dataesr/scientific-paragraphs-categorization huggingface dataset:
Summary and Conclusions An overview about a new data set of satellite-derived CO 2 and CH 4 data products relevant for carbon and climate related research has been presented. The data products have been generated in the framework of the Copernicus Climate Change Service (C3S) and they are publicly and free-of-charge available for interested users Fig. 3  Data quality overview XCO 2 L2 products. From top to bottom: random error, relative accuracy, probability that relative accuracy is < 0. 5 ppm, stability, probability that stability is < 0. 5 ppm/year. From  [8]  Fig. 4  Data quality overview XCH 4 L2 products. From top to bottom: random error, relative accuracy, probability that relative accuracy is < 10 ppb, stability, probability that stability is < 3 ppb/year. From  [8]  including documentation via the Copernicus Climate Data Store (CDS) accessible via the C3S website  [3].
Acknowledgements This study has been funded in parts by the  European Space Agency (ESA)  (via the  GHG-CCI project of ESA's Climate Change Initiative  (CCI, http://www. esa-ghg-cci. org/)),by the  Copernicus Climate Change Service  ( C3S ) implemented by the  European Centre for Medium-Range Weather Forecasts (ECMWF)  on behalf of the  European Commission  (https://climate. copernicus. eu/)and by the  State  and the  University of Bremen. The University of Leicester GOSAT retrievals used the  ALICE High Performance Computing Facility at the University of Leicester. We thank  ESA/DLR  for providing us with SCIAMACHY Level 1 data products and JAXA for GOSAT Level 1B data. We also thank  ESA  for making these GOSAT products available via the ESA Third Party Mission archive. We thank  NIES  for the operational GOSAT XCO 2 Level 2 product and the  NASA/ACOS team  for the GOSAT ACOS Level 2 XCO 2 product.
r e s o u r c e Functions of the rumen microbiome Polysaccharide degradation. Ruminants need efficient lignocellulose breakdown to satisfy their energy requirements, but ruminant genomes, in common with the human genome, encode very limited degradative enzyme capacity. Cattle have a single pancreatic amylase  23  , and several lysozymes  24  which functions as lytic digestive enzymes that can kill Gram-positive bacteria  25. We searched the CAZy database for each Hungate genome (http://www. cazy. org/)  26 in order to characterize the spectrum of carbohydrate-active enzymes and binding proteins present (Supplementary Fig. 2  and Supplementary Table  4 ). In total, the Hungate genomes encode 32,755 degradative CAZymes (31,569 glycoside hydrolases and 1,186 polysaccharide lyases), representing 2.
3 ) highlights the degradation strategies used by different taxa present in our collection. Members of the phylum Bacteroidetes have evolved polysaccharide utilization loci (PULs), genomic regions that encode all required components for the binding, transport and depolymerization of specific glycan structures. Predictions of PUL organization in all 64 Bacteroidetes genomes from the Hungate catalog have been integrated into the dedicated PULDB database  27. The pectin component rhamnogalacturonan II (RG-II) is the most structurally complex plant polysaccharide, and all the CAZymes required for its degradation occur in a single large PUL recently identified in Bacteroides thetaiotaomicron  28. Similar PULs encoding all necessary enzymes were also found in rumen isolates belonging to three different families within the phylum Bacteroidetes (Supplementary Fig.
Gene loss. One curious feature of several rumen bacteria is the absence of an identifiable enolase, the penultimate enzymatic step in glycolysis, which is conserved in all domains of life. Examination of >30,000 isolates from the Integrated Microbial Genomes with Microbiomes (IMG/M) database  32  revealed that enolase-negative strains were rare (<0. 5% of total), and that a high proportion of such strains were rumen isolates belonging to the genera Butyrivibrio and Prevotella and uncharacterized members of the family Lachnospiraceae (Supplementary Table  5 ). In the genus Butyrivibrio approximately half the sequenced strains lack enolase, while some show a truncated form. The distribution of this enzyme in relation to the phylogeny of this genus is shown in Figure  3. This analysis suggests that enolase is in the process of being lost by some rumen Butyrivibrio isolates and that we may be observing an example of environment-specific evolution by gene loss  33.
Biosynthetic gene clusters. We searched the Hungate genomes for biosynthetic gene clusters (Supplementary Fig. 5  and Supplementary Table  7 ) to identify evidence of secondary metabolites that might be used as rumen modifiers to reduce methane production through their antimicrobial activity  34. A total of 6,906 biosynthetic clusters were predicted from the Hungate genomes (Supplementary Note 2). CRISPRs. Identification of CRISPR-Cas systems and their homologous protospacers from viral, plasmid and microbial genomes could shed light on past encounters with foreign mobile genetic elements  35  and somewhat indirectly, habitat distribution and ecological interactions  36. A total of 6,344 CRISPR spacer sequences were predicted from 241 Hungate genomes and searched against various databases (Supplementary Table  8 ).
Comparison with human gut microbiota Many Hungate strains (134/501) were shared between rumen and human intestinal microbiome samples. This is unsurprising, as both habitats are high-density, complex anaerobic microbial communities, producing similar fermentation products, and with extensive interspecies cross-feeding and interaction  41. We performed a comparative analysis against available human intestinal isolates (largely from the HMP), to identify differences that can be attributed to distinct lifestyles and adaptive capacity of rumen microorganisms. The Hungate and human intestine isolate collections were curated to remove redundancy, low-quality genomes and known human pathogens. This resulted in a set of 458 rumen and 387 human intestinal genomes (Supplementary Table  10 ), which was used to identify protein families in the Pfam database that were differentially abundant in isolates from each environment.
DISCUSSION The Hungate genome catalog that we report here includes genomic analysis of 501 bacterial and archaeal cultures that represent almost all of the cultured rumen species that have been taxonomically characterized, as well as representatives of several novel species and genera. This high-quality reference collection will guide interpretation of metagenomics data sets, including genomes recovered from metagenomes (MAGs). The Hungate genome catalog also allows robust comparative genomic analyses that are not feasible using incomplete sequence data from metagenomes. Researchers have access to Hungate Collection strains, which will enable a better understanding of carbon flow in the rumen, including the breakdown of lignocellulose, through the metabolism of substrates to SCFAs and fermentation end products, to the final step of CH 4 formation.
The Hungate genome collection is by no means complete. Some important taxa are missing, especially members of the order Bacteroidales  10, 22. At the start of this project genome sequences were available for strains belonging to 11 (12. 5%) of the 88 genera described for the rumen. Currently, genome sequences are available for 73 (83%) of those 88 genera, as well as for 73 strains that are only identified to the family or order taxonomic level. Of the rumen 'most wanted list' which comprises 70 rumen bacteria 10 , the Hungate Collection has now contributed 30 members. In addition to missing bacteria and archaea, the sequencing of rumen eukaryotes presents considerable technical challenges and although some progress has been made in sequencing of anaerobic fungi  49  , there are no genome data for rumen ciliate protozoa, and only preliminary data on the rumen virome  50.
Microbiome research is moving from descriptive to mechanistic, and to translation of those mechanisms into interventions  51. Using rumen microbiome data to engineer rumens to reduce CH 4 emissions  52  and improve productivity and sustainability outcomes is now in sight  53. The Hungate Collection provides a starting point for this, shedding light on what has been described as 'the world's largest commercial fermentation process'  54. Future studies can use the Hungate resources to improve the resolution of rumen meta-omics analyses, to identify antimicrobials, to source carbohydrate-degrading enzymes from the rumen for use as animal feed additives and in lignocellulose-based biofuel generation, and as the basis for synthetic microbial consortia.
CRISPR-CAS system analysis. A modified version of the Crispr Recognition Tool (CRT) algorithm  61  , with annotations from the Integrated Microbial Genomes with Metagenomes (IMG/M) system  32  was used to validate the functionality of the CRISPR-Cas types (only complete cas gene arrangements were used plus those cas 'orphan' arrays with the same repeat from a complete array within the same genome). This Hungate spacer collection was queried against the viral database from the Integrated Microbial Genome system (IMG/VR database)  73  , a custom global "spacerome" (predicted from all IMG isolate and metagenome data sets) and the NBCI refseq plasmid database. All spacer searches were performed using the BLASTn-short function from the BLAST+ package  74  with parameters: e-value threshold of 1.
0 × 10 -6 , percentage identity of >94% and coverage of >95%. These cutoffs were recommended by a recent study benchmarking the accuracy of spacer hits across a range of % identities and coverage  75. Recruitment of metagenomic sequences. 1,468,357 protein coding sequences or CDS from 501 Hungate isolate genomes were searched using LAST  76  against ~1. 9 billion CDS predicted from 8,200 metagenomic samples stored in the IMG database. Hungate genomes were designated as "recruiters" if the following criteria were met: a minimum of 200 CDS with hits at ≥ 90% amino acid identity over 70% alignment lengths to an individual metagenomic CDS or ≥ 10% capture of total CDS in each genome. The rationale for choosing the minimum 200 hit count was to ensure that the evidence included more than merely housekeeping genes (which tend to be more highly conserved).
Genome comparisons. For rumen versus human isolates comparisons, human intestinal isolate genomes were carefully selected from the IMG database using available GOLD metadata fields pertaining to isolation source (and taking care to remove known pathogens). Genome redundancies within either the human set or the rumen set were eliminated after assessing the average nucleotide identity (ANI) of total best bidirectional hits and removing genomes sharing >99% ANI (alignment fraction of total CDS ≥ 60%) to another genome within that set. Furthermore, low-quality genomes within the human set were flagged and removed based on the absence of the "high-quality" filter assigned by the IMG quality control pipeline owing to lack of phylum-level taxonomic assignment or if the coding density was <70% or >100% or the number of genes per million base pairs was <300 or >1,200 (ref.
All data as well as detailed sequencing and assembly reports can be downloaded from https://genome. jgi. doe. gov/portal/pages/dynamicOr-ganismDownload. jsf?organism=HungateCollection. Hungate Collection and the Global Rumen Census analysis. We used the 16S rRNA gene sequences generated from the Global Rumen Census (GRC)  22  to map the phylogenetic positions of the Hungate Collection genomes onto the known global distribution of Bacteria and Archaea from the rumen. Ten-thousand predicted OTUs were randomly chosen from the total 673,507 OTUs identified from that study in order to construct a phylogenetic tree. The 16S rRNA gene sequences for Hungate Collection genomes were added to the GRC subsample, and all Bacteria and Archaea were checked for chimeras and to ensure they represented separate OTUs using CDHIT-OTU  65  (with a 0.
97% identity Ribosomal Database Project (RDP)  66  followed by visual inspection with JalView 67. Taxonomic classifications were taken from those predicted by the GRC study. A maximum likelihood tree was then separately constructed for the Bacteria and Archaea using two rounds of Fasttree (version 2. 1. 7)  68 : the first round built a maximum likelihood tree using the GTR model of evolution and (options: -gtr -nt); the second round optimized the branch lengths for the resulting topology (options: -gtr -nt -nome -mllen). The resulting phylogenetic trees were visualized using iTOL  55  with the mapped positions of the Hungate genomes.
Carbohydrate-active enzymes (CAZymes). For each of the 501 genomes, the protein sequences were subjected to parallel (i) BLAST queries against CAZy libraries, of both complete sequences and individual modules; and (ii) HMMER searches using CAZy libraries of module family and subfamilies. Family assignments and overall CAZyme modularity were further validated through a human curation step, when proteins were not fully aligned (without gaps) with >50% identity to CAZy records. Conserved single-copy gene phylogeny. A set of 56 universally conserved single-copy proteins in bacteria and archaea  69  was used for construction of the Butyrivibrio phylogenetic tree. Marker genes were detected and aligned using hmmsearch and hmmalign included in HMMER3 (ref. 70) using HMM profiles obtained from Phylosift  71.
genouest. org/sp/ harmonia_axyridis HaxB4 whole genome assembly This paper http://bipaa. genouest. org/sp/ harmonia_axyridis Pool-Seq data (14 pools) This paper SRA: PRJNA474099 RNA-Seq data [26] SRA: PRJEB13023 BAC library This paper https://cnrgv. toulouse. inra. fr/ Library/Asian-ladybird Experimental Models: Organisms/Strains Black-2Spots Gard, France N/A Black-4Spots Gard, France N/A Black-nSpots Ol. Nedved's Czech Republic N/A Red-nSpots Gard, France N/A d CONTACT FOR REAGENT AND RESOURCE SHARING Current Biology 28, 1-7, October 22, 2018 5 (Continued on next page) e1 Current Biology 28, 1-7. e1-e7, October 22, 2018.
Phylogenetic analyses We sequenced nuclear ribosomal DNA internal transcribed spacer (ITS) from 100 samples, large subunit (nLSU, 28S) from 9 samples and translation elongation factor 1-ɑ (tef1) from 44 samples. The resulting sequences are available in INSDC under the accession numbers MG137026-MG137169. We also utilized We constructed four datasets for analyses:  showing which parts should be studied under microscope for comparable results.
RESULTS Phylogenetic analysis of the 28S-ITS-dataset confirms that the Postia caesia complex forms a distinct lineage of closely related species within the genus Postia (Fig. 2 ). The closest, but still distant, relatives of the P. caesia complex in our analysis were P. lactea (the type species of Postia) and P. venata. In the absence of close relatives and small interspecific variation, no firm conclusions can be reached about the earliest diverging species and branching order within the P. caesia complex. Our ITS-dataset separates 19 species with good support (clades with posterior probability≥0. 9): P. auricoma, P. subvirids,  P. arbuti, P. magna, P. coeruleivirens, P. subcasesia, P. bifaria, P. glauca, P. caesia, P. livens, P. yanae, P. cyanescens, P. alni, and P. populi (Fig. 3). In addition, one variable clade that includes P.
dataset does not separate between P. livens and P. subcaesia (Fig. 4 ), while the ITS-dataset clearly does (Fig. 3 ). Second, sequences of P. caesiosimulans form as a clade only in the tef1analysis (Fig. 4 ). The concatenated ITS-tef1-datset includes only specimens, for which both ITS and tef1 were sequenced (Fig. 5 ). It resolves 13 species with excellent support (PP≥0. 99), while failing to treat P. caesiosimulans as a distinct clade from the well-supported P. cyanescens. The ITS-tef1-analysis supports distinction of P. livens from P. subcaesia, a conflict between analysis of ITS (separate clades) and tef1 (one clade). Combining results of these three datasets, we have sequence data available for altogether 24 species in the Postia caesia complex, including 2-3 Southern Hemisphere species we will not treat further here.
Boletus caesius was described based on material from Germany  (Schrader 1794) , and this name was subsequently sanctioned by Fries (1821). Fries's concept of the species and its current synonymy are unclear. No type material survives from Schrader or Fries. Fries (1821) referred directly to two illustrations and indirectly to a third one in his description: All of the above-mentioned illustrations are technically suitable as lectotypes, but are in conflict with Schrader's and Fries's description referring to a blue or bluish fungus and help in no way to anchor the name Postia caesia to modern species concepts. We therefore designate a sequenced neotype from locus classicus for P. caesia. Fries (1821)  considered Boletus coeruleus as a synonyms of Polyporus caesius, and this opinion persists in current literature and mycological databases.
ACKNOWLEDGEMENTS We are indebted to  Frank Dämmrich ,  Ellen Larsson ,  Karl-Henrik Larsson ,  Tuomo Niemelä ,  Beatriz Ortiz-Santana ,  Viktor Papp ,  Dmitry Schigel ,  Gerhard Schuster  and  Petr Vampola  for valuable specimens and sequences. Tuomo Niemelä also commented the manuscript. Sampsa Lommi  prepared the distribution maps. Alix David provided valuable ideas for species delimitation in this complex. We are ever grateful for  Yu-Cheng Dai  and his students for arranging a collecting trip in China resulting in valuable collections. Part of the sequences were produced by the  Finnish Barcode of Life (FinBOL) initiative. CSC -IT Center for Science (Espoo, Finland)  provided computational resources. This research was made possible by the  PolyPEET  project led by  David Hibbett  ( NSF  grant  DEB0933081 ) and the  Commission Marie Curie  grant  PIOF-GA-2011-302349.
(Ryvarden 2016)cribed this species from Ecuador. It is the only yellow-colored representative of the P. caesia complex known so far from the tropics. It differs from similarly colored European species, P. auricoma and P. luteocaesia, in having larger basidiocarps, not turning green when bruised, and smaller pores, 8-10 per mm(Ryvarden 2016). Schleswig-Hollstein, Travemünde,  Hermannshöhe, dicot, 24 Jun. 2007,Miettinen 11703 (H). UK,England,  Hampshire, New Forest, Quercus sp. , 4 Nov. 1995, Legon (O, H). Suffolk, Postia atrostrigosa (Cooke) Rajchenb. , N. Z. Jl Bot. 33: 104. 1995. Basionym: Polyporus atrostrigosus Cooke, Grevillea 19 (89): 2. 1890. Remarks: Rajchenberg (1995) re-introduced this species after morphological and cultural studies of specimens from New Zealand. We sequenced a Tasmanian specimen, which differs by just 1 bp from two Argentinian ITS sequences available in GenBank (JX090109 and JX090110); they represent a unique species that may well be P.
While Bitcoin has indeed no formal governance (there is no constitution or founding principles setting decision-making procedures), a set of practices have emerged, in the interplay of three categories of actors: core developers, miners, and users. Taking over from Nakamoto's initial drafting of the protocol, the core development team enjoys a sort of moral authority over the community, which entrusts it for technical decisions. Core developers control the GitHub repository (https://github. com/bitcoin/) and the domain The second is called a "hard fork", which touches on the fundamental characteristics of the protocol such as block structure or difficulty rules. As it is not backward-compatible, a hard fork requires all full nodes to upgrade, or the blockchain could split between users using the new updated version and those using the older version.
DOES BITCOIN IMPROVE PAYMENT PRIVACY? Finally, one last perceived advantage of Bitcoin over conventional currencies is the better protection of payment privacy that it is supposed to provide, since its decentralised payment system makes it independent of banks or other payment intermediaries, and does not require disclosure of an account holder's identity. Admittedly, this is not a claim that more knowledgeable Bitcoin proponents are likely to make, as it has been at the centre of much criticism. However, it remains a recurrent preconception, at least in popular opinion and among some Bitcoin users, and therefore deserves a brief discussion here. There are many good reasons why people might seek privacy in their transactions. They might wish to avoid mass data collection of their transaction history by private companies for targeted marketing, or they can be political opponents, fearing retribution from authoritarian regimes.
Results A major QTL controls the differences of resistance to VHSV in B57 and A22 fish To understand the mechanisms underlying the differences of susceptibility to VHSV between B57 and A22 isogenic lines, we first looked for the presence of the major QTL we previously identified  [13]. To do so, F2 segregating offspring were produced by backcrossing a B57-A22 F1 hybrid and a parental B57 (BC57-A22). BC57-A22 offspring were then waterborne challenged with VHSV 07-71, and individuals were genotyped for 8 markers (microsatellites or SNP) belonging to the major QTL area on chromosome Omy3 (RT31 linkage group). The presence of a QTL for resistance in the region was then tested using an interval mapping method implemented in the QTLMap software. As shown in Fig. 1a , a highly significant QTL was found in this area, confirming the key role of this genomic region in the difference of resistance to VHSV among lines B57 (resistant) and A22 (susceptible).
Likelihood (LRT) values were obtained using the QTLMap software. The 95% confidence interval (CI) of the QTL was obtained using the Hendge Li method and is indicated in grey. b Conservation of the effect of the QTL on survival rate in BCB57-A22 backcross progeny after infection with VHSV 07-71 by injection. 125 fish from a B57-A22 backcross were injected with VHSV. Mortality was monitored daily and surviving fish were sacrificed at day 28 post infection. The allelic status at Omy1392INRA marker was determined for every fish, and cumulative death curves were built for the two alternative genotypes (B57-A22 and B57-B57) potential contrast between the responses in the two genetic backgrounds. We have previously observed that the type I IFN response to VHSV infection was much faster in B57 cells, with mRNA for the IFNφ1 (aka IFN1) already expressed at 4 h post infection (hpi), while it was just detectable in A22 cells only at 8hpi.
Strong induction of innate immune-related pathways in B57 following VHSV inoculation To analyze the nature of the transcriptomic response to VHSV in both genetic backgrounds, we performed a functional annotation analysis mapping zebrafish homologs of rainbow trout modulated genes to zebrafish pathways in the KEGG database. As shown in Additional file 2, VHSV induced the modulation of metabolic pathways, such as sugar and lipid pathways, as well as global cellular signaling pathways, such as mTOR and MAPK. Interestingly, genes belonging to sugar metabolism were induced in both A22 and B57, in line with a previous observation that glycolytic pathways were induced after VHSV infection in zebrafish  [28]  (Table  1 ). Cell cycle-related pathways were found downregulated also in both cell lines (Table  2 ), which may reflect their common ability to slow cellular growth in response to virus infection.