dataesr/scientific-paragraphs-categorization huggingface dataset:
Data treatment and statistical analysis The package mixOmics 4  was used for statistical treatment of the transcriptomic data sets. The tool has its own tutorial and can be easily used, for a nearly inexperienced R user, through the web site at http://mixomics. org/. Specific functions for genes ontology, pathways tools, etc. were searched using tools available at the ECOCYC website 5  (Keseler et al. , 2017). Clustered heat maps of transcriptomic analysis were performed using the Interactive Clustered map builder freely available at https://build. ngchm. net/NGCHMweb-builder/ (Ryan et al. , 2019). Frontiers in Microbiology 05 frontiersin. org.
ACKNOWLEDGMENTS We thank  Dr. N. Pfanner  for comments on the manuscript and support. We thank  Drs. D. Mokranjac ,  H. -G. Koch ,  J. Song ,  H. Rampelt ,  N. Wiedemann ,  K. N. Doan , and  J. D. Busch  for discussions and materials. Work included in this study has also been performed in partial fulfilment of the requirements for the doctoral thesis of C. P. at the  University of Freiburg. This work was supported by grants of the  Deutsche Forschungsgemeinschaft  (Research Training Group  278002225/RTG2202 ,  BE4679/2-2  project  ID 269424439 , and  SFB1218  project  ID 269925409 ).
In fact, our biophysical and biochemical analyses show that the NR7 LBD does not heterodimerize with the RXR LBD, in contrast to classical heterodimeric RXR partners, such as PPARα, used as a control in our experiments. Nevertheless, we could model a canonical NR7/ RXR heterodimer, if we assume that the unstructured H10'-H11' loop region around Phe361 could change its conformation (Additional file 1: Fig. S5 ). In this model case, we observed that the dimerization with RXR has reduced interface area (900 Ǻ 2 ) as compared to NRs that encompass a fully helical H10-H11 region (for example, 962 Ǻ 2 for RARα/RXRα (PDB code 1DKF, as shown in Additional file 1: Fig. S7 )). Thus, our analyses indicate that the peculiar conformation of the region H10-H11 of NR7 LBD is not in favor of a classical heterodimerization with RXR.
We performed an evolutionary analysis of these various amino acid positions and this reveal that the amino acids effectively change in NR7 further highlighting that NR7 represents a transition state between class I receptors and class II receptors (Additional file 1: Fig. S11 ). S2 ). For each analysis, left panels correspond to the respective chromatograms where the main chromatographic peaks are colored in A blue, B green, C red, and D beige. Right panels correspond to the extracted mass spectra of the main chromatographic peaks. The different charge states of identified NR7 homodimers, NR7-RXR heterodimer, and RXR homodimers all bound to DNA are given in blue, purple, and green respectively while the charge states of NR7 and RXR alone are given in grey and black respectively. The masses corresponding to these identified species are summarized in Additional file 1: Table  S4  Discussion NR7 defines a new conserved NR subfamily located at a pivotal position in NR phylogeny NR7 was initially identified in the genome of the cephalochordate amphioxus  [25] , but, given the paucity of genome sequences available at that time, its phylogenetic status as an independent NR subfamily could only be demonstrated in analyses based on more comprehensive datasets  [7, 9, 13].
Cloning of B. lanceolatum NR7 The sequence of B. floridae NR7 (Table  S1 ) was used to search available B. lanceolatum transcriptome databases  [28]. The resulting B. lanceolatum sequences allowed the design of B. lanceolatum NR7-specific primers (Forward: 5′-TAA ACA ACA TGG CGA GAC A-3′; Reverse: 5′-ATG ACA CCT TAG TCA AAG CA-3′). Total mRNA was extracted from B. lanceolatum adults with the RNeasy Minikit (Qiagen) and was used as template for cDNA synthesis using the Superscript III kit (Invitrogen) and random primers. Subsequent PCR experiments were performed using AmpliTaq Gold (Roche), and amplified fragments were cloned using the pGEM-T Easy system (Promega) before being sequenced on both strands. The resulting NR7 sequence from B. lanceolatum is 1232 bp long and partially truncated at its N-terminus.
Phylogenetic analyses Our backbone dataset for the extensive outgroup was simplified from  [7]. Additional sequences for the NR7 subfamily were retrieved by BLAST against metazoan proteins. Protein sequences were aligned with Muscle  [29] , and alignments were checked by eye and edited with Seaview  [30]. Phylogenetic trees were calculated using PHYML  [31] , a fast and accurate maximum likelihood method, under the LG substitution model  [32]. Node robustness was assessed using approximate likelihoodratio test (aLRT)  [33]. Accession numbers are provided in Additional file 1: Data S1.
The reaction conditions were as follows: 95°C for 3 min followed by 45 cycles of 95°C for 10 s and 60°C for 30 s. Data were collected and curves were generated with the CFX Manager software (Biorad). Each reaction was carried out in technical triplicates. Dissociation analysis was performed at the end of each reaction to confirm the amplification specificity. For each reaction, a reverse transcriptase negative control was performed to test for genomic DNA contamination. To determine primer efficiencies, a template qPCR reaction was performed on adult cDNA for each primer couple and then diluted (with seven dilution points) to generate linear standard curves.
Data collection and phasing Native datasets were collected to a maximum resolution of 2 Å on the ID29 beamline at the European Synchrotron Radiation Facility (ESRF). Data from thiomersal derivatized crystals were collected on the X06DA beamline at the Swiss Light Source (SLS). All data were integrated, indexed, and scaled using XDS  [37]. The crystals showed a primitive trigonal space group, either P3 1 12 or P3 2 12 with unit cell dimensions a=b= 46. 4 Å and c=163. 2 Å. Since amphioxus NR7 does not have direct homologs in model organisms, such as vertebrates, molecular replacement was attempted with several closely related crystal structures, in particular with structures of the RXR LBD with which NR7 has 46 % sequence identity. Initial models were prepared by removing flexible loops and known variable regions such as the β-sheet and the C-terminal helix.
All of the models, except one, failed to give a reasonable MR solution. A weak solution was found in P3 2 12 using the mollusk RXR (PDB code 1XIU) with one molecule per asymmetric unit with reasonable packing, using Phaser  [38]  in the PHENIX suite  [34]. Alternatively, a similar solution was obtained using the BALBES software  [39]. However, the maps were very poor, especially for the lower part of the protein, including helices H6, H7, H10, and H11 and the construction/refinement of the structure stalled at an early stage with no further improvement in the map quality. Therefore, soaking of the crystals with several different types of heavy atom (HA) compounds was undertaken. The best result was obtained by soaking the crystals in a thiomersal solution at a concentration of 1 mM for 24 h.
Two HA sites were found using AutoSHARP  [40, 41]  in the CCP4 suite  [42]. However, the maps were poor and it was not possible to build a model. The partial molecular replacement solution was refined against this derivative dataset which allowed the identification of the mercury sites (one fully occupied dual conformation site and two partially occupied sites (with about 25% occupancy), and placement of the mercury atoms vastly improved the map quality.
Model building and refinement Refinement was performed using Refine in the PHE-NIX suite and BUSTER  [43] , followed by iterative cycles of construction in COOT  [44]. Once the structure had been refined to convergence, it was refined against the best native dataset. Figures were prepared using PyMOL version 1. 7. 4. 0 (Schrödinger, LLC,  [45] ) and the interface area was calculated using CoCoMaps software  [46]. The coordinates and associated structure factors have been deposited in the Protein Data Bank under the accession code 7Q71.
Samples were then infused into the mass spectrometer via an automated chip-based nanoESI source (Triversa Nanomate, Advion, Ithaca, NY) with capillary voltage and gas pressure set to 1. 65 kV and 0. 65 psi respectively. Instrumental parameters of the mass spectrometer were optimized for the detection of labile noncovalent complexes as follows: interface pressure, 6 mbar; cone voltage, 80 V (for mixture analyses), and 120 V (for NR7 LBD alone analysis); m/z range, 1000-10,000; scan time, 4 s. Native MS data treatment was performed using Mass Lynx V4. 1 (Waters, Manchester, UK). Deconvolution was performed using UniDEc  [48]. Relative abundances of the species were calculated from native MS intensities of the deconvoluted data.
25 mL/min over 3 min. The flow rate was then decreased to 0. 10 mL/min over 10 min and finally increased to 0. 25 mL/min over 5 min. The Synapt G2 HDMS was operated in positive ion mode and instrumental parameters were optimized as follows: capillary voltage, 3 kV; interface pressure, 6 mbar; cone voltage, 180 V; m/z range, 1000-10,000; scan time, 1. 5 s. SEC-nMS data interpretations were performed using Mass Lynx V4. 1 (Waters, Manchester, UK).
Size-exclusion chromatography coupled to multi-angle light scattering SEC-MALS/QELS experiments were performed on a multi-angle light scattering detector (miniDAWN TREOS, Wyatt Technologies) coupled in-line with SEC and an interferometric refractometer (Optilab T-rEX, Wyatt Technologies). A Superdex S200 10/300 GL column (total volume 24 mL, GE Healthcare) with a flow rate of 0. 5 mL/min was used to separate the sample before performing the MALLS/QELS measurement. Experiments were done with 50-100 μL samples at concentrations between 1 and 3 mg/mL in a buffer of composition 20 mM Tris pH 8, 120 mM NaCl; 2 mM MgCl 2 and 2mM TCEP. The molar mass was determined by construction of Debye plot using Zimm formalism (plot of K*c/R(θ) as a function of sin 2 (θ/2)) at 1-s data interval. The analysis of the data was performed using the ASTRA 6.
1software (Wyatt Technologies). and its nearest neighbor. The aromatic residue Phe361 of this loop is buried into a hydrophobic pocket formed by leucine residues of the nearest neighbor, stabilizing a peculiar bulge conformation at this location. (C) Comparison of the crystal structure of NR7 LBD (green) with the structure predicted by AlphaFold colab (cyan). AlphaFold predicts that NR7 can nevertheless adopt an agonist H12 conformation with a long, continuous H10-H11 helix. The orange arrow indicates that the small H11 helical part in the crystal structure would interferes with an agonist position of helix H12 as observed in the AlphaFold model. Fig. S6. Functional characterization of amphioxus NR7. (A) Transactivation assay in HEK293T cells of Gal4-NR7 LBD with a UAS-luciferase reporter.
Fig. S7. Heterodimer formation of amphioxus NR7 and RXR. The ligand-binding domains (LBDs) of amphioxus NR7 and RXR create a reduced interface area compared to classical RXR heterodimers. Views from the front and rotated by 90° of a model of amphioxus NR7-RXR (on the left) built by superimposing the crystal structure of the isolated proteins to the human RAR-RXR heterodimer (PDB code 1DKF) (on the right). The loop between helices H10'-H11' is removed from the NR7 structure because of serious steric clashes with RXR and is further considered for interface area calculations. The short helix H10' and helix H12 of NR7 are shown in orange and red, respectively. Fig. S8. Full NR7 forms a homodimer on direct repeat response elements, but not on control DNA. SEC-nMS analyses of full NR7 with (A) DR1, (B) DR4 and (C) Ctrl(-) response elements.
Acknowledgements The authors would like to thank  Bariza Blanquier , manager of the Genetic Analysis facility for her expert assistance ( AniRA platform ,  SFR BioSciences Gerland -Lyon Sud   UMS3444/US8 ). We thank  Pascal Eberling  for the peptide synthesis and  Camille Kostmann  for technical support. We thank the  Structural Biology and Genomics platform of IGBMC , in particular  P. Poussin-Courmontagne  for the SEC-MALLS measurements. We thank  Dr. Patrick Balaguer  ( Institut de Recherche en Cancérologie, Montpellier, France ) for fruitful discussion. We thank the  European Synchrotron Radiation Facility  (proposal MX-1413), SOLEIL (proposal 20120719), and the  Swiss Light Source  at the  Paul Scherrer Institut  for the provision of beamtime,  Daniele De Sanctis  for assistance in using beamline ID29 (ESRF),  Pierre Legrand  for assistance in using beamline Proxima 1 (Soleil), and  Vincent Oliéric  for assistance in using X10SA-PXII beamline at the  Swiss Light Source ,  Paul Scherrer Institut, Villigen-PSI, Switzerland.
Funding This work was funded by the  Agence Nationale de la Recherche (ANR)  grants  ANR-2010-BLAN-1234-01  and by  CNRS ,  INSERM , The  Université de Strasbourg , the  Association pour la Recherche sur le Cancer (ARC)  and l' Alsace contre le Cancer. This study was supported by the grant  ANR-10-LABX-0030-INRT , a  French State  fund managed by the  Agence Nationale de la Recherche  under the  frame program Investissements d' Avenir   ANR-10-IDEX-0002-02. This work of the  Interdisciplinary Thematic Institute IMCBio , as part of the  ITI 2021-2028 program  of the  University of Strasbourg ,  CNRS  and  Inserm , was supported by  IdEx Unistra  ( ANR-10-IDEX-0002 ), and by  SFRI-STRAT ' US  project ( ANR 20-SFRI-0012 ) and  EUR IMCBio  ( ANR-17-EURE-0023 ) under the framework of the  French Investments for the Future Program.
The authors acknowledge the support and the use of the  French Infrastructure for Integrated Structural Biology FRISBI   ANR-10-INSB-05-01  and  Instruct-ERIC , a  Landmark ESFRI project , the  French Proteomic Infrastructure ProFI   ANR-10-INBS-08-03. This study was supported by the grant  ANR-10-LABX-0030-INRT , a  French State  fund managed by the  Agence Nationale de la Recherche  under the  frame program Investissements d' Avenir   ANR-10-IDEX-0002-02. The authors thank  GIS IBiSA and Région Alsace  for financial support in purchasing a Synapt G2 HDMS instrument. BB acknowledges the ARC foundation for funding of his PhD fellowship. MB was supported by a PhD fellowship from the  Région Alsace.
Availability of data and materials GenBank accession number: The sequence data have been deposited to Gen-Bank. Amphioxus NR7: MK976734, sea urchin NR7: MK976735 and leech NR7: XP_009028197. 1 Protein Data Bank accession number: The crystal structure of NR7 LBD has been deposited to the Protein data Bank (www. pdb. org) under the accession number 7Q71.
Data collection In February 2015, daily observations took place between 9 a. m. and 5 p. m. on a total of 13 observation days, with the monkeys being observed for a total of 4-6 h per day. Independent 15 min. continuous focal-animal sampling (Altmann 1974) was used to video record the behaviour of the 17 adult and subadult focal individuals for a total duration of 120 min per individual, using a Panasonic HC-X920 digital video camera. Focal animals were selected following a preset randomised order. Usually, the focus was on individuals from one group in the morning (between 9h:00 and 12h:00) and another in the afternoon (between 13h:00 and 17h:00), and the next day this order was alternated. If a focal subject moved outside the range of vision, the recording was stopped, but the recorded focal time was added to the total sampling time for that individual if it had lasted at least one minute.
e. audible or tactile) depending on recipient's attentional state. To run this analysis also at the individual level, we only kept the data of individuals that produced body acts both in the presence of attending and non-attending recipients (N = 7). Then, we tested the likelihood of body acts being associated with the marker 'response waiting'. Regarding the marker 'goal persistence', we determined whether the form of goal persistence (stop signalling/repeat same signal/ produce new signal) depended on the type of response by the recipient (response or no response). To run this test at the individual level as well, we only kept data of individuals that received both 'responses' and 'no responses' from their recipients (N = 13). Finally, with regards to measuring means-ends dissociation, a preliminary inspection of our data revealed that the two hours of observation per individual provided insufficient data to address this question statistically.
8 elaglenastat (CB-839) has been evaluated in early phase clinical trials, mainly in combination regimens in patients with solid tumors. In a combination study with cabozantinib or everolimus, telaglenastat displayed promising activity in patients with advanced or metastatic renal cell carcinoma, with mostly grade 1 to 2 treatment-related adverse events. 9 A single-agent phase I study has been conducted in patients with hematologic malignancies (NCT02071888) but the results have not yet been reported. Targeting GLS appears to be particularly relevant in the context of ibrutinib resistance. Lee et al. analyzed the impact of ibrutinib in various mantle cell lymphoma lines and found that inhibition of BTK had a profound effect on several metabolic pathways, including glutaminolysis. 10 Importantly, glutaminolysis was found to contribute to over 50% of mitochondrial ATP production.
The timing of pronuclear envelopes scission was scored in embryos expressing mCherry::NPP-22 (blue dots, n=7) while the timing of lamina disassembly was scored in embryos expressing mCherry::LMN-1 (orange dots, n=8). (E) Graph presenting the surface area occupied by the pronuclei starting 200 s before anaphase onset (0 s) in embryos expressing GFP::TBB-2 and mCherry::LMN-1. ( F) Graph presenting the intercentrosomal distance normalized to embryo length starting 80 s before anaphase onset (0 s) in embryos expressing GFP::TBB-2 and mCherry::LMN-1 or mCherry::NPP-22. The online version of this article includes the following video, source data, and figure supplement(s) for figure  1:  Source data 1. Quantification of: (D) The steps of pronuclear envelopes breakdown: pronuclei permeabilization, lamina disassembly (at the poles, between pronuclei), chromosomes alignment, and pronuclear envelopes scission event (membrane gap); (E) The surface area occupied by the pronuclei starting 200 s before anaphase onset (0 s).
Times are in seconds relative to anaphase onset (0 s). All panels are at the same magnification Scale bar, 10 μm. (E, F) Quantification of (E) GFP::LMN-1 or (F) GFP::LMN-1 8A fluorescence signal intensity over time from central single focal planes above background at the nuclear envelope in embryos of the indicated genotype during mitosis. Times are in seconds relative to anaphase onset (0 s). The average signal intensity of GFP::LMN-1 and GFP::LMN-1 8A at 120 s before anaphase was defined as 1. The data points on the graphs are the normalized average signal intensity per pixel results ± SEM for n embryos of the indicated genotypes. Data were collected from three independent experiments. The online version of this article includes the following source data and figure supplement(s) for figure  2:  Source data 1.
Lamina depolymerization and chromosome alignment are prerequisites for membrane gap formation even in the presence of excessive pulling forces Embryos with a stabilized lamina, expressing the non-phosphorylable LMN-1 8A, are systematically defective in pronuclear envelopes scission  (Velez-Aguilera et al. , 2020). We reasoned that the lamina when stabilized, in addition to constituting a physical barrier between chromosomes, could oppose the pulling forces exerted by astral microtubules and could thus prevent elongation of the mitotic spindle during anaphase. To test this model, we measured mitotic spindle elongation in WT versus lmn-1 8A mutant embryos by measuring the intercentrosomal distance during mitosis. In contrast to WT, the spindle did not elongate to the same extent in lmn-1 8A mutant embryos (Figure  5A , Figure  5 -source data 1), indicating that stabilization of the lamina interferes with mitotic spindle elongation and thus that lamina depolymerization facilitates spindle elongation.
spinning disk confocal microscopy to monitor pronuclear membranes configuration in one-cell embryos. As reported previously, pronuclear envelopes scission between the pronuclei was totally prevented in plk-1ts embryos at restrictive temperature  (Rahman et al. , 2020; Rahman et al. , 2015). However, partial RNAi-mediated lmn-1 inactivation was sufficient to restore pronuclear envelopes scission (Figure  6B ). lmn-1 inactivation also suppressed the paired nuclei phenotype of plk-1ts embryos in these conditions (Figure  6C , Figure  6 -source data 1), as reported previously  (Rahman et al. , 2015; Martino et al. , 2017). lmn-1 inactivation not only restored membrane scission and the shape of the pronuclei, but also the normal localization of LEM-2 and EMR-1. In plk-1ts embryos, pronuclei appeared rounded, likely due to the persisting lamina that provides rigidity to the nuclear membrane.
Cycling conditions for qPCR amplification were 95 °C for 2 min followed by 30 cycles of 95 °C for 15 s, 60 °C for 30 s and 72 °C for 30 s. Melting curves were generated after amplification by increasing the temperature from 60 °C to 95 °C. Then, two-tailed ANOVA tests and t-student tests between each group (each gentamicin concentration and each exposure time) and the average between all groups were performed using the ggpubr package in R (Figure  S2  in Supplementary Information).
B) using the Platinum Taq DNA Polymerase (Invitrogen) and the Nextera XT Index Kit V2 (Illumina, San Diego, California, USA). DNA and cDNA were sequenced using the MiSeq System and the MiSeq Reagent Kit v2 (Illumina). Reads were trimmed to meet a quality score of Q20. Then, pair-ended reads were assembled using PANDAseq  [29]  at a sequence length between 410 and 500 bp and an overlap length between 20 and 100 bp using the rdp_mle algorithm. Finally, each of the DNA sequences was annotated to the genus level using the Ribosome Data Project (RDP) database and the RDP Bayesian classifier  [30]  using an assignment confidence cut-off of 0. 6. The genera that had less than 10 associated sequences in the ensemble of DNA or cDNA sequences were removed. Finally, the relative abundances of the remaining genera were assessed and normalized per number of copies of the 16 S rRNA gene or per l of water.
Annealing was performed at 65 °C for 2 min instead of 60 °C for 30 s. Then, amplicons were cleaned-up using AMPure XP beads (Beckman-Coulter, Brea, California, USA) and sequenced using the Nextera XT Library Prep Kit and Indexes (Illumina) according to the Illumina's "Nextera XT DNA Library Prep Kit" reference guide (15031942 v03). DNA sequencing was performed using the MiSeq System and the MiSeq Reagent Kit v2 (Illumina). Metagenomics reads were trimmed using the Fastq Quality Trimmer tool of the FASTX-Toolkit. Nucleotides that did not meet a minimum quality score of Q20 were trimmed from the sequences and sequences shorter than 100 nucleotides after trimming were removed. Forward and reverse reads were blasted separately against the CARD database using Diamond  [33]. The obtained results were filtered at a minimum identity of 90%, a minimum length of 50 amino acids and an e-value of 10 -10.
Average values and the percentage of standard deviation calculated for each condition are shown in Table  S3  (Supplementary Information). Since gentamicin pollution at 800 ng/ml provoked a higher increase of gene abundance and transcription than subinhibitory concentrations, dose-response graphs were created only for sub-inhibitory concentrations for better visualization of the effect of gentamicin pollution at sub-inhibitory concentrations on aminoglycoside resistance gene abundance and transcription. Two-tailed ANOVA tests were performed using the ggpubr package in R.