dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments: C. V. was funded by  Fundação para a Ciência e a Tecnologia (FCT)  grant  SFRH/BD/76169/2011 , co-financed by  FSE, POPH/QREN  and  EU. J. M. was supported by the  EPSRC   Intelligent Imaging Program  Grant  EP/H046410/1. This work was supported by the  US Army Medical Research and Materiel Command  under Contract Agreement no  DAMD17-W81XWH-04-2-0022. Opinions, interpretations, conclusions and recommendations are those of the author and are not necessarily endorsed by the  US Army.
1. A synchrotron X-ray beam with a cross-section of 100 £ 100 microns and a photon energy of 67 keV was used (wavelength D 0. 1839 £ 10 ¡10 m), with the diffraction patterns being recorded in transmission. A 2D detector (Perkin Elmer 1621 AN) was located about 1 m away from the sample, from which Debye-Scherrer rings (Fig. 1 ) were collected. In order to generate 2-theta -Intensity plots, the data was caked into 10 slices centered around the poling direction (C D 0 ), using Fit2D software  [11].
5 mm length) with 6-and multi-holes in the distal zone, which correspond with two commercial models for RFCA: ThermoCool 1 and ThermoCool 1 SF (Biosense Webster, Diamond Bar, CA, USA), data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have read the journal's policy and have the following competing interests: JMG has received educational grants and has participated as speaker in courses organized by Biosense Webster (<10. 000$). The other authors have declared that no competing interests exist. This does not alter the authors' adherence to PLOS ONE policies on sharing data and materials. respectively. The small holes allow the saline solution to continuously flush into the cardiac chamber. In endocardial ablation, the flowing saline mixes with the circulating blood without forming a film around the electrode, differently from what happens in epicardial ablation  [13].
Governing Equations The numerical model is based on a coupled electric-thermal-flow problem, which is solved numerically using the Finite Element Method (FEM) with COMSOL Multiphysics software (COMSOL, Burlington, MA, USA). The governing equation for the thermal problem is the Bioheat Equation, modified by the enthalpy method  [18]  that includes the phase change to model tissue vaporization: @ðrhÞ @t ¼ r Á ðkrTÞ þ q À Q p þ Q m À rcu Á rT ð1Þ where ρ is density (kg m -3 ), h enthalpy, t time (s), k thermal conductivity (W m -1 K -1 ), T temperature (°C), q the heat source caused by RF power (W m -3 ), Q p the heat loss caused by blood perfusion (W m -3 ) and Q m the metabolic heat generation (W m -3 ). Q p can be neglected since it has been demonstrated both computationally  [19]  and experimentally  [20]  that the blood flow away from the coronary arteries does not have significant influence on the temperature distribution during RFCA.
Boundary conditions Fig 2A shows the electrical boundary conditions. We consider a constant power ablation, which is the usual ablation mode for open-irrigated electrodes in RFCA. We implemented a proportional-integral (PI) control algorithm using MATLAB (MathWorks, Natick, MA, USA) and is simulated by means of the COMSOL-MATLAB interface, where we previously exported the FEM structure generated from COMSOL. The behavior of the PI controller is determined by the proportional (K p ) and the integration (K i ) constant. We used the parameters for a Table  1. Thermal and electrical characteristics of the elements employed in the numerical models (data from  [17] ): σ: electric conductivity; k: thermal conductivity; ρ: density; c: specific heat. Element/Material σ (S m -1 ) k (W m -1 K -1 ) ρ (kg m -3 ) c (J kg -1 K -1 ) Electrode/Pt-Ir 4.
Acknowledgments This work was supported in part by the  Basque Government  through the  BERC 2014-2017 program  and by  Spanish Ministry of Economy and Competitiveness MINECO  through the  BCAM Severo Ochoa excellence accreditation   SEV-2013-0323 , and also by the  Spanish "Plan Estatal de Investigación, Desarrollo e Innovación Orientada a los Retos de la Sociedad " under Grant  TEC2014-52383-C3-R (TEC2014-52383-C3-1-R ) and Grant  MTM2015-69992-R.
This work was supported in part by the  Basque Government  through the  BERC 2014-2017 program  and by  Spanish Ministry of Economy and Competitiveness MINECO  through the  BCAM Severo Ochoa excellence accreditation   SEV-2013-0323 , and also by the  Spanish "Plan Estatal de Investigación, Desarrollo e Innovación Orientada a los Retos de la Sociedad " under Grant  TEC2014-52383-C3-R (TEC2014-52383-C3-1-R ) and Grant  MTM2015-69992-R. The funders had no role in study design,.
thaliana to show that the single layer of internal tissue present in the shr mutant had cortical identity while the ground tissue layer of the scr mutant exhibited multiple identities  (Di Laurenzio et al. , 1996; Helariutta et al. , 2000). These markers have many advantages: their simplicity and the possibility of combining secondary antibodies coupled to different fluorochromes to limit overlapping with auto-fluorescence, they do not require genetic transformation and they can be used to complement other classes of markers. In this paper, we first describe a simple medium-throughput protocol for immunolabeling fresh vibratome tissue sections. Using this protocol, we screened radial sections of rice radicles with a large library of 174 cell wall antibodies. Among these, we identified eight cortex-specific markers and demonstrated that rice possesses two types of cortical tissues with distinct identity.
Some specific features of these two subcortical layers were highlighted when the "polar transformer" plugin of the ImageJ software (http://imagej. nih. gov/ij/) was used to view the images of the root sections (Figures  1B, C ;  Schneider et al. , 2012; Lartaud et al. , 2014). The inner cells were characterized by a thick cell wall compared with the outer cells, which exhibited various air-containing cavities resulting from cell wall fusion. The inner cortical cells also exhibited a flattened shape resembling endodermal cells, in contrast to the outer cells, which were rounder. In this transformed picture, the radial cell wall that is wall running from the inner side of the cell to the outer side, autofluorescence of the endodermal and exodermal cells are not visible, presumably due to the presence of Casparian strips.
This signature is exhibited, for example, by squark and gluino production followed by cascade decay chains, and/or decays to heavy SM particles, such as top quarks or W, Z or Higgs bosons, each of which can produce multiple jets in their decays. In contrast to many other searches for the production of strongly interacting SUSY particles, the requirement made here of large jet multiplicity means that the requirement on E miss T can be modest. Previous searches  [8] [9] [10]  in similar final states have been performed by the ATLAS Collaboration at the lower centre-of-mass energies of √ s = 7 TeV and 8 TeV, with integrated luminosities up to 20. 3 fb - 1. The larger energy of the present dataset provides increased sensitivity, particularly to particles with higher masses. This paper closely follows the strategy of those previous studies.
The EvtGen v1. 2. 0 program  [38]  models the bottom and charm hadron decays, as it does for all non-SHERPA-simulated processes mentioned below. The t t simulation is normalised to the cross-section calculated to next-to-next-to-leading order (NNLO) in perturbative QCD, including soft-gluon resummation to next-to-next-to-leading-log (NNLL) accuracy  [39]. Events containing t t and additional heavy particles -comprising three-top, four-top, t t + W, t t + Z and t t + WW production  [40]  -are simulated at leading order in the strong coupling constant α s , using MadGraph v2. 2. 2  [41]  with up to two additional partons in the matrix element, interfaced to the PYTHIA 8. 186  [25, 35]  parton shower model. The A14 tune of the PYTHIA parameters is used  [42] , together with the NNPDF2. 3LO PDF set  [43].
INTRODUCTION Mapping-by-sequencing has become a powerful tool for the genetic mapping of mutants and continuous pipeline development has streamlined such analyses in diploid species  (Schneeberger et al. , 2009; Doitsidou et al. , 2010; Austin et al. , 2011; Abe et al. , 2012; Minevich et al. , 2012). One frequently cited mapping-by-sequencing pipeline, SHOREmap, was originally developed for the diploid plant species Arabidopsis thaliana. SHOREmap uses sequence data from a phenotyped F2 mapping population to identify mapping intervals containing the phenotype inducing mutation. It scans across a reference sequence and locates a region of homozygosity in the mutant mapping population that is conserved with the mutant parent; however, it does not work for a polyploid dataset  (Schneeberger et al.
This pseudo-genome was used as the reference sequence for mapping analyses within this study to highlight the suitability of this methodology for poorly defined polyploid genomes. The pipeline to generate 'reference genomes' based on the two purebred parental lines of the varieties Avalon and Cadenza is shown in Figure  2 (a). Genomic DNA was isolated from each of the parents and separately enriched using our NimbleGen SeqCap EZ wheat exome capture probe set before sequencing using an Illumina HiSeq 2000. The short read sequences were mapped to the Chinese Spring pseudo-wheat chromosomes using short read mapping software Burrows-Wheeler Aligner (BWA)  (Li and Durbin, 2009). Coverage of the reference was similar for both the Avalon and Cadenza sequencing datasets. In both experiments approximately 97% of the reference was covered with uniquely mapping, non-duplicate reads, to an average depth of ~429 (see Table  S1 ).
, 2015). Also, mapping to the three reference genomes individually results in a high level of non-uniquely mapped sequencing reads. Furthermore, here the analyzed cultivars are different from the Chinese Spring-based reference introducing more SNPs and further hindering confident unique mapping. Therefore to maximize mapped sequencing data, and to highlight the suitability of this methodology for poorly defined polyploid genomes where sub-genome assemblies have not been discriminated, we align reads to a collapsed reference genome rather than three. However, for the application of SNP calling to our hexaploid P1 bulk segregant dataset, a homoeologous SNP allele must be categorized as being homozygous or having heterozygosity within the pool. We defined specific thresholds for this categorization as follows; homoeologous homozygous alleles in 50-24% of sequencing reads; borderline SNP alleles in 23-24% of sequencing reads and homoeologous heterozygosity within a pool is defined if SNP alleles are in 10-23% of sequencing reads (default settings shown in Figure  2b ).
These thresholds are relatively relaxed to allow the analysis of a maximum number of positions. We then utilize an algorithm to score regions of interest by prioritizing long homozygous parental haplotypes, the longer the length and the more homozygous the region in the pool, the higher the score generated  (Gardiner et al. , 2014). Of the homoeologous homozygote SNPs that were specific to the Avalon parent, 28 260 of the SNP alleles were conserved in the P1 dataset regardless of allele frequency. Similarly of the homozygote SNPs that were specific to the Cadenza parent, 35 639 of these were found in the P1 dataset. The scoring algorithm was then implemented to calculate a homozygosity score per 500 000 bp window along each pseudo-chromosome at 10 000 bp intervals for SNP alleles that were found in the bulk segregant dataset and were specific to either the Avalon or Cadenza parents (Figure  3 ).
386 to 213. 416 cM. Candidate region contains potential disease resistance genes and associates with the B sub-genome on chromosome 7 We investigated the interval between 13 650 001 and 14 150 001 bp on pseudo-chromosome 7 in more detail; however, here a window size of 100 000 bp was used to calculate homozygosity scores to allow us to analyze the interval with greater precision (Figure  4a ). We also analyzed this peak interval using a BLASTN alignment  (Altschul et al. , 1990)  (minimum E-value of 1e-5) to the BLAST nr nucleotide database with a focus on the identification of potential disease resistance genes. It has been previously observed that disease resistance genes in plants commonly encode nucleotide binding site leucine-rich repeat proteins (NBS-LRR) therefore the matched sequences are strong candidates for stripe rust resistance  (McHale et al.
The single peak in Figure  3  separates into smaller peaks in Figure  4 (a), which is likely to be due to inaccuracies in contig order at a local level. We also scanned the peak interval between 13 650 001 and 14 150 001 bp on pseudo-chromosome 7 for candidate homozygous or borderline SNPs. A list of 145 SNPs was identified that were highly homozygous across the pool and conserved between the bulk segregant dataset and the Cadenza parent (Figure  4b  and Table  S3 ). In total, 51 of these homozygous SNPs are located within the peaks shown in Figure  4 (a) and have disease-resistance functions (highlighted in Figure  4b  and detailed in Table  1 ). The SNPs detailed in Table  1  were defined as synonymous/non-synonymous whenever possible. Their surrounding sequence (AE500 bp) was used in a BLASTX alignment of the translated nucleotide query to the BLAST nr protein database  (Altschul et al.
Therefore the order of the capture design contigs along genome B's chromosomal pseudomolecules 1-7 was preferentially utilized as the greatest number of contigs could be aligned to these sequences. This POPSEQ pseudo-genome contained 116 220 of the 169 345 capture design contigs; 2415 less than the previous Genome Zipper-based design though 970 more than our previously published assembly  (Gardiner et al. , 2014). POPSEQ genetic positions are available for the IWGSC CSS contigs that aided their assembly into chromosomal pseudomolecules. Here, 6043 of these IWGSC CSS contigs also had Genome Zipper assigned genetic positions and these positions are compared in Figure  5. Figure  5  shows, as anticipated, a positive correlation for contig genetic positions between the Genome Zipper and POPSEQ datasets that is conserved across the seven chromosomes.
Mapping-by-sequencing of the Yr6 locus using POPSEQderived pseudo-chromosome reference sequences The mapping-by-sequencing analysis of the Yr6 locus was repeated using the re-designed POPSEQ-based pseudochromosome reference sequence. The same parameters for the mapping and SNP calling pipeline were used as in the previous analysis. Across the three sequencing datasets (Avalon, Cadenza and the bulk), coverage was highly conserved with on average 98% of the reference sequence being mapped to uniquely after removal of duplicate reads. An average depth of coverage of 459 was seen in the parental lines and 609 in the P1 bulk (Table  S1 ). We identified 37 322 Avalon-specific and 58 868 Cadenza-specific homozygous SNPs. Of the homoeologous homozygote SNPs that were specific to the Avalon parent, 23 767 of the SNP alleles were conserved in the bulk segregant dataset regardless of homozygous or heterozygous status.
Similarly, of the homozygote SNPs that were specific to the Cadenza parent, 29 608 of these were found in the bulk segregant dataset. These SNPs were categorized as homozygous, heterozygous or borderline according to the hexaploid-specific thresholds used previously and the scoring algorithm was implemented to calculate a homozygote score per 500 000 bp window along each pseudo-chromosome at 10 000 bp intervals (Figure  S3 ). Using our POPSEQ-based pseudo-chromosome reference we observed a single peak near the end of pseudo-chromosome 7 in Cadenza but not in Avalon at 7 650 001-8 150 001 bp (500 Kbp of genic sequence) (Figure  S3 ). Using the BLAST alignment of the contigs to the POPSEQ pseudomolecules that was used for ordering, the interval could be translated to ~239 000 001-245 000  Using the POPSEQ-derived pseudo-genome, the defined region on chromosome 7 overlaps the Genome Zipperbased result The defined interval using the POPSEQ-based pseudo-genome  (148.
We also analyzed this peak interval using a BLASTN alignment (minimum E-value of 1e-5) to the BLAST nr nucleotide database with a focus on the identification of potential disease resistance genes  (Altschul et al. , 1990). Homologous genes identified within the peak interval included three disease resistance associated genes (Table  S4 ): the first at 7 885 679-7 887 186 bp associating with putative disease resistance; the second at 7 936 847-7 938 817 bp also associating with putative disease resistance; and finally at 8 040 733-8 043, 356 bp associating with a NBS-LRR protein. Two of these disease-resistance-associated gene regions fall in the immediate vicinity of the main peak that can be seen in Figure  4 (c), allowing us to focus on these smaller candidate intervals amounting to around 6 Kbp.
We also scanned the peak interval for candidate homozygous or borderline SNPs. A list of 239 SNPs was identified that were highly homozygous across the pool and conserved between the bulk segregant dataset and the Cadenza parent (267 identified in total, 28 conserved with previous list in Table  S2  and 68 across chromosome 7) (Figure  4d  and Table  S5 ). 18 of these homozygous SNPs were associated with the gene regions that showed disease resistance functions (highlighted in Figure  4d  and detailed in Table  2 ). These SNPs were defined as synonymous/non-synonymous where possible as per previous methodologies, resulting in seven SNPs that were predicted as non-synonymous. Genomes of origin were predicted for the SNPs using previous methodologies; 94. 4% of SNPs were associated with genome B and 5.
6% were associated with genome D. The 18 candidate SNP locations that were defined using the POPSEQ-based pseudo-chromosomes (Table  2 ) were associated with 11. 7 cM on pseudo-chromosome 1 in the Genome Zipper pseudo-genome and as such had not been previously considered as candidates. Furthermore, of the 51 candidate SNPs that were identified using the Genome Zipper pseudo-genome (Table  1 ) 98% were in contigs that were not included in the POPSEQ pseudo-chromosome 7, and the remaining 2% overlapped within 3 Kbp of the 7 650 001-8 150 001 bp interval. This again highlights the complementarity of these approaches for association of SNPs with the interval. Finally, we scanned the peak interval between 13 650 001 and 14 150 001 bp on the Genome Zipper pseudo-chromosome and the interval between 7 650 001 and 8 150 001 bp on the POPSEQ-based pseudo-chromosome for candidate homozygous or borderline SNPs that were conserved between the bulk segregant dataset and the Avalon parent.
Therefore the current POPSEQ wheat chromosomal pseudomolecules provide a likely adequate reference for mapping-by-sequencing analyses  (Chapman et al. , 2015). As such, the mapping-by-sequencing analysis of the Yr6 locus was repeated using these chromosomal pseudomolecules directly as a mapping reference to validate our previous analyses using the pseudo-chromosomes. In this analysis the same parameters for mapping were used as in the previous analyses. For the sequencing datasets Avalon, Cadenza and P1 29, 27 and 41% of the reference sequence respectively was mapped to uniquely after removal of duplicate reads. Coverage is seen to extend beyond the 110 Mb capture space due to the use of paired end sequencing reads and the presence of off target carryover sequence. An average depth of coverage of 59 was seen in the parental lines and 69 in the bulk (Table  S1 ).
This, as anticipated demonstrates a marked decrease in depth of coverage compared to the pseudo-chromosomes due to the inclusion of low coverage off target sequence data, the separation of the sub-genomes and additional mapping losses from non-uniquely mapped reads. As such, SNPs were called as previously but with a minimum depth of 10 for the parental lines and 20 in the P1 dataset. We identified 211 307 Avalon and 237 577 Cadenza specific homozygous SNPs. Of the homoeologous homozygote SNPs that were specific to the Avalon parent, 147 756 of the SNP alleles were conserved in the bulk segregant dataset regardless of homozygous or heterozygous status. Similarly of the homozygote that were specific to the Cadenza parent, 143 462 of these were found in the bulk segregant dataset. The sub-genome discrimination in the wheat reference sequence renders hexaploid wheat effectively as a diploid genome, therefore these SNPs were categorized as homozygous, heterozygous or borderline according to the diploid-specific thresholds used in our previous study i.
DISCUSSION We have studied a yellow rust resistant bulk segregant doubled haploid population that was developed from an F1 cross of parental purebred hexaploid wheat lines. We have performed target enrichment for genic regions and, using mapping-by-synteny, identified a genic region of 500 Kbp and further narrowed this down to ~60 Kbp on chromosome 7B that is likely to be linked to the Yr6 stripe rust resistance locus. It has been noted previously that, at a minimum of 159 coverage, larger pools of ~200 plants generated interval Table  2  Detailing candidate homozygous SNP alleles for stripe rust resistance (defined using a POPSEQ-based pseudo-genome). Homoeologous homozygous SNPs found in 23-43% of reads in the bulk segregant dataset that are within the peak interval (7 650 001 and 8 150 001 bp) and that could be associated with known disease resistance genes.
, 2014)  and applied them to polyploid wheat using a unique homozygote-scoring algorithm that highlights longer homozygous haplotypes shared between the mutant parental line and the bulk segregant mutant dataset. This algorithm was implemented to identify and associate SNPs with the Yr6 locus that is thought to cause stripe rust resistance. The current pipeline is available as a workflow for public use within the iPlant collaborative web portal (see Experimental procedures and Figure  S5  for sample output) (The iPlant Collaborative, 2011). Simple adjustment of the definitions of a homozygous, heterozygous and borderline SNP within the analysis will allow it to be easily adaptable to other polyploid species, particularly those with closely related genomes. Application of this methodology to bread wheat demonstrates a rapid method to identify markers and potentially genes underlying key phenotypic traits.
EXPERIMENTAL PROCEDURES Phenotyping of the Avalon 3 Cadenza doubled haploid population for reaction to an AVRYr6 YR isolate The wheat yellow rust isolate '07/03' is referred to by  (Ma et al. , 2015)  as '03/07' and also referred to in the literature as the 'Brock' isolate. This isolate was obtained from the UK Cereal Pathogen Virulence Survey collection at NIAB (Cambridge) and was used in a replicated inoculated seedling test of Avalon (susceptible to '07/ 03') and Cadenza (resistant to '07/03') parental lines and 201 doubled haploid progeny. Rust symptoms were scored 14 days after inoculation on the 0-9 scale described by  McNeal et al. (1971)  in which a score of 3 or less is considered highly resistant. Sequence capture and sequencing protocol for the Avalon, Cadenza and bulk segregant datasets Genomic DNA was extracted from parental cultivars Avalon and Cadenza along with the bulk segregant sample using the Qiagen DNeasy plant mini kit; 2 lg of genomic DNA for each sample, in a total volume of 130 ll, was sheared for 3 9 60 sec using a Covaris S2 focused ultrasonicator (duty cycle 10%, intensity 5, 200 cycles per burst using frequency sweeping).