dataesr/scientific-paragraphs-categorization huggingface dataset:
DISCUSSION AND CONCLUSION The radiometric data from the 2014 season are coherent enough to provisionally date this part of the OAI1 cemetery to the 9 th -6 th c. BC, which sits within the now solidly founded Bronze Age sequence of 11 th -5 th c. BC from neighbouring Thailand  (Higham, in press ). However, before we can attribute OAI1 to a now radiometrically-quantified Myanmar Bronze Age phase, we must consider that the site's sole bronze artefact comes from S15. This burial, nominally dated to the 4 th -3 rd c. BC, would, both regionally and nationally, typically be considered Iron Age  (Higham, in press, Pryce et al. , 2013). This fits awkwardly with S15's stratigraphy, which suggested it should correspond to an earlier OAI1 subphase of north-south aligned burials, and the burial was also distinguished by containing the highest single concentration of pottery in the cemetery.
The remaining issue we should briefly address with the preliminary dataset is the relation between our putative Myanmar Bronze Age and its regional neighbours; especially, whether our 9 th -8 th c. BC Nyaung'gan proxy, OAI1, is a middle Bronze Age cemetery according to the Thai chronology or an early Bronze Age cemetery within Myanmar's own sequence. By this we explicitly question whether there is a 2-3 century gap between the Thai and Myanmar Bronze Ages, which in the future must be explained in terms of cultural and technological transmission mechanisms, or whether we simply haven't yet straddled the Myanmar Neolithic-Bronze Age transition, which means we need to test more sites. We acknowledged in section two that a majority of previous scholars, based upon their initial impressions of grave good typology, decoration and technological sophistication, anticipated that Nyuang'gan was not an 'early' Bronze Age site and attributed it to the 1 st millennium BC  (White, n.
ACKNOWLEDGEMENTS We wish to express our deep gratitude to His Excellency the  Myanmar Minister of Culture , his staff and the Director General and his staff at the  Department of Archaeology in Naypidaw. In Mandalay we are also indebted to the Director General of the regional Department of Archaeology and his most supportive team. In Yangon we acknowledge the tireless help and backing offered by the  French Embassy and French Institute , in particular that of the  Cultural Attaché ,  M. Charles Bonhomme , his deputy,  M. Sebastien Bris , and his administrator,  Mme Yi Mon. The Mission Archéologique Française au Myanmar is generously financed by grants from the  French Ministry of Foreign Affairs and International Development , as well as contributions from the  CNRS UMR 7055 "Préhistoire et Technologie " based at the  Université de Paris Ouest La Défense.
A critical evaluation of diagnostic and therapeutic procedures was performed, including assessment of the risk -benefit ratio. Estimates of expected health outcomes for larger populations were included, where data exist. The level of evidence and the strength of the recommendation of particular management options were weighed and graded according to predefined scales, as outlined in Tables  1  and 2. The experts of the writing and reviewing panels provided declaration of interest forms for all relationships that might be perceived as real or potential sources of conflicts of interest. These forms were compiled into one file and can be found on the ESC website (http:// www. escardio. org/guidelines). Any changes in declarations of interest that arise during the writing period must be notified to the ESC and updated.
A deep and strand-specific RNA sequencing strategy was adopted in order to experimentally refine genome annotation for strain CFBP 5828R. This approach also allowed the experimental definition of novel ORFs and non-coding RNA transcripts. Using a constitutively active allele of hrpG, a master regulator of the type III secretion system, a HrpG-dependent regulon of 141 genes co-regulated with the type III secretion system was identified. Importantly, all these genes but seven are positively regulated by HrpG and 56 of those encode components of the Hrp type III secretion system and putative effector proteins. Conclusions: This dataset is an important resource to mine for novel type III effector proteins as well as for bacterial genes which could contribute to pathogenicity of X. campestris.
Analysis of the transcriptome of strain CFBP 5828R by RNA sequencing improves genome annotation In order to identify genes co-regulated with the T3S system, strain CFBP 5828R of X. campestris pathovar raphani was transformed either with an empty vector (pBBR1MCS-2) or the same vector expressing a constitutively active form of the hrp master regulator HrpG (HrpG*, mutation E44K). Total RNA was purified from cells growing exponentially in MOKA rich medium and derived from three independent biological experiments. After removal of rRNA by oligonucleotide-capture, these six samples were size-fractionated to discard the smallest RNA fraction (less than 200bp) and were subjected to strand-specific RNA sequencing on an Illumina HiSeq2000 platform. Sequencing yielded from  12  The CFBP 5828R genome sequence was first reannotated taking advantage of this large dataset using Eugene-P software  [37].
euvesicatoria, X. citri pv. citri and X. campestris pv. campestris (10-fold, 700-fold and 400-fold respectively)  [38, 52, 53]. The size of this dataset is also far above the accepted limit (5-10 millions non-rRNA reads per library) for correct expression profiling, gene discovery or gene reannotation  [55]. The RNA reads were first used to improve the structural annotation of the genome using the Eugene-P pipeline. One important difference of our RNA sequencing approach with most of the above-mentioned reports is the use of strandspecific libraries. Such libraries enable to assign individual reads to a specific DNA strand in the genome and therefore allow, for instance, to identify overlapping or antisense RNA molecules: 72 ncRNA overlap with CDS such as the three T3E genes xopR, xopL and xopP in X.
Genome sequencing and assembly Shotgun sequencing of genomic DNA was performed on HiSeq2000 Illumina platform. Paired-end (ca. 300-bp inserts) and mate-pair (ca. 3-kb inserts) libraries were sequenced to generate 101-bp and 51-bp paired reads respectively. Genome assembly was performed using a combination of SOAPdenovo (Short Oligonucleotide Analysis Package, version 2. 04)  [30] , SOAPGapCloser (version 1. 12) and Velvet (version 1. 2. 02)  [31]  assemblers. Contigs obtained were re-ordered into pseudomolecules (corresponding to chromosome or plasmids) with the Mauve software (version 2. 3. 1 build 1)  [60]  based on the reference genome X. campestris pv. campestris strain 8004, and public Xanthomonas plasmid sequences available on NCBI (X. axonopodis pv. citri str. 306 plasmid pXAC64, NC_003922; X.
Genome structural annotation Structural annotation was done using Eugene-P software  [37]. This modular software allows the integration of several sources of high-throughput data such as protein similarities, DNA homologies, predicted transcription terminators and transfer RNA genes and others. We trained Eugene-P with the public annotation of X. campestris pv. campestris strain B100 (available on NCBI website under the accession number NC_010688), X. campestris pv. campestris strain 8004 (NC_007086) and X. campestris pv. campestris strain ATCC 33913 (NC_003902) and at a lower weight with the Swissprot database (version of 04 February 2013). For strain CFBP 5828R, all RNA sequencing libraries were merged and used by Eugene-P to predict structural annotations of mRNA as described  [37]. Identification of core and accessory genes in X.
Phylogeny of X. campestris genomes Phylogenetic analysis was performed based on OrthoMCL analyses. Only groups composed of one single protein in each strain was used to build what we defined as the core proteome. For each of these groups, we aligned the protein sequences using MAFFT software  [65]  and cleaned alignment using trimAl software  [66]  to remove all positions in the alignment with gaps in 10% or more of the sequences. Alignment files were converted in phylip format. Phylogenetic tree was constructed using PhyML  [67]. Identification of candidate type III-secreted proteins in X. campestris strains CFBP 5825R, CFBP 1606R, CFBP 2527R and CFBP 5828R Protein sequence of T3SP from strains X. campestris pv. campestris 8004 and B100, X. euvesicatoria 85-10, X. campestris pv. raphani 756C or X.
Analysis of RNA sequencing results and statistical analyses Mapping of RNA sequencing reads on CFBP 5828R genomic sequence was done using the Glint software (Faraut T. and Courcelle E. ; http://lipm-bioinfo. toulouse. inra. fr/download/glint/, unpublished) integrated in the Eugene-P pipeline. Parameters used were the following: matches allow no gap, a minimum length of 40 nucleotides and no more than one mismatch. We kept only the reads with the best score when several reads mapped to two different positions with different scores. Reads mapping at two different positions with the same best scores were not considered. Differential expression of genes was calculated with R (v2. 13. 0) using DESeq (v1. 4. 1)  [40]. Variance was estimated using the per-condition argument. p-values were adjusted for multiple testing using the Benjamini and Hochberg method  [68].
Acknowledgements We are grateful to Genotoul,  Génopôle Toulouse-Midi Pyrénées  for allowing access to computing resources. We wish to thank  Jeri Barak-Cunningham  ( University of Wiscosin, Madison ) for valuable comments on the manuscript. This work was supported by a PhD grant from the  French Ministry of National Education and Research and French Guyana  to EG, the  LABEX TULIP  ( ANR-10-LABX-41  and  ANR-11-IDEX-0002-02 ) and grants from the  Agence Nationale de la Recherche  ( XANTHOMIX ANR-2010-GENM-013-02  and Xopaque  ANR-10-JCJC-1703-01 ). Author details 1  INRA ,  UMR 441 Laboratoire des Interactions Plantes Micro -organismes (LIPM), F-31326 Castanet-Tolosan, France. 2  CNRS ,  UMR 2594 Laboratoire des Interactions Plantes Micro -organismes (LIPM), F-31326 Castanet-Tolosan, France.
,151,406 (A) flg22 (B) elf18 8004 ATCC33913 Xca5 JX B100 to 23,835,557 reads of 51 bp per sample containing 3-16 % Xcc CN14 CN15 of reads corresponding to rRNAs plus tmRNAs [Genbank XcNP Sequence Read Archive: SRR1025987 to SRR1025992, CFBP 5825R CN16 Xci CFBP 2527R CFBP 1606R Xcr 756C CFBP 5828R Fig. 2Conservation in Xanthomonas campestris of flg22 (a) and elf18 (b) peptides from FliC and EF-Tu PAMP proteins, respectively. Peptides with/ without predicted elicitor activity are in black/grey, respectively. Residues which are essential for elicitor activity and polymorphic in X. campestris are underlined in black http://www. ncbi. nlm. nih. gov/Traces/sra/?study= SRP032762].
Clinical characteristics After excluding individuals receiving anti-hypertensive treatment, the eligible sample size was 7017 (FHS, n = 3679; EGCUT, n = 972; RS, n = 604; InCHIANTI, n = 597; KORA F4, n = 565 SHIP is part of the Community Medicine Research net of the University of Greifswald, Germany, which is funded by BMBF (grants no. 01ZZ9603, 01ZZ0103, and 01ZZ0403), the Ministry of Cultural Affairs as well as the Social Ministry of the Federal State of Mecklenburg-West Pomerania, and the network 'Greifswald Approach to Individualized Medicine (GANI_MED)' funded by the BMBF (grant 03IS2061A). Generation of genome-wide data has been supported by the BMBF (grant no. 03ZIK012). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Discussion Our meta-analysis of gene expression data from 7017 individuals from six studies identified and characterized whole blood gene expression signatures associated with BP traits. Thirtyfour BP signature genes were identified at Bonferroni corrected p<0. 05 (224 genes were identified at FDR<0. 2, reported in the S1 Text). Thirteen BP signature genes replicated between the FHS and Illumina cohorts. The top BP signature genes identified in the FHS (55 genes for SBP and 22 genes for DBP) explained 5-9% of interindividual variation in BP in the Illumina cohorts on average. Among the 34 BP signature genes (at Bonferroni corrected p<0. 05), only FOS  [15]  and PTGS2  [16]  have been previously implicated in hypertension. We did not find literature * rs653178, intronic to ATXN2 and in tight linkage disequilibrium with rs3184504 (r 2 = 1), was also associated with BP in ICBP GWAS and all the 6 genes; + A proxy SNP rs4698412 at LD r 2 = 1 associated with the same trait; $ A proxy SNP rs4389526 at LD r 2 = 1 associated with the same trait; § indicated eQTL were identified from  [12].
Gene expression profiling RNA was isolated from whole blood samples that were collected in PaxGene tubes (PreAnaly-tiX, Hombrechtikon, Switzerland) in FHS, RS, InCHIANTI, KORA F4 and SHIP-TREND, and in Blood RNA Tubes (Life Technologies, NY, USA) in EGCUT. Gene expression in the FHS samples used the Affymetrix Exon Array ST 1. 0. EGCUT, RS, InCHANTI, KORA F4, and SHIP-TREND used the Illumina HT12v3 (EGCUT, InCHANTI, KORA F4, and SHIP-TREND) or HT12v4 (RS) array. Raw data from gene expression profiling are available online (FHS [http://www. ncbi. nlm. nih. gov/gap; accession number phs000007], EGCUT [GSE48348], RS [GSE33828], InCHIANTI [GSE48152], KORA F4 [E-MTAB-1708] and SHIP-TREND [GSE36382]). The details of sample collection, microarrays, and data processing and normalization in each cohort are provided in the S2 Text.
The proportion of the variance in BP phenotypes attributable to the FHS BP signature genes was estimated in the five Illumina cohorts, respectively, and then the average proportion values were reported. In turn, the proportion of the variance in BP phenotypes attributable to the Illumina BP signature genes was estimated in the FHS. Identifying eQTLs and estimating the proportion of variance in gene expression attributable to single cis-or trans-eQTLs SNPs associated with altered gene expression (i. e. eQTLs) were identified using genome-wide genotype and gene expression data in all available FHS samples (n = 5257) at FDR<0. 1 (Joehanes R, submitted, 2014, and a brief summary of methods and results are provided in the S2 Text). A cis-eQTL was defined as an eQTL within 1 megabase (MB) flanking the gene.
Acknowledgments We thank the field staff in Augsburg who was involved in the conduct of the studies. The authors are grateful to the study participants, the staff from the  Rotterdam Study  and the participating general practitioners and pharmacists. We thank  Marjolein Peters, MSc ,  Ms. Mila Jhamai ,  Ms. Jeannette M. Vergeer-Drop ,  Ms. Bernadette van Ast-Copier ,  Mr. Marijn Verkerk  and  Jeroen van Rooij, BSc  for their help in creating the RNA array expression database. This study utilized the high-performance computational capabilities of the Biowulf Linux cluster at the  National Institutes of Health, Bethesda, MD. (http://biowulf. nih. gov).
The  Framingham Heart Study  is funded by  National Institutes of Health  contract  N01-HC-25195. The laboratory work for this investigation was funded by the  Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health. The analytical component of this project was funded by the  Division of Intramural Research, Research) , partner site  National Heart, Lung, and Blood Institute , and the  Center for Information Technology, National Institutes of Health, Bethesda, MD. EGCUT is supported by targeted financing from the  Estonian Ministry of Science and Education  [SF0180142s08]; the  Development Fund of the University of Tartu  (grant  SP1GVARENG ); the  European Regional Development Fund  to the  Centre of Excellence in Genomics  (EXCEGEN; grant  3.
2. 0304. 11-0312 );and through  FP7  grant  313010. AD is supported by  NWO  grant (veni,  916. 12. 154 ) and the  EUR  Fellowship. The  Rotterdam Study  is funded by  Erasmus Medical Center  and  Erasmus University, Rotterdam ,  Netherlands Organization for the Health Research and Development (ZonMw) , the  Netherlands Organisation of Scientific Research NWO Investments  (nr. 175. 010. 2005. 011 , 911-03-012 ), the  Research Institute for Diseases in the Elderly  ( 014-93-015 ;  RIDE2 ), the  Ministry of Education, Culture and Science, the Ministry for Health, Welfare and Sports , the  European Commission (DG XII) , and the  Municipality of Rotterdam. The generation and management of RNA-expression array data for the Rotterdam Study was executed and funded by the  Human Genotyping Facility of the Genetic Laboratory of the Department of Internal Medicine, Erasmus MC , the  Netherlands.
The  InCHIANTI study was  supported in part by the  Intramural Research Program ,  National Institute on Aging. DM was generously supported by a  Wellcome Trust   Institutional Strategic Support Award  ( WT097835MF ). The KORA research platform and the KORA Augsburg studies are financed by the  Helmholtz Zentrum München, German Research Center for Environmental Health , which is funded by the  BMBF  and by the  State of Bavaria. Furthermore , KORA research was supported within the  Munich Center of Health Sciences  ( MC Health ),  Ludwig Maximilians-Universität , as part of the  LMU  innovative and in part by a grant from the  BMBF  to the  German Center for Diabetes Research (DZD). The  German Diabetes Center  is funded by the  German Federal Ministry of Health  and the  Ministry of School, Science and Research of the State of North-Rhine-Westphalia.
Additional support was obtained from the  BMBF (National Genome Research Network NGFN plus Atherogenomics ,  01GS0834 ), by the  DZHK (Deutsches Zentrum für Herz-Kreislauf-Forschung -German Centre for Cardiovascular Research)  and from the  European Commission 's  Seventh Framework Programme  ( FP7/2007-2013 ,  HEALTH-F2-2011 , grant agreement No. 277984 , TIRCON and  HEALTH-F2-2013 , grant agreement No. 603288 , SysVasc). SHIP is supported by the  BMBF (German Ministry of Education and Research)  and by the  DZHK (German Centre for Cardiovascular Research)  within the framework of the  MetaXpress consortium. with prior GWAS, provides a deeper understanding of the molecular and genetic basis of BP regulation, and identifies several potential targets and pathways for the treatment and prevention of hypertension and its sequelae.
| Participants As part of the training course development study, we recruited 12 patients with knee OA and five physiotherapists. Each physiotherapist worked in the UK NHS (National Health Service) and had at least 3 years of experience of treating patients with musculoskeletal pain. They were identified through advertisements in NHS departments. None of the physiotherapists had any previous experience of the CMT intervention and completed 20 h of online learning followed by a 1-day face-to-face workshop. To guide the delivery of the CMT intervention, the physiotherapists were expected to follow a clearly defined protocol, which was designed to lead the patient through an incremental learning process. Patients with knee OA were identified through a volunteer database, through community sites in outpatient clinics and social media adverts.
Each of the 12 patients with knee OA received seven sessions of CMT from one of the physiotherapists, with each physiotherapist delivering to at least two patients. Patients were also provided with access to an online learning platform. The platform included videos and written materials to support the information and learning provided in each clinical session. The videos and materials were developed through an iterative process with 21 patients (described in full in  Preece et al. (2021). An example of one of the videos can be accessed at www. cogmustherapy. com/BMC_example_ 2. Quantitative data on changes in knee pain which happened across the delivery of the intervention are reported in a separate publication  (Preece et al. , 2023). For this study, each of the five physiotherapists was interviewed along with five of the patients.
| Analysis Interviews were conducted online, audio-recorded, and transcribed verbatim. Identifying information was then deleted from the transcripts and pseudonyms were assigned (pseudonyms: Ash, Kelly, Blair, Frankie and Robin). Inductive reflexive thematic analysis  (Braun & Clarke, 2019)  was conducted together by DG and NW. They both familiarised themselves with the data through repeated reading of the transcripts and discussion of initial line-by-line coding, and through an iterative discussion, an analysis plan was developed. The final thematic structure and narrative summaries were developed by DG. Through discussions between DG and NW regarding the narrative summaries, a timeline framework was developed to understand how patients and physiotherapists were conceptualising pain and how this changed throughout their interactions with CMT.
With the advent of new GNSSs, a wider range of attitude control laws arises and a variety of manufacturer-specific conventions for the individual spacecraft coordinate systems has to be handled. As part of its Multi-GNSS Experiment (MGEX;  Montenbruck et al. , 2014) , the IGS already provides early data products for many of the new constellations (including the European Galileo system, the Chinese BeiDou Navigation Satellite System, and the Japanese Quasi-Zenith Satellite System QZSS). Therefore, a need for a uniform and traceable description of the nominal spacecraft attitude as well as the GNSS antenna and SLR retroreflector coordinates has emerged. In response to this need, the present article provides a description and mathematical formulation of GNSS attitude control laws for all satellite navigation systems currently in operation or under construction.
On top of this, an IGS-specific convention for the labeling of spacecraft axes is introduced as an alternative to the manufacturer-specific systems. To the extent possible, the application of this convention enables a uniform description of the nominal (yaw-steering) attitude across all   (ILRS, 2015a; Yang, 2008; Zhang, 2012c). i BeiDou I3, I5 (ILRS, 2015a; Zhang, 2012b). j BeiDou G1 (ILRS, 2015a; Zhang, 2012a). k w. r. t. CoM of 7/2012  (Nakamura and Kishimoto, 2010; Kogure, 2012). l ILRS (2015f) and  Ganeshan (2014). GNSS constellations and spacecraft brands. Limited exceptions such as the orbit-normal mode employed by individual QZSS and BeiDou satellites or the biased yaw-steering mode of IRNSS are identified and described. The body axes conventions introduced here offer a common standard for IGS product generation and data exchange.
Thus, accounting for AS patterns in cancer is becoming an important challenge because specific AS events may represent useful biomarkers while the development of spliceosome-  [21]  and AS-specific  [22, 23]  therapeutic tools are in progress. Here we investigated whether the expression of certain oncogenes and the resistance of AML cells to anti-cancer drugs might be associated with specific exon expression patterns. We used exon array analysis confirmed by exon-specific PCR (ESPCR) to evaluate AML cells expressing various amounts of either DEK or WT1 and AML cells that show sensitivity or resistance to AraC, doxorubicin (DXR) or azacitidine (AZA). Data gathered from cell lines were confirmed in patient-derived samples in which exon-arrays confirmed by exon-specific RT-PCR permitted the identification of specific exon expression patterns that are putatively involved in disease phenotypes and responses to treatment.