dataesr/scientific-paragraphs-categorization huggingface dataset:
monocytogenes extra elongation step at 72 uC for 10 min. Oligonucleotides used in these RT-PCR assays were designed using the software Primer Express v3. 0 (Applied Biosystems) and are listed in Table  S1. Nucleotide sequencing of rsbRSTU and rsbVW-sigB-rsbX operons in DinlG, Dvip and Dvip : : km mutants. Sequencing of the rsbRSTU and rsbVW-sigB-rsbX operons was performed upon PCR amplification of 500-600 bp fragments from chromosomal DNA isolated from wt EGDe strain, the original mutant Dvip : : km  (Cabanes et al. , 2005) , and the Dvip(1) and DinlG(1) deletion mutants constructed for this study. Oligonucleotides used are listed in Table  S1. Whole-genome sequencing. Chromosomal DNA from L. monocytogenes EGDe, Dvip : : km  (Cabanes et al. , 2005) , Dvip and DinlG strains was extracted using cetyl-trimethyl-ammonium bromide and alkaline lysis, as described previously  (Wilson, 2001).
Validation of proteomic data uncovers the presence of additional mutations affecting SigB function in DinlG and Dvip mutants Western blots were performed to validate the proteomic data obtained for the DinlG and Dvip mutants by an alternative method. A DsigB mutant was also included as control. These experiments confirmed that the lack of InlG or Vip correlated with a dramatic decrease of SigBregulated proteins such as InlH, Lmo0610 and Lmo0880 (Fig. 1a ) in the cell wall. This effect was specific since it was not observed for other LPXTG proteins, such as Lmo0160 or surface proteins strongly bound to the peptidoglycan by the LysM domain, e. g. the autolysin P60 (Fig. 1a ). To determine whether these changes reflected a failure of the entire SigB regulon, we monitored the expression of genes positively regulated by SigB but not related to cell wall such as bsh and lmo2695, which encode a bile salt hydrolase and a subunit of the dihydroxyacetone kinase enzyme, respectively  (Abram et al.
ACKNOWLEDGEMENTS We thank  Diana Barroso ,  Pablo Garcı  ´a and  Catarina Correia  for their technical assistance. This work was supported by the following grants: from the  Spanish Ministry of Economy and Competitiveness (Listress ERANet-Pathogenomics   PIM2010EPA-00714 ; to F. G. P. ); from the  Spanish Ministry of Economy and Competitiveness  ( BIO2010-18962 ; to M. G. P. ); from the  Fundaca ˜o para a Ciencia e Tecnologia of Portugal, COMPETE  and  FEDER  programmes ( PTDC/SAU-MIC/ 111581/2009FCOMP-FEDER  and  ERANet-Pathogenomics Listress   ERA-PTG/0003/2010 ; to D. C. );  European Reseach Council  advanced grant  ERC-233348 ,  Fondation Le Roch les Mousquetaires and Listress ERANet-Pathogenomics  ( ANR 2010-PATH-001-01 ) (to P. C. ); and  Listress ERANet-Pathogenomics Project  from the  German Federal Ministry of Education and Research  (to T.
qRT-PCR analysis of freshly isolated HSCs also demonstrated albumin mRNA (Figure  8A ), and in situ hybridization verified coexpression of albumin and GFAP transcripts (Figure  8B ). This direct evidence for albumin expression in freshly isolated HSCs complements data that desmin + cells coexpress E-cadherin (Supplemental Figure  2 ) and, together with the other flow cytometry and PCR data (Figures  7  and 8  and Supplemental Figures  16  and 17 ), confirm that Q-HSCs are epithelioid cells with characteristics of hepatocyte progenitors. It is well accepted that Q-HSCs become MFs in injured livers and during culture. Therefore, we examined day 7 culture-activated HSCs for evidence of albumin expression. We were unable to demonstrate albumin transcripts in day 7 HSCs using FISH (Supplemental Figure  18 ).
LSR II (BD) and FACSDiva software (BD) were used for the acquisition of flow cytometry data, and FlowJo software (TreeStar) was used for analysis. BODIPY staining for lipid content was performed by incubating mouse HSCs with BODIPY 493/503 (4,4-difluoro-1,3,5,7,8-pentamethyl-4-bora-3a,4a-diaza-s-indacene) (20 μg/ml; Invitrogen) for 30 minutes and was analyzed using FITC channel. YFP expression in hepatocytes was analyzed using FITC channel. Antibodies and conjugates are listed in Supplemental Table  2. Statistics. All data were expressed as mean ± SEM. Statistical analysis was performed using Student's t test. All analysis was conducted using Graph-Pad Prism 4 software (GraphPad Software Inc. ). Differences with P ≤ 0. 05 were considered to be statistically significant. Immunohistochemistry.
Negative controls included liver specimens exposed to 1% bovine serum albumin instead of the respective primary antibodies. Sirius red staining and αSMA, desmin, and elastin immunohistochemical staining were assessed by morphometry (MetaView software, Universal Imaging Corp. ). For morphometric quantification, 10 randomly chosen fields at ×20 magnification per section were evaluated for each mouse. GLI2, SOX9, Ki67, and cyclin D1 staining was quantified using similar approaches: for each of these parameters, numbers of cells with stained nuclei were counted in 10 randomly chosen ×20 fields per section per mouse. In situ hybridization. To detect specific transcripts within isolated HSCs and hepatocytes, FISH was carried out using validated probes specific for mouse albumin (VB6-12839, Panomics), collagen 1α1 (VB1-13595, Panomics), and GFAP (VB1-10623, Panomics) mRNAs, according to the manufacturer's protocol.
Acknowledgments The authors, work on interaction between Casuarina and soil symbiotic microorganisms is supported by the  International Foundation for Sciences (IFS , no. AD/22680 ), The  Academy of Sciences  for the Developing World (TWAS, no. 11-214 RG/BIO/AF/AC I ), and the  Institut de Recherche pour le Développement (IRD). Nathalie Diagne  was the recipient of a  CV Raman International Fellowship for African Researchers. The authors thank  Dr. Laura M. Boykin  ( Australian Research Council Centre of Excellence in Plant Energy Biology ) for critical reading of their paper.
Autonomous Curvature Measurements In the tree, internal maturation stresses exists in the three directions but are the highest in the longitudinal direction  [2]. Sawing operations allow to release these stresses. Moreover, within the thickness of each slat, maturation of wood cells induces a gradient of properties. Finally, when slats are sawed, a curvature in the longitudinal-radial plane can occur. Curvatures of hydrated slats were experimentally determined using full field measurements. For that purpose, high definition images (3648 Â 2736 pixels 2 ) of the samples were first recorded immediately after cutting. Then, images were regularly taken for 8 weeks (see Fig. 54. 2). The autonomous curvature of some samples increased with time. The shape of each slat was fitted by a circle using the least squares method with a MATLAB routine  [10].
At the same time, Ago2-bound small RNAs were immunopurified and the lengths of miR-451 were examined by Northern blotting. Whereas three phosphorothioate linkages hindered miR-451 maturation (Figure  4D ), silencing efficiency of the reporter expression was unaltered by the phosphorothioate modification for any of the three reporter constructs (Figure  4E ). These data together suggest that trimming of Ago2-cleaved pre-miR-451 is dispensable for target silencing in vitro and in cultured cells.
Mass spectrometry Analysis Proteins separated by SDS-PAGE were stained with GelCode Blue Safe (Pierce) and the bands of interest were cut out from the gel, followed by in-gel digestion with trypsin. The peptide mixtures were analyzed by a ion trap mass spectrometer (LTQ Orbitrap XL, Thermo Fisher Scientific) equipped with a nanospray ion source, and a splitless nano HPLC system (DiNa, KYA Technologies) with ODS capillary column (100 × 0. 1 mm, 3 μm particle size, KYA Technologies). The tryptic digests were separated in 2% acetonitrile and 0. 1% formic acid in water, using linear gradient from 0% to 80% of a solvent consisting of 70% acetonitrile and 0. 1% formic acid for 30 min at a flow rate of 300 nl/min. Proteins were identified from the protein database of Homo Sapiens by employing MASCOT (Matrix Science) as a search engine for peptide mass fingerprinting.
Western blot analysis Anti-FLAG (1:5000, Sigma), anti-PARN (1:4000, Bethyl) and anti-Tubulin (1:3000, Sigma) primary antibodies were used for detection. Chemiluminescence was induced by Luminata Forte Western HRP Substrate (Millipore) and images were acquired by a LAS-3000 imaging system and quantified using ImageGauge software (Fujifilm Life Sciences).
MZdicer rescue and brain ventricle labeling MZdicer mutant embryos (dicer hu896 allele) were injected at 1-cell stage with 1000 pl of 25 μM stock solution of the indicated hairpin or duplex miRNA. At 30 hpf, embryos were injected in the brain ventricle with Texas Red dextran 70,000 MW (1:20 dilution of a 500 μg/μl stock, Molecular Probes) and imaged as described previously  (Giraldez et al. , 2005). Different focal planes were merged into a single image using Adobe Photoshop CS2 software.
Acknowledgments We thank  Charles Vejnar  for mapping high-throughput sequencing results,  Jesse Reinhart  for mass spectrometry analysis, and  Ian MacRae  for providing recombinant human Ago2 used for additional experiments not presented here. We also thank  Hervé Seitz  and the members of our laboratories for discussions and critical comments on the manuscript. This work was supported in part by a  Grant-in-Aid for Scientific Research on Innovative Areas ("Functional machinery for non-coding RNAs," Grant Number   21115002 ) from the  Ministry of Education, Culture, Sports, Science and Technology of Japan  to Y. T. , the  March of Dimes , the  Pew Scholar , and  NIH  grants  5R01GM101108-02 ,  5R01GM102251-02 ,  5R21HD073768-02  to A. J. G. , a  NIH  grant  K99HD071968-01  to D. C. , and postdoctoral fellowships from the  Japan Society for the Promotion of Science  to M.
We directly sequenced the purified amplicons and compared the resulting sequences with HEV sequences in GenBank  (7)  and those from autochthonous HEV cases from 2008-2011. ClustalW2 (www. ebi. ac. uk/Tools/msa/ clustalw2/) was used to align sequences. MEGA5 (8) was used to construct a phylogenetic tree (300-nt sequences) by the neighbor-joining method. The genotypes and subtypes were identified as described  (7). The 52 men arrived in Central African Republic in several groups during July 2010-June 2011. During May-July 2011, a total of 40 (77%) men had a febrile illness; 9 illnesses were accompanied by digestive signs or symptoms, such as nausea and vomiting (Technical Appendix Table, wwwnc. cdc. gov/EID/article/12-0670-Techapp1. pdf). Only the patient whose case was reported was jaundice.
Early HEV infection was biologically confirmed for 11 (21%) men, including the -patient whose case was reported; 8 of the 11 men had IgM only, 1 was HEV positive according to rRT-PCR and IgM negative, and 2 were HEV positive according to rRT-PCR and IgM positive. The 2 other men with viremia were asymptomatic, but liver enzyme levels were elevated in 1 of them. Illnesses in infected and noninfected men did not differ, and, except for the notified case, we cannot say with certainty that the illnesses were caused by HEV. We found IgG against HEV in 14 (34%) uninfected men, which is close to the prevalence for the general population in India  (2). HEV subtype 1a isolates from the notified case-patient (serum-derived isolate) and a co-worker (stoolderived isolate) were sequenced (GenBank accession nos.
JN863908 and JQ074213, respectively) and found to be 100% similar and to share 97%-99% similarity with other HEV strains in India and Nepal (Technical Appendix Figure). The sequences obtained from persons with autochthonous HEV (GenBank accession nos. JN863909, JN863910, and JQ740782) clustered with HEV subtype 1e and type 2 strains and were closely related to strains from Africa and Mexico (93% and 82% similarity, respectively). Similarity between strains was not as high for the strain from the notified case-patient and those from persons with autochthonous infection (87% similarity with the subtype 1e strain and 77% similarity with the type 2 strain). IgM titers typically rise after the incubation period, which is >3 weeks for HEV (9). Thus, for the purpose of this study, we assumed that men who were positive for IgM against HEV or who had positive rRT-PCR results <3 weeks after their arrival in Central African Republic were probably infected while in India (Table  , study  participants 2-4  and 9 ).
sanguineus. This DNA showed 98% homology with the sequence in GenBank (accession no. AY559843). R. sibirica mongolitimonae with 99. 8% homology for the outer membrane protein gene sequence in GenBank (accession no. DQ097082) was isolated from 1 tick collected from the cat. This tick was identified as Rh. pusillus and showed 99. 7% homology with the sequence in GenBank (accession no. FJ536547). R. massiliae was cultured from an Rh. sanguineus tick, and R. sibirica mongolitimonae was cultured from an Rh. pusillus tick. A cluster of 1 documented case and 2 probable cases of lymphangitisassociated rickettsiosis in southern France was linked to a cat and Rh. pusillus ticks. Infection with R. massiliae for the 2 probable case-patients was unlikely because clinical findings.
Figure. Alignment of partial sequences of human gyroviruses (HGyVs) from healthy blood donors, France. Point mutation corresponding to a nonsynonymous substitution is in boldface (13F1 isolate). Reference sequences and GenBank accession nos. : HGyV1-915, FR823283; HGyV1-CL33, JQ308212; avian gyrovirus (AGV) 2, JQ690763; gyrovirus (GyV) 3, JQ308210). Bar above sequences indicates location of the HGyVsPBp probe; lowercase letters indicate 5′/3′ ends of HGyVsPBs/HGyVsPBr real-time primers; asterisks (*) indicate conserved positions.
1014 Figure. Alignment of partial sequences of human gyroviruses (HGyVs) from healthy blood donors, France. Point mutation corresponding to a nonsynonymous substitution is in boldface (13F1 isolate). Reference sequences and GenBank accession nos. : HGyV1-915, FR823283; HGyV1-CL33, JQ308212; avian gyrovirus (AGV) 2, JQ690763; gyrovirus (GyV) 3, JQ308210). Bar above sequences indicates location of the HGyVsPBp probe; lowercase letters indicate 5′/3′ ends of HGyVsPBs/HGyVsPBr real-time primers; asterisks (*) indicate conserved positions.
For the Sholl analysis following DCX immunohistochemistry, 35 µm floating sections were incubated 30 min with 0,3% H 2 0 2 , then blocked 10% foetal bovine serum in 0. 1M TrisHCl pH7. 4, 0. 15M NaCl (=TBS) with 0. 5% Triton X100 and incubated overnight at 4°C with goat anti-DCX antibody (1/200) (Santa Cruz) in blocking solution. After washes in 0. 1M TBS, sections were incubated in biotinylated bovine anti-goat antibody (1/500) and procedure was finished using the ABC kit and DAB staining procedure from Vector Laboratories. Sections were mounted on slides, dehydrated in ethanol, delipidated in xylene and mounted with Entellan. Sholl analysis was performed on 12 randomly chosen DCX positive hippocampal neurons per brain that presented at least a second order dendrite, using NeuroLucida software (MicroBrightField, Williston, VT) on an Olympus BX51 microscope equipped with a motorized stage device and x100 immersion oil objective.
Videos, kymographs, and analyses were generated with ImageJ software (http://rsb. info. nih. gov/ij/, NIH, USA) and the KymoToolbox plug-in  [30]. The analysis of BDNF transport-dependent secretion was done as described in  [15]. Briefly, hippocampal neurons were electroporated with a non-tagged version of human BDNF. Three days later, neurons were depolarized (treatment for 20 min with neuronal culture media containing 28 mM KCl, 30 mM CaCl 2 , 30 mM NaCl). The supernatant was recovered (K1 fraction). The neurons were washed and incubated 30 min in normal neuronal culture medium and depolarized again. The supernatant K2 was recovered and a whole protein lysate (L) of cells was extracted to assess the general expression of BDNF. BDNF levels were measured by anti-BDNF sandwich-ELISA using BDNF E max Immunoassay system (Promega, France), following manufacturer's instructions.
This work was supported by grants from  Agence Nationale pour la Recherche  ( ANR-08-MNP-039 , FS),  Fondation pour la Recherche Médicale  (FRM, équipe labellisée) (FS),  CNRS ,  INSERM  and the  Institut Curie (FS). SO was supported by the  French Minister of Research. FS and SH are INSERM investigators; AMG, DJD. and PP are respectively professors and assistant professors at  Université Paris-Sud. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Crystal structure features of c-JMJ703 The crystal structure of c-JMJ703 alone or in complex with a-KG (termed as c-JMJ703-a-KG) or with NOG (N-oxalylglycine, a non-catalytic analog of a-KG) and H3K4me3 peptide (termed as c-JMJ703-NOG-H3K4me3) was determined via the molecular replacement method with the modified crystal structure of the core of human JMJD2A (PDB code 2OQ6)  [22]  as the initial searching model. The final model was best at a resolution of 2. 35 A ˚with a final R work value of 19. 3% (R free = 22. 5%). The crystals belonged to the P6 3 space group with a slight change in unit cell parameters among the three crystals. One c-JMJ703 molecule was identified in the asymmetric unit with a Matthews coefficient of 2. 3 A ˚3/Da (corresponding to 46% solvent content)  [23]. There are five solvent-exposed regions in c-JMJ703 structure, including P195-K199, S224-R261, R288-S295, T329-Y349, and Q363-V377, which could not be built due to lack of interpretable electron.
Three of the ten residues in the H3K4me3 peptide (ARTK-me3QTARKS) were visible in the c-JMJ703-NOG-H3K4me3 complex structure (Figure  3 , Figure  5 , Figure  6 ). This complex structure provided a view of the substrate peptide-binding mode of an H3K4 demethylase. Compared with the structure of c-JMJD2A in complex with methylated H3K9/H3K36 peptide, the methylated H3K4 and its two flanking residues adopted a different binding conformation to c-JMJ703. H3K9me3/H3K36me3 and their two flanking residues stretched along the long axis of a-KG in c-JMJD2A-a-KG-H3K9me3/c-JMJD2A-NOG-H3K36me3 structure (PDB code 2Q8C/2Q8E, Figure  7B-7C ), whereas H3K4me3 and its two flanking residues stretched along the short axis of NOG and was almost perpendicular to H3K9me3/ H3K36me3 and their flanking residues (Figure  7A ).
The methyl group binding pocket of JmjC domain is unique among methylated peptide-binding proteins due to the polar rather than hydrophobic environment  [25]. The methyl groups could not be defined properly in the c-JMJ703-NOG-H3K4me3 complex structure because of low occupancy as indicated by obviously higher B-factor for atoms in H3K4me3 peptide. Based on the crystal structure of c-JMJD2A in complex with H3K9me3 (PDB code 2Q8C)  [26] , four of the five residues that have been shown to be important in methyl group binding in c-JMJD2A  [25]  were conserved in c-JMJ703, namely, G376, Y383, E396, and N496. S288 in c-JMJD2A (S335 in Rph1) is substituted by an alanine (A494) in c-JMJ703. G376 had no electron density and was invisible in structure, whereas Y383, E396, A494, and N496 were well-defined and adopted very similar conformations as in c-JMJD2A  [26].
Y321 and N404 showed significant conformational shifts compared with their counterparts in c-Rph1 and c-JMJD2A (Figure  8A -8C and Figure  S5 ). Alternative conformation of the Tyr corresponding to Y321 in other JmjC proteins has been observed in JMJD2D (PDB code 3DXU). Interestingly, substitution of Y321 by alanine decreased H3K4me1 demethylase activity but did not affect that of H3K4me2 and H3K4me3 (Table  1 , Figure  S6 ), whereas substitution by alanine of the corresponding residue in Rph1 leads to loss of the H3K36me3 demethylase activity of the protein  [20]. These data suggested a different NOG-binding mechanism between JMJ703 and Rph1.
T-DNA insertion identification of jmj703 mutant A T-DNA insertion line of JMJ703 (3A-00550) was obtained from the Postech rice mutant database (http://www. postech. ac. kr/life/pfg/risd/). Insertion was confirmed by PCR using the primers muJ3-F and muJ3-R and a T-DNA-specific primer 2715L1 (Table  S2 ).
Histone demethylation assay The cDNA fragment of the J3NCZ region was amplified using primers FAJ3NCZ-F and FAJ3NCZ-R and then cloned into pFA121 vector modified from pBI121 (GenBank: AF485783. 1), in which GUS was replaced by 26FLAG:26HA tag. The pFA121-J3NCZ plasmid was transferred into Agrobacterium tumefaciens strain EHA105 cells for tobacco infection with the help of Agrobacterium cells harboring P19 plasmids  [39]. For in vivo histone demethylation assay, tobacco infection and nuclei isolation were performed as previously described  [27]. The immunostaining protocol was modified from http://sites. bio. indiana. edu/,pikaardlab. Briefly, the nucleus solution was placed on a poly-lysine coated slide, air dried, and then refixed with 4% formaldehyde in KPBS (1. 28 M NaCl, 20 mM KCl, 80 mM Na 2 HPO 4 , 20 mM KH 2 PO 4 , pH7.
X-Ray data collection, processing, and structure determination Diffraction data for apo c-JMJ703 crystals were collected at a resolution of 3. 0 A ˚at 100 K using a MAResearch M165 CCD detector in beamline 1W2A at the Beijing Synchrotron Radiation Facility. The data set for c-JMJ703-a-KG and c-JMJ703-NOG-H3K4me3 were collected at 2. 3 A ˚and 2. 4 A ˚in beamline BL17A (Photon Factory, Japan) and BL17U1 (SSRF, Shanghai, China), respectively, with an ADSC Q315 CCD detector at the wavelength of 1. 0000 A ˚. All data sets were indexed, integrated, and scaled using the HKL2000 package  [40]. The crystals belonged to space group P6 3 with cell parameters a = 53. 0 A ˚, b = 86. 1 A ˚, c = 87. 3 A ˚, and b = 90. 7u. All crystals showed very small shifts in their cell parameters. The molecular replacement method was used to calculate the phases using the PHASER program  [41]  and the modified crystal structure of a catalytic core of the human c-JMJD2A (PDB code 2OQ6) as the initial searching model.
Manual model building and refinement were performed with the programs COOT  [42]  and PHENIX  [43]. Solvent molecules were located from stereochemically reasonable peaks in the sA-weighted 2Fo-Fc difference Fourier electron density map (1. 2 s). Model geometry was verified using the program PROCHECK (Table  S3 )  [44]. Coordinates have been deposited in PDB with accession 4IGP, 4IGO and 4IGQ for apo c-JMJ703, c-JMJ703-a-KG and c-JMJ703-NOG-H3K4me3, respectively.
8 GEP was performed in 4 patients (UPN 2, 3, 6 and 7), according to standard protocol with Genechip Affymetrix HG 133 plus 2. 0 array. 9 he analysis of the Acute Leukemia French Association (ALFA) trials database showed a very low incidence (3 of 1333; 0. 23%) of AML with NPM1-MLF1 among adult AML patients with available karyotype. This incidence is consistent with that reported by Grimwade et al. (<0. 5%). 10 The mean age of patients with NPM1-MLF1 was 24 years. Cytological characteristics showed that a 3lineage dysplasia was present in the great majority of cases, both in peripheral blood and bone marrow smears. Dysmegakaryopoiesis was constantly observed, dysgranulopoiesis was associated with peroxidase deficiency in 3 cases, and dyserythropoiesis occurred in 5 of 7 cases. Flow cytometry analysis showed that blast cells were positive for the myeloid antigens CD117, CD13, and CD33.
Feature selection using test frames In literature, the segmentation is usually processed on all available before and after image bands. In this study, in order to determine the most relevant features for segmentation, input feature selection was carried out through an original generic calibrationlike procedure using a test frame. Moreover, this process aims to automatically optimize the segmentation parameters. The test frames are constructed with n small image samples corresponding to n classes, yielding as much test frames as input features, thus resulting in a multi-band test frame, at the core of our feature selection method. The used data is not included in the validation dataset. The test frames are then segmented by the MS algorithm using either one input feature (single test frame) or multiple normalized features (multi-band test frame) while testing various parameterizations.