysis was done in r v 3. 5. 0 (R Core Team, 2018). We performed principal component analysis (PCA) on web architecture variables (Table  1 ) using the FactoMineR package  (Lê, Josse, & Husson, (2008) ). Capture area and capture thread length were first log-transformed to obtain a normal distribution, and variables were scaled to unit variance so that variable loadings would be more directly comparable. After testing our data for any violations of assumptions of normality, we performed a one-way ANOVA to test for differences among species along axes PC1 and PC2, followed by a post hoc Tukey's honest significant difference (HSD) test controlling for multiple comparisons. To test for differences in site choice (web attachment microhabitat), we performed a nonparametric Fisher's exact test on the number of times each species had been observed building webs on different vegetation groups (fern, grass, shrub, tree or vine).
| Testing for relationships among niche parameters To assess niche divergences between the different Tetragnatha species, we tested relationships between (a) web architecture and isotopic signature, (b) web architecture and gut contents, and (c) isotopic signature and gut contents. We first quantified the variability in web architecture and isotopic composition occupied by each species by constructing hypervolumes for both web and isotope variables. This approach quantifies the multidimensional space occupied by each species using multivariate density kernel estimation  (Blonder, Lamanna, Violle, & Enquist, 2014). This is an improvement over convex hull methods, which are more sensitive to outlier points. Hypervolumes were calculated using the HYPERVOLUME package in r  (Blonder et al. , 2014).
We assessed the relationship between web hypervolume overlap and isotope hypervolume overlap using a Pearson's correlation test. For gut content data, we assessed the degree of pairwise dissimilarity in diet by calculating the Bray-Curtis dissimilarity between pairs of species in VEGAN  (Oksanen et al. , 2010). We used prey data at the ordinal level because order is expected to correspond to broad but important functional traits in arthropods, for example feeding style, life history and mobility. Using the hypervolume overlaps calculated as described above, we then tested for correlations among: (a) gut content and web architecture, and (b) gut content and isotopic signature, using a Pearson's correlation test. If web architecture were driving differences in gut content, or if gut content were driving differences in isotopic signature, then we would expect a negative correlation between gut content dissimilarity and hypervolume overlaps for web architecture and isotopic signature.
| Isotopic differences among species The isotopic data showed significant differences both among species and between the two major clades (Figures  4  and 5 ). These results should be regarded with some caution due to potentially confounding effects of different collecting years and elevations (see Table  S1 ), and because no baseline data (e. g. isotopic signatures of plant leaves or soil) were taken. Nevertheless, significant interspecific and inter-clade differences in isotopic signature persist when datasets are controlled for year and elevation (Figures  S1  and S2 ). Interestingly, another recent study found that spiders' diets do not change over elevational gradients despite differences in the prey community over these gradients  (Eitzinger et al. , 2019) , though isotopic differences due to climatic variation may still occur between different elevations.
| Gut content Our analyses of gut content data showed pronounced differences in taxonomic composition of diets among the spider species (Figure  6 ). Sample sizes were small (n = 5 for web-building species, n = 6 for Spiny Leg species; see Table  S1 ), and the results should therefore not be assumed to reflect the full spectrum of these species' diets. Moreover, the T. filiciphilia samples were collected in a different year from the other species, which could have a confounding effect given that prey may fluctuate in their availability between years and seasons. However, while likely incomplete, our results appear to agree with previous studies on the diets of Hawaiian Tetragnatha spiders. Blackledge et al. (2003)  found a greater proportion of tipulids (order Diptera) than other taxa in the webs of T.
ACK N OWLED G EM ENTS We thank  Seira A. Adams  and  Gregg Stephenson  for contributing specimens;  Todd Dawson ,  Stefania Mambelli  and  Wenbo Yang  for assistance with stable isotope analysis; and  Athena Lam  for help with Illumina sequencing. We are grateful to the staffs of the  Nature Conservancy  and the  Department of Land and Natural Resources on Maui  for access to field sites (permit nos. FHM13-313 ,  FHM14-339 ,  FHM17-422 , and  I1026 ). Many thanks to  Dr. Enrico Rezende , an anonymous editor, and two anonymous reviewers for valuable feedback on earlier submissions of this manuscript. This material is based upon work supported by the  National Science Foundation Graduate Research Fellowship  under Grant No. DGE 1106400 , and the  Dimensions of Biodiversity  Grant No. DEB 1241253.
This governance strengthens the dynamic of observation of coastal erosion and storm surges along the regional coast by improving the networking of the OR2C twenty-eight members. Monitoring strategy is based on an airborne LiDAR technology that provides annual topo-bathymetric data. One of the OR2C first actions was to establish an initial LiDAR acquisition survey (t0) in 2016 along 140 km of sandy coasts. The obtained data are updated every year and freely accessible to the coastal managers. The data are also used in an innovative toolbox of spatial analysis of coastal risks (MAp-RISC), which has an ability to map predisposition of coastal sectors exposed to coastal hazards. MAp-RISC provides several indicators to support decision-making, and could also be used in the future to update policies or strategic documents.
e. more than 100 km of coastline) providing long-term homogeneous quality data, regularly updated. Their main missions are: giving access to the data to a wide audience; conducting scientific studies with the aim of strengthening the scientific knowledge on coastal risks; and, in some cases, carrying out coastal expertise. The OR2C (Observatoire Régional des Risques Côtiers/ Regional Coastal Hazards Observatory) is a new regional observatory of coastal hazards located in the Pays de la Loire region on the Atlantic coast of France. This observatory is the most recent to be set up in France and its main objective is to collect, strengthen, and transmit scientific knowledge and data on coastal erosion and storm surges. The OR2C was set up post-storm Xynthia to improve the existing tools used for coastal hazard management.
Also, it comprises three other members: the first member is from the Pays de la Loire region data center (i. e. GEOPAL, https://www. geopal. org/); the second member is from the coastal observation network Normandie-Hauts-de-France regions ("Réseau d'Observation du Littoral Normandie-Hauts-de-France" or ROL); and the third member is from the OSIRISC regional project in charge of the preliminary study for setting up a coastal regional observatory in Brittany region. The governance of the OR2C is unique in France because it combines public institutions (e. g. SHOM 1  , IGN 2  , ONF 3  ), research centers (e. g. IFSTTAR 4  , CEREMA 5  , University of Nantes), decisional bodies (i. e. State, regional and department authorities), and operational bodies (i. e. PAPI managers). This governance is currently the only one in France that has chosen to include PAPI managers.
A modular structure The actions of the OR2C are conducted according to a modular structure, with six different technical or thematic elements called "Modules" (fig. 5 ). The major aim of Module 1 is to produce a comprehensive inventory of coastal hazards data in the Pays de la Loire region, but also to identify the needs in order to better target and prioritize the acquisitions. This module uses a thorough bibliographic research, questionnaires, and interviews conducted with the twentyeight OR2C members. Module 1 is regularly updated along with an inventory of available equipment for coastal hazards studies and monitoring in the Pays de la Loire region. Module 2 is entitled "Structuring and acquisition of the scientific knowledge of coastal hazards". As its name suggests, this module aims to strengthen the scientific knowledge with acquisition of new data, and also organize and transmit knowledge on coastal hazards.
This module is responsible for the LiDAR airborne acquisitions performed by the OR2C and is intended to provide data chronically (i. e. every year) or following an extreme event. The OR2C website was also designed and created within this module as a major vector for transmitting information and data. Module 3 is thematic and deals with the history of coastal hazards in the Pays de la Loire region. It was carried out in the context of two PhD theses at the University of Nantes. The goal of the first thesis was to provide information on past extreme storm events (i. e. paleo-storms) and reconstruct paleo-storm chronology based on sediment analysis and dendrochronology. The project was achieved using sediment cores sampled in marshes that had not been subjected to humans' impacts before the 19th century  (Pouzet, 2018; Pouzet et al.
First mission: strengthen the scientific knowledge Module 1, from March 2016 to March 2017, provided an overview of available data in the Pays de la Loire region  (Robin and Kerguillec, 2017). This work also showed that some data were missing or not very recent (e. g. some bathymetric data date to the 18th century). In addition, it considered the needs of the OR2C members, and particularly the requirements of local authorities (e. g. PAPI managers). The needs are essentially related to data, equipment, and training. Therefore, this work targeted the need for new data in order to advice the technical committee members about acquisition surveys.