dataesr/scientific-paragraphs-categorization huggingface dataset:
(2012)  for the tropics (see Table  S1  in the supporting information). • Aboveground Litter Carbon comes from the "Global Database of Litterfall Mass and Litter Pool Carbon and Nutrients"  (Holland et al. , 2015). It includes site measurements of among others aboveground litter IIASA/ISRIC/ISSCAS/JRC, 2012). We derived the organic carbon mass using soil density data from the database (http://webarchive. iiasa. ac. at/Research/LUC/External-World-soil-database/HTML/). • The LAI3g product derived from the third generation of the Normalized Difference Vegetation Index (NDVI3g) by the Global Inventory Modeling and Mapping Studies (GIMMS) group. The NDVI3g from the Advanced Very High Resolution Radiometer (AVHRR) sensors was released for the period 1981 to 2011  (Zhu et al. , 2013). The original 15-day time resolution and 1/12°spatial resolution was averaged to a monthly time step and 1°spatial resolution.
39 mgCO 2 /m 2 /s; see Table  2 ) as suggested by the  Domingues et al. (2007)  values for Amazon species that directly reduce assimilation rates (see equation 3). In general, all forested zones have reduced GPPs with the new version of the model (Figure  S1 ). This is also linked to the reduction in Ammax deduced from the  Kattge et al. (2009)  Vcmax values using equation 6 resulting in smaller maximum photosynthetic rates for trees (see Table  2 ). In the boreal forest, GPP is now underestimated. Needleleaf trees in particular, boreal and to a lesser extent temperate, are not productive enough, especially in summer (Figure  S2 ). Here, it is mainly the strong reduction in specific leaf area (SLA see Table  2  from 13. 3 to 5. 0 m 2 /kg) from the TRY database that plays a role. The smaller SLA leads to a smaller area of leaves per unit of carbon assimilated and a reduced area to photosynthesize.
Carbon Pools 4. 2. 1. Vegetation biomass Aboveground biomass in ISBA is calculated as the sum of leaves, stem/twigs, trunk, and the numerical storage pool. Overall, the distribution of aboveground biomass reflects the forest distribution (Figure  12 ). Compared to the  Liu et al. (2015) , both versions of the model tend to overestimate biomass in the boreal 10. 1029/2019MS001886 and temperate forests, although slightly less with ISBA_bgc6 (Figure  S8 ). Data using radar data give even lower estimates for temperate and boreal forest aboveground biomass (Table  S1 ) indicating room for improvement in the model  (Thurner et al. , 2014). Following the changes in NPP, tropical evergreen forests where biomass was too low with bgc5 (Figure  12e ) have now too much aboveground carbon (Figure  12f  and Table  S1 ;  Baccini et al.
Litter Pools There are very few data sets on aboveground litter, let alone belowground litter, to evaluate models. One exception is the "Global Database of Litterfall Mass and Litter Pool Carbon and Nutrients"  (Holland et al. , 2015)  including site measurements of among others aboveground litter carbon dating from 1827 to 1997. To compare our simulation results, we excluded data with reported management. Overall, ISBA_bgc6 simulates much less aboveground litter (Figure  13 ) than ISBA_bgc5 (Figure  S9 ) and has values that are more in the range of the in situ observations on all continents, except N America. This reduction in aboveground litter is mainly due to the effect of fire that consumes aboveground litter (see section 2. 8) and was not represented in ISBA_bgc5. The tropical forest is the only biome with increased aboveground Journal of Advances in Modeling Earth Systems litter because NPP and hence litterfall have increased while humidity limits fire.
Vegetation and Soil Turnover Time Turnover times, estimated as the ratio of a carbon pool to its input flux, may be used as tool to understand how a model might behave in climate change simulations in terms of carbon cycling  (Koven et al. , 2015; Wu et al. , 2018). Here, we chose to estimate vegetation turnover time as biomass/NPP and soil turnover time as "dead carbon"/NPP, where dead carbon represents litter and soil carbon. To be exact, turnover times should be evaluated at equilibrium. But to be able to compare them with the available data set, we use the last 30 years of our simulations. The input flux to the litter and soil carbon pool should be the mortality flux (dead leaves, branches, plants), not available from data. However, at equilibrium, this flux is equal to NPP. This is why we estimate soil turnover time as the ratio of litter and soil carbon to NPP.
Compared to the LAI3g, this reduced peak LAI is an improvement in the tropics, India and S-E Asia where the model used to overestimate LAI (Figures  15e  and 15f ). In the boreal forest, ISBA_bgc6 now slightly underestimates peak LAI, from the Pacific NW to central and E Siberia. For most vegetation types, the smaller peak LAI is related to the reduced maximum photosynthetic rate Ammax, decreasing GPP and NPP and hence LAI, as it results from the carbon balance of the leaves. In the tropical forests, where NPP is actually increasing, the reduced peak LAI is mostly due to the drop in SLA (14. 6-8. 3 m 2 /kg) suggested by the TRY database for tropical evergreen trees. In the boreal forests the strong reduction in specific leaf area for conifers, both boreal and temperate (from 13. 3 to 5. 0 m 2 /kg) from the TRY database also plays a major role that adds up to the reduction in Ammax.
Summary and Conclusions The carbon cycling module of ISBA was greatly/largely updated throughout the 2010 decade. The model now takes into account land cover changes, wild fires, and leaching of carbon from the soil, processes that were neglected in previous versions. The existing processes were also revised, mainly modifying tree leaf dark respiration and using the TRY database for updating photosynthesis and leaf traits parameters. The comparison of the results of two versions of the model with a present-day atmospheric forcing shows that the gross vegetation carbon fluxes (GPP and Ra) are greatly improved through mainly a general decrease in GPP and a strong decrease in Ra for trees. The net flux NPP is also improved mainly for tropical forests. Vegetation  Journal of Advances in Modeling Earth Systems biomass has increased in the tropics where it was underestimated, and the high bias is reduced in the midlatitude to high latitude.
van der Werf et al. , 2017;is compared to the yearly maps at 1°resolution of burnt area derived from satellite data, census data, and vegetation byMouillot and Field (2005). CO 2 emissions from fire come from the Global Fire Emissions Database, Version 4. 1 (GEFD4,van der Werf et al. , 2017; Randerson et  al. , 2017)(https://www. globalfiredata. org/data. html). • The DOC originating from soil carbon leaching is compared to the global, spatially explicit, multielement, and multiform model of nutrient exports by rivers (NEWS2, https://marine. rutgers. edu/globalnews/datasets. htm) described in.
Acknowledgments The authors would like to thank  Stephanie Faroux , and  Marie Minvielle  from the  CNRM  for their important scientific and technical work on the SURFEX modeling platform. The authors are also grateful to the anonymous reviewers. This research was supported by the  "Centre National de Recherches Météorologiques" (CNRM) of Météo-France  and the  "Centre National de la Recherche Scientifique" (CNRS)  of the French research ministry, the  H2020  project  CRESCENDO Coordinated Research in Earth Systems and Climate: Experiments, Knowledge, Dissemination and Outreach , which received funding from the  European Union   Horizon 2020 research and innovation program  under grant agreement no  641816. It was also supported by the  Acceleration of Permafrost Thaw (APT)  project through  BNP Paribas Foundation , grant number  2014-00000004300  and the "Global Earth Observation for integrated water resource assessment" (eartH2Observe) project funding from the  European Union Seventh Framework Programme  ( FP7/2007-2013)  under grant agreement No.
van der Werf et al. , 2017;is compared to the yearly maps at 1°resolution of burnt area derived from satellite data, census data, and vegetation byMouillot and Field (2005). CO 2 emissions from fire come from the Global Fire Emissions Database, Version 4. 1 (GEFD4,van der Werf et al. , 2017; Randerson et  al. , 2017)(https://www. globalfiredata. org/data. html). • The DOC originating from soil carbon leaching is compared to the global, spatially explicit, multielement, and multiform model of nutrient exports by rivers (NEWS2, https://marine. rutgers. edu/globalnews/datasets. htm) described in. This product derived from the Moderate Resolution Imaging Spectroradiometer (MODIS) on board the U. S. National Aeronautics and Space Administration (NASA) Earth Observation System (EOS) satellite Terra has a yearly time step and a 1-km spatial resolution to compare with model results (NASA LP DAAC, 2017).
It covers years 2000- 2013 ( Monfreda, Ramankutty, and Foley (2008)rod/mod17. php) • The Harvested Area and Yield for 175 crops data set described inMonfreda, Ramankutty, and Foley (2008)to compare crop NPP. This land use data set combines national, state, and county level census statistics with a global data set of croplands, on a 5-min × 5-min spatial grid and is representative of the years 2000 (http://www. earthstat. org). • For heterotrophic respiration, we use the data set from Hashimoto et al. (2015) that combines in situ data from the Soil Respiration database (Bond-Lamberty et al. , 2018) and global gridded climate data. It is 10. 1029/2019MS001886 Journal of Advances in Modeling Earth Systems based on data from 1965 to 2012 and has a 0. 5°spatial resolution (http://cse. ffpri. affrc.
Design A health service evaluation survey was carried out. setting The survey was carried out online across Europe. Participants Clinical experts, researchers and policymakers involved in national tinnitus healthcare and decision-making. Outcome measures A survey was developed by the study steering group, piloted on clinicians from the TINNET network and underwent two iterations before being finalised. The survey was then administered to clinicians and policy-makers from 24 European countries. results Data collected from 625 respondents revealed significant differences in national healthcare structures, use of tinnitus definitions, opinions on characteristics of patients with tinnitus, assessment procedures and particularly in available treatment options. Differences between northern and eastern European countries were most notable.
Acknowledgements We are thankful to all participating professionals, who have dedicated their limited time to address our queries. We are also grateful to all project members, work package leaders and management of TINNET ( COST Action , number  BM1306 , a European tinnitus research network funded from 11 April 2014 to 10 April 2018), who disseminated our requests for participation in their respective countries and networks. Special thanks are due to Thomas Fuller who attended some of the discussions in the final stages and offered valuable insight and assistance during consensus voting. Contributors RFFC wrote the first draft of the manuscript and performed the statistical analyses. DK and TB developed and designed the online questionnaire and performed preliminary analyses. DJH provided extensive feedback on the initial draft and cowrote further versions of the manuscript.
We additionally present a draft genome of CCMP470, which is the first genome available for a staurosiroid lineage. 270 Pfams (19%) found in the CCMP470 genome are not known in other diatom genomes, which otherwise does not hold big novelties compared to genomes of non-staurosiroid diatoms. Notably, our DNA library contains the genome of a bacterium within the Rhodobacterales, an alpha-proteobacterial lineage known frequently to associate with algae. We demonstrate the presence of commensal alphaproteobacterial sequences in other published algal genome and transcriptome datasets, which may indicate widespread and persistent co-occurrence.
The diatoms are important primary producers in aquatic ecosystems, being responsible for 20% of global net primary productivity  1  , and play an important role in the biological carbon pump  2. Diatoms are proposed to number within the tens of thousands of species  3  , as has been further supported by analysis of the Tara Oceans dataset  4. The evolutionary diversity of diatoms has been studied extensively: historically by means of morphological and fossil information, and recently also through molecular phylogenetics. Recent phylogenetic studies, using multigene datasets, have consistently recovered the following results: (1) among the ancestral "centric" diatoms, radial centrics are paraphyletic to the polar centric lineages, (2) the polar centric diatoms are themselves paraphyletic to the monophyletic "pennate diatoms", and (3) the pennate clade comprises araphid species, which are paraphyletic, and raphid species, which are monophyletic  5, 6.
Phylogenetic studies of diatoms now routinely use multigene markers, often in a combined dataset with small subunit ribosomal DNA (SSU), the Rubisco large subunit (rbcL), and the photosystem II binding complex (psbC), to reconstruct higher level phylogeny (e. g. , above genus to class relationships)  7. Well-curated culture collections are an ideal resource for phylogenetic studies when one tries to characterize a particular group of organisms, as strains are often tied to various useful information such as sampling sites and dates, suitable culture conditions, and sometimes microscopic images and even gene sequences  8, 9. 1] [12] [13]  ), we obtained the strain CCMP470, which was previously annotated as Leptocylindrus danicus, from the National Center for Marine Algae and Microbiota (NCMA, formerly CCMP).
Draft genome and phylogeny. To better understand the evolutionary placement of CCMP470, we sequenced and assembled a draft genome. The crude CCMP470 genome sequence was separated into two constituent sets of contigs with differing GC contents, with medians of 64% and 51%, respectively (Fig. 2A ; Table  S1 ), indicating that it in fact represents a simple metagenome. These contigs were confirmed using MetaBAT  21  and last common ancestor (LCA) reconstruction analysis  22, 23  to correspond to two, different co-sequenced organisms: the diatom host and a bacterial symbiont (Fig. S1A and Dataset S1). The CCMP470 host genome assembly is 22. 99 Mb and consists of 4,992 contigs, containing 8,970 gene models, slightly fewer than the numbers (11,184-34,500)  annotated in other diatom genomes (Fig.
oceanica, or Fragilariopsis cylindrus (Fig. 5A )  24, [30] [31] [32]. These include two tetratricopeptide domains (PF07926, PF13429) and a methanol dehydrogenase (PF13360), each found in >5 copies in the CCMP470 genome, but absent from all four remaining diatoms (Fig. S2B ). Conversely, we identified 358 Pfams found in all four remaining diatom genomes, but absent from CCMP470, including a pentatricopeptide domain (PF01535) and zinc-binding alcohol dehydrogenase (PF00107), both present in >5 copies in all other diatoms (Fig. S2B ). Next, we investigated whether any genes in the CCMP470 genome have specific evolutionary ancestries that separate them from other diatom lineages. The evolutionary origin of each gene in the CCMP470 genome was investigated using a reciprocal BLAST best hit (RbH) search, integrating published genomic and transcriptomic data from across the tree of life, and divided into 144 sub-categories based on recently published taxonomies  5, 23, 27  (Table  S3 ).
5B ). Seven of the HGT genes occur on contigs containing at least one sequence of verified diatom origin, indicating that they are not contaminants within the diatom sequence fraction (Table  S4 ). The remaining HGT gene (g7872 C) is an apparent chimeric or "S-gene"  34  , consisting of an N-terminal carbonate dehydrogenase domain of apparent verrucomicrobial origin; and a C-terminal Hcf164 domain of diatom origin (Fig. S4 ). Origin and function of the CCMP470 symbiont. Next, we considered the genome of the CCMP470 bacterial symbiont, which was 3. 48 Mb in size and consisted of 3,158 genes (Table  1A ; Table  S1  and Dataset S1). The majority of the bacterial contigs were identified using LCA annotations as resolving within the Rhodobacteraceae, an alpha-proteobacterial group frequently identified as algal symbionts and associated with algal blooms  [35] [36] [37] [38] [39].
In silico analysis of metabolic interactions between CCMP470 and its bacterial symbiont. Since previous studies have shown that CCMP470 can form symbiotic interactions for nutrient exchange with Rhodobacteraceae, e. g. , supplying fixed organic carbon to the species Planktotalea frisia  43  , we explored the potential of metabolite exchange between CCMP470 and its co-sequenced symbiont in silico. We searched for possible metabolic interactions between the two species using ModelSEED  44. This identified 1,201 reactions based on 768 annotated genes for the bacterium, and 1,084 reactions from 502 genes for the diatom (Table  S5  and Dataset S2). We noted that the bacterial commensal encodes the complete pathway for the synthesis of bacteriochlorophyll, from geranylgeraniol and chlorophyllide precursors, suggesting that it is likely to be photo-heterotrophic.
The libraries were then loaded on one PTP and pyrosequenced using the GS FLX Titanium Instrument (Roche) according to the manufacturer's protocol. A total of 2,666,857 reads (795,989,340 bp) were obtained and assembled using Newbler software (version vMapAsmResearch-04/19/2010-patch-08/17/2010) and default parameters. Contigs were separated into those of probable bacterial and of host origin using LCA analysis, as described in  22, 23  , and MetaBAT analysis, as described in  21  ). functional analyses. Protein prediction was based on NCBI ORFinder (https://www. ncbi. nlm. nih. gov/ orffinder/), except that we did not consider start and stop codons within conserved domains. Introns were identified by the generalized mode of GENESCAN  56  for each one of the ORFs. For functional analyses, GO category annotation was generated using the Pfams found by CLADE  28  and refined by GO consortium PFAM2GO (citation http://current.
Furthermore, additional staurosiroid sequences were also appended after  14, 16  who newly sequenced further staurosiroids with the description of new Plagiostriata species, P. baltica. The length of the final datasets was 4,221 bp (1,616 bp for SSU, 1,473 bp for rbcL and 1,132 bp for psbC). RAxML 8. 2. 0 61 was used for ML analyses with the GTRGAMMAI model, with partitions for each codon position for protein-coding gene for which gamma correction values and a proportion of invariable sites were obtained automatically by the program. For each dataset the best scoring ML tree was obtained with 200 replicates of hill-climbing searches; we performed 1,000 bootstrap analyses.
Acknowledgements D. N. acknowledges a fellowship funded by the  Stazione Zoologica Anton Dohrn (SZN)  within the  SZN-Open University Ph. D. program. R. G. D. was supported by a  CNRS   Momentum Fellowship  and E. K. was supported by the  Marie Curie Postdoctoral Fellowship IRONCOMM. We thank  Carmen Minucci  for sequences of psaA of Plagiostriata s0388. Computations were partially performed on the NIG supercomputer at  ROIS National Institute of Genetics, Japan. Work in the Bowler lab  is supported by the  Investissements d' Avenir programmes PSL  and MEMOLIFE:  MEMO LIFE  ( ANR-10-LABX-54 ), and  PSL*Research University  ( ANR-11-IDEX-0001-02 ).
3c ). The Pearson correlation between the P7 and P14 fold change data sets for transcripts expressed above 100 normalized reads was close to 0. 8, indicating that Tbpl2 loss of function similarly altered RNA levels at P7 and P14 stages. We therefore focused on the P14 stage for the rest of the study. In WT P14 oocytes transcripts corresponding to 10791 genes were detected. Importantly, many of these detected transcripts have been transcribed at earlier stages and are stored in growing oocytes  19. As there is no Pol II transcription in Tbpl2 -/-growing oocytes 2 , RNAs detected in the Tbpl2 -/-mutant oocytes represent mRNAs transcribed by a TBP/TFIIDdependent mechanism and deposited into the growing oocytes independently of TBPL2 activity at earlier stages. The proportion of genes (1396) upregulated following Tbpl2 deletion (Fig.
TBPL2-driven promoters are TATA box-containing with sharp TSS selection The promoter usage changes during zebrafish maternal to zygotic transition revealed different rules of transcriptional initiation in oocyte and in embryo, driven by independent and often overlapping sets of promoter "codes"  27. This switch has not yet been demonstrated in mammals and the role of TBPL2 during oogenesis remained to be investigated. To this end, we mapped the TSS usage by carrying out super-low input carrier-CAGE (SLIC-CAGE)  28  from WT and Tbpl2 -/-P14 oocytes. To characterize only the TBPL2-driven promoters we removed the CAGE tags present in the Tbpl2 -/-dataset from the WT P14 dataset, to eliminate transcripts that have been deposited at earlier stages (hereafter called "TBPL2-specific-only"). Conversely, the Tbpl2 -/-dataset corresponds to the TBP/TFIID or TBPL2-independent-only TSSs (hereafter called "TBPL2-independent-only").
Next, we analysed the genome-wide enrichment of T-and/or A-rich (WW) dinucleotide motifs within the -250/+250 region centred on the dominant TSSs of the TBPL2-specific-only and TBPL2-independent-only oocyte TSS clusters (Fig. 4a, b ). TBPL2-specific-only TSS clusters are strongly enriched in a well-defined WW motif around their -30 bp region (Fig. 4a , read arrowhead) (see also Cvetesic et al. , in submission). In contrast, only about 1/3 rd of the TBPL2-independent-only TSS clusters contained WW-enriched motifs at a similar position (Fig. 4b , read arrowhead), as would be expected from promoters that lack maternal promoter code determinants  27   (Cvetesic et al. , in submission). As canonical TATA boxes are often associated with tissue-specific gene promoters, we investigated whether the above observed WW motif densities correspond to TATA boxes using the TBP position weight matrix (PWM) from the JASPAR database as a reference.
All rights reserved. No reuse allowed without permission. above defined two categories confirmed that TBPL2-specific-only TSS are sharper compared to the TBPL2-independent-only TSS clusters (Extended Data Fig. 4c, d ). In order to test whether TBPL2 controls transcription initiation from maternal promoter code determinants, we grouped the expression profiles corresponding to each consensus TSS clusters, to characterise promoter activity profiles among datasets by performing selforganizing maps (SOM) (Extended Data Fig. 4e ). We then focussed on the two most distinct SOM groups: the down-regulated promoters (blue group, containing 9442 consensus TSS clusters) (Fig. 4d ) and the up-regulated promoters (red group, with 6900 consensus TSS clusters) (Fig. 4e ). Motif analyses of these two categories of promoters in their -35/+5 regions relative to the different dominant TSSs indicated that only the core promoters associated to TBPL2-specific-only dominant TSSs belonging to the down-regulated gene promoters contain a well-defined 7 bp long TATA box-like motif (W-box) in their -31 to -24 regions (Fig.
Crystallization and structure determination of TBPL2 C Purified TBPL2 C was screened for crystallization in a range of conditions using the sitting drop method. Crystals obtained in 26% PEG3350, 0. 2 M magnesium formate were harvested flashfrozen in liquid nitrogen and used for data collection at Diamond Light Source, (beamline I04-1). Diffraction data were processed and scaled using software XDS 38 and the structure solved by molecular replacement using software Phenix 39 , with TBP C (from PDBID 1NVP) as a starting model. The structure was iteratively rebuilt and refined. Data and refinement statistics are provided (Supplementary Table  5 ). Structure images were prepared using software PyMOL.