dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgement BN was awarded of a scholarship by the  Austrian Federal Ministry for Science and Research (BMWF). The work was supported by the  Federal Ministry of Education and Research (BMBF) , Grant Number  01KI0710 , " Research on Zoonotic Infectious Diseases" program , " Emerging arthropode-borne viral infections in Germany: Pathogenesis, diagnostics and surveillance ",  Institut Pasteur de Dakar  and  European Union  grant  HEALTH. 2010. 2. 3. 3-3Project 261391 EuroWest Nile (http://eurowestnile. isciii. es/ewn).
The domestic pig karyotype (2n = 38) is composed of 2 sex chromosomes and 18 pairs of autosomes (5 metacentrics, 7 submetacentrics and 6 acrocentrics)  [28]. This karyotypic structure is relatively similar to that of Humans. For this reason, the pig species is a much better animal model for meiotic recombination studies than other mammalian species, like dogs or mice, whose karyotypes contain only acrocentric chromosomes. In this paper, for the first time in the domestic pig, we present unique data on the meiotic recombination of males with normal karyotypes, obtained by direct immunocytological approach. Distribution of the MLH1 foci and the estimated strength of interference on the 18 porcine autosomal pairs were determined by identifying each autosome by multiple specific loci in situ hybridization.
Image and Statistical Analyses After identification of each bivalent, the images were analyzed to determine the length of the synaptonemal complexes (SC), and the positions of the centromere and CO, using MicroMeasure 3. 3 software  [34]. The relative positions of the MLH1 signals and centromeres were expressed as percentages of the total SC lengths, starting from the end of the q arms. The distances between adjacent MLH1 foci (relative distances expressed as % of total SC length) were used to estimate the interference for each chromosome. The strength of interference was estimated by fitting the frequency distribution of the inter-CO distances to the gamma model, as explained in  Broman and Weber (2000)   [35]  and  Lian et al (2008)   [19]. Maximum likelihood estimates of the u parameter of the gamma function were obtained using the free online Wessa software  [36].
The obtained images were divided in earlywood (EW), transition-wood (TW) and latewood (LW) zones as described in the next section, and then the percentage of the stained (i. e. conductive) area was measured in each type of wood with ImageJ image analysis software  (Rasband 2009 ) (Fig. 1 ). Subtracting this area to the total conductive area, the variable named "% of non-conductive area" was estimated assuming that it represents a measure of the proportion of cavitated (embolized) cells in the sample.
Wood microdensity: Microdensity profiles were obtained from wood samples of the 8 selected trees using indirect x-ray microdensitometry  (Polge 1960). The resulting films were scanned and processed with WinDENDRO software  (Guay et al. 1992). A function written in Rlanguage (R Core Team 2014) allowed dividing each 2011 ring into three parts: earlywood, transition-wood and latewood (hereafter EW, TW and LW, respectively). The function firstly identifies the minimum (MID) and maximum ring density (MAD), calculates the average density of these two extreme values and locates it along the x axis (Mdp: red vertical line in Fig. 2 ) as in  Mothe et al. (1998). At this point the ring is divided in two parts, corresponding to the conventional EW and LW portions. Subsequently the R function repeats the extreme average procedure described above in each part of the ring, defining Mdp1 (Mdp1: blue vertical line in Fig.
5 and -4 MPa that caused 50 and 88 % loss of hydraulic conductivity, respectively. After centrifugation, the samples were immediately dropped in liquid paraffin wax and cooled in order to prevent their drying during the x-ray scan. The samples were then placed in the Xray microtomograph (Nanotom 180 XS, GE, Wunstorf, Germany). X-ray source settings were 50 kV and 275 μA. After 3D reconstruction, the field of view was a 6. 2 × 6. 2 × 6. 2 mm 3 with a spatial resolution of 2. 8 × 2. 8 × 2. 8 μm per voxel. One radial-tangential 2D cross section was virtually extracted from the middle of the volume in order to visualize the part of the ring located in the middle of the sample, using VGStudioMax software (Volume Graphics, Heidelberg, Germany). Then, images were analyzed using the ImageJ software in order to compute the percentage of cross section area that was embolized.
Acknowledgements The authors would like to thank  INTA-Programa Nacional-Forestales ,  PNFOR-1104073  and  CONICET  for founding part of this study. The x-ray tomography scans were partly founded by the  PitBulles  project (ANR no. 2010 Blanc 171001 ). Special thanks to  Dr. Victor Mondino  ( INTA-Trevelin ) who facilitated the access to the plant material and helped with the sample collection. Finally we would like to thank the two anonymous reviewers that contributed with their corrections and suggestions.
Identification of the EgDEF1 genomic sequence Using the full-length cDNA sequence of EgDEF1 (accession number AY739700. 1) as a template for 59-oriented primer design, we performed chromosome walking on genomic DNA sampled from a palm of FC166 origin using the GenomeWalker Kit with the Advantage 2 Polymerase (both from Clontech) according to the supplier's recommendations. This first step allowed us to recover a genomic fragment extending from nucleotide positions -1833 to +12 relatively to the ATG of the gene. This genomic fragment was then used as a probe to screen high density filters from an oil palm BAC genomic library constructed from a seedderived individual of L2T origin  [20]. Four positive clones showing identical hybridization patterns were isolated and one, named Eg133H20, was sequenced by Genoscope (Evry, France).
5 mL of the product from this first round was used for a second round of amplification with nested or seminested primer combinations using GoTaq Polymerase (Promega) and a programme of 30 cycles (94uC 30 s, 55uC 30 s, 72uC 1 min). The complete list of bisulfite-specific primers is displayed in Table  S4. The separation of amplification products, their purification, cloning and the selection and sequencing of positive inserts were performed as previously indicated. A minimum of 15 sequenced amplicons per primer pair and per sample was analyzed using the CyMATE software platform (http://www. cymate. org/) [23].
Isolation of the EgDEF1 gene sequence and structure of the genomic region The screening of a BAC library generated from a seed-derived L2T oil palm with EgDEF1's putative promoter allowed the isolation of the Eg133H20 clone (accession number KF142646). The start of the EgDEF1 coding sequence is localized near the middle of this 81. 5 kbp genomic fragment from which the 39 extremity of the gene (corresponding to exons 6 and 7) is missing, due to the presence of a massive intron 5 (36. 3 kbp). Chromosome walking in 39 orientation from the ATG confirmed both the structure and sequence of the EgDEF1 gene. More walking in both 59 and 39 orientation using as reference the 39 extremity of the EgDEF1 cDNA enabled the recovery of the missing exons, the 39end of the 5 th intron matching perfectly the Eg133H20 BAC clone border.
The Southern hybridization pattern obtained using the P1 probe confirmed the occurrence of a single copy of the EgDEF1 gene in both L2T-related (LMC343) and non-L2Trelated (FC2317) oil palm genotypes (Figure  2A ). The recent publication of the complete genome sequence of the oil palm  [26]  has allowed us to confirm the structure of the EgDEF1 gene, which near-perfectly matches a portion of scaffold 00322 (BLASTN E value = 0, identity 98-99%, score 5. 373610 4 bits). The reassembled genomic sequence of the EgDEF1 gene has been deposited in GenBank (accession number KF142645) and the gene structure is depicted in Figure  1A. Further annotation of the BAC clone sequence showed that the genomic region surrounding the EgDEF1 gene contains several sequences with similarities to Transposable Elements.
928610 4 bits), as well as the presence of shorter, partially matching sequences in other genomic locations. As for the copia retroelement, we found over 50 imperfect copies scattered throughout the genome (E value = 0, maximum score 3029 bits). Since the sequenced genome belongs to a pisifera individual  [26]  which relatedness to our tenera (dura x pisifera) hybrids is unknown, we can only assume that this particular copia insertion is variable among oil palm genomes. According to the convention suggested by Wicker et al. [27] , we named these retroelements RLG_Koala_Eg133H20-1 (gypsy element) and RLC_Rider_ Eg133H20-1 (copia element), and they are thereafter refered to as Koala and Rider in the present paper. Both TE sequences have been deposited in GenBank under accession numbers KF142647 and KF142648, respectively.
Analysis of EgDEF1 gene expression The discovery of EgDEF1 gene structure raises the question of possible dysfunctions of either transcription or pre-mRNA processing mechanisms resulting from the extreme size of intron 5. Indeed, our 39-RACE-PCR experiments show that at least two distinct transcripts are produced from the EgDEF1 gene. As illustrated by Figures  1A  and S7 , in addition to the 979 nucleotides-long full-length transcript (hereafter named cDEF) we detect a slightly shorter polyadenylated molecule (845 nucl). This alternate transcript contains exons 1 to 4 and includes the 59 extremity of intron 5 with two small deletions (5 and 13 nucl respectively) inducing two successive frameshifts. Because of the truncated coding sequence of the alternate transcript, we named it tDEF (accession number KF142649).
A BLASTN search in the available oil palm inflorescence transcrip datasets  [26, 28]  confirmed the occurrence of several shorter isoforms similar to tDEF. In the aim of evaluating the potential consequences of structural alterations in tDEF with respect to cDEF, we compared the putative peptidic sequences derived from each transcript (Figure  5 ). The hypothetical product of tDEF is 58 residues shorter than the complete peptide and therefore lacks the C-terminal domain. Moreover, its K domain is modified in the K3 motif since 9 of the 14 aminoacids originating from the partial read-through of intron 5 correspond to altered biochemical properties with respect to the functional peptide. In order to understand the dynamics of EgDEF1 expression in the developing oil palm inflorescence, we designed rt-qPCR primers targeting specifically the cDEF or the tDEF transcript (Figure  S7  and Table  S5 ).
Discussion The present work describes for the first time the structure of the EgDEF1 gene, the oil palm ortholog of the B-class MADS-box genes APETALA3 (Arabidopsis thaliana) and DEFICIENS (Antirrhinum majus). Very large introns (i. e. several kbs long) are commonly found in members of this gene superfamily  [29]. The singularity of intron 5 in the EgDEF1 gene resides in its extreme size of 36. 3 kb, an enlargement which is partially attributable to the insertion of the 10. 9 kbp Koala retrotransposon. The presence of intronic TEderived sequences has been documented for several other large introns of MADS-box genes  [30] [31] [32]  and a survey of AP3-like genes in public databases showed that such remnants are detectable in most of them (Table  S9 ). However, the intronic insertion of Koala is not, in itself, at the origin of the mantled phenotype.
Study design We employed two methods in this study. We analysed data collected from a consumer panel in 2007 that was representative of the French population. This crosssectional dataset did not allow accounting for the dynamics of the life course. Therefore, we conducted a qualitative in-depth survey of shopping routines and biographies of a small number of subjects who resided in Southwest France. During coordination meetings we pooled the results achieved by the quantitative and qualitative analyses and checked their consistency (or tried to explain apparent contradictions).
Statistical data The quantitative arm of the present study consists of a secondary analysis of opinion and purchase data collected from the 2007 consumer panel Worldpanel. 2 The data provider collected the total food purchases of nearly 7000 households over a one-year period. Access to this data enabled a detailed study of certain products: dairy nutraceuticals 3 (health norm), low-fat dairy products (anti-fat dietary norm), vegetables (dietary norm), organic products (environmental norm) and pre-prepared salads (nutritional norm -vegetables -in conflict with environmental norm). We selected these products because of their perceived status as vehicles for innovation. They also offer potential associations with nutritional and/or environmental prescriptions through public, activist or marketing discourses.
Finally, the gaps that exist between standards and prescriptions are probably smaller for the middle classes than they are for the lower classes because prescription producers are, in general, members of the upper classes. Therefore, they may design prescriptions acceptable to other members of the middle and upper classes. These prescriptions may even be consistent with their own standards  (Boltanski, 1971). However, the explanations provided above fail to account for the finding that in our quantitative analysis of purchases (see Tables  1  and 2 ), education solely exerted an effect on organic food purchases. This may have occurred because the interviews revealed respondents' perceptions of standards and practices. In the interviews, respondents may have attempted to be reflexive. The purchase data collected every food they bought over a year.
This approach stresses the fact that gaps exist between standards and practices. The current study employed two complementary empirical surveys. We analysed purchase data collected from a representative sample of over 6000 French households over the year 2007. In addition, we conducted a qualitative in-depth study of a limited non-representative sample of households. We obtained the following results. Firstly, the link that connects a particular practice and one or more prescriptions is socially constructed and proceeds based on the contributions of a variety of agents. This link is not explicit, unique or stable. The quantitative analysis of purchases provided more riddles than answers. We concluded that no straightforward links connect prescriptions and purchases. The analysis of the qualitative fieldwork confirmed that many actors (including consumers) debate about ways to connect practices and prescriptions.
New high-throughput "omics" technologies, such as whole transcriptome sequencing (RNA-Seq) and highresolution mass spectrometry, allow simultaneous examination of thousands of genes, transcripts, proteins, and metabolites, opening new possibilities towards marker discovery and genome-wide identification of signalling molecules, protein functions and interactions. Such technologies were recently applied also to the study of plant-phytoplasma interactions, but in most of these cases only the plant responses to the phytoplasma infection have been investigated, leaving the phytoplasma perspective almost unexplored  [9] [10] [11] [12] [13] [14] [15] [16]. Only two reports took advantage of the new high-throughput technologies to describe the transcriptional and proteome landscape of phytoplasmas: Ji and colleagues provided the first valuable dataset of mulberry dwarf phytoplasma proteins by a shotgun proteomics approach  [17]  and, more recently, Siewert and colleagues  [18]  combined RNA-Seq and shotgun proteomics to provide insights into the expressed genes of 'Candidatus Phytoplasma mali' infecting graft-inoculated Nicotiana occidentalis leaves.
Microarrays were instead used for the first global gene expression study on phytoplasmas, which evaluated the changes in gene expression during 'Candidatus Phytoplasma asteris' "host-switching" between plant to insect hosts  [19]. In the present study, RNA-Seq provided the first comprehensive transcriptomics landscape of FD phytoplasma infecting field-grown cv. Barbera grapevines. An annotated draft genome of the FD92 isolate, covering 85% of the 671 kbp chromosome, has been recently produced using a combination of 454 pyrosequencing and Illumina/Solexa  [20, 21]. In the absence of a complete FD genome sequence, different approaches to separate FD-mapping reads from the eukaryotic ones followed by assemblies and recursive merging of sequence datasets were used to reconstruct the FD transcripts.
Phytoplasma detection, strain characterization and quantification Diagnostic assays confirmed the presence of FD and the absence of stolbur 'Bois noir' (BN) phytoplasma in all three grapevine leaf samples used in this study (120, B68 and B75). In addition, qRT-PCR assays on the most common viruses reported in Piedmont vineyards revealed the presence of Grapevine rupestris stem pitting-associated virus in all samples and Grapevine fleck virus in sample 120 and B75. On the basis of the TaqI-RFLP profiles of the ribosomal 16S gene, samples 120 and B68 were identified as 16SrV-C isolates and sample B75 as a 16SrV-D isolate (data not shown). In the three samples, the phytoplasma titer expressed as number of FD cells/500 mg of plant tissue ranged from 5. 81E+05 to 6. 32E+06.
Reads assembly As a first assembly approach, reads from libraries 120 and 120E were first mapped to the FD92 draft genome (Table  1 ) and then assembled. The number of PE reads mapping in the antisense orientation to the FD92 predicted coding sequences (Table  1 , third row) was below the theoretical maximum number of spurious cDNAs generated during the second-strand synthesis of the reverse transcription (calculated to be 145 reads for library 120E and 189 for library 120), so they were not further analyzed. In each library nearly 0. 01% of the total reads were mapped, confirming the ratio obtained by qRT-PCR. The two separate assemblies obtained from the libraries (dataset 1 and dataset 2) were compared to evaluate the technical reproducibility. Some sequences were unique to each dataset, i.
e. they did not find any significant hits in others, whereas many other sequences found at least one significant hit with 100% identity across the alignment, but with a different length. These results suggested the importance of dealing with at least two technical replicates when studying the genome-wide transcriptome profile of an organism whose sequences represent a very small fraction of the total RNA-Seq library. A merged dataset (dataset 3) was obtained from the assembly of these two initial datasets. The second assembly approach consisted in merging reads from the two libraries, mapping them to the FD92 genome and then assembling them altogether. The resulting dataset (dataset 4) was compared to dataset 3 to determine the best assembly strategy. Sequences from dataset 4 included all the sequences of dataset 3 and were generally longer than the corresponding sequences of dataset 3.
Therefore, the second assembly approach proved to be far more efficient than the first one. A new merged dataset (dataset 5) was obtained from the assembly of dataset 3 and 4. As a final approach, reads from the two merged libraries were first mapped to the V. vinifera genome. The Vitisunmapped reads, which represented nearly 0. 7% of each library, were then de novo assembled. The resulting sequences with significant similarities to known Mollicutes genes (dataset 6) were compared to dataset 5. No unique sequences were identified in dataset 6, but still there were differences in length between some matching sequences from the two datasets. The third assembly approach was found to be less efficient than the second one, both in terms of number and in terms of the average length of the assembled sequences.
However, it was adopted in combination with the second approach to obtain a more accurate description of the FD transcriptome. A final comprehensive FD transcriptome dataset of 347 sequences with an average length of 294 bp was created by assembling dataset 5 and 6 and used for further analyses. Comparison of RNA-Seq transcripts to FD92 annotated genes 334 out of 347 RNA-Seq sequences corresponded to 215 FD92 annotated genes (18 were full-length protein-coding transcripts) (Additional file 2). Of the remaining 13 sequences, 10 were present in the FD92 genome but the matching regions were not yet annotated, and three did not find any match to the FD92 genome but showed significant similarities to Poinsettia branch-inducing phytoplasma sequences (Additional file 2). PCR analyses with specific primers demonstrated that these three sequences truly belonged to the phytoplasma genome (Additional file 3), so they were probably localized in the gaps of the FD92 draft genome.
The 10 unannotated transcripts (Additional file 2) were further analyzed to determine whether they showed significant similarities to known Mollicutes protein-coding sequences or previously characterized ncRNAs. After querying the NCBI "nr" and the Rfam databases, four of them showed significant similarities to three phytoplasma hypothetical proteins and a translation initiation factor IF-3. In addition, contig12 and contig6 showed significant similarities (expected value, E-value ≤ 1E-5) to ncRNAs, namely the catalytically active RNA of a group II intron and the RNA component of a bacterial ribonuclease (RNase) P class B, respectively. The remaining four unannotated transcripts showed putative ORFs spanning the whole length or a part of the nucleotide sequence, but the corresponding predicted proteins did not have any significant similarity to other bacterial sequences.
Phytoplasma in silico gene expression The expression levels of a dataset that included the FD92 annotated genes extended by the newly identified 5′ UTRs and 3′ UTRs and the newly identified transcripts, both coding and non-coding, are shown in Additional file 5. The most expressed transcript, named contig12, corresponded to the catalytic RNA component of a group II intron, which was present in the FD92 genome in at least two slightly divergent copies. It is important to underline that one of these two copies was artificially truncated due to its position at the end of a genomic contig. Even if divided by two, the transcriptional level of this catalytic intron remained the highest in both RNA-Seq libraries. Interestingly, a blastx analysis of contig12 revealed the presence, at the 3′ end of the sequence, of the first 27 amino acids of a putative transposase tra5 for insertion sequence element IS150 (GenBank:WP_015637618.
Expressed transcripts were classified by comparing sequences against the manually curated KEGG GENES database (Additional file 5). Excluding the generic functional category named "Metabolic pathways", the most represented categories during Vitis infection were those related to translation and protein metabolism (ribosome, tRNA and amino acids biosynthesis), DNA metabolism (pyrimidine and purine metabolism, DNA replication, DNA repair) and carbon metabolism (including glycolysis/gluconeogenesis) (Figure  1 ). In particular, all the enzymes of the glycolysis pathway were transcribed. Transport, protein export and secretion categories were also well represented with a total of 16 transcripts. Unfortunately, nearly 30% of the total assembled transcripts were not functionally classified. Where possible, protein-coding transcripts were associated to GO terms by Blast2GO (Additional file 5).