dataesr/scientific-paragraphs-categorization huggingface dataset:
Constraints from LHC The searches performed by ATLAS and CMS on the 7 and 8 TeV LHC data in channels with jets, leptons and missing transverse energy (MET) have already significantly re-shaped our views of the high energy frontier in relation to SUSY. Searches for signatures of production and decay of supersymmetric particles with large MET have failed to reveal any significant excess of events compared to SM expectations. A variety of final states have been probed in LHC searches which are sensitive to the production and decay modes of both strongly-and weakly-interacting SUSY particles. The results of searches for gluinos and squarks of the first two generations are easy to interpret in generic models. The analyses of the almost 25 fb -1 of combined 7 TeV and 8 TeV have led to mass limits in the range of m g > ∼ 1 -1.
The recent observation of a Higgs-like particle with mass 125 GeV at the LHC is opening new perspectives for SUSY searches at colliders. The mass of the newly discovered particle sets some non-trivial constraints on the SUSY parameters. In particular, the relatively large mass value observed implies strong restrictions on the scalar top mass and the mixing in the top sector  [929, 1030]. Heavy scalar top quarks and/or large mixing are required to bring the h boson mass around 125 GeV. The first measurement of the yields (or signal strengths µ) in the decay channels studied so far-including γγ, ZZ * and WW * -(although limited in accuracy and only at the level of upper limits in the important bb and ττ channels) will add further constraints. In particular, if interpreted within the SUSY framework, the data point towards a decoupling scenario, with a relatively heavy A boson.
Much of the accuracy demonstrated by the detailed ILC studies at 0. 5 TeV is preserved at multi-TeV energies, as confirmed by some of the studies carried out for the CLIC CDR [1040], which focused on 3 TeV e + e -collisions. Chargino and neutralino masses in the range 600 -1000 GeV can be determined with a relative statistical accuracy of 1 -2% with unpolarised beams and 2 ab -1 of data  [1040, 1043]. The mass of μR of 1. 1 TeV is again determined to ∼2% with unpolarised beams and 1% with polarised electrons and positrons, accounting for backgrounds  [1040, 1052]. In addition to the weakly interacting SUSY particles, multi-TeV collisions may access scalar quark pair production, providing unique accuracy on their masses. In the case of a 1. 1 TeV right-handed squark of the first generation a detailed study performed for 2 ab -1 of integrated luminosity at √ s = 3 TeV demonstrated a relative statistical accuracy on the mass of 0.
Acknowledgements Several authors acknowledges the support of the  DFG  through the grant  SFB676  'Particles, Strings and the  Early Universe'. This work was supported by  European Commission  through the contract  PITN-GA-2012-316704  (HIGGSTOOLS). This work is supported in part by the  Creative Scientific Research Grant  No. 18GS0202  of the  Japan Society for Promotions of Science (JSPS) , the  JSPS   Grant-in-Aid for Science Research  No. 22244031 , and the  JSPS Specially  Promoted Research No. 23000002. This work is part of the  D-ITP consortium , a program of the  Netherlands Organisation for Scientific Research (NWO)  that is funded by the  Dutch Ministry of Education, Culture and Science (OCW). G. Moortgat-Pick  would like to thank  A. A. Mikhailichenko  for useful discussions and valuable comments on collider aspects.
C. Grojean is supported by the  Spanish Ministry MICNN  under contract  FPA2010-17747  and by the  European Commission  under the  ERC Advanced Grant 226371 MassTeV  and  M. M. Mühlleitner  is supported by the  DFG/SFB-TR9 Computational Particle Physics. M. Asano  acknowledges support from the  German Research Foundation (DFG)  through grant  BR 3954/1-1  and  DFG TRR33  "The  Dark Universe". S. Matsumoto  acknowledges supports from the  MEXT, Japan  through grants Nos. 22244031 & 26287039 , and also from the  WPI Initiative, MEXT, Japan. K. Rolbiecki  has been supported by the  MICINN, Spain , under contract FPA2013-44773-P, Consolider-Ingenio CPAN  CSD2007-00042  and the  Spanish MINECO Centro de excelencia Severo Ochoa Program  under grant  SEV-2012-0249. S. Godfrey was supported in part by the  Natural Sciences and Engineering Research Council of Canada  under grant number  121209-2009   SAPIN.
The work of  S. Y. Choi  was supported by  Basic Science Research Program  through the  National Research Foundation (NRF)  funded by the  Ministry of Education, Science and Technology  ( 2012-0002746 ). The work was partly supported by  Polish National Center for Science,  grant  NCN OPUS 2012/05/B/ST2/03306  ( 2012-2016 ) and the grant  NCN DEC-2012/05/B/ST2/02597 , and by  BMBF ,  DAAD PPP Poland Project 56269947, "Dark Matter at Colliders " ( M. Krawczyk ), grants  RFBR 11-02-00242 ,  NSh-3802. 2012. 2 ( I. Ginzburg ). A. S. Kronfeld is supported in part by the  German Excellence Initiative  and the  European Union Seventh Framework Programme  under grant agreement No. 291763 as well as the European Union's  Marie Curie COFUND program. Fermilab  is operated by  Fermi Research Alliance, LLC , under Contract No.
wisc. edu/index. html) for bacterial 16S sequences searches for sets of short fragments that are uncommon in the phylogenetic group where the sequence is classified, but frequent in other phylogenetic groups. This depends on a robust pre-existing data set. UCHIME  (Edgar et al. 2011) , a chimera check program, is best when two known parental sequences and a high-quality reference database that is chimera free are available. Bellerophon uses a partial treeing analyses to detect 16S chimeras  (Huber et al. 2004 ). Other chimera checking programs are available [see  Fonseca et al. (2012)  for discussion]. Nilsson et al. (2012)  note the high incidence of ITS chimeras in public ITS databases and suggest a mechanism for identifying them by Blast mismatches between the ITS1 and ITS2 regions and by exploring long branches in phylogenetic trees.
They comment that the most frequent site for exchange between two similar templates in a PCR reaction is in the first part of the highly conserved 5. 8S segment. An open source chimera checker for the ITS region has been developed and is available at http://www. emerencia. org/chimerachecker. html  (Nilsson et al. 2010). Using chimera checker to evaluate 12 300 sequences, 1. 5% were identified as chimeric sequences. To better facilitate ITS-based molecular identification of fungi for the scientific community, the UNITE database was established to provide reliable documented ITS sequences for the fungal community  (Kõljalg et al. 2013; Nilsson et al. 2015)  and a reference set of ITS sequences, each representing a species hypothesis is available in several formats including UCHIME  (Nilsson et al.
Two regions of 5 tem- 1 TENN-F-XXXXXX is abbreviated as TENNXXXXXX plate switching events were also observed (Fig. 1 ). It should be noted that the exact point at which template switching occurred cannot be determined in regions where G. dichrous I and II have identical sequence but is between the last 5' diagnostic base pair difference between G. dichrous I and II and the diagnostic base pair at which template switching occurred (Fig. 1 , horizontal arrows). The possibility of identical chimeras occurring in GenBank and thus being interpreted as valid taxa was noted by  Nilsson et al. (2012). The non-random nature of template switching would suggest that some stable mechanism influences template switching. We investigated the possibility that secondary structure formation during the PCR process might lead to non-random chimera formation, perhaps by briefly stalling taq polymerase transcription at the point of secondary folding and allowing template switching.
Questionnaires, other dependent measures, data analysis After exposure to each of the four experimental conditions, participants completed up to five self-report questionnaires assessing acceptability (levels of emotion, motivation, security, fatigue, and familiarity). These questionnaires were devised using classical Likert scale methodology (a horizontal line, on which a subject indicates his or her response by checking tick marks between 0 and 10). Cyber-Sickness and Presence questionnaires were only completed after the two VR conditions, and were tested respectively with the 22-item Cybersickness questionnaire,  28  and the general and spatial presence questionnaire. 29 The questionnaire scores are explained in the notes for Table  1. In order to assess autobiographical memories, we adapted the autobiographical fluency task  30  to the context of the experiment.
The subject's verbal outputs were directly recorded during the experiment and analyzed after the session by a speech therapist blinded to the research protocol. The score derived included the number of memories and number of remember and know recollections. The statistical analysis was carried out using Statistical Package for the Social Sciences version 11. 0 software (SPSS Inc. , Chicago, IL, USA) with a significance level of 0. 05. Values are expressed as the mean ± standard deviation. Mean comparisons between the conditions were performed using the Wilcoxon non-parametric test.
05), motivation not different between the VR conditions and Fam-Photo condition. The FamPhoto condition yielded a higher emotion score than the other conditions (P,0. 05). For the two VR conditions, data from the CyberSickness questionnaire indicated that participants did not experience important sickness (0, no cybersickness; 6, significant cybersickness) with UnknoIBVE (mean 0. 46±0. 1) or FamIBVE (mean 1. 42±0. 3). Scores on the Presence questionnaire were in the medium range (on a scale from 0 to 84). There were no significant differences between the two conditions for either the CyberSickness (P=0. 11) or Presence (P=0. 24) questionnaire. Concerning the autobiographical fluency task, the total number of responses in the FamIBVE and FamPhoto conditions were significantly (P,0. 05) higher than those in the gray and UnknoIBVE conditions.
Determination of complete genome sequences by pyrosequencing Double-stranded RNAs (dsRNAs) were extracted from fresh leaves of GF305 grafted with the 13025 and Pair sources, and from dried leaves of the Aze204 almond. After whole-genome amplification, the amplified fragments were analyzed by 454 pyrosequencing, following the strategy described in Candresse et al. [19]. After demultiplexing, the reads were assembled using the CLC Genomics Workbench 6. 5 (http://www. clcbio. com) and annotated by BlastX and BlastN comparison with GenBank, using a 10 -3 e-value cut-off. Mapping of contigs on the genome of AVCaV (for the 13025 and Pair sources) or of Citrus leaf blotch virus (CLBV) (for the Aze204 source) used as references allowed the scaffolding and ordering of contigs for each viral isolate.
In the 13025 Japanese plum sample, Blast comparisons allowed identification of two viruses: PBNSPaV (two distinct isolates, 43% of the reads) and an isolate of AVCaV, representing 2% of the reads. Seven contigs identified as belonging to AVCaV were manually assembled by mapping against the reference AVCaV genome, thus creating a scaffold of 6,141 nt missing the 5' and 3' genome ends and containing six internal gaps. The genomic sequences of the Pair and 13025 AVCaV isolates were completed by targeted sequencing as described in the Materials and Methods section. The assembled complete genome sequences were deposited in the Gen-Bank database under accession numbers KM507062 and KM507063, respectively. For the Aze204 almond sample, only a few contigs could be identified as having a possible viral origin by BlastN and BlastX analyses.
The assembled sequence was deposited under accession number KM507061 in the GenBank database. Partial sequencing of the AVCaV isolate present in the Iran1 Prunus persica source TNA extracts from the Iran1 P. persica source were submitted to a PDO nested RT-PCR which permits the detection of Trichovirus, Foveavirus, and Capillovirus members as well as of some unassigned Betaflexiviridae members  [28]. In Blast analyses, the 310-nt long fragment obtained showed strong nucleotide identity (92%) with the corresponding fragment of AVCaV  [21]. Using a forward primer located in the PDO fragment and LD-polyT primer targeting the polyA tail of the genome, a 2,883-nt long fragment was amplified, cloned and sequenced on both strands by primer-walking. The assembled sequence of 3,037 nt was deposited under Accession number KM507070 in the GenBank database.
To assess the incidence of both viruses in various Prunus accessions, 412 samples gathered during several surveys were submitted to the polyvalent RT-PCR assays. No additional sample was found to be infected by the new virus. In contrast, three additional samples were found to be infected with AVCaV (S2-S3 Figs lanes 3, 5, and 6), enlarging the natural host range of this virus to P. mume (sample S4), and to P. domestica (sample 381-07-4), and its geographical distribution to China (samples S4 and S15) (S4 Table ). Sequencing of the amplified fragments confirmed the specificity of the detection assays. The unrooted neighbor-joining trees constructed using the partial sequences of the NB gene or of the Pol gene showed that all identified AVCaV isolates appear to form a relatively tight cluster, with the exception of the Iran1 isolate, which is more divergent (data not shown).
Acknowledgments The authors would like to thank  Xavier Foissac ,  Véronique Decroocq  and  David Tricon  ( INRA, Villenave d'Ornon, France ), and  Yoann Brans  and  Pascal Gentit  ( Ctifl, Lanxade, France ) for providing some Prunus samples. The 454 pyrosequencing was performed at the  GeT-PlaGe (INRA, Toulouse, France). Sébastien Carrère  and  Jérôme Gouzy  ( INRA, Toulouse, France ) are also thanked for the help in the initial bioinformatic analysis of the sequence data.
In this way we were able to analyse the pathogen-specific response at each time and also examine how the different pathogens induced common or specific responses during ontological development (Table  S1  and S2 ). To gain an overview of the global responses, principal component analysis (PCA) was separately performed with hybridization datasets for viral and bacterial infections (Fig. 2A, B ). The transcriptomes were separated primarily by developmental stage as seen with dimension 1 (horizontal axis); both eyed eggs (EE) and hatch (H) stages were closely grouped, but were clearly different from first feeding (FF) and even more distant from 3 weeks post first feeding (3wFF). This observation was consistently observed for all fish groups (viral and bacterial infected fish, as well as controls).
Although the smaller number of features used for the analysis at the EE stage can decrease the sensitivity of this approach, these observations suggested that a full interferon response is not expressed early in fry development. To test this hypothesis, we performed a specific analysis of gene expression in Toll-like receptor and RIG-I signalling pathways. We mapped up-and down-regulated genes on KEGG for TLR and RLR pathways at each developmental stage, using a combination of David  19  , Ingenuity pathway analysis (IPA) and direct analysis of the dataset. As shown on Fig. 4B  and Figure  S1 , most inducible genes of both pathways were not significantly up-regulated at EE, but were at later stages. A selection of genes up-regulated by the VHSV infection (comprising probes modulated with the 20 highest FC at least for one developmental stage; "top20" genes) is shown in Table  1.
No significant mortality due to the injection was observed in other groups. The experiments were performed at 10°C. Microarray platform, hybridizations and analysis. The microarray platform was custom designed and derived from rainbow trout EST tentative contigs (TC) from Rainbow Trout Gene Index Release 7. 0 (July 2008). 40,125 oligos from this source were the basis of the array, and were supplemented with further immune related transcripts from more recent releases to NCBI designed using the Agilent e array oligo design software (1,287 oligos). A further 1,417 Agilent in house control features were included. Full details of the array platform are available at EBI array express (http://www. ebi. ac. uk/arrayexpress/ : "Trout_imm_v1"_(Agilent array design 028918) with platform accession A-MEXP-2315.
Study population and treatments The assessment of HRQOL was a secondary endpoint of a multicentric open label randomized phase IIb trial performed to test the hypothesis that the addition of TG4010 to first line roles of these authors are articulated in the 'author contributions' section. Competing Interests: This study was supported by Transgene SAS. This work is a contribution to ADNA (Advanced Diagnostics for New Therapeutic Approaches), a program dedicated to personalized medicine, coordinated by Institut Mérieux and supported by the French public agency Bpifrance. GL, BB and JML are full time employees of Transgene SA. There are no patents related to the quality of life data presented in the publication, however. TG4010 is a product in development, not marketed so far and protected by a family of patents.
This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials. chemotherapy would improve the outcome in patients with advanced NSCLC (NCT00415818). The main eligibility patients' criteria were patients aged 18 years or older with a confirmed stage IIIb or IV NSCLC, chemotherapy naive for this stage of the disease, expressing MUC1, with at least one lesion measurable by CT-scan according to World Health Organization, a performance status (PS) of 0 or 1 and a life expectancy of at least 4 months. Patients were excluded if they had received prior systemic therapy for advanced stage NSCLC, or if they had concomitant brain metastases (unless successfully treated) or history of another malignancy within the past 5 years, apart from basal-cell carcinoma of the skin or intraepithelial carcinoma of the cervix.
Statistical analysis Patient's socio-demographic and clinical characteristics at baseline were described. The percentage of available questionnaires was reported at each assessment. Patients with HRQOL questionnaire fully completed at baseline and those with at least one missing item at baseline were compared according to baseline characteristics and treatment arm in order to detect nonrandom missing data profiles. Scores were calculated using the simple imputation method by the mean following the FACT-L scoring guidelines  [16]. Scores were described by treatment arm at each measurement time using the mean and standard deviation (SD). Mean difference and 99% confidence interval (99%CI) were calculated at baseline. If the outcome data was normally distributed, Student t test was employed. However, if the outcome data was not normally distributed, Mann Whitney test was used instead.
However, when treated by TG4010 with a normal level of aNK cells tended to present a longer TUDD than patients with a high level of aNK cells. Nevertheless, we failed to demonstrate a statistically significant interaction between treatment arms and level of aNK cells, probably due to a lack of statistical power. Moreover, there were more patients with no follow-up measure in the subgroup of high level of aNK cells: it is suspected that these patients had a lower general health status than those with normal level of aNK cells and were unable to complete HRQOL questionnaires. In subgroup exploratory analyses, a deleterious effect on FWB score was observed in patients with high level of aNK cells, but not statistically significant. A phase IIb-III study taking into account the pre-treatment level of aNK cells has been initiated to prospectively validate these clinical results and further analyze the evolution of HRQOL under chemo-immunotherapy with an acceptable statistical power (NCT01383148).
Bioinformatic analyses Data pre-processing and analysis were performed using R/Bioconductor packages. Data quality was assessed using box plots for the distribution of methylated and unmethylated signals, and multidimensional scaling plots and unsupervised clustering were used to check for sample outliers. Quantile-normalized data were used to infer blood cell subtypes based on Houseman's regression calibration, as previously described. 16, 17 Cross-reactive probes, probes mapping to sex chromosomes and probes overlapping with a known single nucleotide polymorphism (SNP) with an allele frequency of at least 5% in the overall population (all ethnic groups) were also removed, as previously described. 18 After background correction and colour-bias adjustment, type I and type II probe distributions were aligned using the intra-array beta-mixture quantile normalization from the wateRmelon package.
01) containing five informative CpG sites at the microRNA hsa-miR-4520B locus. Importantly, aflatoxin-associated loci included growth factor genes such as FGF12 and IGF1, and immune-related genes such as CCL28, TLR2 and TGFBI. In addition, AfMSs included three sites within the TRNA-YW(Wybutosine) Synthesizing Homolog gene TYW3 locus. However, performing pathway/ontology analysis in HM450 data may result in spurious associations due to the unbalanced representation of probes for different genes within the array. 26 To overcome this issue, we adjusted for the number of probes per gene symbol and selected only those genes with at least one CpG site below the FDRadjusted P value threshold of 0. 05 (see Methods). Using this strategy, we obtained 53 unique gene symbols for pathway analysis (out of 71 AfMSs on the original analysis).
RNA quality and concentration were assessed by agarose gel electrophoresis and a NanoDrop ND-1000 spectophotometer (Nanodrop® Technologies, Wilmington, DE, USA). RNA was processed for the use on Affymetrix ARAGene 1. 1ST arrays as described by the manufacturer. In brief, Biotin-labeled cDNA was prepared using the Affymetrix NuGEN PicoSL WTA v2 kit and Biotin Module from 50 ng total RNA. The ss-cDNA was fragmented, denaturized and used for hybridization on the Affymetrix ARAGene 1. 1ST array plate. The Affymetrix HWS Kit for GeneTitan was used for hybridization, washing and staining of the array plates. The array plates were scanned using the Affymetrix Command Console v3. 2 software. All data are MIAME compliant as detailed on the MGED society website http://www. mged. org/Workgroups/MIAME/miame.
Quality control The quality control was performed in the software Affymetrix Expression Console v. 1. 2. 1. In order to minimize the effect of probespecific affinity differences, the Robust Multichip Analysis (RMA-Sketch for gene level analysis) algorithm  [5]  was used for the summarization. Signal intensities were extracted and analyzed using the Bioconductor packages of R  [6]. The data was normalized using the RMA algorithm with the TAIRG v17 cdf file (http://brainarray. mbni. med. umich. edu). A box plot and a correlation heat map were used to detect possible outliers. One replicate of time point 2 h showed the lowest signal and both the box plot and the correlation plot indicated it as an outlier. Therefore, this replicate was removed for further analysis.
Acknowledgment Los Alamos National Laboratory , an affirmative action/equal opportunity employer, is operated by  Los Alamos National Security, LLC , for the  National Nuclear Security Administration of the U. S. Department of Energy  under contract  DE-AC52-06NA25396. This publication is LA-UR-14-28168. Work at  Lawrence Livermore National Laboratory  performed under the auspices of the  U. S. Department of Energy  under Contract  DE-AC52-07NA27344. LANL and LLNL thank the  U. S. Department of Energy's National Nuclear Security Administration, Office of Non-proliferation and International Security , for financial support.