dataesr/scientific-paragraphs-categorization huggingface dataset:
Seven ribosomal proteins (S2, S4, S14, S21, L25, L30, L33) that were absent from >50% of the considered genomes or had paralogous copies making difficult the identification of orthologues were discarded from the analysis. The remaining 47 single protein data sets were aligned with MUSCLE v3. 8. 31  (Edgar, 2004)  with default parameters, and unambiguously aligned positions were selected with BMGE 1. 1  (Criscuolo and Gribaldo, 2010)  and the BLOSUM30 substitution matrix. Trimmed datasets were concatenated by allowing a maximum of 11 missing sequences per taxon into a large character supermatrix (218 taxa and 5551 amino acid characters). PhyloBayes v3. 3b  (Lartillot et al. , 2009)  was used to perform Bayesian analysis using the evolutionary model CAT +GTR+G 4. Two independent chains were run until convergence, assessed by evaluating the discrepancy of bipartition frequencies between independent runs.
, 2010). For each tree topology, log-likelihood per character was estimated by PhyML v3. 0 with the evolutionary model LG+G 4. In order to estimate the AU test p-values associated to each topology, the resulting data were processed with CONSEL v0. 20  (Shimodaira and Hasegawa, 2001)  with default parameters. For the LPS core gene analysis, homologues were searched by using Pfam HMM profiles for LpxA, LpxB, LpxC, and LpxD. The same approach as the one described above for ribosomal proteins was used to assemble a 4-gene supermatrix of 898 unambiguously aligned amino acid characters, which was analysed by PhyloBayes with the evolutionary model CAT+GTR+G 4. Congruence among the four markers was assessed by the IC criterion as described above.
Protein annotation Given the small number of markers analyzed and their frequently limited conservation at the sequence level, we followed a semi-manual procedure for annotation based on a combination of profile-based homology searches, protein domain identification, and genomic synteny. Profile-based homology searches of specific OM markers were performed by using the HMMER package  (Johnson et al. , 2010). Initial searches were conducted by HMM on the local Firmicute genome databank by using standard Pfam domain models corresponding to a given protein of interest. The top-scoring hits were used to build new HMM models and perform a novel search. This process was iterated until no new hits were found. The resulting homologues were aligned and manually inspected in order to confirm homology and to eliminate divergent, partial or non-homologous sequences.
Additional searches with tblastn  (Altschul et al. , 1997)  were used to identify eventually misannotated homologues in some genomes. Protein domains were inspected by querying the Conserved Domain Database (CDD) at NCBI  (Marchler-Bauer et al. , 2015). Genomic synteny was investigated using the interactive web-based visualization tool SyntTax  (Oberto, 2013). Local genomic alignments were generated using EasyFig  (Sullivan et al. , 2011)  with a BLAST cutoff E-value of 0. 0001. For localization prediction, we used the PSORT v3. 0 server (http://www. psort. org/psortb/, Yu et al. , 2010)  with default settings for Gram-negative Bacteria. Protein families were assigned to Clusters of Orthologous Groups by searching the COG database, which was downloaded from the NCBI FTP server (ftp://ftp. ncbi.
Figure3. Conserved genomic locus for cell envelope components. Co-localization of the genes coding for LPS synthesis and transport, OMP assembly and structural OMPs in the Negativicutes and the Halanaerobiales. Representatives of the 2 families of Negativicutes and the 2 families of Halanaerobiales are shown (for full distribution and accession numbers see Supplementary file 1). Genes are colored according to their functional class: LPS synthesis and transport (green), OMP assembly (blue), flagellum (light pink), OM-PG attachment (red), hypothetical (brown), efflux (purple) (see text for discussion). White boxes indicate proteins not known to being related to the OM or non-conserved proteins whose connection with the OM is unclear. The figure was obtained by EasyFig (Sullivan et al. , 2011) , where vertical lines represent BLAST hits with a cutoff of 0.
Acknowledgements LA was the recipient of a postdoctoral fellowship from the  Investissement d'Avenir Grant  " Ancestrome " ( ANR-10-BINF-01-01 ). DP is a scholar in the  Pasteur-Paris University International PhD program. AK wishes to thank  Uwe-G Maier  for allocation of the EM facility in Marburg and  Marion Debus  for technical assistance. We thank the  Collection of Bacteria of the Institut Pasteur  for kindly providing the two strains used in this work for electron microscopy, and the  Centre Informatique pour la Biologie  (CIB, pole cluster) for providing computing facility. We also wish to thank  Patrick Forterre  for discussion during the preparation of this work.
Patient demographics A total of 160 patients were recruited for the study, 80 from each country (France and Spain). None of the patients who were contacted refused to take part in the study or asked for their data to be removed once they had completed the questionnaire. Patient demographics are presented in Table  1  and were similar in both countries. The most notable difference was that 63. 8% of French patients but only 45. 0% of Spanish patients never ate ready-to-use food (Table  1 ). Patient history of taking phosphate-binder medication and reasons for switching are presented in Table  2. Overall, at the time of survey completion, patients in France and Spain had been receiving haemodialysis for an average of 43. 3 months (SD, 45. 6; Table  2 ), and had been taking a phosphate binder (including lanthanum carbonate powder) for an average of 35.
In a survey of 79 patients on maintenance haemodialysis, the preference for lanthanum carbonate in chewable tablet versus granule form was investigated  [29]. In this study, 46. 8% of patients found granules easier to take, while 27. 8% reported that tablets were easier to take and 25. 3% reported no differences between the formulations. This supports the idea that a physically smallersized formulation of lanthanum carbonate may be preferred and could therefore increase adherence. Nevertheless, lanthanum carbonate powder, like other phosphate binders, must be taken together with meals, which may affect adherence if it is not compatible with the patient's lifestyle  [28]. A relatively low level of adherence to phosphate binders has been previously reported in a review of online medical databases searching for predictors of non-adherence to phosphate-binding medication in patients with ESRD  [12].
For oil immersion microscopy, we used oil with a refractive index of 1. 518 (Zeiss). Image capture was carried out with a definition of 1,024 by 1,024 pixels with 8-bit data for each color. Images were analyzed using ImageJ software. Total pixel intensity was quantified using ImageJ software. Chromatin immunoprecipitation. Chromatin immunoprecipitation experiments were carried out as previously described  (21). PCR analysis of inputs or immunoprecipitated DNAs was performed using oligonucleo-tides F-40 (5=-GTT TTC CCA GTC ACG AC-3=) and CAT (5=-CCA TTT TAG CTT CCT TAG-3=) to reveal the integrated WT330 and WT110 IFN-␤ promoters. For the F-40 and CAT sets of primers, PCR conditions were as follows: 1 cycle of 94°C for 5 min; 20 cycles of 94°C for 30 s, 53°C for 30 s, and 72°C for 30 s; and 1 cycle of 72°C for 10 min.
For fold changes in expression of less than 1 (which translates into repression of the gene's expression), inverted values were determined, such that a 0. 5fold change corresponds to a fold change in expression of Ϫ2. The sequences of the primers used for RT-qPCR analysis are shown in Table  1. Statistical analysis was carried out using the Student t test or REST software, which uses a pairwise fixed reallocation randomization test to determine the P value. RNA interference experiments. L929 cells were transfected, using the Lipofectamine 2000 reagent (Invitrogen Life Technologies), with the ON Target Plus Smart pool of small interfering RNA (siRNA) oligonucleotides specific for ␤-catenin (catalog number L-040628-00; Thermo Scientific Dharmacon) or with a pool of control siRNA sequences (catalog number D-001810-10-05; Thermo Scientific Dharmacon) at a final concentration of 50 nM each for 72 h.
For measurement of the cytopathic effect of RVFV, L929 cells that were either not treated or treated with LiCl for 24 h were infected with RVFV ZH548 and incubated under an overlay consisting of DMEM, 2% fetal calf serum, antibiotics, and 1% agarose at 37°C. At 3 days p. i. , the lytic plaques were counted after staining with a solution of crystal violet. Western blotting. For Western blotting, total protein extracts were prepared in radioimmunoprecipitation assay buffer and resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in 4 to 12% precast gels (Life Technologies). Relative quantification of proteins on scanned films of the Western blots was carried out using ImageQuant software. Ethics statement. Experiments on live mice were conducted according to French and European regulations on the care and protection of laboratory animals (EC Directive 86/609 and French Law 2001-486, issued on 6 June 2001) and the National Institutes of Health Office of Laboratory Animal Welfare (assurance number A5476-01, issued on 2 July 2007).
(E, F, G, and I) IFN-␤ mRNA (E and I) and Oas1b or IRF7 mRNA (F) in noninfected L929 cells that were either not treated or LiCl treated (E to G) and at different times postinfection in L929 cells mock or NDV infected and either not treated or pretreated with LiCl (I) were analyzed by RT-qPCR. In panels E to G, the corresponding fold levels of induction with respect to the levels of induction for nontreated cells were calculated; in panel I, the corresponding fold levels of induction with respect to the levels of induction for noninfected and nontreated cells were calculated. Data are for 33 (minimum) to 71 (maximum) nuclei that were counted (C), 42 biological replicates from 13 independent experiments (E), 18 biological replicates from 6 independent experiments (F), and 6 biological replicates (I).
At the same time, the automotive industry needs always to satisfy its customers by keeping up a high performance standard. For that, manufacturers are trying to find a way to fix it, having the hope that the electric car can win in the near future the heart of consumers. Preliminary design of electric vehicles  [2] [3] [4]  can be performed using different tools such as multi-domain a Corresponding author: amir. guizani@supmeca. fr VHDL-AMS, Matlab/Simulink or Modelica. Several studies were performed to improve and optimize models of electric vehicles in order to obtain a more reliable and more efficient vehicle. For example, the authors in  [3]  focused on the modelling and design of the battery package which should contain enough energy in order to have a certain driving range and have a sufficient power capability for the accelerations and decelerations.
A case study for the optimization of electric vehicle We consider the optimization of an electric vehicle with four objective functions and three design constraints: -Objective f 1 : minimizing the mass of the energy storage system in order to choose the optimal battery. -Objective f 2 : maximizing the state-of-charge of the battery at the end of a driving cycle. -Objective f 3 : minimizing the electric power required by the propulsion and the transmission systems in order to choose the optimal electric motor. For the design variables, we will limit our study to the number of series connected cells N s , the number of parallel strings N p , the constant of the electromotive force Emf of the electric motor and the gear ratio R g. In this study, we have combined Modelica modeling language with ModelCenter for the optimization of an electric vehicle.
Methods The non-redundant database of protein sequences at the NCBI was searched using the PSI-BLAST  (Altschul et al. 1997). Profileagainst-profile searches were performed using HHpred (So ¨ding 2005) against different protein databases, including PFAM (Database of Protein Families), PDB (Protein Data Bank), CDD (Conserved Domains Database), and COG (Clusters of Orthologous Groups), which are available via the HHpred website. For phylogenetic analyses protein sequences were aligned with Promals3D (Pei and Grishin 2014) (MCP, SF1 helicase, and pDNAP) or Muscle  (Edgar 2004 ) (ATPase). The alignment was visualized using Jalview  (Waterhouse et al. 2009 ). The quality of the MCP and mCP alignments was evaluated using the Transitive Consistency Score (TCS), a sequence alignment reliability measure which helps to estimate alignment accuracy  (Chang et al.
2014 (Chang et al. , 2015)). Poorly aligned (low information content) positions were removed using the Gappyout function of Trimal  (Capella-Gutierrez et al. 2009). Representative MCP and ATPase sequences were acquired from  Yutin et al. (2015). Representative sequences from different families of SF1B helicases were collected from PFAM database with following accession numbers PF05970 (PIF1), PF05127 (RecD), PF02689 (Herpesvirus UL5). Viral and plasmid pDNAP sequences were collected from GenBank, whereas those from Polintons were obtained from the Repase Update database  (Jurka et al. 2005). Phylogenetic trees were constructed using the PhyML program  (Guindon et al. 2010)  the latest version of which (http://www. atgc-montpellier. fr/phyml-sms/) includes automatic selection of the best-fit substitution model for a given alignment.
The best models identified by PhyML for ATPase, SF1 helicase and pDNAP domains were LG þG6 þI þF. LG, Le-Gascuel matrix; G6 þI þF, Gamma shape parameter: fixed; number of categories: 6; Proportion of Invariable sites: fixed; Equilibrium frequencies: empirical. The best model identified by PhyML for MCP was the same as above but with estimated Proportion of invariable sites. All the alignments used for the tree construction are available from the authors upon request. A Bayesian-like transformation of aLRT (aBayes)  (Anisimova et al. 2011) , as implemented in PhyML  (Guindon et al. 2010) , and non-parametric bootstrapping (1,000 replicates) were used to estimate branch support. Alternative topologies for the SF1 helicase tree were tested using the CONSEL software (Shimodaira and Hasegawa   (Krupovic et al.
Putative integrated transpovirons in B. Natans are PLVs The original analysis of the putative transpovirons of B. natans  (Blanc et al. 2015)  has shown that these elements are considerably larger than the transpovirons associated with the mimiviruses  (Desnues et al. 2012 ) and encompass several viral genes. To better understand the provenance of the putative transpovirons of B. natans and to investigate their link to viruses, we reanalyzed their gene content. BLASTp searches against the NCBI viral database seeded with the protein sequences of the putative transpoviron BnTV26 resulted in a match between protein BnTV26_9 and TVSG_00021 of TVS1(Supplementary Table  S1 ). The latter protein has been recently identified as the putative MCP of TVS1, related to the DJR MCPs of the other PLVs  (Yutin et al.
2014 (Chang et al. , 2015)) ). Collectively, these results suggest that BnTV26_9 is the MCP of BnTV26 (Figure  1A ). Considering that viruses with DJR MCPs typically encode an additional mCP with a single jelly-roll fold, the protein set of BnTV26 was searched against a custom database of PLV proteins  (Yutin et al. 2015). A significant hit was obtained between the mCP of PLV-MED1 and BnTV26_10 (Supplementary Table  S1 ) which is encoded immediately downstream of the MCP (Fig. 1A ). The same arrangement of the two genes is also found in TVS1. As in the case of the MCP, multiple sequence alignment (TCS score 645; Supplementary Figure  S2B ) confirmed the conservation of both sequence and secondary structure in the mCPs of PLV and BnTV26 (Supplementary Figure  S1B ). Other significant matches were identified between proteins BnTV26_5 and A32-like genome packaging ATPase of PLV-MED1, BnTV26_ 13 and GIY-YIG nuclease of PLV-ACE1, BnTV26_18 and Tlr1-like SF1 helicase of PLV-SAF5 as well as between BnTV26_14 and a hypothetical protein of PLV-RED1 (Supplementary Table  S1 ).
Transpovirons associated with mimiviruses evolved from PLVs Transpovirons and some PLVs, including PLV-Bnat, share a gene for the SF1 helicase which is most closely related to the helicase first described in Tlr1  (Wuitschick et al. 2002 ) (Fig. 1 ), indicating that all these elements might be evolutionarily related. Previous analysis has shown that transpoviron helicases form a sister clade to proteins of the PIF1 family which falls into the SF1B group  (Desnues et al. 2012) , a division of SF1 helicases that translocate in the 5 0 -3 0 direction  (Singleton et al. 2007 ). However, at the time of the analysis, several groups of elements encoding Tlr1-like helicases have not been yet identified. To clarify the relationships between transpovirons and other groups of mobile elements, we performed phylogenetic analysis of the Tlr1like helicases jointly with other SF1B helicase families, namely PIF1 (PF05970), RecD (PF05127), and Herpesvirus UL5 (PF02689).
The threshold was defined as the average plus twice the standard deviation of the values of these correlation coefficients. The longest distance at which the Pearson's correlation coefficient between the envelopes of BW and respective averaged AEP was above threshold was considered the maximum distance at which the BW was correctly perceived. Signal averaging was performed with custom-written software (P. J. F. and M. Vieira). This software is available from the authors. The Pearson's correlation analysis was performed with Statistica 12. 0 (StatSoft, Inc. , USA).
J. F. ) in LabView (v8. 2, National Instruments), and consisted of frequency sweeps (0. 01 to 1000 Hz) with a 500 ms duration, repeated 25 times with 100 ms pauses. The output of both the reference and testing hydrophones was simultaneously recorded with the same multifunction board. Comparisons of the reference sound with attenuated sounds were made by computing with the same LabView software the averaged transfer function spectra and the coherence function of the distant hydrophone relative to the reference hydrophone. The sound sampling was delayed relative to the recording of the hydrophone close to the speaker to take into account the sound propagation delay from the speaker to the distant hydrophone. The hydrophone recordings were calibrated by comparison with a Bruël & Kjaer type 8104 hydrophone conditioned by a Sound Level Meter (Mediator 2238) with a linear frequency weighting and set on fast measuring mode.
Enriched CD117 high positive bone marrow cells have previously been described to be highly enriched for mast cells, thus we defined CD117 high positive cells as mast cells  [36]. All samples were analyzed on a FACSCalibur flow cytometer (Becton Dickinson), employing the Cellquest software, and the data acquired analyzed with the FlowJo 7. 6 program. For ROSA cells, apoptosis staining was performed with Annexin V and 7-AAD (BD Bioscience) in Annexin V Binding Buffer (BD Bioscience).
0 software (LI-COR). Western blots where analysed and quantified using Image Studio Software version 2. 1. 10 (LICOR). The protein of interest was normalized to the loading control, β-actin (DM1A, Sigma) or α-tubulin (AC-15, Cell signaling). For ROSA cells, membranes were incubated with HRP-conjugated IgG secondary antibody (Cell Signaling, Danvers, USA), proteins visualized with chemiluminescence (GE Healthcare) in a ChemiDoc MP System (Bio-Rad) using Image Lab 4. 1. Bands were normalized to β-actin and vehicle control.
RNA extraction and qPCR Total RNA was extracted using Trizol (ThermoFischer Scientific) according to the manufacturer's instructions, with the addition of a second precipitation with absolute ethanol. cDNA was synthesized using Maxima Reverse transcriptase (ThermoFisher Scientific) according to the producers protocol. The subsequent qPCR was performed using 200 nM primer (TaqCopenhagen, Copenhagen, Denmark) and SybGreen (ThermoFisher Scientific) on the StepOnePlus Real-Time PCR system (Applied Biosystems). Normalized gene expression was calculated using the CFX manager software (Bio-Rad). The expression was normalized to housekeeping gene GAPDH, and to the DMSO vehicle control.
Transcription factor analysis Transcription factors to analyze were chosen by extensive literature search. HMC-1. 2 cells were treated with 5 μM SAHA or vehicle control for 24 hours, whereafter total RNA was extracted with Trizol and cDNA was synthesized using iScript (Bio-Rad) according to the manufacturer's protocol. Real time PCR was performed using 100 ng cDNA, 200 nM primer (TaqCopenhage) and SybGreen (Bio-Rad) on the CFX96 Touch™ Real-Time PCR. Gene expression normalized to housekeeping gene was calculated using the CFX manager software (Bio-Rad), and thereafter normalized to the DMSO vehicle control. Primer list is shown in Supplementary Table  1.
Primers were for KIT promoter forward 5'GCCTTTTCCGTGATCCATTCA3', reverse 5'GGCGACGAGATTAGGCTGTTA3' , -71 kb of KIT forward 5' TGCCAGAACATCATTGATATCTCTG'3; reverse 5'CAGGCATGTGGTTGTTAGATATTGT'3; -123 kb forward 5' ATG GCT TCT GTC CTT GGA GC'3; reverse 5' GGC CTG ACT GCT TAC TCC TC'3, PDGFRα forward 5' CGCGGTTTTTGAGCCCATTA'3, reverse 5'ATGGAGTAAAGAGCGTGCCC'3, KDR forward 5' GCCTTCAGATGCCACAGACT'3, and reverse 5' TGGCAGCCATATGGAGTTGG'3. For qPCR, 200 nM primer (TaqCopenhage) and SybGreen (Bio-Rad) on the CFX96 Touch™ Real-Time PCR Detection System (Bio-Rad) was used. Normalized gene expression was calculated using the CFX manager software (Bio-Rad). Enrichment was validated by qPCR with primers specific for the KIT gene including sequences in its promoter, as well as a gene upstream (PDGFRα) and downstream (KDR) of KIT.
ACKNOWLEDGMENTS This work was supported by the  Swedish Cancer Society , The  Swedish Research Council-Medicine and Health ,  The Cancer and Allergy Foundation, Ollie and Elof Ericssons Foundation ,  Hans von Kantzows Foundation , the  Swedish Medical Society , the  Åke Wiberg Foundation ,  Marianne and Marcus Wallenberg Foundation ,  Stockholm Cancer Association , and the  Swedish Blood Cancer Association (Blodcancerfonden).
We reduced the duration to a maximum of 3 minutes, in contrast to previous studies  [26, 27] , to avoid difficulties holding older or heavier infants. A midstream urine sample was collected in a sterile container by the third person, a nurse. For illustrative purpose, a movie is available as electronic supplementary data attached to this paper (S1 File). Additional informed consent was obtained from the parents of the patient for whom identifying information is included in this article. Success was defined as the collection of a urine sample within 3 minutes (180 seconds) after starting the stimulation maneuvers. If the first attempt failed, the infant was fed with water, formula or breast milk. A sterile bag was placed onto the child to avoid losing urine samples. Thirty minutes later, both maneuvers were repeated for 3 minutes.
Acknowledgments The authors are grateful to  Fatima Yagoubi  for help in setting up the study procedures, to  Clara Fortier ,  Jonathan Desmontils ,  Diane Demonchy  and  Pauline Brouillon  for help in rigorously including patients according to the protocol, and to the  pediatric emergency unit staff for the implementation of the study procedure in our unit despite the intense and usual activity of a pediatric emergency unit.