dataesr/scientific-paragraphs-categorization huggingface dataset:
Genotyping and Quality Control (QC) EuroTARGET: Genotyping of the EuroTARGET samples was conducted at deCODE genetics (Reykjavik, Iceland). Germline DNA isolated from whole blood with the Chemagic Blood kit (PerkinElmer, Waltham, Massachusetts, United States) was used for SNP genotyping on the Illumina Human OmniExpress BeadChips 12v1-1, 24v1-0, and 24v1-1 (Illumina, San Diego, CA, USA)  [24]. Quality control (QC) checks for Eurotarget were performed using software R version 3. 2. 3 [25]  and PLINK software, version 1. 07  [26]. Individuals were excluded from analyses based on an individual genotype call rate <97%, gender mismatch between reported and estimated sex based on genotypes of the X-chromosome, or excess of heterozygous genotypes (i. e. , inbreeding statistic of F > 0. 1). Genetic markers were excluded based on a SNP call rate <97%, minor allele frequency (MAF) <1%, and a p-value ≤ 10 -7 for the Hardy-Weinberg equilibrium (HWE) goodness-of-fit test.
5 months), respectively. The quality criteria for statistical analysis were met for 679,324 SNPs based on measured genotypes (Table  S2 ). This number was supplemented using SNP imputation procedures using the 1000 Genomes data as reference panel  [29]. A total of 8,148,675 SNPs with a minor allele frequency (MAF) of >2% were analysed for the EuroTARGET cohort. For the RIKEN cohort, median follow-up times of PFS and OS were 10. 6 months (range: 0. 4-69. 7 months) and 12. 3 months (range: 0. 5-69. 7 months), respectively. For the 204 individuals from the RIKEN cohort, QC procedures were performed prior to association analyses. A total of 5,518,066 SNPs with a minor allele frequency (MAF) of >2% were analysed for the RIKEN cohort. Duration of prior drug treatment refers to the number of months that a patient has received an antitumor treatment prior to start with sunitinib that is not a TKI or TKIlike drug as mentioned in Table  S1 , because these patients have already been excluded from analyses.
Genetic Association Analysis For the meta-analysis, results of statistically significant or suggestive association with PFS or OS are presented in Tables  2  and 3 , respectively. The GWAS results for the metaanalysis and separate cohorts are visualized in Manhattan plots in Figures  2  and 3. The associated SNPs in the meta-analysis come from imputed SNPs in the EuroTARGET cohort and are not present in the Japanese dataset. The annotation and interpretation of our findings therefore apply only to European populations. In the meta-analysis, SNP rs28520013 in PDLIM3 (p = 4. 02 × 10 -10 , HR = 7. 26), and SNPs rs2205096 (p = 5. 60 × 10 -9 , HR = 2. 5) and rs111356738 (p = 4. 77 × 10 -8 , HR = 2. 51), both in DSCAM, were significantly associated with PFS. Most of the SNPs in DSCAM show high levels of linkage disequilibrium (R 2 > 0.
Also, the number of analysed SNPs and hence genome coverage differed between the two cohorts. When comparing SNPs across the cohorts allowing for some physical distance, more overlap can be identified in an explorative way. While other approaches are possible, such as gene-based analyses, they were outside the scope of this study. The frequency of the variant T-allele of rs28520013 in PDLIM3 in this study was 2. 3% while the frequency reported in Asians in the NCBI database is 0. 1%  [40]. This suggests that an Asian population can hardly contribute to this SNP association. For the variant A-allele of rs2205096 in DSCAM the MAF reported in this study is 6. 3%, whereas the reported MAF for Asians in the NCBI database is 36%  [40]. SNPs rs2205096 and rs111356738 in DSCAM are moderately to highly correlated (R 2 = 0.
Molecular Procedures Total genomic DNA was obtained with the Plant Genomic DNA Kit (CWBIO, Beijing, China) according to the manufacturer's instructions from collections dried with silica gel. Primer pairs used for amplification were as follows: nuc 28S rDNA D1-D2 domains (28S) with LR0R/LR5  (Vilgalys and Hester, 1990; James et al. , 2006)  and the translation elongation factor 1-α gene (TEF1) with EF1-α-F/EF1-α-R  (Mikheyev et al. , 2006). Polymerase chain reaction (PCR) conditions followed the program of Zhang Y. Z. et al. (2021). PCR products were checked in 1% (w/v) agarose gels. Amplified PCR products were sequenced using an ABI 3730 DNA Analyzer (Guangzhou Branch of BGI, China) with the same primers. Forward or reverse sequences were compiled with BioEdit  (Hall, 1999). All sequences newly obtained in this study were deposited to GenBank 1.
Dataset Assembly A total of sixty-nine DNA sequences (34 of 28S, and 35 of TEF1) from 36 collections were newly generated. Edited sequences were deposited in GenBank; the GenBank accession numbers are listed in Table  1. For the concatenated dataset, the sequences of 28S and TEF1 from new collections were aligned with selected sequences of subg. Cantharellus from previous studies and GenBank (Table  1 ); Cantharellus ibityensis Buyck, Randrianj. and V. Hofst. was chosen as an outgroup inferred from  Buyck et al. (2014). To test for phylogenetic conflict among 28S and TEF1, single-gene phylogenetic trees based on each of these two fragments were analyzed. The results of analyses showed that 28S and TEF1 were not in conflict. Thus, two datasets (28S and TEF1) were aligned with MUSCLE v3. 6  (Edgar, 2004)  and manually optimized on BioEdit v7.
Phylogenetic Analyses The combined nuclear dataset (28S + TEF1) was analyzed using maximum likelihood (ML) and Bayesian inference (BI). Maximum likelihood tree generation and bootstrap analyses were performed with the program RAxML7. 2. 6  (Stamatakis, 2006)  running 1,000 replicates combined with an ML search. Bayesian analysis with MrBayes 3. 1  (Huelsenbeck and Ronquist, 2005)  implementing the Markov chain Monto Carlo (MCMC) technique and parameters predetermined with MrModeltes 2. 3  (Nylander, 2004)  was performed. The best-fit likelihood model of 28S and TEF1 was GTR + I + G and SYM + I + G, respectively. Bayesian analysis of the combined nuclear dataset (28S + TEF1) was repeated for 20 million generations and sampled every 100 generations. Trees sampled from the first 25% of the generations were discarded as burn-in, and Bayesian posterior probabilities (PP) were then calculated for a majority consensus tree of the retained Bayesian trees.
Molecular Data The combined dataset (28S + TEF1) of subg. Cantharellus consisted of 129 taxa and 1,707 nucleotide sites, and the alignment was submitted to TreeBase (S29413). The phylogram with branch lengths generated from RAxML and support values is shown in Figure  2. The topologies of the phylogenetic trees based on the combined dataset generated from ML and BI analyses were almost identical, but there was a slight variation in statistical support. The present molecular data indicate that the Chinese species of subg. Cantharellus were grouped into fourteen independent lineages (Figure  2 ). A total of seven new lineages were identified in this study (Lineages 1-7 of Figure  2 ). Lineage 1 was comprised of one collection (FHMU6845) from central China; lineage 2 was comprised of one material (FHMU4592) from southern China; lineage 3, with strong statistical support (BS = 100%, PP = 1.
Taxonomy Cantharellus albopileatus N. K. Zeng, Y. Z. Zhang, and W. F. Lin, sp. nov. Etymology: Latin "albo-" means white, "pileatus" means pileus, referring to the off-white pileus of our new species. Holotype: China. Hainan Province: Yinggeling of Hainan Tropical Rainforest National Park, elev. 750 m, 28 May 2017, N. K. Zeng3026 (FHMU1987). GenBank accession number: 28S = OM691480, ITS = OM835804, TEF1 = OM811321. Basidiomata are very small to small-sized. Pileus is 2. 5-5 cm in diameter and convex with a depressed center; the margin was strongly incurved, irregular, often wavy, and lobed; the surface is smooth, slightly greasy, and cream (3A1) to off-white (4A1) in color; the context above stipe was 0. 3 cm in thickness, whitish (4A1), unchanging in color when injured. Hymenophore is composed of relatively welldeveloped, decurrent gill folds, branched to furcate, which becomes strongly intervened with age; these folds are about 0.
MycoBank: MB843062 Diagnosis: It differs from other species of subg. Cantharellus by an egg-yolk yellow to bright yellow, shiny pileus, a whitish stipe, a well-developed hymenophore, ellipsoid basidiospores, and a distribution in tropical Asia. Etymology: Latin "chuiweifanii" is named after Chinese mycologist W. F. Chiu; for that, he published the first new species of Cantharellus in China, i. e. , Cantharellus yunnanensis. Holotype: China. Hainan Province: Limushan of Hainan Tropical Rainforest National Park, elev. 650 m, 11 May 2014, N. K. Zeng1524 (FHMU2412). GenBank accession number: 28S = OM717953, TEF1 = OM811347. Basidiomata are very small to medium-sized. Pileus is 2-5 cm in diameter and plano-convex at first but soon depressed in the center; the margin was first very regular and strongly incurved and then became more wavy, the surface is smooth, pale yellow, egg-yolk yellow (1A5) to bright yellow (1A7), sometimes tinged with brownish, and shiny in color; the context above stipe  was 0.
MycoBank: MB843064 Diagnosis: It differs from other species of subg. Cantharellus by a bright yellow to orange-yellow pileus, a cream to grayish yellow stipe, a well-developed hymenophore, broadly ellipsoid to ellipsoid basidiospores, and it is associated with pine trees. Etymology: Latin "pinetorus" refers to the association of the new species with pine forests. Holotype: China. Hunan Province: Yizhang County, Mangshan National Nature Reserve, elev. 750 m, 30 July 2019, N. K. Zeng4180 (FHMU3759). GenBank accession number: 28S = OM691482, TEF1 = OM811323. Basidiomata are small to medium-sized. Pileus is 3. 5-5 cm in diameter and convex when young and then applanate with depressed center; the surface is smooth, bright yellow (3A5) to orange-yellow in color (3A6); the margin is incurved and irregularly wavy; the context above stipe is 0.
MycoBank: MB843065 Diagnosis: It differs from other species of subg. Cantharellus by a yellowish to grayish yellow, dull pileus, a well-developed hymenophore, and ellipsoid basidiospores. Etymology: Latin "ravus" refers to the grayish yellow basidioma of our new species. Holotype: China. Hunan Province: Yizhang County, Mangshan National Nature Reserve, elev. 550 m, 29 July 2019, N. K. Zeng4176 (FHMU6845). GenBank accession number: 28S = OM717944, TEF1 = OM811338. Basidiomata are small to medium-sized. Pileus is 3. 5-8 cm in diameter and plano-convex to infundibuliform; the surface is smooth, yellowish (1A2) to grayish yellow (2A4) in color, and dull; the margin is incurved or downward; the context above stipe is about 0. 3 cm in thickness, yellowish (3A3), unchanging in color when injured.
Species Diversity of Cantharellus Subgenus Cantharellus High species diversity of subg. Cantharellus in China was revealed in this study, and fourteen lineages were identified (Figure  2 ). A total of four (lineages 1, 3-5 of Figure  2 ) were here described as new species: Cantharellus albopileatus, Cantharellus chuiweifanii, Cantharellus pinetorus, and Cantharellus ravus; others represent previously described taxa: Cantharellus cibarius, Cantharellus hainanensis, Cantharellus laevihymeninus, Cantharellus macrocarpus, Cantharellus vaginatus, Cantharellus versicolor, and Cantharellus yunnanensis, whereas three lineages (lineages 2, 6-7 of Figure  2 ) remain still undescribed. Up to now, taxa in subg. Cantharellus are all from northern hemisphere  (Buyck et al. , 2014). Most species of the subgenus included in the present dataset are from temperature areas of northern hemisphere including North America and Europe (Figure  2 ).
Figures 3A,B, 4. MycoBank: MB843063 Diagnosis: It differs from other species of subg. Cantharellus by a cream to off-white basidioma, a well-developed hymenophore, and ellipsoid basidiospores. Etymology: Latin "albo-" means white, "pileatus" means pileus, referring to the off-white pileus of our new species. Holotype: China. Hainan Province: Yinggeling of Hainan Tropical Rainforest National Park, elev. 750 m, 28 May 2017, N. K. Zeng3026 (FHMU1987). GenBank accession number: 28S = OM691480, ITS = OM835804, TEF1 = OM811321. Basidiomata are very small to small-sized. Pileus is 2. 5-5 cm in diameter and convex with a depressed center; the margin was strongly incurved, irregular, often wavy, and lobed; the surface is smooth, slightly greasy, and cream (3A1) to off-white (4A1) in color; the context above stipe was 0.
DATA AVAILABILITY STATEMENT The data presented in the study are deposited in the https://www. ncbi. nlm. nih. gov/GenBank and https: //www. mycobank. org/page/Home/MycoBank repository, accession number of GenBank (28S: OM319632-OM319637, OM691480-OM691495, OM717944-OM717956; TEF1: OM321043-OM321046, OM811321-OM811350; and ITS: OM835791-OM835808) and MycoBank (MB843062-MB843065).
Figures Figures 3A,B, 4. MycoBank: MB843063 Diagnosis: It differs from other species of subg. Cantharellus by a cream to off-white basidioma, a well-developed hymenophore, and ellipsoid basidiospores. Etymology: Latin "albo-" means white, "pileatus" means pileus, referring to the off-white pileus of our new species. Holotype: China. Hainan Province: Yinggeling of Hainan Tropical Rainforest National Park, elev. 750 m, 28 May 2017, N. K. Zeng3026 (FHMU1987). GenBank accession number: 28S = OM691480, ITS = OM835804, TEF1 = OM811321. Basidiomata are very small to small-sized. Pileus is 2. 5-5 cm in diameter and convex with a depressed center; the margin was strongly incurved, irregular, often wavy, and lobed; the surface is smooth, slightly greasy, and cream (3A1) to off-white (4A1) in color; the context above stipe was 0.
K. Zeng3875 (FHMU6842) China OM319635 OM321044 Present study Cantharellus yunnanensis Z. H. Chen MHHNU31318 (FHMU6843) Yunnan, SW China OM319636 OM321045 Present study Cantharellus yunnanensis Z. H. Chen MHHNU32137 (FHMU6844) Hubei, Central China OM319637 OM321046 Present study Cantharellus yunnanensis Yuan 13983 China MW979527 MW999428 Cao et al. (2021) Cantharellus yunnanensis Yuan 13985 China MW979528 MW999429 Cao et al. (2021) Cantharellus yunnanensis Yuan 14539 China MW979514 MW999422 Cao et al. (2021) Cantharellus yunnanensis Yuan 14636 China MW979515 MW999423 Cao et al. (2021) GenBank numbers in bold indicate the newly generated sequences; SW Southwestern China, NE Northeastern China. with obtuse apex. Clamp connections are present in all parts of basidioma. Habitat: Solitary, scattered, or gregarious on the ground in forests dominated by fagaceous trees such as Castanopsis fissa (Champion ex Bentham) Rehder et E.
| Fitness assays Monokaryotic confrontations of F1 were realized between three mycelia originating from monokaryotic cultures (see Study population). The focal mycelium was of type (+) and was presented in all assays with two mating partners of type (-) (Figure  1 ). Implants of standardized size (cut out with a sterilized metal tube) were placed centrally and evenly spaced using a placement pattern in a 5 cm petri dish containing reproduction medium. Dikaryotic selfings of F2 were realized by placing one dikaryotic mycelium implant in the center of a 5 cm petri dish containing either reproduction medium or stress medium. For both F1 and F2, assays were randomized by assigning a random ID number to each dish. All dishes were kept at 26°C in an incubator, with a 12 h/12 h light cycle. For both F1 and F2, fitness proxies measured were: time to reproduction (time in Time to reproduction was estimated by inspecting three times daily (10, 14, 17 h) the lids of petri dishes under a stereomicroscope for the first spores shot (spores are likely not shot during nighttime, see pilot data in Supporting Information S4).
| Spore count Once the first spores had been recorded, assays were left 48 h to shoot spores before the lids were removed for spore collection (most of the spores are shot within this time span making it a good proxy for total spore count, see pilot data in Supporting Information S5). Spore collection on the lid of petri dishes was realized by pipetting 1200 μl of spore harvesting solution (see Supporting Information S3) on the lid. The solution was then collected in a 1. 5 ml Eppendorf and sonicated (Soniprep 150, 9 μm amplitude, 15 s). Spore count was estimated from the number of spores in five drops of 5 μl each of the solution, counted under the stereomicroscope just after agitation. If spore count was high, a 10× dilution in harvesting solution was made to allow accurate counting.
| Statistical analysis F1 fitness proxies were analysed in a dataset with only Selfing and Outcrossing assay types (i. e. , excluding Mate Choice assays). Each fitness proxy was analysed in a linear mixed model with het-v genotype (V or V1), type of assay (Selfing or Outcrossing) and their interaction as fixed effects. Strain identity and strain crossed by experimental batch were added as random effects. F2 fitness proxies were analysed in a linear mixed model with type of F1 parental assay (Selfing or Outcrossing), F2 assay environment (Normal or Stress), het-v genotype, the interaction of het-v and F1 assay, and the three-way interaction of het-v, F1 assay and F2 environment, as fixed effects. Strain identity and strain crossed with F1 parental assay were added as random effects. For F1 and F2 fitness proxies, spore germination probability was analysed in a generalized linear model with a binomial error distribution, while spore count and time to reproduction were analysed in models with a normal error distribution.
Finally, strains appeared to differ from each other in their overall spore count (Figure  S6b ). Spore germination probability was significantly reduced for outcrossing assays (Figure  2c , Table  1 ). It also appeared to differ among strains, with in particular Wa124 showing an overall very low spore germination probability, and a higher germination probability for outcrossing than for selfing assays, a trend opposed to the eight other strains tested (Figure  S6c ). Except for Wa124, strains of the V1 group showed an overall higher germination probability than those of the V group. Because of Wa124, selfing spore germination probability was lowered in the V1 group, resulting in a smaller reduction of germination probability when outcrossing in this group as compared with the V group. In fact, if Wa124 is excluded from the dataset, the reduction in germination probability due to outcrossing is on the contrary more important in the V1 group.
Five strains of het-v genotype V (different from the reference genotype) and four strains of genotype V1 (same as the reference genotype) are assayed. Each measurement was replicated four times per strain per environment. Figure  S7  shows the same data detailed at the level of each strain. to the P. comata and P. pauciseta species (Supporting Information S8). The two remaining strains were not sequenced, but we note that under our culture conditions P. comata is morphologically distinct from P. anserina  (Vogan et al. , 2021) , and that P. pauciseta was never sampled in the Wageningen population. [Correction added on 28 November 2022, after first online publication: 'sub-species' has been replaced with 'species' in the "A potential explanation for … P. pauciseta species. " sentence. ].
This may be due to the increase in the vaccinated population among Mongols and reducing the risk of death upon infection. With vaccinations rolling out, reforms on drug regulations were speeded up since Mongolia has the highest global prevalence of "fake" pharmaceuticals. 29 The Asian Development Bank released $100 million in financial aid to help Mongolia's healthcare system mitigate COVID-19 transmission. The program shall make available essential medicines to improve and safeguard the procurement system of hospital supplies. In most countries, prevalent mismanagement of funds and aid led to undelivered essential medical supplies and services. 30 This was unlikely in Mongolia, where an integrated management system that shares databases across government agencies was implemented to improve response to similar disasters.
This is confirmed by the fact that the lifetime of produced 1 O 2 is approximately constant at ~ 50 μs and that the difference resides in the sixfold reduction of the lifetime of the triplet state of the chromophore (Table  1 ), suggesting that 3 O 2 can more readily quench it. Noteworthy, we did not observe any chromophore phototransformation under our irradiation conditions. Because the triplet state plays an important role in the formation of lumichrome in both RF and FMN  [14, 15] , a more efficient 3 O 2 quenching of the triplets in miniSOG[RF] reasonably reduces the phototransformation efficiency. We then determined the 1. 07 Å structure of miniSOG[RF] and compared it to our previously determined 1. 17 Å structure of miniSOG (PDB entry code: 6GPU)  [10] , to compare the binding modes of FMN and RF.
Electrospray ionization mass spectrometry (ESI-MS) Before ESI-MS analysis, the different miniSOG protein samples were diluted to a final concentration of 10 μM in acetonitrile/water/formic acid (50:50:0. 1, v/v/v) and infused directly in the mass spectrometer by a syringe pump at a flow rate of 10 μL/min. A blank run was carried out infusing only protein buffer diluted at the same ratio as the protein sample in the same solvent system. Data acquisition was carried out in the positive ion mode with spectra in the profile mode and mass spectra were recorded in the 130-1200 m/z range. The mass spectrometer was operated with the following experimental settings: ESI source temperature was set at 325 °C; nitrogen was used as drying gas (5 L/min) and as nebulizer gas (30 psi); the capillary needle voltage was set at 3500 V.
Photophysical characterization Spectroscopic measurements were performed using 1 cm quartz cuvettes (Hellma) under magnetic stirring and at room temperature. Absorption and fluorescence spectra were recorded on a double beam Cary 6000i spectrophotometer (Varian) and a Fluoromax-4 spectrofluorometer (Horiba), respectively. were analyzed by fitting Eq. 1  [22]  to the data using GraphPad Prism 5. where τ T and τ ∆ are the lifetimes of the photosensitizer triplet state and of 1 O 2 , respectively, and S (0) is a quantity proportional to Φ ∆. Flavoprotein Φ ∆ values were determined by comparing the S (0) values of optically matched solutions of the corresponding protein and FMN at 473 nm in deuterated buffer (Φ ∆FMN = 0. 57)  [6]  as described by Eq. 2.
Structure determination X-ray diffraction data were collected at 100 K from flashcooled crystals that have been cryoprotected with 20% glycerol (v/v) beforehand on beamlines ID23-1  [23]  and ID29  [24]  of the ESRF in Grenoble (France). Crystallographic data were indexed, integrated, scaled and merged using the XDS package  [25]. Our previously determined 1. 17 Å structure of miniSOG (PDB entry code: 6GPU)  [10] , was used as starting model for all structure refinement performed with Refmac5  [26]. Models were manually improved in Coot  [27]  by reorientation or modification of amino-acid residues and of the flavin chromophores, and addition of solvent molecules. Data collection and refinement statistics are presented in Table  3. Pymol (http:// pymol. org/, The PyMOL Molecular Graphics System, Version 1.
Acknowledgements The  ESRF  is acknowledged for access to beamlines and facilities for molecular biology via its in-house research programme. AR acknowledges funding from the  French Agence Nationale de la Recherche  (project  SOxygen ,  ANR-11-JSV5-0009 ). SN acknowledges funding from the  Spanish Ministerio de Economía y Competitividad  ( CTQ2016-78454-C2-1 -Rand the  Fundació la Marató de TV3  (Grant No. 20133133 ). This work used the mass spectrometry platform of the Grenoble Instruct-ERIC center (ISBG;  UMS 3518 CNRS-CEA-UGA-EMBL ) within the  Grenoble Partnership for Structural Biology  (PSB), supported by  FRISBI  ( ANR-10-INBS-0005-02 ) and GRAL, financed within the  University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS  ( ANR-17-EURE-0003 ).