dataesr/scientific-paragraphs-categorization huggingface dataset:
DATA ANALYSIS As the data in these analyses represented 55 studies conducted using different methods and for different purposes, we treated 'study' as a random effect. For each trait, we used a random-effect model with 'study' as random factor to calculate a best linear unbiased predictor (BLUP) of the mean trait value (and standard error) for each species. The BLUPs Given the lack of within-species variation for most traits in the dataset and to avoid overfitting, we were unable to fit a general linear mixed model with phylogeny as a random effect (e. g. Ives & Helmus 2011). Instead, for each trait separately, we chose to fit a general least squares model in which the correlation structure was a phylogenetic tree reflecting the relatedness among species (using gls function from 'nlme' package;  Pinheiro et al.
In a second step, we repeated the same approach (accounting for species phylogeny) on a subset of our data excluding observations from plants grown indoors or in pot, in order to test the effect of global climate and soil variables. This time, we included as fixed effects plant growth form, MAT, MAP, soil pH, cation exchange capacity and bulk density in our models for all four traits. Data for all four root variables were log-transformed prior to all analyses, and we determined that model assumptions were met for each model. The interaction effects between MAT and MAP and between soil pH and cation exchange capacity on root traits were also included in the second step of our analyses, but are not presented here as they were consistently found to be non-significant for all four traits. For both steps, no differences were observed between shrubs and trees and observations for these categories were pooled.
Accepted Article This article is protected by copyright. All rights reserved. (using 95% confidence interval range; Fig. 2 ). As a point of comparison, the 20-fold difference in fine-root N (from 1. 7 to 39. 3 mg g -1 ) was twice this of its aboveground analogue, leaf N, in a dataset of comparable size and geographical spread (10-fold difference, from 6. 3 to 58. 7 mg g -1 ;  Freschet et al. 2011). Large trait variation also occurred within local flora, with up to 4-, 9-, 10-and 50-fold differences in mean fine-root diameter, N, tissue density and SRL, respectively (Fig. 2 ), as well as within climatic areas, plant growth forms, N 2 -fixation ability, and plant growth conditions (see Fig. 3 ).
Accepted Article This article is protected by copyright. All rights reserved. stood out with generally lower fine-root N, and tissue density than forbs, shrubs and trees (Fig. 4 ). Second, woody species showed lower SRL than forbs and graminoids owing to higher tissue density. Shrubs and trees did not show any substantial or significant differences in any of our models. Plant N 2 -fixation capacity was positively but weakly related to fine-root N (2% explained variance) and negatively to SRL (1% explained variance; Table  S2 ). Once corrected by phylogenetic relatedness these weak trends disappeared (Table  1 ), mostly because of the constrained distribution of N 2 -fixers to the Fabaceae family (96% of N 2 -fixers in this dataset; Fig. S1 ).
Accepted Article This article is protected by copyright. All rights reserved. dataset, we demonstrate that primarily climate (mean annual temperature and precipitation) and to a lesser extent plant functional types (i. e. , growth form and N 2 -fixation ability) and soil variables (pH, cation exchange capacity, bulk density) account for the global variation in four key fine-root traits. Similar to previous aboveground observations, our results show high root trait variation at local scales among co-occurring species  (Wright et al. 2004; Freschet et al. 2010 ) despite local environmental constraints.
2005). However, this is not supported by other trait variation with cation exchange capacity. The increasing fine-root N observed with decreasing soil pH also suggests that limited nutrient availability for plants favours species with high metabolism  (Roumet et al. 2016). Indeed, across the pH range observed in our dataset (from 4. 5 to 7. 8), decreasing pH implies lower nutrient mobility in soil solution. However, again, this trend was relatively weak and not paralleled with consistent variation in.
Acknowledgements We would like to thank  JC Cahill  and two anonymous reviewers for their constructive assessment of our work. CMT was supported by  EU's Research Executive Agency  for funding through  Marie Curie Actions  ( 657951 ). CMI was supported by the  Biological and Environmental Research program in the U. S. Department of Energy's Office of Science. VGO was supported by grant  14-50-00029  from the  Russian Science Foundation (RNF).
Interestingly, miRNAs transferred via EVs to other cells can alter recipient cell responses, as miRNAs act in catalytic-like fashion and can target multiple critical nodes in intracellular pathways  (2, 39, 44). Illustrative examples of EVs transporting stem cell and parenchymal mRNA, miRNA, and lncRNA are discussed in subsequent sections. Nucleic acids and proteins of EVs have been curated in several databases, including ExoCarta (http:// www. exocarta. org) and EVpedia (http://www. evpedia. info).
Acknowledgments The authors would like to thank members of the  Zhao and Lötvall laboratories  for helpful discussions. This work was supported by grants from the  National Institutes of Health (NIH)  ( 1DP2CA195763-01 ) to W. Z. and from the  Swedish Research Council  (Project no. K2014. 85X-22504-01-3 ), Swedish Heart and Lung Foundation  (Project no. 20120528 ),  Swedish Cancer Foundation  (Project no. CAN 2012/690 ), and  VBG Group Herman Krefting Foundation for Asthma and Allergy Research  (Project no. 20131212 ) to J. L. M. R. was supported by a  National Institute of Neurological Disorders and Stroke  ( NINDS/NIH ) training grant (Award # NS082174 ). The authors apologize to the authors of papers not cited here owing to space limitations.
From rym5 and susceptible varieties, the complete VPg coding region of BaMMV was amplified using the primers and the annealing temperature described in Table  1. Direct sequencing of the uncloned PCR products was performed by Genoscreen (Lille, France). The corresponding BaMMV VPg sequences have been deposited in Genbank with accession numbers KX117164 to KX117182 (S1 Table ). Additionally, some samples were screened for the presence of barley endornavirus (HvEV)  [52]  using the primer set and the annealing temperature described in Table  1.
Each MySeq run integrated between 12 and 22 samples (S2 Table ). Following demultiplexing and quality trimming/filtering of reads, bioinformatic analysis of the sequencing data was performed essentially as described previously  [53]. Information on the number of reads obtained for each sample is provided in S2 Table. Bioinformatic analyses involved either de novo assembly and annotation by BlastN and BlastX against Genbank, or mapping of reads against reference viral genomes using CLC Genomics workbench 7 or 8. Assembled BaMMV and BaYMV sequences showing more than 75% completeness were used for phylogenetic analyses and have been deposited in Genbank (Accession numbers KX117183 to KX117209 and KX831456 to KX831469, S1 Table ).
Viral sequences comparisons and phylogenetic analyses Multiple sequence alignments of contigs obtained from NGS data and of BaMMV and BaYMV sequences (or of deduced encoded proteins) and of European and Asian isolates retrieved from Genbank were performed using the ClustalW algorithm  [54]  as implemented in MEGA 6. 0  [55]. Phylogenetic trees were reconstructed in MEGA 6. 0, using strict nucleotide or amino acid distances and either the Neighbour Joining (NJ) or the Maximum Likelihood (ML) algorithms. Branch support was evaluated by bootstrap analysis (500 replicates).
In contrast, samples originating from susceptible varieties that do not carry any of the rym genes showed more variability at that position, with either an AAG codon encoding a lysine (BaYMV-1, non resistance-breaking), a range of codons encoding an asparagine or a histidine (BaYMV-2, resistance-breaking) or, in three samples, mixes of the BaYMV-1 and BaYMV-2 codons (Table  3 ). This result suggests that although BaYMV-2 is prevalent, BaYMV-1 isolates are still present in a range of environments in France. Complete or near complete genomic sequences for both genomic RNAs of BaYMV and/or BaMMV could be reconstructed from the NGS data of most analyzed samples and were used to compare the isolates found in France with those analyzed in the past or present in other countries and for which genomic sequences are available in Genbank.
In addition, comparison of the phylogenetic trees reconstructed for the RNA1 and for the RNA2 provides evidence for pseudorecombination between the two European clusters (Fig 2B  and 2C ): indeed, the UK-L isolate  [35]  clusters with Table  3. Indexing of selected symptomatic barley samples by next generation sequencing. NGS analyses were performed on highly purified doublestranded RNAs extracted from 21 barley leaf samples. The viruses identified are indicated, with the percentages of total reads mapping to their genome; PCR and NGS results are compared for BaYMV and BaMMV screening. BaYMV type, either Y1 (BaYMV-1) or Y2 (BaYMV-2), was determined from codon at position 132 of VPg in NGS data and in parallel with the dCAPS assay.
Considering that rym5 encodes a modified version of eIF4E  [8, 9] , and that the viral VPg has been shown to be involved in breaking this type of resistance  [7, 43] , the complete sequence of the VPg gene of ten BaMMV isolates detected on symptomatic rym5 varieties was determined. For comparison purposes, the VPg gene sequence of eight BaMMV isolates detected from susceptible varieties were also determined. Four additional samples from Germany were also studied to extend the range of sequences available. The corresponding amino acid sequences were aligned and compared, together with the sequences of reference isolates available in Genbank. No single mutation specific for the rym5-breaking isolates could be identified (Fig  3 ), suggesting that several amino acid positions might independently or in combination contribute to the overcoming of rym5 by BaMMV isolates.
Introduction The genetic diversity of animals meant for food and agriculture is continuously diminishing. Numerous breeds have been disappeared within the last decade and the remaining ones are dramatically endangered. The FAO has adopted an efficient strategy based on the identification and characterization of the existing animal resources, breeds and populations, aiming to preserve these important sources of various products such as meat, milk, wool, etc. More than 8800 domesticated animal breeds, belonging to 38 species, are catalogued in the FAO's DAD-IS database (http://dad. fao. org)  (Leroy et al. , 2017). They could be recognized thanks to a number of phenotypical, geographical and/or cultural specifications. It represent a potential tank that could be used to meet the future challenges of the international market regarding their ability to adapt to the changing production environments The breed constitutes the main subdivision within the domestic species.
Naming according to the geography Numerous names according to cultural and geographical considerations have been reported for the dromedary. The name of the populations is those of the tribe that keeps it or the region it belongs to. Thus, 10 branches exist in Algeria: Tergui, dromedary of the steppe, Reguibi, Aftouh (called also Azawak), Ouled Sidi Chikh, Sahraoui, Châambi, Ait Kebbach, Berbari and Ajjer. This study allows us to identify the pure breeds in their original range and realize morphological measurements as well as blood sampling for genotyping and therefore enrich the genetic database.
Conclusion In Algeria, the dromedary populations and their genetic variability are important yet not well documented. The first studies report the names of the breeds according to the tribes they belong to rather than the phenotypic and productive features. From one region to another, the breeds and the populations are very different due to the geographic and bioclimatic conditions. It is interesting to study the impact of the mode of breeding on the genetic variability under different environments. The identification of the genotypes adapted to different conditions (food availability, heat-resistance, etc. ) as well as the analysis of the phenotypic features will help to establish a valuable database. Such information would contribute positively to a better usage and the promotion of the dromedary resource.
1985). Performance data were collected as follows: live weight (per cow daily), TMR intake (per pen daily), and body condition score (BCS) (per cow weekly). Daily milk production (per cow) was reported as the sum of morning and evening milk yields. Milk was sampled from each cow in the morning and afternoon of d 0, 7, 14, 21, 28, 56, and 84. The morning and afternoon samples were combined for each cow, according to their milk production, and divided into two aliquots of not less than 50 ml each. The first aliquot was analysed for milk components (i. e. , fat, protein, lactose, somatic cell, and urea). Fat corrected milk (FCM, 4%) was calculated as per Gaine's formula (1923): FCM (kg) = 0. 4M + 15 F where: M = milk yield (kg). F = M x fat content (%). The second milk aliquot was analysed for individual fatty acid composition following an in situ preparation of fatty acid methyl esters, separation by gas chromatography and quantification against known standards  (Park and Goins, 1994, Loor and Herbein, 2001).
Statistical analyses All statistical analyses were performed using SAS 9. 3 software (SAS Institute Inc. , 2011). Milk yield, fat content and DHA content were analysed using linear mixed models for repeated measures using proc MIXED procedure. For each the model included the fixed effects for treatment (CON vs AURA), day, and their interactions; for fat content and DHA, the model also included the random effect of cows. For milk yield, each model was subjected to two covariance structures (i. e. , compound symmetry and autoregressive); the model with the smallest Akaike information criterion was then used. Because of the irregular sampling intervals used to determine milk fat and DHA content each of these models was subjected to compound symmetric and spatial power covariance structure. Two-sample t-tests were used to determine between-treatment differences.
Methods Photographs were taken using a Zeiss Stereo Discovery V16 microscope system with Zen software. In most instances, incident and transmitted light were used simultaneously. All images are digitally stacked photomicrographic composites of approximately 40 individual focal planes obtained using the free software Combine ZP for a better illustration of the 3D structures. The line drawings were prepared from photographs using image-editing software (CorelDraw X7 and Adobe Photoshop CS6). Specimen NIGP164757 is housed at the Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences (NIGPAS). Specimen BA16200 is currently in NIGAPS but will be finally deposited in the Lingpoge Amber Museum in Shanghai (China). Specimen SMNS Bu-137 is housed at State Museum of Natural History in Stuttgart (Germany).
Acknowledgements This research was supported (grant nos in parentheses) by the  National Natural Science Foundation of China  ( 41572010 ,  41622201 ,  41688103 ),  Youth Innovation Promotion Association of the Chinese Academy of Sciences  ( 2011224 ), the  Chinese Academy of Sciences President's International Fellowship Initiative  ( 2011T2Z04 ), and the  HKU Seed Funding Program for Basic Research  (201210159058). We offer our sincere gratitude to  Günter Bechly  for providing photos of the specimen SMNS Bu-137; and  Günter Bechly  and three anonymous reviewers for the very useful comments on the earlier version of the manuscript.
e. , "rare" variants) represent 88% of all detected junctions. To investigate whether gene expression level correlates to the amount of detected splice variants, we generated 20 bins of about 1000 genes grouped according to their expression level in our compendium data set. We then measured the average number of distinct splicing events per gene in each expression bin. The total number of detected junctions per gene increases with the gene expression level (with the highest expression bin having on average around 70   C ) For each splice junction, we measured a usage frequency over the whole compendium (see Methods) and assigned it to a usage category (>99%: constitutive; 50%-99%: major; 5%-50%: minor; 1%-5%: secondary; <1%: rare). We then evaluated for each junction what its usage frequency was in each of the individual 1682 RNA-seq runs.
The distribution within each category is represented as pie charts. The breakdown of junctions with a frequency <1% found "nonrare" in individual sets is shown as a stacked graph (see also Supplemental Table  2 ). potential introns); however, if we only count the number of junctions with a usage frequency >1%, we see that the average number of introns per gene is almost invariant (between five and seven) regardless of the expression level (Fig. 2A ). This seems to indicate that these low frequency junctions do not in fact correspond to functional introns but rather to accidental misfiring of the spliceosome. To evaluate the possible functionality of those rare isoforms we analyzed the conservation of all introns boundaries. For each gene with an alternative splice form we retrieved from the WormBase database (http://www.
In the 2011 study, RNA-seq reads were mapped against a database of potential trans-splice sites generated in silico by joining all SL sequences with all annotated acceptor splice sites. In contrast, our detection method is independent of the accuracy of the genome annotation and therefore allowed us to recover trans-splice sites that had been previously missed. In addition to the difference in mapping strategy, we also benefited from using a 1000-fold larger number of reads. Most of the 15% of genes for which we found no SL site are among the lowest expressed genes Introns with low inclusion rate are overrepresented in highly expressed genes. All C. elegans genes were ranked according to their expression level (defined by the highest read count for an intronic junction of that gene) and split in 20 bins of about 1000 genes.
Data sets selection The raw data used in this study are publicly available and downloaded from the NCBI Sequence Read Archive (SRA; https://www. ncbi. nlm. nih. gov/sra; see Supplemental Table  1 ). Sample experiment and run accession numbers and sequence files were downloaded programmatically using the NCBI "E-utilities" tools "ESearch" and "EFetch" (https://www. ncbi. nlm. nih. gov/books/ NBK25501/) and the Unix utility "wget", and read files in FASTQ format were generated using the "fastq-dump" tool from the NCBI SRA toolkit 2. 5. 0. Illumina mRNA-seq experiments were selected with a regular expression search of the experiment descriptions, leading to a final compendium of 1682 data sets (1214 single-end and 468 paired-end). Read files were taken as is; no read processing was performed.
Then, three mapping algorithms were used in succession to determine the genomic locations of the corresponding trans-splice sites. The read portion downstream from the SL portion was first mapped to the C. elegans WS251 genome with TopHat2 (with the options "--min-intron-length 10 --max-intron-length 20000 --read-mismatches 3 --read-gap-length 2 --read-edit-dist 3 --maxmultihits 2 --b2-sensitive --segment-mismatches 2 --segment-length 15 --min-segment-intron 10 --max-segment-intron 20000 --nocoverage-search"), which allows reads to contain introns but requires full alignment. Then, the unmapped SL reads were mapped to C. elegans WS251 RNA transcripts with Bowtie 2, which does not make spliced alignments but allows for partial mapping with soft-clipping. Bowtie 2 was run with the options "--local --sensitive-local" (all other parameters set as default).
Finally, the remaining unmapped SL reads were aligned to the C. elegans genome with GSNAP from the GMAP-GSNAP package release 2017-01-14  (Wu and Nacu 2010) , which allows for both introns and soft-clipping. The following GSNAP options were set as follows (all other parameters as default): "--nofails --novelsplicing=1 --localsplicedist=20000 --novelend-splicedist= 20000 --suboptimal-levels=0 --max-mismatches=3 --indel-penalty= 2 --max-middle-insertions=2 --max-middle-deletions=2 --max-end-insertions=2 --max-end-deletions=2 --input-buffer-size=100000 --output-buffer-size= 100000. " In the above mapping strategy, in case of soft-clipping the genomic position of the trans-splice site was shifted according to the length of the clipped region. Otherwise, it was taken as the mapping position of the 5 ′ end of the SL read (i.
Acknowledgments This work has been funded by  Inserm  (D. D. , N. J. T. ) and the  French Ministry for Higher Education and Research  (J. R. M. M. ). We thank  Dr. Axel Innis  for providing access to his computer cluster at the  IECB , and the  University of Bordeaux  for access to the supercomputer of the  Mésocentre de Calcul Intensif Aquitain (MCIA).
The isolates were further identified as E. kobei by hsp60 typing  [3]. The three strains exhibited similar antimicrobial profiles determined by the agar dilution method (Table  1 ). They showed an extended spectrum β-lactamase-positive and AmpC-overexpression phenotype detected as previously reported  [2]. Multilocus sequence typing with use of seven loci (dnaA, fusA, gyrB, leuS, pyrG, rplB and rpoB) detected a new profile  (3-3-110-32-19-16-17 ) for all isolates, and was assigned as ST591 by the PubMLST database (https:// pubmlst. org/ecloacae/). Isolates were sequenced using Illumina Hiseq2500 (Illumina, San Diego, CA, USA) using 2 × 125-bp pair-end libraries. Genomes were assembled by CLC GENOMIC WORKBENCH v8. 0, and annotated by the RAST service (http://rast. nmpdr. org/). To analyse the resistome, genomic sequences were uploaded to RESFINDER (https://cge.
This stochasticity in sex ratio and genetic contributions of founders add to both the realism and the variation in the dataset. After 24 hr, the founding adults were removed and discarded, leaving the eggs behind to develop into the next generation of adults over a period of 5 weeks. The new adults that emerged were placed on fresh medium and also allowed 24 hr to mate and lay eggs, and this procedure was repeated for eight generations. Using fresh medium each generation, wastes could not accumulate and resource availability remained consistent generation-to-generation. We censused all populations each generation. In evolving populations, the beetles that reached adulthood within 5 weeks were used to found the next generation. Nonevolving populations, in contrast, were censused and then individuals were replaced each generation, one-for-one, using beetles from the source population.
| Statistical analyses To understand the consequences of rapid evolution for extinction in challenging environments, we evaluated whether the probability of extinction over the course of the experiment varied by evolution treatment. There was only one extinction in the favorable environment-in a control population initiated at a founding size of N 0 = 10. Thus, there was no variance in extinction among three treatments in the favorable environment (both founding sizes of evolving populations, and large nonevolving populations) and a full, generalized linear mixed model (GLMM) including environment could not be fitted (the separation problem,  Albert and Anderson 1984). To be able to fit the full model, we used a simple data augmentation approach in which we added one trial with extinction to the dataset for the three affected treatment combinations.