dataesr/scientific-paragraphs-categorization huggingface dataset:
Approximate Strehl ratios S 0 are derived from the ratio between the measured relative peak counts ct(0)/ct 3dia and the expected relative peak flux for diffraction-limited PSFs according to S 0 = ct(0)/ct 3dia f (0)/ f 3dia , where f (0)/ f 3dia is calculated for the VLT (8. 0 m primary mirror telescope with a 1. 1 m central obscuration by the secondary mirror). For a pixel size of 3. 6×3. 6 mas there is f (0)/ f 3dia = 4. 95 %, 3. 66 %, and 2. 44 % for the V-, N_R-, and N_I-filters, respectively. Ratios S 0 between about 9 % and 21 % are obtained for the HD 183143 observations which were taken under good conditions with a long atmospheric coherence time of τ 0 ≈ 8 -9 ms. This kind of approximate Strehl ratio S 0 determination provides a very useful parameter for a simple comparison of the atmospheric conditions and the AO performance of different data Notes.
A second complicating factor are the complex structures of the Hα emission features, composed of small and large, bright and faint clouds, and perhaps even a diffuse emission component. The flux measurements require therefore the definition of flux apertures and appropriate aperture correction factors, and this introduces additional measuring uncertainties. The quasi simultaneous HST data are very helpful to improve and check the ZIMPOL flux measurements but in the HST data some clouds are blended and aperture correction factors differ because of the lower spatial resolution. For this reason we determine here also the total Hα flux for the central 3. 6 × 3. 6 region of R Aqr. This value is independent of the flux aperture definition and correction factors, but needs to account properly for the contribution of the red giant.
Flux measurements for the Hα clouds Absolute flux measurements for complex sources, like the Hα jet clouds around the strongly variable object R Aqr, are difficult to achieve with ground based, extreme adaptive optics measurements because of the strong PSF variations caused by the rapidly changing atmospheric conditions and AO performance. The unique coincidence of quasi-simultaneous HST data provides for our ZIMPOL -SPHERE test data an ideal opportunity for assessing and checking the quality of our measuring procedure and instrument calibrations. The ZIMPOL Hα cloud flux measurements require an analysis of the PSF to account for the non-focussed flux in the extended PSF halo. The derived correction factors are large, of the order of three to ten typically, and depend on the cloud and aperture size.
This is the major source of uncertainty in the absolute flux measurements. The resulting line fluxes from ZIMPOL -SPHERE are about 30 % higher than the fluxes derived from the HST data. The main reason for this discrepancy is most likely a systematic overestimation of the flux correction factors for the ZIMPOL data. Flux ratios between different clouds agree very well σ ≈ 10 % between different ZIMPOL observing dates and different ZIMPOL Hα filters. The agreement is also excellent σ = 7. 5 % between relative cloud fluxes measured in ZIMPOL data and HST data. This indicates that line flux variation can be measured with high sensitivity with ZIMPOL -SPHERE, if one emission component in the field can be used as flux reference. The absolute Hα line flux is a very important diagnostic for the ionized gas in spatially resolved clouds.
On the R Aqr jet The presented SPHERE-ZIMPOL data and WFC3 -HST data provide two most significant advances for the investigation of the R Aqr jet with respect to previous HST imaging observations  (Paresce et al. 1991; Paresce & Hack 1994; Hollis et al. 1997a). First, the SPHERE-ZIMPOL images provide a spatial resolution of about 25 mas (FWHM), which is about three times higher than for the previous and new HST observations. Therefore the SPHERE-ZIMPOL data can resolve the central binary and the innermost jet clouds. Second, the simultaneous WFC3 data provide very sensitive, wide field images of the R Aqr jet for four important diagnostic lines. This combination of high quality data forms a very rich source of observational information about the physical properties of the R Aqr jet. In this work, we focus the analysis mainly on the Hα emission of the innermost jet r jet < 400 AU covered by the ZIMPOL data.
This will help us to understand the interaction between the jet originating from an orbiting source with the red giant wind and answer the important question whether the jet outflow is oriented perpendicular to the orbital plane or not. From an inclined outflow one may expect jet precession that could explain the partly point-symmetric arc structures associated with the NE-SW jet directions. The data presented in this work provide a wealth of new information for the detailed investigation of the physical nature of the jet clouds in the innermost region of the R Aqr jet. For example, it would be interesting to know whether the Hα clouds are ionized gas regions of the slow red giant wind, which are excited by shocks from the fast outflow (e. g. , the clouds in the SW). Alternatively, they might also be radiative shock regions moving with the fast outflow (e.
Acknowledgements. SPHERE is an instrument designed and built by a consortium consisting of  IPAG (Grenoble, France ),  MPIA (Heidelberg, Germany) ,  LAM (Marseille, France), LESIA (Paris, France), Laboratoire Lagrange (Nice, France) ,  INAF -Osservatorio di Padova (Italy) ,  Observatoire de Gen'eve (Switzerland) ,  ETH Zurich (Switzerland) ,  NOVA (Netherlands) ,  ONERA (France) , and  ASTRON (Netherlands) , in collaboration with  ESO. SPHERE was funded by  ESO , with additional contributions from  CNRS (France) ,  MPIA (Germany) ,  INAF (Italy) ,  FINES (Switzerland) , and  NOVA (Netherlands). SPHERE also received funding from the  European Commission Sixth and Seventh Framework Programmes as part of the Optical Infrared Coordination Network for Astronomy (OPTICON)  under grant number  RII3-Ct-2004-001566  for FP6 (2004)(2005)(2006)(2007)(2008), grant number  226604  for FP7 (2009)(2010)(2011)(2012), and grant number  312430  for FP7 (2013)(2014)(2015)(2016).
This work has been carried out within the frame of the  National Centre for Competence in Research "PlanetS"  supported by the  Swiss National Science Foundation. H. M. S. , S. Q. , and C. T. acknowledge the financial support of the  SNSF. A. B. , R. C, S. D. , R. G. , B. S. , E. S. , and M. T. acknowledge support from the  "Progetti Premiali" funding scheme of the Italian Ministry of Education, University and Research. This research has made use of the SIMBAD database, operated at  CDS, Strasbourg, France.
Phylogenetic profile of CYD-TDV vaccine strains and DENV detected in CYD14 and CYD15 trials Full and partial E gene sequences determined directly from serum samples collected in  were aligned with E gene sequences corresponding to the CYD-TDV vaccine strains and sequences from GenBank for which the year and country of sampling were known. Maximum likelihood trees representing subsampled E gene sequence datasets allowed the classification of CYD14/15 viruses to the major intra-serotype lineages (genotypes) previously described for DENV (Figure  2 -figure supplements 1-4). At the country level, CYD14/15 viruses were closely related to publicly available DENV sequences acquired from the same country, an indicator of ongoing local evolution. Figure  2  shows the genotypes detected in the CYD14/15 virus populations according to their country of sampling.
Sequence differences between CYD-TDV vaccine strains and circulating wild-type viruses We quantified the differences between the E gene amino acid sequences in the components of the tetravalent CYD-TDV formulation and viruses from VCD cases in the CYD14 and CYD15 trials. The mean level of E gene amino acid sequence difference between vaccine strains and viruses from VCD cases in CYD14 and CYD15 was <3% for all serotypes (Figure  3  and Supplementary file 1b). To define the nature of these sequence differences, the amino acid positions that varied between CYD-TDV vaccine strains and the E gene sequences sampled in CYD14/15 trials and in the subsampled GenBank sequences were annotated adjacent to the subsampled maximum likelihood phylogenetic trees for each serotype. The DENV-2 E gene phylogeny (incorporating the vaccine strain) of relevance to the CYD14 trial is shown in Figure  4A  and for CYD15 in Figure  4B.
CYD14 We examined amino acid sequence identity between vaccine strains and wild-type CYD14/15 virus sequences at twelve B cell epitopes. The twelve epitopes represent some of the best structurally defined epitopes in DENV that are targeted by potent virus neutralising human mAbs and are thus of particular interest in vaccine development and immune correlate assays  (Fibriansah et al. , 2014; Cockburn et al. , 2012a; Smith et al. , 2013; Fibriansah et al. , 2015a Fibriansah et al. , , 2015b;; Teoh et al. , 2012; Rouvinski et al. , 2015; Costin et al. , 2013; Cockburn et al. , 2012b). Sequence analyses indicated limited variation at these epitope regions in the CYD14/15 sequences, as well as in a global database of wild-type virus sequences (Figure  5  and Figure  5 -figure supplement 1). The conservation of these epitope sequences between the decades-old 'donor' viruses from which the CYD-TDV product was derived and contemporary virus populations suggests that these amino acid sites are not highly prone to evolutionary drift.
Vaccine efficacy by DENV serotype and genotype Given the high degree of overall amino acid sequence identity, including at key epitope positions, between the E protein found in CYD-TDV vaccine strains and contemporary wild-type CYD14/15 viruses, we postulated that vaccine efficacy would be largely independent of virus genotype. We report two levels of intention to treat genotype-level efficacy from the CYD14 and CYD15 trials: the observed estimates and the observed+imputed estimates. The observed estimate refers to vaccine efficacy in the population of VCD cases who had serum samples yielding an E gene sequence that was empirically assigned a genotype. The observed+imputed estimates used the observed genotype data plus imputation to give genotype assignments to VCD cases where the serotype was known but genotype information was absent.
Discussion The pivotal Phase III efficacy trials of CYD-TDV and longer term follow-up have revealed the complex efficacy profile of this vaccine  (Capeding et al. , 2014; Hadinegoro et al. , 2015; L'Azou et al. , 2016). These trials also highlighted generic challenges in dengue vaccine development, e. g. the 100 90-99. 9 75-89. 9 50-74. 9 25-49. 9 0-25  Figure  5. Sequence conservation between the DENV-2 vaccine component and wild-type DENV-2 viruses at epitope locations targeted by virus neutralising human mAbs. Amino acid targets for five neutralising human mAbs  (Fibriansah et al. , 2015b; Rouvinski et al. , 2015)  are coloured as indicated in the key (top) and compared to the vaccine sequence and wild-type sequences obtained within the CYD14 and CYD15 trials (middle), as well as complete E gene sequences from wild-type DENV-2 available on GenBank (bottom).
Comparing wild-type DENV-2 sequences sampled in CYD14/CYD15 to the CYD-TDV vaccine component, only site E83 showed a mismatch in a high proportion of the Asian I population alone. Sequence data obtained from GenBank confirm that, while there is some variability at this site among all contemporaneous DENV-2 lineages, the Asian I lineage is defined by this amino acid difference at E83. An important caveat to these sequence comparisons is that amino acid differences between vaccine strains and wild-type viruses at known B cell epitopes does not necessarily imply that antigenicity (or immunogenicity) is altered -functional assays of antibody binding will be needed for this. Our study had several limitations. These were post hoc analyses and, inevitably, sample sizes became small for genotype-level vaccine efficacy estimates and in particular the age-class (9-16 year olds) subgroup analysis.
Data analysis GS Mapping software (Roche) was used for primer trimming and alignment of reads against reference sequences. Briefly, each read per amplicon was mapped to a reference sequence (DENV-1/VN/ BID-V2732/2007, GenBank accession number GQ199773. 1; DENV-2/VN/BID-V1873/2007, GenBank accession number FJ461321. 1; DENV-3/VN/BID-V1933/2008, GenBank accession number KF955460. 1; DENV-4/KH/BID-V2055/2002 (GenBank accession number KF955510. 1). Sequence quality was high; the Phred scores for E gene sequences are provided in Supplementary file 3. Technical controls were included in all sequencing runs, and showed 100% sequence concordance across the prM and E gene in all cases. CYD-TDV prME sequences from CYD1-CYD4 vaccine components are deposited in GenBank under accession numbers KX239894-KX239897, respectively.
Sequence analysis A total of 664 DENV prM and/or E gene sequences were obtained using the above protocol (DENV-1, 253; DENV-2, 191; DENV-3, 108; DENV-4, 112) (Figure  1 , Figure  1 -source datas 1-4). Sequences were manually aligned using Geneious (v7. 1. 7; RRID:SCR_010519) and validated on both nucleotide and amino acid levels. Due to the availability of a larger, less geographically biased public database of E gene sequences compared to prM/E, we focused analysis on the E gene only (1485 nucleotide/495 amino acids for DENV-1,-2, À4; 1479 nucleotide/493 amino acids for DENV-3), excluding three sequences for which only the prM sequence could be obtained. Thus for each serotype, all full and partial E gene sequences  253; 191; 107; 110)  were aligned to large datasets of publicly available E gene sequences from GenBank for which the country and year of sampling are known.
Maximum likelihood (ML) phylogenies were inferred for nucleotide sequences using RAxML (v8. 0, http://www. exelixis-lab. org/; RRID:SCR_006086) under the GTRGAMMAI model and were visually assessed to determine the genotype of each virus obtained from CYD14 and CYD15. Visual inspection further indicated that all viruses sequenced in this study fell into expected lineages corresponding to previously sampled sequences from the countries from which they were isolated. To investigate DENV sequences from the CYD14 and CYD15 studies in the context of the viruses circulating in their respective countries and make datasets more tractable, datasets were subsampled to include all CYD14 and CYD15 E gene sequences and up to three randomly selected, publicly available sequences per country per year from the countries involved in this study, along with up to five representative sequences of each known genotype  (Goncalvez et al.
, 2002; Twiddy et al. , 2002; Wittke et al. , 2002; Patil et al. , 2012) , regardless of the country from which they were isolated (Total number of taxa used for phylogenetic reconstruction, CYD14: DENV-1, 317; DENV-2, 279; DENV-3, 222; DENV-4, 207. Total number of taxa used for phylogenetic reconstruction, CYD15: DENV-1, 236; DENV-2, 252;  159; 119). Evolutionary models for each dataset were determined using jModeltest (v2. 0; RRID:SCR_015244)  (Posada, 2009). ML trees were then inferred from these nucleotide sequences using RAxML (v8. 0) under the GTRGAMMAI model with 500 bootstrap replications, and p-uncorrected sequence identity (pairwise comparison of genetic differences across the nucleotide and amino acid alignments) was determined using Geneious (v7. 1. 7). To investigate potentially novel amino acid residues or changes suggestive of selection, all amino acid sites showing a difference between two or more CYD14/CYD15 sequences relative to the vaccine or circulating viruses of the same genotype were mapped to the aforementioned phylogenies using Phandango (https://jameshadfield.
VCD cases with missing genotype were imputed using multiple imputation techniques (logistic regression) by serotype with the country included in the model. The twenty imputed (completed) datasets were then analyzed separately and the resultant estimates combined using Rubin's variance rules and their multivariate generalizations  (Rubin, 1987). Analyses were run based on the available data (i. e. no imputed values) and on the imputed data (raw imputation data are shown in Supplementary file 1d). A Chi 2 test (or Fisher's exact test) was used to test the heterogeneity of genotype distribution between vaccine groups. The alternative procedure for pooling chi-square distributed statistics that was proposed by Rubin  (Rubin, 1987)  and further investigated by Li et al. was used on imputed data  (Li et al.
Acknowledgements The authors would like to acknowledge all investigators,  Sanofi Pasteur's Global Clinical Immunology team  and volunteers involved in the clinical evaluation of CYD-TDV. Many thanks also to all  Sanofi Pasteur Dengue Vaccine  team members and in particular to  Helena Aurell ,  Alain Bouckenooghe ,  Laurent Chambonneau ,  Danaya Chansinghakul ,  Diana Leticia Coronel ,  Remi Forrat ,  Carina Frago ,  Etienne Gransard ,  Thelma Laot ,  Josemund Menezes ,  Fernando Noriega ,  Leon Ochiai ,  Eric Plennevaux ,  Paula Perroud ,  Enrique Rivas ,  Melanie Saville ,  Jo-Ann West  and  Jean Lang  for their support. In Vietnam , thanks to  Vi Tran Thuy  and  Huy Huynh Le Anh. We would also like to thank  Hao Chung The  and  Christine Boinett  for assistance with figures. A special thanks to  Bruno Guy  for helpful discussions and critical reading of the manuscript.
, 2015). To our knowledge, the 20 synthetic and 32 natural B. napus accessions in this panel provide the largest available dataset so far available for detailed comparisons of genome structural features between de novo and natural allopolyploids. Common areas under selection were identified in the natural B. napus accessions, representing successful survivors of allopolyploidization. Genes affected by segmental deletions were enriched for gene ontology (GO) terms related to adaptive processes and chromosome stability. Motifs identified in the breakpoints of genomic rearrangements suggest that structural changes arise primarily from meiotic recombination between chromosomes with extended homeologous sections. Rearrangements were directionally biased, leading to systematic reduction of genome size as a result of preferential loss of longer C-subgenome fragments after nonreciprocal exchanges replacing them with smaller, homeologous segments from the A-subgenome.
A detailed description of the development and origin of the synthetic accessions has been described previously  (Girke, 2002; Girke et al. , 2012; Jesske, 2011; Jesske et al. , 2013) , as has a detailed description of the sequence data generation  (Schmutzer et al. , 2015). The full sequence data for all 52 accessions is archived at the European Nucleotide Archive (http://www. ebi. ac. uk/ ena, accessed 3 July 2017) under the project numbers PRJEB5974 and PRJEB6069. The raw Illumina short read sequencing data were subjected to quality control procedures using the software suite FastQC  (Andrews, 2010). Adapters and low-quality bases were removed using cutadapt  (Martin, 2011) , the fastq_quality_trimmer, and the fastq_quality_filter algorithms. Applying the fastq_quality_trimmer with the settings -t 28 and -l 90, trimmed bases with a Phred quality score of <28 followed by removing reads with a length of <90 nucleotides.
Using the fastq_quality_filter algorithm (options:-q 28, -p 90) only reads where more than 90% of the nucleotides had a Phred score of ≥28 were retained. Paired-end reads were synchronized using a custom Perl script provided by the Leibniz Institute for Plant Genetics and Crop Plant Research, Gatersleben, Germany  (Schmutzer and Scholz, 2015).
Detection of Genomic Rearrangements in Natural and Synthetic B. napus Accessions On the basis of the alignment files, we calculated the genome-wide guanine and cytosine content and median normalized coverage in 1000-bp blocks, assuming five copy number levels by using the commands getRead-CountsFromBAM and singlecn. mops implemented in the R package cn. mops  (Klambauer et al. , 2012). Five possible copy number levels were assumed because an allotetraploid can carry between zero and four copies of each allele in the five alternative genotypes AAAA, AAAC, AACC, ACCC, or CCCC  (Voorrips et al. , 2011). Chromosome regions exhibiting copy number variations were identified individually for each line and chromosome by segmenting the normalized 1000-bp blocks, sorted according to their genomic distribution, using the circular binary segmentation algorithm implemented in the R package PSCBS  (Olshen et al.
Single Nucleotide Polymorphism Calling Allelic variants were called by mapping the preprocessed 100-bp paired-end reads to the B. rapa Chiifu-401-42 and B. oleracea TO1000 genome assemblies, using SOAP2 software (http://soap. genomics. org. cn/soapaligner. html, accessed 11 July 2017)with the options -v 2 and -r 1. The alignment file was then converted to binary alignment/map format, followed by filtering of unmapped and nonunique reads by applying the samtools view algorithm  (Li et al. , 2009). High-quality single nucleotide polymorphisms (SNPs) were called by executing the samtools mpileup command with the following options: -Q 13 and -q 20. Homozygous SNPs with a minimum depth of five and a minimum quality score of 50 were extracted by applying the Genome Analysis Toolkit variant filtration algorithm  (McKenna et al.
Segmental Deletions are Conserved in Natural B. napus To investigate common patterns of selection we searched for regions with common rearrangement patterns in a high number of natural accessions. Distinct chromosome segments on chromosomes C01, C02, C04 and C09 were deleted in nearly all investigated natural B. napus accessions (Fig. 2 ; Table  S4 ). Segmental Deletions are Enriched for Genes Associated with Reproduction, Adaption, and Chromosome Stability To characterize the functional impact of segmental deletions, we searched for enriched GO terms in each of the 52 natural and synthetic accessions among genes showing deletions in comparison with the B. rapa Chiifu-401-42 and B. oleracea TO1000 transcriptomes (functionally annotated using Blast2GO version 3. 0. 8). The conditional hypergeometric test included in the Bioconductor GOstats package (version 2.
Using MEME software (with settings -nmotifs 10, -minw 8, and -maxw 20), breakpoint-flanking sequences were subsequently analyzed for enrichment with DNA motifs 8 to 20 bp long. Genomic sequences around putative breakpoints were found to be significantly enriched for poly-A or poly-T stretches and the palindromic GAA-CTT microsatellite sequence (Fig. 3 ). Both of these motifs are associated with recombination hotspots in Arabidopsis thaliana (L. ) Heynh. (Choi et al. , 2013; Wijnker et al. , 2013). By sequencing a bacterial artificial chromosome clone spanning a putative breakpoint for a known HE, we confirmed the breakpoint junction at the transcription start site of an ortholog of the A. thaliana gene SIMILAR TO RCO1 (SRO5; Bra029254/Bo2g164210). Within the promoter sequence of this gene, we identified the GAA-CTT recombination hotspot predicted by the sequence enrichment analysis (Supplemental Fig.
Selective Sweeps Reveal Signatures of Selection for Agronomic Traits Changes in nucleotide diversity and skewed allele frequency spectra provide additional information on selection processes beyond structural chromosome rearrangements. Supplemental   S8. These selective sweeps show unequal subgenomic distribution, For each breakpoint, the genomic sequence 500 bp upstream and downstream was extracted and analyzed for enriched DNA motifs using MEME software. The e-value estimates the expected occurrence (with the given log-likelihood ratio or higher) of motifs with the same size and frequency in a similarly sized set of random sequences. the pl ant genome  november 2017  vol. 10, no. 3 with 172 areas under selection in the C-subgenome and 72 in the A-subgenome. Analysis for enriched GO terms revealed a range of terms strongly associated with traits of relevance for domestication and breeding, including leaf senescence, carbohydrate biosynthesis, lipid metabolism, response to osmotic stress, vernalization response, and root development (Supplemental Table  S9 ).