dataesr/scientific-paragraphs-categorization huggingface dataset:
Library quality was verified with a Fragment Analyzer (Advanced Analytical Technologies) and then quantified by qPCR using the Kapa Library Quantification Kit (Roche Diagnostics Corp, Indianapolis, IN). The enriched male and female pool libraries were then sequenced using a paired-end multiplexed sequencing mode on a NovaSeq S4 lane (Illumina, San Diego, CA), combining both pools on the same lane and producing 2 × 150 nt reads with Illumina NovaSeq Reagent Kits according to the manufacturer's instructions. Pool-sequencing datasets were analyzed with the PSASS-workflow pipeline (https:// github. com/ SexGe nomic sTool kit/ PSASS-workfl ow) that computes on a whole-genome assembly, the fixation index (FS T ), sex-specific single-nucleotide variation (SNVs, heterozygotes in one sex and homozygotes in the other sex), and male/female coverage differences.
RNA sequencing and transcriptome analysis of juvenile and adult gonads. RNA of gonads of one juvenile male (RIN 9. 0) and one juvenile female (RIN 7. 0) arapaima were extracted using the TRIzol Reagent (Thermo Fisher Scientific, Waltham, USA) according to the supplier's recommendation. RNA was then cleaned using RNeasy (Qiagen RNeasy Mini Kit cat#: 74104). Library processing and RNAseq were carried out by NOVOGENE (Cambridge, UK) on a NovaSeq 6000 PE 150, generating 10 Gb of data per sample. Transcriptome sequences of male and female juvenile and adult gonads were mapped to the genome using the RNA-sequence aligner STAR (https:// github. com/ alexd obin/ STAR/ relea ses,-quantMode GeneCounts). Differentially expressed genes between testis and ovary were detected by DESeq2 81 (Bioconductor/R) for juveniles and adults.
Acknowledgements MCA was supported by  Graduate School of Life Sciences (GSLS) PostDoc Plus Funding and MSc by Deutsche Forschungsgemeinschaft (DFG). We would like to thank the team of  Manich Foods Innovations GmbH Kassel/ Germany  for providing samples within the framework of the cooperation with the  Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin/Germany. We also like to thank  Wibke Kleiner  and  Antje Tillack  for help in the lab. A special thanks to  Maud Alix  ( IMR ) for preparing the map of population locations of arapaima. This publication was supported by the  Open Access Publication Fund of the University of Wuerzburg.
Treatment of the Zmpste24 -/-mouse model with this combination led to an improvement in several hallmarks of HGPS, including lifespan  [66]. These pioneering preclinical studies have successfully led to the design of several clinical trials, highlighting the efficiency of the repurposing of these drugs. The first ever clinical trial was launched in 2007 (ClinicalTrials. gov, NCT00425607) using the FTI lonafarnib on a cohort of 25 patients for a minimum period of 2 years, showing encouraging results with an improvement in weight gain, vascular stiffness and bone density  [67]. In 2008, following the identification of the zoledronate and pravastatin effect, a second clinical trial was initiated using these two drugs in 12 patients (ClinicalTrials. gov, NCT00731016) followed by a tri-therapy clinical trial combining lonafarnib, zoledronate and pravastatin in 37 patients (ClinicalTrials.
gov, NCT00879034). Results of this last clinical trial was reported describing no additional improvement of the tri-therapy as compared to lonafarnib alone  [68]. More recently, in late 2015, another phase I/II clinical trial combining the existing drugs lonafarnib and everolimus (Clinical-Trials. gov, NCT02579044) was started in 60 patients, for which results are expected in October 2020 (https://www. progeriaresearch. org/ clinical-trials/). Everolimus is an analog of the antibiotic macrolide drug rapamycin, an mTOR inhibitor, already used against cancer or for immunosuppression and implicated in the regulation of several cellular functions such as cell proliferation, protein synthesis, transcription, cytoskeleton rearrangement and autophagy  [69]. Previous studies had suggested that rapamycin improved lifespan, notably in aged mice, through activation of autophagy, a process that is down-regulated during ageing  [70] [71] [72] [73] [74].
Acknowledgements  I-Stem  and the  Center of Research in Myology  are part of the  Biotherapies Institute for Rare Diseases (BIRD) , supported by the  Association Française contre les Myopathies (AFM-Téléthon ). This research was funded by grants from  INSERM ,  the domaine d'intéret majeur (DIM) Biothérapies, Genopole  and the  European Commission : the  laboratoire d'Excellence Revive (Investissement d'Avenir ;  ANR-10-LABX-73 ),  NeurATRIS: A Translational Research Infrastructure for Biotherapies in Neurosciences (Investissement d'Avenir - ANR-11-INBS-0011 ), INGESTEM: the  National Infrastructure Engineering for Pluripotent and differentiated Stem cells (Investissement d'Avenir - ANR-11-INBS-0009 ), the  University of Paris-Saclay (BiotherAlliance)  and the  French National Agency  ( ANR-18-CE14-0036 ).
Micrographs were taken with 0. 5-to 2. 5-m underfocus at a nominal magnification of 11,000× with a digital pixel size of 4. 86 Å. Micrographs were CTF-corrected using GCTF  (41). All subsequent processing steps were carried out in RELION-3. 0 (42). A small set of particles was manually picked and 2D classified, and the filament-like classes were chosen as a template for AutoPicking. Particles were subjected to further 2D classification before 3D classification and 3D refinement using a negative-stain structure of dynactin (  43 ) as a reference. The cryo-EM structure of dynactin (Protein Data Bank: 5ADX)  (11)  was fit into the 3D negative-stain maps using UCSF Chimera  (44).
Acknowledgments: We thank  P. Lappalainen  and  D. Billadeau  for gifts of DNA constructs,  L. Blanchoin  for the gift of profilin,  P. Mahou  for assistance in confocal microscopy, and  J. Boulanger  for image processing advice. Funding: This work was supported in A. M. G. 's group by grants from the  Agence Nationale de la Recherche  ( ANR ANR-15-CE13-0016-01 ), from the  Fondation ARC pour la Recherche sur le Cancer  ( PGA120140200831 ), and from  Institut National du Cancer  ( INCA_6521 ). E. D. is supported by the  Medical Research Council  ( MC_ UP_1201/13 ) and the  Human Frontier Science Program  ( CDA00034/2017 ). The imaging facility of  Laboratoire d'Optique et Biosciences (Ecole Polytechnique ) is partly supported by  Agence Nationale de la Recherche  ( ANR-11-EQPX-0029 Morphoscope2 ).
The samples were then centrifuged at 10,000× g for 10 min and finally the pellet was removed and the supernatant, containing the Pi released by the enzymatic reaction, was tested as described in Section 2. 4 to study the inhibition of the enzyme. Two control tubes were prepared, one lacking the inhibitor quercetin to obtain the maximum activity of the enzyme, and one lacking both the inhibitor and ATP, which was used as a blank. All tests were performed in triplicate. Inhibitory concentration (IC 50 ) value of quercetin was calculated using GraphPad Prism (GraphPad Software, San Diego, CA, USA). This was achieved by using a curve of the enzymatic activity (%) as a function of log of different concentrations of quercetin (µM).
Statistical Analysis Data were analyzed using GraphPad Prism (GraphPad Software, San Diego, CA, USA) and represented as mean ± SD of at least 3 independent experiments performed in triplicate for each condition. One-way ANOVA tests were performed. Differences were considered significant at p < 0. 05(*), p < 0. 01(**), p < 0. 001(***) and p < 0. 0001(****).
The cells were incubated overnight at 37 • C and 5% CO 2 to ensure adherence. On the day of the experiment, cells were pre-washed with and kept in Hanks' Balanced Salt Solution (HBSS, Thermo Fisher Scientific Inc. , USA) supplemented with 1% (v/v) FCS, 1 mM L-glutamine, 1% (v/v) NEAA, 10 mM HEPES, 0. 55% (w/v) D-Glucose, while imaging. GUVs were pre-incubated with fluorescently labeled FS-Janus lectin for 5 min and applied to the cells with a final lectin concentration of 200 or 500 nM. GUVs and H1299 cell samples were imaged at 37 • C using an incubator stage (Okolab, Italy) mounted onto a confocal laser scanning microscope (Nikon Eclipse Ti-E, A1R). Image acquisition and processing were conducted using the software NIS-Elements (version 4. 5, Nikon).
Statistical analysis Glycan Analysis. The UPLC profiles were separated into peaks and the area under each glycan peak was expressed as a relative percentage area derived from the UPLC total profile. Thus, the logit transformed value was used to map the data onto a more Gaussian distribution as previously described by  Saldova et al. (2014). Peak data were checked for normal distribution using a Kolmogorov-Smirnov nonparametric test. Multivariate analysis of variance with post hoc analysis using Tukey's Honest Significant difference test was then performed using SPSS software (IBM Corp. , Armonk, NY) to identify significant peak differences across groups. The pool of mucus was the experimental unit and the model included fixed effects for ewe breed, type of cycle (synchronized and natural) and their interaction.
Acknowledgments The authors would like to acknowledge the assistance of all the technical and farm staff at  Teagasc Research Centre, Athenry, Ireland, Section  for small ruminant research and herd health,  NMBU-Faculty of Veterinary Medicine, Sandnes, Norway , and the technical staff of the  INRA experimental Unit (UEPAO). The authors would also thank  Anne Donovan  for her assistance during sample collection.
Funding The  European Research Area Network, on Sustainable Animal Production (SusAn ; Grant no. 16/RD/SusAn/ERA-NET ). National funding was provided in Ireland by the  Department of Agriculture, Food  and the  Marine as well as Teagasc , in France, by the  Agence Nationale de la Recherche  ( ANR-16-SUSN-0001 ) and in Norway by the  Research Council of Norway  ( NFR 272338/E50 ).
3A ). Within Ruminococcaceae UGC-002, cluster 11 decreased after each NO pulse, becoming almost undetectable after the third 100 mM NO pulse. The impact of NO on specific groups was measured by quantitative PCR (qPCR). The bacterial biomass, as quantified by the Eubacteria probe, was not drastically impacted by NO exposure, with even 100 mM NO, leading to minor changes (8. 1 Â 10 10 to 5. 7 Â 10 10 bacteria/ml) (Fig. 3C ). In contrast, the C. leptum group, from the Firmicutes phylum, decreased from 2. 3 Â 10 10 /ml to 1. 9 Â 10 9 /ml after the 100 mM NO pulses (Fig. 3C ). Likewise, Faecalibacterium prausnitzii decreased upon 100 mM NO pulses from 5. 3 Â 10 8 /ml to 8. 0 Â 10 7 /ml. No evident variations were identified for the subdominant groups Lactobacillus/ Pediococcus/Leuconostoc and Bifidobacteriaceae (data not shown).
Blank samples were composed of the Griess reagent and supernatants of fresh nutritive medium. The absorbance (optical density) was measured with a microplate spectrophotometer (Epoch; Biotek Instruments, USA) at 540 nm (Gen 5 2. 00 software). Gas and SCFA analysis. Gas overproduction in the atmospheric phase of ARCOL was collected daily into an external bag connected to the condenser outlet. Analysis of O 2 , N 2 , CO 2 , CH 4 , and H 2 was performed using an HP 6890 gas chromatograph (Agilent Technologies, Santa Clara, USA) coupled with a micro-TCD detector (Agilent Technologies, Santa Clara, USA) as previously described  (31). The three major SCFAs (acetate, propionate, and butyrate) were quantified in colonic samples by high-performance liquid chromatography (HPLC) (Elite LaChrom; Merck Hitachi, USA) coupled with a DAD diode as described in reference 31.
Briefly, overlapping reads were merged using PEAR  (37) , and adapters were removed with cutadapt. Reads were then clustered with SWARM  (38) , chimera were detected with VSEARCH (39), and singletons and chimera were removed. SWARM does not use a fixed similarity threshold to pick OTUs but relies instead on an adaptive OTU definition strategy where (groups of) reads are iteratively grown by adding all reads at a distance at most 1 bp from the group, until no group can be grown anymore. All those steps followed the FROGS guidelines and resulted in a 82. 4% read retention rate. Taxonomic assignment was performed against SILVA 132  (40) , and OTUs with affiliations (,95% coverage or ,95% identity) were filtered out. A total of 242 OTUs were obtained. Diversity analyses were performed using phyloseq R package (41) in addition to custom scripts.
Samples were rarefied to even sampling depths (11,898 reads/sample) before computing diversity metrics. We computed both within-sample alpha diversities (observed richness and Shannon) and betweensamples compositional diversities (Bray-Curtis). Principal coordinate analysis (PCoA) was also performed on the Bray-Curtis distance matrix to obtain a two-dimensional representation of the samples. Data are at the SRA repository under Project number PRJNA706948. Metabolomics. From the fermenters incubated with 100 mM NO, 23 samples were collected in triplicates throughout the experiment (before inoculation with fecal samples and during fermentation) and were immediately stored at 280°C. The samples were then sent on dry ice to Metabolon (Research Triangle Park, NC, USA). Samples were prepared using the automated MicroLab STAR system (Hamilton Company).
ACKNOWLEDGMENTS We thank the  Metabolon platform (Research Triangle Park, North Carolina ) and the  Mass Spectrometry platform  ( Centre Hospitalier-Universitaire, Clermont Ferrand, France ). We thank the  INRAE MIGALE bioinformatics platform  for access to computational resources and data storage facilities. We thank  Stéphane Chaillou ,  Rozenn Dervyn , and  Fabienne Béguet-Crespel  for their help during the batch experiments and analysis. We declare that we have no competing interests. This work was supported by an  INRAE  grant of the  Mica Department (MEM). C. B. F. , L. E. -M. , L. L. , S. -L. T. , L. B. , C. M. , J. D. , and S. B. -D. , experiments; M. M. , O. R. , M. L. , and N. R. , data interpretation; S. B. -D. , M. L. , and N. R. , supervision; C. B. F. , L. E. M. , M. L. , and N.
The protein sequence of chicken MSMB3 is highly conserved in avian species The comparison of protein sequences of the three chicken paralogs indicates a moderate sequence identity ranging from 34% (MSMB2 and MSMB3) to 42% (MSMB1 and MSMB2; Fig. 2A ). Among chicken paralogs, chicken MSMB2 possesses the highest percentage of sequence identity with human and porcine MSMBs (46. 8% and 46. 1%, respectively; Fig. 2A ) as well as conserved motifs such as DXKG, HXXN, ISCC, VVEKXD, KTC, CYFXP, and the last W residue that are not recovered in chicken MSMB1 and MSMB3. These observations suggest that chicken MSMB2, porcine, and human MSMBs may be orthologous genes. As expected, using BlastP program  [37] , the highest sequence similarities with chicken MSMB3 were found with proteins from bird species.
Discussion Microseminoprotein proteins are widely distributed in the animal kingdom and display a broad range of biological activities. MSMB genes are present in one single copy in most mammals, while multiple copies have been identified in marsupials (14 paralogs), zebrafish (three paralogs), and chicken (three paralogs)  [1, 4]. The biological significance of these numerous MSMB proteins in some species is still obscure. Chicken MSMB3 paralog has been recently purified, and its protein sequence has been corroborated by mass spectrometry  [26]. However, the genomic localization of the related gene remains controversial because of the withdrawal of MSMB3 gene in the two last chicken genome assemblies (Fig. 1 ). This inconsistency will need to be further corrected as the absence of this chicken MSMB3 in protein databases, including the National Center for Biotechnology Information databank, may introduce some bias when performing proteomics on egg-derived samples.
3B ), and to a lesser extent in the liver (Fig. 3B, E ), and consequently, it may have other physiological functions, besides reproduction. Compared to MSMB1 and MSMB2, MSMB3 is merely expressed in the reproductive tissues of female chickens, especially in the magnum (strong expression) and in the white isthmus (low expression), which is in accordance with the identification of this MSMB3 protein specifically in egg white and eggshell membranes, respectively  [26, 41]. The tissue specificity of MSMB3 strongly supports a role in chicken embryonic development. Recently, a msmb3 gene from Xenopus was described as a potent regulator of neural crest migration  [35]. However, the mature form protein corresponding to Xenopus msmb3 gene as identified in databank only shares 38. 37% sequence identity with mature chicken MSMB3, while it shows 47.
2; Fw-TGGTGATGAGATTGTAGGCTGC; Rev-TGCCACTC CTTTGTTAGCCC), and for 'beta-MSMB-like' (MSMB3, LOC101750704; XM_004942119. 1; Fw-TTCTCTAGGACC CTGTGCGAT; Rev-GTCTTCCACACTGCACCAAA) were designed using Primer-BLAST  [51]  based on the information available in Gallus_gallus-4. 0 (MSMB3) and Gallus_gallus-5. 0 (MSMB1 and MSMB2) assemblies, and purchased from Eurogentec (Angers, France). Their gene specificity was validated by sequencing the corresponding PCR product (GENEWIZ, Paris, France). The cDNA (2. 5 µL) was amplified using SYBR Green I Master Kit (Roche, Mannheim, Germany) and a Light Cycler 480 Apparatus (Roche Diagnostics, Meylan, France). A melting curve program was carried out from 60 to 97 °C in 1 min for each individual sample. Each run included triplicates of control cDNA consisting of a pool of cDNA from all tissues.
All experiments were performed on a dual linear ion trap Fourier Transform Mass Spectrometer (FT-MS) LTQ Orbitrap Velos Pro (Thermo Fisher Scientific, Bremen, Germany) coupled to an Ultimate ® 3000 RSLC Ultra High-Pressure Liquid Chromatographer (Thermo Fisher Scientific, Bremen, Germany), as previously described  [31]. MS/MS ion searches were performed using Mascot search engine version 2. 7. 0. 1 (Matrix Science, London, UK) via PROTEOME DISCOVERER 2. 1 software (Thermo Fisher Scientific) using a homemade database that includes the chicken MSMB3 amino acid sequence. The selected parameters included trypsin as a protease with two allowed missed cleavages and carbamidomethylcysteine (+57 Da), methionine oxidation (+16 Da), amidation (-1), and acetylation (+42 Da) of amino-terminal protein as variable modifications.
3 kV, no sheath, and auxiliary gas flow; heated capillary temperature, 250 °C; predictive automatic gain control enabled; and an S-lens RF level of 70%. The LTQ Orbitrap Velos instrument was operated in positive mode, in the scan range of m/z 400-2000. The MS and MS/MS spectra were performed with a target resolution in the Orbitrap set to r = 100 000. Polydimethylcyclosiloxane (m/z, 445. 1200025) ions were used for internal calibration. Mass spectrometry/MS spectra of interest were manually extracted from Xcalibur and integrated to PROSIGHT PC software v 4. 0 (Thermo Fisher, San Jose, CA, USA) for deconvolution using THRASH (signal/noise : 2) and submitted against the two MSMB3 sequences (with or without G terminal). Lists of monoisotopic masses of ions fragments were extracted and submitted to ProSight Lite tool with a mass tolerance at 10 ppm (at the fragment ion level) in order to note delta mass and scores.
NMR Spectroscopy of MSMB3 MSMB3 was dissolved in H 2 O : D 2 O (9 : 1 ratio) at a concentration of 300 or 50 μM in 100 mM Tris, pH 7. 5, 50 mM NaCl. Ubiquitin, lysozyme, myoglobin, and albumin were purchased from Sigma-Aldrich and dissolved at a concentration of 100 µM in the same buffer as the MSMB3 protein. All NMR experiments were performed on an Avance III HD Bruker 700 MHz Spectrometer equipped with a cryoprobe. NMR data were processed using Bruker's Topspin 3. 2 ™ (Billerica, MA, USA) at 298 K. 1H and 2D 1H TOCSY (T m = 80 ms) spectra were acquired on both samples of MSMB3 in order to assess whether the protein was highly structured. DOSY experiments were acquired on all NMR samples using a standard Bruker sequence and diffusion protocol described in the NMR user manual. Calibration of the gradient strength was performed on a 99.
X-ray structure of MSMB3 MSMB3 was concentrated to 10 mgÁmL -1 before initial sparse matrix crystallization screening using a Mosquito nanoliter pipetting robot (TTP Labtech Ltd. , Melbourn, UK). The crystallization conditions were then manually refined using hanging drops to the final condition: 100 mM phosphate/citrate buffer pH 3. 7, 100 mM Li 2 SO 4 , and 22% PEG1000. The crystals were grown at 20 °C for 2 weeks and then transferred into mother liquor supplemented with 25% ethylene glycol and flash-frozen in liquid nitrogen. 100 K X-ray data were collected at ESRF beamline ID29 and processed using XDS  [52]  and AIMLESS  [53]. The 3D crystal structure of MSMB3 was determined at 2. 14 Å resolution by molecular replacement with Phaser  [54]  of the Phenix suite  [55]  and using protein data bank (PDB) id 3ix0 (PSP94) as a search model.
Acknowledgements We thank  Jacky Ezagal  ( BOA, INRAE, Université de Tours, 37380 Nouzilly, France ) for his help in achieving MSMB3 purification from egg white and  Aurore Thélie  ( PRC, INRAE, CNRS, IFCE, Université de Tours, Nouzilly, France ) for sharing tissues from roosters. We thank the  University of Tours, France , for supporting MB's PhD. We are grateful to the staff of the  ESRF Synchrotron Facility (Grenoble, France)  for the use of ID29 beamline. This work was funded by the  MUSE Project  (Grant No. 2014-00094512 ) from the  Région Centre-Val de Loire, France. The high-resolution mass spectrometer was financed ( SMHART Project ,  35069 ) by the  European Regional Development Fund (ERDF) , the  Conseil Régional du Centre , the  French National Institute for Agriculture, Food and Environment (INRAE) , and the  French National Institute of Health and Medical Research (Inserm).
Gut Microbiota analysis Following DNA extraction and sequencing, raw pairedend reads were processed in a data curation pipeline, that includes a step of removal of low quality reads (Qiime2 2019. 10). 57 Remaining sequences were assigned to samples based on barcode matches, and barcode and primer sequences were then trimmed. The sequences were denoized using the DADA2 method, and reads were classified using Silva reference database (version 132). 58 lpha and beta diversity were computed using the phyloseq package (v1. 24. 2). 59  Principal Coordinate analyses of the Bray Curtis distance and Jaccard index were performed to assess beta diversity. The number of observed species, Chao1, Shannon and Simpson indexes were calculated using rarefied data (depth = 24,000 sequences/ sample) and used to characterize alpha diversity.
Raw sequence data are accessible in the European Nucleotide Archive (accession number:). Differential analysis was performed using the linear discriminant analysis effect size (LEfSe) pipeline. 60 Correlation networks were built using Spearman's correlation and figures were built using Cytoscape V. 3. 8. 0. The connectivity degree of a node is defined by the number of edges of the node. The neighborhood connectivity of a node is defined as the average connectivity of all neighbors of the node.
The LC-MS/MS procedure was performed as previously described. 61 Mass spectra were obtained using an 5500 Q-Trap (Sciex, Concord, Ontario, Canada) equipped with a TurboIon electrospray (ESI) interface set in the negative mode (needle voltage +5000 V) with nitrogen as the nebulizer set at 40 (arbitrary pressure unit given by the equipment provider). Curtain and heater pressures were set at 20 and 40, respectively (arbitrary unit). The ion source temperature was set at 350°C. Declustering and entrance potentials were set at +60 V and +10 V, respectively. The MS/MS detection was operated at unit/unit resolution. The acquisition dwell time for each transition monitored was 25 ms. Data were acquired by the Analyst® software (version 1. 6. 2, -Sciex) in the Multiple Reaction Monitoring (MRM) mode.