dataesr/scientific-paragraphs-categorization huggingface dataset:
When no hit was found, a second search was performed against the NR database using BLASTp. RNAmmer (9), ARAGORN (10), Rfam (11), Pfam (  12 ), and Infernal (13) were used to predict noncoding genes and miscellaneous features. Of the 5,918 predicted genes, 5,863 were protein-coding genes and 55 were RNAs, including 3 5S rRNAs, 3 16S rRNAs, 3 23S rRNAs, and 48 tRNAs. A total of 4,507 genes (76. 87% of protein-coding genes) were assigned a putative function, 94 genes were identified as ORFs with no homologs (ORFans) (1. 60%), and 982 genes (16. 75%) were annotated as hypothetical proteins. Based on 16S rRNA gene sequence proximity, genomes were selected and incorporated with in silico DNA-DNA hybridization (DDH) (14). The DDH values were calculated using the GGDC version 2. 0 online tool (15).
This analysis yielded sequence similarities of 99. 80% with the type strain M. setense DSM 45070 (GenBank accession number JTJW00000000), 89. 80% with the nonpathogenic strain Manresensis (JTLZ00000000), 30. 50% with M. farcinogenes DSM 43637 (CCAY000000000), 30. 40% with M. senegalense CK2 (LDPU00000000), 29. 70% with M. houstonense ATCC 49403 (NZ_FJVO00000000), 29. 40 with M. fortuitum DSM 46621 (ALQB00000000), and 20. 60 with Mycobacterium gilvum PYR-GCK (NC_009338). These results confirmed that strain CSUR47, also known as isolate 74023791 (2), belongs to the M. setense.
species within the M. fortuitum complex. Furthermore, M. setense CSUR47 was more closely related to the clinical M. setense DSM 45070 type strain than to the environmental Manresensis strain isolated from Cardener River in Manresa, Spain, and was shown to be less virulent than M. bovis BCG in immunocompromised mice  (16). Accession number(s). The M. setense CSUR47 genome sequence has been deposited at EMBL under the accession number OEJY01000000.
In contrast, women with HMB showed no increase in VEGF levels during the menstrual phase. The twofold increase in endometrial CXCR4 mRNA concentration during menstruation in women with NMB was similarly absent in women with HMB. As HIF-1 is known to accelerate wound repair via stimulation of mitogenesis and angiogenesis at other tissue sites  23, 24  , we aimed to determine the functional impact of decreased HIF-1α and its downstream targets in the endometrium at menstruation. We measured duration of bleeding as a clinical marker of endometrial repair. Women with HMB were found to bleed for 2 days longer on average than women with NMB, consistent with defective repair (Fig. 1f ). Hypoxia is present in a mouse model of simulated menses. Our observational human data are consistent with a defective hypoxic response in the endometrium at menstruation.
Endothelial cell branching was captured in the same position in each well after 8 h using an inverted Axiovert microscope. Branch points of the formed tubes were counted by an observer masked to the sample origin and an average of the replicates determined after unmasking. Statistical analysis. Analysis was carried out using GraphPad Prism software (San Diego, CA). Analysis of two groups (i. e. histological breakdown/repair scores, densitometry, duration of bleeding) utilised unpaired t tests where the distribution of data was normal and Mann-Whitney test where data were not normally distributed. For comparison of data sets with two variables (i. e. human data: MBL and stage of cycle, mouse data: treatment groups and time) a two way analysis of variance was used with Bonferroni's/Tukey's multiple comparisons test.
Acknowledgements We thank  M. Nicol ,  K. Walker ,  D. Wilson ,  R, Murgai ,  H. Murray ,  L. Boswell ,  A. Carton ,  A. Manderveld ,  K. Brepoels ,  P. Vanwesemael ,  E. Van Dyck ,  R. Martinez-Aguilar  and  A Dearbey  for technical support. We are grateful to  A. Williams  for scoring uterine histology and  P. Brown  for construction of lentiviral vectors. Thanks to  R. Grant  and  S. Milne  for help with figure and manuscript preparation and  C. Murray  and  S. McPherson  for patient recruitment. We are grateful to  S. Walmsley  and  K. Chapman  for critical appraisal of the manuscript. This work was supported by the  Wellcome Trust  ( 100646/Z/ 12/Z  and  ISSF  fund  J22738 ),  Academy of Medical Sciences  ( AMS-SGCL13 ),  Wellbeing of Women  ( RG1820 ) and the  Medical Research Council  ( G0600048 ,  G0500047 ) and was carried out in the  Medical Research Council Centre for Reproductive Health , which is funded by  MRC Centre  grants  G1002033  and  MR/N022556/1.
27 progressed perpendicularly into the cortex with the first positioned at the periosteal edge (Fig  5A ). Spectra were collected in the mid-IR region from 750 cm -1 to 3850 cm -1 using a narrowband mercury cadmium telluride detector, at 8 cm -1 spectral resolution and 128 co-added scans per pixel spectral resolution in transmission mode. A matching background spectrum was collected through clear BaF2. For each sample MMA reference spectra were collected from within the embedding material. All data acquisition was undertaken with Bruker OPUS version 6. 5 and data analysis completed with OPUS version 7. 2. After acquisition, raw spectra for each region and sample were baseline corrected using a 3-point baseline at 1800, 1200 and 800 cm -1. Residual MMA absorbance peaks were then subtracted using the relevant MMA reference spectrum for each sample by iterative manual subtraction.
Acknowledgements The authors thank the staff of the  St. Vincent's Health Bioresources Centre  for excellent animal care and assistance,  Mr Joshua Johnson  and  Mrs Ingrid Poulton  for technical assistance with histology,  Dr Roger Curtain  ( Bio21 ) for technical assistance with BSEM,  Dr Paul Roschger  for advice on BSEM analysis and  Dr Eleftherios Paschalis  for advice on collagen crosslinking analysis. This work was supported by  NHMRC  Grants  1042129  and  1081242  to NAS and TJM, Program Grant  1054618  to GKS, the  Australian and New Zealand Bone and Mineral Society Christine  and  TJ Martin Travel Award  to CV, and a  Brockhoff Foundation Grant  to CV. JSO was supported by an  ARC   Future Fellowship. NAS was supported by an  NHMRC   Senior Research Fellowship. St. Vincent's Institute acknowledges the support of the  Victorian State Government OIS program.
The pump was exchanged weekly for 8 weeks. miR-222 inhibition. LNA-anti-miR injections were performed as previously described  18. Two-month-old C57Bl/6 male mice were subcutaneously injected with 10 mg kg -1 of LNA-modified anti-miR-222 (LNA-anti-miR-222) or scrambled control (LNA-Ctr) reconstituted in saline for three consecutive days after osmotic pump implantation and then weekly after pump exchanges throughout the experiment. LNA-anti-miR oligonucleotides were purchased from Exicon. Echocardiographic studies. Echocardiography was performed on conscious mice by using a GE Vivid E90 with a L8-18i-D probe. Parasternal long-axis views, shortaxis views, and two-dimensional-guided M-mode images of short axis at the papillary muscle level were recorded. The average of at least three measurements was used for every data point from each mouse.
Sample preparation and MIMS data acquisition and analysis. Tissues were fixed with 4% paraformaldehyde (PFA), embedded in LR (London resin) white, sectioned (0. 5-1 μm), and mounted on silicon chips. MIMS analyses were conducted with ion microscopy (NanoSIMS 50 and a large-radius NanoSIMS 50L, Cameca) as described previously  2, 3. Briefly, a focused Cs + ion beam (size <100 nm) is rastered over the sample surface. The impact of the Cs + ion beam on the sample surface generates the sputtering of multiple secondary ions from the probed nanovolume (corresponding to a pixel in the image). For each nanovolume, the secondary-ion intensities for 12 C -, 12 C 14 N -, 12 C 15 N -, and 31 P -were recorded in parallel. The detection of nitrogen requires the use of poly-atomic ions 12 C 14 N - and 12 C 15 N -as a proxy for 14 N and 15 N.
Sections were imaged on a LSM 510 Inverted Confocal (Zeiss LSM 510) and analyzed with Zen lite software (Zeiss). Capillary density and cross-sectional area quantification. Hearts from animals that underwent the above described exercise regimen but that were not used for LR white embedding and MIMS were snap frozen in OCT (optimal cutting temperature) as previously described  18. Thick sections of 6 μm were cut from the frozen tissue and placed on a glass cover slip, air-dried for 5 min, followed by a brief 10 min fixation with fresh 4% PFA. Sections were immunofluorescently stained with both CD31 (BD Pharmingen) and wheat germ agglutinin (488-oregon green, Thermo Fisher Scientific) to analyze capillary density (capillaries/cardiomyocyte) and cross-sectional area using standard procedures. AlexaFluor (555-texas red) fluorescent dye (Thermo Fisher Scientific) was used as secondary antibody.
1% Tween), slides were counterstained with DAPI (4′, 6-diamidino-2′-phenylindol, dichloride; Thermo Scientific/Pierce, Rockford, IL, USA) to visualize the nuclei. Finally, slides were washed and mounted and all quantitative analyses were performed. All images were post-processed in ImageJ (NIH) software. Approximately 14,000 troponin-Tpositive cardiomyocytes were counted for the TUNEL analysis. LR = London Resin OCT = optimal cutting temperature TMR = Tetramethylrhodamine TUNEL = Terminal deoxynucleotidyl transferase dUTP nick end labelled RNA isolation and quantitative real-time PCR. RNA was isolated from both tissue and cell samples using Trizol (Qiagen), and phase separation followed by column purification (Zymo Research). RNA of 1 μg was added to reverse transcription reactions (Applied Bioscience) and quantitative PCR was carried out using SYBR-green (Bio-Rad).
0. Microarray data analysis was performed with Affymetrix Microarray Data Analysis tools. Statistical analysis. Statistical testing was performed using Prism 3. 0/7. 0 (Graphpad). For echocardiographic and morphometric analyses, as well as gene expression, cross-sectional area, capillary density, and cell death/volume, results are presented as mean ± s. e. m. from n = 3-5 animals per group and were compared by using two-sided t tests (significance level p < 0. 05). More than two groups were compared by using one-way analysis of variance with Tukey's correction for multiple comparisons. Data comparing event rates, i. e. ,  15  N-thymidine-positive and -negative cardiomyocytes and non-CMs, were compared using Fisher's exact test based on the total number of cells counted as unit of analysis (significance level p < 0.
Acknowledgements We thank  J. Gannon  and  C. Y. Xiao  for surgical assistance,  Y. Iwamoto  and  D. Capen  of the  Center for Systems Biology at Massachusetts General Hospital  for pathology and histology services, and  C. Heß  and  K. Mühlburger  for technical assistance. C. L. was funded by the  German Research Foundation  ( LE 3257 1-1 ). R. T. L. was funded by the  NIH  ( HL117986 ,  HL119230 , and  HL122987 ) and the  Leducq Foundation. A. R. was funded by the  NIH  ( HL122987 ,  HL135886 , and  TR000901 ) and the  AHA  ( 14CSA20500002  and  16SFRN31720000 ). Confocal microscopy was partly performed in the  Microscopy Core of the Center for Systems Biology/Program in Membrane Biology , which is partially supported by an  Inflammatory Bowel Disease Grant   DK043351  and a  Boston Area Diabetes and Endocrinology Research Center (BADERC)  Award  DK057521.
Statistical analyses Cell quantifications were performed on 3D image reconstructions of the dorso-medial pallium (Dm) for all hey1 knockdown experiments and on telencephalic sections for RG phenotyping in notch3 mutant larvae. Between one and six 1 µm optical sections (average 2. 84, mode 3) corresponding to different rostrocaudal levels were analysed. Only the Dm region was investigated. For each optical section, cell counts were normalized by Dm ventricular zone length to account for span variations along the rostrocaudal axis. They are reported as number of cells per 100 µm of ventricular zone length. Images were analysed using Imaris software (Bitplane) and investigators were not blinded to treatments/genotypes. Balanced ratios of females and males were included in the different experimental groups.
At least 4 ng of total RNA was extracted for each biological replicate. Libraries were constructed using the Totalscript RNAseq kit from Epicentre (discontinued), using the oligodT option, according to the manufacturer recommendations. Paired-end sequencing was performed on a NextSeq sequencer from Illumina. We used 50 bp reads in the experiments on the adult brains and 100 bp reads in the experiment on notch3 mutant larvae. The read quality was assessed with FastQC and the mapping carried out with TopHat2. Read counting was performed with HTSeq and differential analysis with DESeq2. RNAseq data have been deposited in GEO under accession number GSE111765.
Analysis of RNAseq datasets Mapping of sequencing reads Quality of the reads was assessed with FastQC. We aligned raw RNAseq reads to zebrafish genome assembly (Zv9) using TopHat2 [PMID: 23618408] by providing zebrafish gene model from Ensembl (V78) as the reference gene model. The number of mapped reads varied between ∼50 and 63 million pair-ends across each sample that accounted for about 75% of pair-ends reads. Because of the bias they introduce, multiple mapping reads were excluded. Unique mapping reads were selected using samtools (version 1. 3. 1).
Differential expression analyses DESeq2 (v. 1. 14. 1)  (Love et al. , 2014)  Wald test was used to assess differential expression between groups. The input data are pre-filtered matrices in which no reads or nearly no reads have been removed. Each prefiltered matrix contains the raw count data where each row indicates the transcript, each column indicates the sample and each cell indicates the number of reads mapped to the transcript in the sample. P-values for genes surviving independent DESeq2 filtering (see  Love et al. , 2014)  were adjusted for multiple comparison correction using the Benjamini-Hochberg correction for FDR at a threshold of P<0. 05  (Benjamini and Hochberg, 1995). No minimum LFC threshold was applied.
Gene ontology enrichment analyses Tables for each comparison from DESeq2 results were ordered by the Wald statistic values. Zebrafish Gene Symbol and Entrez Ids were added using the org. Dr. eg. db (v_3. 4. 0) and AnnotationDbi (v_1. 36. 2) Bioconductor Packages, using the Ensembltrans as keys. Human orthologs were added to the tables using the human and Zebrafish orthology tables from Zfin website (zfin. org/downloads/human_orthos. txt, downloaded June 2017). Duplicated Human Symbols were then collapsed by keeping the one with highest logFC. gmt files containing the  GO gene collections (c5. mf. v6. 0. symbols. gmt, c5. bp. v6. 0. symbols. gmt) were downloaded from Molecular Signatures Database (software. broadinstitute. org/Gsea/ msigdb, downloaded June 2017). The gene collections were used to perform enrichment analysis using two complementary approaches: First, an over-representation analysis (ORA)  (Khatri et al.
, 2012)  on differentially expressed genes was performed using one-sided Fisher's exact tests implemented in R script (R Development Core Team, 2013) with a Benjamini and Hochberg's multiple testing correction of the P-value. Then a gene set enrichment analysis (GSEA) [functional scoring method (FSC)  (Khatri et al. , 2012) ] type of analysis using the runGSA function in piano R package  (Väremo et al. , 2013)  was performed on the ranked list (see above) of genes.
RT-qPCR RT-qPCR was performed on cDNA from the head (without eyes) of 7 dpf genotyped larvae, and expression of the prkag1 gene was used for normalization. Data are reported as mean fold-change (2 -ΔΔCt )±s. e. m. in notch3 -+-relative to notch3 +/+ larvae. All details are provided in supplementary Materials and Methods and in Table  S13.
Acknowledgements We thank the technical teams running the  FACS Platform at Institut Curie (Orsay, France)  and the IMAGIF sequencing platform ( Gif-sur-Yvette, France ) for their input on cell sorting and RNAseq profiling. We are indebted to  Drs Shahragim Tajbakhsh  and  Benjamin Simons  for discussions and advice during the course of this project, to  Dr Fernando Giraldez  for sharing his inspiring work on Hey1 function, to  François Guillemot  for communicating Hey1 expression data in mouse prior to publication, and to members of the ZEN team for their constant input. Sebastien Bedu ,  Marie-Elise Schwartz  and  Nicolas Chanthapathet  provided expert fish care.
Funding Work in L. B. -C. 's lab was funded by the  Agence Nationale de la Recherche  ( ANR-2012-BSV4-0004-01  and  Laboratoire d'Excellence Revive ), and by the  Centre National de la Recherche Scientifique ,  Ecole des Neurosciences de Paris, Institut Pasteur  and the  European Research Council  ( AdG 322936 ). E. T. -T. was the recipient of a PhD student fellowship from the  Ministry of Science and Education and the Fondation pour la Recherche Medicale. S. M. is a research associate supported by the  Agence Nationale de la Recherche Laboratoire d'Excellence Revive. Deposited in PMC for immediate release.
The spectra were acquired within the m/z mass range of 100-1,200 atomic mass units (amu), using a resolution of 50,000 at m/z 200 amu. The system was calibrated internally using dibutylphthalate as lock mass at m/z 279. 1591, giving a mass accuracy lower than 1 ppm. The instruments were controlled using the Xcalibur software and data was processed using the XCMS software package  (Smith et al. , 2006). Raw data were converted to the mzXML format using MSconvert before analysis. Settings of the xcmsSet function of XCMS were as follows: method = "centWave", ppm = 2, noise = 50,000, mzdiff = 0. 001, prefilter = c(5,15,000), snthresh = 6, peakwidth = c(6,35). Peaks were aligned using the obiwarp function using the followings settings of the function group. density: bw = 10, mzwid = 0. 0025. This allowed the alignment of 2,156 peaks in the positive mode.
Ion identifiers were generated automatically by XCMS as MxxxTyyy, where xxx is the m/z and yyy the retention time in seconds. Selection of major differential ions (peak area > 10 6 , fold > 15) between sporangia and leaf extracts led to a final set of 123 major ions. The integration of each peak was checked manually before validation. T-tests were performed in R with the t. test function. Differential ions with p ≤ 0. 05 were considered for further characterization. The exact m/z and retention time of each metabolite were used for targeted metabolomic analyses using the Excalibur software. For kinetic analysis of P. viticola development, seven major Plasmopara-specific lipids [AA, DAG, EPA, DEPG, TEPG, Cer(d16:1/18:0), Cer(d16:1/20:0)] were selected.
Chlorophyll a content in sporangia extracts (1. 7. 10 4 ± 1. 2. 10 4 arbitrary units) was 4,000 times lower than in leaf extracts (6. 8. 10 7 ± 4. 1. 10 7 arbitrary units), indicating very low levels of contamination. Submission of these 123 ions to the Metlin database  (Smith et al. , 2005)  led to the putative identification of two compounds of particular interest. Indeed, one of the proposed structures for compounds giving the ion n • 10 (M303T44) with the mass-to-charge ratio (m/z) 303. 2316 was eicosapentaenoic acid (EPA). Similarly, ion n • 12 (M305T48) with m/z 305. 2473 was potentially associated to arachidonic acid (AA) (Table  1 ). Both EPA and AA had previously been identified in mycelial extracts of Phytophthora infestans, another phytopathogenic Oomycete causing the late blight of potato  (Bostock et al.
, 2000; Hsu and Turk, 2002; Murphy, 2015)  and obtained with this standard (Supplementary Table  3 ). However, neither its RT nor   1 ) are numbered from 1 to 4 and retention times are indicated. Peak 1: M492T96 = Cer(d16:1/16:0); peak 2: M521T125 = Cer(d16:1/18:0); peak 3: M549T166 = Cer(d16:1/20:0); peak 4: Cer(d16:1/22:0). Identity of Cer(d16:1/16:0) was confirmed by using the corresponding standard. (B) Mass spectrum of putative Cer(d16:1/18:0) (M521T125) from P. viticola. The fragmentation giving rise to the main fragments is indicated. A detailed fragmentation is given in Supplementary Figure  3. its fragmentation corresponded to any of the ions found in P. viticola, excluding the hypothesis that some of these ions may be derived from C18:1 sphingosines. A second set of candidates retrieved from the Metlin database contained C16:1 sphingosine.
Indeed, the four compounds present in P. viticola extracts shared the same specific fragments with m/z 236. 2371 (C 16 H 30 N) and 254. 2476 (C 16 H 32 ON) (Figure  2B ). The formulas of these fragments could be compatible with their being derived from a C16:1 sphingosine  (Lhomme et al. , 1990; Pivot et al. , 1994). Therefore, a commercial standard of the ceramide Cer(d16:1/16:0) was analyzed by UHPLC-HRMS. Both its RT and its fragmentation pattern corresponded to that of the ion M492RT96 (n • 19) found in P. viticola (Supplementary Table  3 ). Furthermore, M492RT96 and Cer(d16:1/16:0) exhibited the same RT in three different chromatographic conditions (data not shown), showing that the ion M492RT96 (n • 19) is indeed derived from Cer(d16:1/16:0) present in P. viticola extracts (Figures  2A, 3 ).
ACKNOWLEDGMENTS We thank the staff of  UE0871 Service d'Expérimentation Agronomique et Viticole (SEAV, INRA, Colmar)  for maintenance of plant material. We are grateful to  Marie-Annick Dorne  and  Marie-Céline Lacombe  ( INRA, Colmar ) for help with downy mildew infections and to  Andy Schneider  ( INRA, Colmar ) for help with lipid extraction and analysis. We thank  Patrick Schaub ,  Florian Wüst , and  Peter Beyer  ( University Freiburg, Germany ) for MS2 analyses.
FUNDING LN was supported by a doctoral fellowship from the  Conseil Interprofessionnel des Vins d'Alsace , the  Conseil Interprofessionnel du Vin de Bordeaux , and the  Comité Interprofessionnel du Vin de Champagne  and from the  Région Alsace. This work was co-funded by the  European Regional Development Fund (ERDF)  in the framework of the  INTERREG IV  and  V Upper Rhine  programs (BACCHUS and VITIFUTUR projects), and by the  Fondation Jean Poupelain (Javrezac, France)  through the  HealthyGrape2 program.
In the case of canned tuna most laboratories used cytochrome b markers of shorter size, 187 and 176 bp  [9, 22] , except for France, which used a short control region fragment of 150 bp  [8]. Primers and PCR protocols are specified in S4 Table. Once checked by agarose electrophoresis in 1-2% agarose gels, PCR products were sequenced. Subsequent DNA sequence analysis was performed as indicated in S3 Table. Briefly, sequences were edited using Chromas (Technelysium), Bioedit  [23]  and GeneDoc  [24]  and matched against NCBI database using the nucleotide BLAST (Basic Alignment Search Tool) and the BOLD (Barcode of Life) database for the COI sequences  [25]. Species were identified using a 99% minimum match criterion, with the exception of Thunnus albacares and T. obesus, where the threshold was 100%  [26].
For an unequivocal identification, laboratories from Spain, France and Germany also constructed Neighbor-Joining trees using MEGA software  [27]  with their own reference sequences using Tamura-Nei distances. Sequences longer than 200 bp were uploaded in GenBank (accession numbers: Germany KJ531289 to KJ531379; France KJ535741 to KJ535783; Spain KJ623816 to KJ623830; Portugal MF067430 to MF067499) and BOLD database in the case of COI sequences (UK and ROI KJ510424 KJ531384 and KJ563141-KJ645864) Samples containing a different species than the one declared in the label were considered mislabelled. When only the commercial name was present, mislabelling records were obtained by following each country's list of approved commercial designation for tunas (S2 Table ). When the scientific name was present, it was the one taken as a reference to compare with the analytical result.