dataesr/scientific-paragraphs-categorization huggingface dataset:
R. M. M. was supported by a  Cancer Research UK  ( C18281/A19169 ) programme grant (the  Integrative Cancer Epidemiology Programme ) and is part of the  Medical Research Council Integrative Epidemiology Unit at the University of Bristol  supported by the  Medical Research Council  ( MC_UU_12013/1 ,  MC_UU_12013/2 , and  MC_UU_12013/3 ) and the  University of Bristol. R. M. M. and A. R. N. are supported by the  National Institute for Health Research (NIHR) Bristol Biomedical Research Centre  which is funded by the  National Institute for Health Research (NIHR)  and is a partnership between  University Hospitals Bristol and Weston NHS Foundation Trust  and the  University of Bristol. This publication presents data from the  Head  and  Neck 5000 study. The study was a component of independent research funded by the  NIHR  under its  Programme Grants for Applied Research scheme  ( RP-PG-0707-10034 ).
The views expressed in this publication are those of the author(s) and not necessarily those of the  NHS , the  NIHR  or the  Department of Health. Core funding was also provided through awards from  Above and Beyond, University Hospitals Bristol Research Capability Funding  and the  NIHR Senior Investigator  award to A. R. N. B. D. and the  University of Pittsburgh  head and neck cancer case-control study are supported by  US National Institutes of Health (NIH)  grants:  P50 CA097190 ,  P30 CA047904  and  R01 DE025712. The genotyping of the HNSCC cases and controls was performed at the  Center for Inherited Disease Research (CIDR)  and funded by the  US National Institute of Dental and Craniofacial Research  ( NIDCR ;  1X01HG007780-0 ). The  University of North Carolina (UNC)  CHANCE study was supported in part by the  National Cancer Institute  ( R01-CA90731 ).
Code availability Two-sample MR analyses were conducted using the TwoSampleMR package (version 0. 5. 5) in R (version 3. 5. 3). Multivariable MR analysis was conducted using both the MVMR (version 0. 2. 0) and MendelianRandomization (version 0. 5. 0) 48 packages in R. A copy of the code used in this this analysis is available at: https://github. com/rcrichmond/ smoking_alcohol_headandneckcancer  49.
Data availability GWAS summary statistics for the SNPs used to estimate the causal effects of smoking initiation, lifetime smoking and alcoholic drinks per week in this study are presented in Supplementary Data 1 and 2. Full summary statistics for the GAME-ON GWAS have been deposited in dbGAP (OncoArray: Oral and Pharynx Cancer; study accession number: phs001202. v1. p1)  30. Published data from this study can also be found in: Lesseur, C. et al. Genome-wide association analyses identify new susceptibility loci for oral cavity and pharyngeal cancer. Nat Genet. 48, 1544-1550 (2016)  30. Smoking initiation and alcohol consumption data (GSCAN study) are published in: Liu, M. Z. et al. Association studies of up to 1. 2 million individuals yield new insights into the genetic aetiology of tobacco and alcohol use.
4. 11. 7), an enzyme that has been shown to be present in blood serum. Although this zinc-containing enzyme is sensitive to inhibition by 1,10-phenthroline and amastatin, the inhibitor studies would not be expected to reveal this since removal of the terminal leucine would be necessary for the enzyme to act. Cleavage of the Lys-Phe bond to produce 1-6 and 2-6 was catalysed by a phosphoramidon-sensitive metallo-endopeptidase. These enzymes belong to the M13 (neprilysin) family of peptidases, as classified by the MEROPS peptidase database  [19] , which includes, in addition to neprilysin (neutral endopeptidase; EC 3. 4. 24. 11)  [20, 21] , peptidyl-dipeptidase A (ACE, angiotensin converting enzyme; EC 3. 4. 15. 1)  [22]  and the erythrocyte Kell protein  [23]. Both peptidyl-dipeptidase A  [7]  and neprilysin  [21]  have been shown to catalyse this cleavage in isolated THF.
MCPyV integration and LT truncation in the MCC Two molecular features characterize MCPyV-associated MCC. First, the virus genome is clonally integrated into the genome of the tumor cells  (Feng et al. , 2008) , and second, the LT antigen coding sequence is always affected in a way leading to expression of a truncated protein  (Shuda et al. , 2008). Applying a combination of whole genome and Sanger sequencing onto DNA isolated from the MCC part, we could detect and confirm integration of MCPyV in chromosome 3 of the tumor genome (Figure  2a  and b ). Moreover, the presence of MCPyV sequences beyond the unique break points suggest integration of a concatemer consisting of one or more viral copies in addition to the sequence between the break points. Sequencing further indicates that even two differently truncated LT proteins may be expressed in the MCC part, one truncation caused by the integration break point at base pair 1956, the other by a deletion spanning base pairs 2248e2542 (both according to GenBank EU375803) (Figure  2b ).
HPS, hematein-phloxin-saffron; KRT, keratin; LT, large T antigen; MCC, Merkel cell carcinoma; MCPyV, Merkel cell polyomavirus; TB, trichoblastoma. DNA isolated from the MCC part of the combined tumor was analyzed by WGS and confirmed by Sanger sequencing. The integration break points in the viral genome (Genbank EU375803) as well as in chromosome 3 (GRCh37; NC000003. 11) are depicted. To note, human sequences adjacent to the integration break points were found to be swapped. Moreover, sequencing revealed a deletion in the viral genome (D2248e2542). Frequently, MCPyV integrates as a head to tail concatemer. In this case, nucleotides 1557e1956 are followed by one or more full length copies (1957e1956), which is predicted to lead to (b) one or two different truncated LT proteins expressed in the MCC part.
Data analysis Demultiplexing of the sequencing reads was performed with  Illumina bcl2fastq (v2. 19). Adapters were trimmed with Skewer, v0. 2. 25  (Jiang et al. , 2014). An initial quality assessment was performed using  FastQC, v0. 11. 5 (Andrews, 2010 , available online at: http:// www. bioinformatics. babraham. ac. uk/projects/fastqc). Low-quality reads were trimmed with TrimGalore, v0. 4. 0 (Krueger, 2012, available online at: http://www. bioinformatics. babraham. ac. uk/projects/ trim_galore/) powered by Cutadapt, v1. 86  (Martin, 2011). The trimmed reads were mapped to the human reference genome (hg19) using BWA mem, v0. 7. 127  (Li and Durbin, 2009)  and sorted and indexed using Picard, v1. 125 (available online at: http:// broadinstitute. github. io/picard/) and SAMtools, v1. 38  (Li et al.
ACKNOWLEDGMENTS The authors thank  A. Balaton ,  L. Durand ,  J. Mabille , and  S. Manela  for their help and contribution. The study was supported by  Fondation ARC pour la recherche contre le cancer, Interdisziplina ¨res Zentrum fu ¨r Klinische Forschung Wu ¨rzburg  ( IZKF B-343 ), and  LEO Foundation  Award to DS. Ligue nationale contre le cancer, Comites 16, 18, 28. The  local Ethics Committee of Tours (France)  approved the study (no. RCB2009-A01056-51 ).
Dangling chains and free chains are also shown. presence of some porous microstructure. For 5 wt% crosslinker the apparent surface roughness increased and the contrast of the surface features captured became sharper. For the two highest cross-linker concentrations, sharp contrast and a morphology showing a nanoporous appearance were observed. For the quantitative analysis of the surface structures, average pore size and pore size distribution, porosity (surface coverage), and roughness values were estimated from AFM images taken at five different spots for each sample. These data are presented in Figure  2  and Tables  1  and 2. Mesh size distributions were estimated using the ImageJ image processing software (version 1. 50b). Each distribution presented in Figure  2  was determined from 200 pores analyzed.
In this study, we used two AFM setups, including a MultiMode 8 AFM instrument (Bruker) supplied by a JV vertical engage scanner and a Dimension Icon microscope (used only to image mechanically stretched samples under tension), both retrofitted with a NanoScope V controller (Bruker). Imaging was performed in the PF-QNM mode to allow to capture topography images at controlled normal forces. The AFM data were collected following a sine-wave sample-tip trajectory with a frequency of 2 kHz and utilizing a peak-force amplitude value of 150 nm. The ScanAsyst optimization in the user interface was set to "on" to acquire high-resolution images at low applied normal forces and to automatically adjust the feedback loop control. Images were captured at constant applied normal forces, employing the "best" scan parameters found by the ScanAsyst for a specific scan area.
Two types of soft, rectangular, silicon-made cantilevers were used, i. e. , OMCL-AC240TS (Olympus) and HQ:NSC19/Al BS (µMasch) with a nominal tip radius of 7 and 8 nm, respectively. Image processing and data analysis were conducted with the NanoScope (version 8. 15-MultiMode 8 AFM, version 9. 4-Dimension Icon AFM) and the NanoScope Analysis software (version 1. 9), respectively. Measurements were performed in air and at room temperature (≈21 °C). Since the AFM measurements are highly sensitive to tip shape, new AFM tips were used in each consecutive experiment. For examples of tip profiles captured with a high-resolution scanning electron microscope (SEM), see Figure  S1  (Supporting Information).
Acknowledgements V. D. , H. G. , M. A. H. , and G. J. V. acknowledge the  University of Twente  for financial support. V. D. , A. A. , and C. N. thank for funding by the project  E2S   UPPA (Energy and Environment Solutions ) and  POCTEFA HEALTH LSR 2017-146  ( Région Nouvelle Aquitaine   1R10103-00013013 ).
From Peugeot' s personnel registration registers, it is possible to find out the number of people hired per year and to conduct analyses based on information about each worker at the time they were hired, including nationality, housing, age, family situation, and their previous employer or occupation. Analysis of these data allows for observations of, for example, whether there were differences between nationalities or whether the profile of Yugoslavs was homogeneous. Moreover, the consultation of approximately 600 foreigners' files at the Departmental Archives makes it possible to follow the trajectories of workers from the moment they applied for a visa. Indeed, the files of foreigners are a very rich source of information composed of, among other things, investigations of morality, identity documents, etc.
At depth, mesoscale activity can be evaluated using eddy available potential energy (EAPE), which measures the energy stored in vertical isopycnal displacements  (Lorenz, 1955; Roullet et al. , 2014). In the Argo-based atlas of  Roullet et al. (2014)  Journal of Geophysical Research: Oceans Figure  2d ). The same hotspot of EAPE is more pronounced in  Vic et al. (2018)  (their Figure  2b ), where an updated version of  Roullet et al. (2014)  database is used. Interestingly, this EAPE maximum is not reproduced by their numerical model (which uses a dx ≈ 6 km resolution). An intense deep mesoscale activity in the central RT is also visible in  Fischer et al. (2018) , from the Argo-based eddy kinetic energy distribution at 1,000-1,500 m depth (their Figure  3b ). A surface, semipermanent anticyclone, centered at 55°N, 12°W, was identified by  Xu et al.
In section 4, we use high-resolution (~2 km) numerical simulations  January, partial transect survey), and 2013 (5 January to 20 January, partial transect survey). Data were acquired using a Sea-Bird 9/11 plus CTD probe, with sampling rate of 24 Hz and temperature and conductivity accuracies of ±0. 001°C and ±0. 0003 S m -1 respectively. Independent temperature and salinity calibrations have been performed on discrete water samples using Sea-Bird SBE-35 digital thermometer and a Guildline Portasal salinometer (Model 8410A), respectively  (McGrath et al. , 2012). Additional surveys and data details are provided in Tables  S1  and S2. Preliminary data processing has been performed with Seabird SBE software. Prior to analysis, all downcast data have been averaged to 1 m bins, compiled into a three-dimensional data array format: pressure/depth, station (latitude/longitude), and time (year), that is, [min:max pressure] × [number of stations] × [number of years].
Satellite Altimetry We use delayed-mode absolute dynamic topography (ADT) altimetry data, coinciding with the ship survey sampling, to explore the possible signature of the deep anticyclone at the surface. ADT data are produced by SSALTO/DUACS (Data Unification and Altimeter Combination System), processed and distributed by the Copernicus Marine and Environment Monitoring Service (CMEMS), and available online (http://www. marine. copernisuis. eu). We apply a simple eddy detection algorithm, outlined in section 2. 3. 3. Similarly to  Halo, Backeberg, et al. (2014 ), Halo, Penven, et al. (2014 ), and Laxenaire et al. (2018) , we use objectively mapped ADT, which represents the sum of sea level anomaly and mean dynamic topography, both referenced to over 20 year time-period in the Ssalto/Duacs 2014 ADT data set  (Laxenaire et al.
Surface Imprint of the Deep Anticyclone To identify the surface imprint of the anticyclone and the surrounding eddy field, we compute the Okubo-Weiss (OW) parameter (after  Okubo, 1970, and Weiss, 1991)  and the relative vorticity (ζ) using the weekly composite ADT. The OW parameter is widely used as an eddy detection method and is applicable to defining vortices in both altimetry and model output data sets (e. g. ,  Chelton et al. , 2011; Gula et al. , 2016a; Isern-Fontanet et al. , 2006). The OW parameter is taken as a quantification of strain versus vorticity and equal to s 2 n þ s 2 s -ζ 2 , where s n is the normal strain component, s s the shear strain component, and ζ is the relative vorticity of the two-dimensional field (u and v the zonal and meridional components), with s n = ∂u/∂x-∂v/∂y, s s = ∂v/∂x+∂u/∂y and ζ = ∂v/∂x -∂u/∂y  (Gula et al.
This link is supported by the Lagrangian tracking of particles, falling within the regional MOW 27. 3-27. 7 kg m -3 density range. The RT anticyclone could be viewed as a prime spot for intermediate water masses modifications, with MOW as a primary contributor, as deduced from our water masses fractions analysis and high AHA and ASA estimations. The Lagrangian investigations, confirmed by CTD data from within the anticyclone, show that particles with densities higher than 27. 3 kg m -3 are predominantly the product of isopycnal/diapycnal mixing between particles with MOW and SAIW characteristics. Exploring the impact of the RT anticyclone on water masses modifications in the region in more details is a next step in our upcoming analyses. Our model-based deductions on vortices generation along the south-eastern RT slope and their propagation north-eastward into the trough, or westward into the wider subpolar NA, could be direct/indirect heat and salt injections into the Iceland and Irminger basins, and Nordic Seas, inflicting warming up and salinification of upper regional waters from below via mixing.
Such eddy-induced fluxes and transports may have an impact for the heat and salt regional and possibly large-scale budgets. This further highlights the importance of the eastern NA boundary dynamics, particularly for the meridional heat and salt transports. (https://climatedataguide. ucar. edu/climate-data/soda-simple-ocean-data-assimilation). WOA18 is available online (https://www. nodc. noaa. gov/OC5/woa18/). We thank all filed and scientific teams for the availability of data products. Model sample data are available online (https://github. com/asmilenova/RT_anticy-clone_JGR_Oceans).
Acknowledgments We thank the captains, technicians, crew, and scientific personnel on board the RV  Celtic Explorer  for acquiring the 2006-2013 wintertime CTD data, part of which used here. A. S. PhD studies were supported by  MI, Ireland Cullen Scholarship (grant-aid  agreement No. CF/14/05 ), funded under the  Marine Research Programme ,  2014-2020 , by the  Irish Government. A. S. kindly acknowledges the  Thomas Crawford Hayes Trust research award  from the  School of Earth and Ocean Sciences, NUIG, Ireland , toward investigations presented here, as part of PhD studies. J. G. and M. L. C. gratefully acknowledge support from  Région Bretagne , from the  French National Agency for Research (ANR)  through  the project ISblue "Interdisciplinary graduate school for the blue planet " ( ANR-17-EURE-0015 ) and the project  French National Agency for Research (ANR) ( ANR-19-CE01-0002-01 ).
Data Availability Statement CTD data (MI, Ireland) are available upon request (https://www. marine. ie/Home/marine-institute-requestdigital-data). Gridded altimeter product details and source are provided within text. Bathymetry data set (NGDC, USA) is available online (http://www. ngdc. noaa. gov/mgg/global/relief/ETOPO2/ETOPO2v2-2006/ETOPO2v2g/). ISAS15 data set  (Gaillard et al. , 2016; Kolodziejczyk et al. , 2017)  is available online (https://www. seanoe. org/data/00412/52367). SODA data set  (Carton & Giese, 2008 ) is available online.
, 2009 , Kutchukian, Lo Scrudato et al. , 2016 , Lawlor, Beggs et al. , 2016 , Shichiji, Biancalana et al. , 2013). During the past decade, our lab and others have used rAAV vectors in XLMTM mice and dogs and demonstrated remarkable therapeutic efficacy, paving the way for a recently initiated clinical trial  (Buj-Bello, Fougerousse et al. , 2008 , Buj-Bello, Laugel et al. , 2002 , Childers et al. , 2014 , Mack et al. , 2017) , (ClinicalTrials. gov identifier NCT03199469). Treated XLMTM dogs showed dose-dependent correction of multiple disease phenotypes, resulting in improved muscle function and survival up to 4 years of age  (Elverman, Goddard et al. , 2017 , Mack et al. , 2017). Here, we explored the transcriptional changes driving this correction of muscle morphology and function in treated XLMTM dogs using an unbiased and comprehensive approach based on RNA-sequencing (RNA-seq).
Gene therapy studies rarely investigate the molecular consequences of target cell transduction. With rAAV vectors injected in new patients every year, now including boys suffering from XLMTM (clinical trial NCT03199469), a better understanding of the molecular mechanisms by which NMDs are corrected will become crucial. Recently, one study reported the normalization of microarray gene expression data after dual rAAV gene therapy in a mouse model of oculopharyngeal muscular dystrophy (OPMD),  (Malerba et al. , 2017) , but the authors did not focus on specific genes or gene sub-populations. Here, we provide for the first time a comprehensive picture of muscle transcriptome remodelling after rAAV gene therapy using RNAsequencing. We used hierarchical clustering to group injected dogs based on the extent of transcriptome remodelling rather than on the dose of rAAV injected in vivo.
Sequencing libraries were validated using DNA Analysis Screen Tape on the Agilent 2200 TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2. 0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (Applied Biosystems, Carlsbad, CA, USA). Sequencing libraries were multiplexed and clustered on flow cell using the cBOT from Illumina. After clustering, flow cell was loaded on the Illumina HiSeq instrument according to manufacturer's instructions. The samples were sequenced using a 2x150 Pair-End (PE) High Output configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS) on the HiSeq instrument. Raw sequence data (. bcl files) generated from Illumina HiSeq was converted into fastq files and demultiplexed using Illumina bcl2fastq program version 2.
17. One mismatch was allowed for index sequence identification. The 13 Vastus-mRNA-derived libraries were sequenced to an average of 60M paired-end reads/sample and the 13 Biceps-mRNA-derived libraries were sequenced to an average of 20M paired-end reads/sample. Data analysis: Initial data analysis, including alignment to reference genome and count table generation, was conducted on the DNAnexus platform (Palo Alto, CA, USA). Specifically, fastq files were first mapped onto the reference genome of Canis lupus familiaris (Genome assembly: CanFam3. 1 (GCA_000002285. 2), downloaded from Ensembl. org) using the Subread mapping package  (Liao, Smyth et al. , 2013 , Liao, Smyth et al. , 2014)  (settings: subread-align -t 0 -T 4 -d 50 -D 600 -i my_index -r read1 -S ff -R read2 -o $output_name). The resulting bam files were fed into featureCounts  (Liao et al.
, 2014)  package to obtain the count-per-gene table (settings: featureCounts -p -P -d 50 -D 600 -t exon -g gene_id -a GTF_file -o $output_name bam_file1 bam_file2 bam_file3 bam_file4 bam_file5 bam_file6 bam_file7 bam_file8 bam_file9 bam_file10 bam_file11 bam_file12 bam_file13). Count tables were further analysed with the open-source RStudio environment for R (https://www. r-project. org/), and the Bioconductor software (https://www. bioconductor. org/). The limma  (Ritchie, Phipson et al. , 2015)  and edgeR  (Robinson et al. , 2010)  packages were used to normalize, fit, and compare the data between groups following the analysis pipeline detailed here  (Law, Alhamdoosh et al. , 2016). Cutoff values for DE gene determination were as follows: Pvalue < 0. 05, and fold-change (FC) > 2. 0. The code used to analyse count tables is comprehensively detailed below: # Import.
csv files: read counts (count_table. csv), information about samples and groups (samples_info. csv), and gene annotation file (gene_info. csv) > samples_info <-read_csv("samples_info. csv") > count_table <-read_csv("count_table. csv") > gene_info <-read_csv("gene_info. csv") # Call the packages necessary for data processing and analysis > library(limma) > library(edgeR) > library(genefilter) > library(pheatmap) > library(viridis) > library(dplyr) # Reformat count_table into a matrix of counts with row. names corresponding to the column of gene_info which will be used for gene annotation (e. g. ensembl identifiers). Requires same number of lines in count_table. Gene ontology analyses were performed on the GO consortium online platform (http://geneontology. org/), using the statistical overrepresentation test and the Bonferroni correction for multiple testing.
Enrichments with a corrected P value lower than 0. 05 were considered significant. Data representation: Heatmaps and PCA plots were automatically generated in R-Bioconductor. Other data representations were realized on Graphpad PRISM 7, and Figures were assembled using the vector graphics Inkscape software. The color palette used in this manuscript to distinguish dog groups was extracted from the viridis package on R-Bioconductor and was carefully selected to be easily interpretable by individuals with colorblindness. (https://cran. r-project. org/web/packages/viridis/vignettes/intro-to-viridis. html).
Data availability: The RNA-Sequencing data from this publication have been deposited to the Sequence Read Archive (SRA) database (https://www. ncbi. nlm. nih. gov/sra), and assigned the Bioproject ID PRJNA49575. The read files are available at the following link: https://trace. ncbi. nlm. nih. gov/Traces/sra/sra. cgi?study=SRP165150.
This data challenge, sponsored by Nvidia, took place in Rouen during CAp2018 1 , the yearly French conference on machine learning that gathers specialists in artificial intelligence. The aim was to encourage cross-fertilisation between linguists and specialists of Artificial Intelligence (AI) and Natural Language Processing. The domains of AI and NLP have a long history in data challenges, or shared tasks, especially in the areas of corpus annotation  (Magerman, 1995) , semantic labelling such as named entity recognition  (Sang & De Meulder, 2003) , opinion mining, sentiment analysis  (Liu, 2012)  etc. The challenges usually consist in automatically predicting specific labels for a given task (such as annotation). A training set includes the labels to be predicted whilst a test set does not.