dataesr/scientific-paragraphs-categorization huggingface dataset:
H-index literature search protocol Information sources. H-index searches were undertaken in January 2012 using Web of Science (WoS)  [18]. Previous work established that results of H-index searches for pathogens undertaken using different bibliographic sources (e. g. WoS, SCOPUS, Google Scholar) are not identical but are highly correlated  [6]. Eligibility criteria. Searches were restricted to the years 1900 to 2010, inclusive. English is used in WoS, however searches also include foreign-language publication title translations. All literature in the WoS database has been published. Searches. Searches were undertaken using search phrases specified in quotation marks (''''), the 'topic' search field and with no lemmatization. Phrases were compiled including pathogen scientific name, alternative names, synonyms and alternative spellings according to NCBI Taxonomy  [19].
H-indices for clinical diseases used clinical terms as well as pathogen phrases for the main pathogens of disease. Virus searches also included synonyms and acronyms from the NCBI Taxonomy database and International Committee on Taxonomy of Viruses  [19, 20] , and the term 'virus', and excluded other entities (viral or non-viral) which shared acronyms. The Boolean operators 'AND', 'OR', and 'NOT' linked multiple search phrases. Example of a search phrase. (''mycobacterium tuberculosis'' OR ''bacillus tuberculosis'' OR ''bacterium tuberculosis'' OR ''mycobacterium tuberculosis typus humanus'' OR ''mycobacterium tuberculosis var. hominis'').
H-indices are likely to underestimate the contribution of scientific literature published in non-English languages, although after translation some publications are included in WoS and consequently in our calculations of H-indices. The literature searching method also doesn't account for the quality of publications in which pathogen names appear and the typical number of citations within different fields, and all bibliographic software packages incorporate newly published literature from different literature sources into their databases at different rates. Finally, H-indices are only a proxy for impact, with the results susceptible to a lag in time-to-publication, and newly emerging pathogens likely to be under-represented. As the strengths and weaknesses of using the H-index method are different to those of other prioritisation methods, it is probably best used in combination with other approaches, for example, to shortlist a set of pathogens for more detailed risk assessment relying on expert opinion or qualitative data.
It may also be used to prioritise diseases for which formal risk assessments are not possible because of data gaps. Our priority lists of pathogens enabled investigation of why infectious pathogens are omitted from disease surveillance and impact quantification work  [8, 9, 10, 11]. We considered several reasons for exclusion, including lack of diagnosis or misdiagnosis  [27] , because the impact of particularly chronic infections is difficult to quantify or they are seen as less important, and because some pathogens are commensals or natural biota causing opportunistic infections in immune-compromised individuals; their Pathogens include those which are zoonotic (Z), non-zoonotic (NZ), emerging (E) and not emerging (NE)  [15, 16] , or given a new status (NS) in this work. Pathogens also included in the list of top 100 animal pathogens are noted (A).
Acknowledgements This manuscript is dedicated to Axel Rethwilm who passed away much too early on July 29 th , 2014. We thank  Thomas Kurth  and his team of the  CRTD electron microscopy facility  for help and advice in the initial electron microscopy analysis. We acknowledge the use of the platforms of the Grenoble Instruct center (ISBG;  UMS 3518 CNRS-CEA-UJF-EMBL ) with support from  FRISBI  ( ANR-10-INSB-05-02 ) and  GRAL  ( ANR-10-LABX-49-01 ). E. M. and M. V. H. were partially supported by a  DIGS-BB  fellowship. G. E. was supported by a postdoctoral fellowship from the  ANRS  (Agence nationale de recherché sur le sida et les hépatites virales. This work was partially supported by grants from the  DFG  ( Li621/3-3 ,  Li621/4-1, Li621/4-2 ,  Li621/6-1 ) to D. L.
The systemic toxicity was assessed by means of a 90-day subchronic oral toxicity study in rodents. A No Observed Adverse Effect Level (NOAEL) was derived, which compared with the dietary exposure results in a sufficiently high Margin of Exposure. The CEF Panel considers that the likelihood of food allergic reactions to this xylanase produced with this genetically modified strain of A. oryzae is low and therefore does not raise safety concern. Based on the genetic modifications performed, the manufacturing process, the compositional and biochemical data provided and the toxicological studies, the Panel concluded that this food enzyme does not raise safety concern under the intended conditions of use.
Chemical parameters The xylanase produced with the genetically modified A. oryzae strain NZYM-FB is a single polypeptide chain of 384 amino acids. The molecular mass derived from the amino acid sequence was calculated to be 40. 8 kDa. Data on the chemical parameters and the protein homogeneity status of the food enzyme have been provided for three enzyme preparation batches and for the food enzyme batch (PPJ 6867) used for the toxicological tests (Table  1 ). The average Total Organic Solids (TOS) of the three enzyme preparation batches was 10. 6 % (w/w); the values ranged from 9. 3 to 11. 6 % (Table  1 ). TOS is a calculated value derived from 100 % minus % water % minus % ash and minus % diluents (stabilisation and formulation ingredients). The three enzyme preparation batches presented in Table  1  are ultra-filtered concentrates, which were stabilised and preserved by addition of potassium sorbate, sodium benzoate, sorbitol and glycerol.
Reaction and fate in food The xylanase catalyses the hydrolysis of 1,4-β-D-xylosidic endo-linkages in xylan (including arabinoxylan, which is xylan branched with arabinose) resulting in the production of (1→4)-β-D-xylan oligosaccharides of different lengths and xylose. Xylanase is specific in its action, not known to catalyse other reactions than this endo-hydrolysis of xylans to shorter xylans chains, xylo-oligosaccharides and xylose. These reaction products are naturally present in xylan-containing foods. The data and information provided indicate that the xylanase is denatured and/or removed during processing under the intended use conditions. The food enzyme was tested for other enzyme activities, i. e. alpha-amylase, glucoamylase, protease and lipase activities, which were below the detection limits of the employed methods.
e. species lists, called floristic relevés) to perform a hierarchical classification of plant community types (syntaxa, i. e. associations, alliances, orders and classes) at regional to continental scale  (Braun-Blanquet 1964 , Westhoff & van der Maarel 1978). As a consequence, phytosociological classifications are widely used by conservation agencies as a basis to habitat classification and ecosystem health assessment. Recently, the emergence of large phylogenetic, phytosociological and trait databases, coupled with the standardization of several computation methods, allows communitylevel studies combining different facets of biodiversity for numerous species, especially in order to compare vegetation units  (Benson et al. 2006 , Kleyer et al. 2008 , de Bello et al. 2010 , Dengler et al. 2011).
Study area The study is based on phytosociological data collected in the French Jura Mountains. This region is characterized by an altitudinal gradient divided into three structural units: first plateau (500-800 m a. s. l. ), second plateau (800-950 m a. s. l. ) and high range (950-1700 m a. s. l. ). Climate is nemoral with a strong suboceanic influence. Predominant soils are cambisols developed on limestone with a variable superficial cover of wind silt depositions. Permanent grasslands, either episodically or regularly mown and/or grazed, represent 22% of the area  (Mauchamp et al. 2013).
Data selection From the Taxa database  (Ferrez 2007) , provided by the CBNFC (Conservatoire Botanique National de Franche-Comté), we extracted 2335 phytosociological relevés recorded in grasslands of the French Jura Mountains. We imported these relevés in Phytobase 8. 1, a relational database devoted to vegetation analysis  (Gillet 2010). For each floristic relevé, performed on approximately 100 m 2 , species abundancedominance codes  (Braun-Blanquet 1964)  were converted into relative percentage cover, summing to 100% for each plot  (Gillet 2010). We first selected the subset of relevés related to permanent grasslands of the Jura Mountains at an altitude between 500 and 1300 m a. s. l. We excluded relevés from uplands (subalpine belt) or wetlands. For each selected relevé, we then performed a diagnosis of phytosociological classes, orders and alliances according to Julve's classification  (Julve 1993 (Julve , 2013) )  and based on species fidelity indices  (Gillet 2010).
Phylogenetic tree The Angiosperm phylogenetic tree was built from a larger number of species, related to the three previously defined phytosociological orders, but observed on additional surveys in the study area. It is composed of 54 families, 207 genera and 426 species, with significant differences in number of species per genus as well as genera per family (electronic appendix 1). The construction of the phylogenetic tree is based on sequences of two genes encoding chloroplast proteins (rbcL and matK). Their complementarity allows a good resolution of the tree for the selected species  (Hilu et al. 2003). The sequences were obtained using the GenBank database  (Benson et al. 2006 ). For species not yet or partially sequenced for the selected genetic markers, we replaced them by the closest available relative in the light of phylogenetic relationships revealed by the recent literature, including APG III classification  (APG 2009).
This represented 13% of the rbcL dataset and 19% for matK. All sequences were first automatically aligned using ClustalX 2. 1 software and then manually using Se-Al 1. 0al software for both markers  (Larkin et al. 2007 , Rambaut 1996). A combined analysis of these two datasets was then performed following the Bayesian MCMC (Monte Carlo Markov Chain) approach using BEAST 1. 5. 3 software  (Drummond & Rambaut 2007). The ambiguously aligned regions of the matK gene have been excluded (11% of 1010 bp). MrModeltest2 v. 2. 0 software was used to choose the model of nucleotide substitution that best fits the data, following Akaike's information criterion  (Nylander 2004 ). The selected model was the general time reversible model (GTR) with among-site substitution rate heterogeneity described by a gamma distribution  (Yang 1994).
These indicator values are grazing tolerance, trampling tolerance, mowing tolerance from Biolflor database  (Klotz et al. 2002) , and the nutrient value, indicating the nitrogen and phosphorus content in the soil as a proxy of soil fertility and grassland productivity, from Flora Indicativa  (Landolt et al. 2010). To assess the relative importance of altitude and vegetation units on the metric values, we performed a partial redundancy analysis (pRDA) with diversity metrics as response variables, vegetation units as explanatory variable, and altitude as covariable  (Borcard et al. 2011). In addition, we tested Spearman rank correlation between altitude and metric values for each phytosociological order independently. The three vegetation units were compared, for each metric and indicator, with a non-parametric Kruskal-Wallis test associated with a post-hoc test for multiple comparisons.
Relative influence of vegetation units and altitudinal gradient on metrics The partial RDA of diversity metrics constrained by vegetation unit and conditioned by altitude reveals that only 0. 79% of the variance is explained by the altitude covariable, while the vegetation unit alone explains 23. 20%. In addition, when split by vegetation unit and after applying Bonferroni-Holm correction, Spearman tests only detect few significant correlations between diversity metrics and altitude (electronic appendix 2B). Thus, in our dataset, the altitudinal effect on diversity metrics is negligible compared to the differences among vegetation units.
Limitations and prospects We are cognizant that several limitations require further studies to confirm the results. As an example, the use of meantrait values retrieved from databases, although often close to the field data values  (Kazakou et al. 2013) , seems less reliable than field measurements when studying fine-scale processes  (Cordlandwehr et al. 2013). Moreover, the knowledge of direct information on land-use history, landscape characteristics as well as a detailed characterization of farming practices, especially when mixed management was applied (i. e. mowing and grazing during the same season) seems crucial to better understand the community assembly. Further analyses using data about management practices applied to grasslands in the study area will be carried out, especially to address the question of the impact of such mixed management regime on biodiversity.
ACKNOWLEDGEMENTS We thank  Yorick Ferrez  and the  CBNFC  ( Conservatoire Botanique National de Franche-Comté ) for the provision of phytosociological relevés. This research was supported by the  Conseil Régional of Franche-Comté  and the  Comité Interprofessionnel du Gruyère de Comté. We are grateful to the two anonymous reviewers who helped us improving the manuscript.
Recovery was expressed as a percentage of the mean peak area of the extracted replicates divided by the mean peak area of non-extracted replicates. The stability of samples in the autosampler tray was tested using blank plasma and brain samples spiked with 10 ng BUP, 10 ng NBUP, and 100 ng d 4 -BUP. The spiked samples were by the procedures described above followed by evaporation, reconstitution with 20 µL ethyl acetate and 20 µL BSTFA with 1% TMS, transfer to vial insert, and placement in the autosampler tray. Every hour 1 µl of the solution was injected from the same sample. The response ratios of BUP and d 4 -BUP of successive injections were compared to that of the first injection. Identical calculations were performed for NBUP. data analysis. Data were collected and analyzed utilizing Thermo Electron GC/MS Solution software (Xcalibur™, version 1.
Phylogenetic Analysis Sequence alignment was generated and phylogenetic methods were performed as previously described  (Tailliez et al. 2010 (Tailliez et al. , 2012)). Briefly, for each bacterial strain, individual gene fragments (recA, 646 nucleotides; gyrB, 864 nucleotides; dnaN, 828 nucleotides; gltX, 913 nucleotides; and infB, 965 nucleotides) were aligned using MUSCLE  (Edgar 2004 ) and then concatenated with the seaview platform (http://doua. prabi. fr/software/seaview, last accessed June 17, 2014). Ambiguously aligned blocks were removed by the Gblocks method  (Castresana 2000)  or the "Guidance" program  (Penn et al. 2010). Maximum-likelihood analysis (phyML 3. 0) was carried out with the general time-reversible model of substitution with gamma-distributed rate heterogeneity and a proportion of invariant sites determined for all five proteincoding sequences by jModelTest, to give the best fit to the data according the Akaike information criterion  (Posada and Crandall 1998).
MUSCLE, Gblocks, PhyML, and bootstrap values were obtained from the phylogeny. fr platform  (Dereeper et al. 2008 ). Five X. poinarii strains, 23 type strains representative of Xenorhabdus species and the Xb strain, the genome of which has been sequenced, were included in this study. Three strains of Photorhabdus and one strain of Proteus mirabilis were used as closely related outgroups. The accession numbers of the individual genes used for building phylogenetic trees are listed in supplementary table  S1 , Supplementary Material online. The Enterobacteriaceae phylogenetic tree was constructed as described above, from the concatenated sequences of 12 conserved individual genes from the core genome  (infB, nusA, polA, pyrD, rpoB, valS, cysS, metK, purA, tpiA, smpB, secY)  of 47 Enterobacteriaceae strains.
The surface of the insect larva was sterilized with 70% (v/v) ethanol before the injection of the bacteria into the hemocoel. The number of bacteria injected into the larvae was checked by plating serial dilutions on LB agar plates. Insect mortality was assessed at regular point times after injection, for the evaluation of LT 50. At least four independent experiments were performed for each strain. For Sp. littoralis assays, statistical analysis was carried out with the Statistical Package for Social Science version 11. 0. 1 (SPSS, Chicago, IL), comparing individual survival times within each group.
Genome Annotation Functional annotation was carried out with the tools of the MicroScope platform  (Vallenet et al. 2013 ) and the annotated genome was implemented in the public XenorhabduScope database (https://www. genoscope. cns. fr/agc/microscope/ home/index. php, last accessed June 17, 2014). We used specific tools for the annotation of specific gene families. The nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) genes were predicted by the "2metDB" method  (Bachmann and Ravel 2009)  implemented at the MicroScope platform. Toxin-antitoxin (TA) systems were predicted with RASTA-Bacteria software  (Sevin and Barloy-Hubler 2007)  and we focused on predicted proteins with a domain characteristic of one of the nine most frequent TA system families: CcdA/CcdB, HicA/HicB, HigB/HigA, HipA/HipB, MazE/MazF, ParD/ParE, Phd/Doc, RelB/RelE, and VapB/VapC  (Pandey and Gerdes 2005).
Gene Remnant Identification We analyzed gene remnants in the Xp_G6 genome by first extracting protein sequences from the Xd genome present in the other two virulent strains, Xn and Xb, but absent from Xp_G6 using results of the Gene Phyloprofile tool from the MicroScope platform and a custom-designed Perl Script. We then compared each of these proteins with the six-frame translations of the complete genome of Xp_G6, using the TBLASTN software, a sensitive method of searching for traces of partial coding regions not annotated in the Xp_G6 genome. A gene was considered to be remnant in the Xp_G6 genome if the corresponding TBLASTN results met the following criteria: HSP (high-scoring segment pair), including one to three different hits displaying at least 40% identity and with an e value <0.
The accession numbers of the sequences of the subsequent amplicons are HG934736 (strain AZ26), HG934737 (strain NC33), HG934738 (strain SK72), HG934739 and HG934740 (strain CU01). reduced genomes in host-adapted symbionts may be due to genetic drift  (Mira et al. 2001; Silva et al. 2001; Nilsson et al. 2005). Indeed, because of sequestration in the host or the occurrence of major lifecycle stages within host, genome of host-adapted bacterial symbionts has reduced opportunity for counterbalancing deletional bias by HGT compared with freeliving bacteria. Moreover, the restriction to specific hosts also promotes small bacterial population size, asexuality and population bottleneck for transmission, favoring the persistence of slightly deleterious mutations (Muller's ratchet). The accumulation of these mutations entails a fitness cost to the bacterium and leads to DNA loss  (McCutcheon and Moran 2012).
Acknowledgments The authors thank  Nadege Ginibre  for assistance with insect pathology assays and  Mathieu Sicard  for his careful reading of the discussion section. They also thank the  INRA MIGALE  bioinformatics platform http://migale. jouy. inra. frfor providing computing resources. The paper benefited from the comments of  John McCutcheon , and three anonymous reviewers. This study was supported by  INRA  (grant SPE  2010-1133-01 , " Genomique comparative et evolutive de nouveaux facteurs d'adaptation de la bacterie entomopathogene Xenorhadus a ses hotes insectes ") and by  UniversiteMontpellier 2  (grant  2011  " Genomique comparative et fonctionnelle de nouveaux facteurs d'adaptation de la bacterie entomopathogene Xenorhabdus ases hotes insectes ").
Literature search Between 22 June 2011 and 25 September 2013, a systematic literature search was conducted in NCBI PubMed, ISI Web of Science, Armed Forces Pest Management Board Literature Retrieval System and Pasteur Institute Media Library. Citations in the identified articles were also examined individually in order to recover additional references. When the article was not found using the databases mentioned above, the corresponding authors and/or journal were contacted to obtain a copy of the publication. Older publications were found through Internet Archive (http://www. archive. org/). Publications were searched regardless of their language, including English, French, German, Japanese and Chinese. Japanese and Chinese publications without a full abstract in English were excluded for practical reasons.
Historical trends. To analyze historical trends in VT research, a first database (database #1) was built that contains all publications related to VT according to the inclusion criteria indicated above. For each individual publication contained in this database, basic bibliographical data, virus taxonomy and study type were recorded. Study type consisted of five categories: 'Experimental' studies looked for evidence of VT based on laboratory experiments under controlled environments; 'Natural' studies attempted to demonstrate VT in nature, by collecting immature, male or overwintering female mosquitoes; 'Both' are studies that conducted both experimental and natural investigations; 'Modeling' studies used mathematical models to evaluate the potential role of VT in arbovirus epidemiology; 'Reviews & Opinion' articles synthesized earlier work and/or commented the possibility of VT.
Evolution of virological assays. In order to examine how the evolution of laboratory assays in virology influenced the outcome of VT studies, two additional databases were assembled. Database #2 consists of 'experimental' studies and database #3 consists of 'natural' studies. Both were derived from database #1, but were restricted to the 'experimental', 'natural', and 'both' types of studies. Additionally, inclusion criteria were more stringent for databases #2 and #3 than for database #1. Databases #2 and #3 only included publications that specified mosquito and virus species tested, sample size and detection technique (the full list of studies included in these databases is provided in Supplementary Table  1 ). A total of 32 and 16 factors were included in databases #2 and #3, respectively, and each unique combination of factors was considered a different entry (the full list of factors recorded is provided in Supplementary Table  2 ).
Historical trends. To normalize the overall scientific production about VT of dengue, West Nile and chikungunya viruses, the yearly number of publications between 1950 and 2013 was obtained through queries to the ISI Web of Science version 15. 13. 1 database, using the keywords 'dengue', 'West Nile virus' and 'chikungunya', respectively. For each virus, the normalized yearly number of publication was calculated as the ratio of the yearly number of publications about VT of this virus over the total yearly number of publications about the virus. The normalized yearly number of publications was analyzed using nonparametric Wilcoxon tests.