dataesr/scientific-paragraphs-categorization huggingface dataset:
Gene sequences used in the study Viral genome linked protein (VPg) was from a variant of PVY isolate SON41 (GenBank accession AJ 439544-2)  [25]. The Eukaryotic translation initiation factor 4E used in this study is encoded by Capsicum annuum Yolo Wonder, a bell pepper inbred line susceptible to PVY (GenBank accession AAN74644-1).
illumina. com). These data were combined with genotypes from previous studies (Matukumalli et al. , 2009; Gautier et al. , 2010), that have been made available in the WIDDE database  (Sempéré et al. , 2015)  which included (i) European Taurine (EUT) belonging to four different breeds, that is Holstein (HOL) (n = 30), Abondance (ABO) (n = 22), Tarine (TAR) (n = 18) and Montbéliard (MON) (n = 30), (ii) West African Taurine (WAT) belonging to four different breeds, that is Baoulé (BAO) (n = 29), Somba (SOM) (n = 44), Lagune (LAG) (n = 44) and N'Dama (NDA) (n = 25), (iii) Zebu (ZEB) individuals from three Indian or Brazilian pure Zebu, that is Nelore (NEL) (n = 21), Gir (GIR) (n = 24), Brahman (BRM) (n = 25) and from African Zebu, that is Fulani Zebu (ZFU) (n = 43), Bororo Zebu (ZBO) (n = 23), Zebu from Madagascar (ZMA) (n = 35) and (iv) individuals from three admixed breeds Borgou (BOR) (n = 45), Kuri (KUR) (n = 47) and Santa Gertrudis (SGT) (n = 24).
The whole data set includes 732 individuals belonging to 23 different breeds  (Gautier et al. , 2010). Raw signal intensities on the 50 309 autosomal-SNP were converted into genotype calls with GenomeStudio (v. 1. 6. 3; Illumina). Among these, we discarded SNP that (i) displayed a minor allele frequency <0. 01 in all samples (ii) were genotyped on <75% of the individuals of one breed and (iii) did not pass Hardy-Weinberg equilibrium tests following the procedure described by  Gautier et al. (2010). The usefulness of 50 309 SNP was examined by characterization of the SNP allele frequencies. Quality control of genotypes was performed within populations to exclude SNP and individuals with more than 10% missing genotypes. The final data set consisted of 41 183 informative SNP with nearly 80. 67% of them being polymorphic with minor allele frequencies (MAF ⩾ 0.
Analysis of population structure To study the genetic relationships between six Algerian and Moroccan cattle populations, we performed the following: (1) Principal Component Analysis, based on individual SNP genotype data, using the R software (R Core Team, 2016), and the ade4 package for the multivariate analysis  (Chessel et al. , 2004). (2) Proportions of individual ancestry for K (number of assumed ancestral populations) ranging from 2 to 10 using the unsupervised model-based approach implemented in ADMIXTURE v. 1. 2. 3. Software  (Alexander et al. , 2009). The proportion of the genotype of each individual in each group or population (q) was estimated with the value K = 3, and the probability of ancestry in other populations. The percentage of individuals correctly assigned to the original populations was calculated for q different threshold values.
(A) World map showing the origin of the collected entomopathogenic nematode strains together with the primary and invasive ranges of the WCR, a specialized maize herbivore (WCR; data from 2012). Note that nematode strains from the invasive range do not share any evolutionary history with WCR, as they were collected before invasion. For detailed information about the different strains, refer to SI Appendix, Table  S1. (B) Chromatograms of plant-derived benzoxazinoids in the body of WCR (Top) and the BCB (Bottom), a generalist root herbivore which does not sequester benzoxazinoids and is mainly present in Central America, Mexico, and the Southern United States, outside of the nematode sampling range. Asterisks indicate significant differences between herbivore species (**P < 0. 01, ***P < 0.
001). For quantitative comparisons, refer to SI Appendix, Fig. S1. (C) Infectivity of nematodes toward WCR and BCB. Infectivity is shown for nematodes with an evolutionary history with WCR of more than 50 y (blue) and nematodes without evolutionary history with WCR (orange). EMMeans and SEs derived from statistical models (Dataset S1) are shown. Different letters indicate significant differences between treatments (false discovery rate corrected P < 0. 05). closely related to H. bacteriophora. In a first experiment, we compared the infectiveness of the different nematode strains toward larvae of the WCR and larvae of the banded cucumber beetle (BCB; Diabrotica balteata). In contrast to the WCR, the BCB feeds on many different plant species apart from maize and does not sequester benzoxazinoids (Fig.
1B  and SI Appendix, Fig. S1 )  (28). The BCB occurs mainly in Central America, Mexico, and the Southern United States, outside of our collection range. Thus, none of the tested nematode strains are likely to share an evolutionary history with this herbivore. Infectivity tests revealed a significant interaction between the host herbivore species and the evolutionary history of the nematodes (Fig. 1C  and Dataset S1). Nematode strains from the primary range of the WCR were able to infect and kill the WCR and the BCB equally well. By contrast, the infectivity of nematodes from outside the primary range was significantly lower for the WCR than the BCB (Fig. 1C ). Thus, nematodes that evolved in the presence of the WCR have an increased capacity to infect and kill this specific herbivore. This pattern was similar when only strains belonging to H.
Upon nematode infection, HDMBOA-Glc is broken down to 6-methoxy-2benzoxazolinone (MBOA), which also reduces nematode survival  (28). In choice experiments, MBOA-Glc reduced the attraction of nematodes that share no evolutionary history with the WCR, while nematodes from the primary range did not show a negative response toward MBOA-Glc (Fig. 2F  and SI Appendix, Fig. S6 ). Physiological doses of HDMBOA-Glc induced mortality in strains that shared no evolutionary history with the WCR but not in strains from the primary range (Fig. 2D ). No clear effects were found for MBOA-induced mortality (Fig. 2E ). Simple linear regression analysis revealed a positive correlation between the avoidance of MBOA-Glc and the benzoxazinoidspecific suppression of nematode infectivity (Fig. 2I ). Model selection applied on a multiple linear regression including all explanatory factors and their interactions resulted in a model with the behavioral response toward MBOA-Glc alone explaining 61% of benzoxazinoid-dependent nematode infectivity across the different strains (Dataset S1).
3E  and SI Appendix, Fig. S9 ). Furthermore, HDMBOA-Glc and MBOA reduced the survival of nematodes selected on the BCB but did not reduce survival of nematodes selected on the WCR (Fig. 3  C and D and SI Appendix, Fig. S9 ). Simple linear regression analysis revealed a correlation between the behavioral response to MBOA-Glc and benzoxazinoid-specific nematode infectivity as well as HDMBOA-Glc and MBOA toxicity and benzoxazinoid-specific nematode infectivity (Fig. 3 F-H ). Multiple linear regression including all explanatory factors and their interactions, followed by model selection and averaging, resulted in a model with MBOA-Glc repellence and HDMBOA-Glc toxicity explaining 82% of the benzoxazinoid-dependent nematode infectivity across strains (Dataset S1). Thus, similar to the pattern observed for the natural strains, nematodes exposed to the WCR for 5 generations do no longer avoid an insect-specific benzoxazinoid breakdown product and become resistant to a sequestered benzoxazinoid and its breakdown product.
The packages used for the different analyses were RVAideMemoire, car, emmeans, MASS, lme4, lmerTest and MuMIn  (65). All of the analyses were conducted in R 3. 5. 1. Data and Materials Availability. Some of the nematode strains were obtained under a materials transfer agreement. The data generated for this manuscript are available on Dryad, https://doi. org/10. 5061/dryad. nk98sf7pf. R codes and results of statistical analyses are available in the form of an R markdown file (Dataset S1).
ACKNOWLEDGMENTS. We thank the following scientists and institutions for sharing nematode strains:  Ralf-Udo Ehlers  (e -nema GmbH, Germany ),  Raquel Campos-Herrera  ( Instituto de Ciencias de la Vid y del Vino, Universidad de La Rioja, La Rioja, Spain ),  Stefan Toepfer  ( Plant Protection and Soil Conservation Directorate, CABI International, Hódmez} ovásárhely, Hungary ),  Alper Susurluk  ( Department of Plant Protection, Uludag University, Bursa, Turkey ),  Selcuk Hazir  ( Department of Biology, Adnan Menderes University, Aydin, Turkey ),  Javad Karimi  ( Biocontrol and Insect Pathology Laboratory, Department of Plant Protection, School of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran ),  David Clarke  ( School of Microbiology, University College Cork, Cork, Ireland ), and  Juan Ma  ( Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Science/Integrated Pest Management Centre of Hebei Province, Baoding, PR China ).
❼ Alongside the neutralization of the provirus described above, the evolution sometimes takes advantage of a viral function to enrich the physiological functions of the host. A well-known example is Syncytin-1 protein, which derives from an HERV-W envelope protein harboring fusogenic activity. Syncytin-1 is expressed during placentation and is required for trophoblast cells fusion into a multinucleated syncytiotrophoblast layer, a critical step of placental development demonstrated an excellent safety profile and promising results in neuroprotection and in myelin preservation in a phase II clinical trial (NCT03239860)  [26••, 30]. This example of HERV-W and MS illustrates how fundamental research can lead to new therapeutic strategies. In MS, approved drugs mainly consist of immunomodulatory agents, the efficacy of which has only been shown to alleviate relapses of early symptoms in most MS cases, but were shown to be ineffective at stalling disease progression.
The particular HERV-W-env genomic copy encoding the pathogenic HERV-W-Env protein involved in T1D remains to be identified. This identification is precluded by extensive interindividual variations existing in the proviral content of some HERV families in human genomes  [96]. Such nonubiquitous copies or somatic DNA rearrangements in chromosomal HERV sequences may explain difficulties to pinpoint the relevant copy in DNA databases of reference human genomes  [96]. The identification of a peculiar HERV copy clustering with T1D, or T1D subtypes, would allow the identification of a potentially critical genetic risk factor that could not have been pinpointed from traditional genetic studies in which this part of the human DNA is not examined with appropriate methods required for multicopy transposable elements  [4, 96••].
unique positioning identifies HERV-W-Env as a new therapeutic target in T1D. A phase IIa clinical trial addressing HERV-W-env-neutralizing humanized antibody temelimab clinical safety and pharmacokinetics endpoints in T1D adults patients has recently been conducted (ClinicalTrials. gov Identifier: NCT03179423) [98]. It has confirmed the very strong safety profile of t e m e l i m a b a n d n o w c a l l s fo r f u r t h e r c l i n i c a l developments in recent-onset T1D pediatric patients.
Information Studies about enteroviruses from D. H. mentioned in this review were supported by Ministère de l'Education Nationale de la Recherche et de la Technologie, Université de Lille (Equipe d'accueil 3610), Centre Hospitalier et Universitaire de Lille, and by EU FP7 (GA-261441-PEVNET). A. B. was supported by a scholarship of Université de Lille.
Funding Information Studies about enteroviruses from D. H. mentioned in this review were supported by Ministère de l'Education Nationale de la Recherche et de la Technologie, Université de Lille (Equipe d'accueil 3610), Centre Hospitalier et Universitaire de Lille, and by EU FP7 (GA-261441-PEVNET). A. B. was supported by a scholarship of Université de Lille.
Acknowledgements We thank  Pr. Claire Remacle  ( University of Liège, Belgium ) for her helpful discussions. We are grateful to the  NanoBio-ICMG platform (FR 2607, Grenoble)  for granting access to the  Electron Microscopy facility. S. L. was recipient of an  ANR  PhD grant from the  "investment for the future" program  ( ANR-10-IEED-0004-01 ).
The PacBio reads and the previously published Illuminabased assembly  (Varadharajan et al. 2018)  were merged together using the PBJelly2 suite  (English et al. 2012 ) using the noSplitSubreads, minMatch 8, minPctIdentity 70, bestn 1 and maxScore 11 parameters. Basic statistics, such as N 50 , L 50 and the length range of the assembled sequences were calculated for each assembly using an in-house  developed script (contig_statistics. pl; available in GitHub). After initial mapping of the assembled scaffolds to the Atlantic salmon genome assembly (described in more detail in the linkage mapping section) and manual curation, some of the assembled scaffolds were split in cases of potential sequencing or assembly errors. Linkage mapping: Male-and female-based linkage maps were built using markers from a single European grayling family originating from the Rhine River (Obenheim, France) that included both parents, 69 female offspring and 44 male offspring that were sequenced using a restriction site associated DNA (RAD) methodology according to previously described protocol  (Amores et al.
2011). The RAD fragments were produced by using the SbfI restriction enzyme and were sequenced using 100 base pair single-end sequencing using the Illumina HiSeq 2500 platform. Quality trimming of the sequence reads was performed with ConDeTri v. 2. 3  (Smeds and Kunstner 2011). The RAD data consisted of a total of 4,167,787 and 7,056,371 reads for the male and female parents, respectively, and an average of 4,041,607 reads for each offspring. Scaffolds containing at least one marker covered 54% of the total length of the hybrid assembly. To identify the RAD markers, we sorted the trimmed reads to separate files according to barcode, removed the barcode sequence, and verified the restriction site sequence using an in-house Perl script named barcodesplitter5. 3. pl (available in GitHub). The reads were then mapped to the hybrid assembly using the Bowtie2 tool  (Langmead and Salzberg 2012).
8 read coverage, a criterion which resulted in removal of four offspring from the analysis. Polymorphic site filtering was completed using R (script "RADstats_final. R"; available in GitHub). The filtered markers were mapped to linkage groups and ordered using the Lep-MAP2 software  (Rastas et al. 2016). Linkage between markers was accepted at LOD $ 9, upon which additional individual markers were added at LOD $ 7. The linkage groups were initially constructed based on recombination frequencies and thereafter improved by testing the alternative ordering of markers using comparative mapping information from Atlantic salmon, a procedure hereafter referred to as salmonization. The latter was performed by first mapping the scaffolds from the European grayling hybrid assembly to the Atlantic salmon genome assembly  (Lien et al.
2016) , downloaded from the NCBI Genome database (RefSeq assembly GCF_000233375. 1), using the nucmer tool in MUMmer 3. 0 aligner  (Kurtz et al. 2004). Prior to the alignment, Atlantic salmon chromosome sequences were repeat-masked using a salmon repeat database (ssal_repeats_v2. 0) and RepeatMasker v4. 0. 3  (Smit et al. 2013 (Smit et al. -2015)). The best matching position for each European grayling scaffold in the Atlantic salmon genome was determined by adding up the number of base pairs in each hit and the number of hits within a scaffold. Second, for each linkage group, markers mapping to the most frequently associated Atlantic salmon chromosome were included in the further salmonization procedure. At each step, the correct map was assumed to be the one with the shortest female map length calculated using Lep-MAP2  (Rastas et al.
In the third step, we investigated the possibility of translocations from these blocks explaining our observations. To do this, we reconstructed each linkage group by permuting the order of the corresponding blocks and selecting the solution with the minimal length as the most parsimonious block order. To test the possibility of inversions in the most parsimonious block order, we then inverted each block and tested whether it further reduced the map length. At the end of this step we validated the final combination of rearrangements by testing if implementing all accepted changes indeed resulted in the minimal map length. The salmonization script "salmonize_final. R" is available in GitHub. As the final step, all maps were further manually curated with special attention given to regions that are known to have.
Repeat library construction and genome annotation A comprehensive repeat library was built by combining de novo identified European grayling-specific repeats as well as repeat elements identified in the Atlantic salmon genome (available at: http://web. uvic. ca/ grasp/salmon_v1. 6). We initially ran the RepeatModeler software v. 1. 0. 11 (available at: http://www. repeatmasker. org/RepeatModeler; last accessed June 8, 2018) with default parameters. To compile a set of LTRs, we used the LTRharvest  (Ellinghaus et al. 2008)  and LTRdigest  (Steinbiss et al. 2009 ) software as described in (http://weatherby. genetics. utah. edu/MAKER/wiki/index. php/Repeat_Library_Construction-Advanced; last accessed: June 8, 2018) and combined the results with the sequences identified by MGEscan-LTR  (Lee et al.
2016). All the identified sequences were combined and filtered to remove redundancy. The resulting de novo set of sequences was combine-queried against the Universal Protein Resource database (UniProt proteins release 2017_08, Consortium 2017) to filter out any known proteins sequences. The remaining unclassified set of sequences was then annotated using RepeatClassifier, the Dfam database and TEclass  (Abrusán et al. 2009 ). An updated reference-based set of transcripts was constructed by first aligning the RNAseq reads to the improved assembly using STAR v. 2. 6  (Dobin et al. 2013 ) followed by Cufflinks  (Trapnell et al. 2010)  for the prediction of transcript sequences. This along with the de novo assembled transcriptome described in  Varadharajan et al. (2018)  was used as an input to the PASA pipeline  (Haas et al.
2003)  to build a comprehensive transcript database. Further, predictions from ab initio gene finders like SNAP  (Korf 2004 ) and GeneMark-ES  (Lomsadze et al. 2005)  were also used as input into MAKER v. 2. 31. 9  (Cantarel et al. 2008). MAKER pipeline was run for two iterations with transcript evidence from PASA transcriptome assembly and protein coding sequences from the Atlantic salmon, GTF outputs from AUGUSTUS and GeneMark-ET resulting from BRAKER  (Hoff et al. 2016) , the UniProt database (UniProt proteins release 2017_08, Consortium 2017) as the protein evidence and the above described repeat library. MAKER was run with default options. Functional annotation was added to the MAKER-predicted gene models using BLAST against UniProt database and domain information was added using InterProScan  (Zdobnov and Apweiler 2001).
MAKERpredicted gene models were then filtered based on Annotation Edit Distance (AED) and the presence of known PFAM domains to retain high confidence set of genes. Genome repetitiveness and repeat element assessment Kmer repetitiveness of the previously published and current genome assemblies of European grayling, Atlantic salmon and rainbow trout (Oncorhynchus mykiss) were calculated using Jellyfish software v. 1. 1. 11 (Marçais and Kingsford 2011) using kmer size of 31. Repetitiveness was calculated by dividing counts of non-unique kmers by total kmers in the assembly. To investigate the European grayling genome in terms of repeat elements, the European grayling repeat library, containing 1,743 de novo repeats, was employed along with the repeats from RepBase v. 20. 05  (Jurka et al. 2005).
Transposable element sequences were curated by first detecting the host genes that were potentially of non-transposable element origin and then classifying the remaining transposable element sequences according to the classification system of  Wicker et al. (2007). Transposable element abundances were estimated for both European grayling and Atlantic salmon. To remove from the final repeat analysis any repeats that potentially originated from host genes instead of transposable elements, the transposable element sequences were compared to two different repeat databases. These databases were the REPET-formatted RepBase v. 20. 05  (Jurka et al. 2005 ) and the Swiss-Prot database available in UniProt (as of June 1, 2018). Comparisons were conducted by using the blastn  (Altschul et al. 1990 ) and blastx  (Gish and States 1993)  algorithms with parameters set to word_size = 7, and to e-value.
1•10 210. A custom script named best_multi_blast_score_parser. pl (available in GitHub) was used to select the highest scoring hits for each potential transposable element sequence. Based on the best-scoring hits, each transposable element sequence was categorized as non-transposable element derived host gene and removed if it had a best-scoring hit to a Swiss-Prot sequence. The rest of the library hits were kept for further analysis. To classify the transposable element sequences, they were compared to the RepBase repeats using both nucleotide sequence and protein similarity. To categorize transposable element sequences to class, order, and superfamily levels, the relevant information from RepBase was used in case a sequence had an acceptable alignment hit with this database. An alignment was accepted if it suggested high similarity between query and reference repeat, defined by  Wicker et al.
(2007). A high similarity alignment was at least 80 base pair long with at least 80% sequence similarity between query and reference repeat sequence, occupying at least 80% of the query repeat length (which we calculated after removing unknown nucleotides from the query sequence length). These thresholds concerned the blastn search. In case of a non-acceptable nucleotide alignment for a transposable element sequence, then this sequence was searched against the RepBase database using the blastx approach, with an alignment considered valid if the hit had e-value , 1•10 210 (following  Lien et al. 2016). The repeat element abundance in the European grayling and Atlantic salmon genomes was assessed for each chromosome separately using the RepeatMasker v. 4. 0. 7 tool  (Chen 2004 ) by using the parameter -qq.
The RepeatMasker-based locations of transposable element sequences in each of the two genomes were annotated with a script named "classifyGoodTEHits. R" (available in GitHub). The elements with marked difference in their abundance between the two genomes were sought out by using a linear model log2(salmon abundancy+1) log2(grayling element abundancy+1) using R (v. 3. 4. 0, R Core Team 2017) and elements that had residuals larger than 1. 96 standard deviations from zero were considered outliers, that is, outside the 95% confidence interval limits. Predicting centromere locations using the location of repeats: Repetitive element content can reveal information about the chromosomal landscapes  (Kaminker et al. 2002; Lien et al. 2016). To estimate the repeat content, copies of the generated repeat library were sought from the European grayling chromosomes using RepeatMasker.
Identification of the European grayling sex chromosome The gene named sdY for sexually dimorphic on the Y-chromosome was searched using a tblastn  (Altschul et al. 1990 ) homology search against the European grayling chromosome assembly. The rainbow trout sdY protein sequence (GenBank: BAM24747. 1) was used as bait in this search. The RAD sequences were then remapped to the chromosome-level assembly and sex-biased loci were detected from the chromosomes.