dataesr/scientific-paragraphs-categorization huggingface dataset:
C. Berge-Thierry et al. Pure Appl. Geophys. Figure  13  (from  Gatti et al. 2018b ) outlines the features of the multi-tool platform that was developed to respond to those needs within the framework of the SINAPS@ project. Among the tools used, the main wave propagation solver is represented by the SEM3D software, which is tailored to efficiently solve wave propagation problems through the spectral element method  (Komatitsch and Vilotte 1998; Komatitsch et al. 2005; Gatti et al. 2018b ). The original core of the SEM3D software allowed the viscoelastic wave propagation problem to be solved in any velocity model, including with anisotropy, intrinsic attenuation, and Newtonian fluid-structure interactions. Moreover, the software makes use of a library called HexMesh (https://github. com/jcamata/ HexMesh.
14, right ). A recent study that involved several project partners provided insight into the advantages of a new, all-embracing, modeling approach of a strong ground motion scenario through a source-to-structure analysis at the regional scale, which accounted explicitly for the uncertainties related to the databases and models  (Gatti et al. 2018a, b). To this end, a suitable case study is represented by the 2007 Mw 6. 6 Niigata-Ken Chuetsu-Oki seismic sequence (west Japan) that damaged the Kashiwazaki Kariwa Nuclear Power Plant. This study described the effects of the wave propagation path within the Earth crust on the seismic response of the nuclear reactor buildings located near to seismogenic source. The multiscale problem was de-coupled into three steps: (1) a parallel simulation of seismic-wave propagation throughout the Earth crust at regional scale (60 km wide, major 3D geological interfaces below the nuclear site), and reliable up to 5.
Further Studies After SINAPS@ A PhD project was activated between CEA, IRSN and ENS with the aim to continue the use of reduced order models to extend their applications to probabilistic seismic loading. A nonintrusive version will be implemented into Cast3 M Finite Element Code. The study undertaken by Th. Heitz within WP5 concerned the identification of structural damping for reinforced concrete, and this will be continued ove the coming years. A doctoral study was activated by ENS-Paris-Saclay in collaboration with Pierre Leger (Ecole Polytechnique de Montreal, Canada). The enormous amount of data acquired during the SINAPS@ project (51Go of data coming from 643 experimental tests, 8 performed in quasi-static and 12 in dynamic conditions) will be further explored, with regard to the effects of nonlinearities on the evolution of damping.
Scientific Challenges of WP4 WP4 partners were challenged: 1. to establish the overall methodological approach for the quantification of the seismic margins of a facility through coordinated implementation to global validation, by confronting the measures and data available for Unit 7 of the Kashiwazaki-Kariwa NPP site, which suffered an earthquake on July 16, 2007 that was beyond its design level; 2. to consolidate the performance of probabilistic risk assessment methods, in terms of uncertainty propagation techniques and probabilistic metamodels, fragility curve calculations, and extreme statistics and Bayesian methods. 5. 2. Limitations at the Beginning of the SINAPS@ Project and Regulatory 'Constraints' Identified in the Topics of the Risk Assessment The general approach of the French safety regulations with respect to seismic safety was of a deterministic nature.
The efficiency of this approach for applications is sensitive to the modeling choices, and in particular the training algorithm might need large computational time to produce adequate precision. Another way to produce meta-models has been evaluated using a Gaussian process model. On a specific nonlinear structural case, it was concluded that satisfactory accuracy and CPU times can be achieved. The implementation of Bayesian analysis methods and extreme statistics for the calculation of fragility curves was studied in particular by  Wang et al. (2017a, b). The main conclusions of the demonstrative case study based on the data from the former benchmark KARISMA (2010) about unit 7 of the Kashiwazaki-Kariwa NPP site of the SINAPS@ project are: 1. The capability to produce synthetic ground motion signals  (Zentner 2014 ) has been shown on the basis of a scenario adapted to the case of the seismic event considered (here the NCOE July 2007 event) using a Campbell-Bozorgnia-type GMPE  (Campbell and Bozorgnia 2008).
Indeed, the motion defined at the 'outcropping rock' is not as affected by the nonlinearity of the superficial soil layers. • The limit of validity of the equivalent linear elastic model (Guidelines ASN/2/01 2006) can be overcome by using a nonlinear soil behavior model. This offers the advantage of being able to represent in 3D the evolutions of all of the components of the fields during a transient, and to identify the amplification and the de-amplification at the free-field of the seismic ground motion, according to the frequency level. However, such models often require more data for the calibration procedure. 4. As explained above, the relevancy of accounting for the degradation of the soil behavior that produces a saturation of the amplitude of the transfer capacity of the seismic motion within the soil column from the substratum was assessed.
Proposals for Recommendations from WP4 Achievements SINAPS@ has led to the emphasis for possible evolution of engineering practices and regulatory approaches: 1. Identify the importance of seismic ground motion data control at the bedrock or outcropping rock instead of the free-field motion. This analysis of the site effects makes it possible to reduce the difficulty and the uncertainty associated with the de-convolution of the signal in a soil column defined by the geological profile of the site, taking into account the degradation of the properties of the soil according to the intensity of the seismic loading, the signal directivity. This approach might be associated with a 'host to target' adjustment of GMPEs. The epistemic uncertainties are also reduced by using a suitable geophysical, geotechnical site data analysis and an appropriate verification and validation procedure for tools and methods.
Scientific Challenges of WP5 Following the Fukushima Daiichi nuclear disaster, an analysis of the cliff effects for extreme events was carried out for nuclear installations in France, particularly with regard to seismic risk. In addition to the experienced feedback analysis, the experimental approach was also able to characterize and model the phenomena that appeared in these extreme situations. Thus, WP5 of the SINAPS@ project provides experimental data from shaking table tests to: • Refine the evaluation of seismic margins in nuclear reinforced concrete buildings by quantification of the various damping mechanisms (IDEFIX test campaign). Indeed, the models of damping used today suffer from lack of physics. In a closed interaction between WP3 and WP5 of the SINAPS@ project, the IDEFIX test campaign was carried out.
This test campaign must therefore create experimental data on building-building interactions to construct a numerical model to estimate the number and magnitude of impacts during an earthquake. In conjunction with the other WPs of the SINAPS@ project, industrial and academic experts from these fields were integrated into the organization of these two original testing campaigns, which made it possible to obtain numerical analyses based on experimental data. In the first phase of these two experimental campaigns, bibliographic studies and numerical analyses were used to design the models and define the measurements and test conditions. A second phase was dedicated to manufacturing and development of models and their set-up. A third phase allowed for the analysis of test data to identify some parameters and refine numerical models.
Tests showing impacts were directly compared with those without impact. Finally, the two structures were subject to higher excitation levels so that yielding occurred at first storey columns of both structures. To obtain accurate measures of the effects of pounding on structures, high frequency and low-tomedium frequency responses were recorded, using dedicated instrumentation. For instance, accelerations were measured using both high frequency (10-4000 Hz) and low-to-medium frequency (0-150 Hz) acceleration sensors. Strain gauges were also mounted on the steel frame columns. As for displacements, LVDT, wire sensors, laser sensors, and video-metric methods were used. In addition the motion of the shake table itself was accurately monitored using additional acceleration sensors. As an overall observation, the experimental data highlighted the important effects of pounding on acceleration time history (Fig.
• A nonlinear numerical hysteretic model with seven parameters was identified and verified in several tests. This model has in particular the ability to represent 'pinch' at a low range of force. Identification of this model was from dynamic tests using an optical measurement system with images correlation; a procedure for identifying non-linear parameters by modal decomposition was used to evaluate the evolution of the damping for each mode during the test. This analysis also made it possible to visualize higher damping when crack openings are small. • The data from the tests carried out at different deformation speeds showed that the value of the damping coefficient changed with deformation speed of the structure, whereas this value was a constant in the regulations. As part of SINAPS@ project, an important work of storage, formatting, classification and communication was necessary to make these data available and exploitable by the scientific community.
Outlook • This experimental campaign generated more than 600 tests that can verify several approaches. Indeed, even if the analyses of these tests carried out as part of the SINAPS@ project are numerous, the exploitation potential of the test data is high, as it would be possible, for example, to use these data to evaluate and improve finite element models. • The test data were obtained on a very simple and 'classical' structure, and they can easily be used for other analyses than the evaluation of damping. • The test method developed for IDEFIX can be extended to other structural elements such as floors, to evaluate the behavior (damping) of plate elements.
Further Studies After SINAPS@ as an Extension of WP5 Research and Development At the end of the project, presentations related to damping identification and the study of buildingbuilding interactions received very positive responses and great interest from the international community, because these topics have been little discussed (in the literature) and are studied as both experimental and modeling through SINAPS@. The database that will be opened to the scientific community is currently under study and must be set up to disseminate the experimental data more widely, which can be used beyond SINAPS@. In this sense, actions have already been launched to reuse the experimental data from WP5: (1) initiation of a PhD (EDF and INSA) on the interactions between buildings; (2) EDF FRAMATOME ENS for the use of IDEFIX data and the possibility to carry out new IDEFIX tests.
The two sessions lasted over one full week, and were structured differently. During the second session, a full day was dedicated to a 'specialized module', where the participants experimented with the scientific topic they choose (e. g. , seismic hazard assessment, experimental and numerical site effect characterization and prediction, SSI, structural and component seismic vulnerability, probabilistic seismic analysis) (working with state-of-the-art databases and tools, with some directly linked with the SINAPS@ products). To summarize, the participants then improved their knowledge and practical experience for: • data, processing, metadata, databases; • Methods; • Uncertainties identification, quantification and propagation; • Continuous seismic risk analysis, with the full physical seismic wave path modeling (from fault, SSI, structure and components); • Contribution of experimental seismic testing (i.
The site and structure specific data are unavoidable and are the key: (1) to investigate accurate and reliable geological and structural models, as performed in SINAPS@ on the Greek Argostoli test-site; (2) to catch in the models the specific physical properties and phenomena of the studied case; (3) to reduce, or at least to better quantify, the uncertainties and their epistemic and random components; and finally (4) to compare and test various competitive models and to use Bayesian methods to rank and weight them. Moreover, SINAPS@ conducted specific experimental campaigns using seismic shaking tables that showed how experimental data and modeling approaches are complementary and mutually serving. The qualification and validation of all of the databases and their openness to the international community are also a strong recommendation from SINAPS@.
Acknowledgements The work carried out under the SINAPS@ project received French funding managed from the  National Research Agency  under the program '' Future Investments '' (SINAPS@ reference No. ANR-11-RSNR-0022 ). SINAPS@ is a SEISM Institute project http:// www. institut-seism. fr/en/. The authors thank all of the SINAPS@ contributors, reseachers, engineers, PhD students, post-doctoral researchers, internships and technicians: the content of this article is based on their work.
Phylogenomic tree for rodent species The Alpine marmot genome was aligned to whole genomes of 15 other rodent species and the human genome as outgroup. Genome assemblies were downloaded from the public NCBI assembly repository (as of January 2015). The genomes were aligned to the Alpine marmot genome using LAST  [37]. The output was screened for ortholog matches using single_cov2 from the MultiZ package  [42]. Pairwise alignments were combined into a multiple alignment using MultiZ. The multiple alignment file (MAF) was screened for blocks aligned in all species. All alignment blocks were concatenated into a multi fasta alignment (length 94 Mbp). We found that 500kbp fragments of the total alignment were sufficient to produce a stable tree topology using the FastTree  [43]  method with the e2 Current Biology 29, 1712-1720.
Gene model prediction To avoid spurious matches to the genome, low-complexity repeat regions were masked from the genome assembly marMar2. 1 using RepeatMasker. The paired-end RNASeq reads were aligned to marMar2. 1 using TopHat v2. 0. 9  [44]. The transcripts were assembled using Cufflinks and merged with Cuffmerge  [45]. The predicted proteomes of human, mouse, rat and thirteen-lined ground squirrel were obtained from Ensembl  [46]  and UniProt  [47]  and the protein sequences of naked mole-rat was obtained from NCBI  [48]  and UniProt respectively. The gene models were predicted with MAKER  [34]  genome annotation pipeline in three iterations (genome browser track: ''Maker''). The predicted proteomes downloaded from UniProt  [47]  were used for the homology search. The assembled transcripts from RNASeq reads were included as experimental evidence in the pipeline.
Second, the CDS models from SPALN were combined with spliced transcripts assembled from RNaseq using Cuffmerge  [45]  This resulted in a high number of possible transcript models, whose open reading frames were annotated by the Transdecoder tool (https://transdecoder. github. io). The transcript models were weighted with scores assigned for the different models based on their origin (highest rank: RNaseq only, lowest rank: SPALN only) and the open reading frames length. In addition, only gene models of at least 50 amino acids in length were retained. The two sets of gene models were manually inspected, and the consensus gene models were chosen as the reference gene models (see track ''protein coding genes''). If the gene models from the two sets were different, individual sources of evidence were utilized in choosing reference gene models.
Functional annotation BLASTP  [39]  was used for Alpine marmot coding sequences against the predicted proteomes of above mentioned species obtained from Ensembl  [46]  and NCBI  [48]  databases. The functional annotation was inferred for Alpine marmot proteins from their best BLAST  [39]  matches. Alpine marmot proteins were also associated to gene symbols from their homologous proteins with functional annotation. The Gene Ontology (GO) terms  [52]  were assigned for Alpine marmot predicted proteins by identifying shared signatures with proteins of known function using InterProScan v5. 17-56. 0 [53]. Alpine marmot protein-coding genes were annotated to their metabolic and cellular pathways by KEGG  [54]  Automated Annotation Server (KAAS). This provides KEGG Orthology annotation to each gene and corresponding pathway annotations.
For orthology annotation (COG/ eggNOG, KO annotation), the predicted protein sequences were compared to the eggNOG 4. 1  [55]  eukaryotic database as well as KEGG  [54]  Release 77 database, using diamond aligner with options ''blastp -k 3 -e 0. 0001-sensitive. '' Results were post filtered using custom Perl scripts, filtering for the best hit with an alignment length of at least 50% of the reference sequence and an e-value cutoff of 1e-10. NOG categories were assigned by linking the relevant COG (http://eggnogdb. embl. de/download/eggnog_4. 1/data/NOG/NOG. members. tsv. gz).
Mitochondrial genome annotation Gene models for the mitochondrial genome were predicted using Open Reading Frame Finder (ORFfinder, http://www. ncbi. nlm. nih. gov/orffinder/). The functional annotations were transferred to predicted ORFs from protein coding genes of known functions from the NCBI non-redundant sequence database  [48]  through BLASTP  [39]. Similarly, mitochondrial tRNAs were predicted with tRNAscan-SE-1. 23  [56].
Sciuridae phylogeny based on mtDNA conservation Complete mitochondrial genomes of members of Sciuridae were downloaded from GenBank (accessed 15 th Feb 2016, although excluding the genome identified as the Daurian ground squirrel (Spermophilus dauricus  [57] , because the phylogenetic placement of this genome suggests misidentification, or introgression between distantly-related species). The complete genomes were aligned with MUSCLE v. 3. 8. 31 [58]  and manually corrected. Because highly variable regions cannot be aligned between sciurid subfamilies, we then extracted non-overlapping coding sequences, according to the annotation of Pallas' squirrel (Callosciurus erythraeus, Gen-Bank: NC_025550), and made a concatenated alignment of 3,786 translatable codons. Phylogeny was estimated via maximum likelihood using RaxML v.
8. 2. 4  [59] , using its GTR+G model and 1,000 rapid bootstraps. The phylogeny shown fits standard taxonomy  [60, 61] ;  [62] , and an identical topology was obtained when we repeated the analysis after excluding the rapidly-evolving third codon positions. Protein coding sequence alignment across species For all predicted marmot protein-coding genes, we obtained DNA and protein sequences of potential orthologs from nine mammals species. Seven genomes were from other rodents plus the rabbit (Oryctolagus cuniculus), and a human genome. Sequence annotations were obtained from the NCBI database  [48]  for human (Homo sapiens, GenBank: GCF_000001405. 29), mouse (Mus musculus domesticus, GenBank: GCF_000001635. 24), rat (Rattus norvegicus, GenBank: GCF_000001895. 5), rabbit (GenBank: GCF_000003625.
3), Upper Galilee mountains blind mole-rat (Nannospalax galili, GenBank: GCF_000622305. 1), chinese hamster (Cricetulus griseus, GenBank: GCF_000419365. 1), naked mole-rat (GenBank: GCF_000247695. 1), thirteen-lined ground squirrel GenBank: GCF_000236235. 1) and damaraland mole-rat (Fukomys damarensis, GenBank: GCF_000743615. 1). Orthologs of the predicted Alpine marmot proteins were identified using best protein BLAST  [39]  hits of each refseq-annotated genome using an expect value (E) threshold of 0. 01 and a minimum percent identity of 65%. Protein sequences were then aligned using MUS-CLE  [58]. Alignment quality at each individual position was measured using the probabilistic framework of ZORRO  [63]  and inconsistent positions (positional score < 9) were removed from the alignment. The filtered protein alignments were then prepared along with their respective coding DNA sequences with PAL2NAL  [64]  to produce codon-based alignments as input for the substitution rate analysis.
Gene set enrichment analysis and pathway enrichment analysis was carried out on these datasets using hypergeometric testing with WebGestalt toolkit  [67]. The multiple testing correction used FDR < 0. 01 as the threshold for significant enrichment. In addition, gene sets involved in functions of interest, namely anti-parasite defense and fatty acid desaturation were prepared. Regardless of enrichment at pathway or gene family level, we also checked all rapidly evolving genes in ''marmot -thirteen-lined ground squirrel'' comparison.
Heterozygosity analysis across species and SNP calling of Alpine marmot individuals Complementing the Alpine marmot data, the paired-end sequence read data, genome assembly data and annotation data of other mammalian species were downloaded from their respective sources (Data S1). Reads were aligned to the genome assembly with bwa -mem v0. 7. 17  [71, 72]. Duplicate fragments introduced by PCR based library preparation were removed using Picard tools' MarkDuplicates (version 2. 12. 1-SNAPSHOT; http://broadinstitute. github. io/picard). For detecting variation in Alpine marmot samples the Genome Analysis Toolkit's (GATK version 3. 6) HaplotypeCaller was used in gvcf mode  [73]. Individual gvcf files were used for joint genotyping with GATK's GenotypeGVCFs tool to build a single variant file containing every Alpine marmot sample.
For comparative analyses of the genic regions between marmot and other mammals the mapped read files were analyzed for variation using GATK's HaplotypeCaller (version nightly-2017-07-11) restricted to regions listed in the respective species' gff file (Data S1). Further filtering was based on base-wise coverages that were determined for these regions with bedtools coverage (v2. 24. 0; doi: 10. 1093/bioinformatics/btq033). The ''vfutils'' script from SAMtools were used to further filter the SNPs. 20% of mean coverage and 200% of mean coverage were chosen as minimum and maximum coverage for variant filtering. We also required to have at least 6 supporting reads for a genotype and that heterozygous allele read are in balance, i. e. , the ratio of reference allele and alternative allele is between 0.
We therefore focused on inference of recent events. Diffusion Approximation for Demographic Inference (DADI) and PCA SNP calling and filtering was carried out for all 12 sequenced Alpine marmot individuals as described above. We filtered the raw SNP dataset by removing non bi-allelic and low quality SNPs (average DP < 10 or > 50, QUAL < 30). We then detected false positive SNPs (FP-SNPs) by using the two independent sequencing datasets of the reference individual. Since both datasets were from the same individual, we reasoned that any position differing by homozygous genotypes was a false positive SNP (mostly due to mapping errors in low complexity and/or duplicated regions). We thus computed the density of homozygous SNPs in 5Kb windows and removed from our dataset any window with more than 1 FP-SNP.