dataesr/scientific-paragraphs-categorization huggingface dataset:
Fine-mapping Fhb1 A large mapping population was developed to genetically narrow down the Fhb1 region and thereby reducing the number of Fhb1 candidates. Polymorphisms for marker design were detected utilizing mapped RNA-seq data from the susceptible Remus to the Fhb1 region of CM-82036. Using only SNPs unique to CM-NIL38-mapped reads with a frequency of >90 %, we detected 30 polymorphisms within predicted coding sequences, which comprise a conservative estimate of SNP in the region (Supplementary Table  S6 ). We used these and SNP identified by mapping reads from a previous RNA-seq project using similar NILs  (Kugler et al. 2013)  to design six KASP genotyping assays. An additional KASP assay was constructed based on resequencing the PCR product of UMN10 from the susceptible and highly polymorphic locus of cv.
A highly similar protein from Aegilops tauschii has been annotated as 'putative disease resistance RPP13-like protein 1' (GenBank accession: EMT27135. 1). The version of the susceptible Chinese spring gene is identical in 898 of 905 amino-acids, leaving room for functional differences (Supplementary File Fig. S7 ). Yet, lack of expression is hard to reconcile with the otherwise suggestive role of this candidate disease resistance gene. How can genes on the Fhb1 contig help explain the higher ability to inactivate DON?  Lemmens et al. (2005)  have associated the Fhb1 locus with the higher ability to metabolize DON into the non-toxic DON-3-O-glycoside, which is a product of the activity of toxin-specific UDP-glucosyltransferases (UGT,  Poppenberger et al. 2003). No such gene is encoded on the Fhb1 contig, gene #6 annotated as a HGA-like UGT does share similarities to the large super family encoding small molecule conjugating UGTs  (Ross et al.
Acknowledgments Open access funding provided by  University of Natural Resources and Life Sciences Vienna (BOKU). We would like to acknowledge  S. Cauet ,  G. Beydon  and  N. Rodde  for assisting in BAC library screening and sequencing in Toulouse,  France. A. Müllner ,  D. Fink  and  S. Zimmerl  have assisted in marker development and fine mapping in Tulln,  Austria. C. Ametz  is acknowledged for bioinformatical support. This work was financed by the  Austrian Science Fund (FWF)  ( SFB F3705 ,  F3708 ,  F3711 ) and the  Deutsche Forschungsgemeinschaft (DGF)  project  LAP3714.
Downregulation of Fn14 by a siRNA (Supplementary Figure  S3A ) abolished TWEAK effects on Pi-induced calcification as compared with scrambled transfected cells (Figure  1b ). To understand how the activation of TWEAK/Fn14 axis promoted Pi-induced h-VSMCs mineralization in vitro, the influence of TWEAK on h-VSMCs osteogenic transition, TNAP activity and matrix metalloproteinase (MMP) activity was evaluated in both non-calcific (1. 1 mmol/l Pi) and pro-calcific (3. 0 mmol/l Pi) conditions. Data obtained by qRT-PCR demonstrated that a 7-day exposure to 100 ng/ml TWEAK reduced by about 70% the expression of the contractile markers acta2 and myh11 in non-calcific conditions (Figures  2a  and b ) and significantly amplified by about three-fold Pi-induced decrease of both markers in procalcific environment (Figures  2a  and b ).
siRNA targeting Fn14, RelA and RelB (Invitrogen) were used at a concentration of 10, 50 and 20 nM respectively. Scrambled siRNA (Ambion, Foster City, CA, USA) served as negative control. qRT-PCR. Total RNA was extracted using the TRI reagent method (Sigma, St Louis, MO, USA). Then 1 μg RNA was reversed transcribed into cDNA using the 'High Capacity cDNA Reverse Transcription Kit' (Applied Biosystems, Foster City, CA, USA) according to the manufacturer's instructions. Predeveloped primer for acta2, myh11, bmp2, spp1, mmp2, mmp9, tnfsf12 and GAPDH were from Applied Biosystems. Quantitative PCR was performed by 7500 Real Time PCR System with the Prism 7000 System SDS Software (Applied Biosystems) and RNA expression of the different genes was corrected for GAPDH. Western blotting. H-VSMCs (60 000 cells/well in six-well plates) were stimulated with Pi and/or TWEAK.
Acknowledgements. We thank the  European Renal Association-European Dialysis and Transplant Association  ( ERA-EDTA ) for awarding valuable support, especially for funding LH with a long-term postdoctoral fellowship. We also thank  Luis Blanco-Colio  for critical reviewing of the paper. AO is supported by  Instituto de salud Carlos III (ISCIII) / Fondo Europeo de Desarrollo Regional (FEDER)  funds  PI13/00047 ,  PI15/00298 ,  PIE13/00051 , European uremic toxins (EUTOX),  Sociedad Española de Nefrolgia ,  ISCIII-RETIC REDinREN RD012/0021 ,  Comunidad de Madrid Consorcio Investigación en Fracaso Renal Agudo (CIFRA)   S2010/BMD-2378  and  Programa Intensificación Actividad Investigadora  ( ISCIII/Agencia Laín-Entralgo/CM ). LH received funding from  ERA/EDTA   LTF 153-2013. ABS, MDS-N and RV-B are supported by  ISCIII  postdoctoral contracts Miguel Servet  MS12/03262 ,  MS14/00133  and  Sara Borrell   CD14/00198.
While alpha-diversity measures (richness and exp(Shannon H)) are hardly affected by contemporary environmental conditions, species (OTU) turnover and community similarity (β-diversity) across taxonomic groups showed strong correlation to environmental parameters. Logistic regression models predicted significant correlations between the occurrence of specific ciliate genera and individual nutrients, the oceanic carbonate system and temperature. Planktonic ciliates displayed distinct vertical distributions relative to chlorophyll a. In contrast, the Tara Oceans dataset did not reveal any evidence that latitude is structuring ciliate communities. Recent results from the circumglobal Tara Oceans expedition impressively demonstrated that heterotrophic protists are even more diverse (and at the same time much less understood) than prokaryotes in the planktonic ocean ecosystem 1.
In specific, we used this global ocean ciliate plankton dataset to test the following hypotheses: (i) Ciliate diversity is a function of environmental variables such as temperature, salinity, oxygen, nutrients and the oceanic carbonate system; (ii) Ciliate diversity is a function of depth (surface waters versus deep chlorophyll maximum); (iii) Ciliate diversity is a function of latitude; (iv) Global marine ciliate plankton diversity is high; and (v) Local diversity covers a small/high proportion of global diversity. Finally, we tested the hypothesis that the extent of ciliate diversity in open ocean waters is still far from being fully appreciated.
Methods Dataset. The genomic and environmental data used in this study were collected during the circumglobal Tara Oceans expedition  21 (2009-2012). Plankton samples were collected from surface waters (SRF) and deep chlorophyll maximum (DCM) at 47 stations in seven oceanic regions (Fig. 1 , Supplementary Table  S1 ). Detailed sampling strategy and methodology are described by Pesant and colleagues  22. In short, plankton samples (at least 0. 1 m 3 seawater) were collected on polycarbonate membranes. Samples were stored frozen until DNA extraction. Detailed information about DNA extraction, PCR amplification and Illumina sequencing of V9 rDNA metabarcodes, as well as subsequent sequence data cleaning and taxonomic assignment can be found in de Vargas et al. 1. In short, DNA was extracted from each polycarbonate membrane and the hypervariable V9 region of the 18S rDNA was then PCR amplified using the universal eukaryotic primers 1389F (5′ -TTGTACACACCGCCC-3′ ) and 1510R (5′ -CCTTCYGCAGGTTCACCTAC-3′ )  23.
Purified PCR products were Illumina-sequenced using a Genome Analyser IIx system (Illumina, San Diego, CA, USA). Subsequent sequence data cleaning included quality checking (Phred score filtering, elimination of reads without correct primers, and removal of chimeras) and conservative filtering (removal of metabarcodes present in less than three reads and two distinct samples). Tara Oceans metabarcodes were taxonomically assigned using the V9 PR 2 database  24. V9 ciliate sequence data used in this study are available from the Dryad Digital Repository (http://dx. doi. org/10. 5061/dryad. c3n62). Ciliate V9 rDNA reads with a minimum length of 100 base pairs were clustered into operational taxonomic units (OTUs) at a 97% sequence similarity threshold using a modified script of usearch quality filter (usearch_qf)  25  and QIIME v.
1. 7. 0  26. Details on the modified script can be found in Oikonomou et al. 27. For final taxonomic Figure  1. Geographic locations of sampling stations. Planktonic ciliate communities from surface waters and deep chlorophyll maximum layer have been sampled in seven oceanic regions. MS: Mediterranean Sea, RS: Red Sea, NIO: North Indian Ocean, SIO: South Indian Ocean, SAO: South Atlantic Ocean, SO: Southern Ocean, SPO: South Pacific Ocean. This map was created with the R package 'maps' v. 2. 3-6 (http://CRAN. R-project. org/package= maps)  68. assignment of the OTUs the representative read (longest) of each OTU was subjected to BLAST analyses  28  against GenBank's nr nucleotide database release 200 in JAguc  29. JAguc employs BLASTn searches with algorithm parameters adjusted for short reads (-m 7 -r 5 -q -4 -G 8 -E 6 -b 50).
Statistical analyses. All statistical analyses were conducted and visualized in R Studio (v. 2. 15. 1, http://r-projekt. org). Rarefaction analyses were performed in R using the 'vegan' package  30. To predict ciliate OTU richness, we calculated the abundance-based coverage estimator (ACE) and the incidence-based coverage estimator (ICE) using the 'fossil' package  31  in R. Alpha diversity for each sample was assessed by the exponential of the Shannon entropy H (exp(H), effective number of species 32 ) using the 'vegan' package  30  in R. Prior to calculating the effective number of species, the OTU abundance table was randomly subsampled to the lowest number of reads present in any sample. Additionally, the ciliate OTU richness (number of OTUs) of each sample was calculated. To investigate differences in ciliate OTU compositions between samples the OTU abundance table was transformed to presence-absence data and the binary Jaccard (J incidence ) index was calculated.
Jaccard distances were then analyzed by non-metric multidimensional scaling (NMDS) using the 'vegan' package in R  30. Environmental parameters were fitted to the ordination using the function 'envfit' of the 'vegan' R package. The fit (R 2 ) of each variable to the ordination was assessed with a Monte-Carlo analysis of 10000 permutations. In general, all data was tested for normal distribution before deciding which statistical test to use (parametric or nonparametric). The Two-Sample t-test was used to test for significant differences in ciliate OTU richness and exp(H) between surface and DCM samples (global dataset). For individual sample comparisons, we used the One-Sample t-test. Spearman's rank coefficients were calculated in R to relate ciliate diversity and environmental data (Supplementary Table  S1 ).
Multiple logistic regression analyses  33  in R modelled the relationship between environmental parameters and presence-absence of ciliate genera. Since the complete set of environmental parameters could not be obtained at all sampling sites, we had to run the logistic regression on two independent sets of environmental parameters. The first dataset included temperature, salinity, oxygen and nutrients (NO 2 -, NO 3 -, PO 4  3-, Si(OH) 4 ) of 42 surface samples  34  (Supplementary Table  S1 ). The second dataset included measures of the oceanic carbonate system (pH, CO 2 , pCO 2 , HCO 3 , CO 3 , total alkalinity, total carbon) of 23 surface samples  35  (Supplementary Table  S1 ). For taxonomic assignment of ciliate OTUs on genus level, we applied a 95% sequence similarity threshold to reference sequences  36.
Identification of novel ciliate sequence diversity. To screen for genetically divergent ciliate OTUs we used the Swarm-network approach  37. First, ciliate reads of the Tara Oceans dataset were dereplicated using the custom script as recommended on the Swarm homepage (https://github. com/torognes/swarm). Then, unique reads were clustered using Swarm v1. 2. 5  38  with d = 1. From the resulting swarms, the "seed reads" (i. e. the most abundant read of each swarm) of the 200 most abundant swarms were BLASTed 28 against GenBank's nr nucleotide database (rel. 200) to identify their taxonomic affiliation. Only swarms assigned to ciliates with a sequence similarity of at least 80% to reference sequences were included into the network analyses. The seed reads were then aligned in Seaview  39  and pairwise sequence similarities between each pair of seed reads were computed with PairAlign  17.
Results Local and global distribution of marine planktonic ciliates. The final ciliate dataset consisted of 6,137,350 high quality V9 SSU rDNA reads, which clustered into 1,274 distinct OTUs called at 97% sequence similarity threshold. The number of reads obtained from the different oceanic regions varied between 207,644 reads (Red Sea) and 2,105,449 reads (Mediterranean Sea), whereas the number of OTUs ranged from 401 in the Southern Ocean to 1,024 in the South Pacific Ocean. For surface waters (SRF) we obtained 3,864,389 V9 reads and for the deep chlorophyll maximum (DCM) 2,272,961 reads. These reads clustered into 1,159 and 1,176 OTUs, respectively. Rarefaction analyses indicated near-saturated sampling for most sampled regions (Supplementary Fig. S1 ) and depths (Supplementary Fig. S2 ).
The occurrences of 20 ciliate genera were related to the oceanic carbonate system (Supplementary Table  S4 ). The final model of each genus contained between one and three parameters for this dataset, with the most important parameter being pH value, followed by total alkalinity and total carbon. Also for the carbonate system, specificity (82%) was higher than sensitivity (49%). The overall percentage of correct predictions was 74% for the oceanic carbonate system data. Ciliate communities in surface waters were notably different from ciliate communities in the deep chlorophyll maximum. J incidence distances among ciliate communities of the DCM were significantly smaller when compared to J incidence distances between ciliate communities from the surface waters and the DCM (p < 0. 001). This result was also mirrored in significant differences (Two-sample t-test: p < 0.
Thus, waters with high chlorophyll content probably attract a higher diversity of predatory ciliates than waters with lower chlorophyll a content. For other environmental variables measured in this study, our analyses rejected the hypothesis that ciliate diversity (OTU richness and exp(H)) is a function of these parameters. However, while alpha diversity measures are hardly affected, ciliate species (OTU) turnover and community similarity (β -diversity) across taxonomic groups showed a strong correlation to contemporary environmental conditions. Community turnover is a result of the reaction of individual taxa to a (combination of) environmental variables as well as biotic interactions  46. While the V9 amplicon dataset of the Tara Oceans project does not allow testing biotic interactions, logistic regression modelling enabled us to assess the effect of multiple environmental parameters to individual ciliate taxa (genera).
Logistic regression has often been used in ecological studies to model and predict the occurrence and distribution of species  47. Also for protistan plankton this approach was applied to predict blooms of the toxigenic diatom Pseudonitzschia  48. In contrast to these studies, the logistic regression for planktonic ciliates in this study is based on V9 rDNA reads instead of abundances of cells or individuals. Since logistic regression requires presence-absence data, we applied a threshold to define the occurrence of a genus at a specific sampling site. This strategy avoided statistical bias based on different rDNA copy numbers in ciliates  18. Our modelling approach achieved high percentages of correct predictions, which ranged from 64. 29% to 95. 24% for the dataset including nutrients, physical variables and hydrochemistry and from 56.
52% to 86. 96% for the dataset of the oceanic carbonate system. Nitrite, oxygen, salinity and temperature were identified as significant factors playing in concerto to contribute to ciliate community assembly. Only few studies have evaluated the effect of (mostly individual) environmental parameters on ciliate taxa. In a north Chinese ocean bay a strong correlation between the distribution of non-loricate ciliates and nutrients, including nitrate and nitrite was observed  49. The significant effect of nitrite on ciliate community assembly that was also observed in our data could be related to the primary nitrite maximum, which forms at the base of the euphotic zone  50  close to the DCM. Oxygen and salinity were identified as strong parameters structuring ciliate communities using metadata from different ecosystems  51.
Likewise, in a recent molecular diversity study Forster et al. 20  found notably different ciliate communities and predicted a higher ciliate OTU richness in the DCM of European coastal waters compared to surface waters. Commonly, ciliates are considered as herbivores. However, at second sight, ciliate communities are composed of variable proportions of more or less distinct trophic guilds  16. While some species are strict heterotrophs feeding on pico-and nanophytoplankton, others are mixotrophic species which, in addition to phagotrophic feeding, sequester and exploit chloroplasts from ingested algae 2. Grazing impacts of planktonic ciliates in the DCM could reach as much as 50% of the primary production  16. Together with these previous studies, the Tara Oceans dataset revealed that also in the (unstratified) upper ocean water column different types of planktonic ciliates display different vertical distributions, relative to chlorophyll a, in a system with a well-defined DCM.
Community properties cannot be understood without biogeographical context. However, while some controversially discussed issues in biogeography are difficult (if at all) to test (for example Baas-Beckings  56  famous "everything is everywhere-but the environment selects" paradigm-one can probably never prove that something is not present), other concepts in biogeography provide a well testable framework. One important and well-testable aspect in geographic structuring of all living organisms is the relation of diversity (species richness) and latitudes  13. We did not find a decline of ciliate plankton diversity with latitude (latitudinal diversity gradient-LDG) in the Tara Oceans dataset as known for most larger animals and plants  13. Likewise, species turnover (community similarity, beta diversity) were not identified as a function of latitude.
This finding corroborates well with previous assumptions that protists in general and ciliates in specific are less influenced by large-scale spatial processes than animals and plants  5, 57. Accordingly, in a meta-analysis of data collected from various literature sources Hillebrand and Azovsky 14 found no LDG for protists compared to larger animals and plants. On the other hand, others  7, 15, 58  reported pronounced LDGs at least for a specific evolutionary lineage of ciliates (marine planktonic tintinnids). Thus, the question whether planktonic ciliates exhibit LDGs or not is currently unresolved. Even though the data obtained from the circumglobal Tara Oceans voyage do not support an LDG for marine planktonic ciliates, this finding is not conclusive. Inference of LDGs from metadata obtained from various publications (such as in Hillebrand and Azovsky  14  ) may be equally critical as using data from the Tara Oceans project: (i) Compiling (meta)data from inconsistent habitat types (e.
g. habitats with strong variation of environmental variables such as pH or salinity), which may overlay and obscure spatial (latitudinal) patterns; (ii) non-uniform protocols to collect and process samples and different protocols to precisely quantify diversity may artificially introduce differences in sample sets from different studies; (iii) lumping together data collected from different seasons may make comparison of data from different studies or samples highly biased  59. Therefore, testing LDGs in ciliate plankton solidly requires a well-designed sampling strategy. Until solid data from such a targeted sampling are available, LDGs for marine ciliate plankton will remain largely speculative and elusive (for an exception see Dolan et al. 58  ). Even though we found no evidence for ciliate LDGs in the Tara Oceans dataset, ciliate communities from the polar regions of the Southern Ocean differed notably in terms of richness and community composition from ciliate communities in all other investigated oceanic regions.
63  is not unbiased. The data obtained from Long Island Sound samples can only be compared to the molecular data available in public database (as a benchmark for the global diversity of Oligotrichea and Choreotrichea). But as shown recently, we are far away from having the full extent of marine ciliate diversity recorded and deposited in public databases. In first place, these databases comprise the genetic signatures of the most common, cultivable and morphological recognisable ciliate species. A different approach is to simply collect data (ciliate diversity) from the global oceans rather than relying on database entries (which do not cover as much diversity as found during the circumglobal Tara Oceans expedition 1. Even if not all Tara-obtained ciliate OTUs can be assigned a species name, these OTUs can be compared among each other to assess the local diversity coverage of the global marine ciliate plankton diversity.
Following this approach, it would be too stringent to require for an OTU to be present at every station to be considered as a cosmopolitan (even if sampling saturation profiles are close to saturation, individual low-abundant taxa can still escape detection in individual samples). Therefore, we defined that an OTU had to occur in at least one sample of each oceanic region to be considered as cosmopolitan. We found that 17% of all detected ciliate OTUs occurred in all oceanic regions under study and that, on average, local ciliate OTU richness represented 27% (± 8% s. d. ) of the global ciliate OTU richness. For all protistan taxon groups analyzed in the Tara Oceans dataset, the local richness covered, on average, 9. 7% (± 4% s. d. ) of the global richness  1. Thus, regardless of the taxonomic resolution (morphospecies or molecular OTUs), for open ocean samples it seems that global planktonic ciliate diversity is low (ca.
Acknowledgements We thank  L. Bittner  and  F. Mahé  for their help with the Tara Oceans dataset. Our gratitude also goes to the captains, crew and scientific teams who sampled the world oceans systematically on board the schooner TARA. This study was funded by a grant from the  Deutsche Forschungsgemeinschaft (DFG)  to TS ( STO414/11-1 ), a grant from the  Forschungsinitiative BioComp  to TS and RK, a fellowship from the  University of Kaiserslautern  to AG and the  French Government 'Investissements d' Avenir' programmes OCEANOMICS  ( ANR-11-BTBR-0008 ).
2013 (Ross et al. , 2014)). While the rate of fixation for neutral mutations is equal to the mutation rate, that of non-neutral mutations also depends on their fitness effect (expressed as selection coefficient) and effective population size  (Kimura 1993). Both theoretical considerations  (Kimura 1968 ) and analyses of empirical data  (Weinreich and Rand 2000; Nielsen and Yang 2003; Popadin et al. 2007; Lartillot and Poujol 2011)  suggest that the majority of mtDNA mutations are deleterious and thus should be eliminated by selection. Although positive selection has also been inferred in the mtDNA of some lineages, usually   animal phylogeny showing variable rates of mt-sequence evolution. Complete or nearly complete mt-genomes from all available nonbilaterian animals and a few selected bilaterian animals were downloaded from the GenBank.