dataesr/scientific-paragraphs-categorization huggingface dataset:
Mass spectrometry-based proteomics Protein bands were excised from colloidal blue-stained gels (Thermo Fisher Scientific), treated with DTT and iodoacetamide to alkylate the cysteines before in-gel digestion using modified trypsin (sequencing grade; Promega). Resulting peptides from individual bands were analyzed by online nanoLC-MS/MS (UltiMate 3000 coupled to LTQ-Orbitrap Velos Pro; Thermo Fisher Scientific) using a 25-min gradient. Peptides and proteins were identified and quantified using MaxQuant (version 1. 5. 3. 17) through concomitant searches against ToxoDB (20151112 version), SwissProt (Homo sapiens taxonomy, 20151112 version), and the frequently observed contaminant database embedded in MaxQuant. Minimum peptide length was set to 7 amino acids. Minimum number of peptides, razor + unique peptides, and unique peptides were all set to 1.
Microarray hybridization and data analysis HFFs, 2fTGH, and U3A were plated at 8-10 × 10 6 cells per 55-cm 2 plate, infected (MOI = 6) for 24 h with 76KG-FP-WT and -ΔTgIST and with 100 U/ml IFN-γ for 6 h. RNA was isolated using TRIzol reagent, followed by phenol/ chloroform/isoamyl extraction. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis. Transcripts were obtained from three biological replicates each. Total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The labeled cRNAs were purified by RNeasy Mini kit (QIA GEN). The concentration and specific activity of the labeled cRNAs (pmol Cy3/µg cRNA) were measured by NanoDrop ND-1000. 1 µg of each labeled cRNA was fragmented by adding 11 µl of 10× blocking agent and 2.
2 µl of 25× fragmentation buffer and then heated at 60°C for 30 min, and finally 55 µl of 2× hybridization buffer (GE Healthcare) was added to dilute the labeled cRNA. 100 µl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 h at 65°C in a hybridization oven (Agilent Technologies). Feature extraction software (version 11. 0. 1. 1; Agilent Technologies) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the Gene-Spring GX version 12. 1 software (Agilent Technologies). After quantile normalization of the raw data, genes that had at least 3 out of 27 samples have flags in Detected ("All Targets Value") were chosen for further data analysis.
Differentially expressed genes with statistical significance were identified through Volcano Plot filtering. Hierarchical clustering was performed using the R software (version 2. 15). GO analysis and Pathway analysis were performed in the standard enrichment computation method. The thresholds were fold change ≥ 2. 0, p-value ≤ 0. 05. GO analysis and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis were performed using the DAV ID Bioinformatics Resources. GSEA and DIRE analysis were performed to identify TFBSs. Microarray data has been uploaded to GEO Datasets under accession no. GSE81613.
Levels of CXCL9, CXCL10, CII TA, MX1, GBP2, IGTP, and SOCS1 mRNAs were determined by RT-qPCR. β2-microglobulin was used for normalization. Data are displayed as fold difference relative to the uninfected cells. The mean of two experiments is shown; error bars represent SEM. This experiment is representative of at least three experiments and was repeated with 76KGFP (WT and Δ) strains with similar results (not depicted).
ACK NOW LED GME NTS We thank  Dr. Geneviève Milon  ( Pasteur Institute ) for her valuable comments. We thank  Pr. Jonathan Howard  ( Lisbon ) for his kind gift of the Irgb6 antibody. This work was supported by the  Laboratoire d'Excellence (LabEx) ParaFrap  ( ANR-11-LABX-0024 ), the  European Research Council  ( ERC Consolidator Grant N° 614880 Hosting TOXO  to  M. -A. Hakimi ), and  Agence Nationale de la Recherche (ANR)  grant  ANR   Blanc 2012 TOX OHD AC  ( ANR-12-BSV3-0009-01 ). Proteomic experiments were partly supported by the  ANR  ( Investissement d'Avenir Infrastructures ,  ProFi  project  ANR-10-INBS-08-01 ). The authors declare no competing financial interests.
KIT mutations and other genetic defects The entire coding regions of KIT were sequenced in 40 of the 53 patients (75. 5%). When a mutation was detected, it was mostly the KIT D816V. Indeed, this mutation was retrieved in 34 of the 40 tested patients (85%), whereas 2 patients (5%) presented another KIT mutation, (p. (Phe504_Asn505delinsLeuLysPhe-LysThr) and p. Ser501_Ala502dup), and 4 patients (10%) displayed wild-type KIT. For 26 patients, including 1 ISM, 2 ASM, 21 SM-AHNMD patients, and the 2 patients with MCL, sequencing data for additional genetic defects were available and are shown in Table  2. Seventeen (65. 3%) of them (including 14 SM-AHNMD, 2 ASM, and 1 MCL patient) exhibited TET2 (n = 12), SRSF2 (n = 8), IDH2 (n = 3), ASLX1 (n = 4), CBL (n = 1), U2AF1 (n = 2), and/or NRAS (n = 1) mutations.
According to their ΔCt to the S6 gene, genes were classified as high-expressed (ΔCt less than 5 cycles), intermediate-expressed (ΔCt from 5 to 15 cycles), low or Bound antibodies were detected with HRP-conjugated anti-rabbit or anti-mouse antibodies, and visualized by enhanced chemiluminescent detection (ECL advance, GE Healthcare). Membranes were stripped for 15 min in Reblot buffer (Millipore), followed by extensive washing in TBST before reblocking with 5 % non-fat dry milk in TBST and reprobing for β-actin determination. Bands were imaged in a LAS-3000 Imager (Fujifilm, Tokyo, Japan) and quantified with Multigauge 3. 0 software (Fujifilm). To allow comparison between different membranes, the density of the bands was referred to that of untreated controls and normalized to the amount of β-actin in the same sample.
Statistical analysis Results are presented as mean values ± S. E. M. of at least three independent experiments. All data were compared using one-way or two-way ANOVA, followed by Tukey's post hoc test (unless otherwise stated). Where stated, randomised block design analysis was performed to minimise the variability due to differences between individual culture responses. Data analysis and plot were performed with GraphPad Prism 5. 0 software (GraphPad Software Inc. , La Jolla, USA). Randomised block design analyses were performed with Minitab 15 Statistical Software (Minitab Inc. , Pennsylvania, USA). A P value <0. 05 was considered to be significant.
Acknowledgements Work in EF's group is also supported by  Generalitat de Catalunya  ( SGR-2009-997 ). The authors would like to thank  J. Chevalier ,  M. Biraud  and  M. Ribeiro-Neunlist  ( INSERM U913 ) for training and technical support on ENS PC preparation;  N. Barba  ( INc from the Universitat Autònoma de Barcelona ) for excellent technical assistance in confocal microscopy imaging and  Drs. L. Grasa  ( Universidad de Zaragoza ),  MT. Abreu  ( University of Miami ) and  R. Herzog  ( University of Florida ) for providing TLR2 -/-, TLR4 -/-and TLR9 -/-tissues for confirmation of antibody specificity.
16S rRNA Gene Sequencing and Data Processing Total metagenomic DNA was extracted from the intestinal section using QIAamp Fast DNA Stool Mini Kit (Qiagen, USA). The samples were sequenced for 16S rRNA genes targeting the V4 region with barcoded 515F GTGCCAGCMGCCGCGGTAA and 806R GGACTACVSGGGTATCTAAT universal primers following the procedure of  Dowd et al. (2008). DNA concentrations were determined using the Qubit system (Invitrogen, USA). Subsequently, dual-index barcodes and Illumina sequencing adapters were joined to the reads using a limited PCR cycle. After purification with Agencourt AMPure beads (Agencourt, USA), libraries were normalized using the Nextera XT protocol. Samples were pooled into a single flow cell for sequencing on the MiSeq sequencing platform (Illumina, USA) following the manufacturer's protocol.
Automated cluster generation and paired-end sequencing with dual index reads were performed in a single run with a read length of 2 × 300 bp. Raw FASTQ files were obtained from the Illumina MiSeq, and paired end reads were collected using PANDAseq  (Masella et al. , 2012). Sequences were cleaned of primers and barcodes. Additionally, all reads with 'N' and those with sequences <200 bp were deleted, and high-quality sequences were dereplicated  (Boissière et al. , 2012). The cleaned sequences were then clustered at k = 10 (97% similarity) followed by deletion of chimeras and singleton reads  (Eren et al. , 2011; Swanson et al. , 2011). Finally, operational taxonomic units (OTUs) were classified using BLASTn against a curated database derived from GreenGenes, RDPII and NCBI. Sequence data of this study is submitted in the NCBI under project no.
Statistical Analysis The OTU biodiversity and richness were calculated using R package phyloseq (1. 7. 24) implemented with non-parametric Chao1 and rarefaction analysis that showed the uniformity and distribution of OTUs in different groups  (McMurdie and Holmes, 2012). R package "rich" (0. 3) was employed for statistical modulations in specie richness and abundance. The Kolmogorov-Smirnov D test was used to ascertain the normality of the data. One-way ANOVA (for parametric data) and nonparametric Kruskal-Wallis and Mann-Whitney tests (for nonnormal data) were performed to identify significantly different bacterial taxa among different groups (Supplementary Figure  S1 ). SPSS version 22 was used for statistical analysis. The VassarStats website 1 was used to conduct pair-wise comparisons of rat weight via the Tukey's HSD test.
Biodiversity and Microbial Richness Alpha diversity was estimated through rarefaction analysis, the Shannon index and the Chao1 index. The lowest OTU richness was observed in the cefaclor-treated groups (NPCef and PCef). The highest Chao1 value was observed for PC followed by NPC and PAzi. Rarefaction analysis indicated variation among samples and showed sufficient data coverage for diversity in the samples (Supplementary Figure  S3 ). The Shannon Wiener index, calculated at 3% dissimilarity, showed the lowest value of evenness (2. 8) for NPCef. The highest value of evenness was observed for NPAzi (4. 4) and NPAmx (4. 2). The identified genera from all sequence reads were compared using UPGMA distance matrix clustering analysis. The pregnant groups treated with antibiotics formed a separate cluster from the non-pregnant groups (Supplementary Figure  S4 ).
4 ). In the absence of fast motion, R 2 /R 1 values directly depend on the average rotational correlation time of the subdomains  16. Average R 2 /R 1 values measured for residues of MapZ extra1 and MapZ extra2 subdomains were 14. 24 and 7. 23, respectively. This large difference in the R 2 /R 1 ratios is in favour of an independent hydrodynamic behaviour of the two subdomains, thus suggesting the absence of a strong interaction between them. The independent mobility of the two domains conferred by the flexible SRL was confirmed by small-angle X-ray scattering (SAXS) data recorded on the full-length extracellular domain at two concentrations (Supplementary Fig. 5A ). Indeed, the Kratky plot derived from the experimental I(s) scattering curves showed a behaviour for s42 nm À 1 in agreement with the presence of a large flexibility (Supplementary Fig.
These data were used to generate 20 low-energy structures (Fig. 2 ) after eight iterations using Crystallography and NMR system (CNS) software  17  and Aria protocols  18. Structural statistics for each of the two subdomains structure calculations are given in Table  1. MapZ extra1 is a 50-Å prolate domain (Fig. 2a ) composed of four helices (H1: 200-213, H2: 225-240, H3: 245-269 and H4: 300-310). The H2 helix consists in a 3 10 helix (225-229) prolonged by an a-helix (230-240), thus inducing a bending of the helix axis. The N-terminal end of MapZ extra1 is connected to the transmembrane segment of MapZ through a flexible linker, from residues 182 to 199, as suggested by { 1 H} 15 N-NOE and R 2 /R 1 relaxation data (Supplementary Fig. 6A ) and in agreement with the IUPred predictions (Supplementary Fig.
1 ). The H3 helix, which extends along the whole subdomain, is flanked by H1 and H2 at its bottom, and H4 at its top. The strong stability of the tertiary structure is ensured by the presence of numerous hydrophobic contacts between the different helices (Fig. 2c ). The majority of the highly conserved residues are not accessible at the surface (Fig. 3 ), but are directly involved in many inter-helices interactions (Fig. 2c ), yielding a very rigid domain. Searches for structural homologues of the MapZ extra1 subdomain prevented us to get further insight into its functional role  19. Indeed, no MapZ extra1 homologues were found in the Protein Data Bank (PDB) and a closest structural alignments were found almost exclusively with eukaryotic a-helix-rich proteins such as VPS4 (PDB 2LXL, Z-score 5.
Unbound and bound fractions were analysed by SDS-polyacrylamide gel electrophoresis subjected to western blotting using mouse anti-histidine-tag antibody. Data-driven docking of MapZ extra2 with muropeptides. The peptidoglycan model is a sixfold repetition of an N-acetylglucosamine (GlcNAc)-N-acetylmuramic acid (MurNAc)-L-Ala 1 -g-D-iGln 2 -L-Lys 3 S. pneumoniae muropeptide. Topology, parameter files and patches for CNS were generated using the GLYCANS software (http://haddock. chem. uu. nl/enmr/services/GLYCANS/) for the oligosaccharidic backbone and complemented to integrate the lactoyl-peptide stems. A starting hexamuropeptide structure was generated with CNS  17  and minimized in explicit water molecules, while restraining the j and c dihedral angles of the b-1,4glycosidic bond to 69°and 12°(±30°), respectively  48.
Acknowledgements This work was supported by grants from the  Agence Nationale de la Recherche  ( ANR-12-BSV3-0008-01  and  ANR-15-CE32-0001 ). N. L. J. was supported by a PhD fellowship from the  CEA. We acknowledge the contribution of the  PLATIM and Protein Sciences platforms of SFR Biosciences Gerland-Lyon Sud  ( UMS344/US8 ). This work used the NMR and isotope labelling platforms of the Grenoble Instruct Center (ISBG;  UMS 3518 CNRS-CEA-UJF-EMBL ) with support from  FRISBI  ( ANR-10-INSB-05-02 ),  GRAL  ( ANR-10-LABX-49-01 ) and a financial support from the  TGIR-RMN-THC   FR3050. Access to the  ESRF SAXS beamline BM29  and technical support for data collection is acknowledged. We gratefully thank  Yves V. Brun  for stimulating discussions and help in the use of FDAAs.
Data availability. NMR chemical shifts and resonance assignments, and atom coordinates are available at the Biological Magnetic Resonance Bank (www. bmrb. wisc. edu) and Protein Data Bank (www. rcsb. org), respectively, under the accession numbers 26052 and 2ND9 for MapZ extra1 and 26053 and 2NDA for MapZ extra2. All other data are available from the corresponding authors on reasonable request.
By thermal shift assay experiments, a 10 °C stabilisation was observed when 5′-vRNAp was added to all the constructs, whereas when 3′-vRNAp was added, the effect was less significant and dependent on the construct. Similar data had already been published  32. We used fluorescence anisotropy to measure the interaction between our truncated polymerase constructs and the conserved vRNA ends by following the fluorescence polarization increase of a fluorescently labelled RNA when it binds the polymerase. For this purpose, we used 5′-vRNAp and 3′-vRNAp, both labelled with fluorescein amidite (FAM) at the opposite extremity of the putative interaction, i. e. at the 3′-end for the 5′-vRNAp and vice versa (Fig. 3  and Table  2 ). At 300 mM NaCl, the Kd for the 5′-vRNAp are similar (sub-nanomolar) for both constructs 1 and 14, whereas for the 3′-vRNAp, a Kd of 36 nM for the construct with PB2 is obtained (Fig.
Remarkably, from this polyprotein construct, PA-PB1 co-purifies with RanBP5, forming a homogeneous and stable heterotrimer (Fig. 2d ). Online SEC-SAXS was used for the characterisation of PA-PB1(1-686), RanBP5 and PA-PB1(1-686)-RanBP5, respectively in solution. Using the Vc determination method  39  on the diffusion data of PA-PB1(1-686) shows a Mw estimate of 146 kDa (Table  3  and supplementary Figure  7 ). The calculated Mw is 166 kDa. The Guinier transform measures a hydrodynamic radius (Rg) of 36. 2 Å and GNOM produces the pair distribution function fit with a Dmax of 128 Å. Further analysis of the SAXS curve (Fig. 4a ) shows a visually adequate correlation with the CRYSOL curve which uses the bat-IAV polymerase structure (PDB id: 4WSB) as a model. To evaluate the statistical similarity between experimental intensities and those computed from a model has been derived.
The high chi  2  values are observed for this dataset, due to a noisy SAXS curve. A slight deviation of the fit is observed above a q range of 0. 8 nm -1 , suggesting conformational differences between the scattering curve and the crystal structure coordinates. Ab-initio modelling was performed using 15 DAMMIF models which were averaged by DAMAVER. Averaged model correlation with the diffusion curve was then checked using the damstart file as a starting envelope for DAMMIN. The polymerase DAMAVER envelope (Fig. 4a ) appears as a pear shaped structure in which the homologous model can be fitted. Additional envelope volume is visible close to the endonuclease domain, implying that it adopts multiple conformations in solution. Using the same methodology, we determine RanBP5 to be a monomer in solution with a measured Mw of 144 kDa close to the theoretical Mw of 126 kDa (Table  3  and supplementary Figure  7 ).
RanBP5 displays an Rg of 38. 8 Å and a Dmax of 136 Å. With a Mw lower than that of PA-PB1(1-686), RanBP5 displays a larger Dmax and Rg indicating an extended structure. We have looked over the Protein Data Base (PDB) and found yeast karyopherin Kap121 40 to be the closest homologue available for RanBP5 (30% sequence identity over 1027 residues). CRYSOL curve fitting using the apo form of Kap121 (PDB id: 3W3T) against the diffusion curve reveals important structural and conformational differences between the two structures (Fig. 4b ). However, envelope modelling confirms an elongated structure of RanBP5 in solution, comparable in size with yeast Kap121 in the crystal structure. Analysis of PA-PB1(1-686)-RanBP5 describes a significantly larger complex in solution with an Rg of 51. 8 Å and a Dmax of 181 Å.
SEC-MALLS-RI analysis. All MALLS runs were performed using a S200 increase SEC column (10/300 GL, GE Healthcare). Sample injection and buffer flow was controlled by a Hitachi L2130 pump, following the SEC column was a L-2400 UV detector (Hitachi), Optilab T-rEX refractometer (Wyatt technologies) and a DAWN HELEOS-II multi angle light scattering detector (Wyatt technologies). Prior to injection, columns and systems were equilibrated in 5 to 10 column volumes of running buffer. 50 μL injections were performed using protein samples concentrated at a minimum of 2 mg. mL -1 , constant flow rate of 0. 5 mL. min -1 was used. Accurate MALLS mass prediction was performed with the Astra software (Wyatt Technologies). Curves were represented with Graphpad (Prism). Electron microscopy. Samples (0. 1 mg.
SAXS analysis. All datasets were collected on BM29 (ESRF). The initial trials using direct sample measurement showed a slight concentration dependency of the Guinier estimated Rg. Online SEC-SAXS was therefore used for all experiments in order to limit the contribution of partially aggregated, oligomeric or dissociated protein to the experimental curve. The experimental setup consists of a High Pressure Liquid Chromatography (HPLC) system connected to an analytical S200 increase column (5/150 GL, GE Healthcare) followed downstream by the SAXS sample capillary. SAXS measurements were performed every second with a Pilatus 1 M detector at distance of 2. 87 m allowing a q range of 0. 03 to 4. 5 nm with a wavelength of 0. 01 nm. Following data collection, experimental curves were subtracted and analysed using Primus (ATSAS) or Scatter (Bioisis) programs suits  56.
To verify the molecular mass, the Rambo and Tainer method was used  39, 57. Rg predictions using the Guinier extrapolation were plotted against the elution volume to select the most monodisperse part of the protein elution peak. SAXS datasets within this zone were then scaled and averaged to produce one unique I(q) curve. GNOM  58  was then used to produce a P(r) function which was subsequently used by DAMMIF  59  to generate 15 ab-initio models. DAMAVER  60  was then used to generate an average model. Consistency of the DAMAVER averaging with the original experimental curve was assessed by using DAMMIN  41  and using the damstart. pdb envelope as a starting model. Homologue PDB structure comparison was assed using Crysol  61. Multiple diffusion curve ab-initio modelling was performed using Bunch  62.
The first membrane was Protran BA 85 membrane (Whatman) to retain the polymerase and the second one is a nylon Hybond-N + membrane (Amersham Bioscience) to retain unbound nucleic acid. Both membranes were pre-incubated 1 h at room temperature within the protein buffer prior to use. After blotting, another 180 μL of protein buffer were run through the membranes to wash any unbound RNA before letting the vacuum dry the dot-blots for 30 seconds. Both membranes were then dismounted from the dot-blot apparatus and exposed to a storage phosphor screen (BAS storage phosphor screen, GE Healthcare) overnight. Revelation of the phosphor screen was then performed with a Typhoon Trio imaging system (GE Healthcare). Dot blot phosphorescence intensity was integrated using the Image J software. A derived bound ratio was then calculated using the following formula (1): = + Br Ibound Ibound Ifree (1) Where I bound is the integrated intensity of protein/RNA complex which is retained by the protran membrane and I free is the unbound RNA retained by the nylon Hybond-N + membrane.
Acknowledgements We are very grateful to  Daphna Fenel ,  Francine Gérard ,  Raphaelle Germi ,  Laurence Grossi ,  Darren J Hart ,  Marc Jamin ,  Thomas Lunardi ,  Hélène Malet ,  Stefan Reich  and  Adam Round  and for their help. We thank  Kausiki Datta ,  Klaus Klumpp  and  Christoph Bieniossek  for discussion. We thank  Juan Ortin  for the gift of the RdRp antibodies. CS was funded by the  Hofmann-La Roche pRED external collaboration program , AM by the  Région Rhône-Alpes  ( ARC 1 Santé ) and AL through the Labex GRAL. This work was supported by the  French agency for Research  through the  ANR Flunucleovir  ( ANR-2010-Blanc-1307-1301 ), the  ANR RNAP-IAV  ( ANR-14-CE09-0017 ) and the  European Commission projects Flupharm  (contract number  259751 ) and ComplexINC (contact number  279039 ).
This study used the platforms of the Grenoble Instruct centre (ISBG;  UMS 3518 CNRS-CEA-UJF-EMBL ) with support from  FRISBI  ( ANR-10-INSB-05-02 ) and  GRAL  ( ANR-10-LABX-49-01 ) within the  Grenoble Partnership for Structural Biology  (PSB).
Traditionally, Leptospira have been classified serologically into 25 serogroups and over 300 serovars using Microscopic Agglutination Test (MAT) and Cross agglutination absorption test (CAAT) analysis, respectively  [1, 8]. More recently, a genetic classification based on DNA-DNA hybridization complemented by molecular methods and experimental studies have confirmed the existence of at least 22 Leptospira species  [9]. The congruence between serological and molecular classifications is poor  [1] : one serogroup can be linked to several Leptospira species while serovars can vary within a given clone or lineage, an observation considered as probably resulting from horizontal gene transfer  [10]. Among the various molecular tools currently used to genotype Leptospira, multilocus sequence typing (MLST) has emerged as a method of choice as it provides data produced at a local scale that can be further compared to genotypes obtained all over the world and made freely accessible to the scientific community through public databases.