dataesr/scientific-paragraphs-categorization huggingface dataset:
Identification of staphylococcal virulence factors among subjects-Each contig from the all-inclusive co-assembly was screened for the presence and expression of specific virulence factors produced by S. aureus and S. epidermidis that are vital for pathogenicity, specifically the following six genes: (1) Phenol-soluble modulin α (PSMα1: fMGIIAGIIKVIKSLIEQFTGK  (Williams et al. , 2019) (2) Staphopain A (scpA [GenBank: CAD61962. 1]) (3) Staphopain B (sspB [GenBank: AAG45844. 1]) (4) Extracellular cysteine protease (ecpA [GenBank: AJ298299]. Assembly ORFs were called on all contigs using FragGeneScan (version 1. 16), and read counts for each ORF across all samples were obtained by mapping reads to predicted ORFs using clc_ref_assemble_long in CLC Assembly Cell (CLC bio, version 3. 22. 55705) using the method as described in  (Dupont et al.
, 2015). These ORFs were also searched against PhyloDB (version 1. 076) using Blast (Evalue threshold < 1e-03) to establish phylogenetic annotation. Additionally, the ORFs were also searched against the Pfam and TIGRfam custom database using HMMER  (version 3. 0)  to establish functional annotation. For Pfam and TIGRFAM assignments, only matches with scores above the model trusted cut-off score were considered. Finally, all phylogenetic and functional annotation results were merged with the read counts for all ORFs across all samples. Quantification of live staphylococci and collection of isolates from skin swabs -For quantification of live staphylococci and collection of clinical isolates, swabs were rapidly thawed, vortexed, serial diluted and plated onto mannitol salt agar (MSA) selection plates supplemented with 3% egg yolk.
QUANTIFICATION AND STATISTICAL ANALYSIS All figures utilized non-parametric unpaired Kruskal Wallis analysis, Student's t tests, and One/Two-way ANOVAs for statistical analysis as indicated in the figure legends. All statistical analysis was performed using GraphPad Prism Version 8. 0 (GraphPad, La Jolla, CA). All data is presented as mean ± standard error of the mean (SEM) and a P value ≤ 0. 05 considered significant. Each dot represents a swab sample. Different numbers of swabs were collected for the different subjects depending on the number of visits they had during the time of the study. See also Figure  S4. (D) Pearson correlation between the trypsin activity induced in neonatal human epidermal keratinocytes (NHEKs) after culture for 24 h with 5% supernatant of clinical S. aureus (SA) isolates from NS skin and the relative abundance of psmα mRNA level in the same SA isolates.
Study population and follow-up. All liveborn singleton children born between 1st January 2011 and 31st December 2014 were eligible for inclusion. The mother had to be covered by the national health insurance general scheme for salaried workers (which represents 75% of the French population) and to have had at least one health expenditure reimbursement over the 2 years preceding the onset of pregnancy. We excluded children who could not be linked to their mother's data, those with missing data for sex, gestational age and birth weight and those with a diagnosis of brain malformation (ICD-10 codes Q00 to Q04 and Q05. 0 to Q05. 4) during their stay in the maternity unit. When the mother had several deliveries during the study period, only the first single liveborn child during the study period was included.
Strengths and limitations. This study, based on the largest cohort of children exposed to AEDs in utero, constitutes a major source of information on the risk of NDs associated with prenatal exposure to these drugs. Up until now, studies on this risk have generally been limited to a small number of drugs and much smaller sample sizes. Linking the mother and child data from the national SNDS databases allowed this study to be conducted on a large unselected population, for which exposure to AEDs was measured without memory bias, in contrast with previous studies generally based on retrospective exposure data derived from registries. The data available in the SNDS also allowed the analysis of various indicators of NDs based on diagnoses or health care utilization. Finally, the available information allowed to account for differences in terms of sociodemographic characteristics, maternal health status and neonatal characteristics according to exposure to the various AEDs considered.
, 2009). Using DMS values as guides for structure modeling, we reconstructed two alternative conformations for this 5 0 UTR: at 26 C, the structure adopted an ''open'' conformation, where the SD sequence was available for ribosome binding, whereas at 37 C, the 5 0 UTR rearranged to a ''closed'' conformation See also Figure  S2  and Table  S3. Cell Reports 30, 4027-4040, March 24, 2020 4029 (legend continued on next page) with the SD sequence hidden in an RNA hairpin  (Figures 3A and S3A). This was especially evident after a transient shift from 26 C to 37 C. To study the putative effect of the rearrangement on translation, we introduced mutations in the cspA 5   3D ). These data were further verified by performing DMS-MaPseq of in-vitro-synthesized cspA 5 0 UTR that was denatured and refolded at 26 C or 37 C.
See also Figure  S5  and Table  S5. that the trans-acting sRNA RoxS is able to bind and prevent degradation of the yflS mRNA, by binding at its extreme 5 0 end  (Durand et al. , 2017). With this in mind, we performed a whole-genome search for sequences complementary to the identified DMS footprint using the CopraRNA software (Table  S5 ;  Wright et al. , 2014). Unexpectedly, the best match was in the 3 0 UTR of the hly (lmo0202) mRNA, encoding LLO. Expression of the hly gene is directly regulated by PrfA and is much higher in the prfA* strain than in the WT strain  (Figures S5A and S5B; Ripio et al. , 1997). Our data thus suggested a base-pairing interaction between the 5 0 UTR of prsA2, encoding the chaperone, and the 3 0 UTR of hly mRNA, encoding its substrate. To validate this interaction, we introduced complementary base substitutions in the chromosome corresponding to the proposed site of interaction between the prsA2 5 0 UTR (M1) and the hly 3 0 UTR (M2) (Figure  4A ).
, 2009). Hence our data strongly indicate that the full-length hly mRNA acts in trans by a direct interaction with the prsA2 mRNA. hly Protects prsA2 mRNA from RNaseJ1-Mediated Degradation In contrast with the LhrA-lmo0850 interaction (Figure  3E ), we did not observe increased DMS protection of the prsA2 SD sequence upon interaction with hly, indicating that the hly-prsA2 interaction does not affect ribosome binding (Figure  4A ). Furthermore, abolition of the interaction between the prsA2 and hly mRNAs decreased the quantities of both prsA2 mRNA and PrsA2 protein equally, suggesting that the hly-prsA2 interaction might instead affect the stability of the prsA2 mRNA (Figures  4B  and 4C ). To examine this, we measured prsA2 mRNA stability following addition of rifampicin to prevent new transcription initiation.
monocytogenes virulence. Mice were infected by tail vein injection with 2 3 10 4 colony-forming units (CFUs) of the indicated strain. At 72 h post-infection, livers and spleens were harvested, homogenized, and plated for bacterial burdens. Boxplots are shown where each dot represents one mouse. Data were obtained from eight animals. An asterisk (green) indicates statistical significance estimated by two-tailed Wilcoxon rank-sum test when M1 and M2 strains were compared with WT or M1+M2 strains (*p < 0. 05, **p < 0. 01, ***p < 0. 001). ŧ (light blue) indicates that one mouse succumbed to infection prior to 72 h for WT strain. (D) The interaction site between prsA2 and hly mRNAs is conserved in all Listeria species carrying the hly gene (L. monocytogenes, L. ivanovii, and L. seeligeri, respectively).
Although we did not comprehensively assess the performance of our 5 0 UTR enrichment strategy, it allowed us to discover functional elements by sequencing DMS-MaPseq libraries of moderate size (z10 million sequencing reads). Because lmo0850 and prsA2 are expressed only at low levels, the 5 0 UTR enrichment was necessary to observe differences in DMS reactivity between different conditions. Larger libraries would increase the depth and might aid in the identification of more complex regulatory events. Also, the datasets obtained by FUSE in different conditions stems from few replicates. Despite this, we were able to confirm the discoveries made by FUSE using other methods. In summary, we have identified RNA regulatory interactions through the targeted structural analyses of L. monocytogenes 5 0 UTRs in vitro and in vivo.
Analysis of DMS-MaPseq and FUSE data The sequencing reads were mapped to Listeria monocytogenes EGD-e genome (NC_003210) with Bowtie 2 aligner using the -endto-end-very-sensitive mode  (Langmead and Salzberg, 2012). The coordinates of mismatches were extracted from the CIGAR string of the SAM files. The coordinates of transcriptional start sites were obtained from  Wurtzel et al. (2012)  and verified using our data. Genome regions corresponding to non-coding RNAs, 5ʹ UTRs and the first 30 nucleotides of coding sequences were selected for further analysis. For each adenine and cytosine nucleotide position of these regions, the coverage was calculated as the number of reads mapped at that position. The mismatch rate (MR) of position i in sample j was calculated as the ratio between the number of mismatches (mis) and coverage (cvg) at that position: MR ij = mis ij cvg ij Our DMS treatment conditions resulted in the average mismatch rates for adenine and cytosine nucleotides ranging from 3 to 6% in different samples.
The calculated p-values were adjusted for multiple comparisons  (Benjamini and Hochberg, 1995) , and positions with the adjusted p-values < 0. 05 were selected for further analysis. Among the statistically significant differences only the differences with a high effect size were regarded as significant. The effect size criterion demanded that the relative difference between the samples' DMS values should be larger than 20% and that the absolute difference between the values should be larger than 0. 1. The results of the performed comparisons are represented in Table  S4. To discover structural rearrangements, we manually searched for the regions where nucleotides with pronounced changes of DMS reactivity were located close to each other. Data manipulation was performed with custom Python scripts using HTSeq framework  (Anders et al.
coli. (PDB: 1HQ1) (Batey et al. , 2001). The evolutionarily conserved nucleotides are colored according to the differences of DMS values between in vivo and in vitro samples. Intensive red color indicates nucleotides with strongly decreased DMS values in vivo. (C) The SD sequences are protected by ribosomes in vivo. The average DMS values in the vicinity of the start codon are shown in vitro (blue line) and in vivo (red line). Because the start codons always have a U at the second and a G at the third position, DMS values cannot be calculated for these positions. The distribution of SD sequence locations is plotted as a green line. See also Figure S2 and TableS3.
001). (C) The abolishment of the interaction between prsA2 and hly mRNAs attenuates L. monocytogenes virulence. Mice were infected by tail vein injection with 2 3 10 4 colony-forming units (CFUs) of the indicated strain. At 72 h post-infection, livers and spleens were harvested, homogenized, and plated for bacterial burdens. Boxplots are shown where each dot represents one mouse. Data were obtained from eight animals. An asterisk (green) indicates statistical significance estimated by two-tailed Wilcoxon rank-sum test when M1 and M2 strains were compared with WT or M1+M2 strains (*p < 0. 05, **p < 0. 01, ***p < 0. 001). ŧ (light blue) indicates that one mouse succumbed to infection prior to 72 h for WT strain. (D) The interaction site between prsA2 and hly mRNAs is conserved in all Listeria species carrying the hly gene (L.
ACKNOWLEDGMENTS J. J. was supported by  Umea ˚University, Swedish Research Council  grant  2016-03313 , the  K. A. Wallenberg Foundation , the  Wenner-Gren Foundations, Stiftelsen Olle Engkvist Byggma ¨stare , and  ERC  starting grant  260764-RNAntibiotics. D. I. was supported by the  UCMR postdoctoral program. S. D. and C. C. are supported by funds from the  CNRS and Universite de Paris  to  UMR 8261 , the  Agence Nationale de la Recherche (ARNr-QC and BaRR) , and the  Labex (Dynamo) program (France). L. C. and N. F. were supported by  NIH  grants  R01 AI083241  and  AI083241-03S1  to  NEF (United States ). We are grateful to  Drs. A. Le Rhun ,  L. Broglia , and  A. Escalera  for critical reading of the manuscript and to  Prof. F. Narberhaus  ( Ruhr University Bochum ) for sharing the pBAD2-bgaB plasmid.
DATA AND CODE AVAILABILITY All sequencing data are deposited in NCBI's Gene Expression Omnibus  (Barrett et al. , 2013). The accession number for the sequencing data reported in this paper is GEO: GSE118387 (https://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE118387). The scripts are deposited at GitHub under the project name 5ʹ-UTR-structure-elucidation' (https://github. com/dimaignatov/ 5-UTR-structure-elucidation).
5S RNA in E. coli. (PDB: 1HQ1) (Batey et al. , 2001). The evolutionarily conserved nucleotides are colored according to the differences of DMS values between in vivo and in vitro samples. Intensive red color indicates nucleotides with strongly decreased DMS values in vivo. (C) The SD sequences are protected by ribosomes in vivo. The average DMS values in the vicinity of the start codon are shown in vitro (blue line) and in vivo (red line). Because the start codons always have a U at the second and a G at the third position, DMS values cannot be calculated for these positions. The distribution of SD sequence locations is plotted as a green line. See also Figure S2 and TableS3.
Introduction Since decades, nanoparticulate forms are developed to overcome the limitations of drugs by decreasing their intrinsic toxicities and/or by improving their efficacy. Therefore, many nanoparticles were preclinically tested and showed promising results on various therapeutic areas with an unmet medical need such as oncology, orphan diseases, infectiology, etc. However, almost all failed to be transposed in clinical trials due to an overestimated efficacy, an unfavourable toxicological profile or difficulties concerning the scalability of the manufacturing process. [7] [8] [9] [10]  SRP is currently implicated in two Phase II clinical trials on brain metastases (NANO-RAD2, NCT03818386 and NANO-STEREO: NCT04094077) and one phase Ib clinical trial on advanced cervical cancer (NANO-COL, NCT03308604).
Then, the T 1 value was used to estimate the concentration, C (mM), of Gd 3+ ion in the lungs as follows: 37 C ¼ 1 r 1 1 T 1post À 1 T 1pre � � where T1 pre and T1 post are the longitudinal relaxation times before and after nebulisation of the tracer and r 1 is the longitudinal relaxivity induced by gadolinium ion. The measurements of SNR values in the region of interest (ROI) and the generation of maximum intensity of projection (MIP) were performed using OsiriX (Geneva, Switzerland). The computing of T 1 values was realized using open-source SciLab software (ESI, Paris, France). Further information is provided in the Supplementary Information. Lastly, samples of lung parenchyma (two pieces of 1. 5 g each per lobe for each tracer) were used to quantify gadolinium concentration using ICP-MS (NexIon 2000, PerkinElmer, Wellesley, MA, USA).
Statistical Analyses Statistical analyses were performed using GraphPad Prism 8 (GraphPad Software Inc. , San Diego, CA, USA). For the aerosol size and output determination, a one-way ANOVA with Tukey's post hoc multiple comparison test was performed. For the quantitative assessment of regional radioaerosol deposition in the ex vivo model, a two-way ANOVA with Sidak's post hoc multiple comparison test was used. For MRI quantitative assessment, multiple t-tests were used and p-values were adjusted with Holm-Sidak's method. For all tests, significance was fixed at 5%. The data are presented as mean value ± standard deviation (SD).
Funding The aerosol size and output determination and the scintigraphic assessment of the regional aerosol deposition were funded by the  French Agency for Research  [ ANR-17-CE19-0002-01 ]. The MRI studies were carried out within the  IBIO (Institut de Bio-Imagerie de Bordeaux ) and were achieved within the context of the  Laboratory of Excellence TRAIL   ANR-10-LABX-57. NH TherAGuIX ® supported the cost of radionuclides for the radiolabelling of the AGuIX ® nanoparticles with 111In.
Distribution of RAG1L-RAG2L gene pairs across phyla To search for additional RAGL transposons in disparate phyla, RAG1L and RAG2L amino acid sequences from invertebrate deuterostomes  [9, 17, 19]  were used to scan recently updated databases including Whole-Genome Shotgun Contigs (WGS), High Throughput Genomic Sequences (HTGS) and Transcriptomic Shotgun Assembly (TSA). Scans were performed on all metazoan invertebrate and jawless vertebrate projects available before February 2019. RAG1L proteins, possibly because of their direct role in catalysis, exhibit greater evolutionary conservation than RAG2L proteins, and detecting evolutionarily-distant RAG2L homologues using existing genome-wide blast techniques is challenging. For example, using tblastn  [24, 25]  and mouse or human RAG2 as query does not detect RAG2L from amphioxus WGS data (data not shown), and standard blast searches failed to identify RAG2L sequences in the purple sea urchin genome  [17].
Overall, the RAG1L phylogeny corresponds to the consensus species phylogeny (Fig. 3 ) except for some RAG1L sequences from the pearl oyster P. imbricata. The findings suggest that a duplication occurred in the Bivalvia clade, which led to the RAGL_B_Bivalvia1 and RAGL_B_Bivalvia2 subfamilies (Additional file 3: Figure  S3c ). Based on the RAG1L family tree, two distinct RAGL families were found in N. geniculatus, RAGL_B and RAGL_D (Figs. 1c, 2b ). Interpretation of our findings (see Discussion) is limited by the availability of data in the databases (Fig. 3  and Additional file 6: Table  S1 ). For example, we cannot be confident about the absence of RAGL sequences in some groups, as the number of sequenced species is not homogenous among clades.
Protostomes encode intact and potentially functional RAG1L and RAG2L proteins The ProtoRAG-encoded BbeRAG1L-BbeRAG2L proteins from the cephalochordate amphioxus together constitute an active endonuclease/transposase in vitro and in vivo Phylogenetic trees were built using the Maximum Likelihood as described in Methods using MEGA X  [27]  and WAG with Freqs. (+) correction model  [28]. The bootstrap numbers next to branches are the percentage of branches in which the associated proteins clustered together. Branches with a bootstrap value below 50% were collapsed together. Branch lengths represent the number of substitutions per site, with positions with gaps or missing data being ignored. The protein sequences used for these analyses were chosen as representative of the monophyletic group to which they belong.
Bold indicates proteins from protostomes and contain domains corresponding to all of the functionally essential "core" subdomains of jawed vertebrate RAG1 and RAG2 (Fig. 4 )  [19, 22]. These core subdomains are: the nonamer binding domain (NBD), the dimerization and DNA binding domain (DDBD), the Pre-RNase H domain (PreR), the catalytic RNase H domain (RNH), two zinc binding domains (ZnC2 and ZnH2) that together coordinate a zinc ion, and the Cterminal Domain (CTD) (Fig. 4 ). The RAG1 C-terminal tail (CTT) is not required for catalytic activity  [4] , while Fig. 3  Bilaterian evolutionary tree and RAG evolutionary history. Tree was built with species for which there are at least one WGS and/or TSA project in the NCBI database. The species in which there are no RAG-like sequences found were regrouped into larger groups (Xenacoelomorpha, Platyhelminthes, Nematoda, Tardigrada, Arthropoda phyla), and the Gnathostome species were grouped as well, as RAG is domesticated in all of these species.
Analysis of protein-DNA and protein-protein interaction surfaces The availability of RAG1L-RAG2L sequences from protostomes provided an opportunity for a broad Fig. 5  Alignment of RAG1L sequences from protostomes and deuterostomes. RAG1L sequences from 3 deuterostomes (the cephalochordate amphioxus (Bbe), echinoderm purple sea urchin (Spu), and hemichordate P. flava (Pfl)), 2 mollusk RAGL_B subfamilies (eastern oyster (Cvi) and pearly oyster (Pim)), and a nemertean N. geniculatus RAGL_D family representative (Nge) were aligned to mouse (Mmu) RAG1. Domains, sequence motifs, secondary structure assignment (helices -wavy lines; beta sheet -arrows, other -straight line), protein-protein and protein-DNA contact interactions (within 5 Å) displayed above the alignment derive from the BbeRAG1L cryo-EM structure (PDB: 6B40).
Acidic catalytic residues, red; active site residue mouse H795, purple; zinc coordinating residues within ZDD (*) and ZnC2 and ZnH2 (#) are indicated above the sequences. Locations at which coding sequences span exon boundaries are underlined. Amino acid color code: hydrophobic aliphatic, yellow; hydrophobic aromatic, orange; positively charged, blue; negatively charged, red; neutral polar, light blue; glycine and prolines, grey; cysteine, purple; histidine, dark purple. Sequences displayed are BbeRAG1L_B (GenBank: KJ748699. 1), PflRAG1L_B (TSA:GDGM01438088. 1), SpuRAG1L_B_Ech1 (Uniprot: Q45ZT6), and CviRAG1L_B_Biv1_0007, PimRAG1L_B_Biv2_3145, and NgeRAG1L_D_2322 from this study (Additional file 7: Alignment S1a). evolutionary examination of the conservation of interaction surfaces in the complexes formed by these proteins with each other and with DNA.
Fig. 6  of RAG2L sequences from protostomes and deuterostomes. RAG2L sequences are aligned and displayed as in Fig. 5. Domains, beta sheet regions of each kelch-type blade, the GG motif, secondary structure (helixes -wavy lines; beta sheet -arrows, other -straight line), proteinprotein interactions (5 Å threshold) displayed above the alignment derive from the BbeRAG2L cryo-EM structure (PDB: 6B40). Sequences displayed are: BbeRAG2L_B (GenBank: KJ748699. 1), PflRAG2L_B (TSA:GDGM01438088. 1), SpuRAG2L_B_Ech1 (Uniprot: Q45ZT5) and CviRAG2L_B_Biv1_0007, PimRAG2L_B_Biv2_5135, and NgeRAG1L_D_2322 from this study (Additional file 7: Alignment S1b). These RAG2L proteins are the transposon pairs of the RAG1L sequences displayed in Fig. 5  except that PimRAG2L_B_Biv2_5135 was used instead of PimRAG2L_B_Biv2_3145 due to merge uncertainties in the 3145 sequence; these two sequences are 98% identical on their counterpart RAG1L core.
Potentially active RAGL transposons in protostomes Numerous findings described here support the conclusion that the RAGL transposon is present in the genomes of protostomes and has been active during protostome evolution: 1) Multiple elements with sequence similarity to known RAG1/RAG1L and RAG2/ RAG2L genes of deuterostomes are present in protostome sequence databases; 2) protostome RAG1L and RAG2L genes often lie in close proximity in convergent transcriptional orientation; 3) many of these RAG1L-RAG2L gene pairs are flanked by TIRs and TSDs; 4) the TIRs resemble the sequence of the RSS heptamer and TIRs of deuterostome RAGL transposons; 5) protostome RAGL transposon TSDs are five bp in length; 6) predicted protostome RAG1L and RAG2L proteins often contain critical active site and structurally important amino acid residues and all of the domains required for activity by RAG or BbeR-AGL; 7) conservation in protostome RAGL proteins extends to include non-essential but important regulatory domains at the N-terminus of RAG1/RAG1L and the C-terminus of RAG2/RAG2L of deuterostomes; 8) two different families (RAGL_B and RAGL_D), several RAGL_B subfamilies, and multiple degenerate copies of RAG1L and RAG2L sequences are detected in the genomes of protostomes, arguing for instances of transposon movement followed by inactivation.