dataesr/scientific-paragraphs-categorization huggingface dataset:
(http://www. ap242. org/)This extension is the result of an initiative to favour common effort, as an alternative to previous work on AP203 and AP214, by extending them to new topics (such as 3D printing) and other information supported by CAD models, including GD&T  (Sarigecili et al. , 2014)  and PMI  (Lipman and Lubell, 2015) , resulting in a convergent application protocol. STEP AP242 contains both presentation and representation of GD&T information as referenced in  (Lipman and Lubell, 2015). The presentation of tolerances is standardised by ASME Y14. 41-2012 (A. Y14. 41, 2012 ) and ISO 16792:2021 (ISO, 2015)  and can for example be visualised by polylines or tesselated geometries. The main technical requirements for STEP AP242, apart from information exchange and archiving, are to provide a consistent data model for XML exchange  (Boy et al.
Literature review methodology To obtain a clear understanding of the usage of ontologies, a literature review was conducted according to the following steps: • A list of keywords was prepared according to the context of this study, i. e. , considering the data storage context into a PLM or PDM system. This study investigates the semantic contained into 3D CAD models by using ontologies. So, the selected keywords are PLM/PDM, as well as CAD/CAM, 3D file format, interoperability related to 3D models, and ontology. • The keywords were used to query into some well-known elec- tronic databases, including Elsevier (Scopus and ScienceDirect), Inderscience, IEEEXplore, Springer (SpringerLink) and Taylor & Francis. • The papers whose terms are related to one of the keywords and ontology were reviewed and selected.
Paper analysis and classification A preliminary effort on evaluating papers on low-level CAD models enrichment was made by: • Grouping all the articles found in Elsevier, Inderscience, IEEEXplore, Springer and Taylor & Francis, and then applying an impurities removal filter for the duplicates found in more than one database, as well as in surveys, reviews, or non-scientific papers such as magazine articles. The number of papers considered relevant for these reviews was further reduced in this phase; and then • Screening the remaining papers considering the title, the abstract and finally the full text. After the application of these filters, the most relevant papers were classified in descending order of published year, according to the users' expectations as listed in Table  2 , as well as with the reasons and motivations for their selection.
VAQUERO for Semantic CAD enrichment, using of OntoSTEPAP242, textual annotations of low-level CAD models VAQUERO (Visual Ontology bAsed QUERy) for CAD enrichment system was proposed as a first edition as a demonstrator to proof the usage of OntoSTEPAP242 for CAD semantic annotations. The system would allow the semantic enrichment of low-level 3D models from semantically rich STEP AP242 standard. (https://gitlab. utc. fr/ snzetcho/semantic_enrichment. git) This system should enable the evolution of these 3D models as valuable approach to improve data communication and information exchange. As it can be seen on Fig. 1 , it should be proposed an open access application that allows interoperability between different systems in order to favour the enrichment of 3D models. The use of ontology in VAQUERO for CAD enrichment system allows to ensure a certain taxonomic uniformity of the added semantic information because it is modelled based on STEP AP242 which covers the whole product life cycle.
Vaquero for CAD enrichment includes applications such as: • A PDM system such as Windchill PDMLink for allowing the re- trieval of 3D models that will be used for the primary view (Fig. 1E ). • The 3D model visualization in primary view must be through a 3D viewer such "ShareCAD" embedded into VAQUERO. That 3D viewer could open all the low-level CAD models (Fig. 1D ). • An ontology based on STEP AP242 standard (OntoSTEPAP242) is proposed and available at: https://gitlab. utc. fr/snzetcho/ semantic_enrichment. git. User navigates in the ontology from tree-structures and graph from the dedicated panels. Quick selections called "Category" are proposed to navigate easily in the ontology (ontological Category panel, Fig. 1A ). A graph representation of the ontology is proposed to clearly identified relations between concepts (panel in the middle, Fig.
Conclusion This paper proposes a literature review allowing to highlight the need to develop Ontologies for low-level CAD model enrichment (i. e CAD model available in frozen geometry). STEP AP242 is considered as a high-reference standard. It means containing both geometry and expert information for rich CAD models. The research statement defended in the contribution is to use an ontology based STEP AP242 called OntoSTEPAP242. The usage of this kind of ontology will allow to standardise textual annotations enrichment of low-level CAD model. Indeed, the technical interoperability of these CAD models could be improved. A first demonstrator called VAQUERO for CAD enrichment has been developed an available at https://gitlab. utc. fr/ snzetcho/semantic_enrichment. git. The contribution has been fully dedicated to CAD models opening in primary view.
A future work will be to consider CAD models used in secondary view (such as PDM viewer). In fact, JT, which is now standardised and used for industrial practises, could also be considered as a rich viewer CAD format. It was initially developed by Siemens PLM Software and standardised as ISO14306  (Beckers et al. , 2016; Katzenbach et al. , 2013; Handschuh et al. , 2013). But it should be mentioned that technical solutions has to be found for enrichment of low level CAD viewer.
Briefly, the DNA molecules were cleaved by a transposase and barcoded tags were attached to the cleaved ends. The barcoded samples were then pooled and Rapid Sequencing Adapters were added to the tagged ends. The pooled libraries were sequenced into a FLO-MIN106 (R9. 4. 1) flow cell for a 48h run according to manufacturer's instruction. After the run, fast5 files were basecalled on the MinIT using default settings in MinKNOWv21. 02. 5 and Guppy v4. 3. 4 and a Fast Basecalling. For the Illumina sequencing, libraries were prepared starting from 30 ng of genomic DNA using the Illumina DNA prep kit (Illumina, USA) following the manufacturer's instruction. Briefly, genomic DNA was tagmented using Bead-Linked Transposomes which fragments and tags the DNA with adapter sequences. After a post tagmentation clean-up, tagmented DNA were amplified using a 12 cycle PCR program and IDT® for Illumina® DNA/RNA UD Indexes Set A to adds the index and adapter sequences.
(Illumina). Raw sequences generated by MinION nanopore sequencing were assembled using meta-flye v. 2. 9, an assembler supporting metagenomic data that was specifically developed for the assembly of third-generation long-read sequences  [32]. The resulting draft assemblies were then polished with Illumina short reads by using multiple rounds of Pilon v1. 24  [33]. Four genomes were thus assembled: those of the B. aphidicola and S. symbiotica symbionts composing the di-symbiotic system of S. maydis (hereafter BaSm and SsSm) and those of the B. aphidicola and S. symbiotica symbionts of P. lyropictus (hereafter BaPl and SsPl). The four assembled genomes were annotated with the Prokaryotic Genome Annotation Pipeline (PGAP)  [34]. The genome sequences were deposited on the MicroScope platform  [35, 36]  and their metabolic capabilities compared using MicroCyc, a collection of microbial Pathway/Genome Databases (PGDBs) based on the MetaCyc database and specifically dedicated to the analysis of microbial pathways  [37].
Genome annotation and comparative analyses Virulomes of both S. symbiotica symbionts were analyzed with the virulence factor database (VFDB, http://www. mgc. ac. cn/VFs/)  [40]  integrated on the MicroScope platform using BLASTp (with a threshold of minimum 50% aa identity, 80% align. Coverage). Secretion systems were identified with MacSyFinder  [41]. PHASTER was used to predict the intact prophage regions  [42]. Assemblies and annotations are available on GenBank (BioProject accession numbers: PRJNA835797 for BaSm, PRJNA837269 for SsSm, PRJNA837360 for BaPl and PRJNA837363 for SsPl.
Molecular phylogenetic analyses To examine the evolutionary relationships of SsSm and SsPl with other S. symbiotica symbionts and other bacteria in the genus Serratia, a phylogenetic tree was built using a set of single-copy core concatenated protein sequences shared across all S. symbiotica strains for which complete genome sequences are publicly available. S. symbiotica and outgroup genomes used for phylogenetic analysis are listed in Table  S2  in the supplemental material. Genomes were downloaded from the NCBI Assembly Database on June 2 nd 2022. All protein sequences of the different species and strains were analyzed with OrthoFinder (version 2. 0)  [43, 44]  to identify groups of orthologs. A set of 235 protein sequences encoded by single-copy genes present in each bacterial strain was then used for phylogeny estimation.
Acknowledgments The authors thank  Karen Gaget  for her help with the aphid pictures and the whole  BF2I  laboratory for the stimulating discussions about the topic. This study was financially supported by  FNRS  grant no. 1B374. 21. This paper is publication BRC 393 of the  Biodiversity Research Centre (Université catholique de Louvain). BF2i laboratory  was specifically supported by  INSA Lyon  and  INRAE. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
e. , flash heating, bulk melting and viscous flow mechanisms) that best fit the data in a given slip range. We analyze data resulting from a large set of laboratory experiments performed on silicate-built and calcite-built rocks. Flash heating and bulk melting are investigated for silicate-built rocks, while flash heating and dislocation creep or flash heating and diffusion creep are investigated for calcite-built rocks. Furthermore, we present a novel way to model and interpret the measured temperature at high acquisition rates with optical fibers inside the slipping zone  (Aretusini, Núñez-Cascajero, et al. , 2021). This approach helps to validate the assumptions made when modeling temperature from the mechanical data and interpret the possible contribution to the temperature rise of the investigated weakening mechanism.
Slip, slip-rate and shear stress were determined using the methods outlined in  Niemeijer et al. (2011)  and  Tsutsumi and Shimamoto (1997). The original mechanical data were acquired with a constant time step (between 0. 04 and 4 ms). We resampled our data to obtain a constant slip step of Δx = 0. 001 m for all the experiments so that, during the fitting and optimization procedure, the data points during the acceleration stage are not overrepresented with respect to those during the plateau at constant velocity. This comprehensive data set offers a unique opportunity to integrate and discuss dynamic fault weakening mechanisms at high slip-rates for each lithology and loading conditions.
The fully coupled partial differential equations are solved using a 1D finite difference explicit method implemented in ® Matlab. This is an approximation of the cylindrical geometry, but the results do not differ substantially as discussed in  (Nielsen, Mosca, et al. , 2010). The model domain z is orthogonal to the fault plane, and it was discretized in 50 nodes equally spaced Δz = 0. 001 m outside the melt layer w or slipping zone t (see Section 3. 1 and 3. 2). The melt layer and the slip zone t where discretized using Δz = 1 μm. Due to the symmetry of the experimental setup, we modeled only one-half of the sample assembly. In our model the fault is represented by a single point at z = 0. At each time iteration, the time step Δt was equal to Δx/V(t). With the only exception of the melt lubrication model (Section 3.
Here we present geophysical (swath bathymetry, acoustic profiles) datasets and a compilation of previously published sediment core data collected on the outer sector of the cross-shelf trough off Clyde Inlet (Baffin Island) and its adjacent continental slope of western Baffin Bay that together demonstrate the existence of an ice shelf in northern Baffin Bay-the Northern Baffin Bay Ice Shelf (NBBIS)-during the last glacial episode (Fig. 1 ). This geomorphological evidence and the reinterpretation of sediment cores allow defining the extent of the LIS on the continental shelf at the LGM and examining the potential impact of an ice shelf collapse on the evolution of ice streams of the three marine-terminating ice sheets in Baffin Bay.
A second diamicton overlying the red brown laminated muds is observed immediately below BBDC-1 in cores north of Clyde Trough  45, 69  , representing glacigenic debris-flow deposits correlated to a smaller localized advance from northeastern Baffin Island ice streams to the shelf break prior to 14. 2 kyr BP  45. To our knowledge, no sediment core has been collected or published from the Greenland side of northern Baffin Bay to allow direct comparison with Baffin Island continental slope assemblages. In southern Baffin Bay, sediment core data show similar sequence as those from the Baffin Island continental slope  34, 70, 71. However, widespread foraminifera assemblages and bioturbation during the LGM interval suggest the presence of perennial sea-ice  61  and/or a nearby ice shelf margin  62, 72, 73.
6  Sediment assemblages in Baffin Bay and along the Baffin Shelf. Lithology of piston cores from Baffin Bay modified from various published datasets (see 'Methods'). Radiocarbon ages are reinterpreted in calendar years using the online software Calib 8. 2 with the Marine20 radiocarbon age calibration curve  87  and a local reservoir correction (ΔR) of 87 ± 20  88. In addition, relative paleointensity (*) chronology is also presented for core 16PC 59 and 77PC  26. Correlations are based on Baffin Bay detrital carbonate (BBDC) beds and are compiled from original publications. BBDC events are represented by the brown shaded areas-ages are from Simon et al. 57   ~800 m, hence continually calving icebergs throughout the LGM  76. Such a constant calving in northern Baffin Bay is, however, not compatible with the sedimentary record from the slope and deep basin off Baffin Island (Fig.
Although geophysical data from the Greenland continental shelf do not allow confirmation, it is probable that the ice shelf had a similar extent across the entire Baffin Bay. The relatively deep troughs (<500 mbsl) on the Greenland side of northern Baffin Bay possibly prevented the formation of ice shelf lateral moraines. Similarly to northeastern Baffin Island, ice streams located off the GrIS may have merged with the NBBIS. The exact extent of the NBBIS in southern Baffin Bay remains unknown; sediment assemblages  45, 60  show similarities to those of northern Baffin Bay, while the record of marine productivity during the LGM suggests openings in sea-ice as polynias and/or advection under a proximal ice-shelf margin  34. It is therefore possible that, while northern Baffin Bay was covered by a basin-wide ice shelf system, southern Baffin Bay was characterized by fringing ice shelf and/or perennial sea-ice along both continental shelves, which could also explain the presence of ice shelf lateral moraines off Home Bay.
Methods Geophysical data along the Baffin Island continental slope. Swath bathymetric data was collected in 2017 during expedition MSM66 of the RV Maria S. Merian 85 using a Kongsberg Simrad EM122 (12 kHz) system, which allowed the coverage of Clyde Trough. This dataset is complemented by swath bathymetric data from ArcticNet cruises collected during transits from 2003 to 2016 onboard the CCGS Amundsen, equipped with a Kongsberg Simrad EM302 (30 kHz). These datasets were processed for anomalous data points and artefacts removal using Caris Hips and Sips software and gridded at a 10 m cell-size resolution. They were then imported into ESRI ArcGIS software for geomorphological mapping and landforms identification. The International Bathymetric Chart of the Arctic Ocean (IBCAO) data  86  , gridded at a 500 m cell-size resolution, was also used to show overall bathymetry of Baffin Bay and its adjacent shelves.
Parasound profiles were acquired onboard the RV Maria S. Merian using a Teledyne-Reson Parasound DS P-70 (secondary low-frequency ca. 4 kHz). The raw data were recorded into ASD and PS3 format and then converted into SEGY using ps32segy software of Dr. Hanno Keil (University of Bremen). The shallow-acoustic profiles were then imported into the IHS Markit Kingdom software for processing and interpretation. Seismic lines 78029_AG_274_1516 and 80028_AG_RAYT_257_0200 were acquired by the Geological Survey of Canada during airgun surveys in 1978 and 1980, respectively. Extraction and interpretation were done using the LizardTech GeoViewer® software. Both acoustic and seismic data were then transferred into Adobe Illustrator® for figure production. Thicknesses and water depth were calculated using a velocity of 1500 m/s.
For full description of the cores, readers are referred to the original publications-16PC 57 ; 34PC and 36PC 56 ; 61PC, 64PC, 73PC, 74PC and 77PC 45 ; 67PC 21 ; SL174  60. Radiocarbon ages were calibrated within the age-depth modelling process using the online software Calib 8. 2 with the Marine20 radiocarbon age calibration curve  87  and a local reservoir correction (ΔR) of 87 ± 20  88  commonly used on northeastern Baffin Island  26, 45, 57, 60  (Supplementary Table  1 ). This reservoir correction is in line with the one currently used for radiocarbon date calibrations of central West Greenland  34, 71  , that indicate a reservoir correction (ΔR) of 140 ± 35 years  89. We recognize that an offset caused by a well-mixed ocean was most likely variable through time and the appropriate ΔR reservoir correction for the region might have been larger than the one used and provide younger ages.
Acknowledgements We are thankful to the captains, crews and scientific participants on the different cruises for their help and support during the expeditions. This project was funded by the  ArcticNet Network of Centers of Excellence, Natural Sciences and Engineering Research Council of Canada (NSERC)  and  Sentinelle Nord (Apogée Canada ) grants to P. L. , the  Deutsche Forschungsgemeinschaft (DFG)  grants to B. D. , C. G. and  D. H. for ship-time and to D. H. for the  International Research Training Group "ArcTrain " (IRTG 1904), as well as  Université de Strasbourg  grants to P. O. C. We also thank  ArcTrain Canada  for providing financial support to this project. This paper benefited from fruitful discussions with  D. B. Praeg  and  C. Ó Cofaigh. The final version of this manuscript was greatly improved by thoughtful reviews from  M.
Data availability The swath bathymetric data collected in 2017 during expedition MSM66  85  have been deposited in the PANGAEA repository, available under https://doi. org/10. 1594/ PANGAEA. 902341. The swath bathymetric data from ArcticNet cruises can be visualized on the Université Laval Géoindex + website (http://geoindex-plus. bibl. ulaval. ca). The Parasound profiles collected in 2017 during expedition MSM66  85  have been deposited in the PANGAEA repository, available under https://doi. pangaea. de/10. 1594/PANGAEA. 944843. The seismic reflection data along with the acquisition specifics are available on the Marine Data Holding public repository of National Resources Canada (http:// geogratis. gc. ca/).
Actinobacteria are important cave inhabitants, but knowledge of how anthropization and anthropization-related visual marks affect this community on cave walls is lacking. We compared Actinobacteria communities among four French limestone caves (Mouflon, Reille, Rouffignac, and Lascaux) ranging from pristine to anthropized, and within Lascaux Cave between marked (wall visual marks) and unmarked areas in different rooms (Sas-1, Passage, Apse, and Diaclase). In addition to the 16S rRNA gene marker, 441 bp fragments of the hsp65 gene were used and an hsp65related taxonomic database was constructed for the identification of Actinobacteria to the species level by Illumina-MiSeq analysis. The hsp65 marker revealed higher resolution for species and higher richness (99% operational taxonomic units cutoff) versus the 16S rRNA gene; however, more taxa were identified at higher taxonomic ranks.
Actinobacteria communities varied between Mouflon and Reille caves (both pristine), and Rouffignac and Lascaux (both anthropized). Rouffignac displayed high diversity of Nocardia, suggesting human inputs, and Lascaux exhibited high Mycobacterium relative abundance, whereas Gaiellales were typical in pristine caves and the Diaclase (least affected area of Lascaux Cave). Within Lascaux, Pseudonocardiaceae dominated on unmarked walls and Streptomycetaceae (especially Streptomyces mirabilis) on marked walls, indicating a possible role in mark formation. A new taxonomic database was developed. Although not all Actinobacteria species were represented, the use of the hsp65 marker enabled species-level variations of the Actinobacteria community to be documented based on the extent of anthropogenic pressure.
Additionally, the length of the amplified hsp65 fragment (441 bp) is sufficient for amplicon sequencing. While this marker has been used to assess some Actinobacteria groups from environmental samples, it has mostly been used with regard to particular groups, such as Nocardia  (Vautrin et al. , 2021)  or Mycobacterium (van der  Wielen et al. , 2013). Therefore, considering these features, the hsp65 gene may be a good candidate for detailed assessments of the whole Actinobacteria community in extreme environments, such as caves. To make this possible, a reference database encompassing the Actinobacteria taxonomic group is required, which should be publicly available for taxonomic identification. Since the 1960s, the Lascaux Cave has undergone several microbial outgrowth events until recently and has been subjected to (often unsuccessful) chemical treatments, which have resulted in the formation of various visual marks (including stains on walls) that have threatened the Paleolithic artwork (F.
The objective of this study was to assess the usefulness of hsp65 to complement 16S rRNA gene sequence data using a metabarcoding approach for a deeper, species-level appraisal of the Actinobacteria community in caves, and to assess variation according to cave condition and human disturbance  (Mammola, 2019). We compared communities belonging to the phylum Actinobacteria between pristine limestone caves (Reille and Mouflon Caves) and anthropized caves (Lascaux and Rouffignac Caves), and within Lascaux Cave between marked (wall visual marks) and unmarked areas in different rooms (i. e. , Sas-1, Passage, Apse, and Diaclase). The second objective was to create an hsp65-based Actinobacteria database that is accessible to the scientific community. Bastian et al. , 2010; De La Rosa et al. , 2017; Martin-Sanchez et al.
| Processing and analysis of sequence data Paired sequence reads obtained from sequencing were merged using Fast Length Adjustment of Short reads (FLASh;  Magoč & Salzberg, 2011)  with a maximum of 25% mismatches in the overlapping region. The sequences were then filtered and aligned using reference alignments of hsp65 gene sequences (this study) or 16S rRNA gene sequences from the Silva database V132  (Quast et al. , 2012). Chimeric sequences were removed using the integrated Vsearch tool  (Rognes et al. , 2016)  according to the MiSeq standard operating procedure  (MiSeq SOP, February 2018; Kozich et al. , 2013)  in Mothur v1. 39. 5 software  (Schloss et al. , 2009). Sequence libraries were taxonomically assigned in Mothur using the hsp65 reference database for hsp65 sequences and the recreated SEED database subset of the Silva Small Subunit rRNA Database, release 132  (Yilmaz et al.