dataesr/scientific-paragraphs-categorization huggingface dataset:
Data selection The search is performed as a "blind" analysis, i. e. data in the signal region were not used to define the reconstruction and selection procedures. The analysis is based on a data sample corresponding to an integrated luminosity of 5. 3 fb -1 of proton-proton collisions at √ s = 7 TeV, obtained in 2011. The data were collected with a trigger selecting events containing at least two muons, one with p T > 17 GeV/c and one with p T > 8 GeV/c. In the offline analysis, events are selected by requiring at least one primary vertex reconstructed with at least four tracks and with its z coordinate within 24 cm of the nominal collision point. Offline muon candidates are built using tracks reconstructed in the inner tracker matched to track segments in the muon system, using an arbitration algorithm  [55].
The rate of prompt double J/ψ production in the data sample is extracted by extrapolating in the plane of the transverse lifetime ct xy of the two J/ψ candidates and their measured invariant masses. The rate thus obtained from data is used to normalize the simulation, which is produced using the double parton scattering (DPS) J/ψ pair production process in the PYTHIA 8. 108 event generator  [64] , applying the same selections as applied to the data. This calculation provides an estimate of the background rate due to prompt double J/ψ production in the signal region. To evaluate the systematic uncertainty, this normalization factor is recalculated separately for each of the four ranges of the invariant masses m 2J/ψ of the two J/ψ candidates: 6-13, 13-22, 22-35, and 35-80 GeV/c 2. Although the control samples overlap with the data sample used for the search, for none of the benchmark models considered are the control samples significantly contaminated with the signal.
Summary A search for non-standard-model Higgs boson decays to pairs of new light bosons, which subsequently decay to pairs of oppositely charged muons (h → 2a + X → 4µ + X) has been presented. The search is based on a data sample corresponding to an integrated luminosity of 5. 3 fb -1 collected by the CMS experiment in proton-proton collisions at √ s = 7 TeV in 2011. No excess is observed with respect to the SM predictions. An upper limit at 95% confidence level on the product of the cross section times branching fraction times acceptance is obtained. The limit is valid for new light-boson masses in the range 0. 25 < m a < 3. 55 GeV/c 2 and for Higgs boson masses in the range m h > 86 GeV/c 2. Although the results have been interpreted in the context of the NMSSM and the dark-SUSY benchmark models for m h < 150 GeV/c 2 , it is possible to extend them by smoothly extrapolating the model-independent cross section limit to higher masses.
Acknowledgments We would like to thank  Joshua Ruderman  ( LBNL and University of California at Berkeley ) for his guidance with the theoretically motivated benchmark samples of dark SUSY and useful discussions. We wish to congratulate our colleagues in the CERN accelerator departments for the excellent performance of the LHC machine. We thank the technical and administrative staff at  CERN  and other CMS institutes, and acknowledge support from:  FMSR (Austria) ;  FNRS  and  FWO (Belgium) ;  CNPq ,  CAPES ,  FAPERJ , and  FAPESP (Brazil) ;  MES (Bulgaria) ;  CERN ;  CAS, MoST , and  NSFC (China) ;  COLCIENCIAS (Colombia) ;  MSES (Croatia) ;  RPF (Cyprus) ;  Academy of Sciences  and  NICPB (Estonia) ;  Academy of Finland ,  MEC , and  HIP (Finland) ;  CEA  and  CNRS/IN2P3  (France);  BMBF ,  DFG , and  HGF (Germany) ;  GSRT (Greece) ;  OTKA  and  NKTH (Hungary) ;  DAE  and  DST (India) ;  IPM (Iran) ;  SFI (Ireland) ;  INFN (Italy) ;  NRF  and  WCU (Korea) ;  LAS (Lithuania) ;  CINVESTAV ,  CONACYT ,  SEP , and  UASLP-FAI (Mexico) ;  MSI (New Zealand );  PAEC (Pakistan) ;  SCSR (Poland) ;  FCT (Portugal) ;  JINR (Armenia, Belarus, Georgia, Ukraine, Uzbekistan) ;  MST  and  MAE (Russia) ;  MSTD (Serbia) ;  MICINN  and  CPAN (Spain) ;  Swiss Funding Agencies (Switzerland) ;  NSC (Taipei) ;  TUBITAK  and  TAEK (Turkey) ;  STFC  ( United Kingdom );  DOE  and  NSF (USA).
The Al target was cleaned with Ar plasma before each deposition in order to remove the contamination of target surface induced during the substrate loading process. The structure of the AlN layers was investigated by highresolution xray diffraction (HRXRD) with a Bruker AXS D8 Advance four-axis diffractometer using Cu Kα 1 incident radiation. The layer grain size was estimated from the full-width at half-maximum (FWHM) of the AlN(0002) reflection peak of the 2θ/ω-scan by means of Scherrer's  formula  [17]. The surface roughness of the AlN layers was measured by atomic force microscopy (AFM) in the tapping mode with a Veeco Dimension 3100 microscope. Data visualization and processing were carried out using the WSxM software  [18].
Molecular characterization Reverse transcription PCR (RT-PCR) using NP3/NP4 N genes primers' , targeting the N protein gene was carried out in combination with nucleotide sequencing as previously described  [13]. The nucleic acid sequences obtained from PCR products were aligned with PPRV sequences retrieved from GenBank. Multiple aligments of the N gene were performed by using the ClustalW algorithm of the Mega 4 software package  [14]. Phylogenetic analysis based on the 255 nucleotides of the N gene was done  [6]  with MrBayes V. 3. 2 software, using the default chain for two million generations with the GTR+G+I nucleotide substitution model  [15]. Trees were sampled every 100 generations, resulting in 20 000 saved trees, the first 5000 saved trees being discarded as burn-in.
Phylogenetic analysis Partials N gene sequences of 303 bp located on the C terminus end of nucleoprotein of virus were obtained. The 10 nucleotide sequences from the three sick animals were identical. Three nucleotide sequences (Gabon Aboumi 1, Gabon Aboumi 2 and Gabon Aboumi 3), each from a different animal, were aligned with PPRV sequences available in Genbank, and were themselves submitted to GenBank (Accession numbers JX079994 -JX079996). Phylogenetic analysis revealed that the Aboumi outbreak strain clustered in lineage IV, along with Asian strains (Figure  2 ). Moreover, this strain was closely related (95% nucleotide sequence identity) to the Cameroonian strain, with which it formed a distinct cluster (Figure  2 ).
Background and purpose. -Long-term results of decompressive laminectomy in degenerative lumbar stenosis have been studied in only six prospective studies. The objective of our study was to evaluate the functional outcome at long term of patients after decompressive laminectomy in lumbar stenosis and to determine predictive factors of favorable outcome. Methods. -A prospective cohort data were collected by an independent observer five years after decompressive laminectomy for degenerative lumbar stenosis. The endpoint was the assessment of the Beaujon score for functional evaluation. The result was considered as favorable if the Beaujon score increased by at last five points between the preoperative stage and at follow-up examination. Logistic regression was then performed with univariate and multivariate analysis to reveal predictive factors of good long-term outcome (P ≤ 0.
Statistical analysis Descriptive statistics were performed using JMP (version 6. 0. 3, SAS Institute Inc. ). Quantitative variables (age, BMI, Beaujon score, walking distance, Charlson score, measuring the diameter of the spinal canal on imaging, number of levels reached and recalibrated) considered as continuous numeric variables were expressed as mean ± standard deviation (SD) and compared using the Student t test. Some variables (age ± 67 years, BMI ± 30, Beaujon score ± 10, Charlson score ± 3, the walking distance ± 500 m, the spinal canal diameter ± 1. 4 cm, the muscle diameter ± 3. 91 cm, the number of levels achieved and recalibrated ± 2) were dichotomized. Other values were qualitative such as gender, predominant symptom (back pain or radiculopathy), the presence of neurological deficit, type of stenosis (global or lateral), the levels or recalibrated, the presence of fusion and/or fixation and the concept of early recovery or re interventions within five years.
E. huxleyi isolate differences were assessed further by Illumina sequencing of ten additional strains. Although sequenced at lower coverage, these strains were estimated to be 91-95% complete (Supplementary Tables 6, 7 and Supplementary Data 7). Direct mapping of reads from the 13 strains to CCMP1516 revealed a 'core genome' containing about two-thirds of the genes predicted in the reference genome (Supplementary Information 2. 6. 2 and Supplementary Data 5), a core  a, E. huxleyi has five well-characterized calcification morphotypes and an overcalcified state  1. b, Cladogram showing the distinct branch occupied by the haptophyte lineage on the basis of RAxML analysis of concatenated, nuclear-encoded proteins after addition of homologues from CCMP1516 and a pico-prymnesiophyte-targeted metagenome  8.
METHODS SUMMARY The diploid genome of CCMP1516 (isolated from the Equatorial Pacific (02. 6667S 82. 7167W)) was Sanger sequenced and assembled using the Arachne assembler. Gene models were predicted and validated using computational tools, experimental data (including transcriptomics; Sanger and Illumina sequenced) and NimbleGen tiling array experiments. Thirteen additional strains were sequenced using Illumina and mapped to the reference genome. A detailed description of materials and methods is in Supplementary Information.
Materials and Methods A medial wedge of 10° was removed from the femur of a female cadaver (aged 78 years at death with weight of 64 kg and body mass index of 21. 9 kg/m 2 ) to model a three-part peritrochanteric fracture (31-A2, AO classification  6  ). The angle of the fracture line with the shaft of the femur was assigned a value of 43° and the intrusion distance into the fracture complex was assumed to be 60% (Fig. 1 ). The CT scan of the femur was converted to a mixed hexahedral/tetrahedral mesh with Simpleware software suite (Simpleware Ltd, Exeter, United Kingdom) and imported into an FE solver (Abaqus; Simulia, Providence, Rhode Island). A linear relationship between Hounsfield units and ash density was assumed, and we chose the following density-elasticity relationship to convert apparent density (ρ, in g/cm 3 ) into Young's modulus (E, in MPa)  7  : E = 6950ρ  1.
We then modify the code so that the action adds the corresponding resource to the environment and obtain the code on lines 13 and 14. Mutually exclusive narrative actions can be explicitly suggested using the choice connective & in the declaration of the initial conditions. These can be used to encode key turning points in the narrative that are broadly recognized as such, which is frequently the case when using existing stories as a baseline. We use this connective to model Emma's choice to attend the ball (see line 18). Once the narrative modelled, it is run using Celf and the proof-terms obtained are post-processed for causality analysis. Following a long tradition of analysing causality via graphs  [6] , we developed a prototype tool, CelfToGraph 2  , that automatically transforms proof terms generated by Celf into directed acyclic graphs.
Such graphs represent narrative plots, structured by narrative causality, where nodes are narrative actions and edges represent inferred causality relationships. One advantage of modelling narratives using a programming language is the ability to iteratively fine tune the model: a programmer alternates between coding and testing phases, which is facilitated by the frontend that we developed: in addition to the generation of causal graphs representing narratives, CelfToGraph queries can exhibit plots with specific characteristics. One can also verify if the generated set has a varied output (differing significantly from the original plot), test the impact of more narrative drive on the generation (for instance by comparing the effect of affine vs. linear models of narrative actions), or fine-tune resource threshold quantities.
Generated Plots The entire code corresponding to the excerpt on Figure  1   encoded one branching choice, the variety of outputs is due to the linear semantics of narrative actions (producing resources that may be contended) and forward chaining variability. The code described allows to generate 72 different narrative sequences for 100 attempts. After an automatic comparison of the corresponding plots using CelfToGraph, , we can exhibit 41 different plots (characterised by different generated causal structures), meaning that a number of different narrative sequences share the same causal structures. This allows the characterisation of classes of true story variants. Figure  2  shows a story variant among those generated, which has been exhibited by the tool: in this story, Emma jumps through the window following the departure of Rodolphe.
The cardiac and thoracic dimensions, the mass and the pressure exerted by the left and right cardiac protrusions on the subjacent pulmonary parenchyma were compared between preand postoperative moments using a two-way analysis of variance for repeated measures. Because the collapsed pulmonary parenchyma fraction was not normally distributed, the comparison between the lower lobe segments located beneath and outside of the heart protrusion limits during pre-and postoperative moments was performed using the Wilcoxon matched-pairs signed-rank test. The post-hoc analysis following the analysis of variances was performed using the Bonferroni method. The statistical analysis was performed using the SPSS 20 statistical package (SPSS Inc. , Chicago, IL, USA). All of the parametric data were expressed as means 6 SD, unless otherwise specified.
Numerical parameters The Fortran code DDSCAT 7. 1, developed by Draine and Flatau, is used for calculating extinction of light by irregular particles based on the DDA  [17]. DDSCAT offers the possibility of editing new shapes. Therefore, we edit the cylindrical shape to include the adhesion layer and the roughness. To simulate a realistic roughness, a uniform probability law is used to remove or to add a dipole from/to the surface, or to keep it unchanged. Therefore, the root of mean square roughness is RMS= (-2) 2 + 0 + 2 2 3 ≈ 1. 6 nm, that is close to the RMS that can be observed in MEB images of samples in abundant literature and websites. The inter-dipole distance d = 2 nm is smaller than 2. 6 nm that ensured the validity of the calculations in  [19]. The target precision for the inversion of the matrix of coupling between dipoles is 10 -3.
The method uses a robust fit of the results of the parametric study. The algorithm uses iteratively reweighted least squares with the bisquare weighting function (Matlab). Similarly, the position of the LSPR (nm) can be deduced from Eq. 6 as a function of D (nm) and h (nm): λ 0 (LSPR) ≈ 160 + D + 3. 86h 0. 319 + 0. 0084h (7) A comparison of the simple model (Eq. 7) and experimental data in  [21]  shows a good agreement. Equation 7 seems to be a good approximation of the variation of the LSPR as a function of the geometrical parameters D and h, for a grating of rough gold cylinders with adhesion layer (e = 2 nm) and P = 200 nm (Fig. 1 ). The specific case of homothetic cylinders with h = D, removes a degree of freedom and leads to a simpler formula: λ 0 (LSPR, h = D) = 160 + 4. 86D 0. 319 + 0.
Phage whole genome sequencing Phage DNA was prepared using the rapid protocol described above and the quality was checked by restriction enzyme digestion, followed by gel analysis. Then 5 mg were sent to the CNRS sequencing facility in Gif sur Yvette (IMAGIF) for preparation of a library and sequencing on the Illumina platform (Illumina Genome Analyzer IIx). Paired-end 75 bp reads were produced, from mean insert length around 300 bp. The BioNumerics tools (Applied Maths, Sint-Martens-Latem, Belgium) were used for assembly and comparison of genome sequences. For the de novo assembly, two algorithms were applied to produce contigs, namely Velvet  [33]  and Ray  [34]. Both are implemented in the 6. 6 version of the BioNumerics software, in the "Power Assembler" module. A single contig was obtained without any gap and the distribution of reads along this contig was analysed.
After alignment with published sequences large regions of deletion were verified by PCR amplification using primers selected in flanking sequences. Annotated sequences were deposited at EMBL-EBI under accession number HE983845 for phage vB_PaeM_C2-10_Ab01, and HE983844 for phage vB_PaeP_C1-14_Or01. Additional information is available at the web site http:// bacteriophages. igmors. u-psud. fr.
At the 8 sites we found a short conserved sequence which consensus is GTCATAGTAC (Fig. S3B ). Upon alignment of the P1-14 Or01 genome with sequenced genomes present in Genbank, the closest phages were WMR299-2 with 97% average nucleotide similarity  [10] , PaP3 with 95% average similarity  [41] , and LUZ24 with 90% average similarity  [42]. The differences were not evenly distributed but were concentrated into several regions with 84 to 94% identity with the closest phage genome WMR299-2. An approximately 3000 bp fragment showed 97% similarity with phage PaP3 and 86% similarity with phage WMR299-2. It encompassed 3 hypothetical open reading frames (orf10 to orf13), two of which (orf12 and orf13) encode constituents of the phage particle. Another region of about 660 bp showed 91% identity with WMR299-2 and 92% identity with LUZ24 and encompassed orf17 encoding a putative phage particle protein.
Common spacers were observed in strains belonging to clusters defined by MLVA (Fig. S5  and S6 ). A search for sequences homologous to spacers by BLAST in Genbank gave a 100% match for 40% of the spacers, corresponding mostly to temperate phages or prophages but in a few cases to sequences of plasmids, pyocins or pathogenicity islands. A given CRISPR often contained several fragments of a particular phage. In order to compare the CRISPR of our strains with those described in the literature we produced a combined dictionary of spacers found in the study of Cady et al. [39]  and the spacers described in the present study (Table  S2 ). Twenty six of our strains possessed spacers that were previously found in other strains. We also investigated the presence of the type I-E (Escherichia) CRISPR-Cas by amplification using primers in the cas1 gene.
in the two sequenced genomes. Cady et al. analysed the prevalence of the two CRISPR-Cas systems in P. aeruginosa and showed that the 132 viral spacers with matches in sequence databases matched temperate bacteriophage/prophages capable of inserting into the host chromosome; none matched extrachromosomally replicating lytic P. aeruginosa bacteriophages  [39]. They later reported that the type I-F (Yersinia) CRISPR region of P. aeruginosa strain UCBPP-PA14 plays a role in immunity against specific temperate phages  [24]. In the strains used here, the majority of spacers with homologues in databases also match temperate phages. We observed some matches with chromosomal sequences such as pyocins and genes of pathogenicity islands, both of which often appear to have their origins in temperate phages.
Acknowledgments We are grateful to  Mzia Kutateladze  and  Marina Goderdzishvili  ( Tbilisi, Georgia ) for the pyophage and to  Annick Jacq (Orsay)  for her expertise and support. We thank  Julien Navarro  and  Christophe Tourterel  for their help with genome sequence analysis, and  Danielle Jaillard  and  Luvidine Houel  at the  Electron Microscopy platform of University Paris Sud  for performing EM examination. We thank  Victor Krylov  and  Elena Pleteneva  for testing their phage collection on some strains. This work has benefited from the facilities and expertise of the high throughput sequencing platform of  IMAGIF (Centre de Recherche de Gif  -www. imagif. cnrs. fr).
This study was performed with the financial support of the association  Vaincre La Mucoviscidose  (Grant Nu  2010/IC1020 ). The development of tools for the surveillance of bacterial pathogens is supported by the  French Direction Generale de l'Armement (DGA). CE holds a fellowship of  Agence Universitaire de la Francophonie. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Data collection & outcome measures One investigator reviewed and abstracted the data from the medical records. Demographic information, CO-poisoning history, comorbidities, blood gas measurements, and sedation protocol were extracted. The patients' hemodynamic profile comprising heart rate (HR), systolic blood pressure (SBP) and diastolic blood pressure (DBP) were also reviewed. Values measured from one of the patients' arm using an Oscill Mate 1630 automated device (CASMED® Inc. , Branford, CT, USA) were recorded every five minutes and averaged to obtain mean value during HBOT1, HBOT2, and HBOT3. Also, pulse blood pressure (ΔBP) was further assessed by calculating the difference between SBP and DBP.
Data analysis Data are expressed as the median value and the 25th and 75th percentiles, and analyzed using non-parametric methods with the SAS 9. 2 software (SAS Institute, Cary, NC, USA). Within-group comparisons between HBOT were performed using the Friedman analysis of variance; following a significant F value, post hoc comparisons were made using the Wilcoxon t-test (two-tailed). The statistical significance was set at α = 5%.
The study cohort To analyze the recombinome of the human MLL gene, 1622 prescreened acute leukemia samples were obtained from the above-mentioned centers over a period of one decade (2003-2013). Successful analysis of the direct MLL fusion could be performed for all patient samples except 19 cases, where only a reciprocal MLL fusion allele could be characterized. In these cases we identified only the reciprocal MLL fusion allele to guarantee MRD experiments. Of those 1622 cases, 1590 entered this study because we obtained all the critical information that was necessary for data processing (gender, age at diagnosis, disease type and subtype or information about de novo or secondary leukemia). A total of 32 cases was excluded from our study because relevant information about these patients were missing; they had the following MLL rearrangements: 9 Â MLL-MLLT3/AF9; 5 Â MLL-AFF1/AF4; 4Â MLL-MLLT1/ENL; 4Â MLLMLLT10/AF10, 3 Â MLL-MLLT4/AF6, 2 Â MLL-MLLT6/AF17, 1 Â MLL-GAS7, 1 Â MLL-EPS15, 1 Â MLL-LOC100128568, 1 Â LOC387646-MLL and 1 Â MLL-partial tandem duplication (PTD).
This has to be investigated in more detail in the future to understand these observations. An important translational aspect of this study is the establishment of patient-specific DNA sequences that can be used for monitoring MRD by quantitative PCR techniques. Owing to the fact that a given MLL fusion allele is genetically stable and a monoallelic marker for each tumor cell, a more reliable quantification and tracing of residual tumor cells becomes possible. For each of these 1622 acute leukemia patients at least one MLL fusion allele was identified and characterized by sequencing. Several prospective studies were already initiated and first published data verified the reliability of these genomic markers for MRD monitoring. 4  Therefore, the use of these MRD markers will contribute in the future to a better stratification of leukemia patients, which will help to further improve the outcome.
ACKNOWLEDGEMENTS We thank all local doctors and biologists who provided clinical information and material. This work was made possible by and conducted within the framework of the  International BFM Study Group. This study was supported by Grant  DKS 2011. 09from the  German Children Cancer Aid  to RM. TB was supported by Grants  R 12/09  and  R 10/37f  from the  German JoseCarreras Leukemia Foundation. PM is an  ICREA Professor  from the  Catalunya Government. This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3. 0 Unported License. To view a copy of this license, visit http://creativecommons. org/licenses/by-nc-nd/3. 0/.