dataesr/scientific-paragraphs-categorization huggingface dataset:
Isolation of Microdochium Strains and Their Primary Characteristics Twenty-one strains that were preliminary attributed to Microdochium genus according to the mycelium morphology were isolated from winter rye. All strains are maintained in the collection of the Laboratory of Plant Infectious Diseases in the Federal Research Center "Kazan Scientific Center of Russian Academy of Sciences". The strains are referred to as 1-21 throughout the paper; the corresponding accession numbers in the collection are given in Table  S11  (Supplementary All three variants together were revealed only in R-samples (8. 6%, 0. 7%, and 0. 4% of fungal dataset for M. OTU1, M. OTU2, and M. OTU3, respectively). In the GL-and DL-samples, M. OTU3 was absent. M. OTU1 and M. OTU2 were represented rather equally in GL-samples (9.
Isolation of Microdochium Strains and Their Primary Characteristics Twenty-one strains that were preliminary attributed to Microdochium genus according to the mycelium morphology were isolated from winter rye. All strains are maintained in the collection of the Laboratory of Plant Infectious Diseases in the Federal Research Center "Kazan Scientific Center of Russian Academy of Sciences". The strains are referred to as 1-21 throughout the paper; the corresponding accession numbers in the collection are given in Table  S11  (Supplementary Materials). Nineteen strains were isolated from leaves and two (No. 7 and 17) were isolated from roots. Strains differed in their morphology. Mycelium color was whitish, creamy, or light pink depending on the strain (Figure  6 ). Most (but not all) strains produced a (pale) yellow-ochraceous exudate.
OTU4 and M. OTU5, respectively (Table  S14 , Supplementary Materials). M. OTU3 (that was revealed as a minor OTU among the OTUs that belonged to Microdochium sp. in the microbiome of rye) was not revealed among the isolated strains. To rank the isolated strains to the particular species of Microdochium genus, the ITS2 sequences corresponding to M. OTU1-M. OTU5 were compared with the most similar sequences in NCBI nucleotide database (Tables S15-S19, Supplementary Materials). Although ITS2 is extensively used for phylogenetic classification of fungi, some authors doubt that this DNA region is suitable for the distinguishing of closely related M. majus and M. nivale sensu stricto species  [84]. To check if the analyzed 164 bp region contains unique, M. nivale sensu stricto or M. majus species-specific positions, corresponding DNA regions of 24 M.
Human pulmonary and bronchi preparations Human pulmonary and bronchial preparations were collected in Bichat Hospital (Paris) after obtaining patients' informed consent with Ethics Committee approval from INSERM and AP-HP (CEERB du GHU Nord) Institutional Review Board (n° IRB00006477). These investigations conform to the principles outlined in the Declaration of Helsinki. Control preparations were obtained from patients (20 males, 4 females and 8 anonymous donors) who underwent surgery, mostly for lung carcinoma, while PH preparations were obtained from patients (26 males, 9 females) who had undergone surgery for lung transplantation. Patient categories are PH due to lung diseases and/or hypoxia [Group-III of PH classification  [3] ], with detailed characteristics presented in supplemental data (Table  S1 ), and control patient characteristics were presented in Table  S2.
Statistical analysis All results obtained from different patients (n) were expressed as mean ± standard error of the mean (SEM). After testing normality and equal variances of the data, we performed Student or Mann Whitney-Rank Sum tests and calculated Pearson or Spearman correlation coefficients (r). For all statistical tests, P-values less than 0. 05 were considered statistically significant. Statistical analyses were performed using SigmaStat version 3. 5 (Systat Software, Point Richmond, CA, USA). ELISA measurements were performed in duplicate and an average taken in each sample to calculate the final mean data.
Acknowledgement We would like to thank the  Anapathology laboratory  and the secretary of the  Department of Anaesthesia and Intensive Care, CHU X. Bichat  for their help. We would like to thank  United Therapeutics  for an educational grant supporting  Yasmine Amgoud  thesis and the  European Union 's  Horizon 2020 research and innovation programme  under the  Marie Skłodowska-Curie  grant agreement No:  665850  supporting Heba Abdelazeem thesis.
Between 4% and 13% of phages could be assigned to a host this way. Finally, the program WiSH bases its predictions on the similarity of the phage genome to that of its hosts. It uses a probabilistic approach that compares the composition in subsequences of nine nucleotides, or 9-mers, in phage and bacterial genomes, and reaches good prediction even for short 3 kb-long phage contigs, which is not the case for other methods. Using the same large data set as Paez-Espino et al. 41  , WiSH predicted a host at family level for 59% of the contigs. 42 Using a mix of these approaches, recent studies indicate that the spectrum of the bacterial hosts of the dominant phages reflects the microbiome composition. 29, 43 Indeed, among 180 persistent phage clusters identified, about one third could be linked to a bacterial genus, all of them belonging to abundant taxa, such as Faecalibacterium and Bacteroides.
With respect to antibiotic resistance genes (ARGs), their presence within phage genomes is debated. Most reports are flawed by either excessive bacterial DNA contamination of the virome samples  [71] [72] [73] [74]  or inappropriate thresholds used for the similarity search against ARG databases. 75 When both pitfalls were eliminated, ARG were rare in phage genomes (around or <1 gene among 10 5 genes analyzed, on phage genomes and phage metagenomic contigs respectively),  76  confirming an ancient observation. 77 Further illustrating the potential of prophages to confer fitness advantages to their bacterial hosts, a very recent study analyzing sponge-associated virome suggested that some prophages encoding ankyrin-repeat proteins may provide anti-inflammatory properties to their bacterial host and foster host-microbe symbiosis.
2500 m a. s. l. ), where steep slopes and rainfall favor dense forest and gravitational instability. At high elevation, where farming is absent (>3800 m a. s. l. ), morphologic features are often well preserved and can be revealed by DEM and field analyses, but their accessibility can be limited because of rare tracks and toughness of hiking over large distances at high elevations. To obtain the most complete picture over the 1000 km 2  zone, we performed the morphotectonic analysis of a 4 m pixel-resolution DEM (Proyecto SIGTIERRAS) 2 draped over the geological maps  (Longo and Baldock, 1982). Field data were acquired during five 2 weeks campaigns between 2009 and 2016 at key areas. Like in classical preliminary analyses, we looked for morphological features, their alignment and continuity of lineaments to delineate fault strands.
Earthquake Surface Ruptures and Their Recurrence We recompiled the original radiocarbon ages obtained in  Baize et al. (2015)  trench, together with the measured vertical offsets. Soil samples 14 C ages are calibrated with OxCal software (Bronk Ramsey, 2009), using the IntCal13 calibration curve  (Reimer et al. , 2013)  to infer the possible range of paleo-earthquake dates. We provide details of this analysis in Supplementary Material. The geological interpretation of the trench T2 (Figure  12A ), located a few tens of meters south of the trench visible on Figure  2 , led to propose a series of 4 paleoearthquakes, i. e. , a recording of 3 complete earthquake cycles bracketed by E4, E3, E2, and E1 within the last ∼8000 years (Figure  12B ). Based on the calibrated ages (see Supplementary Material), we come out with the most probable following dates: E4 = 4250 BCE, E3 = 2400 BCE, E3 = 400 CE and an historical earthquake (post-1000 CE; Figure  12B ).
DISCUSSION We estimate that multiple-segment ruptures could occur along the Pallatanga fault system. Biasi and Wesnousky (2017, 2016) , based on a worldwide historical database, propose that the likelihood of rupture propagation is linearly related to the width of surface steps and gaps in strike-slip faults. For instance, they determine a 30% probability of rupture propagation across 5 km wide steps or gaps. In the same way, they also explore the influence of fault bends in rupture propagation and conclude that changes in strike play a significant role on rupture propagation when exceeding 25 •. However, recent events suggest that those rules can be significantly overstepped, such as the 2016 M7. 8 Kaikoura, New Zealand, earthquake during which the rupture jumped over large distances (10-20 km) from the Canterbury faults to the Marlborough faults.
, 2005a,b)  and the northernmost section (Holocene slip rates around 10 mm/yr according to  Tibaldi et al. (2007)  along the Chingual section). In Figure  13  and Table  1 , we report the whole set of slip rate values estimated from both our field data and available datings or stratigraphic information. The Pallatanga fault is active at least since the beginning of the Igualata volcano building (∼376 ka), and probably largely before if we assume a connection with the Puna fault in the Guayaquil gulf  (Witt et al. , 2006). We ranked the values of slip rates obtained in the previous section with respect to their reliability, roughly estimated based on the robustness of the age of displaced markers and the precision or accuracy of the piercing lines. We consider the slip rate reliable when the age is estimated for a dated marker ( 14 C or K-Ar) and when the piercing line is geometrically well-constrained.
CONCLUSION The primary objective of this work is to contribute to seismic hazard analyses for a densely inhabited area of central Ecuador. To achieve this aim, we provide a detailed description of available and newly acquired data on one major and fault zone, the Pallatanga fault, and its related structures. This compilation is a first step in building realistic fault models for future Probabilistic Seismic Hazard Analyses in Ecuador, providing updated and comprehensive fault maps and related earthquake geology parameters, such as slip rates, timing and magnitude of past earthquakes and their uncertainties. We are aware of the heterogeneity of the data and further studies will have both (1) to enrich the existing fault database in terms of geology (mapping, trenching, drilling, dating), geophysics (sub-surface profiling), geodesy (GNSS, InSAR) and seismology (near-fault monitoring, relocating clusters) information, and (2) to expand this endeavor to other parts of the same seismotectonic province.
For instance,  Chartier et al. (2019)  developed a method coupling information from seismology and earthquake geology, for example where parameters such as geometry and slip rate are specified for each fault segment. Then, one can relax the rupture segmentation and calculate the rate of multiple segment ruptures based on geological constrain in consistency with seismological datasets. This approach is a relevant way to explore the behavior of the faults of concern. We suggest that it would be worth to develop similar earthquake geology approaches across the continent of South America, in parallel to geophysical data acquisition. The instrumental and historical record of earthquakes (covering several hundred years at best) and the geodetic measurements, fail to capture alone the behavior of crustal faults, to describe their complete earthquake productivity rate and the long recurrence of large events.
FUNDING Field work expenses were funded by the " Laboratoire Mixte International Séismes et Volcans des Andes du Nord " of " Institut pour la Recherche et le Développement " (LMI-SVAN), by the " Agence Nationale pour la Recherche " project  ANR-REMAKE (N •   ANR-15-CE04-0004 ), and by proper funds from the  "Institut de Radioprotection et Sûreté Nucléaire. ".
This scheme has been designed keeping in mind the differentiability requirement. The adjoint is obtained by automatic differentiation and manually optimized to provide the capacity to work for long time periods (up to several consecutive years) over large spatial areas, with fine resolution. This requires a memory efficient and fast code. The distributed parameters of the GRD model are calibrated over a French Mediterranean catchment, the Gardon d'Anduze, using rainfall radar data and the discharge data from the outlet gauge station. The discharge data from other gauge stations available in this catchment are used for cross-validation (10 years, being split in two periods). Thus, the major questions addressed in this paper are: (a) can we, in principle, benefit from considering the spatially distributed set of coefficients given by the method instead of the uniform (homogeneous) set of coefficients, and, if so, to what extent? In particular, does it help to improve the discharge prediction over the catchment area including "ungauged" locations? (b) What are the major difficulties associated with this approach (insufficient data, structural deficiency of the model, identifiability issue, etc.
Study area and data A French watershed, the Gardon d'Anduze, has been considered for testing our model and calibration algorithm. Located in the western Mediterranean region, this catchment and its surrounding have been deeply studied in the framework of the HyMeX program  (Drobinski et al. , 2014)  to understand the processes leading to flash floods. For instance, some studies exploited a number of very detailed field measurements during severe storm events  (Braud et al. , 2014; Vannier et al. , 2014). Others tested hypotheses using physically distributed models, for instance the MARINE model  (Roux et al. , 2011; Garambois et al. , 2013 Garambois et al. , , 2015;; Douinot et al. , 2016 Douinot et al. , , 2018) )  or the CéVeNnes (VCN) model  (Braud et al. , 2010; Vannier et al. , 2016).
This area is governed by a transitional Mediterranean-oceanic climate with warm and dry summers, alleviated by the oceanic influence, followed by recurrent short, intense but persistent heavy rainfalls in autumn and winter, known as épisode méditerranéen, generating flash floods. This watershed is well gauged: at least five stations with continuous data collection are operational here (see Fig. 2  and Table  1 ). For numerical experiments, the discharge data have been extracted from the HYDRO database of the French ministry in charge of the environment. Rainfall gridded data have been provided by Météo France. It is a pseudo-realtime reanalysis (ANTILOPE -ANalyse par spaTIaLisation hOraire des PrEcipitations -J+1, i. e. , available 1 d after the current date), merging radar rainfall estimation with in situ rain gauges.
Acknowledgements. This research has been done in the framework of the  2010-2020 HyMex program. It contributes to the  French national PICS  ( Prévision immédiate intégrée des impacts des crues soudaines)  project. The authors wish to thank  Etienne Leblois  ( IN-RAE Lyon ) for having provided the flow direction map used in this study. The editor and the four anonymous referees are also thanked for their constructive comments and suggestions. Financial support. This research has been supported by the  "Agence nationale de la recherche"  ( ANR-17-CE03-0011 ), the  Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA, now INRAE ), and by the French ministry in charge of the environment. Review statement. This paper was edited by  Véronique Ducrocq  and reviewed by four anonymous referees.
Results Recurrent horizontal transfer of the A1d1a haplotype. We assessed the frequency of mtDNA capture in a cohort of 539 CTVT tumours collected from 43 countries across all inhabited continents (Supplementary Data 1). By comparing phylogenetic trees constructed using nuclear and mtDNA sequences (whole exomes  13  and full-length mtDNA genomes, respectively), we identified nineteen horizontal transfer events (Fig. 1a , Table  1 , Supplementary Fig. 1 , Supplementary Fig. 2 , Supplementary Data 2). Remarkably, eleven of these mtDNA captures involved a single canine haplotype, known as A1d1a (Fig. 1a , Table  1 , Supplementary Fig. 1 , Supplementary Fig. 2 , Supplementary Fig. 3 , Supplementary Data 2)  14. Despite the relatively high prevalence of A1d1a in the CTVT host dog germline population, it is evident that this haplotype is enriched for horizontal transfers to CTVT relative to other canine haplotypes (p < 0.
The libraries were sequenced with 75-bp pairedend reads on an Illumina HiSeq4000 instrument (Illumina, San Diego, CA, USA) to an average depth of ~168×  13. Samples were processed in three batches (Supplementary Data 6A). Substitution calling and post processing. Substitutions in nuclear genomes were called using Platypus 36 v0. 8. 1 as part of a bespoke computational pipeline (Somatypus v1. 3, https://github. com/baezortega/somatypus)  13. Substitutions in mitochondrial genomes were called using the same bespoke computational pipeline as above, with the following modifications in the individual filtering and merging step, and in the final filtering step: substitution called if ≥3 supporting reads with mapping quality ≥ 20 and base quality ≥ 20 were detected, and base qualities within 10 bp of the ends of reads were set to 0.
Indel calling. Small insertions and deletions (indels) in mitochondrial genomes were extracted from whole exome sequencing data using samtools and bcftools  37, 38. Samtools v0. 1. 18 mpileup with options '-C50' and '-gf' was used to create raw bcf files from indexed bam files, and indels were called with bcftools v0. 1. 17 view, options '-bvcg'. Phylogenetic analyses. For maximum likelihood topology inference, the mitochondrial DNA (mtDNA) phylogenetic tree represented in Fig. 1a  and Supplementary Fig. 2  was constructed with 539 CTVTs, 494 dogs (Supplementary Data 1 and 2), the CanFam3. 1 canine mitochondrial reference sequence, and rooted with two coyote genomes (GenBank accession numbers: DQ480510. 1, DQ480509. 1). We phased and extracted distinct haplotypes in heteroplasmic tumours using variant allele fractions or, in tumours belonging to HT3, using PacBio sequencing (see section 'MtDNA recombination analysis'), and each haplotype was included in the tree as a separate sample (Supplementary Data 2).
2. 9. For tanglegram construction, correspondence between equivalent CTVT tumours on mtDNA and nuclear trees was assessed using a tanglegram constructed in Dendrocope 40 v3. 5. 10. For horizontal transfer group inference, mtDNA horizontal transfer was inferred if discordance was observed between mtDNA and nuclear phylogenetic trees. Heteroplasmic horizontal transfer was inferred in tumours carrying two or more distinct mtDNA haplotypes, all present at more than 10% frequency, and not explained by the matched host haplotype (Table  1 , Supplementary Data 2). Heteroplasmic tumours carried haplotypes from the parental CTVT and the newly transferred haplotype, except for the HT3 group, which carried a heteroplasmic mixture of recombinant haplotypes. Groups of CTVTs were inferred to belong to a single horizontal transfer event if they clustered together on both the mtDNA and nuclear phylogenetic trees (Fig.
1a , Supplementary Figs. 1  and 2 ). Dog haplotype assignment. The haplotype naming system was adapted from the cladistic canine mtDNA phylogeny nomenclature proposed by Fregel et al. 14. An mtDNA phylogenetic tree was constructed with 495 dogs (Supplementary Data 1), the CanFam3. 1 canine mitochondrial reference sequence, and rooted with two coyotes (GenBank accession numbers: DQ480510. 1, DQ480509. 1) (Supplementary Fig. 3 ). The tree inference was performed with RAxML 39 v8. 2. 9 using a maximum likelihood method with a GTR substitution model. The tree topology was used to assign dogs into one of the following 18 haplotypes: A1, A1a1, A1b, A1c, A1d1, A1d1a, A1d2, A1e, A1f, A1h, A2, A4, A5, A6, B1, B2, C1 and C2 (Fig. 1b , Supplementary Fig. 3 , Supplementary Data 3). Timing analysis of horizontal transfer events.
The simulation was performed in R  41  over 10000 repetitions, with randomisation seed set to 76. The empirical p value was derived from the proportion of simulations with the number of A1d1a horizontal transfers equal to or exceeding the observed value. A more conservative analysis was performed that included only matched tumour-host pairs. The code used for this analysis is available at https://github. com/TransmissibleCancerGroup/Mixed. A1d1a mtDNA copy number. MtDNA copy number was calculated for normal canine ovarian (n = 42) and testicular (n = 41) tissue, as well as for CTVT tumours (n = 337) (Supplementary Fig. 5 ). The following equation was used to calculate the mtDNA copy number: (mtCOV-T/nuclCOV-T) × P, where mtCOV-T = average coverage across the mitochondria × mtDNA tumour fraction, nuclCOV-T = average coverage across the nuclear genome × nuclear tumour fraction, and P = ploidy.
Ploidy was estimated as two for both CTVT tumours and dogs  42. MtDNA tumour fraction was estimated from variant allele fraction (VAF, i. e. number of reads supporting the substitution variant as a fraction of the total number of reads covering the substitution variant position). Nuclear tumour fraction was estimated from whole exome sequencing data using the following equation: (mode of T-VAF) × 2, where T-VAF = somatic tumour variant allele fraction  13. Statistical significance was tested using an unpaired two-tailed Student's t test implemented in R  41. Nuclear relationships of A1d1a dogs. A neighbour-joining cladogram was constructed using 136,880 canine germline variants genotyped across 495 CTVT host dogs (Supplementary Data 1) and 7 wolves obtained from the Dog Genome SNP Database (ftp://download.
big. ac. cn/dogsd/bam/)  43  (Sample IDs: ISW, CRW, CHW, LUPWRUS00001, LUPWRUS00002, LUPWRUS00003 and LUPWCHN00001) (Supplementary Fig. 6 )  13. To account for the presence of heterozygous and homozygous variants, distances between the aligned sequences were calculated using the p-distance metric, as implemented in the 'dist. p' function of the phangorn 44 v2. 3. 1 package for R. The phylogenetic tree was constructed using the neighbour-joining algorithm, as implemented in the 'NJ' function of the phangorn package. A1d1a-specific substitutions and indels. Substitutions and small insertions and deletions (indels), which were common and unique to A1d1a and, in some cases, the related A1d1 haplotype, were identified through filtering against other CTVT and dog samples (CTVTs belonging to HT3, which has undergone recombination between CTVT_HT1 and A1d1a, were not considered in defining A1d1a-specific variants) (Supplementary Data 1 and 5).
Indels were validated visually using Integrative Genomics Viewer (IGV)  45, 46. Annotation was performed using Variant Effect Predictor 47 (Supplementary Data 5), and the functional relevance of each variant was assessed, where possible, by aligning the region to humans and assessing variants using Mitomap  48. Somatic occurrence of each A1d1a-specific genetic variant was assessed in the set of 495 CTVT tumours (Supplementary Data 1 and 5). MtDNA recombination analysis. Potential recombinant samples were identified by searching for outliers on the mtDNA phylogenetic tree, and by visualising mtDNA VAF plotted against mtDNA genome coordinate. Standard PacBio genomic libraries were created using 5 µg of genomic DNA from samples 559T and 1315T, belonging to HT3, not utilising shearing or amplification techniques  12.