dataesr/scientific-paragraphs-categorization huggingface dataset:
Deposit in a culture collection Strain Marseille-P2825 T and strain Marseille-P3257 T were deposited in the Collection de Souches de l'Unité des Rickettsies (CSUR, WDCM 875) under numbers P2825 and P3257, respectively. Fig. 1. Phylogenetic tree showing the position of A. bouchesdurhonensis sp. nov. , strain Marseille-P2825 T and A. mediterranea sp. nov. , strain Marseille-P3257 T relatives to other phylogenetically-close neighbours. Sequences were aligned using Muscle v3. 8. 31 with default parameters and phylogenetic inferences were obtained using the neighbor-joining method with 500 bootstrap replicates, within the MEGA6 software. Only bootstrap values greater than 95% are displayed. The scale bar represents a 1% nucleotide sequence divergence.
Patients' selection and ethical approval This retrospective cohort-study was conducted from July 2005 to April 2016 in the 34-bed infectious diseases department at Nice University Hospital (France). The medical dashboard of our ward records prospectively 28 characteristics of each hospitalization including hospitalization motive, final diagnosis, comorbidities, microbiological data including blood culture and all antibiotics prescribed  [10]. Patients are classified regarding the site of infection; in case of bacteremia without any organ infection detected they are included in the BUO group. The dashboard classifies infective endocarditis or spondylodiscitis in other groups. In France no ethical approval is required for non-interventional study. The medical dashboard of the Infectious Diseases Department of Nice University Hospital is authorized by the French National Commission on Informatics and Liberty (Number of Registration: 1430722).
Prion inoculation and GDLs treatment Inoculations were performed with either infectious brain lysate (RML6) or non-infectious brain homogenate (NBH). Slices were inoculated (as free-floating sections for 1 h at 4˚C) with 100μg brain homogenate per 10 slices. After washing in GBSSK, they were cultured on a 6-well Millicell-CM Biopore PTFE membrane insert (Millipore) according to previously published protocol  [60]. Drug-treated tga20 slices were maintained until 45 dpi, fixed and analyzed by NeuN morphometry (analySIS vc5. 0 software). Neurotoxicity was defined as significant NeuN + neuronal layer loss over NBH treatment. Slices prepared from GRM5 -/-, GRM5 +/-and GRM5 +/+ littermates were maintained until 60 dpi, fixed and analyzed by NeuN morphometry (analySIS vc5. 0 software). Neurotoxicity was defined as significant NeuN + neuronal layer loss over NBH treatment.
Brain homogenization and immunoprecipitation Adult Prnp o/o , tga20 +/+ (tga20), and C57BL/6J mice were euthanized and their brains were dissected. Brain samples were snap frozen in liquid nitrogen. Samples were subsequently homogenized in ice cold Lysis Buffer (1% Igepal (NP-40) in 1x PBS, pH 7. 4) supplemented with protease (EDTA-free) and phosphatase inhibitor cocktail mix (Roche). Protein concentration was determined using the bicinchoninic acid assay (Pierce). Following immunoprecipitation of PrP C with a specific anti-PrP monoclonal antibody (POM1 or POM2) and addition of Dynabeads M-280 Sheep anti-mouse (#311201D, Thermo Fischer Scientific), samples were prepared in loading buffer (NuPAGE, Invitrogen) and incubated at 37˚C for 30 min. For the immunoprecipitation data shown in S4B and S4C Fig, the samples were incubated at 95˚C for 5 min; this resulted in disruption of dimers of mGluR5.
Histology and immunohistochemistry Stainings were performed on sections from brain tissues fixed in formalin and treated with concentrated formic acid to inactivate prions. Partially protease-resistant prion protein deposits, astrogliosis and microglia deposition were visualized by staining brain sections with the SAF84 antibody (1:200, SPI bio), GFAP (1:1000, Millipore) and IBA1 (1:2500, WAKO) respectively on a NexES immunohistochemistry robot (Ventana instruments) using an IVIEW DAB Detection Kit (Ventana), after preceding incubation with protease 1 (Ventana). Images of DAB stained sections were acquired using the NanoZoomer scanner (Hamamatsu Photonics) and NanoZoomer digital pathology software (NDPview; Hamamatsu Photonics). Quantifications of IBA1, GFAP staining and vacuoles in mouse sections were performed on acquired images; regions of interest were drawn on a Digital Image Hub (Leica Biosystems) and analyzed as previously described  [77].
Non-parametric Mann-Whitney test was performed in Fig  7  to measure the statistical differences between the distributions. GraphPad Prism (GraphPad Software) was chosen for the statistical analysis. , Grm5 +/-and Grm5 -/-mice inoculated i. c. with 5 log LD 50 units of RML6, n = 4-6 males per group. Each dot corresponds to a mouse. Two-way ANOVA per each time point revealed a non-significant difference between Grm5 +/+ , Grm5 +/-and Grm5 -/-groups. (B) Total brain extracts from mice inoculated with NBH and received control or MPEP food, as well as control WT brain lysates, were subjected to western blot analysis to evaluate whether MPEP treatment changes the expression of mGluR1 receptor. No differences were observed in the mGluR1 expression levels between the samples. (C) Cerebellar extracts from Grm5 -/-, Grm5 +/-and Grm5 +/+ mice, collected at postnatal day 10 (comparable with the organotypic slices), were subjected to western blot analysis to control for endogenous levels of mGluR5.
Acknowledgments We thank  Rita Moos ,  Petra Schwarz ,  Ahmet Varol ,  Irina Abakumova ,  Isaac Barwon  and  Delic Mirzet  for technical help,  M. Bieri ,  N. Wey  and  A. Wethmar  for imaging and software development,  Dr. Claudia Scheckel  for critical comments and  Dr. Pawel Pelczar  for revitalization of Grm5 +/-embryos.
Funding: AA is the recipient of an  Advanced Grant  of the  European Research Council , a  European Union   Framework 7 Grant  (NEURINOX), the  Swiss National Foundation , the  Clinical Research Priority Programs "Small RNAs" and "Human Hemato-Lymphatic Diseases", SystemsX. ch(PrionX and SynucleiX) , and the  Novartis Research Foundation. AKKL is a recipient of grant from Synapsis be a therapeutic option to alleviate the neurological symptoms, thereby ameliorating the quality of life in patients having prion infection. foundation. AT and ANS contributions were supported by the  ERC « Plastinhib » grant , the  ANR "Synaptune " grant, and by the  Program 'Investissements d'Avenir' :  ANR-10-LABEX-54  MemoLife. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Cell Studies GC1-spg cells were used as previously described  (Baptissart et al. , 2014). Cells were treated for 24 hr with vehicle (DMSO, 1:1,000) or 10 À6 M GW4064 (Sigma-Aldrich). Cells were then harvested 4 hr later, and mRNA or protein extractions were performed. The data presented were obtained from four independent experiments with n = 3 per group per experiment.
ACKNOWLEDGMENTS This work was funded by  Inserm ,  CNRS ,  Clermont Universite,  Ministere de l'Enseignement Superieur et de la recherche  (to M. B. ),  Ligue contre le Cancer (ComitePuy de Do  ˆme to D. H. V. ),  Nouveau Chercheur Auvergne  (no. R12087CC  to D. H. V. ),  ANR Jeune Chercheur  (no. 1103  to D. H. V. ), and  Plan Cancer -Cancer-Environnement InCa/Inserm  ( C14012CS  to D. H. V. ). We also thank Anipath platform from the  GReD  and the animal house staff ( Sandrine Plantade ,  Philippe Mazuel , and  Khirredine Ouchen ).
METHODS The propagation phase-contrast X-ray synchrotron microtomography of the cone was obtained by one of us (PT) in 2007 on the beamline ID17 at the European Synchrotron Radiation Facility (ESRF), Grenoble, France. The data were acquired with a beam set of 90 keV and a propagation distance of 5 m between the specimen and the detector. Voxel size is 31 µm. The resulting images were cropped with the Fiji software (Image J 1. 45, NIH©) and corrected manually to remove external elements such as air bubbles or traces of glue adhering to the fossil. The 3-D images of the cone were reconstructed with the Avizo v. 7 software, VSG©. Two sporophyll-sporangium units were virtually extracted from the rest of the cone using Avizo segmentation tools, and subsequently visualized with volume rendering.
ACKNOWLEDGEMENTS We are very much indebted to  J. Irving ,  R. Derrick  and  I. Percival  ( Geological survey of New South Wales ) for the information they kindly provided on the history of the Barraba plant fossil locality and on the geology of the area. Many thanks to  P. Gerrienne  for his insightful comments on an early version of the manuscript and to  L. Grauvogel-Stamm  for her helpful advice about the structure of the spores. We thank  Dermot Henry  ( Museum Victoria, Melbourne ) for the loan of the specimen. Claude Gril  ( Electronic microscopy Service, University of Montpellier ) is acknowledged for his technical help. Finally, we are very grateful to the two anonymous reviewers for their comments and suggestions that greatly improved the original manuscript.
Identification of Individuals with Mutations and Deletions of YY1 Upon the identification of the initial individual with a de novo mutation in YY1 (GenBank: NM_003403. 4) by exome sequencing,  1  an additional cohort of 500 individuals with unexplained ID was tested for mutations in YY1 by standard Sanger sequencing approaches on DNA extracted from peripheral blood. Primers are available upon request. DNA of the parents was tested for assessing the de novo occurrence of the identified mutations. In addition to the two above-mentioned individuals, the remaining eight individuals with de novo mutations in YY1 were detected by exome sequencing in various cohorts of individuals with unexplained ID (Table  1 ), sequenced in different centers in Tokyo (n ¼ 500), Zurich (n ¼ 350), Oslo (n ¼ 100), Houston (n ¼ 5,500), Gaithersburg (n ¼ 6,709), and Aliso Viejo (n ¼ 1300), leading to a total cohort of 14,969 individuals with ID.
26  Exome capture was performed with the SureSelect Human All Exon Kit V4 or V5, Agilent Clinical Research Exome Kit (Agilent Technologies), IDT xGen Exome Research Panel V1. 0, or VCRome 2. 1 (Roche NimbleGen). 27 Sequencing was performed on a MiSeq, HiSeq 2000, or HiSeq 2500 (Illumina) or SOLID 5500XL (Life Technologies). Data annotation and analysis were performed with the Burrows-Wheeler Aligner for read alignment. 28 Variant calling was performed with the Genome Analysis Toolkit,  29  XomeDx, or in-house developed tools as described previously. 30, 31 he ten individuals with de novo mutations in YY1 were detected by exome sequencing in a total cohort of 14,969 individuals with ID. We calculated the probability of observing ten de novo mutations in YY1 in 14,469 individuals as described previously  32  and corrected for the total number of tested genes (19,280, enrichment Agilent V5).
Individuals with deletions that included (part of) YY1 were identified from DECIPHER  33  and our in-house database containing data from over 8,000 individuals with ID. Microarray analysis was performed with the 44K, 60K, or 400K Agilent array '(Agilent Technologies) or 250K NspI SNP array (Affymetrix) according to the manufacturer's protocol. Detailed phenotype information of individuals with YY1 mutations and deletions was collected. This study was approved by the institutional review board of the.
In all cases and unless otherwise specified, the number of mapped reads was used as the library size, and edgeR v. 3. 12. 1 (with exact test) was used for assessing the statistical significance of the changes at the specific windows. consistently underweight þ Recurrent infections À þ À À À À À À À À Because such an analysis rests on the assumption that the readcount distributions are globally similar, and the H3K27ac data showed signs of a global decrease, for the analysis of this dataset, we excluded regions called as having increased H3K27ac in the probands because these were likely to be artifacts of the normalization.
RNA-Seq Analysis and Differential Expression Analysis RNA-seq libraries were prepared according to Illumina protocols (TruSeq Stranded Ribo-Zero depletion). Sequencing was performed with a HiSeq 2000. We performed paired-end 50 bp sequencing on independently cultured replicates of each line (see Table  S1  for a summary of the samples and experiments). Only one of the two batches clustered by genotype, whereas the other showed high levels of variability partly attributable to broad variations in EP300 and a large amount of its targets. For this reason, and because the first batch represented the same cultures from which the IPs were performed, we first focused on this one. However, we then used the replicated datasets, along with the subset of HapMap LCLs, in a meta-analysis. Because the replicate samples were not fully independent (i.
e. , could not be considered additional individuals) yet were informative of the technical, stochastic, and epigenetic variability, we then focused on the high-confidence differentially expressed genes (DEGs) that were statistically significant both in the main dataset (with adjusted p value < 0. 05) and in the meta-analysis (with adjusted p value < 0. 1). We performed RNA-seq quantification directly from the reads with Salmon 6. 1,  36  which we have shown to be excellent in tracking relative gene expression differences,  37  by using hg38 and the RefSeq annotation complementing the sequences of the ERCC spike-ins and Epstein-Barr virus. All differential expression analyses were performed with DESeq2 1. 10. 1  38  with the geometric normalization and the Wald test, considering only genes that had at least 20 reads in at least four samples.
Enrichment Analyses Gene Ontology (GO) enrichment analyses were performed with the goseq R package,  39  including correction for eventual RNAseq transcript-length bias and exclusion of genes without annotation. Categories with at least 10 but no more than 1,000 genes were considered, and Fisher's test was used. In the main figures, we filtered out the parent categories with significantly enriched offspring categories to maximize the specificity of the enrichments. The unfiltered enrichments are available in Table  S4. TF target enrichment analysis based on published ChIP-seq data was performed with the hypergeometric distribution. DNA motif enrichment analysis was performed with Homer v. 4. 8. 40 Unless specified, the background used for enrichment analysis was the set of expressed and tested genes used for testing DEGs, and all genes were used otherwise.
2% TBS-T (50 mM Tris [pH 7. 5], 150 mM NaCl, and 0. 2% Tween-20) and 5% milk prepared with 0. 2% TBS-T. Primary and secondary antibodies were diluted in 5% milk and 0. 2% TBS-T. Western blots were performed with the following antibodies and detected by peroxidase-based chemiluminescence (GE Healthcare Life Sciences): YY1 (sc-1703, 1:500; Sigma) and b-tubulin (ab6046, Abcam). Densitometry was performed with ImageJ software.
Structural Optimization of the C-Terminal Portion of YY1 Affected by De Novo Mutations The 3D coordinates of the YY1 zinc domain structure were obtained from the Protein Data Bank (PDB: 1UBD  43  ). Hydrogens were added, and the structure was optimized with GROMACS 5. 1  44  and force field Amber99-ILDN  45  through 200 steepest descent minimization steps and 300 conjugate gradient minimization steps. The structures of probands 1-4 and 7 were built by Modeler 9. 16. 46 Surface accessibility was measured with GROMACS 5. 1 with default parameters, whereby the protein was soaked in water explicit solvent with the TIP3P model. 47, 48 ifferences in binding energies resulting from point mutations were measured with Autodock Vina. 49.
External Datasets Used The following published ChIP-seq datasets were used: d GEO: GSM935294 (p300 in GM12878) d GEO: GSM935611 (CTCF in GM12878; post-filtering q < 10 3 10 À10 ) d GEO: GSM803391 (PAX5 in GM12878) d GEO: GSM935583 (CoREST in GM12878; post-filtering q < 10 3 10 À5 ) d GEO: GSM935613 (ZNF143 in GM12878; post-filtering q < 10 3 10 À10 ) d GEO: GSM733772 (H3K4me1 in GM12878) d GEO: GSM1003448 (HDAC1 in K562) d GEO: GSM1003574 (CBP in K562) In all cases, ENCODE 2014 unified narrowPeak calls were downloaded and lifted over to hg38, eventually with the indicated post-filtering. The list of chromatin interactions from GM12878 (called by the HiCUP Hi-C pipeline  50  ) was downloaded from GEO: GSE63525 (file ''GSE63525_GM12878_primaryþreplicate_HiCCUPS_looplist. txt. gz'') and lifted over to hg38.
The two remaining mutations were the early frameshift c. 385delG (p. Asp129Ilefs*127) and nonsense c. 535A>T (p. Lys179*). Importantly, none of these mutations are present in dbSNP 139, our in-house database containing exome data of over 7,000 individuals, or the Exome Aggregation Consortium (ExAC) Browser. By mapping all known variation over the primary structure of YY1, we observed that all variants found in healthy individuals involve the unstructured amino-terminal portion of the protein, and none of them involve its zinc-finger domains (Figure  1A ). We subsequently mapped the probands' mutations over residues 295-408 of the 3D structure of YY1 (PDB: 1UBD) to gain insight into the mechanisms of action of these variants, which are predicted to result in loss of function (Figure  2 ). In brief, c.
42 We performed a large number of permutation analyses to identify genes often differentially expressed between healthy individuals (see Figures  S10A  and S10B  and Material and Methods). 55 mportantly, the HapMap dataset revealed important variations in chromatin regulators, including YY1 itself, as well as some of its key partners, such as EP300 and CREBBP, which explained a large proportion of the transcriptomic variance (Figure  S8C ). Although broad variation suggests that LCLs might not be the ideal cell type for studying these pathways, it also offers an opportunity to detect associated expression patterns. We therefore harnessed this variability to identify a large set of genes (6,687) that were significantly associated with YY1 levels (see Material and Methods) and that significantly overlapped YY1bound genes (Figure  4E ; see Figure  4D  for the GO enrichments of the intersection).
Finally, we performed a meta-analysis of the two RNA-seq datasets in this study (D) Top most-specific GO enrichments of the YY1-bound genes that show a significant association with YY1 mRNA levels across HapMap LCLs. (E) Overlap between the DEGs and YY1-bound and YY1-associated genes. (F) Top most-specific GO enrichments of all DEGs. (G) Expression of high-confidence DEGs (consistently dysregulated in the meta-analysis with the HapMap LCLs), along with eventual YY1 bindings at their TSS. In (C) and (G), expression is shown as Z scores of log-transformed normalized counts, and YY1 binding is indicated in light brown if it was detected in only one of the two IPs and in dark brown if it was detected with both antibodies. (18 samples) and an equally sized subset of the HapMap LCLs by selecting the samples that had YY1 levels comparable with those of our control samples (see Material and Methods).
Acknowledgments We are grateful to the individuals and their parents for their participation. We thank  Lone Laulund  ( Department of Pediatrics, Odense University Hospital ) for additional clinical information about deletion case 263711. We thank  Giuseppe D'Agostino  from the  Testa lab  for his help in creating the summary figure. This work was supported by the  European Commission (GENCODYS  grant  241995  under  FP7  to A. T. V. -v. S. and B. B. A. d. V. ), the  European Research Council  (grant  DISEASEAVATARS 616441  to G. T. ), the  Telethon Foundation  (grants  GGP13231B  and  GGP14265  to G. T. ), the  Associazione Italiana per la Ricerca sul Cancro  (investigator grant to G. T. and fellowship to M. G. ), the  Regione Lombardia (Ricerca Indipendente   2012  to G. T. ), the  Umberto Veronesi Foundation  (P.
-L. G. ), the  Italian Ministry of Health (ERANET-Neuron  grant to P. -L. G. and  Ricerca Corrente  grant to G. T. ), the  Japan Agency for Medical Research and Development  (research grant to K. K. ), the  Australian National Health and Medical Research Council  (grant  1091593  to J. G. ), and the  Dutch Organization for Health Research and Development (ZON-MW  grants  917-86-319  and  912-12-109  to B. B. A. d. V. ). Received: December 21, 2016 Accepted: May 4, 2017 Published: June 1, 2017 Web Resources dbSNP, https://www. ncbi. nlm. nih. gov/SNP/ Exome Aggregation Consortium (ExAC) Browser , http://exac. broadinstitute. org/ NHLBI Exome Sequencing Project (ESP) Exome Variant Server , http://evs. gs. washington. edu/EVS/OMIM, http://www. omim. orgRCSB Protein Data Bank, http://www. rcsb.
The FBA protein sequence does not contain any secretion-export signal and is predicted to be cytosolic. The Francisella proteins possess two signature motifs of FBA II according to Prosite database (PS00602 and PS00806) and bear a conserved C-terminal lysine like the FBA of N. meningitidis, suggesting that they are genuine IIB FBA (Supplementary Fig. 3 ). We constructed an isogenic deletion mutant of fba in F. novicida by allelic replacement (Methods section) and first evaluated the impact of fba inactivation on bacterial growth in chemically defined medium (CDM  30  , supplemented with various carbohydrates (Fig. 2 ). We included in these assays a ΔglpX mutant  31  lacking the strickly gluconeogenic enzyme fructose biphosphatase (FBPase; Supplementary Fig. 1 ). The Δfba mutant (like the ΔglpX mutant) was unable to grow in media supplemented with gluconeogenic substrates such as pyruvate, glycerol, or succinate, a metabolite of the TCA cycle.
The ROS content was ~20% lower with the Δfba mutant compared to WT, at both time points (Supplementary Fig. 10A ). As positive control, NI cells were stimulated with 5 µg mL -1 of lipopolysaccharide from E. coli K12 (LPS-EK) Standard. LPS stimulation provoked an increase of ROS production that was up to 1. 5-fold higher than that in WT-infected cells, at both time points tested. DCFDA levels were also visualized using fluorescence microscopy. The percentage of fluorescent cells was significantly higher in WT-infected cells (33%) or LPS-stimulated NI cells (63. 5%) than in Δfba-infected cells (8. 5%) (Supplementary Fig. 10B ). Altogether, these assays further supported a direct correlation between the FBA -mediated repression of KatG expression and cellular ROS production. These data led us to hypothesize that FBA functions might extend beyond metabolic functions.
novicida (WT) and Δfba mutant. Total RNA was analyzed by quantitative RT-PCR with katG and fba gene. For each gene, the transcripts were normalized to helicase rates (FTN_1594) (**p < 0. 01). e J774. 1 cells were infected for 24 h with wild-type F. novicida (WT) and Δfba mutant in DMEM supplemented with glucose and glycerol (25 mM). The supernatants were analyzed by ELISA to detect the amounts of IL-6 produced at 24 h in pg mL We could identify 1372 proteins across the 9 samples analyzed, which represent 80% of the predicted F. tularensis proteome. For statistical analysis, we kept 1154 proteins robustly quantified (data are available via ProteomeXchange with identifier PXD006908). An ANOVA test identified 26 proteins whose amount significantly differed between the three strains. Of note, most of them were conserved in the subspecies holarctica and tularensis.