dataesr/scientific-paragraphs-categorization huggingface dataset:
Data recorded by IMS-MS suggested that P. tricornutum proteins carry a unique canonical Man-5 isomer. For confirmation, the structure of P. tricornutum Man-5 isomer was further investigated by ESI-MS n with n = 2, n = 3 and n = 4. ESI-MS n of the doubly charged [M+2Na] 2+ ion of permethylated 2AB Man-5 (m/z 882. 5) from P. tricornutum revealed a fragmentation pattern m/z 882. 5 → m/z 1302. 8 → m/z 1084. 7 → m/z 866. 6 → m/z 648. 5 that is consistent with the canonical isomer of permethylated 2AB Man-5 (Fig. 2 ). Similar pattern of fragmentation was observed for [M+2Na] 2+ precursor ion of permethylated 2AB Man-5 obtained from bovine ribonuclease B (Supplemental Fig. 3 ) and differed from the ESI-MS n fragmentation pattern of the permethylated 2AB Man-5 obtained from C. reinhardtii proteins  (Vanier et al.
Analysis by IMS-MS of P. tricornutum oligomannosides The structural analysis of P. tricornutum oligomannosides was extended to the other oligomannosides going from Man-6 to Man-9. Analysis of the whole diatom N-glycan population was investigated by IMS-MS taking advantage of data recorded for Man-6 to Man-9 oligomannosides isolated from bovine ribonuclease B for which structures of each isomer have been already reported. Indeed, bovine ribonuclease B is N-glycosylated by unique isomers of Man-5, Man-6 and Man-9 respectively, whereas different positional isomers of Man-7 and Man-8 have been structurally characterized by proton NMR  (Fu et al. , 1994) , mass spectrometry coupled to liquid chromatography  (Costello, Contado-Miller, & Cipollo, 2007)  and ESI-MS n  (Prien et al. , 2009)  (Supplemental Fig.
Acknowledgements The authors are grateful for generous and financial support from theEuropean Union's  Horizon 2020 Research and Innovation programme  under the Grant Agreement 774078 (Pharma-Factory); the  IUF (Institut Universitaire de France ,  2014-2019 ); the  Normandie Université (NU) , the  Centre National de la Recherche Scientifique (CNRS) ,  Université de Rouen Normandie (URN) ,  INSA Rouen Normandie ; the  European Regional Development Fund (ERDF)   N • HN0001343 , the  Région Normandie , and the  Laboratoire d'Excellence (LabEx) SynOrg  ( ANR-11-LABX-0029 ), France. M. L. W. B. fellowship is supported by the  European Union 's  Horizon 2020 Research and Innovation programme  under the Grant Agreement 774078 (Pharma-Factory).
heimbachae, P. rettgeri, P. rustigianii, P. sneebia, P. stuartii, P. thailandensis, P. huaxiensis, and P. vermicola  [4] [5] [6]. P. vermicola was first isolated from a nematode Steinernema thermophilum collected in soils in India in 2006. Its name means (ver. mi co. la. L. n. worm; L. suff. -cola of L. n. incola inhabitant; N. L. n. vermicola inhabitant of worms)  [7]  and is very rarely found as an etiological agent in humans, with only one described case of diarrhea in a 37-year-old patient in India  [8]. Providencia species are reported to be found mainly in environments such as water and are mostly involved in infections of birds, fish, and certain insects such as fruit flies  [3, 9]. Prior to this study, there was no available genome of P. vermicola in the NCBI database. Here, we describe the first complete genome sequence of a clinical multi drug resistant (MDR) P.
Bioinformatic Analysis The genome assemblies were performed using the A5-pipeline on the Illumina reads and using Unicycler for the hybrid assembly, which includes both Illumina and nanopore reads  [10, 11]. Genome annotation was performed using the prokka (rapid prokaryotic genome annotation) pipeline  [12]. Circular genome representations of P. vermicola chromosome and plasmid and their comparisons by BlastN with the closest sequences were performed using the CGview Server  [13]  and locally downloaded EasyFig v2. 2 software. Proteome comparison of P. vermicola with those Providencia species was performed using the "get_homologues. pl" pipeline  [14]. Moreover, the average nucleotide identity (ANI) between P. vermicola and downloaded genomes was determined using the OrthoANI program (AOT software)  [15].
Genome Features For P. vermicola P8538, the genome size was estimated to be 4,432,495-bp and composed of one chromosome 4,280,811-bp in size and 40. 80% GC and one plasmid (pPV8538_NDM-1) 151,684-bp in size and 51. 93% GC. Genome annotation revealed 4166 predicted genes composed of 3991 CDS, 11 rRNAs, 74 tRNAs, 89 miscRNAs, and 1 tmRNA gene (Table  2 ). As shown in Figure  1 , genome comparison with 10 published Providencia genomes revealed multiple mobile genetic elements (MGEs) in the P. vermicola P8538 chromosome. Indeed, three complete prophage regions were identified from the PHASTER database, including Phage_Entero_mEp460 "54. 42-Kb, 39. 96% GC", Phage_Salmo_Fels_2 "59. 9-Kb, 41. 21%GC", and Phage_Escher_HK639 "41. 7-Kb, 42. 31%GC", respectively. Additionally, a complete siderophore biosynthesis NRPS (39.
62-Kb, 33. 92%GC) composed of 19 genes can be identified (Figure  1 ). As presented in Supplementary Figure  S1 , this siderophore NRPS was only identified from the NCBI database in three genomes including P. stuartii PRV00010, Morganella morganii VGH116, and Salmonella enterica 2014AM-3158 with average % homology of 96%, 44. 37%, and 33. 89%, respectively (Supplementary Table  S1 ). The identified Type-I-F CRISPR-cas3 system (10. 9-Kb, 43. 63% GC) appeared to be specific to the P. vermicola P8538 isolate since it was not identified in any of the 10 compared genomes (Figure  1 ). Interestingly, a complete Type VI secretion system (T6SS) encoding gene was harbored in the P. vermicola P8538 chromosome and was partially detected in the compared genomes (Figure  1 ). However, in addition to the MGEs identified from the P.
Some specific MGEs have been identified in this particular P. vermicola P8538 isolate, including a glutathione detoxification system from the plasmid pPV8538_NDM-1 which was detected by BlastN from the NCBI database in very few bacterial plasmids from Salmonella enterica, Proteus mirabilis, Serratia marcescens, Enterobacter hormaechei, Klebsiella quasipneumoniae, and michiganensis. As reported in the literature, this system is involved in the glutathione-dependent process of formaldehyde detoxification  [22, 23]. Moreover, we identified from the P8538 chromosome a NRPS cluster for siderophore biosynthesis which has only been identified in three other enterobacterial genomes, namely P. stuartii PRV00010, M. morganii VGH116, and S. enterica 2014AM-3158, and was absent in the two genomes of P.
vermicola recently deposited in the NCBI database. As reported, siderophore systems are low molecular weight molecules which are widespread in the bacterial and fungal world, with more than 200 biosynthetic and diverse types. They play the role of capturing, solubilizing and delivering essential Fe(III) ions in the cytoplasm  [24]  and are involved in the growth and development of microorganisms but also in bacterial virulence, as described in E. coli in urinary tract infections  [25]. They are also involved in bacterial dissemination by induction of inflammation in the lungs  [26, 27]. The T6SS acts as a virulence factor in the majority of proteobacteria with the ability to attack eukaryotic and prokaryotic target cells through a complex process, secreting toxic effectors through a contact mechanism into neighboring bacteria or eukaryotic cells, causing cell lysis or growth arrest  [28, 29].
Background: Smoothened (SMO) inhibitors, blocking the sonic hedgehog pathway, have been approved for advanced basal cell carcinoma (aBCC). Safety analyses reveal a high rate of adverse events (AEs) and, most of the time, vismodegib is most commonly stopped when the best overall response is reached. The long-term evolution of aBCC after vismodegib discontinuation is poorly described. The aim of this study is to evaluate the efficacy and safety of the SMO inhibitors (SMOis) available (vismodegib and sonidegib) following rechallenge after complete response (CR) following an initial treatment by vismodegib. Materials and methods: This real-life, retrospective, multicenter and descriptive study is based on an extraction from the CARADERM accredited database, including 40 French regional hospitals, of patients requiring BCC systemic treatment.
Results: Of 303 patients treated with vismodegib, 110 achieved an initial CR. The vast majority of these patients (98. 2%) stopped vismodegib, notably due to poorly tolerated AEs. The CARADERM database provided a median follow-up of 21 months (13. 5-36. 0 months) after CR. Of the 110 patients, 48. 1% relapsed after a median relapse-free survival of 24 months (13. 0-38. 0 months). Among them, 35 patients were retreated by an SMOi and the overall response rate was 65. 7% (34. 3% of CR and 31. 4% of partial response). The median duration of retreatment was 6. 0 months (4. 0-9. 5 months). Conclusion: Our real-life study, carried out on patients with complex clinical pictures, shows that after treatment discontinuation, 48. 1% of patients achieved CR relapse within an average of 24 months (13. 0-38.
9 Subsequently, sonidegib, a new SMO inhibitor (SMOi), was approved for aBCC in 2016. 1] [12] [13]  Nevertheless, safety analyses revealed a high rate of adverse events (AEs) (98%). Thus, most of the time, to limit toxicity, SMOi was prescribed intermittently or stopped as soon as the best overall response (BOR) was achieved. 13 n view of the increase in the number of current patients on vismodegib, maintaining CR after treatment discontinuation is of interest. So far, the long-term evolution has rarely been reported. 14 Herms et al. studied, as a secondary objective, the relapse management [including rates, relapse-free survival (RFS), treatment modalities and efficacy]. The authors showed that in 27 patients with rechallenge, the BOR rate was 85%, but tolerance was not described. 15 he aim of this study, based on a national, real-life database, is to evaluate the efficacy and toxicity of the SMOi available (vismodegib and sonidegib) rechallenge, and the median duration, in relapsing aBCC, after discontinuation of vismodegib and initial CR.
Study design and patients This real-life, retrospective, multicentric, observational and descriptive study is based on an extraction from the CAR-ADERM (RAre DERMatological CAncers) accredited database. 16 ARADERM is a French national hospital network database on rare skin cancers, gathering 40 referent centers. BCC patients included into the CARADERM database have an inoperable or metastatic histologically confirmed BCC or Gorlin syndrome with systemic treatment by SMOi. The non-inclusion criteria were: under 18 years of age and lack of consent. Among the patients with aBCCs and mBCCs from November 2013 (initiation of the database) to 27 May 2020, we selected those with rechallenge due to a relapse during follow-up after an initial CR. CR was defined clinically or, more rarely, histologically by the local investigators.
Statistical analysis Continuous variables were described using the mean and standard deviation or the median and interquartile range (IQR). Categorical variables were expressed by frequency and percentage. The RFS was estimated using the KaplaneMeier method. Relapse or death was considered as events. The database lock was 27 May 2020, and some patients were censored. The statistical analyses were carried out with SAS software version 9. 4 (SAS Institute Inc. , Cary, NC).
27, 28 Stratigos et al. reported in a phase II single arm-trial an ORR of 31% on 84 patients with a novel PD-1 inhibitor REGN2810 used in aBCCs, metastatic or not after SMOi (due to progression or intolerance). 29 A second phase II trial is in progress, using pembrolizumab with or without vismodegib (ClinicalTrials. gov identifier: NCT02690948). This study obviously presents some limitations as all retrospective studies, with data missing and lost to followup. The different assessments were not centrally reviewed, and CARADERM being recent, the number of patients is limited, particularly those with rechallenge. However, these data remain relevant, reflecting the current population in 40 comprehensive cancer centers in France, from the largest to the smallest ones.
Plant Material Experiments were performed on Arabidopsis thaliana accession Columbia 0, unless specified otherwise. Plants were grown in growth chamber with a 100 µmol. m -2. s -  light intensity with 8 h to 16 h of illumination per day for short and long day photoperiods, respectively. T-DNA insertion mutants tt8-6 (N2105594), tt2-5 (N2105593), tt2-1 (NW83), and myb5-1 (N2106725) were obtained from the NASC. The tt2/myb5 double mutant was obtained from a cross between tt2-1 and myb5-1 and a homozygote individual was backcrossed three times in Col 0. Sequence data from this article can be found in The Arabidopsis Information Resource under the following accession numbers: AT2G26150 (HSFA2), AT3G35550 (TT2), AT3G13540 (MYB5), AT5G24520 (TTG1), AT4G09820 (TT8), AT1G61720 (BAN), AT4G22880 (LDOX), AT5G42800 (DFR), AT1G56650 (PAP1).
Bio-Informatic Analyses Genevestigator software was used for publicly available microarray data analyses  [19]. Coregulated genes were determined using the coregulations tool with a 0. 8 Pearson's coregulation coefficient cutoff. Genes' descriptions and promoter sequence consensus were the ones of TAIR10 (www. tair. com, accessed on February 2016). Promoter motif enrichment was analyzed using the MEME suite V4. 12. 0  [20]. MEME was used for de novo motif prediction and AME was used for detecting the enrichment of known motif.
Protoplast were prepared as previously described  [22] , and transformed with 5 µg of each intended plasmid. Protoplast fluorescence was determined 48 h after transformation using flow cytometry. Protoplast suspensions were filtered through a 30-µm mesh. Flow cytometry was performed on a Partec CyFlow®Space instrument (Sysmex France, 93420 Villepinte, France), with a 488 nm solid sapphire 20 mW laser for excitation and using a FloMax®data acquisition and analysis software (Sysmex France, 93420 Villepinte, France). Green fluorescence was detected with a FITC 527nm/30nm band-pass filter (FL1 channel). Red chlorophyll-based fluorescence from living protoplasts was detected with a 610nm/30nm band-pass filter in the FL2 channel. The side light scatter (SSC) detector high voltage was set to 161.
Promoters of HSFA2 Coregulated Genes Are Enriched in the Site II Element Motif To gain insight into the regulation of HSFA2, we used publicly available gene expression data (www. genevestigator. com, accessed on October 2015  [19] ) and searched for HSFA2 co-regulated genes. Genes showing a Pearson correlation coefficient above 0. 8 were extracted. As expected, HSFA2 was part of expression clusters strongly correlated during heat treatment (101 genes), cold stress (75 genes), hypoxia (178 genes), and salt stress (67 genes). One of the clusters, consisting of 43 genes, is systematically co-regulated with HSFA2 and therefore called "HSFA2 common stress cluster" (Figure  1a , Supplementary Table  S3 ). The HSFA2 common stress cluster is enriched in gene ontology terms "response to stress" and "protein folding" (Panther TM V12) and comprises several known HSFA2 targets (Figure  1b , Supplementary Table  S1 ).
during heat treatment (101 genes), cold stress (75 genes), hypoxia (178 genes), and salt stress (67 genes). One of the clusters, consisting of 43 genes, is systematically co-regulated with HSFA2 and therefore called "HSFA2 common stress cluster" (Figure  1a , Supplementary Table  S3 ). The HSFA2 common stress cluster is enriched in gene ontology terms "response to stress" and "protein folding" (Panther TM V12) and comprises several known HSFA2 targets (Figure  1b , Supplementary Table  S1 ). Search for cis-elements in the promoters of the HSFA2 common stress cluster, using the MEME suite software  [20]  revealed two significantly over-represented motifs, the Heat Shock Element and the Site II element, hereafter called HSE and SIIE, respectively (Figure  1c, d ). The HSE (5'-nGAAn-3' repeats) was previously shown to be enriched in the promoters of HSFA2 and its targets  [7, 23] , thereby validating the method (Figure  1d ).
It was suggested that SIIEs interact with the TEOSINTE BRANCHED-1/CYCLOIDEA/PCF 20 (TCP20) factor  [27]. However, in vivo experiments showed that TCP20 was not present in the region of SIIE motifs [28]. Search for cis-elements in the promoters of the HSFA2 common stress cluster, using the MEME suite software  [20]  revealed two significantly over-represented motifs, the Heat Shock Element and the Site II element, hereafter called HSE and SIIE, respectively (Figure  1c, d ). The HSE (5'-nGAAn-3' repeats) was previously shown to be enriched in the promoters of HSFA2 and its targets  [7, 23] , thereby validating the method (Figure  1d ). Unexpectedly, we found that the majority (65. 91%) of promoters (p = 4. 4 × 10 -12 , Figure  1c ) were also enriched in sequences corresponding to the SIIE motif (5'-(A/T)TGGGC(C/T) -3'  [24].
Data Availability Statement: All the data supporting the results of this paper are present in the paper and/or the supplementary materials. The RNA-Seq data analysed in this article have been deposited in NCBI's Gene Expression Omnibus (GEO) and are accessible through GEO Series accession number GSE171922 (https://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE171922). All the materials and relevant data are available from the corresponding author on request.
Values are mean ± SD from four independent and duplicate transfections and were compared by nonparametric Mann-Whitney U test (GraphPad Prism 6 software). *P < 0. 05. than TNFR1, at an apparent molecular mass of 49 kDa (Fig. 1b ). In agreement with translation by an internal initial codon, no change was observed when we mutated the first methionine to valine (c. 1A>G) and no protein expression was detected when Met109 was mutated (c. 171A>G in TNFR1-d2, corresponding to c. 325A>G in TNFR1). This result suggests that the translation of TNFR1-d2 was initiated at a start codon localized in exon 4, in-frame with TNFR1 and leading to a putative new protein variant of TNFR1 lacking the peptide signal (i. e. , the first CRD [CRD1] and the three quarters of CRD2). Identification of the putative internal ribosome entry site (IRES) element in TNFR1-d2.
Cellular localization of TNFR1 and TNFR1-d2. We first determined the cellular localization of TNFR1-d2-GFP with or without transfection with TNFR1-mcherry (Fig. 2 ). We found no redistribution of TNFR1 or TNFR1-d2 when the proteins were co-expressed as compared with each alone. In addition, we observed a complete cytoplasmic co-localization of TNFR1-d2 and TNFR1 (M1, co-localization index calculated by the Manders' coefficient 29 = 0. 9, data not shown). Because TNFR1-d2 can be functionally active in a cell compartment different from that of TNFR1 and because different subcellular localizations have been detected in vitro for TNFR1  30  , we compared the subcellular location of TNFR1 and TNFR1-d2. The cDNAs of TNFR1 and TNFR1-d2 fused to the Flag tag were overexpressed in HeLa cells, then underwent immunofluorescence assay with Flag antibody and antibodies for proteins located in specific subcellular compartments.
Fluorescent and phase-contrast images were monitored using the IncuCyte live cell imaging system (Essen Bioscience). Histograms represent the GFP intensity of both transfection conditions over 24hours without (b) or with TNF stimulation (c) in two independent experiments. Each dot corresponds to one well microscopic field. (d,e) To detect spontaneous activation of the endogenous NF-κB transcription factor, HEK293T cells were transiently transfected with the indicated amount of TNFR1 and TNFR1-d2 vectors either alone (d) or in combination (e). Relative firefly luciferase activity of each condition was normalized to β-galactosidase activity and subtracted by basal luciferase activity obtained with the vector without consensus sequence of the NF-κB transcription factor. Values are mean ± SD from four independent experiments performed in duplicate and were compared by nonparametric Mann-Whitney U test (GraphPad Prism 6 software).
Conditions that provide similar expression levels of proteins were 1:2:4 as determined by fluorescence and western blot analyses of TNFR1, TNFR1-d2 and TNFR1-d2-p. (Thr79Met), respectively. For HeLa cells, the medium was replaced by complete DMEM without antibiotic at 6 h post-transfection. Genetically modified organisms were declared at the national competent authority (agreement no. 2436). Plasmid construction. The pcDNA6/V5-His vector containing TNFR1 cDNA (NM_001065. 3) was used to generate all TNFR1 vectors (a gift of the McDermott laboratory  59  ). The TNFR1-d2 cDNA (GenBank accession no. JN172914  25  ) was obtained by RT-PCR from human kidney total RNA (human Total RNA Master Panel II, Clontech). Vectors expressing TNFR1 and TNFR1-d2 cDNAs fused to Flag tag (Figs. 1b, 3, 4a, d  was obtained by Pfu-mediated amplification with 5′ phosphate-modified and mispaired oligonucleotide primers described in supplemental Table, followed by a DpnI digestion.
The normalized GFP Integrated intensity, was taken every ten minutes during next 2 hours after the cell seeding, following every one-hour during 14 hours (b). Histograms represent the GFP intensity of both transfection conditions at 12 hours (c). (d) HEK293T cells were transiently transfected with the indicated amount of TNFR1 or TNFR1-d2 carrying or not the p. (Thr79Met) disease-causing variant. Relative firefly luciferase activity of each condition was normalized to β-galactosidase activity and subtracted by basal luciferase activity obtained with the vector without consensus sequence of the NF-κB transcription factor. Values are mean ± SD from four independent experiments performed in duplicate and were compared by nonparametric Mann-Whitney U test (GraphPad Prism 6 software). *P < 0. 05, **P < 0.
Acknowledgements We thank  Pr Mickael McDermott  ( Leeds Institute of Rheumatic and Musculoskeletal Medicine ) for the gift of the pcDNA6/V5 vector. We thank  Dr Anne Catherine Prats  ( Inserm and University of Toulouse ) for the gift of the pCREL and pCRHL vectors and for helpful discussions on IRES machinery. We are grateful to  Elodie VIDAL  and  François CAROL  for technical contributions.
To answer this question, the authors again used cells lacking centriolar satellites. CEP90 was correctly localized at centriole distal ends in these cells, and DAs were formed, supporting a direct requirement for the centriolar pool of CEP90 in DA assembly. Putting all their data together, Kumar et al. proposed the following model: First, MNR is recruited to elongating centrioles, which, in turn, triggers the recruitment of OFD1 to arrest elongation at the end of the first cell cycle. MNR and OFD1 then recruit CEP90, which initiates the recruitment of DA components, including CEP83, at the end of the following cell cycle (Fig. 1 ). Thus, the DISCO complex allows for coupling the arrest of centriole elongation to centriole maturation across successive cell cycles. Besides OFD1 and MNR proteins, Kumar et al.
also identified a protein called FGFR1OP N-Terminal Like (FOPNL or FOR20) as a potential CEP90 interactor (4). Interestingly, this interaction was confirmed in a recent study describing that a complex containing CEP90, OFD1, and FOPNL localizes at the distal end of Paramecium centrioles and is necessary for the recruitment of DA components and centriole docking in Paramecium and human cells  (9). FOPNL was previously found in complex with MNR and OFD1 and shown to facilitate their interaction  (8). Together, these data suggest that the DISCO complex could also include FOPNL. The functional similarities of some of the components of the DISCO complex between Paramecium and humans strongly suggest that the role of DISCO in centriole maturation and ciliogenesis is broadly conserved across species.