dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical procedure The inputs to the likelihood fits are the m bb distributions (not transformed) in the 28 p V T intervals of the 2-tag signal regions. Additional inputs are the event yields in the five p V T intervals of the 2-tag e-µ control region and the 26 p V T intervals of the 1-tag control regions. For the tt background, a single floating normalisation is determined by the global fit, instead of one in each of the 0-, 1-, and 2-lepton channels. In addition to the other floating normalisations mentioned for the 8 TeV data analysis, the MJ background normalisation is also left freely floating in all regions of the 1-lepton channel, except in the 2-tag 3-jet regions where the statistical power of the data is not sufficient to provide a reliable constraint. In these regions, an uncertainty of 30% is assigned to the MJ background normalisation, using a method similar to what is done for the analysis of the 8 TeV data.
Nominal results The nominal results are obtained from global fits using the MVA for the 8 TeV data and the dijet-mass analysis of the 7 TeV data. Distributions of the BDT V H discriminant and of M V 1c, with background normalisations and nuisance parameters adjusted by the global fit to the 8 TeV data were already presented in section 7. 4. Dijet-mass distributions in the 7 TeV data analysis were shown in section 10. Agreement between data and estimated background is observed within the uncertainties shown by the hatched bands. Figure  19  shows the 95% CL upper limits on the cross section times branching ratio for pp → (W/Z)(H → bb) in the Higgs boson mass range 110-140 GeV. The observed limit for m H = 125 GeV is 1. 2 times the SM value, to be compared to an expected limit, in the absence of signal, of 0.
8. For the 8 TeV (7 TeV) data only, the observed and expected limits are 1. 4 (2. 3) and 0. 8 (3. 2), respectively. The probability p 0 of obtaining from background alone a result at least as signallike as the observation is 8% for a tested Higgs boson mass of 125 GeV; in the presence of a Higgs boson with that mass and the SM signal strength, the expected p 0 value is 0. 5%. This corresponds to an excess observed with a significance of 1. 4σ, to be compared to an expectation of 2. 6σ. For the 8 TeV data alone, the observed and expected levels of significance are 1. 7σ and 2. 5σ, respectively. For the 7 TeV data alone, the expected significance is 0. 7σ and there is a deficit rather than an excess in the data, as can be seen in figure  18. Figure  20  shows the p 0 values in the mass range 110-140 GeV, as obtained for the 7 TeV and 8 TeV combined dataset.
The fitted µ values for m H = 125 GeV are shown in figure  21  for the 7 TeV, 8 TeV and combined datasets. With all lepton channels and data-taking periods combined, the fitted value of the signal-strength parameter is 11 µ = 0. 51±0. 31(stat. )±0. 24(syst. ). For the 8 TeV data, the fitted value of the signal-strength parameter is µ = 0. 65 ± 0. 32(stat. ) ± 0. 26(syst. ). For the 7 TeV data, it is µ = -1. 6 ± 1. 2(stat. ) ± 0. 9(syst. ). For a Higgs boson with a mass of 125. 36 GeV, as measured by ATLAS  [98] , the signalstrength parameter is µ = 0. 52 ± 0. 32(stat. ) ± 0. 24(syst. ). Fits are also performed where the signal strengths are floated independently for (i) the W H and ZH production processes, or (ii) the three lepton channels. The results of these fits are shown in figures 22 and 23 respectively.
The consistency of the fitted signal strengths in the W H and ZH processes is at the level of 20%. For the lepton channels, the consistency between the three fitted signal strengths is at the level of 72% for the 7 TeV data, and of 8% for the 8 TeV data. The low values of the fitted signal strengths for the ZH process and in the 0-lepton channel are associated with the data deficit observed in the most sensitive bins of the BDT V H discriminant in the 0-lepton channel, shown in figure  12(a). Observed (solid) and expected 95% CL cross-section upper limits, normalised to the SM Higgs boson production cross section, as a function of m H for all channels and data-taking periods combined, as obtained using the dijet-mass analysis for the 7 TeV dataset and BDTs trained at each individual mass for the 8 TeV dataset.
The expected upper limit is given for the backgroundonly hypothesis (dashed) and with the injection of a SM Higgs boson signal at a mass of 125 GeV (dotted). The dark and light shaded bands represent the 1σ and 2σ ranges of the expectation in the absence of a signal. For all curves shown, the results obtained at the tested masses are linearly interpolated. Figure  24  shows the data, background and signal yields, where the final-discriminant bins in all signal regions are combined into bins of log(S/B), separately for the 7 and 8 TeV datasets. Here, S is the expected signal yield and B is the fitted background yield. Details of the fitted values of the signal and of the various background components are provided in table  8.
Cross-check with the dijet-mass analysis The distributions of m bb in the dijet-mass analysis, with background normalisations and nuisance parameters adjusted by the global fit to the 8 TeV data were already presented in section 7. 3. Agreement between data and estimated background is observed within the uncertainties shown by the hatched bands. In the dijet-mass analysis, a µ value of 1. 23 ± 0. 44(stat. ) ± 0. 41(syst. ) is obtained for the 8 TeV dataset. The consistency of the results of the three lepton channels is at the level of 8%. Using the "bootstrap" method mentioned in section 9. 2, the results for the 8 TeV data with the dijet-mass analysis and with the MVA are expected to be 67% correlated, and the observed results are found to be statistically consistent at the level of 8%. The observed significance in the dijet-mass analysis is 2.
Cross-check with the diboson analysis To validate the analysis procedures, V Z fits are performed, the technical details of which were discussed in section 9. 3. The measured signal strength for the 8 TeV dataset with the MVA is µ V Z = 0. 77 ± 0. 10(stat. ) ± 0. 15(syst. ). This result is consistent with the observations already made on figure  25. The signal strengths obtained for the three lepton channels are consistent at the 85% level. In the dijet-mass analysis at 8 TeV, a µ V Z value of 0. 79±0. 11(stat. )±0. 16(syst. ) is obtained. The correlation of the systematic uncertainties on µ V Z and µ is 35% in the MVA and 67% in the dijet-mass analysis. Fits are performed with the same final discriminants as used to obtain the results for the Higgs boson based on the 8 TeV dataset, but with both the V Z and Higgs boson signal-strength parameters µ V Z and µ left freely floating.
A value of µ V Z = 0. 50 ± 0. 30(stat. ) ± 0. 38(syst. ) is obtained for the 7 TeV dataset. The signal strength obtained for the combined 7 and 8 TeV dataset is 0. 74 ± 0. 09(stat. ) ± 0. 14(syst. ) The V Z signal is observed with a significance of 4. 9σ, to be compared to an expected significance of 6. 3σ. The fitted µ V Z values are shown in figure  26  for the 7 TeV, 8 TeV and combined datasets, and for the three lepton channels separately for the combined dataset, all with the MVA used for the 8 TeV data. A measurement of V Z production in pp collisions at √ s = 8 TeV in final states with b-tagged jets was recently reported by the CMS Collaboration  [99]. The analysis is carried out in event categories based on the numbers of leptons, jets, and jets tagged as originating from b-quark fragmentation, and on the transverse momentum of the vector-boson candidate.
Acknowledgments 13 Acknowledgements 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 ;  ISF, MIN-ERVA, 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 ROSATOM, 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.
However, the current state of TE annotation does not facilitate such distinctions, ✓ ✓ ✓ ✓ ✓ ✓ ✓ [81] Cyprinus carpio (common carp) Animal (bony fish) ✓ ✓ ✓ TEClass [82] Esox lucius (northern pike) Animal (bony fish) ✓ ✓ ✓ Genbank, UniprotKB/SwissProt Custom [83] Oryza glaberrima (African rice) Plant (monocot) ✓ ✓ ✓ ✓ MSU Repeats, custom (rice-specific) Custom [84] Callithrix jacchus (common marmoset) Animal (primate) ✓ ✓ [85] Gossypium arboreum (cultivated cotton) Plant (dicot) ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ [86] Nicotiana tabacum (common tobacco) Plant (dicot) ✓ ✓ TIGR, SGN (Solanaceae-specific) [87] Glossina morsitans (tsetse fly) Animal (insect) ✓ ✓ ✓ ✓ Genbank RECON, TARGeT [88] Oncorhynchus mykiss (rainbow trout) Animal (bony fish) ✓ ✓ ✓ ✓ ✓ E-inverted, Manual [89] Tetrao tetrix (black grouse) Animal (bird) ✓ ✓ [90] Pinus taeda (loblolly pine) Plant (gymnosperm) ✓ ✓ ✓ ✓ ✓ PIER 2.
Why and how should researchers contribute? The success of this effort depends on buy-in from the TE community to create and contribute benchmark data sets, to use them in their own work, and to promote their adoption. Because of the multiple challenges involved in the creation of these benchmarks, it is unlikely that any first version will be completely satisfactory; however, this should not be used as an argument to dismiss this type of effort but rather to contribute to its improvement. In the coming months, we would like to initiate discussions with the wider TE community on the ideal format of a first set of TE benchmarks and to begin collecting data sets. We invite the entire TE research community to join us in this effort by providing feedback on the issues raised in this article, by commenting on specific benchmark data set proposals as they are made available, and by contributing their own benchmark data set proposals.
The use of different fluorescent labels allows to multiplex the PCRs. The use of a collection of VNTRs for typing purposes is called MLVA for Multiple Locus VNTR Analysis. MLVA provides data in a numeric form which can be easily stored in databases accessible via internet such as http://mlva. u-psud. fr [50, 51]. Some databases, such as for the Brucella MLVA database, contain data from thousands of strains, independently produced by many laboratories. In Table  1  are summarized some recent study cases of genotyping of phytopathogenic bacteria, including P. syringae, for which MLVA has shown promising results  [52] [53] [54] [55] [56] [57] [58] [59] [60] [61]. We here take advantage of published Psa genome sequence data to explore VNTRs and to test them on an extended collection of Psa strains from the areas of the world where the pathogen is already established.
Tandem repeats identification and design of VNTR primers A preliminary analysis of the WGS data from three geographically separate Psa strains available in the NCBI database (Italian strain CFBP 7286, Chinese strain CH2010-6 and Japanese strain M302091) was carried out to identify suitable tandem repeats (TRs). The sequence data were imported into The Microorganisms Tandem Repeats Database (http://tandemrepeat. upsud. fr/) [50]  and screened using the following parameters: tandem repeat array from 50 to 1000 bp, repeat unit length from 5 to 300 bp, and >80% similarity within the copies of the tandem repeat array. Potentially useful VNTRs were selected as those with predicted size polymorphism among the three genomes. Right and left flanking regions of about 100 bp each were used to confirm by BLAST searches that these regions were present in all the WGS sequences available for Psa.
VNTR analysis by capillary electrophoresis The QIAxcel capillary electrophoresis system (QIAGEN, Milan, Italy) was used to estimate the amplicons size. For all but one VNTR locus, we applied method OM700, recommended for amplicons up to 500 bp, that uses the High Resolution cartridge and the following run parameters: 10 s of sample injection time; 5 kV of sample injection voltage; 3 kV of separation voltage for 700 s of separation time. Only for the VNTR locus Psa-09, due to its dimension, we applied method OM500, recommended for amplicons up to 1 kb, that is characterized by higher separation voltage (5 kV) and shorter separation time (500 s). Results were analyzed and interpreted by means of the Screengel software (QIAGEN), which gives estimates of both size and concentration of amplicons.
org. uk/cgibin/DICI/DICI. pl). The Bayesian clustering software STRUCTURE version 2. 3. 4  [63] [64] [65] [66]  was used to infer the overall population structure. Following the recommendations reported in Evanno et al. [67] , we carried out 20 independent runs for each of the putative number of populations (K), from 1 to 13, using 750000 burn-in replicates and 500000 MCMC (Markov Chain Monte Carlo) simulations per each run. STRUCTURE was run with the following options: admixture model, that assume correlation between alleles frequencies of data, without prior population information. The posterior probability of the data for a given K was calculated and labeled as L(K). The MLVA data were analyzed as a "character" dataset to draw minimum spanning trees (MSTs) using BioNumerics version 7. 5 (Applied Maths NV).
VNTR loci Eleven potentially effective VNTR loci, Psa-01 to Psa-11 were identified from the in silico analysis. Together with the eight loci previously reported by Gironde & Manceau  [55] , they were tested for their discriminatory power using the "diversity panel" of ten Psa strains, chosen for being isolated from different infection sites in the world and at different times. Six loci, two from our selection and four from the panel used by Gironde & Manceau, were monomorphic in the "diversity panel" and were not further explored. The 13 other VNTR loci were tested on the whole Psa panel of 142 strains. The primers for PCR amplification of these VNTR loci, the position of the corresponding amplicons on the circular chromosome of ICMP 18884 (accession number NZ_CM002751. 1) and, when present, the putative function of overlapping genes are indicated in Table  3.
The tandem repeats in 10 out of 13 cases fall within intergenic sequences (reported as unknown) of the reference genome used. In Psa-09 and Psa-10 the repeats are included partially in hypothetical proteins. Only in the MLVA locus GM-1834 the tandem repeats are totally included in a gene coding for a specific protein, and, as expected for intragenic loci, the repeat unit has a size of 6 bp, multiple of 3 bp. The VNTR loci were named as recommended by  [44, 45, 46]  to include the full allele coding convention: name of the locus_length of repeat unit in bp_in silico length of the whole amplicon in bpin the reference genome_assigned number of repeats (convention including partial final repeat) in U, according to a specific genome. In our assay, for instance, Psa-01_7bp_202bp_9U means that locus Psa-01 has a 7 bp long repeat unit, the whole amplicon is 202 bp in ICMP 18884 accession number NZ_CM002751.
1 sequence data when using the primers indicated in Table  3  and by convention this allele is called 9U (Table  4 ). Eight loci yielded a unique amplicon in all strains. A failure in amplification was observed at locus Psa-04 on six Japanese strains isolated from 1982 to 1988, as well as the Italian strain isolated in 1992. Loci Psa-06, Psa-07, Psa-09 and GM-254 failed to amplify the Psa4 "Low Virulence" strains investigated from NZ and Australia. Locus Psa-09 also failed to amplify 15 Korean strains (see footnotes, Table  4 ). One hundred and fifty-nine alleles were sequenced as controls to check the exact amplicon size. A string of 13 integer numbers representing the repeat copy number of each VNTR, in which the lack of amplification was coded as "-1", was defined for each strain (S1 Table ).
Sanger sequencing allowed to detect several single nucleotide polymorphisms in the flanking regions of Psa4 "Low Virulence" strains with no impact on allele size and consequently on MLVA analysis (data not shown). In contrast very few differences were found in amplicons from other Psa strains. The left flanking region of VNTR GM-254 is 133 bp long in European, Chinese, Chilean and New Zealand virulent strains, whilst it is 125 bp long in Japanese and Korean strains. This flanking 8 bp microdeletion could be conveniently coded as a VNTR variation since the VNTR has a 8 bp repeat unit. MLVA data confirmed by Sanger sequencing were compared with the number of repeats as obtainable from WGS for those ten strains of our selection for which genome sequence data are available in Genbank (Table  5 ).
Arrangement of VNTRs in sets for analysis and main haplotypes grouping We then used the MLVA dataset derived from the 142 strains to identify a panel of loci able to correctly assign strains to the four Psa biovars in agreement with previous studies and current knowledge. We propose a set of six loci, Panel 1, composed of Psa-01, Psa-04, Psa-07, GM-254, GM-1553 and GM-4076). Fig  1.
shows a comparison between the dendrogram obtained by McCann et al  [37]  based upon more than 15000 SNPs from draft genomes of twenty-eight Psa strains belonging to the four known biovars and the dendrogram obtained using Panel 1 on twenty strains selected in order to have geographic and time origins identical or equivalent to those of the strains considered in the dendrogram of the paper of McCann et al  [37]. Panel 1 data from the whole collection of strains was therefore used to evaluate the presence of additional populations using the same criterion. In the STRUCTURE analysis (  a the low virulence strains have a seven nucleotides gap in right flanking region when using the indicated primers. b the low virulence strains have a two nucleotides gap in left flanking region when using the indicated primers, resulting in a 164 bp allele.
Deepening analysis within main populations The full MLVA-13 (Panel 1 + Panel 2) data of each of those groups were separately submitted to the same clustering analysis reported above and UNJ dendrograms were chosen for the graphical representation of the relationships between strains. The group "Ubiquitous HV" (Fig  4 ) is constituted by all 50 highly virulent strains linked to the recent global pandemic of Psa. The use of the complete set of 13 VNTR loci allows the distinction of genotypes in agreement with their geographic origin: China, New Zealand, Europe and Chile. The second group is constituted by most Chinese strains (except for the five Chinese strains in the "Hyper-Virulence" group). These fifty-two strains are divided in three main branches of the UNJ dendrogram obtained from the complete dataset analysis, congruently with CCs in the MST based on Panel 1 data, but further groupings are recognizable within (Fig 5 ).
The assay distinguishes Australian strains from New Zealand ones due to a one repeat unit difference at the highly variable locus GM-1834. The data produced was used to create a dedicated resource on the internet by taking advantage of MLVAbank (http://mlva. u-psud. fr). The cooperative Pseudomonas syringae pv. actinidiae database comprises PSA_in_silico, deduced from in silico MLVA typing of WGS data, and PSA_Italia, made from the present MLVA data.
In the present study, the availability of WGS data of strains having different geographical and temporal origins permitted us to develop a MLVA assay in which 13 VNTR loci have been successfully recognized and used to arrange properly the haplotypes derived from the analysis of a wide collection of Psa strains. If needed, additional VNTRs may be identified, with shorter repeat units and/or overall array length. Our results are congruent with the distinction in four populations (biovars) outlined in previous studies. We demonstrated that the six VNTR loci, constituting MLVA Panel 1 are sufficient to attain this identification level. Psa biovar 4 is confirmed as quite different from the others, as demonstrated by the very high number of TR differences of corresponding strains with closest relatives, and the lack of amplification of four among the 13 loci.
By this same approach and with the support of STRUCTURE results, it was also suggested that, rather than four, at least ten different populations can be defined within Psa"sensu latu". Whole genome sequence analysis of the corresponding strains will be necessary to confirm this suggestion. The complete set of MLVA data proved also its effectiveness in distinguishing Psa subpopulations and illustrating their correlation mainly with geographical origins but also with isolation time as well as with pathogenicity level. In the present investigation aimed at setting up the assay, monoplex PCRs and capillary electrophoresis were used. In the future, multiplex PCR will obviously be an interesting option. Each panel can easily fit in a single multiplex PCR, as illustrated by earlier works  [74, 75].
From a technical point of view, the incongruities reported between WGS and true VNTR sequences demonstrated that tandem repeats are poorly analyzable with short reads WGS sequencing. However, this problem is progressively being solved by the availability of much longer reads  [84]. Finally, the chance to generate a haplotypes database accessible via the internet (MLVAbank), in a way which makes simple similarity queries very straightforward and user-friendly for worldwide research community makes MLVA even more promising. This could be of even greater importance considering that the assay presented here is not a closed system. It can be seen as a starting point that could be improved, by the addition of new VNTR loci effective in resolving the complex evolution of a pathogen such as Psa. In this view, MLVA would be used as first-line assay, followed by WGS analysis of relevant samples.
Background. Food allergy (FA) is an important health problem in Western countries but there is limited data on the prevalence of food allergy in the Middle East. The main objective of our study is to assess the prevalence of self-reported food allergy in Lebanon. Methods. The survey was conducted by Telephone Calls questionnaire through random selection of landline phone numbers from the white pages all over Lebanon. A study questionnaire addressing the main objectives of the study was filled during the telephone call conversation. Results. Food allergy prevalence is estimated to be 4. 1% in infants and children and 3. 2% in adults. 65% of patients suffering from food allergy are females and 35% are males. Skin reactions are the most common symptoms among food allergy sufferers, reported in 86% of the cases.
Without comprehensive data on the prevalence of food allergy, it will be impossible to develop appropriate local diagnostic tools and avoid the incidence of anaphylaxis to food. A clear understanding of the extent of food allergies will help public health services to be reactive rather than proactive  [5]. The main objective of our study is to assess the prevalence of selfreported food allergy in Lebanon. Secondary objectives include describing the principal food allergens, reporting the symptoms of food allergy in our group, the diagnostic tools, and the presence of concomitant allergic diseases.