dataesr/scientific-paragraphs-categorization huggingface dataset:
Mostly, more than four comparison stars were used in obtaining the standard magnitude of V838 Mon. The log of all the photometric data of V838 Mon is provided in the CDS table (see Table  2  for representative lines), and the measurements are presented in Fig. 1. The errors in Table  2  for the TO and SAAO data are a combination of the Poissonian error of instrumental magnitudes and the uncertainties of the colour transformation. For our main dataset from NOT the errors in the BVRi are the standard deviation of V838 Mon standard magnitudes when using several comparison stars. The errors of instrumental magnitudes are negligible in these filters. In U band the Poissonian noise of the instrumental magnitudes was also taken into account; during the start of our NOT observations, when V838 Mon was as faint as 21 mag, the noise was considerable.
26 Å pix -1 (R ∼ 9000 at 6600 Å). The exposure times usually varied between 500 and 1200 s guaranteeing a S/N ≥ 100. In addition, a spectrum from September 2007 with the similar set-up is used in this work for comparison purposes. All spectra obtained with NOT were observed with the slit at the parallactic angle. The standard data reduction steps were performed with the MIDAS software package in the context of long-slit spectra. The flux calibration is based on the matching of the synthetic photometry of the instrumental flux in the NOT ALFOSC U BVRi bands to the quasi-simultaneous high-precision photometry (cf. Sects. 2. 1, 3. 1, and 3. 2). For synthetic photometry and brightness zero-point fluxes we used the database provided by the Spanish Virtual Observatory 9. For clearer demonstration of the evolution of spectral shape (spectrophotometric gradient) of V838 Mon (cf.
Sects. 3. 3. 1 and 3. 3. 2) we performed relative flux normalisation using points selected in the stellar continuum at 7560 Å and 6577 Å, which we expect are close to the real continuum, for the grism 4 and 17 settings, respectively. Telluric correction was omitted due to the strong contamination with the stellar molecular absorption bands. The dates of the spectral observations are indicated in Fig. 1. A complete log as well as the data can be acquired from the NOT FITS Header Archive 10. The representative example of reduced spectra is available at the CDS.
Conclusions We present new extensive and homogeneous observational datasets of the intriguing object V838 Mon. Before calibrating the photometric data we performed a solid stability check of the comparison stars. Our photometric and spectroscopic monitoring of this peculiar target over more than a decade reveals impor-tant insights into its temporal evolution. We note a brightening in photometry, in particular in the blue bands, and a simultaneous weakening of the molecular absorption bands. The resonance lines of Ca i and Li i consist of two absorption components, a blue-shifted one tracing the expanding shell and a red-shifted one originating from the ongoing but steadily weakening wind from the SG. The continuous strengthening of the Hα emission traces the gentle reappearance of the hot companion.
A good match between the literature (black) and our (blue) values is visible. M02 refers to data from  Munari et al. (2002) , K02 to  Kimeswenger et al. (2002) , C03 data to  Crause et al. (2003) , and TO to data from this work. from the rather small telescope size and from the faintness of the V838 Mon during the past ten years in bluer bands. On the other hand, the possible reason for the small systematic offset may be related to the exact position and shape of filter transmittance curve relative to the sharp-edged spectral features of V838 Mon. However, because our measurements fit well with other published data during the 2002 outburst, we consider our calculated standard magnitudes to be reliable. Moreover, we restrict our analysis of the light curve from 2009 onwards to the homogeneous data collected with NOT because these data were obtained with a uniform telescope and instrument setting.
Acknowledgements. We thank the anonymous referees for the constructive suggestions that helped to improve the manuscript. Based on observations made with the  Nordic Optical Telescope , owned in collaboration by the  University of Turku and Aarhus University , and operated jointly by  Aarhus University , the  University of Turku  and the  University of Oslo , representing  Denmark, Finland  and  Norway , the  University of Iceland  and  Stockholm University  at the  Observatorio del Roque de los Muchachos, La Palma, Spain , of the  Instituto de Astrofisica de Canarias. The data presented here were obtained with ALFOSC, which is provided by the  Instituto de Astrofisica de Andalucia (IAA)  under a joint agreement with the  University of Copenhagen  and NOT. Observations on 2019 November 29 were done as part of the  NOT science school  for upper secondary school students organised in  Tuorla Observatory.
In addition, this paper uses observations made at the  South African Astronomical Observatory (SAAO). Analyses done in this paper use a GAIA shoftware. GAIA is a derivative of the Skycat catalogue and image display tool, developed as part of the VLT project at ESO. Skycat and GAIA are free software under the terms of the GNU copyright. The 3D facilities in GAIA use the VTK library. For further details, see http://starlink. eao. hawaii. edu/starlink T. L. , M. K. , and B. D. acknowledge financial support from the  Czech Science Foundation (GA ČR , grant numbers  20-00150S  and  19-18647S ). The Astronomical Institute of the  Czech Academy of Sciences  is supported by the project  RVO : 67985815. This project has received funding from the  European Union 's  Framework Programme for Research and Innovation Horizon 2020  ( 2014-2020 ) under the  Marie Skłodowska-Curie Grant  Agreement No.
e. eIF4E_Arm_ P00). For each new haplotype detected, the number after "P" was incremented ("P01", "P02", …). For both coding and amino acid sequences levels of homozygosity, heterozygosity, haplotypic richness and the presence of variations were evaluated and compared between groups and subgroups using Chi-square tests (χ 2 tests) statistical analyses performed by XLStat software v. 2020. 1. 3. Frequencies of haplotypes and amino acid variations were also calculated and were called rare haplotypes and rare amino acid variations when their occurrences were less than 5%. Genetic diversity parameters. Genetic diversity estimates were calculated using DNAsp v. 5. 10. 01 software  40. The haplotype diversity (Hd), the nucleotide diversity (π), the ratio of non-synonymous to synonymous substitutions (dn/ds ratio) and the Tajima's D statistic were calculated from allelic data for each main group and subgroup.
The Datamonkey online database (http:// www. datam onkey. org) was used to test the selection pressure on (i) the whole gene sequences with the RELAX test to analyze whether the strength of the selection has been relaxed or intensified along the phylogeny of the sequences and the BUSTED model (Branch-site Unrestricted Statistical Test for Episodic Diversification) to provide a gene-wide test for positive selection at at least one site on at least one phylogenetic branch, and (ii) at sequence sites with the FUBAR test (Fast Unconstrained Bayesian AppRoximation) for large data sets with a Bayesian approach to infer the dn/ds ratio on a per-site basis and detect positive or negative pervasive selection at the amino acid level assuming the selection pressure for each site is constant along the entire phylogeny  41.
Predicting effects of amino acid variations on protein conformation/function. To predict the potential effect of amino acid variations on the protein conformation and/or function, three computational methods were used: (i) Meta-SNP (https:// snps. biofo ld. org/ meta-snp/ index. html) a random forest-based binary classifier predictor combining predictions of four methods (SNAP2, SIFT, PANTHER, PhD-SNP) and four elements extracted from the PhD-SNP protein sequence profile based on training dataset derived from SwissVar 42 , (ii) MutPred2 (http:// mutpr ed. mutdb. org) an algorithm able to quantify the pathogenicity of amino acid substitutions and describe how they can affect the protein function by modeling a broad repertoire of structural and functional alterations from amino acid sequence  43  and (iii) PredictSNP (https:// losch midt.
chemi. muni. cz/ predi ctsnp1/) a consensus classifier combining eight prediction methods (MAPP, PhD-SNP, PolyPhen-1/-2, SIFT, SNAP, nsSNPAnalyser, PANTHER) to provide a more accurate and robust alternative to the predictions based on accession integrated tools and weighted by the method-specific confidence scores  44. Even though these softwares based their predictions on mammal (mostly humans) databases (no such plant-specific predictors exist), they enabled the classification of amino acid variations found along the eIFiso4E protein for Armeniaca, Amygdalus and Persica accessions to select variable haplotypes for testing PPV infection in the greenhouse.
Technical replicates consist in the same accession grafted on three independent PPV-susceptible rootstocks. One vegetative cycle consists in a succession of 3 months of dormancy in a cold chamber followed by 3 months of growth in the greenhouse. To look for the presence of the virus in the leaves, viral particles were quantified by ELISA, providing optical density values (OD). When OD was at least twice higher than the OD value of the negative control (the non-infected cultivar GF305), the sample was considered as infected. In this case, a score of 1 was attributed to the sample. Otherwise, the score was 0. After each cycle, the average response score was calculated from the two ELISA measurements while at the end of the phenotyping tests, the global average score was obtained by averaging data from the three complete cycles.
Statements. Most of the samples used in this study were collected before October 2014, in the frame of the FP7 IRSES-246795 "STONE" project. Appropriate permissions from responsible authorities for collecting and using Prunus samples from Central Asia, Caucasia and China were obtained by the local collaborators. The rest of the samples were kindly provided, with due authorizations, by the curators of the French INRAE Genetic Resources Centre (GRC, Bourran), the US ARS-USDA repository, the Lednice germplasm collection; further details are available on their respective databases.
Acknowledgements The authors wish to pay their respects to the late  Dr Raul Karychev , former scientist of the  Kazakh Research Institute of Horticulture and Viticulture (Almaty ) who helped tremendously to initiate this work and did not have the chance to see its completion, even though he was an important contributor to this project. We acknowledge the European FP7  IRSES-246795  " STONE ", the  ANR-13-KBBE-0006  " COBRA " and the  PRIMA FREECLIMB  (#  1813-2 ) grants. S. L. was recipient of a  Chinese Scholarship Council PhD  grant. V. D. and S. L. thank the  French Embassy in Beijing  for accommodation and research support in China ( Xu Guangqi  program  2016-2018 ) and the  Research Federation on Integrative Biology and Ecology of Bordeaux University  for a travel grant. The authors wish to acknowledge all the people who helped in collecting the samples.
| Structural organization of IMPDH chimeras Oligomeric state analysis prompted us to assess the structural characterization of IMPDH chimeras into more detail by x-ray crystallography and cryoelectronic microscopy (Cryo-EM) single-particle analysis to correlate at the molecular level allosteric regulation transfer between Classes I and II IMPDHs. Crystals were only obtained for the chimera IMPDH CDec BDpa (Figures  5a-c  and S8a-k and Table  S3 ). The best diffracting crystals afforded the determination of the 3D structures of the apo form (PDB code 7QBJ), and of the IMP-(PDB code 7QEM) and MgATP-bound (PDB code 7QDX) forms. A clear octameric organization is detected for all these structures by the PISA server  (Krissinel & Henrick, 2007). The catalytic domains are clearly visible in all monomers while the Bateman domains are only partially visible.
The first two structures (apo form and IMPbound form) are highly similar, the only difference is the presence of visible IMP molecule in the catalytic domain of the structure of the IMP-bound IMPDH CDec BDpa while the remaining of the structure superimpose perfectly. These two structures adopt a flattened octamer as previously described  (Labesse et al. , 2013)  in the apo-form or inhibitor-bound form of other IMPDHs. On the contrary, the MgATP-bound form shows a more spherical octameric architecture although not to the extent of the MnATP-bound form of the wild-type IMPDHpa (PDB code 4DQW). In agreement, two ATP molecules bind to each Bateman domain in a highly similar manner in both structures. This suggests that manganese was actually a good mimic for magnesium, and this allows matching the small magnesium cation in the electron density (Figure  S8g, h ).
Noteworthy, the structural changes observed at atomic resolution match the changes detected in solution by AUC and SAXS. This confirms that little crystal packing artifacts (if any) are at play here. To get insights into the oligomeric state of the other chimera IMPDH CDpa BDec and its regulation by MgATP, we collected, after unsuccessful crystallization trials for this variant, cryo-EM data of the enzyme in the absence and presence of this nucleotide. In the apo form (Figure  6  and Table  S4 ), we observed the dual presence of octameric and tetrameric species of the chimera. Figure  6  shows crystallographic models fitted into the obtained 3D cryo-EM maps of the octamers (Figure  6a-d ) and tetramers (Figure  6e -g) at 3. 52 and 7. 01 Å resolution, respectively. For both, the Bateman domains seem to be floppy and are only visible in some 2D and 3D classes corresponding to the octamers (Figures  6a  and S9 ).
coli strain in minimal M63B1 medium, since bacteria can only rely on de novo synthesis of nucleotides and not the salvage pathway in these culture conditions, and therefore in need of IMPDH to finalize guanine nucleotide synthesis. Our results showed that deletion of the Bateman domain altered bacterial fitness. Chimera complementation showed similar growth rates for strains expressing an IMPDH containing the same Bateman domain (wild-type or chimera). These observations suggest that the Bateman F I G U R E 7 Growth curves in M63B1 medium at 37 C of JW5401 strains transformed with different pCmcI857 constructs encoding wild-type or chimeric IMPDHs. Optical density was measured at 600 nm every 15 min for 12 h. For each strain (expressing either wild-type IMPDHec, IMPDH CDpa BDec, wildtype IMPDHpa, or IMPDH CDec BDpa as indicated above the curves), mean data curves are shown, with error bars representing standard deviation of five independent experiments.
| Enzymatic assay and kinetic characterization Enzyme activity of each IMPDH variant was measured in a total volume of 0. 5 mL of the corresponding optimal kinetics buffer (noted buffer K, see Table  S1 ) at various concentrations of IMP and NAD + , with or without 5 mM MgATP. After addition of IMPDH diluted in buffer K (final concentration range: 0. 1-2 μM), initial velocity values were determined at 30 C on an Eppendorf ECOM 6122 photometer by monitoring the formation of NADH at 340 nm. Experimental data of at least three individual experiments were fitted using GraphPad Prism (GraphPad Prism Software, Inc. ) and KaleidaGraph (Synergy Software, Inc. ) according to the Michaelis-Menten equation (Equation  1 ) or in the case of substrate inhibition at high substrate concentrations to Equation (2) (Equation  2 ), where v 0 is the initial reaction rate, V m the maximum reaction rate, [S] the NAD + or IMP concentration, K m the Michaelis constant, and K i the inhibitory constant.
| Crystallography and x-ray diffraction data collection Crystallization condition screenings and hits optimization were performed at the Crystallography Core Facility of the Institut Pasteur  (Weber et al. , 2019). Crystallization screens were carried out for two chimeras (IMPDH CDec BDpa and IMPDH CDpa BDec) using the sitting-drop vapor diffusion method using a MosquitoTM nanoliterdispensing system (TTP Labtech). Reservoir solutions were 150 μL in volume and sitting drops were composed of 200 nL of protein (20 mg/mL) and 200 nL of reservoir solution, which was provided from different commercially accessible kits. The crystallization plates were stored at 18 C in a Rock-Imager1000 ® (Formulatrix) automated imaging system. For further optimizations, some of the conditions of interest were reproduced manually via the hanging drops method in Linbro plates.
Diffracting crystals were only obtained for the chimera IMPDH CDec BDpa. Best crystals were obtained in the presence of 0. 1 M Tris pH 8. 5, 8% (wt/vol) PEG 8 K and 1 mM IMP (PDB code 7QBJ); 0. 05 M HEPES pH 7, 12% (wt/vol) PEG 3350, 1% tryptone, 0. 001% NaN 3 , and 10 mM IMP (PDB code 7QEM); or 10% (wt/vol) PEG 3 K, 0. 1 M NaCacod pH 6. 5, 0. 2 M MgCl 2 , 5 mM MgATP, 4 mM NAD + (PDB code 7QDX). The collection of x-ray diffraction data from flash-cooled single crystals was conducted at Synchrotron SOLEIL, beamline Proxima 1 or 2A, (Saint-Aubin, France). Structures were solved by molecular replacement using Phaser AutoMR  (Nimmesgern et al. , 1999)  with previously published IMPDHpa structures (PDB 6GJV for the apo form  [Alexandre et al. , 2019]  and PDB 4DQW MgATP-bound form  [Labesse et al.
, 2013] ) as search probes. Model refinement was conducted with several types of refinement approaches using the current Python-based Hierarchical Environment for Integrated Crystallography (Phenix) software  (Afonine et al. , 2010; Burnley et al. , 2012; Liebschner et al. , 2019)  and with alternating manual rebuilding in COOT  (Emsley & Cowtan, 2004). Data processing and model refinement statistics are shown in Table  S3. All structural figures were generated with the PyMol Molecular Graphics System, Version 1. 3r1 (Schrödinger, LLC).
I G U R E 5 X-ray structures of the IMPDH CDec BDpa chimera (a-c) and comparison with the previously published structures of the wild-type IMPDHpa structures (d-f). (a) apo form (PDB code 7QBJ), (b) in the presence of IMP (PDB code 7QEM), or (c) in the presence of MgATP (PDB code 7QDX). The polypeptide chains (catalytic domains in green and Bateman domains in blue) are shown as ribbons. IMP molecules, each bound to the catalytic sites, are shown as orange spheres. MgATP molecules, each bound to the Bateman domains are shown as dark blue spheres. For both ligands, there is a full occupancy of the binding sites. (d) Superimposition of the structures of the apo forms of the IMPDH CDec BDpa chimera (shown in red) and the wild-type IMPDHpa (shown in bronze; PDB code 6GJV [Alexandre et al. , 2019]).
(e) Superimposition of the structures of IMPDH CDec BDpa chimera in complex with IMP (shown in orange) and the wildtype IMPDHpa (shown in bronze; PDB code 6GJV [Alexandre et al. , 2019]). (f) Superimposition of the structures of the IMPDH CDec BDpa chimera (shown in blue) and the wild-type IMPDHpa (shown in purple; PDB code 4DQW [Labesse et al. , 2013]) in complex with MgATP.
ACKNOWLEDGMENTS This work was supported in part by the  Centre National de la Recherche Scientifique (CNRS) , the  Institut National de la Santé Et de la Recherche Médicale (INSERM) , and the  Institut Pasteur. This work was also supported by the  French Infrastructure for Integrated Structural Biology (FRISBI)  ( ANR-10-INBS-0005 ). Antoine Gedeon  and  Nour Ayoub acknowledge PhD  fellowships from the  Médicament, Toxicologie, Chimie et Imageries PhD  school (MTCI, ED 563),  Université Paris Cité. We thank  Jean-Marc Ghigo  for providing the E. coli ΔguaB strain ( JW5401 ) from the Keio collection. We thank  Zakaria Jemouai  for his participation in the optimization of protein expression and purification conditions. We thank  Pierre-Olivier Vidalain ,  Alexandre Chenal  and  Nicolas Wolf  for fruitful discussions.
The authors are grateful to the staff of the " Plate-Forme de Cristallographie " for robot-driven crystallization screening. We thank beamline scientists from the  Synchrotron SOLEIL (St. Aubin, France)  for advice in x-ray diffraction data collection on PROXIMA-1 and PROXIMA-2A beamlines, and SAXS data collection on SWING beamline. The NanoImaging Core at  Institut Pasteur  is acknowledged for support with sample preparation, image acquisition, and analysis. The NanoImaging Core was created with the help of a grant from the  French Government 's  Investissements d'Avenir program  ( EQUIPEX CACSICE -Centre d'analyse de systèmes complexes dans les environnements complexes ,  ANR-11-EQPX-0008 ). We acknowledge the staff from the  Instruct Image Processing Center (I2PC) at the National Centre of Biotechnology-CSIC (Madrid)  for support with cryo-EM image analysis.
Grant/Award Number:  ANR-10-INBS-0005 ;  Médicament, Toxicologie, Chimie et Imageries PhD  school (MTCI, ED 563);  French Government's Investissements d'Avenir program  ( EQUIPEX CACSICE -Centre  d'analyze de systèmes complexes dans les environnements complexes, Grant/Award Number:  ANR-11-EQPX-0008 ;  National Centre of Biotechnology-CSIC (Madrid).
F I G U R E 5 X-ray structures of the IMPDH CDec BDpa chimera (a-c) and comparison with the previously published structures of the wild-type IMPDHpa structures (d-f). (a) apo form (PDB code 7QBJ), (b) in the presence of IMP (PDB code 7QEM), or (c) in the presence of MgATP (PDB code 7QDX). The polypeptide chains (catalytic domains in green and Bateman domains in blue) are shown as ribbons. IMP molecules, each bound to the catalytic sites, are shown as orange spheres. MgATP molecules, each bound to the Bateman domains are shown as dark blue spheres. For both ligands, there is a full occupancy of the binding sites. (d) Superimposition of the structures of the apo forms of the IMPDH CDec BDpa chimera (shown in red) and the wild-type IMPDHpa (shown in bronze; PDB code 6GJV [Alexandre et al. , 2019]).
Here, we investigate the impact of overlooked but widely used parameters associated with the prokaryotic remineralization (e. g. CF, PGEs) on the magnitude of the discrepancy. Our aims are: 1) to highlight the most sensitive parameters for which the determination of an accurate value is critical in the context of balancing of mesopelagic carbon budget; 2) to perform a mathematical inversion method to estimate the most plausible in situ values of the most sensitive parameters from a limited field dataset; 3) to discuss our results in the context of mesopelagic carbon budget and carbon sequestration by the BCP.
In situ Data Most of the data used in this study originated from the DY032 (June-July 2015) cruise at the PAP (Porcupine Abyssal Plain) site in the North Atlantic onboard the RRS Discovery. Some data unavailable for DY032 were estimated from a previous PAP cruise,  D341 (July-August 2009). Most of the in situ data were compiled from already published cruise data (e. g. Giering et al. 2014; Belcher et al. 2016; Baumas et al. 2021; Fuchs et al. 2022). Their post-treatments to suit our study framework are described below. Additionally, we used data (ecto-enzymatic activities along with total hydrolysable amino acids and carbohydrates, depth profile of heterotrophic prokaryotic production and respiration under in situ pressure versus atmospheric) from the PEACETIME cruise  (Guieu et al. 2020 ) that occurred in May 2017 in the Mediterranean Sea to illustrate some points in our discussions (see supp data).