dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments Marie-Emmanuelle Saint-Macary  and  Océane Frelin PhD  fellowships were funded by the  French Ministry of Industry and Bayer CropScience  ( CIFRE fellowship ). We are grateful to  Dominique Job ,  CNRS, UMR MAP, Lyon , for continuous interest and critical readings and  François Villalba ,  Bayer CropScience, Lyon  for helpful discussions and comments.
82 Mb  (14) , and larger than those of other spiroplasmas of the same clade, 1. 38 and 1. 55 Mb for S. melliferum IPMB4A  (11)  and S. kunkelii  (37) , respectively. Nevertheless, it is significantly smaller than the 2-Mb size estimated by pulsed-field gel electrophoresis for S. poulsonii strain DW-1  (38). Variation in the number of prophage sequences is thought to be partially responsible for the difference in chromosome size between these two S. poulsonii strains. It is notable that S. citri and related genomes contain numerous viral sequences and range from 1. 6 to 1. 9 Mb  (39) (40) (41). The draft S. poulsonii genome has a GϩC content of 26. 6%, The superscript letter a indicates that for S. chrysopicola, S. melliferum, and S. poulsonii, putative pseudogenes were annotated with the "/pseudo" tag in gene feature as suggested by the NCBI GenBank guidelines and were not included in the total number of protein-coding genes.
9 to 27. 5%). GϩC content variation in spiroplasmas from the Citri clade is usually attributed to the proportion of prophage sequences, which are AT biased. In general, insect bacterial symbiont genomes tend to be highly AT biased. In addition to the 10 chromosomal contigs, two small contigs, A and B, could not be placed on the chromosome by optical mapping (Fig. 1A ). These contigs correspond either to extrachromosomal DNA (plasmid) or to chromosomal sequences that are too small to be placed on the chromosome by the MapSolver software. Spiroplasma species that are members of the Citri clade, S. melliferum KC3 and S. citri GII3-3X (but not S. melliferum IPMB4A), contain plasmids that often carry potential virulence factors  (10, 11, 14). The fact that contigs A and B contain several genes that are found in plasmids in other Spiroplasma species  (42) , like Soj and those for several ARPs (adhesion-related proteins), suggests that they could also be extrachromosomal DNA sequences.
poulsonii MSRO confirms its position in the Poulsonii clade and is identical to that of DW1 isolated from D. willistoni, NRSO isolated from D. nebulosa, and SPHY isolated from D. hydei (Fig. 2 )  (22, 46). Among the 2,263 predicted genes found in the S. poulsonii draft genome, only 401 encode well-characterized proteins, 859 encode hypothetical proteins, 82 are pseudogenes, 94 are viral coding sequences, 3 encode rRNA, and 31 encode tRNAs. The length distribution of predicted amino acid sequences in S. poulsonii is lower than that in other spiroplasmas, indicating that the number of pseudogenes is probably underestimated. However, since these short hypothetical proteins have no functional domain/database hit, it is extremely difficult to determine their function (Fig. 1C ). According to the clusters of homologous genes (COG) classification, ~81% of the S.
poulsonii. Drosophila hemolymph containing S. poulsonii was extracted and incubated in phosphate buffer alone or complemented with glucose, fructose, trehalose, or arginine. Bacterial shape was then monitored by fluorescence microscopy. Representative images (A) and percentages of helical cells compared to the total cell counts after 7 days (B) are shown. S. poulsonii maintains its helical shape for 1 week in the presence of glucose but not fructose, trehalose, or arginine. Shown is the mean Ϯ the standard error of the mean of data pooled from three independent experiments (n ϭ Ͼ100; ***, P Ͻ 0. 0001). ity that cardiolipin produced by Spiroplasma bacteria could also be involved in the pathological effects observed in old flies. Adhesins and surface membrane proteins. Like other members of the class Mollicutes, Spiroplasma bacteria lack a cell wall and their plasma membrane is directly exposed to the external environment.
Whole-genome mapping was performed by OpGen. Contigs obtained by HGAP alignment were placed into optical mapping by in silico alignment with OpGen MapSolver Software 3. 2. 0. Figure  1B  was obtained with Geneious 7. 0. 6 software. To examine the extent of genome rearrangement in Spiroplasma and other, related, bacteria, we used MAUVE 2. 3. 1  (73) , S. melliferum.
ACKNOWLEDGMENTS We thank  Steve Perlman  and  Elodie Ramond  for stimulating discussions. We thank  Keith Hartshman ,  Maroun Bou Sleiman , and  Petr Dostál  for biostatistics help and the  Lausanne Genomic Technologies Facility (UNIL Switzerland)  for DNA sequencing. The Lemaitre lab work was funded by the  ERC  advanced grant ( 339970 ). Chih- Horng Kuo  was supported by research grants from  Academia Sinica  and the  National Science Council of Taiwan  ( NSC 101-2621-B-001-004-MY3 ). Laure Béven  was supported by grants from  Structure Fédérative de Recherche Biologie Intégrative et Ecologie.
The MAEL domain (Fig. 1A ) is composed of a central β-sheet composed of five strands (β 1 -β 5 ), where β 2 is antiparallel to the others. The β-sheet is flanked on one face by three helices (α 8 -α 10 ) and on the other by two helices (α 6 and α 7 ). The bottom of the sheet is capped by helix α 5. This basic configuration is strikingly similar to that found in DEDD family nucleases, as represented by the ε-subunit of Escherichia coli polymerase III (PDB: 1J53)  (Hamdan et al. 2002) , which can be superimposed with a RMSD of 1. 6 Å for 74 of a possible 174 Cα atoms (Fig. 1B ). Despite this overall resemblance between MAEL and DEDD nuclease domains, one striking difference is the presence of a Zn 2+ ion in the MAEL structure that bridges the bottom of the β-sheet and the loop connecting α 9 and α 10 , which encompasses η 2 (Fig.
Biophysical studies Sedimentation velocity experiments (Plateforme Biophysique, Partnership for Structural Biology) were done on an analytical ultracentrifuge XLI (Beckman Coulter) with a rotor speed of 42,000 rpm, at 4°C, using a rotor Anti-60, and double-sector cells of optical path length 12 mm with Sapphire windows. Acquisitions were made using absorbance at 280 nm and interference optics. The reference is the buffer (25 mM MES, 150 mM NaCl, and 5 mM DTT [pH 6. 0]) used for the sample. The analysis was done with the SEDFIT software, version 14. 4fb and Gussi 1. 0. 8d. The RNA-binding studies were carried out using fluorescence spectroscopy. Fluorescence emission measurements of 50 nM fluorescently labeled RNA (5 ′ -FAM-Ex-5-UAUACCUCUGCUUCUG CU-3 ′ ) with increasing concentrations of BmMael constructs were monitored at 25°C (excitation at 495 nm and emission at 515 nm) in the reaction buffer containing 25 mM MES (pH 6.
NOTE ADDED IN PROOF We note that the Lassa virus nucleoprotein (PDB: 4GV9), which is an active 3 ′ -5 ′ exoribonuclease, has both the ECHC and the DEDD motifs required for Zn and Mn/Mg coordination, respectively. This again highlights the importance of DEDD motif for nuclease activity, as we showed here for the MAEL-domain protein from amoeba.
DnaQ is the nuclease domain from the ε subunit of E. coli Pol III. The secondary structure elements: α-helices, 3 10 helices (η), and β-strands are shown above (for BmMael) and below (for DnaQ from Pol III; PDB: 1J53) the alignment. The arrowheads indicate conserved residues required for catalytic activity (red) and Zn 2+ coordination (magenta). (D) A time-course of nuclease activity with EhMael. Time in minutes (min) or hours (h) is indicated.
Crystallographic data collection and refinement statistics by the National Science Foundation International Research Experiences for Undergraduates program under grant no. CHE-1263336. We are grateful for fellowships from the EMBL Interdisciplinary Postdoc Programme (EIPOD) under Marie Curie COFUND Actions (K-M. C. and R. R. P), and European Molecular Biology Organization (EMBO) (R. R. P. ). We acknowledge use of the Grenoble Instruct center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) platforms supported by the French Infrastructure for Integrated Structural Biology Initiative FRISBI (ANR-10-INSB-05-02). This work was supported by grants from Fondation Recherche Médicale (DEP20131128529), Agence National de la Recherche (GuidedMethylation), and National Institutes of Health (1R01HD069592-01A1) to R.
As shown by the autoluminescence image of Fig. 6A  and the quantification of the autoluminescence signal in Fig. 6B , WT accumulated lipid peroxides after 28 h of such stress treatment. The increased oxidation of lipids was confirmed by the amount of hydroxy octadecatrienoic acid (HOTE, the hydroxy fatty acid derived from the oxidation of linolenic acid, the most abundant fatty acid in Arabidopsis leaves), which drastically increased in WT leaves (Fig. 6C ). In striking contrast, the SPS1oex lines were much less sensitive to the light stress, with a noticeable reduction of lipid peroxidation (Fig. 6A-C ). Extensive leaf bleaching was observed in WT plants, but not in the SPS1oex lines (data not shown). The increased phototolerance of SPS1oex lines is confirmed by the maintenance of higher PSII photochemical efficiency (Fv/Fm) compared to WT (Fig.
RNA concentrations were measured on a NanoDrop2000 (Thermo Scientific, USA). Quantitative RT-PCR (qRT-PCR) was performed with cDNA synthesized with the Prime Script TM Reverse Transcriptase (Takara) from 500 ng of total RNA. Design of the specific primers was done for each gene (see supplemental Table  1 ) with the Primer3plus software (www. bioinformatics. nl/cgi-bin/primer3plus/primer3plus. cgi). qRT-PCR was carried out using the LightCycler 480 SYBR Green I Master (Roche) in the quantitative PCR thermal cycler (LightCycler 480 real-time PCR system; Roche). Reaction preparation (total volume of 5 μ l): 2 μ l of cDNA diluted 10-fold, 2 μ l of SYBR Green I Master, and 1 μ M forward and reverse primers. The amplification profile was 95 °C for 10 min and 45 cycles (95 °C/15 s, 60 °C or 56 °C (depending on the gene)/15 s, and 72 °C/15 s).
Lipid peroxidation was imaged by measuring autoluminescence emission. The latter signal is attributed to the spontaneous decomposition of lipid peroxides  68. Spontaneous photon emission from whole plants was measured after a 2-h dark adaptation period using a cooled charge-coupled device (CCD) camera, as explained in  68. Integration time was 20 min and pixel binning was 2 × 2. The images were analyzed with the ImageJ software.
Acknowledgments VTE1oex Arabidopsis seeds were a kind gift from  Peter Doermann  ( University of Bonn, Germany ) and the plastoquinone-9 and plastochromanol-8 standards were obtained from  Jerzy Kruk  ( Jagiellonian University, Krakow, Poland ). They are gratefully thanked for their help. We would also like to thank the members of the GRAP platform ( CEA/Cadarache ) for their help in growing and stressing the plants.
Acknowledgements This paper arose from a workshop held at the  Wissenschaftskolleg zu Berlin (Wiko). We thank the  Wiko  and the  Otto  and  Martha Fischbeck Stiftung  for financial and logistical support and R. Meyer-Kalkus  for encouragement. H. Kokko ,  J. Reinhardt ,  K. Paczolt ,  K. Miller-Hesed  and two anonymous reviewers provided comments that helped improve the manuscript.
e. , upland crops and wetland-rice, grassland and livestock system. We compiled 3 databases of GHG emissions and SOC change for cropland, grassland and livestock systems, and through statistical meta-analysis of paired datasets, the technical mitigation potential of individual management practices were estimated. Statistical meta-analysis methods have been developed for quantitative analysis of research results, from multiple independent experiments  (Guo and Gifford, 2002). They have been used effectively to estimate the effect of different management practices and land use changes on soil carbon stock change and GHG emissions  (Guo and Gifford, 2002; Van Groenigen et al. , 2011; Linquist et al. , 2012; Feng et al. , 2013). These methods usually provide advantages over narrative reviews or quantitative reviews that lack sampling rigor and robust statistical methods  (Johnson and Curtis, 2001).
Database collation 2. 1. 1. Cropland (database 1) and grassland (database 2) Data were extracted from 53 studies on CH 4 emission, 48 studies on N 2 O emission and 50 studies on SOC dynamics (Appendix A) of Chinese rice agricultural ecosystems with different management practices from literature published in both English and Chinese. For upland crops, the database included 27 studies for N 2 O analysis and 62 studies for SOC change analysis (Appendix A). The grassland database consists of 8 and 41 studies on GHGs and SOC change experiments, respectively (Appendix B). The following 3 criteria were applied to select appropriate studies. (1) Studies had to report treatment plot data and control plot data. (2) Studies included in our database were only field experiments; no data were included from pot or laboratory experiments.
(3) The duration of experiment to study the effect of management on SOC change had to be at least 3 years. Reporting standard deviation and number of replicates was preferable, but not essential. For SOC data where no standard deviation or standard error was reported, we assigned standard deviations that are 1/10th of means  (Luo et al. , 2006). If the number of replicates were not reported, the number of replicates was assumed to be 3. The database was prepared in Microsoft Access and includes detailed information on location, climate, land use, treatment, management, fertilizer date and application rate, experiment duration, soil physical and chemical character, depth wise SOC data, GHG emission data, yield data and references.
Livestock (database 3) The livestock database used for this meta-analysis has been described in detail by  Veneman et al. (2015). In brief, a global search was made of relevant databases (including databases of Chinese literature) to identify published research on mitigation of CH 4 from ruminant livestock. For each paper identified, metadata including study design, animal husbandry, diet, mitigation strategy and CH 4 emissions was collated and added to the MitiGate database. To date, the global database contains 294 papers covering in vivo mitigation data for a wide range of animals, production systems, and mitigation strategies. Although a concerted effort was made to identify studies specific to China, very few studies are available, hence a relevant subset of the global database was used for this analysis (Appendix C).
Grazing and mixed farming systems reliant on a predominantly roughage-based diet dominate Chinese ruminant livestock production  (Li et al. , 2008). As diet has a large impact on ruminant enteric CH 4 emissions, and therefore also on the mitigation potential of those emissions, a restricted meta-analysis was performed using only studies where the livestock were fed a mainly roughage/forage based diet (<40% concentrates included). Included in the database were only studies where emissions were reported as g CH 4 kg À1 DMI or where data could be transformed to the same units. In total, 139 studies were included in this analysis including 30 studies from Asia (predominantly Japan). Only 3 studies were identified from China for this analysis.
, 2011). A weighted meta-analysis was done using Meta-Win software  (Rosenberg et al. , 2000). Mean effect size was calculated, with 95% confidence interval (CI). With meta-analysis, we tested the impact of management on the variables of interest i. e. , CH 4 , N 2 O and SOC change, and we also tested whether there are significant differences in mean response ratio among various categories such as region, climate, sub-management. In a procedure analogous to the partitioning of variance in analysis of variance, the total heterogeneity for a group comparison (Q T ) is partitioned into within-class heterogeneity (Q w ) and between-class heterogeneity (Q b ), such that Q T = Q w + Q b. The Q statistic follows a chi-square distribution, with K-1 degrees of freedom  (Johnson and Curtis, 2001; Guo and Gifford, 2002)  For each management and for each variable (SOC, CH 4 and N 2 O), overall mean response and CIs were calculated.
Rice The rice database included 229 data points for SOC change, 267 data points for CH 4 emission and 204 data points for N 2 O emission from soil. The change in CH 4 emission, N 2 O emission and SOC was estimated for different management practices. 3. 1. 1. 1. Impact of fertilizer management on GHG emissions from rice. With growing concern about the adverse environmental impacts of the overuse of N fertilizer  (Ju et al. , 2009; Peng et al. , 2010) , our aim was to see the effect of reduction of N fertilizer application on GHG emissions. Reducing N fertilizer application rate to an amount that would not decrease crop yield could be a potential mitigation option, not only to decrease direct N 2 O emissions from soil, but also to reduce demand for N fertilizer, which would lead to less indirect GHG emissions during N fertilizer production.
Upland crops Managing upland agricultural systems to optimize soil C storage and minimize N 2 O emissions can have a significant effect on future radiative forcing. The upland crop database included 330 data points for SOC change and 169 data points for N 2 O emissions. et al. , 2010) , will result in overall mitigation potentials of 0. 16, 0. 27, 0. 39 and 0. 94 t CO 2 -eq ha À1 yr À1. This analysis does not include reduction in GHG emissions due to fertilizer production, or other losses through NH 3 volatilization or NO 3 leaching. However, N loss due to NH 3 volatilization or NO 3 leaching was included in the economic analysis  (Wang et al. , 2014). Use of N inhibitors such as DCD (dicyandiamide), NBPT (N-(nbutyl) thiophosphoric triamide), and HQ (hydroquinone) could decrease N 2 O emissions from maize by 50% compared to urea-only treatments.
1 ). Exon 1 encodes the signal peptide, whereas exons 2, 3, and 4 encode the extracellular domains, a1, a2, and a3, of the heavy chain, respectively. Exons 5 and 6 encode the transmembrane and cytoplasmic domains. Exon 7 is never present in the mature mRNA, due to the presence of a stop codon in exon 6, and exon 8 is also not translated  [9]. The HLA-G gene promoter has an enhancer A (enh A), S and X1 sequence slightly different from that of other class I genes, and a few alternative regulatory elements to regulate HLA-G gene transcription  [10]. The 3 0 -UTR of the HLA-G gene also contains several regulatory elements, including AU-rich motifs and a poly-A signal, influencing mRNA stability, turnover, mobility and splicing patterns  [9]. HLA-G displays only limited polymorphism, with 50 alleles (IMGT HLA database, December 2013) and 16 proteins, far fewer than for some of the more highly polymorphic HLA class I molecules.
In all the analyses, the best model was considered to be the one with the lowest corrected Akaike information criterion (AICc)  (Burnham and Anderson, 2002; Hurvich and Tsai, 1995). R software (R Core Team, 2015) was used for statistical analyses, with the lme4 package for the linear mixed-effect model  (Bates et al. , 2011)  and the MuMin package for the implementation of the AICc  (Burnham and Anderson, 2002).
Acknowledgments Thanks to  Gerard Duvallet ,  Karine Mouline ,  Clément Gouagna , for helpful discussions within the LAMIVECT frame. Also thanks to the general direction of CIRDES, the entomology field team, the technical staff of the  CIRDES insectarium ,  Christophe Estienne  and  Bernadette Tchikaya  from tsetse insectarium in Montpellier. We deeply thank the referees for the time spent on the first version of the manuscript which helped to considerably improve it.
Enriched domains include secretory lipases, and two domains of unknown function, DUF23 (glycosyl transferase 92) and DUF1034 (Fn3-like). DUF23 (PF01697) was present in five copies in M. lychnidis-dioicae and was only present otherwise in Mixia osmundae and S. roseus in our comparison; three of these five genes were mapped to the GT2 CAZY family expanded in M. lychnidis-dioicae (see below). Both M. lychnidis-dioicae and the rusts contain a large number of proteins with the DUF1034 domain; 8 of the 10 M. lychnidis-dioicae proteins with a DUF1034 domain also contained a subtilase family protease domain. Phylogenetic analysis of proteins with the DUF1034 domain suggested that independent gene family expansions occurred in different species; the rusts formed a separate clade from Microbotryum that is further subdivided, mostly along species lines (Additional file 17).
Domains depleted in M. lychnidis-dioicae relative to other basidiomycetes were also identified, including Cytochrome p450, NACHT, and F-box domains (Table  3  bootstrap replicates; all nodes were supported by at least 99 % of replicates. Ortholog conservation (right panel) highlights genes conserved in all species (core, green), genes conserved in at least two species (conserved, blue), genes unique to the Pucciniomycotina or Microbotryomycetes (orange and red, respectively) and genes unique to a given species (species-specific, yellow) of the three Microbotryomycetes to the other species within the Pucciniomycotina identified additional expansions and depletions common to the species in this lineage. A fungal trichothecene efflux pump (PF06609) gene family was enriched in M. lychnidis-dioicae and S.
Families of structurally-related carbohydrate catalytic and carbohydrate-binding modules (or functional domains) are described in the CAZy database (www. cazy. org) [64]. Such enzymes break down, modify, or build glycosidic bonds. The assignment of the predicted proteins derived from a genome to CAZy families helps to shed light on the particular glycobiological features of an organism  [65]. A total of 236 M. lychnidis-dioicae protein models were mapped to protein families in the CAZy database based on sequence conservation (percentage identity over CAZy domain length) (Additional file  19). The CAZy family profile of M. lychnidis-dioicae was then compared to that recently published for 33 basidiomycetes  [66] , in order to identify expanded and reduced families (Table  4 , Additional file 20).
lychnidis-dioicae, of which four are predicted secreted proteins (MVLG_02682, 04072, 04073, 4074). Part two of the pathway requires polygalacturonase; a total of six M. lychnidis-dioicae proteins contain the polygalacturonase GH28 (PF00295) domain, of which MVLG_02498 is highly induced (over 1,000 fold) in MI-late. The homogalactorunan degradation pathway of M. lychnidis-dioicae may thus perform a similar role as pollen in anther dehiscence when the flowers bloom, since during teliospore formation of M. lychnidis-dioicae, host pollen is no longer available to perform that function. Multiple classes of transporters are expanded in M. lychnidis-dioicae (Table  3 ), enabling uptake of diverse substrates. Major facilitator transporters, sugar transporters, and the fungal trichothecene efflux pump are present at high copy number relative to other Pucciniomycotina.
The M. lychnidis-dioicae genome contains a total of 26 potential sugar transporters, with multiple high identity matches to Srt1 and Hxt1, which may fulfill similar roles. One additional contrast between M. lychnidis-dioicae and the two plant pathogenic rust fungi examined suggests a difference in the relative importance of response to superoxides. Reactive oxygen species (ROS), including superoxides or H 2 O 2 produced by the host plant, are a canonical part of the defense response to pathogens. Microbotryum lychnidis-dioicae is depleted in domains for Peroxidase (PF01328) and copper/zinc superoxide dismutase (PF00080); the two other Microbotryomycetes also lack proteins with these domains. Despite the reduced repertoire of such predicted proteins in M. lychnidis-dioicae relative to the rust fungi, six proteins (MVLG_00980, MVLG_03089, MVLG_03931, MVLG_02439, MVLG_03568, and MVLG_04684) were identified as containing peroxidase 2 (PF01328), peroxidase (PF00141), redoxin (PF08534), or Glutathione peroxidase (PF00255) domains.