dataesr/scientific-paragraphs-categorization huggingface dataset:
Given the high identity between LE3 and LE4, we decided to further focus our analysis on LE4. Of the 81 ORF of LE4, only 31 (38%) had a predicted function assigned according to BLASTp, PFAM or COG (Table  1 ). Accordingly, the majority of genes encode for proteins of unknown functions. Following the genome annotations, it was apparent that the phage genomes displayed a modular organisation which is common for the majority of tailed bacteriophage genomes such as LE1  8. There are distinguishable gene modules whose products are predicted to be involved in DNA replication, structure/morphogenesis, and DNA packaging (Table  1 , Fig. 4 ). It was not possible to identify genes encoding integrase, capsid proteins, or proteins involved in the process of host cell lysis (holins and lysins), further confirming that the majority of the phages' genes remain uncharacterized.
Proteomic analysis of LE3 and LE4. To further characterize LE3 and LE4 and identify major structure proteins, we decided to perform bottom-up proteomics experiments on purified phages prepared in biological replicates. A homemade protein sequence database composed of (i) the 83 and 81 different putative protein sequences deduced from LE3 and LE4 genomics data; (ii) the L. biflexa Uniprot database (UP000001847, 3723 entries); and (iii) usual proteomics contaminants was used for the search. We processed 2 to 3 replicates per phage and analyzed all 5 samples. The liquid chromatography/tandem mass spectrometry (LC-MS/MS) analysis reproducibly detected 8 and 11 proteins in LE3 and LE4, respectively (Supplementary Table  1 ). All the proteins found in LE3 were also present in LE4 confirming that the two phages are closely related.
Alternatively, high-sensitivity LC-MS/MS may have lowered detection limits, making it possible to analyze not only structural proteins but also encapsidated enzymes. Taken together, our data show that, even if bacteriophages are hugely abundant and crucial for various ecosystems  23  , their genomic sequences are underrepresented in public databases, comparatively to bacteria. This is particularly true for leptophages. Search of LE4-like prophages in Leptospira genomes. The phages LE3 and LE4 revealed strong DNA sequence identity, whereas no homologies to previously-known phage sequences were uncovered-even at the protein level. Comparison of the sequences of known or putative phages and prophages in Leptospira genomes suggested their partition into three main groups: the LE1-like (similar to the circular plasmid Laicp  14  ), the Mu-like prophages  11  , and the LE4-like prophages.
The strain 200901116 consists of two circular chromosomes (3,815,263 bp in chromosome 1 and 307,019 bp in chromosome 2) and two circular plasmids of 94,000 bp (p1_L200901116) and 53,283 bp (p2_L200901116) exhibiting homologies to the LE1-like and LE4-like prophages, respectively. The LE4-like plasmid, p2_L200901116, has a GC content of 39. 9% and contains 86 predicted CDS, with 74 CDS on the sense strand. Phage-related encoded proteins include a bacteriophage resistance factor (PF05565 family), phage terminase large subunit GpA-like protein, phage tail protein, phage tail tape measure protein, phage late control protein D, and phage tail collar protein. Again, genes encoding capsid proteins or lytic enzymes were not identified (Supplementary Table  S2 ). At the protein level, 16 out of 86 predicted p2_L200901116 products are 49.
Concluding Remarks In summary, the present study suggests that Leptospira possess an unknown diversity of phages, of which most have no homologues with in public databases. LE3 and LE4 are genetically distinct from the temperate phage LE1. Leptospira genome sequencing revealed LE4-like prophages existing as circular plasmids in the pathogens L. interrogans and L. mayottensis. We suggest that LE4 is the founder of a new group of phages, to which LE3, lcp3, and p2_L200901116 also belong. This study is also the first to demonstrate that LPS is a receptor for leptophages and suggests that LPS structure dictates host succeptibility. Prophages play an important role in the genetic evolution and diversification of bacteria, including the emergence of virulence  26, 27. Since prophages are ubiquitous in the genomes of pathogenic Leptospira strains  11  , it is likely that they have contributed to the adaptation of pathogens to their hosts.
Peptides were first eluted using a 3 to 22% gradient of solvent B for 112 min, then a 22 to 38% gradient of solvent B for 35 min and finally a 38 to 56% gradient of solvent B for 15 min all at 250 nL/min flow rate. The instrument method for the Q Exactive Plus was set up in the data dependent acquisition mode. After a survey scan in the Orbitrap (resolution 70,000), the 10 most intense precursor ions were selected for HCD fragmentation with a normalized collision energy set up to 27. Charge state screening was enabled, and precursors with unknown charge state or a charge state of 1 and >7 were excluded. Dynamic exclusion was enabled for 45 s. All data were searched using Andromeda with MaxQuant software  35  version 1. 5. 3. 8. Five amino acids were required as minimum peptide length and 1 unique peptide was required for protein identification.
Genome sequencing. Phages purified by a caesium chloride gradient were dialysed in Leptospira Medium Base EMJH (dialysis cassette 2000 MWCO, Thermo Fisher). Phage solutions were treated with DNase and RNase, and EDTA was used to terminate the reactions. Phage DNA was then extracted using the QIamp Minelute virus spin kit (Qiagen) and amplified with Repli-g mini kit (Qiagen). For whole genome sequencing of L. biflexa Patoc strains, DNA was extracted using a MagNA Pure 96 Instrument. Next-generation sequencing was performed by the Mutualized Platform for Microbiology (P2M) at Institut Pasteur, using the Nextera XT DNA Library Preparation kit (Illumina), the NextSeq 500 sequencing systems (Illumina), and the CLC Genomics Workbench 9 software (Qiagen) for analysis. Genomic DNA of L. mayottensis strain 200901116 was extracted with the Genomic tip 100 g kit (Qiagen) from a 35 ml culture according to manufacturer protocols and the complete genome sequence was obtained using SMRT (Pacific Biosciences) technology.
PacBio sequencing was performed at the Génome Québec Innovation Centre (McGill University, Montreal, Canada) using a Pacific BioScience RS II system. The sequencing reads were de novo assembled using HGAP  36  through SMRT Analysis. Bioinformatics analysis. Genome annotation was performed with the MaGe interface (https://www. genoscope. cns. fr/agc/mage)  37. LE3 and LE4 sequences are available in this interface. Similarity searches were performed using BLASTp  38  (with a BLASTp e-value of 1 × 10 -3 as a cut-off) and conserved domains. ORF denomination in Table  1  and Supplementary Table  S1  correspond to MaGe nomenclature. We compared the Single-nucleotide polymorphisms (SNPs) of mutant RLE4 against the wild-type parental strain. Sequence reads were aligned with the annotated L. biflexa serovar Patoc strain Paris I genome (accession numbers CP000786, CP000787 and CP000788  39  ) by using the Burrows-Wheeler Alignment tool (BWA mem 0.
5. Since some (pro)phages do not share 10 ORF, the average similarities values were multiplied by (n/10), where n is the number of shared ORF. The resulting square matrix was clustered using heatmap. 2 from the statistical package R  44. The map of LE4 and the tblastx results presented in Fig. 6  were visualized using circleator version 1. 0. 0  45. Nucleotide sequence accession number. The LE1 bacteriophage genome accession number is BX571876. The nucleotide sequences of LE3 and LE4 bacteriophages have been deposited in the GenBank database as accession numbers MF974396 and MF974397, respectively. The sequence of Leptospira mayottensis strain 200901116 was deposited in GenBank under the accession number CP024871 (chromosome I), CP024872 (chromosome II), CP024873 (plasmid p1_200901116), and MF974398 (plasmid p2_200901116).
Acknowledgements This work is part of a PhD thesis of O. S. who received financial support from " Université Paris Diderot " and " Sorbonne Paris Cité ". We thank  Olivier Gorgette  ( Ultrapole, Institut Pasteur ) and  Soizick Lucas Staat (BMGE Unit, Institut Pasteur)  for assistance in electron microscopy and phage purification, respectively. We thank  Nathalie Armatys  for technical support in control experiments. We thank  Isabelle Saint Girons  who layed the foundation for this work at the  Institut Pasteur , and  Robert Gaultney  for proofreading the manuscript.
Bo et al. (53)  conducted a meta-analysis on GM-CSF and G-CSF treatment for sepsis. Among 12 RCT identified, only four were GM-CSF-related studies (n = 147 patients). Mortality was consistently found to be unchanged. A multicenter prospective randomized controlled trial is now ongoing in France (NCT02361528). Use of GM-CSF in sepsis studies is characterized by a small number of patients and high heterogeneity of diagnosis and clinical presentation. To date, results of clinical trials show no benefit of GM-CSF treatment during sepsis. At least, there are no major adverse events observed after nearly 20 years of clinical use. It is insufficient to conclude in a lack of safety threat but still there is no big signal of risk and there are potential benefits. There is no definitive answer to the appropriateness of GM-CSF as an immunotherapy for certain subgroups of septic patients.
Mortality does not differ between groups but the rate of liver dysfunction and elevation of troponin raises in the G-CSF group. Thus, G-CSF appears not only to be non-beneficial but detrimental in septic patients. These results point out the risk of increasing inflammation without precise guidance. In the meta-analysis of the impact of G-CSF during sepsis conducted by Bo et al. (53) , G-CSF appears to have overall no effects on mortality and is not associated with a significant rate of adverse events. One trial is ongoing (NCT01913938) evaluating the impact of G-CSF treatment on septic patients with cytopenia with a special interest on the occurrence of hemophagocytosis. The limits of the described trials are nearly the same for G-CSF than for GM-CSF. The main difference is that GM-CSF is a better candidate to the reversal of various features of SIS, while G-CSF is only effective on neutrophils.
Soluble IL-7R (sIL-7R or sCD127) levels are higher in non-surviving septic shock patients  (103). Venet et al. demonstrated the potential of IL-7 to treat T-cell exhaustion during sepsis  (104). In this study, IL-7 levels are augmented in septic shock patients, while it is not correlated to survival or ICU acquired secondary infections. sCD127 levels are, there again, correlated with survival but also with nosocomial infections. IL-7 is highly efficient to promote stimulated T-cell proliferation and IFNγ production. The first "proof of concept" clinical trials on IL-7 during sepsis are conducted in USA and Europe. The two studies are twins as they share the same design. The results are much awaited to evaluate IL-7 potential as a future tool for sepsis immunotherapy (IRIS-7-A and B trials, NCT02797431 and NCT02640807).
EPO at low dose are detrimental in endotoxinic shock  (116). This may be related to dose related response to EPO and variable sensitivity of the target cells. Erythropoietin impedes lymphoid cell apoptosis after CLP without major effect on mortality in rats  (117). The effects of EPO treatment on critical illness-associated anemia and especially sepsis-associated anemia are debated. Two major clinical studies show conflicting results  (118, 119)  and a recent meta-analysis concludes that the effect on anemia is small  (120). Pearl discusses the negative results of EPO in trials and suggests that the doses are insufficient  (121). However, when used in brain injury patients, EPO is associated with increased thrombo-embolic events (122) that could counterbalance any beneficial effects. One clinical trial is ongoing to test the effect of EPO on microcirculatory alterations (NCT1087450) during sepsis (Table  1 ).
Number of patients with absolute lymphocyte controlled double lymphopenia (below recombinant Interleukin-7 counts increased by more than 50% from blinded prospective 900 lymphocytes/ (CYT107) (10 µg/kg once or baseline at Day 42 trial mm3) twice a week for 4 weeks) 2. Kinetic of immune restoration through weekly measures of Absolute Lymphocyte Counts NCT02640807 30 Randomized Septic patients with Two dosing frequencies of 1. Number of patients with absolute lymphocyte controlled double lymphopenia (below recombinant Interleukin-7 counts increased by more than 50% from blinded prospective 900 lymphocytes/ (CYT107) (10 µg/kg once or baseline at Day 42 trial mm3) twice a week for 4 weeks) 2. Kinetic of immune restoration through weekly measures of Absolute Lymphocyte Counts NCT1087450 29 Two phases: Septic patients Phase 1: 3 subjects per dose Changes in sub-lingual micro-circulatory blood 1.
Data analysis For each session, one operator blindly prepared the blood samples, performed the tests, and read the results. Another operator performed a second blind read to maintain objectivity. A third operator was solicited for consensus if the results were discordant  [35]. Readings were performed according to the time defined by the manufacturer, which generally called for an early and late reading. Specificity, sensitivity, and their corresponding exact binomial 95% confidence interval were estimated using standard methods. Data analysis was performed using Excel and Vassarstats (www. vassarstats. net; 2018).
Specificity of the results Results for the specificity obtained for the 200 negative samples are presented in Table  4. For two samples, only one of the three operators observed a very weak signal (with HIVTOP) that was therefore concluded to be negative. The overall specificity ranged from 98. 5 to 100%. EXACTO PRO TEST HIV, HIVTOP, and VIKIA HIV 1/2 had the lowest specificities (98•5%, 99•0%, and 99•5%, respectively), as well as Alere HIV Combo (99•5%), due to reactivity on the antigen line for one sample. Complementary analyses -plasma viral load (Abbott) and p24Ag (Vidas, bioMerieux) -were all negative, excluding a true positive p24Ag result for the latter sample (data not shown). All false reactivities were verified and the samples were still reactive upon two retests.
We cannot exclude that failures in antibody detection may occur on rare occasions in patients with undetectable plasma viral load for years; however, this may not represent an important public health issue, because such individuals do not correspond to those targeted by these tests. We report a frequent failure to diagnose patients infected with divergent variants. For HIV-2, the BioTechMed web test detected only 54% of mono-infections. Another challenge for rapid tests is to discriminate between HIV-1 and HIV-2 infections, as confirmed here using HIVTOP and BioTechMed. Although this point has been previously reported  [24, 41] , such tests are still largely used in diagnosis and typing algorithms  [42, 43]. Previous data and those here highlight the need of manufacturers to improve these tests and that type-specific molecular tools are the only way to accurately diagnose a mono-or dual infection.
Ligated cDNAs were amplified following 15 cycles PCR and PCR products were purified using AMPure XP Beads  (Beckman Coulter Genomics, ref. A63881). The quantitative and qualitative analysis of the library was carried on Agilent_DNA 1000 chip and qPCR (Applied Biosystems 7500, SYBR Green). The sequencing was performed on a HiSeq2500 in paired-end 2x125nt mode. RNA-Seq reads are available at the NCBI-SRA under the BioProject accession number PRJNA378178.
Quality Control Quality control and initial cleaning of the reads was performed with the filter by quality program (version 1. 0. 0) based on FASTX-toolkit  (Blankenberg et al. 2010). Reads with less than 90% of bases with Phred quality score inferior or equal to 30 were discarded (probability of 1 incorrect base call out of 1,000, and a base call accuracy of 99, 9%). Adaptors used for sequencing were removed using the cutadapt program version 1. 6  (Martin 2011).
Mapping of the Reads against the Reference Genome Each sample's paired-end sequencing reads were independently mapped (i. e. , unique reads) to the S. mansoni's reference genome version 5. 2  (Berriman et al. 2009; Protasio et al. 2012 ) using TopHat2 software  (Kim et al. 2013). The alignment was performed in single reads with intron length parameter set between 20 and 50,00 bp. We authorized one mismatch in the anchor region of spliced alignment, applied a microexon search because of the presence of microexon genes in schistosome genomes  (DeMarco et al. 2010) , and used the very sensitive Bowtie2 option  (Langmead et al. 2009 ). The GTF annotation file (S. mansoni sex-specific transcriptome) produced in a previous work  (Picard et al. 2016 ) served as the reference (http://ihpe. univ-perp.
SNPs Calling in the Transcriptomic Data Using SAMtools  (Li et al. 2009) , we produced mpileup files with read coverage information and call quality from the TopHat2 alignment BAM files. We then performed SNPs calling by using VarScan software (version 0. 1) on the mpileup files  (Koboldt et al. 2012). The minimum depth at position to make a call was set to ten reads, the minimum supporting reads for alternative allele at position were set to two. The minimum base quality to count a read was set to 15, minimum variant allele frequency threshold was set to 1%, and the p-value threshold for calling variants was set to 5%. The number of reads, the number of variant allele, and the alternative base identity were visually checked for ten randomly selected SNPs in each sample with the Integrative Genomics Viewer (IGV) software  (Thorvaldsd ottir et al.
Annotation of the Transcriptome The transcriptome file (extracted from the GTF reference  [Picard et al. 2016] ) was de novo reannotated on the local server of the laboratory by searching protein databases using a translated nucleotide query (BlastX) against the nonredundant protein sequence database (nr). The 25 best hits were then used to search for gene ontology terms using the Blast2Go program  (Conesa et al. 2005). Correspondence between transcript and current version of genome annotation was manually checked using IGV software  (Thorvaldsd ottir et al. 2013).
Quantitative PCR Validation of Z-Specific Scaffolds Simple or double copy of genomic DNA was assessed with male (ZZ) and female (ZW) DNA extracted from adult worms to verify the Z-specific status of unplaced scaffolds containing genes with monoallelic paternal expression. DNA of single adult worms of each sex was extracted as recommended from the QIAGEN QIAamp DNA Micro Kit protocol for isolation of genomic DNA from tissues. Final elution was performed using 40 ml of buffer AE (10 mM TrisÁCl, 0. 5 mM ethylenediaminetetraacetic acid, pH 9. 0). Primers were designed using the online Primer3plus program  (Rozen and Skaletsky 2000)  and aligning the primers against S. mansoni's reference genome v5. 2 to verify for high specificity. We used a known Zspecific (double copy in ZZ males and single in ZW females) and an autosomal (double copy in each sex) genomic region as internal control.
Acknowledgments We would like to thank  Anne Rognon  and  Nathalie Arancibia  for rodent and snail maintenance, and  Jean-Francois Allienne  for technical assistance. We also acknowledge the contribution of the MGX-Montpellier GenomiX sequencing platform. This work was funded by the region  Languedoc Roussillon  ( Chercheur d'avenir Schistosex , recipient: JB).
Combination of Rapalogs With the Histone Deacetylase (HDAC) Inhibitors The FDA-approved HDAC inhibitors, panobinostat (LBH589) and vorostinat have been shown to prevent Akt signaling through mTORC2 in several cancer cell lines including DLBCL  (148). As expected, DLBCL cell lines co-treated with rapamycin and the panobinostat (LBH589), display a synergistically inhibited phosphorylation of p70S6K and 4E-BP1 accompanied by an impaired cell survival  (148). Temsirolimus or Everolimus also synergizes with vorostinat, in the treatment of MCL cell lines  (121, 149). A phase I trial confirmed the effectiveness of this combination in a variety of refractory/relapse lymphomas, but with a cost of significant toxicity  (150). A phase 2 study evaluating Everolimus and LBH589 in the treatment of refractory/relapsed DLBCL was aborted for toxicity reasons (NCT00978432).
A phase 2 study combining Temsirolimus, Rituximab and high doses of cytarabin-based chemotherapy (DHAP), is currently ongoing in refractory/relapsed DLBCL [NCT01653067,  (151) ]. Not only purine and pyrimidine but also folic acid is necessary for the production of nucleotides. Methotrexate binds and inactivates an enzyme of folic acid metabolism, the dihydroxyfolate reductase (DHFR). This causes a decrease in DNA and RNA synthesis. Methotrexane is clinically used to prevent central nervous system relapse in patients with DLBCL. The combination of mTOR inhibitors and methotrexane were tested in acute lymphoblastic leukemia where it was synergistically effective  (152). Administration of Temsirolimus and methotrexane leads to an increase OS and durable remission in immunocompetent mice xenografted with human AML patient samples  (152).
In the clinic, indirect proof-ofconcept of Metformin efficacy in DLBCL is demonstrated by a significant increase in PFS and CR of diabetic DLBCL patients on metformin compared to non-diabetic DLBCL patients  (166). Phase 1 and phase 2 studies combining a rapalog and Metformin are currently ongoing in the treatment of several advanced solid cancers (NCT02048384; NCT01797523; NCT01529593), including lymphomas (NCT00659568). Upon inhibition of glycolysis, mTORC1 sustains cell viability by reprogramming metabolism toward glutaminolysis and OxPhos metabolism. Inhibition of mTORC1 signaling decreases cellular respiration of glycolysis-independent cells. Co-targeting glycolysis and mTORC1 thus prevents metabolic escape and synergistically inhibits xenograft tumor progression  (167). Although LDH-A represented a promising target for anti-cancer therapy  (168, 169) , none of the LDH-A inhibitors progressed in the clinic.
Severe adverse events associated with L-asparaginase reduced its clinical utilization in adults. Nevertheless, phase 2 studies evaluating L-asparaginase are currently ongoing for the treatment of multiple adult NH B-cell lymphomas and adult leukemias (NCT00018954 and NCT00002471). In vitro co-targeting of extracellular glutamine/asparagine and mTORC1 has, at least, additive effect, resulting in a stronger reduction of ALL cell lines viability  (152). A phase 1 study is ongoing to evaluate the feasibility of combining Everolimus with chemotherapeutic agents including PEG(pegylated)-asparaginase in patients with ALL (NCT01523977). Similarly, L-arginase hydrolyses arginine and might further prevent mTORC1 activation in combination with rapalogs. It is worth mentioning that recombinant human arginase is under clinical evaluation in solid cancers (hepatocellular carcinomas, NCT00988195; liver cancers, NCT NCT00988195; melanoma and prostate adenocarcinomas, NCT02295101), in pediatric solid tumors, AML and ALL (NCT03455140) and in adult refractory/relapsed AML (NCT02899286).
CB-839 is currently tested in a phase 1 trial in advanced and/or treatment refractory hematologic malignancies including NH lymphomas (NCT02071888) and is evaluating in combination with Everolimus in a phase 2 study in clear cell renal cell carcinomas (NCT 03163667). It is important to note that therapeutic strategies combining rapalogs with anti-metabolic drugs hold potential as effective therapies only if we can better characterize the tumor metabolic state to address the best-adequate combination.