dataesr/scientific-paragraphs-categorization huggingface dataset:
Spectra were recorded in the positive linear mode for the mass range of 2,000 to 20,000 Da (parameter settings: ion source 1 (IS1), 20 kV; IS2, 18. 5 kV; lens, 7 kV). A spectrum was obtained after 675 shots at a variable laser power. The time of acquisition was between 30 seconds and 1 minute per spot. The twelve JC110 T spectra were imported into the MALDI BioTyper software (version 2. 0, Bruker) and analyzed by standard pattern matching (with default parameter settings) against the main spectra of 3,769 bacteria, which were used as reference data, in the BioTyper database. The method of identification included the m/z from 3,000 to 15,000 Da. For every spectrum, a maximum of 100 peaks taken into account and compared with spectra in the database. A score enabled the identification, of the tested species: a score > 2 with a validly published species enabled the identification at the species level, a score > 1.
7 but < 2 enabled the identification at the genus level; and a score < 1. 7 did not enable any identification. For strain JC110 T , no significant score was obtained, suggesting that JC110 T was not a member of a known species or genus. We incremented our database with the spectrum from strain JC110 T (Figure  4 ). The gel view allowed us to highlight the spectra differences with other of Coriobactericeae family members (Figure  5 ).
Genome project history The organism was selected for sequencing on the basis of its phylogenetic position and 16S rRNA similarity to other members of the Coriobacteriaceae, and is part of a "culturomics" study of the human digestive flora aiming at isolating all bacterial species in human feces. It was the sixth genome of a species within the Coriobacteriaceae and the first genome of Senegalemassilia anaerobia gen. nov. , sp. nov. A summary of the project information is shown in Table  3. The EMBL accession number is CAEM00000000 and consists 8 scaffolds. Table  3  shows the project information and its association with MIGS version 2. 0 compliance.
Genome annotation Open Reading Frames (ORFs) were predicted using Prodigal  [35]  with default parameters. The predicted bacterial protein sequences were searched against the Genbank database and the Clusters of Orthologous Groups (COG) databases using BLASTP. The tRNAScanSE tool  [36]  was used to find tRNA genes, whereas ribosomal RNAs were found by using RNAmmer  [37]  and BLASTn against GenBank. ORFans were identified if their BLASTp E-value was lower than 1e-03 for alignment length greater than 80 amino acids. If alignment lengths were smaller than 80 amino acids, we used an E-value of 1e-05. To estimate the mean level of nucleotide sequence similarity at the genome level between S. anaerobia and other members of the Coriobacteriaceae and among members of this family, we compared genomes two by two and determined the mean percentage of nucleotide sequence identity among orthologous ORFs using BLASTn Orthologous genes were detected using the Proteinortho software  [38].
Figure1. Phylogenetic tree highlighting the phylogenetic position of Senegalemassilia anaerobia strain JC110 T relative to other type strains within the Coriobacteriaceae family. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences were made using the maximum-likelihood method within the MEGA software. Numbers at the nodes are percentages of bootstrap values (500 repetitions) to generate a majority consensus tree. The scale bar indicates a 1% nucleotide sequence divergence. The red square groups sequences that exhibit degrees of similarity > 99% with S. anaerobia (same species), whereas that in the dashed-line square is 97. 2% similar (same genus).
The 16S rRNA and genome sequences are deposited in Genbank and EMBL under accession numbers JF824809 and CAEM00000000, respectively. The G+C content of the genome is 60. 9%. Habitat: human digestive tract. The type strain JC110 T (= CSUR P147 = DSMZ 25959) was isolated from the fecal flora of a healthy patient in Senegal.
Thrombus formation was subsequent to chamber dilation and aggravated over time (Figure  9C, D ). In one case, atrial myocardial rupture and pericardial blood effusion was observed on ultrasound analysis, and led to the death of the mouse. Atrial dilation was unlikely to be due to mitral valve dysfunction, because the Doppler mitral inflow pattern was normal (data not shown). Similarly, left-ventricular failure was not the cause, because the fractional shortening was normal. These data led to the hypothesis that death was due to the accumulation of large thrombi in the left atrium and/or its rupture.
Acknowledgments We warmly thank  Prof. Constantinesco  for his help, and  Drs. Stephane Zaffran  and  Gae ¨lle Odelin  for their constructive criticism. IY, SC and MK were supported by  Region Ile-de-France , the  Fondation pour la Recherche Medicale and the Ligue contre le Cancer  ( Comitede l'Oise ), respectively. HCE was supported by  Nevus Outreach, Inc. and  Naevus 2000 France-Europe. We thank members of the animal colony and imaging facilities of the  Institut Curie. We dedicate this manuscript to the memory of  Christine Larue.
Of note, the highest incidence of cataract was recorded for the p. D1424H substitution, even if further data are needed to confirm the more deleterious effect of this mutation compared to the other genotypes (Table  5 ). Thrombocytopenia and bleeding diathesis-In MYH9-RD, the routine automated platelet counting overestimates the severity of thrombocytopenia, as cell counters fail to recognize the very large platelets of these patients. The actual platelet count (PLTC) can be assessed only by counting upon phase-contrast microscopy  [Balduini et al. , 2011]. In our case series, the median PLTC measured by cell counters in all the 255 patients was 31 x10 9 /L (IQR 16-53). Microscopic PLTC was available for 167 patients, and the median value was 70 x10 9 /L (IQR 40-95). In the same patient population, the median automated PLTC was 26 x10 9 /L (IQR 13-46).
Experimental Crystal data  Hydrogen-bond geometry (A ˚, ). D-HÁ Á ÁA D -H HÁ Á ÁA D Á Á ÁA D -HÁ Á ÁA C5-H5Á Á ÁO4 i 0. 95 2. 42 3. 337 (3) 161 Symmetry code: (i) Àx þ 1; y À 1 2 ; Àz þ 1. Data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell refinement: CrysAlis RED  (Oxford Diffraction, 2006) ; data reduction: CrysAlis RED; program(s) used to solve structure: SIR97  (Altomare et al. , 1999) ; program(s) used to refine structure: SHELXL97  (Sheldrick, 2008) ; molecular graphics: ORTEP-3 for Windows  (Farrugia, 2012) ; software used to prepare material for publication: PARST  (Nardelli, 1995). The authors acknowledge the CRIST (Centro di Cristallografia Strutturale, University of Firenze), where the data collection was performed. Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: YK2089).
Computing details Data collection: CrysAlis CCD  (Oxford Diffraction, 2006) ; cell refinement: CrysAlis RED  (Oxford Diffraction, 2006) ; data reduction: CrysAlis RED (Oxford Diffraction, 2006); program(s) used to solve structure: SIR97  (Altomare et al. , 1999) ; program(s) used to refine structure: SHELXL97  (Sheldrick, 2008) ; molecular graphics: ORTEP-3 for Windows  (Farrugia, 2012) ; software used to prepare material for publication: PARST  (Nardelli, 1995). where P = (F o 2 + 2F c 2 )/3 (Δ/σ) max < 0. 001 Δρ max = 0. 15 e Å -3 Δρ min = -0. 22 e Å -3 Absolute structure:  Flack (1983) , 767 Friedel pairs Flack parameter: 0. 038 (18) Special details Geometry. All s. u. 's (except the s. u. in the dihedral angle between two l. s. planes) are estimated using the full covariance matrix. The cell s.
KBMA P. aeruginosa activates and injects antigens into human dendritic cells, which then stimulates antigen-specific CD8 + T cells The DC maturation process coordinates the regulation of antigen processing and presentation, the expression of costimulatory molecules, and the secretion of cytokines that prime CD8 + and CD4 + T-cell responses. We evaluated whether DC maturation occurred when they are exposed to KBMA P. aeruginosa delivering the flu M1 antigen. Immature day 5 moDCs displayed typical morphology and an immature phenotype (moderate levels of CD80, CD86, CD40, and CD83) (data not shown). Immature moDCs were incubated for 3 hours with one of three IPTG-induced OSTAB strains: live (MOI 5:1), KBMA (MOI 100:1), or HK (MOI 100:1). Functional features were assessed 24 hours later. Phenotypic analysis revealed that stimulation with both the KBMA S54-M1 and HK S54-M1 strains led to increases in the surface expression levels of costimulatory molecules (CD80, CD86, CD40) and maturation-associated (CD83) molecules (Figure  5a ).
5 mg/ml bovine serum albumin to test for the presence of the secreted fusion protein S54-OVA. A control strain (not exposed to UVA) was conserved at 4 °C and OD600 = 1 during the PCT of the other strains. When necessary, we quantify the relative amount of OVA by densitometry analysis with ImageJ software (Rasband, W. S. , ImageJ, U. S. National Institutes of Health, Bethesda, MD; http://imagej. nih. gov/ij/, 1997-2012). We also tested for the presence of the OVA antigen, as previously described by Derouazi et al. ,  42  to verify its secretion in all vaccination protocols (ELISPOT or Tumor challenge vaccination). For the Bla injection assay, 37 HL60 cells were washed once in a complete RPMI medium without antibiotics and were seeded in 48-well tissue culture plates at 2. 105 cells/well in a complete RPMI medium without antibiotics.
4 mm pinholes per head) using the following parameters. CT acquisitions were performed at 45 keVp, with 240 projections and 1 second per projection. SPECT acquisitions were performed using a 140 ± 20% KeV window, with 24 projections and a 10-or a 30-minute scan. CT and SPECT acquisitions were reconstructed fused and analyzed using dedicated software (InVivoScope, Bioscan). moDC analysis. Human moDCs were incubated for 3 hours in RPMI 1,640-10% fetal bovine serum with P. aeruginosa strains at MOIs of 5:1 or 100:1. The DCs were then incubated with 250 µg/ml of gentamicin (Sigma, St Louis, MO) to kill live bacteria for an additional 24 hours in RPMI 1,640-10% fetal bovine serum. The moDCs were then washed three times with PBS. For the positive controls, moDCs were matured with 1 µg/ml of soluble recombinant human CD40L and 1 µg/ml of enhancer following the manufacturer's instructions (Alexis Biochemicals, San Diego, CA) or 1 µg/ml of lipopolysaccharide (Sigma).
IL-1α, IL-1β, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, Kc, IL-9, IL-10, IL-12p40, IL-12p70, IL-13, IL-17, Eotaxin, G-CSF, GM-CSF, IFN-γ, MCP-1, MIP-1α, MIP-1β, RANTES, and TNF-α were measured using Luminex technology according to the manufacturer's instructions (BioRad Laboratories, Hercules, CA). The plasma samples were diluted 1:4 and were tested in duplicate. Data collection and analysis were performed on a Bio-Plex 200 instrument equipped with Bio-Plex Manager software (version 4. 1) (BioRad Laboratories) using a fiveparameter non-linear regression formula to compute sample concentrations from the standard curves. The cytokine detection limit ranged between 0. 2 and 45,000 pg/ml. Concentrations outside the detection limit were assigned the lowest or highest value from the corresponding standard curve.
Statistical analysis. Results are expressed as the means ± SD unless stated otherwise. Statistical comparisons between two groups were evaluated by the Student's t-test and corrected by ANOVA for multiple comparisons. A P value of <0. 05 was considered to indicate statistical significance. Unless otherwise indicated, all experiments were conducted at least twice. Logrank tests (Mantel-Cox) were used to compare the Kaplan-Meier tumor survival curves and were performed using GraphPad Prism (version 5. 00 for Windows, GraphPad Software, San Diego, CA; www. graphpad. com). For multiplex cytokines analysis, Mann-Whitney test statistical analysis was performed.
ACKNOWLEDGMENTS The authors thank  O Epaulard  and  AL Fiser  for their assistance in developing this manuscript, and  G Baptist  and  J Geiselmann  for their assistance with the live/dead BacLight experiment. This work was supported by  GRAVIT  grant number  081202  and Ligue contre le cancer (comité ardèche). The authors thank the " Etablissement Français du sang " for the gift of amotosalen S-59, the access to ELISPOT reader. Finally, authors thank  Ina Attree  at  CEA (Grenoble)  for the access to the moFlo FACS. ALG, BP, and BT declare competing financial interest. They are the cofounders of APCure, a start-up that produces immunotherapy treatments for patients with cancer. The work was done in Grenoble, France.
Methods This retrospective study included women with chronic hypertension delivered between 1 January 2004 and 31 December 2007 who were identified from the hospital computer databases of two university hospital centers (CHI Creteil and AP-HP Cochin Port-Royal Paris). Every medical chart was reviewed to collect the data. The criteria used to select women with chronic hypertension was a diagnosis of hypertension that needed a treatment before the onset of the pregnancy. Exclusion criteria were: women with multiple pregnancies, women with secondary hypertension, women with proteinuria at less than 20 weeks' gestation, women considered as having a chronic hypertension but without any treatment at first prenatal visit, women transferred from other maternities, pregnancies complicated by fetal malformations.
The data collected from medical records included: age, prepregnancy BMI, parity, ethnic origin, tobacco use during pregnancy, duration of hypertension, past obstetric history, antihypertensive treatment, treatment with low dose aspirin, maternal systolic and diastolic blood pressure at booking, presence or absence of proteinuria at first prenatal visit, maternal and neonatal outcomes. The blood pressure was obtained with automated device, patient in sitting up position. The mean arterial pressure was calculated from brachial systolic and diastolic blood pressure (BP), according to the following formula: Mean arterial pressure = [systolic BP+(2*diastolic BP)]/3. Superimposed preeclampsia was defined as a new onset proteinuria (0. 3 g of protein or more in a 24-hour specimen) after 20 weeks' gestation and without proteinuria early in pregnancy (less than 20 weeks' gestation).
Fetal growth restriction (FGR) was defined as a birth weight ,5th percentile  [9]. Abruptio placenta was diagnosed according to clinical findings and/or placental examination. HELLP syndrome (hemolysis, elevated liver enzymes, low platelet count) was defined according to Sibai's criteria  [10]. We analyzed the risk factors that may influence the rates of superimposed preeclampsia. Categorical variables are presented as percentage, and continuous variables as mean and SD. Categorical variables were compared with X 2 square or Fisher's exact test and continuous variables with a two-tailed student t test. Variables with a p,. 1 were included in a logistic regression analysis. Data are expressed as odds ratio (OR) with 95% confidence interval (CI). P,. 05 was considered as significant. Positive likelihood ratio with 95% CI was calculated for the prediction analysis.
Statistical analyses For each type of restriction (water or light), we compared the various treatment groups. Chi-squared tests were used to compare bud burst distributions as a function of bud location on the stem between groups. For all other variables, groups were compared by one-way analysis of variance (ANOVA), or by nonparametric Kruskal-Wallis tests if the data were not normally distributed or the condition of homoscedasticity was not satisfied. All statistical analyses were performed with the SAS software (V. 9. 2, SAS Institute), using the glm, npar1way and freq procedures.
Acknowledgements We would like to thank  O. Douillet  ( UMR IRHS ),  B. Perrin ,  E. Le Coz  and  M. Penn  ( UMR IRHS trainees ) for helpful suggestions concerning the protocols and for experimental measurements,  G. Guillemain  and  G. Sintès  ( UMR IRHS ) for helpful suggestions concerning the protocols and for maintaining growth conditions, and  M. Laffaire  and  C. Bouffard  ( UMR IRHS ) for plant multiplication. We also thank  L. Crespel  ( UMR IRHS ) for useful suggestions on the manuscript and  J. Sappa  (scientific translator,  Alex Edelman & Associates ) for reviewing the paper for English usage.
, 2009; Viñas et al. , 2012)  were genotyped for mapping because of the relevance of sex determination for turbot industry (Table  S1 ). In total, 37 microsatellite markers from  Ruan et al. (2010)  were genotyped to be integrated into the new map. Primers and PCR conditions for amplification were as previously described in  Ruan et al. (2010). Markers with positive amplification were first genotyped in parents and grandparents of the reference families, and then genotyped in the offspring of the most informative family. Genotyping was carried out in an ABI 3730xl DNA sequencer using the GENEMAPPER 4. 0 software (Applied Biosystems).
Mapping Novel genotype data were coded as JOINMAP type HAP population with linkage phase unknown (HF family), and as type CP population with known-phase (DF family). This genotype data set was added to the original data from  Bouza et al. (2012 ), Rodríguez-Ramilo et al. (2013)  and  Viñas et al. (2012). Mapping procedures were the same as those from  Bouza et al. (2012). Briefly, a consensus genetic map was constructed using JOINMAP 3. 0 (van Ooijen and  Voorrips, 2001)  starting from the nine reference families (HF, DF, QF1-7). A LOD threshold of 3. 0 and a recombination frequency threshold of 0. 4 were used. Graphics were generated with MAPCHART 2. 2  (Voorrips, 2002).
QTL analyses Given the high increase of genetic markers in DF family and the relevance of sex determination in this species, we considered it important to refine QTL identification and marker association in the DF family to sex  (Martínez et al. , 2009). We followed a linear regression method implemented in the GridQTL program (www. gridqtl. org. uk; Seaton et al. , 2006)  using the SPportlet, as in our previous work  (Martínez et al. , 2009). Two approaches were employed: first, a single QTL was assumed at each LG; secondly, a two-QTL model was tested within each LG. GridQTL implements a linear regression methodology, considering the linkage phase between markers according to pedigree information. The  Haseman and Elston (1972)  method for QTL linkage analysis was applied, and the chromosome-wide significance thresholds at P = 0.
, 2012) , and by the short length of adjacent microsatellite sequences available in GenBank. In fact, the percentage of successful hits was much lower than that observed by  Bouza et al. (2007)  also based on anonymous microsatellite sequences (22. 7%). The consistent macrosyntenic pattern between turbot and Acanthopterygii model fish genomes, reported in  Bouza et al. (2012) , was confirmed for the 14 significant hits of new mapped markers in this study. Only one matched consistently to a different chromosome than predicted with three model fish genomes. Several genes showed significant secondary hits with other model fish chromosomes in addition to that expected according to macrosyntenic patterns, likely due to the existence of paralogous genes. Conversely, the predictive positions obtained through comparative mapping for non-mapped TR markers were mostly concordant with the correspondence obtained between the TB and TR maps.
Acknowledgments This study was supported by the projects:  Consolider Ingenio Aquagenomics  ( CSD200700002 ),  Spanish Ministerio de Ciencia e Innovación  ( AGL2009-13273 ). We are indebted to  Lucía Insua ,  María Portela ,  Susana Sánchez ,  María Villar ,  Mónica Otero  and  Sonia Gómez  for technical assistance. Also, we wish to thank  Antonia Ford  for help with editing the English version of the manuscript.
GENERATION OF FUSION PROTEIN CONSTRUCTS The Abmdh or Abmpd C-terminal GFP fusion constructs were generated by fusion PCR (Figure  2 ). Using A. brassicicola genomic DNA as a template, the respective ORFs and 3 flanking regions were amplified with relevant primer combinations (Table  1 ). In parallel, a fragment containing the GFP cassettes and Hyg B cassettes were amplified from the plasmid pCT74  (Lorang et al. , 2001). The resulting PCR fragments were mixed and subjected to second fusion PCR. A linker containing 3 glycine residues was introduced at the 3 end of the respective ORFs to replace the stop codons. The final PCR products were transformed in the A. brassicicola wild-type to make AbMpd-and AbMdh-GFP fusion proteins. The transformants with expected genetic integration events were identified by PCR and Southern blot analyses (data not shown).
NMR ANALYSIS For nuclear magnetic resonance (NMR) metabolite analysis, 500 μl of the D 2 O-samples were transferred to a 5 mm NMR tube, then analyzed on a BRUKER Advance DRX 500 MHz spectrometer equipped with a multinuclear QNP probe (Bruker, Wissembourg, France). Proton-decoupled 13 C NMR spectra (sweep width = 31 450 Hz) were recorded at 125 MHz excitation frequency, 30-degrees pulse angle (6. 5 μs pulse duration) at 2 s intervals. The free induction decays were collected as 32 K data points and processed with a 1-2 Hz exponential line broadening for 13 C NMR. Maleic acid (δ CH 130. 4 ppm) was the external reference for chemical shifts. Identifications were made by comparison with spectra of pure known standards. For brassicicolin A, 1 H (500 MHz) and 2D NMR spectra (HMQC and COSY) were recorded in CDCl 3 in a capillary probe (Bruker TXI 1.
CHARACTERIZATION OF Mpd AND Mdh GENES IN A. brassicicola AND GENERATION OF REPLACEMENT MUTANTS The presumed Mpd and Mdh loci were identified by a homology search against the A. brassicicola genome assembly (http:// genome. jgi-psf. org/Altbr1/Altbr1. home. html) with genes previously described in A. alternata  (Velez et al. , 2007). AbMdh and AbMpd sequences (GenBank accession No JX403801 and JX403800, respectively) consisted of 851 and 1173 nucleotides, respectively. Blast search on the whole genome sequence and Southern analyses suggested the presence of only one copy of each gene (Figure  3B ). Among the putative regulatory elements identified on sequences upstream of the ATG, consensus sequences for the binding of transcription factors involved in response to thermal, osmotic and oxidative stresses (Msn2p/Msn4p, HsF2) were found on the two genes.
SUSCEPTIBILITY OF REPLACEMENT MUTANTS TO STRESS CONDITIONS Mannitol has been proposed to act as a potent protective metabolite against oxidative stress. As the mannitol contents of conidia and mycelia from the different mutant genotypes were significantly different from that of the wild-type, the effects of AbMpd and AbMdh inactivation in A. brassicicola on conidia germination and initial mycelium growth in the presence of oxidative stressors were examined. Analysis of nephelometric growth curves revealed that under non-stress conditions (PDB medium), no significant phenotypic differences in conidia germination (based on the lag time parameter) or mycelium growth (based on the maximum growth rate parameter) were detected in any of the tested mutants as compared to the wild-type (data not shown).
Note that after 24 h of exposure to ITC, the mannitol content of wild-type mycelia was 1. 4-fold higher than in control and a 3-fold increased expression of AbMpd was recorded in cultures after 3 h of ITC treatment, while the AbMdh expression level remained unchanged (data not shown). Based on these susceptibility patterns, comparing the response of the four genotypes to H 2 O 2 on one hand and to menadione or ITC on the other suggested different modes of action for these oxidants. This was further supported by comparing the effects on the cell viability of non-germinated and germinated conidia of low-time exposure to H 2 O 2 and Al-ITC at their respective IC 50 (Figure  6 ). On germinated conidia, treatment with Al-ITC resulted in PI-positive hyphae suggesting a loss of cell viability. No PI staining was observed in non-germinated conidia exposed to Al-ITC.