dataesr/scientific-paragraphs-categorization huggingface dataset:
In order to investigate our hypothesis, we assessed the existence of circulating antibodies against the F. hepatica Fas2 antigen in patients diagnosed with liver cancer by conducting Fas2-ELISA, an accurate serological test based on the detection of circulating immunoglobulin G (IgG) antibodies elicited in infected individuals against Fas2. A total of 13 serum samples were analyzed. These biospecimens were previously obtained from an HCC study conducted at the Instituto Nacional de Enfermedades Neoplásicas (INEN). All the samples corresponded to patients diagnosed with liver cancer at INEN between 2014 and 2015. Written informed consent was obtained from each patient before sample collection. Demographic data was also recorded, which included the sex, age, tumor type, place of current residency, and place of birth.
A color reaction developed when 3,3',5,5'-tetramethylbenzidine (TMB) was incorporated into the reaction, which was stopped by adding 50mL of 2M H 2 SO 4. The optical density was measured at 450nm in a microplate reader (Benchmark Bio-Rad). Negative and positive controls were used. The results obtained using Fas2-ELISA were analyzed considering the demographic and relevant clinical data of each patient.
Ancestry and evolutionary age of the Amazon molly. A low level of genomic decay in the asexual species could be expected if new lineages are repeatedly produced from hybridization of the parental species. Previous studies based on small fractions of mitochondrial or nuclear genomes showed conflicting origins as to a single  14  or multiple F 1 hybrids or backcrosses  14, 29. We performed ancestry estimates for P. formosa using our highquality single-nucleotide polymorphism (SNP) data set (292,324 sites). In total 53,175 sites display fixed nucleotide differences between the parentals, of which 47,359 were inferred to be heterozygous in P. formosa for the two parental alleles confirming an F 1 hybrid origin. All P. formosa isolates consistently display a heterozygosity (H) index of 0. 5 (Supplementary Table  23 ).
However, the P. latipinna and P. mexicana genomes were only annotated for gene content with the NCBI pipeline  62. In both annotation processes gene models were supported or novel based on RNA sequencing (RNA-seq) data from P. formosa, P. mexicana and P. latipinna independent tissues (see NCBI annotation report: https://www. ncbi. nlm. nih. gov/genome/annotation_euk/Poecilia_formosa/101/) for the full list of tissues. For the Ensembl P. formosa gene build only the RNA-seq data from liver, brain, skin ovary, gills and embryonic tissues were used. The final Ensembl P. formosa gene set comprises models based on orthologous proteins from the vertebrate division of UniProtKB, longest translations of some stickleback gene models from Ensembl 73, as well as models from RNA-seq data. RNA-seq data were used to further improve gene model accuracy by alignment to nascent gene models to delineate boundaries of untranslated regions as well as to identify genes not found through interspecific similarity evidence from other species.
The within-species per-site nucleotide diversity was calculated for sequenced genomes of each species using VCFtools  65  and was averaged over all the SNP sites. Tajima's D values were calculated for each 50 kb non-overlapping genomic window using genome-wide SNP data sets in the software VCFtools, and subsequently a genome-wide average was calculated. To validate a previous study that claimed backcrossing has occurred we used INTROGRESS as in ref. 29  to analyse the introgression of genotypes between divergent, hybridizing lineages, including estimating genomic clines from multilocus genotype data and testing for deviations from neutral expectations. DNA sequences described in population sequencing for P. formosa, P. latipinna and P. mexicana from 5 individuals were each aligned with the homologous reference of each at an average input sequence coverage of 11× using BWA-MEM.
Total SNPs were called by GATK HaplotypeCaller and GenotypGVCFs  66. All SNPs were used to report expected LoFs classified as single-base substitutions that disrupt splice acceptor, splice donor, stop loss or gain codons using the VAAST software  67. To filter variants that were shared across all samples in either of the sexual parents we removed LoFs that were shared in all. We reasoned the likelihood of fishes having LoFs fixed among different populations is very rare. However, we did allow LoFs to be shared across all in the P. formosa samples. As they are clonal it is feasible that the LoFs could remain fixed over many generations.
45 min for each step, 72 °C 12 min. PCR products were mechanically hydro-sheered and cloned into shotgun libraries before Sanger sequencing. Sequences were first assembled into contigs using the phred/phrap assembler (www. phrap. org/phredphrapconsed. html) and then contigs further merged using the cap3 assembler (http://seq. cs. iastate. edu/ cap3. html). Remaining gaps were closed by additional PCRs. Whenever aligned shotgun sequences indicated potentially conflicting sequence data, fragments were re-amplified and re-sequenced by specific direct PCRs. The mitochondrial genomes from NGS data were assembled with the Geneious program version 8. 1. 7 (http:// www. geneious. com/) (map to reference algorithm, medium/low sensitivity, up to 5 iterations) using the P. reticulata mitochondrial genome (Genbank Accession number AB898687.
1) as outgroup reference. Consensus sequences were edited with Bioedit (http://www. mbio. ncsu. edu/BioEdit/bioedit. html) and analyzed using MEGA (genetic distances) (http://www. megasoftware. net/) and PopART (mitochondrial haplotype minimum spanning network) (http://popart. otago. ac. nz). Repeat analyses. Repeat (TEs and non-TEs) libraries of P. formosa, P. mexicana and P. latipinna were established using an automatic annotation with RepeatModeler1. 0 http://www. repeatmasker. org, combined with manual search of known TE proteins and phylogenetic classification. For comparison we used the genomes of platyfish (Xiphophorus maculatus)  68  and guppy (P. reticulata) (http:// www. ncbi. nlm. nih. gov/assembly/GCA_000633615. 2). TE superfamily classification is based on a universal classification  69.
TE contents in genome assemblies were estimated using RepeatMasker 3. 3. 0 (http://www. repeatmasker. org). The relative age of TE copies in poeciliid genomes was calculated through Kimura distance analyses (http://www. repeatmasker. org/genomicDatasets/RMGenomicDatasets. html). The proportion of sites with transitions (p) and transversions (q) were transformed as follows: (K = -½ ln(1 -2p -q) -¼ ln(1 -2q)). Transcriptome assembly of the Amazon molly was masked to evaluate the proportion of transcribed TE superfamilies. For phylogenetic analyses, nucleotide sequences were first translated using Augustus  70. TE proteins (reverse transcriptase or transposase) were then aligned using MUSCLE  71  in PhyML package  72  and phylogenetic trees were reconstructed with the maximum likelihood method using approximate likelihood ratio test (aLRT) non-parametric branch supports.
Pairwise relative genetic distance was calculated using the program MEGA v. 6. 06. For each gene mean values for individuals or species were calculated and compared using ANOVA. ANOVA and Scheffé Posthoc test were done with STATISTICA v. 13 (Dell Inc. ). Selection analysis (dN-dS; N, nonsynonymous; S, synonymous base exchange) were done using MEGA v. 6. 06. Allele-specific gene expression analysis. Six P. formosa RNA-Seq sequencing files were downloaded (liver: SRR629501, SRR629518; skin: SRR629511, SRR629503; gills: SRR629508, SRR629510) from SRA and were filtered P. latipinna (GCF_001443285. 1) and P. mexicana (GCF_001443325. 1) reference RNA sequences were downloaded from NCBI. To assign ancestral alleles of P. formosa genes, sequence homology between ancestral alleles and P. formosa genes were identified using Blastn  73.
When multiple representation of homology was observed, the ancestral allele that generated the longest sequence alignment was kept to represent one ancestral allele of a P. formosa gene. Of the 25338 coding genes in the P. formosa genome that have a genome feature as 'mRNA' , 22118 genes can be assigned to both P. latipinna and P. mexicana alleles. Short sequencing files generated from P. formosa RNA-seq reads were mapped to the ancestral allele reference sequences that are generated by combining sequences of both ancestral alleles using Bowtie2  74  Customized Perl script was used to retrieve and quantify the short reads that only aligned to one of the ancestral alleles  73. Differential expression between parental alleles was tested using edgeR http:// bioconductor. org/packages/release/bioc/html/edgeR.
html (P. latipinna alleles were used as control). Log 2 (P. mex / P. lat) was used to label the relativize expression of both ancestral alleles. The false discovery rate (FDR) < 0. 05 was used to determine whether a gene shows allelic expression bias towards one ancestral allele. Overall P. formosa gene expression was assessed by mapping the RNA-seq sequence reads to the P. formosa genome (GCF_000485575. 1) using tophat2 (http://ccb. jhu. edu/software/tophat/index. shtml), and read counts quantified using featureCounts  75. A gene was determined to be expressed if at least one sample of the two biological replicates reached a library size-normalized read count (that is, count per million reads) of 0. 5.
formosa samples, Supplementary Figs. 11  and 12  for the parental P. latipinna and P. mexicana samples). We defined segmental duplications (SDs) as at least five consecutive windows of non-overlapping non-masked sequences with copy number values higher than the mean plus three standard deviations, allowing one of the windows to have a copy number value that is larger than the mean plus two standard deviations. Cutoffs were defined on a per sample basis. Furthermore, regions with an absolute copy number above 100 in any sample were excluded. Gaps were removed from the called intervals in downstream analysis. GO enrichment analyses on the set of duplicated genes were performed using R and the topGO package on a per species basis. First, the Ensembl IDs of the duplicates genes were mapped to the corresponding GO terms using the biomaRt package.
We also required at least 20% of the reads supporting each SNP derived from the minor allele. In the absence of introgression allele frequencies should be approximately 50% of the sites. In the case of paternal introgression a distorted frequency is expected skewed towards alleles that are present in the paternal species. We identified putative paternal introgression events as bimodal distributions of the reference allele frequency that result from the presence of an extra copy inherited from the male host. We confirmed that the inferred copy number throughout the identified scaffolds was higher in the samples where the paternal introgression was detected. To trace back the imbalanced allele to the corresponding paternal species, sequencing data derived from five P. mexicana and five P. latipinna fishes was used to call SNPs using the approach described above.
Data availability. All assemblies are available at Genbank under the following accession numbers: GCF_000485575. 1 (Poecilia_formosa-5. 1. 2) BioProject PRJNA89109, GCA_001443325. 1 (Poecilia_mexicana-1. 0) BioProject PRJNA196869, and GCA_001443285. 1 (Poecilia_latipinna-1. 0), BioProject PRJNA196862. Accession numbers for population sample genome reads are given in Supplementary Table.
Acknowledgements We thank  E. G. Ávila  for assistance and help in the field,  I. Schlupp  for P. formosa samples from Texas and discussions,  M. Niklaus-Ruiz  for help in preparation of the manuscript, and  R. Agrawala  for consultation on the assisted assembly aspects of this project. This work was supported by grants to W. C. W. (NIH:  2R24OD011198-04A1 ),  M. W. H. ( NSF   DBI-1564611 ), M. S. ( German Research Foundation DFG  projects  Scha408/10-1  and  Scha408/12-1 ),  M. St. ( Heisenberg-Fellowship   STO 493/2-2  of the  German Science Foundation/DFG) ,  T. M. B. ( MINECO BFU2014-55090-P (FEDER) ,  U01 MH106874 grant ,  Howard Hughes International Early Career ,  Obra Social 'La Caixa' and Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya ) and R.
Statistical analyses All statistical analyses were carried out with Statistica (Dell). The "Non-parametric Tests" module (Kruskal-Wallis tests) was used to evaluate differences of susceptibility to P. minitans among isolates of S. sclerotiorum as characterized by the different criteria described above. Wilcoxon-Mann-Whitney tests were used to evaluate the specific effect of P. minitans on each individual isolate by comparing colony diameter and production of daughter sclerotia from sclerotia of S. sclerotiorum previously incubated with the mycoparasite and from control non-inoculated sclerotia. These tests were also used to compare the susceptibility of the group of S. sclerotiorum isolates from the North to that of isolates from the South of France. Finally, polynomial regression analyses were implemented with the "General Linear Model" module to examine possible relations between the various criteria used to characterize the susceptibility of the 75 isolates of S.
Whatever the group of respondents considered the word terroir to mean, it was amongst the most cited words. The consumer corpus from Le Fur and Gautier's study  [3]  reported above was complemented with Swiss respondents in order to compare French and Swiss conceptions of minerality. These results showed that minerality represented different things to Swiss and French consumers. Swiss consumers had a richer vocabulary and higher declared wine knowledge than French  [4] , and the data concerning the definition of minerality showed that both groups cited mainly terroir and stone related terms. However, Swiss consumers cited many terms related to palate sensations that were virtually absent from the French corpus (saltiness; fizziness), while the proportion of respondents that declared not knowing anything about wine minerality was much higher in the French group.
Concerning the results for white wines, orthonasal minerality scores from both panels were significantly correlated with three Rieslings the most mineral wines of the sample set. Minerality differences in the full tasting condition were significant only for the wine producers. However, nose only and full tasting condition scores were not significantly correlated for wine producers. The same panellists carried out a sensory profile on the samples, the data used to predict minerality scores from the sensory attributes. The merchant/sommeliers' data did not produce any robust regression model on white wines. On the other hand, the wine producers' data yielded a robust regression model only for full tasting minerality scores. The negative predictors of minerality were tannin concentration (used here as a sensory descriptor) and balance, while the data concerning positive predictors showed unexpected results.
To determine the drivers of perceived mineral character in their selected white wines, the authors associated statistically the physico-chemical data with the sensory data gathered from the procedures undertaken by their (i) wine professionals and (ii) trained panellists. Wine professionals' judgments of mineral were positively associated with malic and tartaric acids, and to a lesser degree with free and total SO 2. Free SO 2 was also a positive predictor of mineral judgments by the trained panellists, recalling that the sensory data described above suggested that these participants were more aroma-driven than taste-driven when judging mineral character. Parr and colleagues  [62]  also report an investigation in which wine composition and wine sensory data were statistically associated in an attempt at elucidating the key aspects of wine physico-chemical composition driving perception of minerality in Sauvignon blanc wines from France and NZ.
The authors associated their global tasting-condition data (i. e. , the data from the full tasting condition involving orthonasal, retronasal, taste, and trigeminal sensations) reported in their earlier study  [43]  with a comprehensive set of wine composition data. These latter data included measures of wine standard parameters including non-volatile organic acids, elemental composition (18 cations), 33 volatile aroma compounds including varietal thiols and volatile sulphur compounds associated with pungent aromas, isobutyl methoxypyrazine and volatile organic acids. As well as absence of fruit/flavour and presence of stony/soil notes, the researchers were particularly interested in reductive phenomena and qualitative aspects of acidity, these often reported in wine-industry media as potential drivers of perceived minerality  [53, 67].
An even more comprehensive wine composition analysis was undertaken  [55]  in the study relating sensory and chemical aspects of minerality in Chablis wines (Chardonnay) from two vineyard locations, the left and right banks of the Serein River, reported above in Section 4. 1. Physico-chemical analyses in this study included wine standard parameters, non-volatile organic acids, 76 aroma compounds, phosphorus, as well as 10 metals. The results demonstrated several relevant wine-composition differences as a function of vineyard location. Left bank wines on average showed higher concentrations of methanethiol, a compound implicated as a source of mineral character in wine  [64]  and linked to shellfish aroma  [55]. This result is in keeping with Rodrigues and colleagues' orthonasal sensory data which showed left bank Chablis wines to be judged as more mineral than right bank wines.
The electrodes were cleaned and tested each day, before and after each set of measurements, according to the procedure indicated by Husson et al. [22]  with a Hach (Loveland, Colorado, CO, USA) 220 mV redox buffer solution (ref LZW9400. 99), and in the same solution diluted (1%) in 0. 1 M KCl solution. All redox potential data presented are actual Eh (mV) vs. standard hydrogen electrode (SHE), The measured E (mV vs. Ag/AgCl 3M) values have been corrected to Eh (mV) as a function of the temperature through the equation: Eh (mV) = E (mV) + 225. 8 -0. 73 t ( • C) derived from the table provided by Radiometer Analytical (Vaux-en-Velin, France) for the REF 321 Ag/AgCl KCl 3M electrode. Soil pH and temperature were taken with a Hach 5014T pH combined electrode (LZW5014T. 97. 002) directly inserted in the humid soil, and connected to WTW 3110 pHmeter.
In season III plants were sown 12 August 2016 and fertilized with NPK. In season IV plants were sown 2 December 2016 and fertilized with Hoagland solution. Measurements were made on the middle part of the last fully expanded leaf of the main tiller. Mean temperature and solar radiation at the day of measurement are indicated. Data for the plant ages 39 and 40 were pooled, details and pairwise comparisons are given in Table  S4. F and p values of the ANOVA are indicated. Values followed by different letters indicate significant difference between varieties at 95% confidence interval (REGW-Q test).
Farmers and their advisors were asked to implement the HHPM programme and have at least three meetings per farm in Sweden and four in France over a period of 12 months. Budget limitations prevented to do the same number of meetings in both countries. These meetings were conducted without the researcher, with the objective to mimic as much as possible a real advisory situation. Participant selection Organic dairy farmers involved in an ongoing research project were invited to participate in the current study. Inclusion criteria were that farms had to have been certified as organic for at least 1 year before the study, participate in the official milk recording scheme and farmers had to give their consent to participate in the study and share their farm data. Farmers were promised that the data would be treated anonymously.
Answers to questions, where a Likert scale (1 to 6) was used, were transformed into agree or disagree answers for the analysis. The scores 1 to 3 were converted into disagree and scores of 4 to 6 were converted into agree. A maximum of three reminders to fill in the questionnaire were sent. Reasons for not responding to the questionnaire were not recorded. Evaluation of the Herd Health and Production Management programme' impact on herd health. To assess the effective- ness of the HHPM programme in terms of improvement in herd health, changes in health situations before and after the intervention were evaluated and compared with the herd health situation in control farms from the corresponding countries. Subsequently, differences between French and Swedish farms were assessed. Farm data from the national recording systems were retrieved to calculate herd health and production indicators in a harmonized way, using the methodology described by  Krieger et al.
(2017). Data were obtained from the official milk recording schemes, artificial insemination databases and the animal identification and registration databases. The national recording systems are not harmonized and record keeping is different across countries, including the amount of information that is recorded. Therefore, the choice of herd health indicators was determined by data availability in both countries. For example, in contrast to Sweden, in France there is no information available on lameness. As a consequence, this health disorder was excluded from the evaluation even though lameness was one of the five health domains targeted by the HHPM programme. Nine indicators were retained to calculate herd health and production performances in both countries. For milk production, the average daily milk yield produced per cow per herd was used.
Between periods 1 and 2, meeting 0 were performed to introduce the HHPM programme on the farms. Data were randomly missing for certain farms for the calculation of certain indicators in both countries, even though data availability was a selection criterion. In France, for 15 control herds and five herds in the intervention group, milk recording data were missing. In Sweden this data were missing for 13 control herds. For the calculation of the calving interval data from one intervention farm was missing in France, in Sweden this was the case for 17 control farms and one intervention farm. To calculate the indicator interval calving-first artificial insemination, data from one control and one intervention farm was missing in France, in Sweden data were missing for three control farms. To calculate calf mortality, the data of four and two control farms was missing in France and Sweden, respectively.
Ile447Asp amino acid change (Supplementary Fig. 5 ). Third, knockdown of expression of TaWAKL4 but not TaWAKL3 through virus-induced gene silencing (VIGS)  31, 32  compromised Stb6mediated resistance in CS and Cad wheat (Fig. 2 , Supplementary Figs. 6  and 7 , and Supplementary Tables  1  and 2 ). Fourth, we took advantage of the Targeting Induced Local Lesions In Genome (TILLING)  33  population of Cad and the corresponding database cataloging mutations identified in 1,200 mutant families through exome resequencing  34, 35. Mutant families with predicted nonsense and missense mutations in TaWAKL3 and TaWAKL4 were tested for resistance to Z. tritici IPO323, and mutations were verified by targeted sequencing (Supplementary Tables  3  and 4 ). All ten families with mutations in TaWAKL3 remained resistant to this fungal isolate (Fig.