dataesr/scientific-paragraphs-categorization huggingface dataset:
Genome-wide nuclear phylogeny A nuclear phylogeny was inferred from the genomeskimming data generated here, using the methods described in  Olofsson et al. (2016). A total of 753,190   1 ). nCBI GenBank accession numbers are given for samples sequenced in previous studies. Within T. triandra, branches are coloured based on geographical origin. the scale is given at the bottom for a scenario that incorporates or ignores the microfossils. the origins of C 4 grasslands are plotted based on each scenario. perennial. Previously, T. quadrivalvis has been considered as a potential synonym of T. triandra  (Veldkamp 2016). However, if speciation is relatively recent, we would predict similar patterns for savanna species to what we observe in our phylogenies  (Pennington and Lavin 2016)  with a monophyletic daughter species (T.
Figure2. Dating the divergence within Themeda using chloroplast data. Posterior probabilities are indicated near nodes (>0. 8), and bars represent the 95% HPD of the estimated dates. the clade that each Themeda species represents is indicated (a-H; table 1). nCBI GenBank accession numbers are given for samples sequenced in previous studies. Within T. triandra, branches are coloured based on geographical origin. the scale is given at the bottom for a scenario that incorporates or ignores the microfossils. the origins of C 4 grasslands are plotted based on each scenario.
Actin buckling: A universal mechanism? Because the buckling issues we address are potentially applicable to many contexts, we sought supporting evidence in existing datasets from other cell types. Keratocyte migration has been imaged using interference reflection microscopy, which identifies differences in height of distinct regions of an object in contact with a glass surface  (Oliver et al. , 1999; Gabella et al. , 2014). Interestingly, when keratocytes were plated on a glass coverslip, the lamellipodia displayed a thin line at the tip of the edge in close contact with the substrate, separated from a large region at the back by a gap of ∼1-2 µm (higher region relative to the glass substrate; Fig. 11  a in  Oliver et al. [1999]  and  Fig. 3 D in Gabella et al. [2014] ). This gap is not mentioned in the articles, but the phenomenon could be analogous to the buckling observed in our fibroblast cell system.
Scalar variables represent the rest length of each segment, analogous to the amount of actin in each segment. These scalars for the actin segments provide a coarsely discretized representation of actin dynamics: continually increasing actin in the outermost segment represents actin polymerization with elongation of the outermost segment, and transfer of actin from segment to segment represents retrograde flow. The equations and parameters are provided in the text as well as in Table  2. The differential equations are solved numerically in Matlab with an explicit Runge-Kutta method. Mechanics of the lamellipodium. Fig. S5 (E  and F ) shows the computational model configurations for two or three adhesions, respectively. Actin segments (A1, A2, and A3) are modeled as viscoelastic solids with a linear viscous dashpot and linear elastic spring in series.
Acknowledgments We thank  Michael P. Sheetz ,  Benoit Ladoux ,  Barbara Hissa ,  Paolo Maiuri ,  Víctor González , and members of Gauthier's group for help and fruitful discussions. This work was supported by the  Mechanobiology Institute  (cofounded by the  National Research Foundation Singapore  and the  Ministry of Education of Singapore ), by an  Istituto Fondazione Italiana per la Ricerca sul Cancro di Oncologia Molecolare (Milan, Italy ) starting grant to Gauthier's group,by the  Brazilian agencies Conselho Nacional de Desenvolvimento Científico and Fundação de Amparo à Pesquisa do Rio de Janeiro , by the  Spanish Ministry of Economy and Competitiveness  ( BFU2016-79916-P ), and by the  European Commission  (Grant Agreeement  SEP-210342844 ). The authors declare no competing financial interests.
Details of ethics approval Our study was non interventional. The CERES approved the realization within our centre of an observational study not modifying patients' management. Every patients consulting for an inflammatory breast during our inclusion period was informed the data collected might be used for medical and / or research purpose and gave oral consent. Written consent was not required nor asked as the study was non interventional. All patients were sent information letters offering them the possibility of refusing to have their data included. All clinical investigation has been conducted according to the principles expressed in the Declaration of Helsinki.
Patients All consecutive patients referred for inflammatory breast to the Breast Unit of our tertiary University hospital department of Obstetrics and Gynecology between September 2013 and December 2015 were prospectively included. Inflammatory breast was defined as a red and hot breast often associated with pain  [3, 4]. All relevant clinical and imaging data were recorded at the time of inclusion. We excluded women who were pregnant or in the postpartum period. All patients were initially examined by a gynecologic oncologist. Clinical examination consisted of breast palpation and investigation for pathologic lymph nodes. Imaging, including ultrasonography of the breast and the axilla associated with a bilateral mammography when feasible, was done for all included patients. Most imaging exams were performed and interpreted in the Radiology Department of the hospital by breast imaging radiologists.
Several authors have assessed the performance of MRI for the diagnosis of IBC  [16, [18] [19] [20]. This exam is usually prescribed after ultrasonography and mammography in case of doubt. Sixteen patients with IBC underwent a breast MRI in our cohort. Presence of mass, local enhancement and suspicious lymph nodes were strongly evocative of a malignant lesion. While some authors  [1, 3]  have developed algorithms for the management of inflammatory breast, we believe that the need for such an algorithm is questionable. The main issue at hand is to rapidly identify all cases of IBC, a particularly aggressive cancer, in women presenting with inflammatory breast syndrome. Unfortunately, our data were limited regarding the time lapse between first clinical contact and the diagnostic of an IBC in our cohort and we were not able to assess the efficiency of the management of such patients using French guidelines.
Next, we quantified the translational response of the TOP mRNAs (CYYYY sequence is in the promoter   supplement 1B ). These data assured us in the ability of our approach to quantitatively characterize the translational properties of individual TSSs. We next analyzed the translational response of individual promoters following the GS stress. For this we determined the ribosome occupancy (RO, the ratio between the reads in the Heavy+Light polysomal fractions to the polysome-free fraction) of transcripts emanating from each promoter and calculated the effect of GS on the RO (referred to as the RO effect) for each experiment. A promoter was considered as translationally affected if its RO was affected by at least two-fold in each of the two biological repeats (Supplementary file 1). With these settings, we found that following glucose starvation, 22.
Deep sequencing data mapping and analysis Reads were mapped to the mouse genome (mm9 assembly) using STAR aligner and to the GFP and luciferase sequences using Bowtie2. The BAM file was altered to contain just the first base of the alignment using a custom Java script (Supplementary file 2) and coverage tracks were prepared using genomeCoverageBed. The tracks were then normalized by the numbers of reads mapping to the GFP/LUC (spikes) and the polysomal normalization factors. The numbers of reads mapping to each TSS defined by the FANTOM5 project (phases 1 + 2, permissive set) was counted using htseqcount. Log2-transformed ratios were computed after adding a pseudo-count of 0. 5 to the each normalized read number. Promoters were assigned to Ensembl 75 transcript models (ENSTXXX). A promoter was considered the 'annotated' promoter of a transcript if it was within 100 nt of its 5' end and 'Exonic' if it overlapped exons of the 5'UTR of the transcript.
Ribosome occupancy was defined as the ratio of Light+Heavy fractions and the polysome-free fraction. RO effect= ROGS ROcont ; mRNA levels change after GS= The data can be accessed in Gene Expression Omnibus (GEO) accession no. GSE93981 or tracked using UCSC genome browser at: ftp://ftp-igor. weizmann. ac. il/pub/hubANA. txt Cells, antibodies, plasmids and siRNA studies MEFs from a WT mouse (from Benois Viollet, INSERM, Paris) and HEK293T (from ATCC) were maintained in DMEM supplemented with 10% fetal calf serum, 100 units/ml penicillin, 100 mg/ml streptomycin and 1 mM Sodium pyruvate (for MEFs only). Cells were tested negative for mycoplasma by PCR. Cells were harvested after the indicated period of glucose starvation [glucose free media (11966025, Gibco) with 10% dialyzed FBS] or 24 hr after transfection and lysates were subjected to SDS-polyacrylamide gel electrophoresis followed by western blot.
Capped RNA oligos were chemically synthesized as previously described  (Lavergne et al. , 2008; Thillier et al. , 2012). For the label-free fluorescence measurements, purified eIF4E (300 nM) in TPA buffer with 0. 1% Pluronic F-127 (NanoTemper) and 50 mg/ml yeast tRNA, was mixed with increasing concentrations of cap analog (1. 25 nM to 10 mM; S1407, NEB) or capped RNA oligos (1. 25 nM to 5 mM). The reaction was centrifuged at 12,000 rpm for 5 min and then premium-coated capillaries (MO-Z005, NanoTemper) were loaded with the samples, and intrinsic fluorescence measurements were performed in a Monolith NT. LabelFree instrument (NanoTemper). Data analysis was performed with the Monolith NT. Analysis software (NanoTemper). 5 0 -Rapid Amplification of cDNA Ends (5 0 -RACE) Total RNA extracted from control and 8 hr glucose starved cells was used as a template to create cDNA with superscript II (Invitrogen) according to the manufacturer's instructions using gene-specific primers.
Acknowledgements We are grateful to  Hadar Sinvani  and  Ora Haimov  (our lab) for assistance, reagents and plasmids used in eIF4E experiments,  Shira Albeck  from the  Structural Proteomics Unit (WIS)  for the gel filtration of eIF4E,  Yoav Lubelsky  ( Biological Regulation, WIS ) for his help in library construction,  Shlomit Gilad  ( G-INCPM, WIS ) for the deep sequencing,  Haleli Sharir  ( G-INCPM, WIS ) for helping with the fluorescence measurements studies, Theo  Guez  for his technical assistance in the synthesis of capped RNA oligos,  Gideon Schreiber  ( Biomolecular Sciences, WIS ) for helpful advice and  Franck Martin  ( UniversiteDe Strasbourg ) for the His-eIF4E construct. This work was supported by grants from  Israel Science Foundation  (# 1168/13 ) (RD),  ISF-INCPM  ( 2359/15 ) (RD) and the  Minerva Foundation  (# 712278 ) (RD), Alon Fellowship (IU),  European Research Council (Project 'lincSAFARI') (IU) ,  Israeli Science Foundation  ( 1242/14  and  1984/14 ) (IU), the  I-CORE Program of the Planning and Budgeting Committee  and  The Israel Science Foundation  (#  1796/12 ) (IU), the  Minerva Foundation (IU) , the  Fritz-Thyssen Foundation (IU) ,  The Abramson Family Center for Young Scientists (IU).
RD is the incumbent of the Ruth and Leonard Simon Chair of Cancer Research. IU is incumbent of the  Sygnet Career Development Chair for Bioinformatics. Additional information Funding Funder Grant  reference number  Author Israel Science Foundation   1168/13   Rivka Dikstein Minerva Foundation 712278 Rivka Dikstein Israel Science Foundation   INCPM 2359/15   Rivka Dikstein European Research Council lincSAFARI Igor Ulitsky Minerva Foundation Igor Ulitsky Alon Fellowship Igor Ulitsky Israel Science Foundation   1242/14 Igor Ulitsky Israel Science Foundation 1984/14 Igor Ulitsky Israeli Centers for Research Excellence 1796/12 Igor Ulitsky Fritz Thyssen Stiftung Igor Ulitsky The Abramson Family Center for Young Scientists Igor Ulitsky The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
The use of Raman spectroscopy for histological analysis of cervical tissue cuts is discussed in  [60]  and  [64]. The Raman spectral mapping of the unstained histological cuts was performed with the spatial resolution of 18 µm. The spectral Raman data set was evaluated by K-means cluster analysis (KMCA). The regions with similar spectral and hence biochemical properties were clustered on a generated pseudocolor map. In the spectrum averaged over the pixels from stromal layer cluster the Raman peaks at 853, 921, 938 and 1245 cm -1 were assigned to collagen, which is the major component of this layer. The accumulation of glycogen in the mature squamous cells of intermediate and/or superficial layers manifested itself by peaks at 480, 849 and 938 cm -1 in the spectrum averaged over the pixels from corresponding clusters.
Mueller polarimetry There is an emerging set of optical techniques based on the detection of changes in the polarization of light instead of (or together with) intensity measurements. Apart from the intensity and wavelength of probing light its polarization can carry important information about the sample. Many research groups work in the field of biomedical applications of polarized light  [94] [95] [96] [97] [98] [99] [100] [101] [102] [103]. Even the simplest orthogonal state contrast (OSC) polarimetric techniques provide data about the polarimetric characteristics of the sample. Typically, the sample is illuminated with linearly or circularly polarized white light. Two set of measurements are performed, detecting the intensity of signal after interaction with sample through another linear or circular polarizer, set parallely ( ) and orthogonally ( ) to the polarization state of the illuminating light.
Using Kaleida-Graph (Synergy Software), dissociation constants were derived by fitting the binding isotherms to a 1:1 binding model of RNA and protein according to Equation (  2 ) f b = L + P + K D -(L + P + K D ) 2 -4 * L * P 0. 5 2 * L (2) where f b represents the fractional concentration of bound RNA, L the total concentration of labelled RNA, P the concentration of protein and K D the dissociation constant. Dissociation constants of influenza B polymerase and v3 RNA at increasing concentrations of v5 RNA were determined in plate-mode format (Figure  1C ). Indicated concentrations of influenza B polymerase (pre-incubated with an equimolar concentration of v5 RNA nucleotides 1-18) and constant 0. 01 M 5 -(FAM-Ex-5)-labelled v3 RNA (nt 1-18) and 0, 0. 02, 0. 05, 0. 2, 0. 5 or 1 M v5 RNA (nt 1-18) were incubated in binding buffer (50 mM HEPES/NaOH, 0.
Remarkably, only small side-chain movements (e. g. PB2 Arg40, Lys43; PB1 Met227 and the Motif B loop 409-410) allow the 3 end to thread through the narrow template entry tunnel. Although the detailed interactions of the template with the entry tunnel cannot be elucidated with certainty at the current resolution, the electron density suggests that highly conserved residues from the anti-parallel ␤-strands at the base of the fingertips loop and from the N-terminus of PB2 are involved (Supplementary Figure  S14B ). Only the phosphate of U1 has electron density, the rest of the nucleotide being disordered as well as the adjacent tip of the priming loop (646-PAHG-649 lack density). Superposition of the polymerase active site with that of Norwalk virus polymerase primertemplate/substrate (CTP) complex (PDB: 3BSO, (30)) suggests that the 3 extremity is positioned not for terminal initiation but advanced one position (Figure  7E  and F ).
(E) Overall view of the promoter bound to the PB1 subunit (cyan ribbons) showing the priming loop (purple) and active site motif C (red). The unobserved 3 terminal base (U1, red) is modeled. Based on superposition with the Norwalk virus polymerase primer-template/substrate (CTP) complex (PDB: 3BSO, (30)) the initial ApG of the product (orange), the incoming CTP (black) and the two catalytic divalent ions (green spheres) are modelled. (F) As (E) but only showing the RNA.
ACKNOWLEDGEMENTS This work used the platforms of the Grenoble Instruct center (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). We thank  Dr. Joanna Timmins  for access to her technical facilties. We are grateful to members of the  ESRF-EMBL Joint Structural Biology Group  for access to European Synchrotron Radiation Facility beamlines.
, 2017). An artificially generated noise recording was used for the experimental exposure with a spectral energy distribution reflecting typical urban noise profiles  (Lohr, Wright, & Dooling, 2003; Pohl, Slabbekoorn, Klump, & Langemann, 2009). A low-pass filter was applied to a white noise file with a random energy in order to create this urban-style noise recording, using Matlab 7. 5 (Mathworks, Inc. , Natck, MA, U. S. A). The noise file had a high-pass cut-off frequency at 100 Hz and a spectral energy decrease of 6. 5 dB/kHz toward the higher frequencies  (Halfwerk & Slabbekoorn, 2009; Halfwerk, Bot, et al. , 2011). Based on values of noise levels reported close to the highways  (Dooling & Popper, 2007)  and in order to be able to compare current research with results from a previous study (Huet des  Aunay et al.
Poisson and binomial models used for the eggs and the CSDs appeared able to fit the variance of the data with these random effects (estimated overdispersion scale parameter close to 1). Theses analyses were performed in R version 2. 10. 1 (the R Foundation for Statistical Computing, Vienna, Austria) with the function lmer and glmer implemented in package lme4 for GLMMs. Estimates of the overdispersion with respect of the fitted models were obtained with function "dispersion_glmer" (package "blmeco"). Estimates of the coefficients accounting for the different fixed effects are reported ± SE and derived p-values allowed to assess their statistical significance (i. e. , non-null coefficients). Sample means are given ± SE throughout the results section.
Quantification of cell Death Two hundred thousand cells were seeded in 24-well plates and treated with Stifenia during 20 h as described above. Cells contained in the culture medium were harvested by centrifugation (400 g, 5 min) and then suspended in 300 µL of PBS containing propidium iodide (PI) (10 µg mL -1 ). PI-stained cells were detected using a LSR II flow cytometer (BD Biosciences) and acquisitions were performed during 45 s using BD FACSDiva Software 6. 1. 2. Flow Jaw was used for figure drawing.
acKnOWleDgMenTs The authors thank Anaïs Gérard, Siham Hichami for technical help, Tatiana Lopez for zebrafish breeding, Dr. Jean-Paul TaBle s1 | cytokine concentrations in culture medium of stifeniaexposed peripheral blood mononuclear cells. Cytokines were measured in the culture medium 20 h after the addition of Stifenia at the indicated concentrations using a multiplex kit (ProcartaPlex human simplex, Affymetrix, France) according to the manufacturer's instructions on blood donor CHR026_91. C, concentration; IF, induction factor; CTR, control non-treated cells. FigUre  s1  | effect of stifenia il-1β production and metabolic activity (Ma). Peripheral blood mononuclear cells were exposed to different concentrations of Stifenia added in the culture medium for 20 h. Cell MA (white bars) was estimated by the XTT assay, and IL-1β (gray bars) was measured in the culture medium.
Acknowledgements This work was supported by the  Wilson and Amelia Wong Endowment Fund, Research Grants Council of Hong Kong  ( AoE/ M-05/12 ),  Innovation Technology Fund of the Innovation Technology Commission (Support to Partner State Key Laboratories in Hong Kong)  and  HKU CRCG awards  ( 0910159039 ,  1007160002 ,  1511159010 ). PL was supported by a  University Postgraduate Fellowship  and a  Postdoctoral Fellowship  from the  University of Hong Kong.
Microscope image acquisition Images were acquired at room temperature using a TCS SP5/AOBS inverted confocal microscope (Leica Microsystems) for the embryos and a TCS SP2/UV inverted confocal microscope (Leica Microsystems) for PGCs and ESCs with a Plan Apo CS 63× (NA 1. 4) oil-immersion objective (Leica Microsystems). The following fluorescence settings were used: DAPI (excitation 405; emission 410-470),  GFP (489; Cy3 (558; and Cy5 (650;  when needed. The acquisition software was LAS AF Lite 2. 6. 3, build 8173 (Leica Microsystems). No gamma adjustments, deconvolution, or reconstitutions were performed. Recording was sequential to avoid bleach-through. Images for this manuscript were formatted using Adobe Photoshop CS4 or ImageJ.
Acknowledgments We thank  Marie-Christine Birling  ( Institut Charles Sadron, Strasbourg ) for helpful discussions during the design of the knockin mice. Work in the Schneider laboratory is supported by the  Helmholtz Gesellschaft  and the  EpiTrio project. Work in the Hajkova laboratory  is supported by the  Medical Research Council, European Research Council   Consolidator Grant  "dynamic modifications," and the  EpiGeneSys Network. P. Hajkova  is a member of the  European Molecular Biology Organization Young Investigator Program ;  P. W. S. Hill  was a recipient of the  Medical Research Council Doctoral award. M. -E. Torres-Padilla  acknowledges funding from  EpiGeneSys ,  European Research Council.
16S rRNA Gene Analysis DNA was extracted from isolated colonies of the different F. prausnitzii strains by alkaline lysis in 50 µL of NaOH 0. 5 M during 30 min and 50 µL of Tris 1M pH7 and 100 µL H 2 O were added. 16S rRNA sequences were amplified using FP1 and FP2 primers (Table  2 ) and PCR products purified with the Wizard SV Gel. PCR Clean-Up system (Promega) was used to obtain bidirectional partial 16S rRNA gene sequences by using primers FP1, FP2, FP3, FP4, and FP5 (Table  2 ). All DNA sequences were confirmed by sequencing (Eurofins MWG Operon, Ebersberg, Germany). Sequences for the novel isolates were deposited in the NCBI database under the accession numbers MF185398 to MF186168. Phylogenetic analysis based on 16S rRNA were performed using the multiple sequence alignment-CLUSTALW  (Thompson et al.
, 1994)  integrated in MEGA6 software  (Tamura et al. , 2013). After that, the most appropriate evolutionary model was defined and the evolutionary history was inferred approach and all positions containing gaps and missing data were eliminated. The tree with the highest log likelihood  (-3073. 67 ) is shown (Figure  3 ). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 36 nucleotide sequences. There were a total of 1090 positions in the final dataset. In this analysis, sequences used by Lopez-Siles et al. (Duncan et al. , 2002; Ramirez-Farias et al. , 2009; Lopez-Siles et al. , 2012)  were included with the objective of compare the new strains to the two phylogroups proposed by that study. Eubacterium desmolans was used to root the tree.
Finally, three antibiotics (not included in the EFSA guidance) were also analyzed due to their importance in the clinical treatments: trimetroprim, linezolid, and cefpirome. All strains were resistant to trimethoprim, as expected for an anaerobic bacteria (MICs >32 mg/L; data not shown), while they tended to be susceptible to linezolid (MICs ranging from 0. 032 to 3. 3 mg/L) and resistant to cefpirome (from 4. 66 to >256 mg/L) which, when linked to the general susceptibility to ampicillin, might indicate that the penicillin binding proteins of Faecalibacterium are poorly recognized by cephalosporins. Remarkably, CNCM I-4543 and CNCM I-4574 isolates were resistant to cefpirome, a fourth-generation cephalosporin  stable against most plasmid-and chromosome-mediated betalactamases  (Wiseman et al.