dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements To the  Bill and Melinda Gates Foundation  for funding this study through Grant No. OPP1019962  to  HarvestPlus. To Jaime Borrero  from  Alliance Bioversity-CIAT Rice Breeding program ,  Luis Londoño  from  HarvestPlus -Alliance Bioversity-CIAT  and  Katherine Loaiza  from  FLAR  for helping with the production, sample preparation and physical characterization of the rice samples. James Stangoulis ,  Lyndon Palmer  and  Georgia Guild  from  Flinders University  for the analysis of minerals by  ICP-OES.
Eighty interviews with randomly selected processors were conducted, as a minimum sample size to conduct quantitative analysis. Processors individually ranked quality characteristics in importance (using simple or pairwise ranking), for the raw material, at each stage of processing and for the final product. Data on the least liked quality characteristics; technological, physico-chemical and sensory characteristics; gender roles; household decision-making; and marketing information were also collected. Economists conducted market interviews with purposively selected traders and retailers to collect data on different consumer groups and their preferences for particular quality characteristics and varieties, and projected future trends of the product. The following market interviews were conducted: at least eight in rural areas, 10-15 in towns and 30 with retailers in towns and urban areas.
Data analysis Since there are extensive qualitative and quantitative data gathered in Steps 2, 3 and 4 of the methodology, data analysis is complex. Its presentation in meaningful form is essential to achieve Food Product Profiles that can be effectively used by biochemists and breeders. Each manual includes recommendations on how to summarise and analyse data for most effective use. For Step 2, Gender food mapping, the focus group discussions and interviews were transcribed, and qualitative and quantitative data were inputed into an Excel database. Excel was used as it was the most accessible software for the research teams, but qualitative software such as Atlas. ti and NVivo are recommended. Qualitative data were coded according to the interview guide, and relationships between concepts and categories (e.
For Step 3, Processing diagnosis, qualitative and quantitative data were collected. Qualitative data were collected during processor interviews using a questionnaire on quality characteristics and processing: Discussion guideline with processors before, during and after processing. Quantitative data were collected by measuring several parameters to compare the processing ability of each variety and assess its technological properties. Typically, but also depending on the crop/ product process with different unit operations, the parameters to be measured can include the dry matter losses, the duration of each unit operation, the evolution of pH and temperature during fermentation, the evolution of the cooking temperature and the evolution of the yield during the whole process. For Step 4, Consumer studies, an analysis of variance (ANOVA) is carried out to identify whether significant differences of overall liking scores are observed between the four to five products tasted by consumers.
Acknowledgments The authors are indebted to the significant and iterative contributions of the interdisciplinary teams of our partner organisations in the  RTBfoods  project, whose research findings are part of this special issue:  P. Marimo  ( Bioversity-CIAT, Uganda );  B. Otegbayo ,  O. Oroniran  and  O. Fawehinmi  ( Bowen University, Nigeria );  G. N. Newilah ,  C. Vepowo  ( CARBAP, Cameroon );  S. Mayanja  ( CIP, Uganda );  C. Ebah Djedji  and  K. A. Landry  ( CNRA, Ivory Coast );  S. Adetonah ,  Y. Assogba ,  J. Bakpe  ( IITA, Benin );  N. H. Tchuente Takam ,  E. Biaton Njeufa ,  I. L. Nguiadem Chomdom  ( IITA, Cameron );  Busie Maziya-Dixon ,  B ela Teeken ,  B. Abolore ,  O. Olaosebikan ,  A. O. Osunbade ,  D. Owoade , ( IITA, Nigeria );  J. Hounouighan ,  N. Akissoe ,  L. Adinisi  ( Universit e d'Abomey, Benin );  R.
Data availability statement The methodology presented in this paper is openly available in Agritrop open repository of CIRAD publications. The manuals can be accessed through the DOIs listed below. Forsythe, L. , Fliedel, G. , Tufan, H. (2018). RTBfoods Step 1: State of knowledge guidance document. Montpellier, France: CIRAD-RTBfoods Project. https://doi. org/10. 18167/agritrop/00568. Forsythe, L. , Fliedel, G. , Tufan, H. , Kleih, U. (2018). RTBfoods Step 2: Gendered food mapping. Montpellier, France: CIRAD-RTBfoods Project. https://doi. org/10. 18167/agri trop/00569. Fliedel, G. , Tufan, H. , Bouniol. A. , Forsythe, L. (2018). RTBfoods Step 3: Participatory processing diagnosis and quality characteristics. Montpellier, France: CIRAD-RTBfoods Project. https://doi. org/10. 18167/agritrop/00570.
| Color of ata and popizza fritters Instrumental determination of surface and inner color of ata and popizza fritters was carried out using the CM-600d colorimeter (Konica Minolta, Tokyo, Japan) supported by SpectraMagic NX software (Konica Minolta, Tokyo, Japan). Lightness (L*), redness (a*), and yellowness (b*) were determined. All color determinations were replicated four times. 2. 9 | Specific volume of ata and popizza fritters Specific volume was determined by rapeseed displacement, as in AACC method  10-10 (AACC, 2000). The determination was performed in triplicate.
| Image analysis of ata and popizza fritters Ata and popizza fritters were cut in two halves, and the image of the inner was acquired by a Canon 600d DSLR camera (Canon, Tokyo, Japan), equipped with a Sigma 17-70 mm f/2. 8 (Sigma Corporation, Kawasaki, Japan), saved in TIFF format with no compression, and processed by ImageJ software (National Institutes of Health, Bethesda, USA). Each image was converted into 8-bit grayscale, and a section of 25 × 25 mm was cropped from the center of the product, then it was filtered by thresholding function in order to obtain the best cell resolution. Image analysis was performed to detect the cells with an area >0. 05 mm 2 and circularity in the range 0-1, where 1 is the value attributed to perfectly circular cells and 0 to thin thread-like cells. The total number of cells, mean area of all the observed cells, and cell density (number of cells/mm 2 ) have been measured according to  Scheuer et al.
ACKNOWLEDGMENTS The authors thank  Dr Danila Di Rella ,  University of Bari, Italy , for the skillful technical assistance in performing the analyses. This research has been performed within the project " LEgume GEnetic REsources as a tool for the development of innovative and sustainable food TEchnological system " supported under the " Thought for Food" Initiative by Agropolis Fondation (through the "Investissements d'avenir" programme with Reference   ANR-10-LABX-0001-01 "),  Fondazione Cariplo , and  Daniel and Nina Carasso Foundation. This research is a collaborative activity with another " Thought for Food" Initiative project entitled  " Increasing COwpea value chain sustainability in West Africa through Product and procEss innovation. ".
In the 1990s, after the cessation of Slu sovice cooperative, Dá sa Veselý licensed the strain exclusively to the company Biopreparáty for the production of the biological fungicide Polyversum. Two other P. oligandrum strains were previously sequenced by Illumina technology, Po37  (Berger et al. 2016 ) (Genbank LSAJ 01000000) and CBS 530. 74  (Kushwaha et al. 2017 ) (Genbank NAJK00000000). However, our ATCC 38472 sequencing project is the first long-read genome of a P. oligandrum strain. We expect that this reference genome will be used for genomic comparison of plant beneficial or commensal Pythium spp. such as ATCC 38472 with other mycoparasitic Pythium spp. to foster the identification of key genetic determinants shaping this lifestyle whereas comparison with plant pathogenic or zoopathogenic species will illuminate Pythiales genomic adaptations for pathogenesis toward widely diverse hosts.
The initially generated raw sequencing reads were evaluated in terms of the average quality score at each position, GC content distribution, quality distribution, base composition, and other metrics. Sequencing reads with low quality were also filtered out before the genome assembly and annotation of gene structure. Finally, microbial DNA potential contamination was excluded after comparison by blast of the draft assembly of the first SMRT cell against a 16S ribosomal RNA sequences data bank (Bacteria and Archaea). The subreads were assembled with the Pacific Biosciences software SMRTanalysis version 2. 3. 0 using default settings with a minimum subreads length of 3 kb to exclude smaller sequenced reads and a read score of better than 0. 8 to enrich in reads with a low error rate.
Data availability This Whole Genome Shotgun project has been deposited at DDBJ/ENA/ GenBank under the accession PRJNA528861. The RNA-Seq consisting of 3 samples has been deposited in NCBI; raw reads were stored as SRA format under the accession SRR8923103. Supplemental materials are uploaded to figshare. Table  S1  lists P. oligandrum 15,007 predicted proteins and their annotation. Table  S2  lists P. oligandrum 1,617 predicted secreted proteins and their annotations. Table  S3  is the REVIGO analysis table of the GO term occurrence related to the biological process axe of the putative secreted proteins. Table  S4  is the REVIGO analysis table of the GO term occurrence related to the molecular function axe of the putative secreted proteins. Table  S5.
Genome annotation We performed a RNAseq based annotation to predict protein-coding genes using Augustus version 2. 6. 1  (Stanke and Morgenstern 2005)  and 15,007 protein-coding gene were predicted, among which 95,25% showed expression evidence in RNAseq data. Sequencing completeness was estimated using BUSCO version 3  (Simão et al. 2015)  based on a set of 234 common stramenopile genes, aka Benchmarking Universal Single-Copy Orthologs (BUSCOs). A total of 227 complete single-copy BUSCOs and 5 duplicated BUSCOs were found, leading to two missing BUSCOs in P. oligandrum ATCC 38472 which suggest a complete genome sequence assembly. The predicted proteome was functionally annotated using the InterProScan software version 4. 8 and KEGG pathway. A total of 10,657 (71%) predicted proteins were successfully annotated with a domain InterPro (Table  S1 ) while 3,912 (26%) show positive hits in KEGG (Table  S1 ).
ACKNOWLEDGMENTS This work was funded by the  ANR  project  LabCom BioPlantProtec  ( ANR14-LAB7-0001-01 ), collaborative project  BioPlantProducts  with  DE SANGOSSE (Agen, France). This work was performed in collaboration with the  GeT core facility, Toulouse, France  (http:// get. genotoul. fr),and was supported by  France Génomique National  infrastructure, funded as part of " Investissement d'Avenir" program  managed by  Agence Nationale pour la Recherche  (contract  ANR-10-INBS-09 ) and by the  GET-PACBIO program  («  Programme opérationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020  »).
8, with a 1% LOD permutation threshold of 3. 6, Figure  1B , top; Source data 1). Second, we performed genome-wide association mapping using 44 winged and 44 wingless males collected across the U. S. from alfalfa (Medicago sativa) fields (Supplementary file 1). We pooled the 44 winged and wingless males separately and performed Illumina resequencing to high coverage for a total of 68X and 70X coverage, respectively. F ST analysis between the winged and wingless sequenced pools revealed a single, large F ST value (Figure  1B , bottom; Source data 2) close to the LOD peak from the QTL analysis. We further refined the api region by assaying restriction fragment length polymorphism (RFLP) markers on a panel of 40 F2 individuals that each carried a recombination event between the previous closest api flanking markers  (Braendle et al.
This analysis revealed that approximately half of the inserted sequence showed similarity to another region of the reference genome (scaffold utg000238I; Figure  1 -figure supplement 4), which is on an autosome. Thus, most of the inserted sequence at api is derived from a duplication of an autosomal region. The remainder of the insertion is largely composed of complex repeats which are likely the result of mobile element insertions that occurred after the duplication event. A candidate follistatin gene in the inserted sequence Annotation software  (Augustus v. 3. 3. 1) predicted 12 open reading frames (ORFs) in the wingless api insertion. The gene models located within the insertion in Figure  2a  are from this annotation; models outside the insertion are the genome v3. 0 annotations  (Li et al.
We found no nonsynonymous polymorphisms in these genes that perfectly segregate with the api phenotype across the pool-seq and biotype data. Any mutations that contribute to the winged and wingless males would, therefore, likely be regulatory. We therefore measured the expression levels of the five genes (as1, as2, sam50, frs2, and cdg) using RT-qPCR. We focused on two developmental stages, embryos and first instar nymphs, as the likely critical times as explained above. as2 is not expressed in males at these stages. Of the four other genes (as1, sam50, frs2, and cdg), none were significantly differentially expressed after multiple comparison correction (Figure  2 -figure supplement 2, although as1 embryos had an uncorrected t-test p-value=0. 013; Source data 3). We therefore found no strong evidence that these genes contribute to the male wing dimorphism.
Evolution at the api locus To investigate the evolution of the api region within the pea aphid species complex, we used the 23 individually sequenced pea aphid genomes from nine biotypes discussed above. Of these genomes, all 14 wingless individuals carried the insertion (Figure  3 -figure supplement 1) and the nine winged individuals did not (Figure  3 -figure supplement 2). Phylogenetic network analysis using a region of the aphid genome outside of api (Source data 4) showed that genetically distinct biotypes, such as those feeding on Lathyrus pratensis (Lap1-3) and Vicia cracca (Vc1-2), group together and are separated by relatively long branches (Figure  3A , top). The other biotypes exhibited little network structure, suggesting that there is gene flow among these biotypes, as reported previously  (Peccoud et al.
0035 (orange distribution, Figure  3B ; Source data 6). In contrast, the three expressed genes with exons within the apiadjacent region had dS values between winged and wingless alleles that are an order of magnitude higher than the average of all genes: 0. 045 (as1), 0. 035 (sam50), and 0. 036 (frs2) (vertical dashed line in Figure  3B ). Even more strikingly, dS between fs-3, the follistatin copy in the WL insertion, and fs-2, the follistatin copy at the autosomal origin, was 0. 068 (Figure  3B , vertical dashed line). These high dS values also support the hypothesis that the api WL insertion is considerably older than the biotype diversification. We next estimated the age of the insertion relative to the divergence between the pea aphid and the rose aphid (Macrosiphum rosae). The pea aphid and rose aphid display an average dS of 0.
It will be interesting to interrogate other, closely related wingless and dimorphic species to determine whether or not the insertion is present in them and thus responsible for the wingless phenotype in other species. To explore contemporary frequencies of the two alleles, we estimated the winged allele frequency from 12 different pea aphid biotypes. To do this, we focused on a noncoding SNP in the api region that segregates perfectly with the male wing phenotype across all 23 sequenced genomes from the nine biotypes, and which is 95% associated with the male phenotype in the alfalfa-biotypespecific, pool-seq data. We examined this SNP from pre-existing pool-seq data collected from each of the 12 biotypes  (Guyomar et al. , 2018)  to estimate the winged allele frequencies. Each pool contained from 14 to 35 individuals from France, which has high host plant diversity, and each pooled individual had a distinct, multilocus genotype  (Guyomar et al.
, 2018). The majority (9/12) of the biotype lineages exhibited both alleles, with the ancestral, winged allele frequency ranging from 5% to 94% (Figure  3C ). In the remaining three biotypes (Gs, Mes, and Vc), the derived, wingless allele has gone to fixation in the samples of our dataset. This inter-biotype variation raises the intriguing idea that specialization on distinct legume hosts may influence male wing dimorphism variation. The winged and wingless alleles have been maintained within the pea aphid lineage for millions of years. This variation may have been maintained within one or more biotypes as we see in modernday sampling, or alternatively, the pea aphid species complex has maintained both alleles for thousands of years, but the alleles have moved between individual biotype via introgression.
We crossed F1 females to F1 males, collected fertilized eggs, sterilized them in 1% calcium propionate on Whatman paper, and placed them in an incubator that alternated between 4˚C for 12 hr light and 0˚C for 12 hr dark. After 90 days, eggs were removed from this incubator and placed in a 19˚C incubator that alternated between 16 hr light and 8 hr dark. F2 hatchlings were transferred to individual plants for asexual reproduction to establish a line of that F2 individual. Genomic DNA from 164 F2 females was isolated, quantified, and diluted to 2 ng/ml and subjected to multiplexed shotgun genotyping  (Andolfatto et al. , 2011). The final amplified libraries were sequenced on an Illumina Genome Analyzer. We generated parental X-chromosome genomes for the MSG software pipeline (https://github.
com/YourePrettyGood/msg; copy archived at https:// github. com/elifesciences-publications/msg; Pinero et al. , 2020)  by updating a recently published assembly of the pea aphid genome  (Li et al. , 2019)  with short sequence reads generated from wingless and winged males from the F1 strain and a custom script (available upon request). MSG produced genotype posterior probabilities that were imported directly into the genotype data structure of R-qtl  (Broman et al. , 2003)  using a custom script (https://github. com/dstern/read_cross_msg; copy archived at https://github. com/elifesciences-publications/read_cross_msg; Stern, 2020). We performed QTL analysis assuming a single additive locus for winged versus wingless males using the R-qtl command scanone using Haley-Knott regression  (Haley and Knott, 1992).
In addition, the reads were mapped to our WL genome using bowtie2  (Li and Durbin, 2009 ) using default parameters. Reads were filtered for a mapping quality of 20 and BAM files were sorted by coordinates using samtools. The coverage of both W and WL libraries mapping to our WL genome was calculated using the samtools depth function. The pool-seq reads are deposited under BioProject PRJNA562690, SRA SRR10030338 for the winged reads and SRA SRR10030337 for the wingless reads.
Basecalling was completed using ONT Albacore Sequencing Pipeline Software version v2. 2. 6. 14 GB of Nanopore reads were generated for the winged line and 7 GB reads were generated for the wingless line. OntCns, a customized version of MECAT  (Xiao et al. , 2017)  was used to assemble the Nanopore reads of the W line. All parameters were kept the same as the example included in the package manual except for the OntCns2Consensus step, in which the coverage cutoff (-c) was set to 5. Mini-map2  (Li, 2018)  and Miniasm2  (Li, 2016)  was used for genome assembly of the WL genome. An additional 36 GB of WL/WL Pacbio reads were combined with the 7 GB of Nanopore reads. Preset parameters (-x ava-pb) were used in the Minimap step. Assembly polishing was performed slightly differently for the two assemblies.
Other genomes We sequenced the genome of the rose aphid (Macrosiphum rosae) using 2 Â 150 nt Illumina reads to approximately 105x coverage. Abyss 2. 13 was used to assemble the genome, with kmer set to 107 and other parameters left as default. This Whole Genome Shotgun project has been deposited at GenBank under the accession BioProject: PRJNA576965. We used publicly available data for the peach-potato (Myzus persicae), the soybean (Aphis glycines), and the bird cherry-oat (Rhopalosiphum padi) aphid genomes, available at Aphidbase. com. We also used information from a genome produced by the 10XGENOMICS company (here renamed Carolinaia spp. based on its COI sequence) available at their website: https://support. 10xgenomics. com/de-novo-assembly/datasets/ 2. 0. 0/aphid).
Association and F ST analysis Two mpileup files were created from the W and WL male BAM files, mapping to either the genome recently published chromosome-length genome  (Li et al. , 2019)  or to the WL genome assembly we produced here using the samtools mpileup function with the -B option to disable BAQ computation. They were further processed by the mpileup2sync. jar script in PoPoolation2 v. 1. 201 (Kofler et al. , 2011)  to generate synchronized mpileup files (sync files), with fastq type set to sanger and minimum quality set to 20. For association analyses, Fisher's exact tests were performed on the mapping to our WL genome using the fisher-test. pl script included in PoPoolation2 with a window-size of 1, step-size of 1, minimum coverage of 2, and minimum allele count of 2. F ST values were calculated on the mapping to the whole-X-chromosome assembly  (Li et al.
dS biotype calculations The bedtools (v. 2. 26. 0) getfasta function was used to extract CDS sequences from the consensus sequences of the Lap1 and Ms3 genomes based on the annotation file AphidBase_OGS2. 1b_-withCDS. gff3, available at aphidbase. com. A modified perl script of SNAP (Synonymous Non-synonymous Analysis Program, v. 2. 1. 1), (Korber, 2000)  was used to calculate dS values with the Jukes-Cantor correction. Results were filtered to only include CDS lengths greater than or equal to 300 and less than or equal to 3000.
The maximum likelihood tree was constructed from 2,378 bp of DNA sequence from elongation factor 1a, 18S rRNA, 12S rRNA, cytochrome b, and cytochrome c oxidase subunit I collected from Genbank. (C) Maximum likelihood tree of the different copies of follistatin (fs) nucleotide sequences. Nodes with bootstrap values < 80 are collapsed. (D) RT-PCR analysis of fs-3 and fs-2 gene expression across different developmental stages (E: embryo cDNA, 1: 1 st instar nymph cDNA, 2: 2 nd instar nymph cDNA; +: genomic DNA, -: no cDNA) of wingless males, winged males, daughters of crowded adult wingless females ('winged' females, which are predominantly winged females), daughters of uncrowded adult wingless females ('wingless' females, which are predominantly wingless female samples). Females here are heterozygous for the api locus, and thus have fs-3 as indicated by the positive band in the female gDNA lanes.
Acknowledgements We gratefully thank  Jen Keister  for technical assistance. This research was supported by award  R01GM116867  from the  National Institute of General Medical Sciences  to JAB. Pool-seq sequencing was performed at the  University of Rochester Genomics Research Center. JCS was supported by the  Agence Nationale de la Recherche  (grant  ANR-11-BSV7-007 ) and France genomique (project  62.
The following datasets were generated: Database and Author(s) Year Dataset title Dataset URL Identifier Binshuang Li, Ryan 2019 Nanopore sequencing of an https://www. ncbi. nlm. NCBI Sequence Read D Bickel, Benjamin Acyrthosiphon pisum line nih. gov/sra/SRR8306868 Archive, SRR8306868 J Parker, Omid Saleh Ziabari, Fangzhou Liu, Neetha Nanoth Vel- lichirammal, Jean- Christophe Simon, David L Stern, Jen- nifer A Brisson Binshuang Li, Ryan 2020 Nanopore sequencing of an https://www. ncbi. nlm. NCBI Sequence Read D Bickel, Benjamin Acyrthosiphon pisum line nih. gov/sra/SRR10028116 Archive, SRR100 J Parker, Omid (aphicarus W/W) 28116 Saleh Ziabari, Fangzhou Liu, Neetha Nanoth Vel- lichirammal, Jean- Christophe Simon, David L Stern, Jen- nifer A Brisson Binshuang Li, Ryan 2020 Paired end sequencing of pooled https://www.