dataesr/scientific-paragraphs-categorization huggingface dataset:
Mass spectrometry detection was performed using a micrOTOF-Q (Bruker Daltonics, Bremen, Germany). The mass spectrometer was equipped with an electrospray ionization probe operated in positive mode. Spray voltage was 4. 5 kV. Mass range was 70-1500 Th and acquisition rate was 1 spectrum 2 s À1. MS spectra were calibrated using a 10 lM lithium formiate solution. Comparing retention time, accurate mass and fragments with the commercial drug standard identified PSN2 and PSN11. Elemental formulas were calculated using the generate molecular formula module of the Data Analysis software (Bruker Daltonics). Extracted ion chromatograms at 400 O5-{[3-(2-chlorophenyl)-5-methylisoxazol-4-yl]carbonyl} -1,3-benzodioxole-5-carbohydroximamide PSN2 Maybridge SPB0273 C 16 H 13 ClN 4 O 3 S 377 O4-{[3-(2-chlorophenyl)-5-methylisoxazol-4-yl]carbonyl}-2-methyl-1, 3-thiazole-4-carbohydroximamide PSN3 Maybridge CD03092 C 16 H 16 ClN 3 O 3 334 2-[({[3-(2-chlorophenyl)-5-methyl-4-isoxazolyl]carbonyl}oxy)imino]piperidine PSN4 Maybridge CD02622 C 15 H 10 Cl 2 N 2 O 4 353 O5-(3,4-dichlorobenzoyl)-1,3-benzodioxole-5-carbohydroximamide PSN5 Maybridge CD02598 C 8 H 8 N 2 O 3 180 N 0 -hydroxy-1,3-benzodioxole-5-carboximidamide PSN6 Maybridge SEW05933 C 13 H 12 ClN 3 O 3 294 4-chloro-N 0 -{[(3,5-dimethylisoxazol-4-yl)carbonyl]oxy}benzenecarboximidamide PSN7 Maybridge SPB02369 C 18 H 13 Cl 2 N 3 O 3 390 O1-{[5-(4-chlorophenyl)-3-methylisoxazol-4-yl]carbonyl}-4-chlorobenzene- 1-carbohydroximamide PSN8 Chembridge # 7991375 C 18 H 14 ClN 3 O 3 356 N 0 -({[3-(2-chlorophenyl)-5-methyl-4-isoxazolyl]carbonyl}oxy) benzenecarboximidamide PSN9 Chembridge # 5919370 C 18 H 13 ClN 2 O 4 357 N-1,3-benzodioxol-5-yl-3-(2-chlorophenyl)-5-methyl-4-isoxazolecarboxamide PSN10 Chembridge # 7984462 C 19 H 14 ClNO 5 372 1,3-benzodioxol-5-ylmethyl 3-(2-chlorophenyl)-5-methyl-4-isoxazolecarboxylate PSN11 Maybridge SB01885 C 11 H 8 ClNO 3 238 3-(2-chlorophenyl)-5-methylisoxazole-4-carboxylic acid Table  2  List of the forward and reverse primers (5 0 to 3 0 ) Gene AGI F R Arabidopsis ACP5 AT3G17790 TTTGACATAAGAGTTGCGAGATG GTGAGCTTCAGAGATTTATAGAGCC AMT1.
taking care of the plants; E. and C. Girard-Smith for their advice regarding the chemical properties of the PSN-like compounds. H. Javot, E. Marin, B. P eret, M-C. Thibaud and anonymous referees for their comments on a first version of the manuscript. Support was provided by the H elioBiotec platform, funded by the European Regional Development Fund, the R egion Provence-Alpes-Côte-d'Azur, the French Ministry of Research, and the Commissariat a l'Energie Atomique et aux Energies Alternatives. Financial support: CEA-IRTELIS PhD grant, ANR-09-BLAN-0118, ANR-08 KBBE-041451.
Acknowledgements We thank  S. Cutler  for providing the LATCA library;  Y. Poirier  ( PHO1-B1 );  R. Paz-Ares  (pPHF1::GUS, pACP5::GUS, pIPS1:: GUS),  F. Gaymard  (phr1-3;phl1-2),  G. C. MacIntosh  (pRNS1: GUS),  P. Wu  (pSPX1::GUS & pSPX3::GUS),  L. Herrera-Estrella  (pPLDf2::GUS),  H. Ohta  (pMGD3::GUS),  P. J. White  (pSQD1:: GUS),  J. Rothstein  (pSTP13::GUS),  F. Cellier  (pCHX17::GUS); the  Groupe de Recherches Appliqu ees en Phytotechnologie  for.
Statistical analysis Data were expressed as mean ± SEM. Tests were performed in triplicate and each experiment was independently repeated at least three times. One-way and two-way analyses of variance were performed with Bonferroni correction for multiple comparisons. Statistical significance was chosen at 0. 05 with p<0. 05 ( Ã ), p<0. 01 ( ÃÃ ), and p<0. 001 ( ÃÃÃ ). Statistics and graphics were generated using PRISM GraphPad 5. 0. (GraphPad Software, San Diego).
Acknowledgments Particular thanks to PhD student  Kristaq Gazeli  for the spectroscopic analyses of GIWs,  Dr Paul Monsarrat  for its helps in statistical analysis, and  Dr Toufic Renno  for critical reading of the manuscript. This work was funded by the  ANR (Agence Nationale de la Recherche) ,  PLASMINF  ( SVSE5 ) and  PLASMAVIV  ( ANR-10-BLAN-0950 ) projects.
The  French National Research Agency   1 -PLASMAVIV ANR-10-BLAN-0950  http://www. agencenationale-recherche. fr/en/anr-funded-project/?tx_ lwmsuivibilan_pi2%5BCODE%5D=ANR-10-BLAN-0950 Understanding of the interaction mechanisms between plasma produced atomic nitrogen and living matter FC UPPA-IPREM :  LCABIE UNIVERSITE DE PAU ET DES PAYS DE L'ADOUR 2-PLASMINF ANR-12-BSV5-0006  http://www. agence-nationalerecherche. fr/en/anr-funded-project/?tx_lwmsuivibilan_  pi2%5BCODE%5D=ANR-12-BSV5-0006 Plasma  gas.
Chromosome arm sequencing, assembly and validation MDA-amplified DNA (500 ng) was used to prepare single end (SE) and 3-kb long mate pair (LMP) libraries using the GS FLX DNA library preparation kit, following the manufacturer's instructions (Roche Diagnostics). Libraries were sequenced across four and two full runs, respectively, using the Genome Sequencer FLX Instrument (Roche Applied Science, Penzberg, Germany) at Indear (CONICET, Rosario, Argentina). De novo assembly was performed using the software Newbler 2. 6 with default parameters. While other assembly software (including Mira, ABySS and WGS) were tested and analyzed, this dataset worked better with Newbler, as expected. The contig construction step was executed in single processor mode to avoid any possible problem created by the processing subdivision on low coverage sequencing.
LMP reads were included in the contig step as single end reads to increase the coverage, obtaining a better representation of the chromosome content. Scaffolding was executed using Newbler 2. 6 with default parameters. Chromosome arm coverage was assessed using the Kmer Analysis Toolkit (KAT) (http://www. tgac. ac. uk/kat) by counting k-mer occurrence considering an index of 20-mer sized words representing the primer sequence of high confidence insertion site-based polymorphism (ISBP) markers, which represent unique single loci in the genome, thus revealing the underlying sampling distribution for unique motifs. ISBPs were designed using the ISBP Finder script  [24]  on preliminary SE contigs (data not shown). In order to validate the LMP library efficiency, the read distance in the LMP was assessed by mapping paired reads against the SE contigs using the software Bowtie under default parameters  [25].
Chromosome completeness was assessed by measuring the representation of wheat 4D chromosome bin-mapped ESTs  [26] , on both, assemblies and raw data using NUCmer  [27]  and kmer mapping approaches. On the other hand, chromosome 4D scaffolds and contigs were compared against the Ae. tauschii survey sequence genome and physical map, including SSR and SNP genetic maps  [16, 19]. Sequence comparisons were performed using the Mummer3 software package  [27]  with the following parameters: maxmatch -l 50 -g 50 -c 500. The datasets used in these comparisons are detailed in Table  S1. Supplementary Table  S1  related to this article can be found, in the online version, at http://dx. doi. org/10. 1016/j. plantsci. 2014. 12. 004.
Gene prediction and annotation The annotation of protein-coding genes with evidence-based quality indexing, and the identification of conserved non-coding sequences were performed using the structural and functional automatic annotation pipeline TriAnnot  [28]. Given that the concept of the pipeline is the identification of full-length genes, only scaffolds of 6 kb or more were used to identify gene models. In silico gene predictions were combined with searches based on similarity using the algorithm BLAST  [29]  against full-length cDNAs, unigenes, and ESTs from Triticeae and other members of the Poaceae family, and the rice (Oryza sativa) proteome. Repeats and transposable elements were identified in wheat specific repeat databases, as described by Leroy et al. [28]. The gene models obtained from Tri-Annot were classified into three categories: (1) high-confidence genes: full-length genes with well-established start and stop codons as well as exon-intron junction boundaries supported by biological evidences; (2) low-confidence genes: full-length genes in which start/stop codons and/or exon-intron junction boundaries are not well established; (3) putative pseudo-genes: predicted genes that would encode a sequence corresponding to <70% of a known protein.
The gene models predicted by the TriAnnot pipeline were functionally annotated as follows: BLASTX (e-value cut off ≤10e-10) searches were performed against the NCBI Viridiplantae protein database first. Then, the sequences with no hits were used to perform a BLASTX search against the NCBI nr protein database in order to make an assessment of the putative identities of the sequences. Annotation and mapping were done using the software BLAST2GO  [30] , which assigns Gene Ontology terms  [31]  (http://www. geneontology. org). GO annotation was completed by running the full suite of InterProScan under default parameters  [32]. InterProScan combines different protein signature recognition methods native to the InterPro member databases into one resource that searches for the corresponding InterPro and GO annotations.
Construction of a syntenic build based on gene order in brachypodium, rice and sorghum The GenomeZipper workflow  [34]  was applied with some adjustments. The comparison and integration of the 4DS and 4DL contigs into a linear reference gene order was achieved by exploiting the synteny with Brachypodium distachyon (Bd), Oryza sativa (Os) (rice), and Sorghum bicolor (Sb) (sorghum) sequenced genomes. Repetitive DNA was identified using Vmatch (http://www. vmatch. de) against the MIPS-REdatPoaceae v9 repeat library. The MIPS repeat library contains known grass transposons from the Triticeae Repeat Database, as well as de novo detected LTR retrotransposon sequences from several grass species. Vmatch was run with the following parameters: 70% identity cut-off, 100 base pairs minimal length, seed length 14, exdrop 5 and e-value 0.
001 and each identified repeat was masked by "N's". Only sequences with a minimum of 100 base pairs non-masked nucleotides were considered for the subsequent steps. All the repeat-free 454 contigs from 4DS and 4DL were compared to Brachypodium, rice and sorghum proteins using BLASTX. As stringent filtering criteria (a) only the first best hit with, (b) a minimal alignment length of 30 amino acids and (c) a minimal sequence identity of 75% (Brachypodium)/70% (rice, sorghum) was used in each case. In-house software called ChromoWIZ was used to calculate the degree of synteny between the above-mentioned datasets. ChromoWIZ is based on a sliding window approach. For each genetic position (window 0. 5 Mb, window shift 0. 1 Mb) the number of conserved genes was calculated and heat maps were constructed.
Setting the virtual gene order A genetic map of T. aestivum chromosome 4D based on SNPs  [35] , was used as a backbone to order and position the contigs along with wheat ESTs from the HarvEST database (http://harvest. ucr. edu), wheat full-length cDNAs from NCBI and TriFLDB  [36]  (http://trifldb. psc. riken. jp/v3/download. pl) and 822 4D wheat gene models predicted by the TriAnnot pipeline (this study). The orthologous genes were anchored to the backbone via bi-directional BLAST hits. The genes that gave positive matches but were not associated to any "marker" were located according to their position in the corresponding reference genome. The virtual gene order established using GenomeZipper was compared with the scaffold order obtained using Ae. tauschii genetic maps  [16]. All comparisons were visualized using the software Circos  [37]  (http://www.
Rates of coding sequence evolution The gene models predicted by the TriAnnot pipeline were used to create a set of orthologs using the orthoMCL software version 2. 0. 9  [38]  under default parameters. We compared wheat 4D predicted proteins, B. distachyon and Ae. tauschii proteomes as follows: the protein sets were pairwise aligned using ClustalW2 program version 2. 1  [39]  and the CDSs were translated and aligned using tranalign tool from the EMBOSS package version 6. 3. 1  [40]  to generate alignments of nucleic sequences from aligned proteins. Alignments consisting of more than 20% gaps were removed. To estimate the rate of coding sequence evolution, the non-synonymous to synonymous substitution ratios (dN/dS ratio) were calculated for all possible comparisons using the method of Yang and Nielsen  [41]  as implemented in the PAML package (estimating dN/dS ratios).
S5 ). Supplementary Fig. S5  related to this article can be found, in the online version, at http://dx. doi. org/10. 1016/j. plantsci. 2014. 12. 004. Wheat chromosome 4D arm scaffold assemblies were contrasted against Ae. tauschii genome datasets  [16, 19] , as a complementary strategy for assessing chromosome completeness under the assumption that these are related genomes with a high level of sequences conservation. Due to the high amount of repetitive elements in wheat/Ae. tauschii sequence comparisons, the likelihood of misleading results was minimized by using the Mummer software  [43]  with a conservative approach defined by self-comparison of the 4D scaffold sequences (Fig. S6 ). In this way, 4D scaffolds were observed as non-repetitive and therefore redundant matches were avoided. Using this approach, the 65 Mb wheat 4D assembly was aligned to: (1) 180 Mb Ae.
tauschii chromosome anchored scaffolds  [16] ; and (2) ∼7 Mb Ae. tauschii chromosome Several of these sequences probably belong to chromosome 4 but could not be assigned to a particular chromosome in the whole genome sequencing approach followed previously by Jia et al. [16]. The remaining 108 scaffolds (1%) showed similarity to bacterial genes or unknown sequences, as revealed by BLASTN searches against nucleotide databases. These could come from organelle DNA or simply contamination and were excluded from the 4D sequences. Supplementary Fig. S6  related to this article can be found, in the online version, at http://dx. doi. org/10. 1016/j. plantsci. 2014. 12. 004.
aestivum as a marker backbone  [35]. All syntenic genes associated with SNP markers (based on the best bidirectional BLAST hit) were anchored to the backbone and additionally tagged genes without marker associations were ordered following the concept of synteny and closest evolutionary distance. The 4DS and 4DL GenomeZipper-based tentative gene order including associated information is provided as a Supplemental Excel file (Table  S3 ). Supplementary Table  S3  related to this article can be found, in the online version, at http://dx. doi. org/10. 1016/j. plantsci. 2014. 12. 004. Wheat ESTs obtained from the HarvEST database (http://harvest. ucr. edu) wheat full-length cDNA orthologs to Bd, Os and Sb, and gene models predicted by TriAnnot (270 (45. 4%) for 4DS and 111 (48. 9%) for 4DL) were also integrated on the virtually ordered linear map.
fcu-4D  [17, 62, 63, 66, 67] , and (iv) quality-related genes -Lpx1  [68, 69]. Recent major advances in gene discovery and building of a highly saturated genetic map were achieved by Ae. tauschii genome survey sequencing  [16]. In that study 30,697 protein coding genes were uniquely anchored to chromosomes with an integrated high density map including 2915 genes tagged at chromosome 4 obtained from 2568 scaffolds covering 180 Mb. Additionally, Luo et al. [19]  reported an Ae. tauschii genome physical map spanning 520 Mb of chromosome 4 defined by 267 anchored contigs carrying 799 markers. The availability of comprehensive genomic datasets for Ae. tauschii chromosome 4 provides an excellent opportunity to thoroughly validate scaffolds/contigs belonging to T. aestivum chromosome 4D obtained by flow cytometry sorting.
These genes were similarly distributed between both chromosome arms, with slightly more orthologous genes identified on 4DL. Noticeably, the proportion of orthologous genes that were supported by the three reference genomes was near 50% for 4DL and 25% for 4DS, suggesting that chromosome 4DS could have been more affected than 4DL by evolutionary changes. A linear gene order model for the entire wheat chromosome 4D was further constructed including wheat full length cDNA orthologous to Bd, Os and Sb, the public SNP map from T. aestivum, the wheat ESTs obtained from the HarvEST database (http://harvest. ucr. edu) and the gene models predicted by the TriAnnot pipeline resulting in 902 and 1092 loci for 4DS and 4DL, respectively, that could be virtually mapped. Thus, the gene maps of 4DS and 4DL were combined into one non-redundant map leading to a complete chromosome length of 98.
Rates of coding sequence evolution We assessed the dN/dS rates for pairwise comparison of 136 orthologous genes (the set of 4D TriAnnot gene models), considering bread wheat (W) -Brachypodium (B) -Ae. tauschii (T) to identify genes with evidence of positive selection (dN/dS >v1)  [41]  and found 94-95% of BW and BT pairwise comparisons with less than 0. 5 values (averages = 0. 219 and 0. 218, respectively). These data are in agreement with dN/dS values obtained from pairwise comparisons of 1022 orthologous sets of genes from chromosome 3A syntenic genes considering bread wheat, Brachypodium and rice (averages BW = 0. 24, RW = 0. 17, BR = 0. 17)  [79]. In contrast to previous data, WT gene pairs showed higher average (0. 388) and a binomial distribution for the dN/dS ratios, with one peak at 0.
Conclusions Here we provide valuable information of wheat 4D chromosome obtained by pyrosequencing of both flow-sorted and multiple displacement amplified chromosome arms, available at NCBI (JROL00000000). A combination of different approaches using GenomeZipper, TriAnnot and EST bin maps allowed the prediction of 5649 genes on Chinese Spring 4D chromosome, comprising 2190 genes on 4DS and 3459 on 4DL. Comparison with other members of the wheat homeologous group 4 (4A and 4B) obtained from the IWGSC gave us an insight about the structure of this group of wheat chromosomes. The comparison showed higher level of collinearity between 4D and 4B compared to 4A, and confirmed that 4A underwent a pericentric inversion during bread wheat evolution. The resulting gene order data may become a valuable marker source for mapping, positional gene cloning and physical map anchoring, especially in cases where traditional mapping suffers from a lack of polymorphism for marker development, being an excellent tool for plant breeding programs.
Acknowledgements We thank  Dr. Bikram Gill  ( Department of Plant Pathology, Kansas State University, Manhattan, USA ) for seeds of double ditelosomic line 4D of bread wheat cv. Chinese Spring. We are grateful to our colleagues  Marie Kubaláková ,  Jarmila Číhalíková ,  Romana Šperková  and  Zde ňka Dubská  for assistance with chromosome sorting and DNA amplification. We also want to thank the  International Wheat Genome Sequencing Consortium  for generating the wheat chromosomes 4A and 4B survey sequences and making them available for the analysis in advance of publication. This work was supported by the following Argentinean Institutions:  CONICET  ( International Cooperation Grant Res. D456  ( 10/2/2011 )),  ANPCyT  ( Préstamo BID 2012 ,  PICT 0660 ),  INTA  ( Res. 418/2012 ,  AEBIO 245001.
Different search channels are used in order to cover a broad parameter space: the events are selected by different requirements on the transverse momentum (p T ) of the leptons, either using low-p T leptons (referred to as the "soft" lepton selection), or high-p T leptons (referred to as the "hard" lepton selection). Each of these categories is further subdivided into a single-lepton and a dilepton search channel. The soft-lepton and hard-lepton channels are complementary, being more sensitive to supersymmetric spectra with small or large mass splittings, respectively, while the different lepton multiplicities cover different production and decay modes. To enhance the sensitivity to gluino or squark production, high and low jet multiplicity signal regions are defined. Previous searches in these final states have been conducted by the ATLAS  [22, 23]  and CMS  [24]  collaborations using their full 2011 dataset at a centre-of-mass energy of 7 TeV.
In this paper, the analysis is performed on the full 2012 ATLAS dataset at a centre-of-mass energy of 8 TeV, corresponding to an integrated luminosity of up to 20. 3 fb -1. All signal regions defined in this search are optimised for this dataset. The paper is organised as follows. After a brief description of the ATLAS detector in section 2, the simulation of the background and signal processes used in the analysis is detailed in section 3. Section 4 discusses the trigger strategy and the dataset used, while the object reconstruction and the event selection are addressed in sections 5 and 6. The background estimation and the systematic uncertainties are discussed in sections 7 and 8. The fitting procedure used is described in section 9 and the results are presented in section 10. Finally, section 11 presents the conclusions.
Signal event samples The signal models considered cover simplified  [26, 27]  and phenomenological SUSY models, as well as a minimal Universal Extra Dimension (mUED) scenario  [28, 29]. Some of these models were also probed by other ATLAS searches based on the 8 TeV pp dataset, using different final-state selections  [30] [31] [32] [33] [34]. The simplified models studied here include the pair production of gluinos or first-and second-generation squarks with different hypotheses for their decay chains, as well as gluino-mediated top squark pair production. In these models, the LSP is always the lightest neutralino. The phenomenological models include scenarios for minimal super-gravity-mediated SUSY breaking (mSUGRA/CMSSM)  [35] [36] [37] [38] [39] [40] , bilinear R-parity violation (bRPV)  [41] , natural gauge mediation (nGM)  [42]  and a non-universal Higgs-boson mass with gaugino mediation (NUHMG)  [43].
3 For each signal region, the results are also shown split by lepton flavour to allow for comparison with new models which could favour a specific lepton flavour. In this table the value of CL B , the confidence level observed for the background-only hypothesis, and the one-sided discovery p-value, p(s = 0), are also given; the latter represents, for each signal region, the probability that the event yield obtained in a single hypothetical background-only experiment (signal s = 0) is greater than that observed in this dataset. CL B and p(s = 0) are obtained using different test statistic definitions: the former has a conditional likelihood calculated with a signal strength µ set to 1, while the latter uses µ = 0. For an observed number of events lower than expected, the discovery p-value is truncated at 0.
Acknowledgments We thank  CERN  for the very successful operation of the LHC, as well as the support staff from our institutions without whom ATLAS could not be operated efficiently. We acknowledge the support of  ANPCyT , Argentina; YerPhI, Armenia;  ARC, Australia ;  BMWFW  and  FWF , Austria; ANAS, Azerbaijan; SSTC, Belarus;  CNPq  and  FAPESP, Brazil ;  NSERC ,  NRC  and  CFI ,  Canada ; CERN; CONICYT, Chile; CAS,  MOST  and  NSFC , China; COLCIENCIAS, Colombia; MSMT CR, MPO CR and VSC CR, Czech Republic; DNRF,  DNSRC  and  Lundbeck Foundation , Denmark; EPLANET,  ERC  and  NSRF ,  European Union ;  IN2P3-CNRS ,  CEA-DSM/IRFU , France; GNSF, Georgia; BMBF,  DFG ,  HGF ,  MPG  and  AvH Foundation, Germany ;  GSRT  and  NSRF, Greece ;  RGC, Hong Kong SAR, China ;  ISF, MINERVA, GIF, I-CORE and Benoziyo Center, Israel ;  INFN, Italy ;  MEXT  and  JSPS, Japan ; CNRST, Morocco; FOM and  NWO, Netherlands ;  BRF  and  RCN, Norway ;  MNiSW  and  NCN , Poland; GRICES and FCT, Portugal; MNE/IFA, Romania;  MES of Russia  and  NRC KI , Russian Federation; JINR; MSTD, Serbia; MSSR, Slovakia; ARRS and MIZŠ, Slovenia; DST/NRF, South Africa; MINECO, Spain;  SRC and Wallenberg Foundation, Sweden ;  SER ,  SNSF  and  Cantons of Bern and Geneva, Switzerland ;  NSC, Taiwan ;  TAEK, Turkey ;  STFC , the  Royal Society and Leverhulme Trust ,  United Kingdom ;  DOE  and  NSF ,  United States of America.