dataesr/scientific-paragraphs-categorization huggingface dataset:
Hence, we decided to classify as ARG all the proteins reporting at least one hit in any of the four databases. We classified each of the integron pangenome families as ARG or non-ARG, which resulted in homogeneous results within families (i. e. , same number of databases reporting a hit), except for two families where a small fraction of genes (resp. 6% and 2%) had fewer hits than the other members. As a final criterion, we classified as ARG all the pangenome families for which at least 90% of the members had at least one hit in any of the four databases.
Distribution of Integrons across Bacteria We used IntegronFinder v2 to search for integrons in the complete genomes of the Ref-Seq NCBI database, including 22,301 replicons named chromosomes and 21,520 replicons named plasmids (the few remaining were phages or not classed). The time that takes to run IntegronFinder is extremely dependent on the existence of attC sites in the genome. Genomes lacking attC sites run very fast, e. g. , 3 s for a genome of Bacillus subtilis 168 with a genome size of ~4 Mb on a laptop. If the genome contains attC sites, then the use of the most accurate covariance model can slow down analyses, up to almost 4 min for the genome of Vibrio cholerae El Tor N16961 where there is one super-integron  [12]. The entire database used in this study is almost ten times larger than the one used for the publication of version 1 (2484 genomes,  [10] ) and took around 150 CPU hours on a standard laptop.
Given the difference in size to the previous database, we started by assessing integron distribution in the new much broader dataset (Figure  2A ). We found 3116 genes coding for IntI and 56,994 attC sites. The classification of the elements by IntegronFinder v2 indicated the presence of 2760 complete integrons, 356 In0, and 2961 CALIN. These numbers are around ten times larger than those obtained 6 years ago, which is in rough proportion to the difference of size of the two datasets. However, we found a ratio CALIN/integron of almost 1, whereas it was almost 2 six years ago. This is caused by the change in the default parameters to identify CALIN that now require the presence of two attC sites. Among genomes that encode an integron, the frequency of In0 elements relative to integrons is also smaller in the new version.
This is because the IntI protein is searched using appropriate thresholds (gathering thresholds) that diminish the rates of false positives, and this affects much more the counts of In0 than those of complete integrons (which also have neighboring attC sites and are therefore much less likely to be false positives). For example, 6 years ago, we identified two In0 in Actinobacteria. Since we found no complete integron in the clade, this suggested that our hits were false positives. We now find only one In0 (and still no complete integrons) with a much larger dataset that should have resulted in proportionally more false positives. Among genomes encoding at least one IntI, 22% encode more than one. This result confirms the observations made at the time of IntegronFinder v1. 0, 6 years ago, where 20% of the genomes had more than one of the three  [10].
RHBSTW-00464 plasmid 5 (46 kb). The second largest plasmid integron was in Enterobacter hormaechei subsp. steigerwaltii BD-50-Eh plasmid pBD-50-Eh_VIM-1 and was reported before  [52]. Hence, while we had previously used 19 attC sites as a threshold to delimit mobile from sedentary integrons, our present results suggest that using a 10 attC sites threshold could be more adequate. The taxonomic distribution of integrons follows previously described trends  [10, 16, 33]. The vast majority of complete integrons (93%) are found in γ-Proteobacteria, a percentage that largely exceeds the representation of these genomes in the database (38%) (Figure  2D ). In line with previous work, we did not identify integrons in Chlamydiae nor in Tenericutes, despite the good representation of these two phyla in our dataset (respectively, 170 and 400 genomes).
However, the much larger dataset analyzed in this work, as well as some changes in taxonomy and species classification, led to the identification of several clades that lacked integrons six years ago and now have a few. For example, we found 2 CALIN elements in the phylum Nitrospira, both occurring in the genome of Candidatus Nitrospira inopinata, a bacterium known to perform complete ammonia oxidation to nitrate  [53]. The newly defined phylum Acidithiobacillia has 2 complete integrons and 8 CALIN over a total of 11 genomes. Finally, while only In0 had been detected in Bacteroidetes in our previous study, we identified complete integrons in the Bacteroidetes/Chlorobi group. More precisely, on top of the ones found previously in Chlorobi and Ignavibacteriae, we identified a complete integron in Salinibacter ruber M1  [54] , a halophilic bacteria that belongs to Bacteroidetes.
Our previous study failed to identify complete integrons in Actinobacteria, Firmicutes, and Alpha Proteobacteria. We now identify a few elements in these clades. However, their frequency is extremely small relative to the high frequency of such genomes in the database. Firmicutes account for 22% of the genomes, Alpha Proteobacteria for 6%, and Actinobacteria for 10%. The only complete integron in Firmicutes was found in Limnochorda pilosa strain HC45, and a few CALIN were found in different genera across the phylum. The 6 complete integrons in Alpha Proteobacteria were found in species of Sphingobium and Agrobacterium. As mentioned above, Actinobacteria lack complete integrons, have only one In0, and a few CALIN. These results show that while integrons, or their components, are not altogether missing in these clades, in line with previous works  [55, 56] , they are indeed extremely rare and the observed occurrences may represent recent acquisitions.
Considering the presence of integrons in very diverse clades and their ability to spread within plasmids and transposons, the lack of integrons in certain clades remains intriguing as it suggests the existence of some incompatibility between integrons and the genetic background of these large bacterial clades. A recent preprint revealed the presence of integrons in metagenome assembled genomes (MAGs) of Archaea, but not in complete genomes  [25]. Since this study used a combination of a pre-release of IntegronFinder 2. 0 and HattCI  [24] , we wished to understand if the novel version of IntegronFinder alone, which is better suited to study MAGs, could identify these systems. We also failed to identify complete integrons, CALIN, or In0 in the genomes of Archaea present in our database. This is not unexpected since the clades where the integrons have been identified are very poorly represented in RefSeq.
Therefore, we downloaded five MAGs of the study cited above and searched them for integrons. We confirmed the presence of two complete integrons, one CALIN, and one In0 whereas one complete integron in  [25]  was detected as a CALIN in our analysis. Hence, if Archaea are found to encode integrons like those suggested by the recent analysis of MAGs, IntegronFinder version 2 is expected to be able to identify them.
Recent Spread of Integrons in K. pneumoniae To exemplify the use of the novel version of IntegronFinder, we analyzed a large collection of draft genomes of Klebsiella pneumoniae (Kpn). Kpn is a Gram-negative bacterial species belonging to the Enterobacteriaceae family, naturally occurring in soil, freshwater, and mammalian gut and is considered an opportunistic pathogen  [57]. It is a member of the ESKAPE pathogens, the list of high-risk multi-resistant nosocomial pathogens from the World Health Organization. Aside from having the largest known mobile integron in the RefSeq database (see above), Kpn is also an interesting example of a nosocomial bacteria that is thought to have recently acquired integrons carrying antibiotic resistance genes. While the presence of integrons in the species is well known  [58] , its characterization has not been done at the species level.
Hence, we collected 3980 genomes of the species, re-annotated them uniformly, and searched for complete integrons in the draft genomes. The analysis by IntegronFinder took 14 h using 5 CPUs on a standard desktop computer. We identified 1855 complete integrons, 2590 CALIN, and 405 In0 in 2709 of the 3980 genomes, resulting in a (CALIN+In0)/complete ratio of 1. 61 (Table  S4 ). As our dataset mostly comprises draft genomes, it was expected that some complete integrons would be divided in several contigs, leading to an increase of the proportion of CALIN and In0. This phenomenon may be enhanced by the presence of attC sites very similar in sequence, which complicates the assembly of contigs harboring integrons. For comparison, among the 730 K. pneumoniae complete genomes comprised in our database extracted from RefSeq (see previous section), 492 complete integrons, 282 CALIN, and 21 In0 were identified in 435 genomes.
The (CALIN+In0)/complete ratio is 0. 62 in this dataset, which seems to confirm that analyses of draft genomes will tend to overestimate the frequency of In0 and CALIN. To further investigate how many complete integrons may have been split between contigs, we looked for occurrences of In0, complete integrons, and CALIN where the integrase or a gene cassette was the first gene in a contig. We found 819 isolates harboring at least one CALIN together with one complete integron or In0 at the border of a contig. Among these, we found 339 In0 and 532 complete integrons. These might correspond to true complete integrons that were split between contigs during assembling. Hence, the analysis of genomes that are not fully assembled may result in the underestimation of the number of cassettes, incomplete integrons, and spurious identification of CALIN elements.
For the following analysis, we decided to focus on the 1855 complete integrons identified in 1677 genomes. In other words, around 42% of the genomes of our Kpn in the database have an integron (all data in Table  S3 ). In genomes carrying integrons, the number of integrons per genome is usually one but can be higher. Notably, the genomes of strains AR_0039 (GCF_001874875. 1) and DHQP1002001 (GCF_001704235. 1) carry four complete integrons each. To study the distribution of integrons across the species, we built a phylogenetic tree and plotted the presence of integrons in function of the sequence type (ST) (Figure  3 ). This analysis revealed no clear pattern of aggregation, since integrons are found across the species. This suggests multiple independent acquisitions of integrons in the species recent past.
Integrons in Kpn have been studied because they have a few well-known antibiotic resistance genes  [59, 60]. One might thus have expected to find little genetic diversity among them. To assess the diversity of these integrons, we analyzed their gene repertoires. The integrons in Kpn encoded a total of 5763 protein coding genes, with the largest elements having up to 15 genes or 7 attC sites. Hence, we could not find in this dataset integrons as large as the one found in the complete genomes of RefSeq. This may be caused by different samplings or because integrons in draft genomes may be split in several contigs. We used PanACoTA  [31]  to compute the pangenome of the integrons and identified 165 different gene families. Hence, the integrons of Kpn are small, as expected from mobile integrons, but carry a large diversity of gene families.
We computed saturation curves for the integrons' pangenome and observed that it is open, i. e. , after analyzing almost 2000 elements, the curve does not show evidence of saturation (Figure  4 ). Further genomic sampling of Kpn will thus likely reveal novel gene cassettes. We then detailed the functions of the genes encoded in the cassettes of integrons (IntI being obviously the most frequent protein of integrons). Expectedly, most of the largest gene families in cassettes are associated with antibiotic resistance genes (ARG). To study them in detail we used four databases of ARGs: CARD, ARG-Annot, ResFinder, and AMRFinderPlus. The integrated analysis of the results (see Methods) resulted in the identification of 50 families of ARG. An analysis of the 20 most frequent gene families reveals 12 that are ARGs, including multidrug transporters and enzymes associated with resistance to antiseptics, aminoglycosides, diaminopyrimidine (e.
Conclusions Many of the improvements in IntegronFinder version 2 will be almost invisible to the user because they involve software engineering, but they will facilitate its maintenance in the next decade. This is important because funding for software maintenance is almost inexistent. The novel most visible capacities of IntegronFinder will allow it to better tackle large datasets of genome, which tend to be composed of draft genomes, and metagenomes. Here, we have exemplified its use with the database of complete genomes and a large dataset of Kpn draft genomes. As it stands, we regard speed as a major limitation to the use of the program in exceptionally large datasets, e. g. , in metagenomes or in datasets with hundreds of thousands of genomes. The current deadlock is the use of the covariance model that is computationally expensive in its most accurate version.
In particular, a simple direct analytical formula is derived in order to compute the stress in a given phase once the effective behavior of the laminate has been determined. Furthermore, the code to compute the effective behavior and the stress distribution in an arbitrary N-phase laminate is made freely available (see Supplementary Material at the end of the document). The paper is organized as follows. Section 2 reminds the expressions of incompatibility stresses in a two-phase laminate from which the effective compliance, effective plastic strain and effective thermal expansion tensors can be deduced. Then, Section 3 presents an explicit method to find the effective behavior and the stress distribution for a general N-phase laminate based on the solutions of the two-phase laminate. Section 4 is dedicated to the validation of the proposed method by comparisons with finite element simulation results on a same boundary value problem.
Section 3. 1), this means that the stresses in the phases are also not sensitive to the stacking order of the phases. Besides, the numerical implementation of the proposed method is very straightforward and is provided as a Matlab code (see Supplementary materials). It contains two functions, one that computes the tensor    (cf. Equation (  7 )) from two elastic compliance tensors and a volume fraction value and one that computes the effective properties of a 2-phase laminate according to Equation (15). The main code is just composed of a single iterative loop that calls the two aforementioned functions in order to compute the properties of the new phases step by step as described in Figure  1. At step , the effective behavior of the N-phase laminate is known through Equation (  23 ) and the stresses in any phase can then be directly computed from Equation (  25 ).
The FE simulation was performed thanks to the use of the open source software suite freefem++  (Hecht 2012). A structured mesh made of 270 000 triangular quadratic Lagrangian elements was used for the meshing of a bar of length 100 (see Figure  3 ), which corresponds to 4 nodes along  1 and  3 and 5001 nodes along  2. Periodic boundary conditions were imposed along the lateral sides. Arbitrary and fixed velocities were imposed on the bottom and upper faces of the bar ( 1 = -0. 05,  2 = 0,  3 = -0. 1 on the bottom face,  1 = 0. 05,  2 = 0. 1,  3 = 0. 1 on the top face). Phase 1 was affected to the region 75 <  2 < 100, phase 2 to 65 <  2 < 75, phase 3 to 35 <  2 < 65, phase 4 to 15 <  2 < 35 and phase 5 to 0 <  2 < 15. A first simulation was performed in pure elasticity in order to determine the most stressed systems and then a second simulation was performed considering static plastic strains in each phase.
The stress tensor in a given phase is then directly deduced from the stress concentration tensor 𝜎 𝑚 𝑖 = 𝐵 𝑚 𝑖 𝑗 Σ 𝑗. (30) For ease of direct comparisons with the results of the laminate model, this set of equations was also implemented in the Matlab software. The results of Figure  5  were then compared with the maximum von Mises stresses obtained from elastic self-consistent models considering oblate spheroidal grains ( =  > ) of different aspect ratios (Figure  6 ), the small axis of the oblate spheroids being parallel to the interfaces normal in the laminate model. A convergence towards the laminate solution is observed by increasing the aspect ratio / of the oblate spheroids, both for the case with 100 000 orientations and for the specific case with two orientations only. For the case with 100 000 orientations, it is seen that, as long as elongated grains are considered, the laminate model provides fairly good qualitative trends for the variation of the maximal von Mises stress with a rotation of the uniaxial macroscopic stress.
Moreover, the Eshelby tensor     in an anisotropic medium cannot be expressed analytically and must be computed numerically. For this work, the Eshelby tensor was computed thanks to the Matlab code provided by Cai 2018 where     is obtained from the Hill P tensor  (Hill 1965b ) which is itself computed from numerical integrals that are performed using the quadv function in Matlab. On the contrary, the expression of the tensor    in Equation (  7 ) is fully analytical and hence very simple to code. Actually, it can be shown that the Eshelby stress solutions can be directly obtained from the tensor    by appropriate integrations  (Richeton and Berbenni 2014). In order to illustrate the numerical differences between the two types of model, the effect of the number of phases on the computation of the effective stiffness tensor, as well as the effect of the absolute tolerance value set in the quadv function in Matlab to evaluate the Eshelby tensor was analyzed.
The code to compute the effective behavior and the stress distribution in an arbitrary N-phase laminate is made freely available for download (link in the Supplementary materials section). Besides, the correctness of the proposed method is checked by comparisons with finite element simulation results on a same boundary value problem, showing excellent agreements. An application of the method is also performed for a near- titanium alloy with elongated grains, by comparing, for different elastic loadings, the level of internal stresses within a N-phase laminate made of 100 000 orientations and a 2-phase laminate with maximal elastic contrast. Interestingly, the maximum von Mises stress of the 2-phase laminate is always the lowest despite the strong elastic contrast considered, which is explained by a volume fraction effect.
Introduction A vast area of research in historical science concerns the quantitative analysis of empirical facts extracted from historical sources, their description, and the interpretation of possible causes, influences, and evolutionary trends. This kind of research requires a holistic data management approach that supports historians in all the different activities involved in their research processes, from digitizing the (usually hand-written) archival sources, to curating the transcribed data and performing quantitative analysis and exploration. Current practice nearly exclusively uses spreadsheets or simple relational databases to organize the data as rows with multiple columns of related parameters, such as prices for kinds of goods in certain harbours at certain times, for the case of maritime history.
The information sources used in SeaLiT range from hand written ship log books, crew lists, payrolls and student registers, to civil registers, business records, account books, and consulate reports, gathered from different authorities and written in different languages, including Spanish, Italian, French, Russian, and Greek. We showcase the use of the described tools using these data sources. Below, we start by describing how the archival sources can be transcribed and curated using FAST CAT and FAST CAT TEAM, then we detail the modelling and transformation of the transcribed and curated data into a rich semantic network, and finally we describe the data exploration functionalities of the ResearchSpace system.
Fig. 17. 1 shows the home page of FAST CAT, where the user is shown a table containing all the available templates. For each template, the table provides some basic information, in particular the "title" of the template, "related categories" (keywords that represent the type of the included information), "related organizations" (responsible for the data entry process), and the "source languages". The user can select a template and create a new record to start digitizing a particular archival source. For creating the record, the user first needs to provide some basic information by filling a small form. This information is different for each template. For instance, for a record of type "Logbook" the user must provide the following information: Type of Ship, Name of Ship, Date of Document (From/To), Author of Record, the latter being the name and surname of the historian performing the data entry.
This is crucial for reliability of the research results as well as validation. FAST CAT offers a special environment, called FAST CAT TEAM, through which the historians can collaboratively perform the above curation steps without changing the original transcribed data. Fig 17. 4  shows the home page of FAST CAT TEAM. In the home page, the user is shown a table containing all the publicly shared FAST CAT records whose data can be curated. The curation steps are organized into two categories, accessible through the left menu: i) management of vocabularies; and ii) management of entity instances (Legal Entities, Locations, Persons, and Ships, in our case). When visiting the "Vocabularies" menu item, the user is shown a table with all vocabularies whose terms appear in the transcribed data (Fig.
If the user is not sure about the exact location, she/he can tick the checkbox "Location certainty" and optionally include a comment. Linking the locations to coordinates is very important for enabling the visualization of the transcribed data on a map. In the context of the SeaLiT project, the total number of vocabularies available for curation is currently 52. Examples include: ship type, flag, marital status, religion, military service status, nationality, profession, reason of death, wind direction, and wind strength. As regards the number of entity instances, there are currently 72,093 person instances, 7,638 location instances, 1,876 ship instances, and 1,137 legal entity instances. Since the investigation process is still open and new records are created, and also the manual instance matching process made by the historians is still in progress, the number of distinct instances in each entity type is expected to be different at the end of the data entry and curation processes.
Data Modelling and Transformation to a Semantic Network The transcribed and curated data is now ready for transformation into a rich semantic network of "Linked Data"8 that will allow for advanced exploration and analysis of the historical information that appears in the archival sources. The objective is to model and semantically represent the curated data and metadata using established and standard data models, for supporting data exchange, interoperability, and long-term validity and reuse. For this, we need: a) to decide on the domain schema (ontology) to use for representing the data of the FAST CAT records b) to create the schema mappings for each template in  FAST   c) to run the transformations considering the designed schema mappings and the domain ontology, and then ingest the produced semantic data (RDF triples9) to a semantic repository (RDF database), from where data analysis and exploration can be initiated.