dataesr/scientific-paragraphs-categorization huggingface dataset:
¥ • Select similar artifacts having a given dimension property (width, height, length or volume) value difference less than a given threshold: A SPARQL query over Xlendi artifact dataset to crawl the dimension property values and select the similar ones based on the threshold. As can be seen in Listing 3, the height value corresponding to an instance of the concept 'Amphorae' can be retrieved via object property 'hasHeight' which is inherited (inferred) from the concept 'SpatialObject' in the Arpenteur ontology. Listing 3: A SPARQL query to retrieve artifacts having height distance less than 5 cm from 'Amphore A02' PREFIX a r p :< h t t p : / / www. a r p e n t e u r. o r g / o n t o l o g y / A r p e n t e u r. owl#> SELECT d i s t i n c t ? s i m i l a r N a m e ? d i s t a n c e WHERE { ?amp a ? t y p e ; a r p : hasName " Amphore A02 " ; a r p : h a s H e i g h t ? h1.
? s i m i l a r a ? t y p e ; a r p : hasName ? s i m i l a r N a m e ; a r p : h a s H e i g h t ? h2. BIND (ABS ( ? h1 -? h2 ) AS ? d i s t a n c e ). F i l t e r ( ? d i s t a n c e < 0. 0 5 ). F i l t e r ( ? t y p e IN ( a r p : Amphorae , a r p : G r i n d i n g S t o n e ) ). F i l t e r ( ? s i m i l a r ! = ?amp ). } ¥ • Get the survey images for the source artifact for a given excavation: While artifacts desciption are stored in the artifacts dataset, the photographs information are stored within different temporal datasets corresponding to survey dates. Hence, for a selected source artifact, a federated SPARQL query is performed over: the artifacts dataset to retrieve the bounding box corresponding to the selected source. the temporal dataset to select the set of 3D points that fits into the bounding box and return the corresponding photographs.
Listing 4 shows an example of a query performed directly over the SPARQL endpoint (HTTP query interface) of the temporal dataset while an embedded SPARQL service will allow queering the Xlendi artifact dataset in the body of the same query. For a given 3D point, the corresponding photograph can be retrieved via the ontology properties path: 'hasImagePointManager/hasASetOfObservation/hasPhotog raph/hasFullFileName. Listing 4: A federated SPARQL query to retrieve photograph corresponding to 'Amphore A02' PREFIX a r p : < h t t p : / / www. a r p e n t e u r. o r g / o n t o l o g y / A r p e n t e u r. owl#> SELECT d i s t i n c t ? p h o t o g r a p h WHERE { ? pt3D a r p : hasX ? x ; a r p : hasY ? y ; a r p : hasZ ? z ; a r p : h a s I m a g e P o i n t M a n a g e r / a r p : h a s  Most often a 2D representation in plan is better than a 3D representation.
In addition, the lack of standard to express 3D models makes portability difficult. Nevertheless the 2D representations must be generated from 3D models to ensure the necessary accuracy. In this work we have opted for the two modes of representation: 2D using the orthophotos themselves generated from the 3D models resulting from photogrammetric surveys. Figure  4  is obtained from an orthophoto produced with the photogrammetric survey obtained in 2014. We used the Raphaöel JavaScript Library 17 to represent the 2D implementation of different artifacts in Xlendi site. We have chosen not to directly use the orhtophoto as an interface to the end user because, despite the metric qualities of such a document, a key aspect of this work is missing: the human interpretation of the knowledge-based site.
The drawing produced here is by Mrs. Gina De Angelis, architect, who interpreted the orthophoto and produced this drawing by identifying each artifact. The two blue squares are the quadrats used for the excavation in 2018, the colors code the year of removal of the artifacts. The 3D Web tool is accessible via the URL 18. We provide a 3D view of the different models corresponding to Xlendi artifacts. The artifact positions map the 3D views of the Xlendi orthophotos corresponding to a given site survey period. The 3D viewer is powered by 3DHop  (Potenziani et al. , 2015). As described in Section 4. 1, an advanced information analysis of the Xlendi site is presented to the user via different user-friendly queries (SPARQL queries are performed in back-end of the Web tool). Moreover, the web tools contain download options for 3D files corresponding to Xlendi artifacts and their typologies.
We draw the reader intention that our main intuition behind our Web tools is to provide a panoramic bird's-eye view for Xlendi shipwreck to allow a maximum exploitation of the available CH information by users (typically archaeologists). Let us take the 17 https://dmitrybaranovskiy. github. io/raphael 18 http://www. lsis. org/groplan/hop/xlendiTimeLine/ xlendi. html Figure  6 : A Sparql query result tab view of the morphological attributes corresponding to Amphorae A02 as the selection in the Figure  4  Figure  7 : An image display tab of artifacts in the Xlendi 2D Web tool corresponding to the Amphorae A02 as the selection in the Figure  4  example of amphorae A02, a panoramic view of this artifacts consists of: • a drawing view of the Xlendi orthophoto where the amphorae A02 is colored in red, see Figure  4.
CONCLUSION This paper presents an approach for retrieving, via the Web, photogrammetric data as well as non graphical data without any computation but only with querying on several semantic datasets acquired over the time. This is performed following Semantic Web best practices, where Xlendi data is modeled by the Arpenteur ontology and stored in an online published linked open dataset providing an online SPARQL service. The web approach presented here offers request on surveys data made on Xlendi wreck from 2009 to 2018. This project addresses two types of problems: first the link between representation and the site. We see it in the 2D interface that is proposed, the statement while relying on a precise 3D measurement technique here is a 2D interpretation of the photogrammetric model. The interpretation is performed by a human, a specialist in the field who relies on incomplete metrics and his knowledge of the field.
This 2D document, produced by an expert, highlights the geometry of the artifacts studied and represents only that one. In the 3D interface also proposed in this project, both the web interface and the Virtual Reality interface, the 3D model is there as an interface to non-graphical data and also supports the expression of useful model visible parts, among others, to evaluate the ratio measure/deduction. Hence, in this project, we chose a knowledge graph solution in which the semantic data are stored in a database of graphs and represented by a set of aligned ontologies. This approach allows us to turn resolutely towards an approach that allows sharing, exchanging, reusing and analysis of archaeological data in an effort to standardize formats. Parallel to the website with a 2D/3D interface we are currently working on a virtual reality interface.
The stem was tied to a stake every 20 cm. To avoid stem damage due to stem growth, we regularly slightly loosened the rigid ties. In February 2016, most stems were tilted at 45°(see column "Day of tilt" in dataset,  Ghislain et al. 2019). Ties were added throughout the experiment to maintain the apex at 45°. Eventual sprouts were cut during the whole experiment, to ensure that the main stem continues reacting and producing tension wood. Sprout production was mainly observed in The trees that did not grow or died during the experiment were removed from the study. The number of trees per species is indicated in Table  1. Trees were processed when their diameter had increased by at least 50%. Depending on their growth rate, trees were kept tilted for 47 to 315 days (see column "Time of tilting" in dataset,  Ghislain et al.
RESULTS Capsid interactions in hexamers versus pentamers. Currently, two atomic models of the entire capsid core are available in the Protein Data Bank (PDB) archive (PDB identifiers [ID]: 3J3Q and 3J3Y)  (31). Both were built using an integrative combination of computational techniques (molecular dynamics flexible fitting, molecular modeling, and all-atom molecular dynamics simulations) and experimental data from cryoelectron microscopy (cryo-EM), cryo-electron tomography (cryo-ET), X-ray crystallography, and NMR spectroscopy. Using these models, we analyzed the statistical prevalence of molecular interactions at the interface of neighboring CA molecules in pentameric or hexameric units (see Fig. S1  in the supplemental material). One interaction is significantly more frequent at the pentameric interface than at the hexameric interface: a hydrogen bond (H-bond) between the E28 of helix 1 (H1) in one CA NTD and the K30= in helix 1= (H1=) of the neighboring CA NTD.
This interaction is present in 86. 7% of pentameric interfaces compared to 24. 2% hexamer interfaces (Table  1 ). The distances between C␣ atoms of E28 and K30= in neighboring subunits in these structures are also smaller in pentamers than in hexamers. A similar trend is seen in 20 subnanometer cryo-ET structures from intact virions  (30) , showing closer proximity of E28 to K30= C␣ in pentamers than in hexamers (Table  1 ). This interaction is at the bottom of a pocket between CA residues from neighboring N-terminal domains (CA NTD s) (Fig. 2B  and C ). Here, we use the term "NDI pocket" to refer to this N-terminal domain interface pocket. Consistent with this observation, the interaction is not observed in the X-ray structure of the native wild-type (WT) CA in hexameric form (PDB ID: 4XFX)  (48)  or in any of the hexameric CA X-ray crystal structures available in the PDB, i.
e. , dehydrated, mutated, or bound to a ligand or peptide. An interaction between E28 and K30= mediated by water molecules is observed in the X-ray crystal structure of the crosslinked hexamer (PDB ID: 3H47) (28) (see Table  5  in reference 48). One structural feature could explain the absence of this interaction in the X-ray crystal structures: the crystal lattice is flat and does not fully recapitulate the core's characteristic curvature. This curvature is expected to impact the relative orientations of neighboring CA NTD s  (30)  within pentameric or hexameric assemblies  (37)  and to be more pronounced in the presence of pentamers  (29, 31). The only available X-ray crystal structure of a pentamer also does not show a hydrogen bond at this site. It is cross-linked through engineered cysteines at positions 21 and 22 in the H1 helix (PDB ID: 3P05)  (29).
The resulting disulfide bond is at the top of the NDI pocket, between position Cys21 of the H1 in one monomer and Cys22= of the H1= in the neighboring monomer. This engineered constraint brings E28 and K30= closer at the end of the helices, requiring a reorientation of their side chains to avoid steric clashes. E28, K30, and R18 are highly conserved. Residues E28, K30, and R18 are highly conserved, with 99. 4%, 98. 8%, and 99. 4% sequence identity across the subtype reference sequences available in the Los Alamos National Laboratory HIV mutation browser (http://hivmut. org [49] ). Only three isolates, 03GH173_06 (subtype 06_cpx; GenBank accession number AB286851 [https://www. ncbi. nlm. nih. gov/nuccore/AB286851]), nx2 (subtype 08_BC; GenBank accession number HM067748 [https://www. ncbi. nlm.
nih. gov/ nuccore/HM067748]), and A32989 (subtype BF1; GenBank accession number AF308491 [https://www. ncbi. nlm. nih. gov/nuccore/AF308491]) show substitutions at those positions with K30R, E28D/K30E, and R18K, respectively (see Table  S1  in the supplemental material). In order to determine whether similar interactions at the E28ϳK30= site are formed in other subtypes, 100-ns molecular dynamic (MD) simulations of pentamers of hexamers (POH; one pentamer surrounded by five hexamers) were performed for the WT (HXB2), 03GH173_06, and nx2 isolates. We extracted one POH from the WT core structure (PDB ID: 3J3Y) and used it as a template to model the POH of the isolates named above. The characteristic curvature was maintained by constraining the positions of three atoms in each hexamer (see Materials and Methods and Fig.
There was an indirect water-mediated H-bond interaction between E28 and K30= in the R18A crystal structure (Fig. 6B ); a similar interaction was observed in the crystal structure of the cross-linked hexamer (PDB ID: 3H47), while the E28A, R18A/E28A, and WT CA structures lacked this interaction. Furthermore, these mutations do not appear to have significantly affected the 3-fold interactions between hexamers (Fig. 6C ). Overall, the R18A, E28A, and R18A/E28A X-ray crystal structures demonstrated that the mutations neither affected the folding of the CA protein nor dramatically altered the CA hexamer assembly. The structures also showed, as in previously determined structures of CA assemblies, that the E28ϳK30= interaction was part of a larger cluster of charged interactions at the site (Fig.
7 ). There appeared to be a facile reorganization of side chains to form salt bridges and alternate interaction in the hexamers, depending on the detailed configuration of the subunits. This is consistent with the alternative ring of interactions observed at this site in our MD simulations of the nx2 isolate. MD Simulations of CA dimers. To observe whether the E28ϳK30= H-bond impacts the dynamics of the pentameric and hexameric interfaces, we performed two 100-ns MD simulations for the WT using two neighboring dimers extracted from the central pentamer of POH and a hexameric dimer extracted from the native CA X-ray hexamer crystal structure (PDB ID: 4XFX). Similar simulations were performed for the E28A mutant in both cases. By combining all the conformations extracted from the simulations at each frame (20,002 conformations for both WT and E28A), complete backbone deformation (N eq ; see Materials and Methods) profiles were quantified for both the WT and mutant dimers (Fig.
8 ; see also Table  S3 ). Note that the dimers used for these computations did not correspond to the CA symmetric dimers (D sym ) solved in solution NMR by Deshmukh et al. (PDB ID: 2M8L)  (34). Here, the dimers were extracted from formed pentamers and hexamers. Consequently, monomers A and B of the dimer did not show the same flexibility as the positions involved at the interface, and the positions exposed to solvent were not the same for each monomer. In pentameric dimers, positions surrounding the residues forming the H-bond (positions 30 and 31 from monomer A and positions 29 and 30 from monomer B) showed a slight increase of ϳ1 N eq unit in deformation in the mutant dimers. Also in the pentamers, the ends of helix H1 and helix H1= (positions from 28 to 31) in the WT dimer were connected via the E28ϳK30= H-bond in 85.
S4B  and C ). Our results suggest that E28A affects neither the formation of the D sym and the TOD nor their polymerization, as we observed tubes in vitro (Fig. 5 ). However, we showed that E28A affects the incorporation of pentamers. We thus propose that proper pentamer formation in the CA lattice requires specific flexibility of the H10/H11 loop at the free end of the CA CTD (Fig. S4D ). Moreover, we propose that the E28ϳK30= H-bond between the adjacent monomers in the pentameric dimer is the key to this flexibility. Lemke et al. (41)  previously identified the K30R substitution as a resistance mutation corresponding to the BM compounds, a family of CA assembly inhibitors that act primarily by blocking the assembly of mature conical capsids. The X-ray crystal structure of CA NTD in complex with BM-4 (PDB ID: 4E92) showed binding in a hydrophobic pocket at the bottom of the CA NTD , just behind H1 and K30, that slightly reorganized the bottom of the helix bundle in the CA NTD.
MATERIALS AND METHODS NDI pocket identification. The NDI pocket was identified in the CA hexamer X-ray crystal structure (PDB ID: 4XFX  [48] ) using AutoSite  (68). In this method, energetic grid points in space combined with a clustering algorithm are used to select high-affinity groups of points around the receptor. Clusters are then scored and ranked to provide a list of potential binding sites. Fifteen unique pockets were identified on the surface of the CA hexamer. The NDI pocket was scored in the top three pockets in terms of AutoSite score (AS score, 33. 90; Nbr points, 186; RadGyr, 4. 39; buriedness, 0. 89). Modeling and MD simulations. The CA pentamer and pentamers of hexamers (POH) models were constructed using MODELLER (69) as follows. The WT POH and CA pentamer coordinates were from PDB ID 3J3Y (pdb-bundle  21 chains c, d, e, f,  and g ).
pymol. org/). Similarly, a pair of monomers was extracted from the X-ray crystal structure of the CA hexamer with PDB ID 4XFX. The missing parts of the structure (positions 6 to 10 and 222 to 231) were modeled using MODELLER  (69). This hexameric dimer structure was used to model the mutant E28A hexameric dimer by replacing the side chains of residue 28 in PyMOL. MD simulations were performed with GROMACS (70) using the AMBER99sb force field  (71). Each structure was immersed in a periodic dodecahedral box using TIP3P water molecules (72) and neutralized with Na ϩ counter ions. The system was energetically minimized with a steepest-descent algorithm for 10,000 steps. The MD simulations were performed in an isotherm-isobar thermodynamics ensemble (NPT) with temperature fixed at 300 K and pressure at 1 bar.
A run of 1 ns was performed to equilibrate the system using the Berendsen algorithm for temperature and pressure control  (73). A production step of 100 ns or 200 ns was carried out using the Parrinello-Rahman algorithm (74) for temperature and pressure control, with coupling constants of Tϭ0. 1 ps and Pϭ4 ps. All bond lengths were constrained with the LINCS algorithm  (75) , which allowed an integration step of 2 fs. The PME algorithm (76) was applied for long-range electrostatic interactions using a cutoff value of 1 nm for nonbonded interactions. Coordinates were saved every picosecond. Trajectory analyses were performed with GROMACS software and in-house R scripts. Nonbonded interactions of the bottom of H1 pentamer helices were computed using the g_energy command from GROMACS software.
After that step, excess fluid was removed, and grids were washed with water, fixed in a drop of 2% uranyl acetate, and dried before visualization using a JEOL JEM 1400 transmission electron microscope at magnifications of ϫ2,500, ϫ20,000, and ϫ40,000. Each reaction was repeated at least three times. Crystallographic structures of CA mutants. Crystals of the CA mutant proteins grew at 18°C in hanging drops, containing 2 to 5 mg/ml of protein, 6% to 9% polyethylene glycol (PEG) 3350, 2% to 6% glycerol, sodium iodide, and sodium cacodylate. Hexagonal plate-like crystals appeared after 5 days, and crystal growth was completed over 2 weeks. Crystals were briefly dipped in paraffin oil before cryocooling in liquid nitrogen was performed. Data were collected on a Dectris Eiger-16m detector at Advanced Photon Source (APS) beamline 23-ID-B, Argonne National Laboratory.
Datasets were collected and processed using XDS  (84). The data were examined for the presence of systematic absences. However, no characteristic patterns were observed. Thus, the crystals were indexed in hexagonal space group P6 with one CA molecule in the asymmetric unit. No twinning was present, as determined by the use of either POINTLESS  (85)  or XTRIAGE  (86). Space group and twinning were also verified in ZANUDA  (62). Initial phases were obtained by molecular replacement via PHASER (62) using WT CA (PDB ID: 4XFX) as the starting model. Several rounds of iterative model building and refinement were carried out using Coot  (87)  and PHENIX  (86) , REFMAC  (62, 88) , or PDBREDO (https://pdb-redo. eu/). Structure validation of final models was performed with.
ACKNOWLEDGMENTS P. C. acknowledges  Jean-Christophe Ducom  for his support with high-performance computing resources. This is manuscript 29704 from  TSRI. Use of the  Advanced Photon Source , an  Office of Science User Facility  operated for the  U. S. Department of Energy Office of Science by Argonne National Laboratory , was supported under contract  DE-AC02-06CH11357. This work was supported in part by  National Institutes of Health  grants  U54 GM103368  (to D. S. G. , J. R. W. , S. G. S. , and A. J. O. ) and  R01 AI120860  (to S. G. S. ). The funding agencies had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Method (PDB IDs) No. of dimers % dimers with E28ϳK30= H-bond C␣-C␣ distance (Å) Modeling (3J3Q and 3J3Y) b Hexamer 2,412 24. 20 14. 45 (Ϯ2. 02) Pentamer 120 86. 70 11. 91 (Ϯ0. 98) Cryo-ET (5MCX ¡ 5MCZ, 5MD0 ¡ 5MD9, and 5MDA ¡ 5MDG) c Hexamer 104 13. 64 (Ϯ0. 34) Pentamer 5 10. 05 (Ϯ0. 04) a H-bonds were identified using a distance threshold of 3. 35 Å between E28 carboxyl oxygen and K30= amine nitrogen. b ΔC␣-C␣ (hexamer Ϫ pentamer) (Å), 2. 54. c ΔC␣-C␣ (hexamer Ϫ pentamer) (Å), 3. 59.
(2019)  found no obvious mismatch when comparing colocated CO 2 and NO 2 plumes from OCO-2 and TROPOMI observations. A follow-up study for quantifying the effect of NO x chemistry would certainly be desirable. Since the shape and extent of the plume can be imaged more accurately with an NO 2 instrument on the CO2M satellites, the NO 2 instrument can also be used to assess and correct transport simulations and improve these simulations through data assimilation.
Code and data availability. Column-averaged dry air mole fractions of all simulated tracers are available both as 2-D fields and as synthetic satellite products through ESA. The total threedimensional model output amounts to 7. 5 TB and is archived on Empa servers. Selected fields or time periods can be made available upon request. The TNO/MACC-3 inventory can be requested for research purposes from Hugo Denier van der Gon (TNO, the Netherlands). The TNO-CAMS CO 2 emission inventory is publicly available at https://doi. org/10. 5281/zenodo. 112889 (Kuenen et al. , 2017). The emissions inventory of Berlin was kindly provided by Andreas Kerschbaumer, Senatsverwaltung Berlin, and is available for research upon request. The global CO 2 simulation, which provided the lateral boundary conditions, was conducted in the framework of the European Earth observation program Copernicus and can be retrieved from ECMWF's MARS archive as experiment gvri, stream lwda, class rd.
Acknowledgements. This study was conducted in the context of the project SMARTCARB funded by the  European Space Agency (ESA). The views expressed here can in no way be taken to reflect the official opinion of  ESA. The work was supported by a grant from the  Swiss National Supercomputing Centre (CSCS)  under project  ID d73. We acknowledge the contributions of the  Federal Office for Meteorology and Climatology (MeteoSwiss) , the  Swiss National Supercomputing Centre (CSCS)  and  ETH Zurich  to the development of the GPU-accelerated version of COSMO. We would like to thank  Oliver Fuhrer  (MeteoSwiss), who supported the porting of COSMO-GHG to GPUs and the setup of the model on the supercomputer at  CSCS. We would like to acknowledge  Richard Engelen  and  Anna Agusti-Pannareda  (ECMWF) as well as the European Earth Observation Program Copernicus and the  EU  project  CHE  for providing support and access to global CO 2 model simulation fields.
The TNO/MACC-3 emissions inventory and temporal emission profiles were kindly provided by  Hugo Denier van der Gon (TNO , the Netherlands). We would also like to thank  Jochen Landgraf  and  Joost aan de Brugh (SRON)  for providing the orbit simulator. We are also very grateful to  Andreas Kerschbaumer ,  Senatsverwaltung Berlin , for providing the emission inventory of Berlin and additional material as well as for being available for discussions on its proper usage. Financial support. This research has been supported by the  European Space Agency  (contract no. 4000119599/16/NL/FF/mg ). Review statement. This paper was edited by  Ilse Aben  and reviewed by two anonymous referees.