dataesr/scientific-paragraphs-categorization huggingface dataset:
ACKNOWLEDGEMENTS We thank  Fabien Duveau  for critical reading of the manuscript and for signal quantifications from microscopy images,  Grégory Batt  for fruitful discussions,  Maria Teresa Texeira  for strains,  Sandrine Mouradian ,  Véronique Barateau  and  SFR Biosciences Gerland-Lyon Sud  ( UMS344/US8 ) for access to flow cytometers and technical assistance, and developers of R, Bioconductor, VMD and Ubuntu for their software. This work was supported by the  European Research Council  under the European Union's  Seventh Framework Programme   FP7/2007-2013 Grant Agreement n°281359. AUTHORS CONTRIBUTIONS Constructed plasmids and strains, performed flow cytometry and yeast experiments: H. D-B. Performed qPCR and human cell experiments: G. T. Performed PMF computations: M. S.
When we presented each component of Mix+ATP individually, we found that blood-sensitive neurons are a heterogenous population and that different neuronal subsets within each female can respond to distinct blood components (Figure  S3A, B ). Moreover, all components except 4. 5 mM glucose reliably activated subpopulations of stylet neurons when presented individually. Unsupervised hierarchical clustering of this dataset was performed to group neurons into 5 clusters according to their functional response profile (Figure  5G ). For each neuron in a cluster, we calculated a ratio of peak ΔF/F response to Mix+ATP compared to the peak ΔF/F response to any individual ligand (Figure  5H ). We found that the first 3 clusters represent neurons reliably activated by an individual component: ATP, sodium bicarbonate, and sodium chloride, respectively (Figure  5I ).
Ir7a and Ir7f mark functionally distinct populations of blood-sensitive neurons We next asked if these functionally distinct blood-sensitive subsets are transcriptionally-defined populations. To identify candidate genetic markers for neuronal subsets, we searched for transcripts expressed only in the female stylet and not in tissues that do not directly contact blood. We profiled gene expression in the female stylet using RNA-seq and compared it to the male stylet and the female labium. To identify female stylet-specific transcripts, we analyzed the intersection of genes significantly enriched in the female stylet compared to both the female labium and the male stylet (Figure  S4A ,B, fuchsia data points). We further filtered for transcripts that were expressed at very low levels (< 0. 5 transcripts per million, TPM) in a comprehensive transcriptome dataset that included other sensory appendages, brain, and ovary (Figure  S4C )  (Matthews et al.
Females readily ingested all three sugars when the labium directly contacted the meal in the nectar-feeding assay, where no host cues are present (Figure  7B ). In contrast, they rejected these same sugars in the blood-feeding assay when the stylet directly contacted the meal in the presence of heat and CO2 (Figure  7C ). In control experiments we showed that blood stimulated robust consumption in the blood-feeding assay (Figure  7C ). These results lead to the question of whether stylet neurons can detect these nectar sugars at all. When we examined the RNA-seq dataset, we found the female labium expresses all predicted orthologues of Drosophila melanogaster canonical sugar receptors (Figure  7D ). However, none of these sweet gustatory receptor transcripts were detected in the female or male stylet (Figure  7D ).
We do not yet understand the mechanism of developmental patterning that permits variable cell body position along the proximal-distal axis of the stylet. Variability in the exact distance of the cell to the stylet tip may be tolerated because all stylet neuron dendrites terminate at the tip, irrespective of cell body position. By generating two female stylet-specific driver lines, we revealed non-overlapping blood-sensitive neurons belonging to two functionally distinct subsets: Ir7f blood mixture-sensitive neurons and Ir7a sodium bicarbonate-sensitive neurons. Together, these driver lines reveal the molecular identity of approximately one quarter of total stylet neurons. Future work will allow us to determine if Ir7a and Ir7f transcripts, along with additional putative chemosensory receptors identified in our stylet RNA-seq dataset, contribute to blood ligand detection.
This dataset is also an important resource to help identify genetic markers for sodium chlorideand ATP-sensitive subsets and to resolve the complete molecular landscape of stylet neurons. A major finding of this work is that four ligands previously shown to increase the probability of initiating blood-feeding behavior do indeed directly activate the stylet. When presented as a mixture, these four blood components-ATP, glucose, sodium bicarbonate, and sodium chloride-are sufficient to initiate blood-feeding behavior and activate the same neurons as blood. It is surprising that females will so readily engorge on Mix+ATP because it does not contain the proteins required for egg development. It may be that proteins are not an ideal substrate for blood recognition because their amino acid sequences and structures can evolve over time and across species.
Images were acquired at 10 frames/sec using Basler Pylon 5 software running on Ubuntu 18. 04. Each female was recorded for 700 sec regardless of engorgement status. Images were processed using custom code written in Python (available from Github: https://github. com/felixhol/biteOscope) using SciPy  (Virtanen et al. , 2019) , TrackPy  (Allan et al. , 2019) , and OpenCV  (Bradski, 2000)  packages to determine the presence and location of a mosquito. Engorgement status of a mosquito was determined by measuring abdominal size by fitting an active contour model to its abdomen. Stylet piercing events were scored by manual visual analysis of the images. TO-PRO-3 staining: 7 to 14-day old animals were anesthetized on ice. Tissue fixation followed modification of previously published methods  (Matthews et al.
Perfusion ligand delivery: Two independent ValveBank8 Pinch Valve perfusion systems (Automate Scientific #13-pp-54) with BubbleStop8 60 mL Syringe Heater (Automate Scientific #10-8-60-G) were automatically controlled by NIS-Elements software (Nikon). To ensure full perfusion chamber exchange, ligands were perfused for 30 sec followed by a 45 sec recovery period before the next ligand. Ligand delivery switched from water (baseline) to ligand of interest with the following exceptions. Since ATP is rapidly hydrolyzed in water, ATP was always delivered in a buffer of 25 mM NaHCO3. 25 mM NaHCO3 was delivered for 30 sec to establish a baseline, after which ATP dissolved in 25 mM NaHCO3 was applied. Responses above the baseline were considered ATP responses. In control experiments, we demonstrated that ATP dissolved in PBS activated these same neurons after pre-equilibration in PBS (see raw data at GitHub: https://github.
com/VosshallLab/Jove_Vosshall_2020). In Figure  7F ,G stylets were pre-equilibrated in 298 mM cellobiose for 30 sec prior to the isomolar sugar of interest to control for osmotic effects. 298 mM cellobiose was behaviorally inactive in both the blood-and nectar-feeding assays  (Matthews et al. , 2019)  (see: https://github. com/VosshallLab/Jove_Vosshall_2020).
Analysis of GCaMP6s data: All calcium imaging data were processed with Nikon Elements software. Regions of interest (ROIs) were selected based on the dTomato fluorescence intensity and used for analysis of GCaMP6s signal. Great care was taken to draw ROIs on the cell body of interest and not on en passant processes or slightly overlapping cell bodies. To exclude background noise, a cut-off of 0. 25 peak ΔF/F0 was set as the minimum threshold for activation. This cut-off intentionally filters for clear activation and does not distinguish between background noise and weak activation. Occasionally (less than 1 cell body per animal) it was difficult to avoid the halo, especially if baseline GCaMP fluorescence was very low in a given cell body. In these rare cases, the cell body was not considered to be activated.
All traces with sample motion, as determined by dTomato fluorescence instability, were discarded. Once raw fluorescence values were extracted for each neuron/stimulus (ligand) pair, ΔF/F0 calculations were performed using a custom R script (R version 3. 6. 0) where ΔF/F0 = (F -F0)/F0. To determine the baseline fluorescence (F0) 5 frames (~2 fps) were averaged before stimulus presentation. To determine peak F to a given stimulus, the average of 3 frames at the peak during stimulus delivery was determined for each stimulus. This process was repeated twice for each stimulus so that the peak ΔF/F0 value represented in all plots is the average peak ΔF/F0 for 3 independent stimulus presentations. Stimulus trains were delivered so that each stimulus was only presented once per trial. Therefore, the final value represents the average peak stimulus response collected from three trials.
Once all averages had been calculated, the dataset from individual females were analyzed and represented in multiple ways. Heat maps in Figure  4G , Figure  5D , Figure  6G ,H, and Figure  S3A  were generated using a custom R script. Each box represents average peak ΔF/F0 to a given stimulus as described above. The heat map color scale is log2 to increase dynamic range and the minimum and maximum color value was set to 0. 25 and 3 respectively. Plots in Figure  4J , Figure  5E , and Figure  7G  were plotted using Prism 8 (GraphPad) and a neuron was considered activated if peak ΔF/F0 > 0. 25. Peak ΔF/F0 scatter plots in Figure  4H , Figure  5F , Figure  6J ,L, and Figure  7H -J were generated using Prism 8 (GraphPad). Custom R script available at Github: https://github. com/VosshallLab/Jove_Vosshall_2020.
This work was supported in part by grant # UL1 TR000043 from the National Center for Advancing Translational Sciences (NCATS, National Institutes of Health (NIH) Clinical and Translational Science Award (CTSA) program. VJ was supported in part by NIH T32-MH095246. This work was supported in part by a grant to The Rockefeller University from the Howard Hughes Medical Institute through the James H. Gilliam Fellowships for Advanced Study program to VJ. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. NSF DGE-1325261 to VJ. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. The work was supported in part by a Career Award at the Scientific interface (CASI) from the Burroughs Wellcome Fund (FJJH), the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 841893 -PiQiMosqBite (FJJH), Jane Coffin Childs Postdoctoral Fellowship (TRS), Kavli Neural Systems Institute postdoctoral fellowship (TRS), NIDCD R00-DC012069 (CSM).
Data and software availability: All data in the paper with the exception of raw GCaMP data files are available on Github at https://github. com/Voss-hallLab/Jove_Vosshall_2020. All plasmids described in this paper are available at Addgene. Scripts for merged genome annotation and calcium imaging analysis are available on Github at https://github. com/VosshallLab/Jove_Vosshall_2020.
The fragment was inserted into pUC-AD20 (pUC-prA3-stA3)  [21]  between EcoRI and MfeI. To allow continuous expression of the gene upon baculovirus infection of cells, this fragment was inserted downstream of the Bombyx mori A3 promoter (prA3) and upstream A3 stop (StA3) (GenBank accession number U49854). The whole cassette containing the A3 promoter, the or3-gfp fusion gene, and the A3 terminator was excised with XbaI and inserted into the baculovirus transfer vector pVT/gp37, at the gp37 locus  [22]. All constructs were verified by their restriction profiles. Both transfer vector DNAs were purified using NucleoBond® Xtra Midi (Macherey-Nagel, Hoerdt, France). For the construction of a single plasmid cassette, both components of ANCHOR3 TM were inserted in the pAcUW2B transfer vector  [23] , by substituting the p10 promoter moiety by the prA3-or3-gfp-A3term cassette, then, the ANCH3 sequences were inserted at the EcoRV site located upstream of the polh promoter.
The fragment was inserted into pUC-AD20 (pUC-prA3-stA3)  [21]  between EcoRI and MfeI. To allow continuous expression of the gene upon baculovirus infection of cells, this fragment was inserted downstream of the Bombyx mori A3 promoter (prA3) and upstream A3 stop (StA3) (GenBank accession number U49854). The whole cassette containing the A3 promoter, the or3-gfp fusion gene, and the A3 terminator was excised with XbaI and inserted into the baculovirus transfer vector pVT/gp37, at the gp37 locus  [22]. All constructs were verified by their restriction profiles. Both transfer vector DNAs were purified using NucleoBond ® Xtra Midi (Macherey-Nagel, Hoerdt, France). For the construction of a single plasmid cassette, both components of ANCHOR3 TM were inserted in the pAcUW2B transfer vector  [23] , by substituting the p10 promoter moiety by the prA3-or3-gfp-A3term cassette, then, the ANCH3 sequences were inserted at the EcoRV site located.
Statistical analyses In vitro NDF digestibility values, the estimated rates, DMd, OMd, pH and VFA were analysed as response variables by the GLIMMIX procedure of SAS using a factorial arrangement of forage, medium, yeast and all interactions. Run was added as random factor with time treated as repeated measure. The highest order interaction (dose Â medium Â forage Â time) was removed from the model because non-significant and because its presence did not result in an improvement of the Bayesian Information Criterion  (Kass and Raftery, 1995; Schwarz, 1978). The control parameters for NDF were the digestibility and rates of NDF digestion, when forages were fermented alone. Differences between means and the control were declared significant at P 0. 05 using the least squares means and the Tukey adjustment.
Many PSI genes from Arabidopsis were not induced in response to 27 h of LP in grapevine In this study on grapevine, we identified a set of 301 and eight DE genes that were down and up-regulated respectively in all scion/rootstock combinations. Surprisingly, there were few of the PSI genes of Arabidopsis  [8]  in this dataset, this is partly because the grapevine orthologues have not been identified (e. g. [34] [35] [36]. However, after 28 d of LP, the expression of orthologues of four Arabidopsis PSI genes was up-regulated relative to HP suggesting that the response to LP at 27 h represents the early stress-related changes in gene expression. A set of 309 genes that were DE in response to LP in all scion/rootstock genotypes was identified The down-regulation of gene expression in response to LP was well-conserved between the four scion/rootstock combinations studied (301 genes), whereas the expression of only eight genes was up-regulated in response to LP across all scion/rootstock combinations.
RNA sequencing RNA sequencing libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina), according to manufacturer's instructions. These libraries were then sequenced using Illumina Hiseq 4000 to produce 50 bp paired-end reads following Illumina's instructions. The RNA-seq data has been deposited in the ArrayExpress database (http://www. ebi. ac. uk/ arrayexpress  [65] ) under the accession number E-MTAB-8678.
Pre-processing of RNA-Seq data Adapter dimer reads were removed using DimerRemover (https://sourceforge. net/projects/dimerremover/) and quality of each sample was assessed with FastQC v0. 11. 2  [66]. Transcript abundance was quantified using salmon v0. 13. 1  [67]  with the flags --seqBias --gcBias --fldMean 50 --fldSD 1 --validateMappings -rangeFactorizationBins 4. Quantification results were concatenated to a count matrix using tximport R package  [68]. After quality verification, one sample was identified as outlier and discarded from subsequent analysis.
Genome functional annotation Gene models of the V3 annotation  [69]  were searched against the Araport11 (release 06. 17. 16, https://www. araport. org/) protein database with the blastx function of the DIAMOND version 0. 9. 19 software set to default parameters and reporting alignments in the 1% range of the top alignment score  [70]. For each V3 gene model, the best blast hit was kept (1-to-1) and for multiple hits with the same score (1-to-many), the first hit was kept as representative keeping the other hits accessible. The corresponding gene annotations were obtained from the Araport11 gff file (release 06. 22. 16 ) and correspondences for V1 IDs were downloaded (https://urgi. versailles. inra. fr/Species/ Vitis/Annotations).
| Mapping To understand the specifics of each case study (see section below) and landscape, we also mapped the different case studies when possible, using available data provided by OpenStreet Map, OS Open Rivers, National Records of Scotland (NRS), National Biodiversity Network Atlas (NBN Atlas) and the Tayside Beaver Survey 2018. The maps displayed here are therefore intended to give a better understanding of relevant issues, and have been updated to take into account the latest developments which occurred after the study was completed.
Based on our study aim, these locations therefore formed the basis for analysing the interviews (Table  2 ). Before the interview, all aspects of the research were discussed with interviewees, who were given information about the purpose, methods and intended uses of the research prior to any data collection. In addition, each interviewee was asked to complete a confidentiality and consent form and data were analysed and reported accordingly. To ensure consistency and to allow quantitative and qualitative data analyses, all interviews were carried out following an interview guide (see Annex 1 in Supplementary Material) based on our framework and tested following a pilot interview. In all, 10 interviews were carried out face-to-face. To match the interviewees' availability, and to cover a wide range of Scotland within a limited time, 14 interviews were carried out on the phone, and one on skype.
| Analysis The material from the interviews was analysed using NVivo (v. 12) software. The transcripts of the interviews were imported into NVivo and coded, using different 'nodes' which represent the variables relevant to the study aims  (Ishak & Bakar, 2012). A total of 39 nodes and 88 sub-nodes were used in the analysis (see Annex 2 in Supplementary Material for full list of the nodes and sub-nodes). While having so many nodes and sub-nodes presented a small risk of lack of consistency in coding, it was best suited to analyse the extensive qualitative material gathered. TA B L E 2 Distribution and codes of interviewees based on their geographical focus in terms of knowledge and role in the reintroduction. Some interviewees were more knowledgeable and involved in a specific area (the Highlands, Tayside, other), whereas others had a broader understanding of the issues at a national scale (National).
Sequencing Viral RNA was extracted from viral cultures using the NucleoSpin ® RNA Kit (Macherey-Nagel, Düren, Germany). The nucleotide sequences were obtained either by the Sanger method on an Applied Biosystems ® Sanger Sequencing 3500 Series Genetic Analyzer (Hitachi High Technologies, Naka, Japan) or by next-generation sequencing (NGS) on Thermo Fisher Scientific's Ion Proton instrument (Thermo Fisher, Carlsbad, CA, USA). The reads obtained by NGS were cleaned with Trimmomatic 0. 36 software  [29] , then assembled by mapping on reference genomes using Burrows-Wheeler Aligner software (version 0. 7. 15-r1140  [30] ) and by de novo using the SPAdes and MIRA programs (versions v3. 10. 0  [31]  and 4. 0. 2 [32] ). A single consensus sequence per viral segment was generated by combining the contigs produced using both methods with Vector NTI Advance 11.
Phylogenetic Analyses of HA-, NA-and M-Encoding Genes The sequences obtained in this study, and sequences of other swIAVs isolated in France and previously deposited in public databases, were compared to swIAV sequences retrieved from the Influenza Research Database (IRD) (available at https://www. fludb. org/). Phylogenetic trees were generated by a Bayesian approach using BEAST v1. 8. 4  [33] , with the substitution models 'HKY + Gamma + Codon Position (CP)' for HA-and NA-genes or 'GTR + Gamma + CP' for M gene, improved by the sample collection years  [34]. A Markov chain Monte Carlo (MCMC) method of 10,000,000 samplings for every 1000 was performed. The quality of the posterior distribution of each setting was checked through the Effective Sample Size (ESS) with Tracer v1. 6  [33] , with 10% of burning.
Amino Acid Sequence Analyses DNA sequences were translated into amino acid sequences with Seaview 4. 6. 1  [38]. For all segments, amino acid positions were numbered from the first methionine. Thus, the amino acid numbering included the signal peptide for HA. The variability of peptides in protein sequence alignments was measured by the entropy values with the Antigen Variability ANAlyzer 0. 31 (AVANA) software with default parameters  [39]. Genogroup-specific amino acid mutations were identified using two methods: (i) the genogroup pairwise comparison in AVANA to identify all genogroup-specific mutations without a priori; (ii) the R 3. 4. 0 analysis only of residues identified to be involved in change of pathogenicity, virulence or fitness of IAVs, according to the literature (Table  S2 ).
Genetic and Antigenic Evolution of HA-1C (H1 av Ny) swIAVs Isolated in France Between 2000 and 2018, 182 out of 838 H1 av Ny strains were sequenced. One hundred and thirty four of these (116 H1 av N1 and 18 H1 av N2), for which at least both HA-and NA-encoding genes were completely sequenced, were included in phylogenetic analyses. Phylogenetic analyses revealed that the HA-encoding genes of H1 av Ny strains isolated in France since 1980 classified into different clades (Figure  2 ). According to the swIAV H1 classification  [7] , the swIAV sequences from the oldest virus strains isolated in France and retrieved from public databases, i. e. , A/Swine/Marseille/2260/1980(H1 av N1) and A/Swine/Finistere/2899/1982(H1 av N1), belonged to clade 1C. 1, within the 1C "Eurasian avian lineage". From 1980 to 2000, strains from this clade, as well as from 1C.
4. 2). strains also presented many mutations in antigenic sites: L88I, PNH->LSY at positions 141-143, H155N, G172D, N173S, K180Q, T183K, K186R, D202Y and G219V for the Southwestern strains; P141E, V151G, A152S, H155R, A158T, N159K, L178I, N185D, K186R, D202Y, I207A, N211S, G219V and S220T for the Northwestern strain. Finally, three strains with H1 from clade 1C. 2. 2 were identified in the Eastern part of France (Figure  3A ). They harbored 22 mutations in HA (data not shown), including S179I in an antigenic site. The antigenic relationships of 146 H1avNy viruses, for which the HA1 sequences were obtained, were tested in HI assays using a selection of swine antisera produced against virus strains representative of the different HA-1C clades encountered in France over time. Hyperimmune serum (HIS) containing antibodies directed against strain Fin2899/82 (clade HA-1C.
Supplementary Materials: The following are available online at http://www. mdpi. com/1999-4915/12/11/1304/s1, Table  S1 : Genbank accession numbers for swIAV sequences isolated in France and used in this study, Table  S2 : List of residues identified as possibly involved in changing the pathogenicity, virulence or fitness of IAVs, Table  S3 : HI titers of hyperimmune antisera directed against reference H1 av , H1 hu , H1pdm and classical swine H1 viruses when tested to swIAV of (A) H1 av Ny or (B) H1 hu Ny lineage isolated in France between 2000-2018, Table  S4 : Specific mutation patterns identified with AVANA software which characterize deduced amino acid sequences of internal proteins from strains of the three genogroups A, B and C within HA-1C.