dataesr/scientific-paragraphs-categorization huggingface dataset:
Analysis of the ERA interim data-set The previous section suggests that the Gulf Stream warm tongue has an impact on the ascending motion embedded in cyclones travelling in the northwest Atlantic, but it was only based on a single case study. To investigate whether this impact can also be detected in a climatological sense, we now analyse the ERA interim reanalysis data-sets over the 1979-2012 period (December through February). This data-set provides a gridded estimate of the state of the global atmosphere (here used on the native T 255 truncation, approximately equivalent to a 80 km horizontal resolution) through a four-dimensional variational analysis and a 12-h analysis window  (Dee et al. , 2011). We do not expect the reanalysis data to capture the dynamics present in the simulations discussed in Section 2 because of its relatively coarse resolution.
Indeed, the vertical motion is mostly downward in this part of the cyclones and this tends to restrict the vertical penetration of the oceanic influence there (e. g. Vannière et al. , 2017). In summary, application of a dynamical diagnostic to the environmental conditions provided by the ERA interim data suggests that the Gulf Stream warm tongue is the region where vigorous ascent from low levels should be most frequently observed in the Northwest Atlantic in winter. The occurrence of such events is comparable (5-10% of the wintertime based on Fig. 8b ) to Fig. 9. Number of back-trajectories (circles) with heights z ≥ 5 km at t = 24 h and reaching low levels over the ocean at t = 0 h (from Table  1  for all experiments): red for CNTL, blue for COOL and green for SMTH. The arrows indicate a measure of oceanic forcing when comparing CNTL/SMTH or CNTL/COOL (see main text).
Acknowledgements The authors are grateful to  Susanne Neubert  for her help in generating the crosses,  Viktoria Kantner  and  Martin Frauenlob  for genotyping, and  Tobias Seethaler  and  Catarina Fernandes  for plant propagation and seed harvesting. The project was supported by grants of the  Austrian Science Fund  and the  French National Research Agency projects FWF-SFB   F3707-B22  and  ANR-FWF I 1725-B16.
Ccr2 was found to be the chemokine receptor displaying the highest upregulation upon wounding (Fig. 1d  and Supplementary Data 1). We performed also RNA sequencing on sorted fetal eGFP þ cells from the peripheral blood obtained from wounded and unwounded pregnant mice. Since fetal cells show a very early peak in the blood (at day 1) after wounding, we first selected genes that displayed high expression (4100 count per million) in wounded mothers. Then we selected the genes that were overexpressed in circulating fetal cells from wounded mice as compared to unwounded mice (41. 25-fold change). Using these thresholds, we retrieved a list of 558 genes that were overexpressed in circulating fetal cells from wounded mice. Among these genes, 16 corresponded to surface receptors and the only chemokine receptor was Ccr2 with 376 versus 261 counts per million reads in wounded versus unwounded conditions leading to a fold change of 1.
Meanwhile, the levels of Ccl8, another Ccr2 ligand, peaked later in the wound, on day 3 (Fig. 1j ). Thus Ccl2/Ccr2 signalling corresponds with the observed early peak of postwounding fetal cells. We investigated the specific populations secreting Ccl2 in skin wounds by measuring Ccl2 levels in various types of cells sorted from the wounds. Marked Ccl2 overexpression was detected in CD45 þ leukocytes from day 1 wounds (Fig. 1m ). We carried out double immunofluorescence staining on day 1 wound sections on day 1: F4/80 þ monocytes and CD31 þ endothelial cells expressed Ccl2, whereas GR-1 þ neutrophils did not (Fig. 1l ). These data suggest that monocytes and endothelial cells secrete Ccl2 during the initial stage of skin wound healing. Ccl2 recruits fetal cells to maternal wounds. Given the overexpression of Ccr2 in FMCs upon wounding, the high percentage of FMCs expressing Ccr2 on their surface and the overexpression of Ccl2 in wound tissue during early stages of healing, we hypothesized that Ccl2 mediates the early recruitment of FMCs to wounds.
The resulting suspension was washed with PBS and filtered through a cell strainer with 40 mm pores (BD Pharmingen). The antibodies used for cytometry were CD34-eFluor660 (1:100; eBioscience), CD11b-PERCP-Cy5. 5 (1:100; eBioscience), CD31-PE-Cy7 (1:100; eBioscience) and CCR2 (1:100; Santa Cruz) crossed with an anti-goat-Alexa 555 (1:1,000 Invitrogen). Flow cytometric data were acquired with a BD LSRII (BD Pharmingen) machine and sorting was performed on a MoFlo cell sorter (Beckman Coulter). The cells were then analysed with the FlowJo software (Treestar, San Carlos, CA). In order to assess the specificity and sensitivity of FACS technique, we performed a dilution curve of eGFP þ splenocytes in WT splenocytes ranging from 100% to 0. 0001%. FACS analysis always showed the expected amount of eGFP cells, even in very diluted specimens.
For immunofluorescence, we used the following secondary antibodies: goat anti-rabbit IgG labelled with Cy3 or Alexa 488, donkey anti-rat IgG labelled with Alexa 488 or Cy3 and rabbit anti-goat Alexa 555 (1:1,000; Invitrogen). Slides were counterstained with 0. 3 mg ml À 1 4,6-diamidino-2-phenylindole (Sigma-Aldrich). Microscopic scoring and measurements. We used a Nikon Eclipse 90i fluorescence microscope equipped with a Nikon DS-Fi1C digital camera (Nikon, Tokyo, Japan). For cell scoring, we took photographs of three different fields and counted the labelled cells by fluorescence densitometry, reporting the number of cells as a percentage of the total (assessed as the total number of nuclei). The mean percentage of labelled cells was calculated for each specimen. Measurements were made with the ImageJ software (NIH, Bethesda, MD).
RNA extraction quantitative PCR and RNA sequencing. Total RNA was extracted from cells or tissues with Trizol reagent, in accordance with the manufacturer's (Invitrogen) instructions. For low amount of cells, RNA was extracted with the NucleoSpin RNA XS Kit, in accordance with the manufacturer's (Macherey-Nagel) instructions. It was then reverse-transcribed with the iScript cDNA Synthesis Kit (Bio-Rad). The resulting cDNA was used for PCR with the SYBR-Green Master PCR Mix (Roche). PCR and data collection were performed on a LightCycler 480 (Roche). The levels of gene expression in the samples were normalized against that of the housekeeping gene (b-actin). All the primers were from Qiagen (QuantiTect). RNA sequencing was performed on sorted fetal cells from the peripheral blood obtained from wounded and unwounded pregnant mice.
15. PCR array for chemokines and receptors and angiogenesis. Changes in chemokines and receptors or angiogenesis levels were measured with an RT 2 Profiler PCR Array for mouse chemokines and receptors PAMM-022ZA or mouse angiogenesis PAMM-024ZR (Qiagen, Hilden, Germany). Total RNA was extracted from sorted eGFP þ cells from BM. The expression of 86 cytokine and chemokine genes was analysed with the Lightcycler 1536 system (Roche Diagnostics, Mannheim, Germany), according to the manufacturer's instructions. The data obtained were analysed with the RT 2 Profiler PCR Array Data Analysis Template (Qiagen). Data were normalized against five housekeeping genes (Actb, B2m, Gapdh, Gusb, Hsp90ab1), and relative expression levels were calculated by the 2 À DDCt method. PCR array analyses were performed at the Hopital La PitieSalpetriere ICM, with a LightCycler 1536 (Roche) and RT 2 Profiler PCR Arrays.
Acknowledgements This work was supported by grants from  SocieteFranc¸aise de Dermatologie and AREMPH. Z. W. was supported with a  Region Ile de France (DIM Stempole ) postdoctoral funding. M. C. and M. S. received support from the  French Ministry for Education (MEN). We also thank  Annie Munier ,  Tatiana Ledent  and  Olivier Bregerie  for their help in FACS and animal facilities.
Background: Histones and histone variants are essential components of the nuclear chromatin. While mass spectrometry has opened a large window to their characterization and functional studies, their identification from proteomic data remains challenging. Indeed, the current interpretation of mass spectrometry data relies on public databases which are either not exhaustive (Swiss-Prot) or contain many redundant entries (UniProtKB or NCBI). Currently, no protein database is ideally suited for the analysis of histones and the complex array of mammalian histone variants.
Results: We propose two proteomics-oriented manually curated databases for mouse and human histone variants. We manually curated >1700 gene, transcript and protein entries to produce a non-redundant list of 83 mouse and 85 human histones. These entries were annotated in accordance with the current nomenclature and unified with the "HistoneDB2. 0 with Variants" database. This resource is provided in a format that can be directly read by programs used for mass spectrometry data interpretation. In addition, it was used to interpret mass spectrometry data acquired on histones extracted from mouse testis. Several histone variants, which had so far only been inferred by homology or detected at the RNA level, were detected by mass spectrometry, confirming the existence of their protein form.
Then, they are proteolyzed with proteases to form short peptides, which are then analysed by MS/MS. The acquired MS/MS spectra are interpreted and converted into amino acid sequences, from which the identity of the original histone protein and the possible presence of post-translational modifications on specific residues can be determined  [35]. However, these analyses still remain restricted for a number of reasons. One of these is that the interpretation of MS/MS spectra relies on matching experimental data to theoretical peptide sequences obtained by an in silico proteolysis of a list of proteins. Therefore, the content of the theoretical protein sequence database conditions the interpretation of the experimental spectra and the subsequent identification of histones. Classical databases such as Swiss-Prot, trEMBL and NCBI are usually used with success.
However, histones have not been precisely annotated in these resources. Manually curated databases such as Swiss-Prot lack several histones, while others, such as trEMBL or NCBI protein database, are more extensively populated with non-reviewed data. The latter contain more histone entries, but the degree of redundancy and the precision of the descriptions can make protein identification results difficult to interpret. Finally, naming of histones has been recently revisited with a new unified nomenclature  [36]. The recent release of HistoneDB 2. 0 consolidated the sequence information of a large variety of histones and their sequence variants in many organisms  [37]. However, it has not yet been integrated in the above databases and the same variant can go by different names. For instance, the coding gene H2afb1 refers to proteins H2A.
L. 2 or H2A. Lap3 in the literature and to H2A-Bbd type 1 in the NCBI RefSeq and UniProtKB databases  [38, 39]. In addition, a different protein coded by Gm14920 is also named H2A. Bbd. 1 in other publications  [40]. Here, a unified name is presented to identify uniquely each ambiguous entry and is also associated with its other names to facilitate its relationship with previously published work. We have collected redundant histone entries from a number of public databases, gathering >700 entries for mouse and >1000 entries for human histones. We manually curated these lists to obtain a final count of 83 and 85 histone entries for mouse or human, respectively. Their annotations have been revisited to match the current histone nomenclature in accordance with the new resource "HistoneDB 2. 0-with variants"  [37].
MS_HistoneDB, a resource containing unique and non-redundant histones Our initial aim with this work was to generate an exhaustive and non-redundant resource that would facilitate histone analysis by MS. We identified and collected all the information available on human and mouse histones from the public databases of NCBI, Ensembl and UniProtKB (Table  1 ). This work was aided by the recent release of an updated version of the Histone Database, named "HistoneDB 2. 0-with variants"  [37]. This database contains 38,664 entries from 1624 species, with 761 and 1039 entries for mouse and human, respectively. In addition, several histones were also considered based on published articles  [41] [42] [43] [44] [45]. The dataflow is presented in Fig. 1a. This curating process is exemplified with human H2A.
Z on Fig. 1b. A total of 23 entries were collected from Swiss-Prot, Uniprot-trEMBL and NCBI databases. Fourteen were duplicated and removed to obtain nine unique entries, which were annotated as H2A. Z. 1 and eight spliced isoforms of H2A. Z. 2 using the release R86 of the Ensembl database (Fig. 1c, d ). In summary, the following rules were applied. First, each entry is protein-centric and therefore defined by the final product, a unique mature protein. Second, it must be associated with gene, transcript and protein accession numbers in NCBI and/or Ensembl, unless published data document its existence. Third, histone names are not always consistent within the existing public databases. Some were renamed following the Talbert et al. nomenclature and in agreement with the HistoneDB 2. 0 resource as detailed in the following sections  [36, 37].
Histone variants are mostly replication-independent In contrast to canonical histones, almost all histone variants are synthesized independently of the cell cycle and named "replication-independent"  [49]. Their mRNA is polyadenylated and these histones are incorporated into chromatin at any time of the cell cycle. Two exceptions are the testis-specific (TS) histone variants TS H2A and TS H2B, which possess a 3′ stem-loop in their mRNA. For this reason, they have been classified as replication-dependent  [49]  even if expressed in differentiating Their protein names have been adapted to improve their identification and analysis by mass spectrometry. Indeed, the column "Entry name for MS analysis" represents the information present in the FASTA file (Additional file 1) used as a database to identify peptides and proteins after an MS analysis.
The last column indicates studies on histones that described evidence of transcript and/or protein existence. For the sake of completeness, histone entries lacking a related publication were retained and the classification currently proposed by the Ensembl database was specified, as follows * "Protein coding", genes and/or transcript that contains an open reading frame (ORF) ** "Nonsense mediated decay", transcript is thought to undergo nonsense mediated decay *** "Pseudogene", genes containing frameshift and/or stop codon(s) that disrupt the ORF The term "Short" indicates that the putative protein is significantly smaller than conventional histones; its incorporation into chromatin and its biological function is then doubtful. Additional file 4 presents links to gene, transcripts and protein entries to Ensembl and UniProtKB databases  ).
H1 histones H1 histones (or linker histones) are different from core histones with respect to their structure, function and evolution. Therefore, it is not possible to single out one of its isoforms as canonical. H1 variants are known to Hist4h4 P62805  [41]  Please refer to the Table  2  for legend. The corresponding FASTA file is presented as Additional file 2. Additional file 5 presents links to gene, transcripts and protein entries to Ensembl and UniProtKB databases encompass isoforms named H1. 0-H1. 10. H1. 1-H1. 5 from histone gene cluster 1 and orphan genes H1. 0 (H1°) and H1. 10 are usually referred to as somatic variants  [36]. The linker variant H1. 0 has been described to be involved in cell differentiation (for review  [2, 52] ). H1. 10 has been identified in human and plays an essential role for mitotic progression  [53].
H3 variants H3 has several isoforms: H3. 1 and H3. 2 are replicationdependent; H3. 3 is considered to be a replication-independent histone variant, while TS H3. 4 and H3. 5 are TS Fig. 3  Phylogenetic tree of the mouse and human H2A. L, H2A. B and H2A. P histone variants  [74, 75]. Several new isoforms of H3. 3 were included in the database developed here along with two other human H3 histone variants, H3. X and H3. Y  [44]. CenH3/CENPA is a well-known centromeric H3 variant with many spliced isoforms. Its name has been the subject of heated discussion, which is out of the scope of our work  [36, 76, 77]. We therefore propose to use both names, cenH3-CENPA, until a consensus has been reached by the community.
Generation of MS-based databases De novo MS data interpretation methods are naive and do not rely on pre-existing databases. However, MS data acquired on histones are generally matched to a database containing all the protein sequences that could theoretically be found in the sample. Using this approach, a given histone protein cannot be identified if its sequence is not present in the database explored by the MS/MS data interpretation software. We used MS_HistoneDB to create a new search space dedicated to the analysis of histones. Basically, mouse or human non-redundant and well-annotated Swiss-Prot FASTA files were cleared of their histone sequences and then repopulated using MS_HistoneDB. This resource is included as Additional files 1 and 2, providing resources to study histones in mouse and human samples, respectively.
Other MS-based studies Not MS-based studies described in publications, which provide clear evidence of their existence at mRNA and protein levels, they may not have been identified by MS yet. This could explain their poor annotation status in UniProtKB. At the RNA level, almost all histone variants have been detected in the testis  [38-40, 55, 57, 68, 78-81]. Moreover, the expression profile of the mouse H2A. L. 1 isoforms which are described in this study has been explored. RNA-seq data from nine mouse tissues have been obtained from a recently published dataset  [82]. Expression data were available for 7 out of the 8 H2A. L. 1 mouse histone entries and confirm that all of them are mainly expressed in the testis, similarly to H2A. L. 2 and H2A. P (Fig. 4a )  [38, 39]. Gene expression profiles during spermatogenesis have been obtained from Ref.
Conclusions MS is a powerful technique to identify histones, their variants and their post-translational modifications but relies on databases with contradictory naming and excessive redundancy. Here we exhaustively collected histone sequences for mouse and human and used manual curation to establish a protein-centric list, MS_HistoneDB, dedicated to the proteomic study of mouse and human histones. Histone variants whose protein status is uncertain in UniProtKB and NCBI but whose protein existence has been established by experimental evidence described in the literature have been included. This work confirmed the expression of isoforms of previously identified TS histone variants and allowed the detection of one H3. 3 isoform whose status was so uncertain that its record had been deleted from the NCBI protein database.
Sample preparation and analysis by MS Histones were reduced and alkylated as described previously  [89]. Histones were either derivatized with propionic anhydride before and after in-gel trypsin digestion    2  and Additional file 4 from a dataset downloaded from Expression Atlas  [87]  and published in Ref. [82]. b Expression profiles of a selection of H2A. L, H2A. B and H2A. P genes during mouse spermatogenesis, revealing a maximum expression in the post-meiotic stage. Data have been obtained from Ref. [83]. Lepto leptotene, Zygo zygotene. c Coomassie-stained SDS-PAGE gel loaded with histones extracted from whole testis and elongating spermatids. d Peptides of the mouse H2A. L histone variants identified by mass spectrometry analysis (identified peptides are highlighted in red boxes)  [90] , or only submitted to trypsin digestion  [89].
Protein sequence database search and manual verification MS RAW files produced by LC-MS/MS analysis of proteolyzed histones were processed as follows. All MS/MS spectra were submitted to the Mascot program (version 2. 5. 1) for searching against the MS_HistoneDB protein sequence database. The parse rules for MS_HistoneDB Fasta files in Mascot are using the accession rule >\([^]*\) and the description rule \(. *\). In addition, the taxonomy and sequence report sources are indicated as "Swiss-Prot FASTA" and "FASTA file", respectively. No taxonomy was specified when using MS_HistoneDB with Mascot Daemon. Classical histone modifications were included in the variable modifications: N-terminal protein acetylation; Lys acetylation; and Lys and Arg mono-or di-methylation. For all Mascot searches, the tolerance on mass measurement was set to 5 ppm for peptides and to 0.
6 or 0. 025 Da for fragment ions when considering LTQ-Orbitrap or Q Exactive acquisitions, respectively. Up to four tryptic missed cleavages were allowed for samples that were not propionylated in vitro, as trypsin does not cleave acetylated lysine, a frequent modification. The enzyme ArgC and up to two missed cleavages were specified for the interpretation of data acquired on propionylated samples. All MS/MS spectra leading to the identification of tryptic peptides specific to newly described variants were carefully manually examined: all major intensity fragment peaks had to be interpreted in terms of y/b ions; a continuous sequence of at least five amino acids had to be read in all cases for validation. Proteomics data are available from ProteomeXchange (PXD005489).
Funding This work was supported by the  Fond d'Intervention of the University Grenoble Alpes  (to JG), the  Agence Nationale de la Recherche  ( ANR-11-PDOC-0011  to JG), and the  European Union   FP7 Marie Curie Action "Career Integration Grant " (304003 to JG). This study also received financial support from the  French National Research Agency   ANR-10-INBS-08  ProFI,  Proteomics French Infrastructure. This research was supported by the  Intramural Research Program of the National Library of Medicine, National Institutes of Health.
-PCR) or at the protein level (e. g. by WB or MS) was further completed with publications NB northern blot, WB western blot, MS mass spectrometry Name (other names) Protein status Accession number Method of detection References TS H1. 6 (H1t) Transcript P22492 WB [41] TS H1. 7 (H1T2, HANP1) Transcript Q75WM6 NB; WB [110] OO H1. 8 (H1oo) Transcript Q8IZA3-1 RT-PCR [111, 112] H2A. 1. ps Inferred Q92646 H2A. B. 1 (H2A. Bbd) Transcript P0C5Y9 WB [118, 119, 130] H2A. B. 2 (H2A. Bbd) Transcript P0C5Z0 WB [118, 119, 130].
The Ni chemical purification of samples was based on a two-step chromatography separation. A first set ion-exchange chromatography columns was filled with 2 mL (wet volume) of anionic resin AG1-X8 in 6 M HCl (BioRad® 100-200 mesh). This resin retained Fe, Zn, and a high  Application of a three-dimensional data reduction procedure was used to determine the true isotope ratios of the samples  (Siebert et al. 2001 ). In addition, each sample analysis was bracketed by the measurements of the spiked standard Ni NIST SRM 986 solutions at the same concentration and same spike/ standard ratio as the samples. The ratios of δ 60 Ni were expressed in per mil and normalized with the average value of the bracketing standard SRM-986 (Eq. 1;  Gramlich et al. 1989). H 2 O KCl [cmol(+)kg -1 ] [ w t % ] [ w t % ] [ m g k g -1 ] Site 1: Szklary Massif (N 50°39′09.
Acknowledgements This research was financed by  Polish National Science Center  ( Jakub Kierczak , project No  2012/ 05/D/ ST10/00529 ). Artur Pędziwiatr is grateful for  Human Capital Operating Program of European Union  (project No  POKL. 04. 01. 01-00-054/10-00 ). The authors would like to thank  Jerzy Raczyk  and  Gaël Monvoisin  for support during chemical analysis. We are grateful also to  Olivier Rouxel  for the Ni double spike preparation, as well as to  Agnieszka Koczur  and  Anna Pietranik  for valuable comments for the manuscript. The authors wish to thank the three anonymous Reviewers, which allowed us to significantly improve the manuscript.