dataesr/scientific-paragraphs-categorization huggingface dataset:
1% and 50 μL of CH 3 CN/H 2 O/TFA 80/20/0. 1%. Then 1 μL of sample was injected into the nanoLC-nanoESI-MS/MS system for analysis. Tryptic peptides were analyzed by mass spectrometry performed using a LTQ Velos instrument (Dual Pressure Linear Ion Trap) equipped with a nanospray source (Thermo Fisher Scientific) and coupled to a U3000 nanoLC system (Thermo Fisher Scientific). Using the software Xcalibur 2. 1 (Thermo Fisher Scientific), a MS survey scan was acquired over the m/z range 400-1600 in Enhanced resolution mode. The MS/ MS scans were acquired in Normal resolution mode over a dynamic m/z range for the 20 most intense MS ions with a charge of 2 or more and with a collision energy set to 35 eV. The spectra were recorded using dynamic exclusion of previously analyzed ions for 0. 5 min with 50 millimass units (mmu) of mass tolerance.
In silico proteomic data analysis Protein identification was performed with the MASCOT 2. 2. 4 Algorithm through the Proteome Discoverer software v1. 1 (Thermo Fisher Scientific). The P. lividus proteome database, comprising 124,032 entries, was used for that purpose. This protein dataset results from the translation of the genome and transcriptome of P. lividus. The nucleic acid sequences were formerly generated in the frame of the 'Arca di Noe' sea urchin network, a subset of the NOI (Network Of Excellence) "Marine Genomics Europe (MGE)", a consortium comprising 44 institutions from 16 countries within and outside Europe. The different datasets on P. lividus are in restricted access on the website of the Villefranche-sur-Mer Marine Laboratory (UMR CNRS-UPMC 7009, see http://octopus. obs-vlfr.
fr/) but are accessible upon request and will be publicly available soon. Another interrogation was performed with an in-house unpublished non-redundant dataset made from the collection of about 800 proteins associated to calcium carbonate biominerals of several metazoans, from sponges to vertebrates (hen eggshell and fish otoliths). In this dataset, echinoderms are represented by the sea urchins S. purpuratus, Lytechinus pictus, Hemicentrotus pucherrimus, Heliocidaris erythrogramma and Heliocidaris tuberculata. The protein hit sequences obtained were further characterized via the following proteomics tools: ClustalW, InterProScan, ProtParam, which are available at www. expasy. org/proteomics/.
Proteomics of the test matrices The biochemical characterization performed in this study was complemented by a proteomic analysis that emphasized the role of a limited number of protein families in the biomineralization of P. lividus test. The ASM and AIM test extracts were analyzed by nano-LC-MS/MS after trypsin digestion and the peptide sequences were used for screening the Basic Local Alignment Search Tool, using the proteome database of P. lividus at http://octopus. obs-vlfr. fr. To ensure the reproducibility of the results, we separately analyzed two batches of ASM and AIM, numbered batch I, and batch II. The results are outlined in Table  2  and in Supplementary Table  S1 , while some of the rough spectra data are also shown in Supplementary Fig. S2. all the protein hits found in batch I.
lividus test, from 9 contigs and 8 sequences (Table  2 ). They include five lectins, three members of the MSP130 family, two almost identical carbonic anhydrases, one matrix-metalloproteinase, actin and myosin. These proteins can be consequently clustered in four different groups: (I) C-type lectins, a class of glycoproteins that are able to bind monoand disaccharides  [30] , (II) proteins of the MSP130 family, (III) metallo-enzymes and (IV) cytoskeletal proteins. The lectin sequences identified in the P. lividus proteome dataset correspond to contigs6474, 14265, 14621 and 15948 and to the sequence s36065. They all contain a calcium-dependent (C-type) lectin domain either in their N-terminus (contigs15948, 6474, and 14621), middle (sequence s36065), or C-terminus (contig14265). A search for homology using BLASTP against the whole UniprotKB database shows that all of them match, at different degrees, to lectins from various sea urchins: for example, contig14265 is 81% identical to the spicule matrix protein SM29 from S.
purpuratus (Q8MUL0_STRUPU) and that contig14621 is 73% identical to SM41, the spicule matrix protein from Hemicentrotus pulcherrimus (Q26264) but exhibits also similarities with SM50 and SM32 from S. purpuratus (respectively P11994 and Q9MUL1) and with SM34 from L. pictus (Q05904). The sequence s36065 is 86% identical to PM27, the 27-kDa spicule matrix protein from S. purpuratus (Q26616), and 83 and 81% identical to the two PM27 sequences of H. tuberculata and erythrogramma, respectively (Q95W97_HELTB and Q95W86_HELER). Interestingly, contigs15948 and 6474, identified both in ASM II and AIM I, correspond to two sequences that exhibit similarities with two uncharacterized lectins from S. purpuratus, Sp-Clectin/PMC1 (W4ZI92_STRPU, database entry Glean3:27906) and Sp-Clect_76 (W4YDJ5_STRPU, database entry Glean3:13825), respectively.
The contig17159 is identical to sequences s72921 and s13733. They exhibit an 80% identity with MSP130 protein from the sea urchin H. tuberculata (Q9GP17_HELTB) and 78%, with that from H. erythrogramma (Q9GP19_HELER). The contig17238 exhibits a high degree of similarity to sequence s11289. Both are 72% identical to the MSP130-related-2 protein of S. purpuratus (Q8MUK7_STRPU). Finally, the sequence s8835 is 72% identical to the MSP130-related-1 protein of the same species (Q8MUK8_STRPU). Concerning the metallo-enzymes, two distinct protein families were identified: at first, two sequences (contig14487 and s75885) encoding for carbonic anhydrase were obtained in the P. lividus proteome dataset: Although of different length sizes, their overlapping parts are almost identical and differ only by one aa residue (valine versus alanine) at the C terminus (10th position upstream the last leucine residue of contig14487).
Secondly, another identified sequence, s77447, encodes for a protein that is 87% identical to two uncharacterized matrix metalloproteinases (MMP) of S. purpuratus (W4YD41_STRPU, W4YD42_STRPU). Furthermore, s77447 exhibits lesser similarities with a large set of other matrix metalloproteinases of diverse sources, including an uncharacterized MMP from the giant owl limpet Lottia gigantea (V4B204_LOTGI), MMP-17 of the edible oyster Crassostrea gigas (K1R1S7_CRAGI), MMP-14 of the parasitoid Fopius arisanus (A0A0C9QER8_9HYME). Finally, three sequences encoding cytoskeletal proteins were obtained by blasting peptide data against the proteome dataset of P. lividus. These sequences include contig20288 that encodes for myosin, and contig20740 and sequence s10890, both encoding for actin.
purpuratus, listing a total of 110 different proteins in the matrix of test and spines  [13]. One may claim that the paucity of protein hits may be the result of three different combined factors: the quality of the dataset used for the interrogation; technical aspects of the trypsin digestion; the abundance of proteins with RLCDs (Repetitive Low Complexity Domains) in the matrix of P. lividus. The first possibility may be ruled out since the proteome dataset of P. lividus, with 124,032 entries, is rather complete, and since all the 'biomineralization proteins' (sensu lato) identified in S. purpuratus were identified in P. lividus proteome. Secondly, about the technical aspects of trypsin digestion, one often asserts that bulk digestion ('in-solution') have a lesser efficiency on protein mixtures than in-gel digestion  [30].
Acknowledgments This work has been fully supported by the  EU-ITN   BIOMINTEC  Project, contract number  215507  to  V. Matranga. The first author,  K. Karakostis , has been the recipient of a  Marie Curie ITN program  fellowship in the frame of the aforementioned project, which allowed three short-term scientific missions in Biogeosciences research unit, Dijon, France. The authors thank  Prof. Dr. F. Wilt ,  Graduate School Division of Cell and Developmental Biology, University of Berkeley, USA  for providing SM30 and SM50 antibodies. The authors also thank the researchers of different European Marine Biology Institutions who contributed to the construction of the Paracentrotus lividus libraries; they include  P. Cormier ,  J. Morales ,  I. Arnone  and  P. Oliveri. Additional support of the work of  K.
The importance of complement activation in reperfusion injury prompted the initiation of clinical trials to test the benefits of an anti-C5 antibody (Eculizumab) to prevent DGF (Delayed Graft Function) (NCT01403389; NCT01919346), which are still ongoing. In the current study, we tested the benefits of a recombinant human C1 inhibitor (rhC1INH)  [11]. Therapeutic strategies centered on C1 have shown significant benefits in models of myocardial IR  [12]  as well as in lung transplantation models  [13]. This strategy downregulated the expression of surface receptors on endothelial cells, reducing the immune response  [14]. Endogenous C1 inhibitor (C1-INH) has a plasma concentration ∼240 mg/l, corresponding to 1 U/ml  [15]. It belongs to the serpin family (serine protease inhibitors) and while it targets the classical pathway, recombinant C1 inhibitors have been shown to target the lectin pathway as well in myocardial IR models  [16] , and to have several inhibitory activities on the alternative pathway, particularly through C3b  [17].
Morphological study Immunofluorescence: biopsy samples of kidney cortex were processed for cryosectioning. Antibodies: Anti Factor B (Novus Biologicals, UK), anti C4d, anti C1q (AbD Serotec, France), anti C3c, anti C5b-9 (DAKO, France), anti MBL, anti MASP2 (Cliniscience, France). Each slide was semi quantitatively evaluated by a trained nephropathologist. Immunohistochemistry: biopsies were preserved in formalin. Antibodies: anti-vimentin (Cell-Marque, USA), anti-αSMA (alpha smooth muscle actin); (Sigma, St. Louis, MO), anti-Calprotectin reacting with Monocyte/ Granulocytes/Macrophages (MAC-387, AbCam, France) and anti-CD3 (SouthernBiotech, Birmingham, Alabama, USA). Fibrosis was analyzed by Sirius Red staining. Staining quantification was performed in silico (Visilog 6. 9 software): fibrosis: percent of stained area per field; inflammation: number of positive immune cells per field.
Our results suggest that treatment likely protects against the consequences of IRI on the inflammatory response, activated in autotransplanted kidneys, likely on the innate arm of the response. It would thus affect the ability of the kidney to recover from the injury, rather than the level of the injury itself, hence the absence of difference until day 3 (IRI effects at the tissue level) but increased recovery after day 3 (unimpeded repair). Thus, while rhC1INH treatment demonstrates evident benefits to graft outcome, combining this strategy with other methods directed at cold ischemia could be even more beneficial. Ruconest has already been tested in clinical trials, concerning its safety (NCT00851409) and the treatment of Hereditary Angioedema (NCT00262301,  [33] ) and it is currently under further clinical evaluation for this pathology.
Acknowledgements The authors wish to express their gratitude for the financial support from the  Région Poitou-Charentes , the  CHU de Poitiers , the  Inserm  and the  Fondation de l' Avenir. The authors also wish to acknowledge the invaluable technical help from  Mrs. Virgine Ameteau ,  Mrs. Maïté Jacquard  and  Mrs. Sandrine Joffrion.
Sulfatases cleave sulfate groups from various molecules and constitute a biologically and industrially important group of enzymes. However, the number of sulfatases whose substrate has been characterized is limited in comparison to the huge diversity of sulfated compounds, yielding functional annotations of sulfatases particularly prone to flaws and misinterpretations. In the context of the explosion of genomic data, a classification system allowing a better prediction of substrate specificity and for setting the limit of functional annotations is urgently needed for sulfatases. Here, after an overview on the diversity of sulfated compounds and on the known sulfatases, we propose a classification database, SulfAtlas (http://abims. sb-roscoff. fr/sulfatlas/), based on sequence homology and composed of four families of sulfatases.
The formylglycine-dependent sulfatases, which constitute the largest family, are also divided by phylogenetic approach into 73 subfamilies, each subfamily corresponding to either a known specificity or to an uncharacterized substrate. SulfAtlas summarizes information about the different families of sulfatases. Within a family a web page displays the list of its subfamilies (when they exist) and the list of EC numbers. The family or subfamily page shows some descriptors and a table with all the UniProt accession numbers linked to the databases UniProt, ExplorEnz, and PDB.
-) or an oxidative mechanism (dioxygenase EC 1. 14. 11. -)  [23]. We propose to revise the nomenclature of all sulfatases present in the UniProt databank to improve the accuracy of their functional annotation, creating four families based on sequence similarities, and dividing the family of the formylglycine-dependent sulfohydrolases (FGly-sulfatases) into substrate-specific subfamilies. This classification system is implemented in an online database dedicated to sulfatases, SulfAtlas (http://abims. sbroscoff. fr/sulfatlas/). Thus, it is possible to distinguish four families of sulfatases: the FGly-sulfatases  [24] ; the alkylsulfodioxygenases, represented by the alkylsufatase AtsK from Pseudomonas putida S-313  [25] ; the alkylsulfohydrolases, represented by the alkylsulfatase SdsA1 from Pseudomonas aeruginosa PAO1  [26] ; and the arylsulfohydrolases, represented by the arylsulfatase AtsA from Pseudoalteromonas carrageenovora 9 T  [27].
Upon substrate binding, the formyglycine is activated for nucleophilic attack on the sulfur by an aspartate (Asp317, AtsA numbering, PDB: 1HDH; Uniprot: P51691). The sulfoenzyme intermediate is formed, and desulfation most likely occurs by elimination from the remaining FGly-diol hydroxyl (E2), catalyzed by a histidine base (His115) (Fig  2 )  [35, 38]. Thirty-six FGly-sulfatases, mainly from mammals, have been currently characterized at the level of their cDNA, mRNA or gene products and for their substrate specificity (Table  1 ). However, thirty of these enzymes represent only 9 EC numbers (the six remaining enzymes have not been attributed EC numbers). Most of these enzymes were studied in the context of severe metabolic disorders in man and other mammals. Genetic defects in GAG-specific FGly-sulfatases provoke various mucopolysaccharidoses  [39] [40] [41] [42] [43] [44] [45] [46] , while absence or malfunctioning of cerebroside sulfatase and sterylsulfatase results into metachromatic leukodystrophy and X-linked ichthyosis, respectively  [47] [48] [49].
In less studied organisms or ecosystems, an annotation only based on the similarity with the currently characterized sulfatases (Table  1 ) is likely to incorrectly predict substrate specificity. In order to improve the predicted sulfatase substrate specificities we have undertaken an extensive census of the sulfatase sequences available in the Uniprot database. Multiple alignments were calculated in order to determine or update the consensus sequences conserved in each family of sulfatases. These alignments were also used for phylogenetic analyses. Notably in the family of FGly-sulfatases the sequences diverge into 73 clades that coincide with their substrate selectivity. Most of the clades do not encompass characterized FGly-sulfatases, supporting the existence of subfamilies of FGly-sulfatases with novel unidentified substrate specificities.
Materials and Methods Sulfatase sequences were extracted from the UniProt database in August 2009 using the BlastP program  [70]. Alkylsulfohydrolases (370 proteins) and arylsulfohydrolases (15 proteins), which belong to the metallo-β-lactamase superfamily, were identified by at least 30% sequence identity over ~600 residues with the characterized enzymes alkylsulfatase SdsA1 (Uniprot code: Q9I5I9) and arylsulfatase AtsA (P28607), respectively, and by the presence of the pattern HxHxDH, which is involved in the coordination of two catalytic zinc ions. Fe αKG-dependent alkylsulfodioxygenases (111 proteins) were identified by at least 30% sequence identity over ~300 residues with the characterized alkylsulfodioxygenase AtsK (Q9WWU5) and by the presence of the pattern HxD/Ex n H (n = 39 to 154) involved in the coordination of the Fe ion  [23].
The proteins encompassing several FGly-sulfatase modules were divided into distinct sequences corresponding to each catalytic module. Due to the huge number of sequences, it is impossible to directly obtain a reliable multiple alignment of this large group of sequences. Therefore, the FGly-sulfatase sequences were first divided into 81 groups and 32 orphan sequences, on the basis of sequence identities using the BlastP program. A multiple sequence alignment was obtained for each of these groups using MAFFT  [71]  with the iterative refinement method L-INS-i and the scoring matrix Blosum62. Then these 81 multiple sequence alignments were manually stacked on each other by matching similar zones using Jalview  [72]. The alignments were manually improved using Jalview on the basis of the sequence alignment derived from the superposition of available crystal structures of sulfatases (Table  1 ).
After this refinement step, the poorly conserved regions were removed from the multiple sequence alignment. The different phylogenetic trees were derived from these refined alignments using Maximum Likelihood method with the program RAxML with the MTMAMF or WAG as substitution matrix  [73]  or with the program MEGA 5. 2. 2  [74]. The reliability of the trees was always tested by bootstrap analysis using 100 resamplings of the dataset. The trees were displayed with MEGA 5. 2. 2  [74]. For the FGly-sulfatase sequences, the program MatGat  [75]  was used and two identity matrices were generated, one for the full length proteins and the second matrix corresponding to the edited multiple sequence alignment. The logo sequences were built using WebLogo via the PROSITE databank  [76].
Analyses of alignment of formylglycine-dependent sulfatases (family S1) From 211 FGly-sulfatase sequences used as seed (104 sequences from R. Baltica SH1 T , 71 sequences from Z. galactanivorans Dsij T and the 36 FGly-sulfatases with a known substrate specificities; Table  1 ), 4058 FGly-sulfatases were extracted from the UniProt database (August 2009). The FGly-sulfatases belongs to the alkaline phosphatase superfamily. They are easily identified using tools such as PFAM or PROSITE which propose the signatures PF00884 (sulfatase) or PS00523 and PS00149. However, these signatures were defined on a limited number of seed sequences (57 for PF00884, 58 for PS00523 and 50 for PS00149) and our multi-alignment shows that these signatures are no longer completely correct. Therefore, we have updated the two signatures, PS00523 and PS00149 (Fig 4A  and 4B ).
Moreover, we have identified three additional conserved signatures, which can be modelled according to PROSITE syntax and illustrated by sequence logos (Fig 4C  -4E ). Updating of the PROSITE signatures. The PROSITE database describes the consensus pattern PS00523 for the catalytic site. This signature contains the two essential amino acids    [32]. Nonetheless, this glycine is replaced by other small residues, a serine in 30 sequences or an alanine in 14 sequences. Finally, the insertion "x(0,6)" is due to the sequence A9UYU7 from the Choanoflagellida Monosiga brevicollis. The insertion "x (0,6)" was removed to generate the sequence logo shown in Fig 4A. On the model of the PRO-SITE consensus pattern PS00523, we have updated this pattern, called the catalytic site pattern (Fig 4A), as [SAPG]-[LIVMSTPAR]-[CS]-[STACGMV]-[PA]-[STAGF]-R-x-{PRFWYH}- [LIVMFWYHQ](2)-[TASL]-G.
This new catalytic consensus pattern recovered 9339 sequences from TREMBL database (July 2016), including 8949 true FGly-sulfatases (96%). From our global alignment, the consensus sequence corresponding to the second PROSITE signature (PS00149) is G 94 -x(0,1)-Y 93 -A 12 -T 84 -x(0,42)-A 31 -x(0,3)-L 18 -x(0,13)-I 24 -x(0,3)-G 95 -x (0,5)-K 94 -x(0,3)-W  59   With the exception of the four residues mentioned above (Gly105, Tyr106, Gly112 and Lys113), the signature PS00149 is poorly conserved and presents many insertions between some residues (S1B Fig). Between the residues Gly105 and Tyr106, the "x(0,1)" position is due to 18 sequences, 14 of which are from various species of Drosophila that display an arginine at in reference sequence (AtsA P51691). The corresponding consensus sequences in multi-alignment are shown below the logo sequences.
The first position "x(0,1)" is due to four sequences of which D5EPW8 from C. akajimensis 04OKA010-24 T is also responsible for the insertion at the second position "x(0,1)". The positions "x(0,34)" and "x(0,5)" are due to the sequences B2AAG4 from Podospora anserina strain S and A9VAR3 from M. brevicollis, respectively. After removing of these six sequences, we have defined the consensus pattern P- From the global alignment, other highly conserved amino acids were found. This is the case for the amino acids Asp291 (98% of conservation) (numbering of the sulfatase AtsA from P. aeruginosa PAOI as reference, P51691), Lys375 (96%), Asp409 (98%), Thr413 (91%), Gly437 (91%) and Asp495 (95%). Based on the inspection of the crystal structure of the sulfatase AtsA from P. aeruginosa PAOI (PDB: 1HDH), Asp291, Asp409, Thr413, Gly437 and Asp495 are likely crucial for protein folding.
This enzyme was used as query sequence (accession number Q9WWU5) with the algorithm BLASTP to detect the other alkylsulfodioxygenases present in the UniProt database. AtsK displays some similarities with proteins annotated as taurine dioxygenase-related proteins (TauD) and with 2,4-dicholorophenoxyacetate dioxygenase-related proteins (TfdA). An alignment of 469 proteins belonging to the dioxygenase superfamily was realized. A characteristic sequence of the dioxygenase superfamily is the presence of the signature HxD(E)x n H (where n is a number comprised between 39 to 154). This signature contains the residues His108, Asp110 and His264 that are involved in the coordination of the Fe ion (numbering of the P. putida alkylsulfatase AtsK Q9WWU5 as reference; Fig  1D )  [23]. The multi-alignment reveals that the residues involved in the coordination of the Fe ion are included, on one hand in the consensus sequence W 96 -H 99 -T 71 -D 99 -V 66 -T 68 -F 60 and, on the other hand in the consensus sequence Q 56 -H 100 -Y 51 -A 89 -V 29 -A 25 (subscript numbers indicate the percentage of conservation in dioxygenase alignment and amino acids involved in coordination of Fe are represented in bold).
From this consensus sequence, we have defined the PROSITE-like pattern [DEN]-[NQTSKRGAED]-L-[WRV]-[AV]-[VLIMRTE]-H-[TSGDN]-[NF]-x(0,1)-{SGNFWYCMI}-[YFAG]-x(0,2)-[DES]-[YLQH]. This pattern has recovered 668 sequences from the TREMBL databank (July 2016), all annotated as "Dioxygenase", "Alkylsulfatase" or "Uncharacterized protein" (including the 111 sequences contained in the AtsK clade of the phylogenetic tree). A logo sequence was built using the multi-alignment of alkylsulfatases (Fig 6A ). Contrary to the FGy-sulfatases that are found throughout the tree of life (with the exception of land plants), the alkylsulfodioxygenases have been found only into three bacterial phyla. Of the 111 alkylsulfodioxygenases detected by phylogenetic analysis, 58 belong to the phylum Proteobacteria, 50 belong to the phylum Actinobacteria and three sequences to the phylum Cyanobacteria.