dataesr/scientific-paragraphs-categorization huggingface dataset:
When dealing with a large amount of spectral data, complex structures and non-linear relationships can arise which may compromise linear regression approaches  (Dardenne et al. , 2000). In practice, using a linear classifi-cation or regression to predict a complex database would lead to degraded results  (Bertran et al. , 1999; Ni et al. , 2014). As a consequence, linear methods are challenged on large amounts of data. Furthermore, some methods, called local methods, exploit data based on a restricted neighbourhood of individuals which greatly improves prediction quality  (Dardenne et al. , 2000; Pérez-Marín et al. , 2007; Davrieux et al. , 2016; Naes et al. , 1990). These methods can be used to overcome non-linearity problems under the assumption that with a restricted neighbourhood, the relationship between spectra and variables becomes linear.
Spectral acquisitions Spectral data of the prepared leaf samples were acquired in the reflectance mode by using a laboratory-based line scanning Hyperspectral Imaging System (HIS). The HIS system was composed of a linear halogen light (Haloline, Osram, 150 W), a translation rail (Linear Unit LES 4, Iselautomation, Germany), and a detection system. The sample was placed on a translation rail, synchronised with the acquisition software (NEO Hyspex, Norsk Elektro Optikk AS) which can record images when sample was scanned under the hyperspectral camera (NEO Hyspex VNIR-1600 with 30cm-objective, Norsk Elektro Optikk AS, Skedsmokorest, Norway). Spectral data were acquired in the 400 -1000 nm wavelength range with 3. 7 nm intervals. For each sample, the reflected light intensity (I s (λ)) was measured at each wavelength.
Dark current image (I b (λ)) was also recorded for each measure. A white reference (SRS99, Spectralon ®) was used as a reference (I o (λ)) to standardize images from non-uniformities of all components of the instrumentation (light source, lens, detector). From these measurements, reflectance (R s (λ)) was calculated for each sample: R s (λ) = I s (λ) -I b (λ) I 0 (λ) -I b (λ) (1) For all hyperspectral images, vegetation pixels were selected to form a spectral data set. This selection was made by a threshold procedure (Fig. 1 ). Indeed, vegetation and background pixels were easily identified by comparing their reflectance value at 800 nm to a threshold defined here at 30%. Leaf spectra were collected from the 28 hyperspectral images, representing more than 1,300,000 spectra.
Data analysis Two methods were used to compare their ability to discriminate sunflower genotypes. Both methods were applied to a similar data set, called test set, built out of the spectra database. Calculations were performed with the R software (version 3. 6. 1 (Core Team, 2013)) and rnirs package (https:// github. com/mlesnoff/rnirs) was used for classical discrimination methods (PLSDA).
ParSketch-PLSDA method The other strategy was to apply the parSketch-PLSDA method  (Metz et al. , 2020) , an extension of the K-Nearest Neighbours (KNN)-PLSDA method for massive data processing  (Lesnoff et al. , 2020). ParSketch-PLSDA was used to combine an indexation strategy (parSketch) and the PLSDA. An approximation of the neighbourhood was defined for each spectrum to be classified. This neighbourhood was then used to compute a PLSDA model and to predict which class belong new spectra. ParSketch was performed in three steps: dimension reduction, grid creation, neighbourhood approximation. Three method parameters (v, s, m) were defined, corresponding to these three steps, and are described below. First, a dimension reduction was achieved by calculating the matrix T corresponding to the sketch of the matrix X as follows: T = XP (3) Where P was a matrix of size (p,v) containing values of -1 or 1 according to a random selection.
Evaluation strategies and method parameterization The data set was divided into two independent data sets: a calibration set and an independent test set. The calibration set was formed with the 14 images acquired on P1 plants and corresponding to about 650,000 spec-tra. The PLSDA model and parSketch-PLSDA method were both calibrated using all spectra of this calibration set. The test set was formed with the other 14 images acquired on P2 plants (independent from P1). 1000 spectra were randomly selected in each image totalling 14,000 spectra for the test set. Spectra that could not be predicted by parSketch due to lack of neighbours were removed from the test set. In the end, the same test set were used for parSketch-PLSDA and for PLSDA. For both methods, validation steps were performed on the calibration set in order to minimize overfitting.
Consequently, the model prediction error decreases to a value of 13%. This implies that parSketch-PLSDA model performs better than the reference discriminant strategy. This improvement in the classification results demonstrates the advantage of using a limited number of neighbours to create a model. As the methods used are locally linear, this improvement confirms the hypothesis that with a limited number of neighbours, the problem becomes linear. The prediction improvement obtained with parSketch-PLSDA method highlights the presence of non-linear relationships between spectra and a class variable in the whole data set. which can be encountered when building a large spectral database.
Conclusion In this study, we compared the two classification strategies on the same calibration and test data sets. For both methods, classification results are encouraging and confirm the interest of VIS-NIR spectroscopy for variety discrimination. Results showed that parSketch-PLSDA method outperforms PLSDA by improving prediction qualities by 10%. The use of the parSketch-PLSDA procedure in the exploitation of massive spectral data is confirmed and shows the interest of using a close neighbourhood of the spectra to be predicted. It would be interesting to test such methods on a larger number of genotypes. This increase in the spectral database can potentially lead to an increase in complexity hence reducing the data set quality. Therefore, it would be interesting, in perspective, to evaluate other methods dealing with non-linearity.
In the framework of plant breeding, hyperspectral imaging or field microspectrometers as tools for high-throughput plant phenotyping could be considered in real time with this method. In an applicative aspect, parSketch procedure is parallelisable, which shows the possibility of fast real-time prediction of a large amount of data. We used parSketch-PLSDA on spectral data for close-range plant phenotyping. Other applications to plant breeding (disease, biotic/abiotic stress) or other applications related to precision agriculture could be considered. More generally, this method can be applied to any other application in analytical chemistry or metabolomics.
collected and organized spatial data to a number of GIS applications: namely Google Maps, DARIAH Geo-Browser, Gephi, Palladio and ArcGIS. Through empirical experimentation with spatial data and their implementation in different platforms, our paper charts the ways in which contemporary GIS applications may be implemented to cast new light on ancient understandings of identity, space, and place. In the past decades, Geographic Information Systems (GISs) has been used extensively in archaeology  (Conolly and Lake, 2006; Landeschi, 2019; Trepal et al. , 2020; Rajani, 2021)  and other humanities disciplines  (Dunn, 2019). By locating historical data on a map, space becomes place, imbued with additional meaning. The capacity to identify, aggregate, organize, and to map spatial data in documents is particularly valuable when researching historical modes of spatial thinking beyond the Cartesian, or bird's eye, view that has dominated post-Enlightenment cartography.
Through empirical and experimental implementation of spatial data in different GIS platforms, our paper charts the ways in which contemporary GIS may help elucidate ancient understandings of identity, space, and place. 2 Working Method: From Semantic Annotations to Geovisualizations and Analytics Recogito (https://recogito. pelagios. org) is an opensource web-platform tool essentially a semantic annotation tool for texts and other documents. Developed within the Pelagios project, with its legacy carried out by the Pleagios Network; Recogito enables the researcher to annotate three kinds of entities-places, peoples, and events-in texts and images. Recogito provides a personal workspace for users to import or upload different text and image formats and to collect and organize source materials-texts, images, and tabular data-and to collaborate  (Simon et al.
The Digital Periegesis' team has a private instance of Recogito which operates with a range of customized gazetteers connected directly to the archaeological and A. Foka et al. Digital Scholarship in the Humanities, 2021 2 of 9 art historical record. At the moment the most granular topographic, archaeological and heritage data can be found in the Topostext gazetteer that is available via the website (https://topostext. org/TT-downloads). For art historical artefacts and heritage monuments we use Judith Binders Art History Gazetteer and the German Archaeological Institute's (https://www. dainst. org/en/) Pausanias's specific gazetteer for archaeological record on the ground (e. g. districts, temples, statues, etc. ). If no appropriate match can be found, the team utilizes a yellow flag option in the gazetteer interface and the comments' box for further details that are then returned to the gazetteer developers.
While Recogito keeps track of version history and edit provenance it also supports a range of export formats. The options presented in our private instance relate to downloading annotations in CSV, as a data table for importing into spreadsheet software or a GIS. There is further the possibility to download annotations and document metadata as RDF, encoded using Open Annotation and Dublin Core, in JSON-LD RDF/ Turtle RDF/XML formats. For places, the user is able to download confirmed geo-located places in the document as a GeoJSON FeatureCollection. Geolocated places can finally be downloaded as a KML file, for viewing in GIS applications such as Google Earth, for example. Recogito is being extended continuously to offer a growing number of integrating options with external sources and developing standards, such as IIIF or TEI, the latter of which is also good for social network visualization  (Pelagios Network, 2021).
For Digital Periegesis, we use Recogito's CSV exports for relations, where the origin and destination nodes are listed under 'from_quote' and 'to_quote' columns, respectively, and the edges under 'relation' column. In the special instance of working with the graph visualization software, Gephi, two separate CSV files can be exported from Recogito, one being for the nodes and the other for the edges. Moreover, Recogito itself offers a simple map view feature that enables the users to display all geo-annotations that are linked to one of its patron gazetteers. There are three basemaps based on contemporary aerial imagery and places as well as ancient places. The map view enables a 'jump to text' feature from place point to references in Pausanias's text. Visualization is minimal in Recogito: relational annotations and time animation are not visualized at all.
cc/perie gesis, categorized all place annotations under volume number and a search box interface feature. The DARIAH Geo-Browser enables a dynamic visualization of spatial and temporal data, by uploading or linking multiple KML files or spreadsheets to draw correlation implications based on visual comparisons of temporal animations of place-based objects. On https://geobrowser. de. dariah. eu/?csv1¼ https://geobrowser. de. dariah. eu/storage/803386, we demonstrate how a Recogito export of all ten volumes can be animated on the DARIAH interface, based on annotations and their timestamps. The Dariah Geo-Browser enables uploading basemaps. Visualizing Recogito data from a social network or relational perspective can be achieved by Gephi and Palladio. Gephi is not primarily a GIS application but is one of the leading open-source software in working with graphs and networks.
Rich libraries of chronological expressions have been compiled, most noteworthy being the structured authority files for time periods of PeriodO (http://www. perio. do), which is a public domain gazetteer of historical, art-historical, and archaeological periods. While linking among datasets that define periods differently may be an interesting exercise, the resource is at the time of writing by no means complete, although it helps scholars and students see where period definitions overlap or diverge. An additional concern is the concept of temporality across times and cultures and the division of time more generally. Contemporary terms (e. g. Hellenistic or Classical period) and their associated date ranges seldom map neatly to Pausanias's narrative which tends to establish a working chronology by using known events such as battles or Olympiads.
Fortunately, Wikidata is rich in such items. A way to tackle this issue in order to use Palladio is to annotate, e. g. the 102nd Olympia mentioned by Pausanias with its Wikidata ID, Q57337793, and extract the year date as a temporal expression, 'tx : 372 BCE'. To conclude, Palladio, and to some extent the DARIAH Geo-browser assisted our temporal information organization and analysis by forcing us to think of ways to organize time numerically while staying true to the text. Last but not least, ArcGIS, a commercial platform of numerous software, applications, and services developed by Esri, or, 'the Cadillac of mapping software, including online and desktop mapping tools'  (Irwin, 2018)  was extensively utilized within the project Digital Periegesis, especially through the use of the desktop application ArcGIS Pro integrated with the cloud-based SaaS ArcGIS Online (AGOL).
' Having tested several applications in terms of their capabilities based on Recogito exports throughout our progress, we believe we can shed light on the said complexities and their contribution to humanities. Our preliminary findings (see Table  1  and the StoryMap on our hub site gis. periegesis. org) on the use of each platform, namely Google My Maps, DARIAH Geo-Browser, Gephi, Palladio, and ArcGIS, Moreover, using AppStudio, we also plan for creating a native mobile app that will allow for visualizing Periegesis in Augmented Reality (AR), as AR can be  a critical link among historical and modern travel geographies and humanities while some challenges remain  (Kounavis et al. , 2012; Barrado-Timon and Hidalgo-Giralt, 2019). The quest will also continue by testing other applications such as Nodegoat, StoryMap JS, Neatline, and QGIS-not least to draw comparisons among free and open-source versus commercial software.
Visualizing Pausanias's Description of Greece Digital Scholarship in the Humanities, 2021 5 of 9 reveal some of the comparative features and skills. While ArcGIS offers the most comprehensive platform for data analysis, the opportunity to draw attention to and understand better the underlying topological connections in the narrative-the links that Pausanias makes between places, objects, and peoples-were best served by network visualization tools such Gephi and Palladio. Our future work involves overcoming this issue by exporting Gephi's graphs through the SHPExporter plugin (SHP being the abbreviation for ArcGIS's native file format-shapefile) as well as testing the recently released ArcGIS Pro Intelligence software that promises to provide the user with interactive visualizations and advanced analyses of relations (Esri, 2021).
CFD Validation The presented CFD tools are here compared with respect to experimental data of commonly adopted benchmark cases (i. e. , free-jet and jet impinging on a cylinder)  [27, 28]. In Section 3. 1, the free-jet validation case is presented, whereas in Section 3. 2 the validation of the case of jet impinging on a cylindrical obstacle is summarized. It is worth noting that in this paragraph the considered tools are FLACS, KFX and a generic 2D Fluent approach. The Fluent validation is performed in 2D to save computational time, taking advantage of the case studies' regularity, and considering that only the jet evolution along the jet axis is of interest. Unfortunately, FLACS and KFX permit only 3D simulations; hence, the three-dimensions domain is considered. Since SBAM is a 3-D model, useful for large, congested domains, it is used in Section 4, where the realistic case of the O & G offshore platform is analyzed.
Results In FLACS and KFX, the following simulation conditions are set: a 3-D transient solver is used to solve the Reynolds-Averaged N-S equations (in fact KFX allows modeling 3D processes), the Standard k-ε model is employed to model the turbulence of the flow (in fact the k-ε turbulence model is the only turbulence model implemented both in FLACS Energies 2021, 14, 8117 6 of 16 and KFX). More details about the numerical models are given in the previous work  [19]. A cartesian grid is built since this is the only one type of grid available in the two software programs. This kind of grid is used also in the next test case, although there is a round shape. This is possible since the two software programs use the Porosity Distributed Resistance (PDR) approach; see details in  [19]. In Fluent, the following simulation conditions are set: 2D steady simulation using a RANS formulation of the Navier-Stokes equations with a Standard k-ε model as the turbulence closure equation, in order to be consistent with the simulations implemented in FLACS and KFX.
Results In FLACS and KFX, the following simulation conditions are set: a 3-D transient solver is used to solve the Reynolds-Averaged N-S equations (in fact KFX allows modeling 3D processes), the Standard k-ε model is employed to model the turbulence of the flow (in fact the k-ε turbulence model is the only turbulence model implemented both in FLACS and KFX). More details about the numerical models are given in the previous work  [19]. A cartesian grid is built since this is the only one type of grid available in the two software programs. This kind of grid is used also in the next test case, although there is a round shape. This is possible since the two software programs use the Porosity Distributed Resistance (PDR) approach; see details in  [19]. In Fluent, the following simulation conditions are set: 2D steady simulation using a RANS formulation of the Navier-Stokes equations with a Standard k-ε model as the turbulence closure equation, in order to be consistent with the simulations implemented in FLACS and KFX.
2 × 10 6 , 4. 5 × 10 6 and 9 × 10 6 elements. It is worth mentioning that the results obtained with SBAM are only due to the mesh discretization for the dispersion simulations, whereas the SB module is considered as a "black-source"; instead, as customary in FLACS and KFX the whole release-dispersion CFD simulation is performed. Results are: • FLACS: GCI = 7. 8%, f 0 = 163 m 3 • KFX: GCI = 10. 6%, f 0 = 199 m 3 • SBAM: GCI = 1. 2%, f 0 = 83 m 3 With respect to f 0 , it is interesting to note that FLACS and KFX provide more conservative results with respect to SBAM, to cover the simplifying modelling assumption adopted (and overcome by SBAM): f 0 estimated by KFX is >100% larger than for SBAM, whereas f 0 estimated by FLACS is ~100% larger than for SBAM, which means that the energies and damage towards which countermeasures and barriers are to be designed for are much larger than what they actually should be.
Estimated Recombination Rates Decreased in the Inbred Line If punctuated regions of elevated heterozygosity are maintained due to deleterious alleles linked in repulsion (pseudooverdominance), these regions could also show decreased rates of recombination  (Waller 2021). To further investigate the elevated heterozygosity maintained in our inbred line, we estimated the recombination landscape using the pooledsequencing pipeline in the software package ReLERNN  (Adrion et al. 2020). We were initially unable to get fine-FIG. 2. The phentypic effects of inbreeding included (A) a decrease in the mean reproductive output that was not recovered after 300 generations of breeding at large population sizes. There was (B) no influence of inbreeding on longevity but the Recovery lines evolved an increase in longevity when compared with the Ancestral and Inbred lines.
Adams et al. doi:10. 1093/molbev/msab330 MBE scaled recombination landscapes with our filtered, highconfidence SNPs. After expanding to all possible polymorphic sites, we obtained fine-scaled recombination estimates for the Inbred line and coarse-scaled recombination rates for the Ancestor (fig. 9A-C ). The average recombination rate for the Ancestor was comparable to previously reported averages in C. elegans  (Rockman and Kruglyak 2009). In comparison, the Inbred line had severely reduced recombination rates across the genome. Due to the reduced recombination rate and patterns of retained heterozygosity, we used the Haplovalidate software  (Franssen et al. 2017; Otte and Schlotterer 2021)  to identify haplotypes in the Inbred and Recovery populations but the haplotypes were not statistically significant.
Effective Population Size Did Not Recover We used the software package poolSeq  (Taus et al. 2017 ) to estimate the effective population size in the Inbred and Recovery lines. The effective population size of wildcollected C. remanei has been previously estimated to be $1,000,000  (Cutter et al. 2006). The effective population size for the Inbred line was estimated as 28 (supplementary table 3, Supplementary Material online). The three Recovery lines had a mean effective population size of 90 after 100 generations and 148 after 200 generations (supplementary table 3, Supplementary Material online).
Selection Scans Identified Significant Parallel Changes in Recovery In order to detect any possible genetic recovery from inbreeding, we used two methods to identify significant, parallel, allele frequency changes across Recovery lines. First, we fit a generalized linear model (GLM) with quasibinomial error distribution to the allele frequency changes across the Inbred line, generation 100 Recovery, and generation 200 Recovery according to  Wiberg et al. (2017)  recommendation for best practices with pooled sequencing data. Second, we performed a Cochran-Mantel-Haenszel (CMH) test to analyze parallel changes in allele frequencies between the Inbred and Recovery lines at generation 100 and 200 with the software package PoPoolation2  (Kofler et al. 2011). All sites that were significant in the quasibinomial-GLM analyses were also significant with the CMH test, and we retained all significant sites for analysis.
The quasibinomial-GLM revealed 102 SNPs with significant parallel changes across the three Recovery lines (q-value < 0. 05). Of these 102 SNPs, 36 were contained within 30 genes. Genomic locations, log q-values from the quasibinomial-GLM, and snpEff annotation  (Cingolani et al. 2012 ) for these genes are given in table 2. InterProScan protein domain annotations  (Jones et al. 2014)  and Caenorhabditis orthologs (identified with the OrthoFinder software package; Emms and Kelly 2015) for these genes are listed where available. Several genes had no identifiable domain annotations or orthologous proteins in other species. Seventeen of the sites were characterized as Intron Variants with potential modifier effects. Nine sites were characterized as Synonymous Variants of low effect. Seven sites were characterized as Missense Variants of moderate impact.