dataesr/scientific-paragraphs-categorization huggingface dataset:
Study population This ancillary study, planned a priori, was performed in one (Henri Mondor University hospital, Creteil, France) of the nine centers participating in the B-type natriuretic peptide (BNP) for the fluid Management of Weaning (BMW) trial  [12]. The BMW study was a randomized, controlled trial comparing a biomarker-guided depletive fluid management strategy to usual care during ventilator weaning. A detailed description of the BMW study design (NCT00473148) has been published previously  [12]. Inclusion criteria of the BMW study were those allowing early initiation of ventilator weaning in patients receiving mechanical ventilation for at least 24 h. Permanent non-inclusion criteria were: pregnancy or lactation, age < 18 years, known allergy to furosemide or sulfonamides, tracheostomy at inclusion, hepatic encephalopathy, cerebral edema, acute hydrocephalus, myasthenia gravis, acute idiopathic polyradiculoneuropathy, decision to withdraw life support, and prolonged cardiac arrest with a poor neurological prognosis.
Statistical analysis The data were analyzed using SPSS Base 20 (IBM-SPSS Inc, Chicago, IL, USA). Categorical variables were expressed as numbers (percentage) and continuous data as medians (25th-75th percentiles), unless otherwise specified. We used the Chi-squared or Fisher exact test to compare categorical variables between groups and the Student's T test, Mann-Whitney test or Wilcoxon paired test to compare continuous variables, as appropriate. A p value of < 0. 05 was considered statistically significant.
0 (Roche Nimblegen). The 64 enriched megabases were sequenced using an Illumina HiSeq 2500 system in rapid run paired-end mode (2x100bp). Raw data (bcl files) was converted to FASTQ files using bcl2fastq v1. 8. 4 (Illumina). Sequences were analyzed as recommended by GATK best practices: mapping was performed using BWA-MEM, variant calling using GATK (haplotype caller). Annotation and filtering steps were performed using VariantStudio (Illumina). Variants files of parents and index case were confronted: only variants that fulfilled recessive inheritance pattern were selected. Among them, variants with allele frequencies above 1% in ESP6500 exome project, and variants not predicted to be deleterious were excluded. The established variants were cross-checked with the 1000 genomes database (http://www.
1000genomes. org/), with the Exome Variant Server (http://evs. gs. washington. edu/EVS/), HGMD (http://www. biobase-international. com/product/hgmd) and with the « clinvar » database (http://www. ncbi. nlm. nih. gov/clinvar/). Upon WES, we detected a homozygous mutation c. 1027C > T; p. Gln343* in exon 8 of the WDR62 gene (Fig. 2a ). Findings from Whole Exome Sequencing (WES) were confirmed by Sanger sequencing. Reference sequence identifier for wild-type WDR62 was obtained from GenBank; Accession: NG_028101, Version: NG_028101. 1. Primers of exon 8 of WDR62 (NM_001083961) were designed using Primer express software V3. 0. The exon 8 of WDR62 gene was amplified with Taq PCR Master Mix Kit (Qiagen Valencia, CA) using a standard amplification protocol, the sequencing reaction was set up with Big Dye Terminator 3.
1 (Applied Biosystems) and remaining dye nucleotides were removed with SephadexTM G-50 superfine (GE Healthcare). Analysis of the amplicons was performed on automated sequencer Applied Biosystems Segregation of the mutation in the family was confirmed by sequencing which showed, as expected, this mutation in the affected children and demonstrated that their parents carry this mutation in heterozygous state (Fig. 2b ). This mutation was previously unreported in various databases (dbSNP, 1000-genomes, Exome Variant Server) and also in our 40 samples of Moroccan exome data results (personal data). This mutation leads to a stop codon 343.
The ab initio potentials computed with MOLCAS  (Aquilante et al. 2010 ) are described in  Hollands et al. (2017). A&A proofs: manuscript no. 34067 The potentials we used were computed by ab initio approaches with the MOLPRO package  (Werner et al. 2012). As for the triplet states  (Allard et al. 2016a ), a pseudo-potential with large core was used for Mg  (Fuentealba et al. 1983) , and core valence correlation effects were taken into account with the operatorial CPP. A large basis set (10s, 9p, 6d, 3f,3g) was optimized for Mg, starting from one involving quite high Rydberg states  (Khemiri et al. 2013) , together with the rather large He one of  Deguilhem et al. (2009). MRCI calculations, with single and double excitations, were performed after a CASSCF with four electrons in six orbitals  (CAS 4, 6)  to obtain both the energies and the transitions dipole moments.
Acknowledgements. One of us (NFA) would like to acknowledge  V. Alekseev  for kindly providing the Mg-He molecular potentials and dipole moments before publication. The authors thank the referee for helpful comments and suggestions that have improved the clarity of the paper. This work used observations made with the  NASA/ESA Hubble Space Telescope , and obtained from the  Hubble Legacy Archive , which is a collaboration between the  Space Telescope Science Institute (STScI/NASA) , the  Space Telescope European Coordinating Facility  ( STECF/ESA ) and the  Canadian Astronomy Data Centre  ( CADC/NRC/CSA ). Support for MAST for non-HST data is provided by the  NASA Office of Space Science via  grant  NNX09AF08G  and by other grants and contracts. This work has made use of data from the  European Space Agency (ESA) mission Gaia  (https://www.
cosmos. esa. int/gaia),processed by the Gaia Data Processing and Analysis Consortium (DPAC, https://www. cosmos. esa. int/web/gaia/dpac/consortium). Funding for the DPAC has been provided by national institutions, in particular the institutions participating in the Gaia Multilateral Agreement. This work has made use of the Montreal White Dwarf Database (Dufour et al. 2017).
For EFRs located entirely within the CH, the intensity histogram was bimodal, one mode each for the CH and EFR pixels. The cut off threshold was then the local minimum after the CH peak in the intensity distribution. The intensity thresholds used to identify CH, quiet Sun, and EFR for R1-R7 varied by ∼20%, depending on whether the EFR was fully surrounded by CH or a mix of CH and quiet Sun. A number of EFRs were excluded from the study because they contained too few EFR intensity pixels (< 50) e. g. R7 in Figure  2 (e) and (i) and R6 in Figure  2(f). The effect of instrumental stray light is estimated to be ∼2% of the typical counts for Fe xii observations of the quiet Sun (see Hinode/EIS Software Note No. 12). For CH observations, the effect is likely to be slightly higher. Based on the intensity histogram in Figure  3 , the threshold for CH pixels is 150 erg/cm 2 /s/sr compared to 400 erg/cm 2 /s/sr for quiet Sun pixels, therefore we estimate the stray light effect to be 4-5%.
Subsequently, Fe xii atomic data has been updated and improved by Del Zanna & Storey (2012) so that now the densities are in agreement for the two ions (Fexii and Fe xiii). These results provide solid evidence that the Hinode/EIS is likely to be sampling the same plasmas since Si x, S x, and Fe xii have the same formation temperature of 1. 6 MK. The CHIANTI Atomic Database, Version 8. 0  (Dere et al. 1997; Del Zanna et al. 2015)  was then used to carry out the calculations of the contribution functions, adopting photospheric abundances of  Grevesse et al. (2007)  for all of the spectral lines while assuming the previously measured densities. The emission measure distributions were computed from the Fe lines using the Markov-Chain Monte Carlo (MCMC) algorithm available in the PINTofALE software package  (Kashyap & Drake 2000)  and then convolved with the contribution functions and fitted to the observed intensities of the spectral lines from the low-FIP element Fe.
515-1G>T PRDX1 mutation in all five cases, and confirmed the maternal transmission of the PRDX1 mutation with the secondary epimutation in one case (Supplementary Table  1 ). The c. 515-1G>T variant was present in seven individuals of European ancestry out of 66,000 individuals reported in the Exome Aggregation Consortium (ExAC) database (estimated frequency in the general population 1. 052 × 10 -4 ). The epimutation results from PRDX1 antisense transcription. MMACHC belongs to a trio of reverse (R1)-forward (F2)-reverse (R3) genes with dual partial overlaps of MMACHC by CCDC163P and PRDX1 at its 5′ and 3′ ends, respectively. The two mutations in PRDX1 affect the canonical splice acceptor site of intron 5, 1 and 2 bp apart, respectively. They are predicted to disrupt normal splicing and to produce skipping of exon 6 and the polyA transcription termination signal of PRDX1.
Control populations. The Asthma BioRepository for Integrative Genomic Exploration consortium (Asthma BRIDGE consortium, USA ) is an open-access collection of cDNA and DNA from more than 1450 well-characterized subjects participating in ongoing genetic studies of asthma and an accompanying database of phenotype, genome-wide SNP genotype, gene expression, and methylation data  11. The Caucasian population of the MARTHA (MARseille THrombosis Association) cohort was recruited in the Thrombophilia Centre of La Timone University Hospital (Marseille, France) between January 1994 and October 2005  12. The MH450K profiling data of the sperm DNA from the control population in Utah are publicly available at the Gene Expression Omnibus under #GSE64096, Utah cohort  13. Studies in skin fibroblasts. We measured the cellular incorporation of the label from 1-[ 14 C]propionate and 5-[ 14 C]methylTHF into cellular macromolecules that precipitated in 5% trichloroacetic acid at 5 °C to evaluate the metabolic functions of methylmalonylCoA mutase (MUT) and methionine synthase (MS), respectively.
SNVs and short indels were called using GATK haplotype caller (version 3. 4-46). All variants were annotated with ANNOVAR and in-house scripts, and most likely protein damage variants (nonsense, splice site, frameshift indel, and missense) were considered for further analysis. The variants were also annotated for the allele frequency in public databases such as ExAC (http://exac. broadinstitute. org/), the National Heart, Lung, and Blood Institute (NHLBI) exomes (V. 0. 0. 14, http://evs. gs. washington. edy/EVS/ ), the 1000 Genomes Project database, and our in-house database of >2000 exomes. In order to remove common variants and sequencing artifacts, variants with MAF >0. 001 in any of the aforementioned databases were removed from further analysis. Whole-genome ChIP-Seq. ChIP-Seq was performed in patient's fibroblasts and control fibroblast lines without inherited metabolic defects in the cobalamin pathway.
ChIP-Seq libraries were prepared using the Kappa Library Preparation Kit Illumina Platforms (Kappa Biosystems) and Illumina TruSeq adapters (Illumina) according to the manufacturer's instructions. DNA clean-up and size selection was performed using Ampure XP Beads. Samples were then sequenced using the HiSeq 2000 with selected read length of 50 bp. Sequence reads were aligned as explained for the WGS bioinformatic analysis. Duplicated reads were removed using PICARD. Peaks were called using Model-based Analysis of ChIP-Seq MACS2 with input DNA as control and using the broad peak mode (--broad --broad-cutoff 0. 1)  35. In order to generate Wiggle (WIG) and Tiled Data Format (TDF) files, HOMER (4. 7)  36  and igvtools (2. 3. 67; http://software. broadinstitute. org/software/igv/igvtools) were used.
We established a list of tail-to-tail SAGPs using a systematic search through the United Sense-Antisense Gene Pairs Database and retrieved 385 gene pairs  30. Each gene pair was visually inspected (RefSeq Genes 105v2) in order to look for the presence of a flanking gene that meets the two criteria of sense-antisense trios of genes: (1) antisense with one of the tail-to-tail SAGPs and (2) sharing a CpG island with the proxy gene (CpG Islands 2009-03-08, UCSC)  30, 31. Among the 385 manually inspected gene pairs, 99 had a triplet gene configuration according to a reverse(R1)-forward(F2)-reverse(R3) pattern (n = 82) or a forward(F1)-reverse(R2)-forward(F1) pattern (n = 17), with a CpG island in the promoter of R1/F2 and R2/F1, respectively. Statistical analyses. The comparison of CpG beta values between the cases and controls was carried out using a t-test, and multiple testing corrections were performed using the Bonferroni adjustment.
The top 10 principal components (eigenvectors) were calculated with their respective eigenvalue (EV). Population stratification was assessed both in 2-dimensional and 3-dimensional visualization based on the eigenvalues of the top two and three principal components, respectively. All analyses were performed using the SNP & Variation Suite (SVS) 8. 4. 2 (Golden Helix, Inc. Bozeman, MT, USA). valuable contribution and help in the collection of data and samples used to study the entire family, and the scientists of the McGill University and Genome Quebec and the Genomic Platform of the FR3209 CNRS-Inserm, University of Lorraine, for expert advice and performing high throughput sequencing. W. K. C received support from the Simons Foundation and the JPB Foundation.
In contrast, when used at a high dose, puromycin reduced the NEDD8 response to HS similarly to the CHX treatment (Fig. 1b ). Short-term inhibition of HSP70, which is expected to increase the production of misfolded newly synthesised proteins  35  , also induced NEDDylation, consistent with the data obtained with puromycin (Supplementary Figure  1A ). Pulse labelling experiments, where newly synthesised  35  S-labelled NEDD8 was isolated by immunoprecipitation, showed that the increase in NEDDylation upon stress is not due to an increase in NEDD8 synthesis (Supplementary Figure  1B ). To determine the state of stress-induced NEDDylated proteins, we performed a subcellular fractionation in untreated and HS cells, separating soluble (cytosol, nucleoplasm) from insoluble (pellet) fractions. NEDDylated substrates showed a transition from the cytosolic soluble into the insoluble pellet fraction during HS, indicating aggregation of the modified substrates (Fig.
2a ). Peptides for approximately 1500 proteins were quantified in two replicate experiments (Supplementary Data 1). Consistent with the western blot and immunofluorescence analysis, ubiquitin and NEDD8 increased in abundance in the formed insoluble inclusions upon HS (Fig. 2b ). Increased abundance was also observed for SUMO-1, 2 in accordance with the established role of SUMOylation in the HS response (Fig. 2b ) and the emerging concept for the cross-talk between ubiquitin and Ubls upon stress conditions  22, 37, 38. A striking observation was that among proteins with increased abundance in the aggregates, RNA transport and ribosomal proteins (RPs) were the two major groups, accounting for approximately 40% of the total number (Fig. 2b, c ). Having determined the composition of the HS-induced aggregates we then assessed the potential role of NEDD8 in the stress-induced nuclear protein aggregation.
Proteasomes were purified with streptavidin beads as described in Methods and the binding to HA-RPL7 was monitored by western blotting. Exposure of cells to HS induced the RPL7-proteasome interaction, which was further stimulated upon NEDD8 knockdown (Fig. 8c ). Repression of NEDDylation by overexpression of NUB1 also promoted RPL7 interaction with the proteasome, especially under HS conditions (Fig. 8d ). In these interaction experiments we did not detect modified RPL7, most likely due to rapid deconjugation during the experimentation, as protease inhibitors were not included in order to isolate active proteasomes. The data suggest that proteotoxic stress promotes modification, at least of a fraction, of RPL7 both with NEDD8 and ubiquitin through HUWE1 and prevents targeting of RPL7 to the proteasome.
After blockage, cells were incubated with the appropriate primary antibody diluted in 0. 05% tween-20 + 1% Goat serum in PBS for 1 h at room temperature (or overnight at 4 °C). After 3 × 10 min washes with 0. 05% Tween-20 in PBS, cells were incubated with corresponding secondary antibodies diluted in 0. 05% Tween-20 + 1% Goat serum in PBS for 1 h at room temperature in the dark. Samples were washed 3 × 10 min with 0. 05% tween-20 in PBS, and then stained with DAPI (1/20,000) for 20 s at room temperature in the dark. Slides were washed 3× with PBS, mounted with Vectashield Mounting Medium (H-1000, Vector), sealed, and viewed under the microscope Leica DM6000 or Leica SP5-SMD using metamorph software. The images were analysed by ImageJ64 software. The 3D rendering experiment was performed from z-stacks (Leica SP5-SMD) using Imaris 8.
63. Peptides were analysed online by nano-flow HPLCnanoelectrospray ionisation using a Qexactive Plus mass spectrometer (Thermo Fisher Scientific) coupled to a nano-LC system (U3000-RSLC, Thermo Fisher Scientific). Desalting and preconcentration of samples were performed online on a Pepmap® precolumn (0. 3 × 10 mm; Dionex). A gradient consisting of 0-40% B in A for 140 min (A: 0. 1% formic acid, 2% acetonitrile in water, and B: 0. 1% formic acid in acetonitrile) at 300 nl/min was used to elute peptides from the capillary reverse-phase column (0. 075 × 150 mm, Pepmap®, Dionex). Data were acquired using the Xcalibur software (version 4. 0). A cycle of one full-scan mass spectrum (375-1500 m/z) at a resolution of 70,000 (at 200 m/z), followed by 12 datadependent MS/MS spectra (at a resolution of 17,500, isolation window 1.
2 m/z) was repeated continuously throughout the nanoLC separation. Raw data analysis was performed using the MaxQuant software (version 1. 5. 5. 1) with standard settings. Used database consists of Human entries from Uniprot (reference proteome UniProt 2017_03) and 250 contaminants (MaxQuant contaminant database). Relative proteins quantifications were calculated on the median SILAC ratios. For further analysis we consider only proteins with at least two peptides. Perseus (version 1. 5. 5. 1) was used for graphical representation of the data, based on the mean value of log2 ratio (only for proteins quantified in duplicate) after elimination of contaminants and reverse entries. Functional enrichment on KEGG pathway was determined using STRING database with a confidence interaction level of 0.
7. The False Discovery Rate was calculated from the STRING database analysis on overrepresented KEGG pathways with a confidence interaction level of 0. 7. 35 S-Methionine labelling and immunoprecipitations. Cell labelling was performed as described  41. Briefly, cells were seeded in 6 cm plates and serum starved for 1 h with Methionine/Cysteine-free medium. 350 μCi/plate of 35 S-Methionine was added and cells were either incubated at 37 °C or heat-shocked for 20 min. Cells were washed in PBS, lysed in 400 μl of NP40 lysis buffer and extracts were precleared with protein G beads or GST beads. Immunoprecipitations were performed with 2 μl of NEDD8 antibody or 5 μg of GST-GFPtrap (in house) and 20 μl of either protein G beads or GST beads overnight before washing the beads 3× with 500 μl NP-40 lysis buffer.
Acknowledgements We are grateful to  Olivier Coux  for his assistance in the proteasome activity assays, the  Montpellier Rio Imaging (MRI)  facility for the microscopy,  Prof. Ron Kopito  and  Dr. Lan Huang  for cell lines. The study was financially supported by the  Labex Epi-GenMed , an " Investissements d'avenir" programme , reference  ANR-10-LABX-12-01 ,  INCa  ( PLBIO16-251 ), the  ATIP/AVENIR programme, INSERM  and the  COST Action (PROTEOSTASIS BM1307-European Cooperation in Science and Technology ).
The most commonly used datasets for abstractive summarization, namely the Gigaword corpus  (Graff and Cieri, 2003)  and the CNN Dailymail news dataset  (Hermann et al. , 2015) , comprise short articles from the news domain, representing only one of the many genres of written text. Target summaries in both these corpora are extractive where either the first sentence or some key points are combined together to train the model. In particular, there have been no resources covering user-generated content until now, severely limiting the range of applications of summarization research and technology on the web. Social media platforms and search engines alike rely on showcasing contents to their users in order to maintain and increase user engagement. Besides the intelligent, personalized recommendation and retrieval systems which retrieve the right content at the right time, they mostly resort to extractive summarization techniques for presentation.
Data The competition can be immediately started, since its training dataset is already available  (Völske et al. , 2017). We have mined Reddit for user postings that include a TL;DR summary, collecting a total of 4,044,501 content-summary pairs (see Table  1  for an example). In terms of size, our dataset matches the state-of-the-art Gigaword corpus. This dataset covers a wide range of everyday topics, drawing examples from 32,778 subreddits, each of which focuses on a particular topic. The mining process was carefully adjusted to include and extract the many syntactical variants of TL;DR summaries while excluding automatically generated postings and summaries by bots. To ensure high quality, we frequently reviewed large samples of the data, adjusting the mining process until at least 95% of the samples were of sufficient quality.
Each item of the dataset is a pair of posting and summary written by the same author. For the competition, we will use a subset of this dataset comprising 3,084,410 of the contentsummary pairs to harmonize the length distributions. In this subset, the average length of a posting is 211 words, ranging from from 100 to 400 words, and that of a summary is 25 words, ranging from 10 to 200 words. Participants are free to split this into training and validation sets as deemed fit. The test dataset comprises 1000 items held out from the training data, each of which has been carefully reviewed by at least three human annotators for quality. Of these, 800 will be used in the initial automatic evaluation runs, and the remaining 200 in a final round of manual evaluation.
Automatic evaluation scores will populate the public leaderboard. The final portion of the test set will only be used in the manual evaluation round, so that overfitting against the leaderboard scores can be avoided. To ensure blind evaluation, and reproducibility, the trained summarization models will be submitted as working software that performs summary inference given a set of input texts. Participants will deploy this software and all required dependencies on a virtual machine provided by the challenge organizers. The test dataset will not be accessible to participants while the competition is running; test set summaries will be generated offline on the aforementioned virtual machine, without direct input from the participants. All evaluation runs will be started from a clone of the participant's virtual machine, without network access, such that no test set data can be leaked.
Each generated summary will be judged by at least three annotators to ensure accuracy; annotators will rate individual summaries, as well as pairs of summaries from different participants to establish preference and break ties. The final ranking, and the winner of the TL;DR challenge, will be derived from the human annotators' quality judgments. The crowdsourcing evaluation phase will employ 200 test samples not used during the automatic evaluation phase. Based on the number of submitted summarization systems, participation in the crowd evaluation phase may be limited to the top performers on the automatic evaluation leaderboard-based on our projections, up to approximately thirty submissions will be considered for crowd evaluation. Some time after the conclusion of the competition, all testing data and annotator decisions will be made available to the research community at large; we expect that the analysis of the resulting data, and how it correlates with automatically computed ROUGE scores, will benefit the development of better evaluation metrics.