dataesr/scientific-paragraphs-categorization huggingface dataset:
This is because malaria pharmacology is a subcategory of pharmacology, which is in accordance with the approach taken with the previous GtoImmuPdb expansion. Instead, a project specific tag has been introduced to identify ligands and targets of interest to malaria pharmacology and that are to be included in the GtoMPdb. The established curation protocol employed for the GtoPdb (described in previous updates and reviewed in  (33) ) required modest adaptations to allow capture of antimalarial ligands and targets as database entries. Papers were selected for curation when they had: an explicit chemical structure and at least one of the following; quantitative potency for antimalarial activity in vitro, activity data (where available) against a purified Plasmodium target, and in vivo and/or clinical data.
guidetomalariapharmacology. org/GRAC/ LigandListForward?type=AntiMal&database=all) lists are accessible on the website. Targets. Antimalarial targets is a new target family, encompassing targets identified and validated in the Plasmodium parasite. It has been introduced as a subfamily un-der other protein targets, within the hierarchical classification of target families used by GtoPdb. In accordance with GtoPdb targets, individual Plasmodium targets use a UniProtKB/SwissProt Accession as their primary identifier. The nomenclature adopted is derived from information available from PlasmoDB (www. plasmodb. org), a genome database for the genus Plasmodium that is part of the Eu-PathDB Bioinformatics Resource Center (www. eupathdb. org)  (34, 35). The pragmatic decision was taken to link the gene symbol to the P.
Comparison with ChEMBL content. A major utility offered by GtoMPdb is the prompt surfacing of new lead compounds, their metadata and associated molecular targets from the literature, but its value is also strengthened by the relative lack of similar open-access resources that curate data on malaria pharmacology. Indeed, comparing our coverage with that of ChEMBL  (37) , highlights a few distinctions. For our 30 Plasmodium targets, only six have UniProt IDs in common with ChEMBL. We suggest two reasons for this, the first being we have picked up more recent publications. The second is the challenge to assign a UniProt ID based only on the author's target description in their paper. This is compounded by the problem that even the reference strain P. falciparum 3D7 has only 165 proteins annotated to the Swiss-Prot standards whereby naming equivocality is reduced (but cannot be eliminated) but for all P.
Modifying the GtoPdb schema for malaria pharmacology A number of changes have been made to the database structure and web interface to improve both the capture and presentation of antimalarial data. To fully describe the activity and target interactions of antimalarial compounds requires the display of additional information, some of which is specific for the malaria parasite. We have extended the database schema and modified the interactions table display to accommodate these requirements (see Figure  6A ). A new 'whole organism' assay type has been introduced to capture data from the high-throughput whole cell screens used routinely in antimalarial drug discovery  (39). As already mentioned, many antimalarial compounds have a poorly understood mechanism of action and an unknown molecular target.
The Plasmodium parasite has a complex lifecycle  (40) , and the goal to eradicate malaria will require the discovery and development of new antimalarial medicines that target multiple stages of the parasite lifecycle and in particular the transmission cycle  (39, 41, 42). Capturing quantitative interaction data for the activity of an antimalarial ligand against the different developmental of the parasite was identified as a key requirement for the GtoMPdb. With guidance from the group of scientific advisors, a set of top-level lifecycle stages was defined (see www. guidetomalariapharmacology. org/GRAC/ ParasiteLifecycleStagesForward for further details) against which ligand interactions can now be annotated in the database. These are collective categories, for one or more developmental forms of the parasite, and which form the basis of organising, navigating and searching for parasitic lifecycle activity data.
Accessing and viewing antimalarial data Portal. A new dedicated portal has been developed, giving open and optimized access to the antimalarial data in the GtoPdb. In designing and building this portal, we have drawn on our experience from the GtoImmuPdb project, with the provision of a dedicated domain for the GtoMPdb (www. guidetomalariapharmacology. org) and the design of a distinct identity (logo, menu-bar and colour scheme). In addition to the existing ligand and target browse/search functionality available on the parent GtoPdb site, customized views of the data have been developed that include parasite lifecycle and target species activity. These have been designed in consultation with malaria researchers to deliver data returns that they find the most useful. Access to all data is from the menu-bar or from panels on the portal homepage.
The site search, available in the top-right corner of all database pages, has been extended to incorporate the new antimalarial data. The search algorithm has also been modified for queries from GtoMPdb pages to increase the ranking of results for entities with the malaria project tag. A description of navigating and viewing data using the GtoM-Pdb portal is provided in the following subsections. Targets. The targets panel links directly to the new antimalarial targets family. From there, the user can browse and navigate to individual target pages and find detailed information about each target and its interactions. For individual target pages, the overall style and layout used by the parent database was retained with the intention of providing a familiar interface for users who are already acquainted with the GtoPdb.
A new comments section has been added, allowing information of relevance to malaria to be highlighted. Ligands. The ligands panel provides customized access to the ligand lists page, with tabs for different categories of antimalarial ligands in the database, such as approved antimalarial drugs and antimalarial ligands with a Target Candidate Profile (TCP). The TCP describes the key attributes of a new molecule from the MMV global malaria portfolio, as it enters clinical development  (41, 42). For individual ligand summary pages, we have again retained the style and layout of the parent database. A new malaria tab has been implemented (Figure  6B ) and this is displayed on the summary page for GtoMPdb tagged ligands. This view provides information of relevance to malaria pharmacology and a separate table containing TCP information (where this is available).
A link to the GtoPdb ligand family page, with the antimalarial ligands category highlighted (www. guidetomalariapharmacology. org/GRAC/LigandFamiliesForward), is available from the menu-bar. Parasite lifecycle stages. The parasite lifecycle stages panel is one of the tailored routes developed for accessing antimalarial information in the GtoMPdb. Clicking on the home page link takes the user to a summary page that includes general information about the lifecycle of the Plasmodium parasite and a list of our top-level lifecycle stage categories. The same list of links to top-level categories is provided in the parasite lifecycle stages panel and from the menu-bar. Clicking on one of these categories links to a new page providing a description of the lifecycle stage and all interactions contained in the database that are associated with it (Figure  7 ).
Target species. The target species panel is another new route for accessing antimalarial information. Clicking on the target species home page link takes the user to a summary page that includes background information about Plasmodium species that are of clinical or experimental importance, links to individual pages for Plasmodium species for which data are presented in the GtoMPdb, and a list of useful resources. The same list of species links is provided in the target species panel and from the menu-bar. Clicking on one of these species links takes the user to a new page providing a description of the species and all interactions contained in the database that are associated with it (Figure  8 ). Resources. The portal homepage provides links to a number of supplementary resources, including a news panel and links to the GtoPdb Twitter feed.
Help pages developed specifically for the GtoM-Pdb (www. guidetomalariapharmacology. org/malaria/ gtmpHelpPage. jsp) can be accessed from the menu-bar. In  The modified interactions table provides data from whole cell assays, with information available for the parasite lifecycle stage activity (given in the dropdown information for each row) and Plasmodium species (pop-up window in the species column). The table shown is for a ligand with an unknown target (ganaplacide, GtoPdb Ligand ID 9946; https://www. guidetomalariapharmacology. org/GRAC/LigandDisplayForward?tab=biology&ligandId=9946). (B) The malaria tab displays curator comments of particular relevance to malaria, including summary information about the potential target or mechanism of action, and a table containing TCP details (example shown is (+)-SJ733, GtoPdb Ligand ID 9723; https://www.
SynPharm Links are now in place on appropriate target and ligand pages to SynPharm (http://synpharm. guidetopharmacology. org/), a database of drug-responsive protein sequences  (44) , derived from the interactions in GtoPdb and using data from the RCSB Protein Data Bank (PDB)  (45). SynPharm is an open-access, web-based tool that integrates pharmacological and ligand-protein binding information to present data on the drug-binding domains of proteins in a manner useful to synthetic biologists. Its strengths as a bioinformatic tool to facilitate the design of drug-responsive proteins are demonstrated in a recent paper that discusses engineering druggability into the Cpf1 effector of CRISPR gene editing  (46).
Database links and interoperability We maintain a list of database link-outs from GtoPdb target and ligand pages and this can be viewed at www. guidetopharmacology. org/helpPage. jsp#databaseLinks. Since 2018, we have added links to Immunopaedia and D1018 Nucleic Acids Research, 2020, Vol. 48, Database issue PlasmoDB, and updated our out-links to ChEMBL (37), thereby adding ∼800 new links. The GtoPdb has recently been included in the External Links service at Europe PMC (EPMC) (https://europepmc. org/LabsLink). On EPMC pages, links to target and ligand entries have been added to the papers curated by GtoPdb that include a quantitative description of the ligand-target interaction. It is possible to retrieve all these references at EMPC by running an 'Advanced Search' and selecting 'IUPHAR/BPS Guide to Pharmacology' from the 'External Links' drop-down list (LABS PUBS:'1969') as the cross-reference query.
External profile Disseminating information about GtoPdb (as one of our routes to impact) is done in a number of ways. We regularly publish peer-reviewed articles covering database updates, curation challenges and guides to accessing data (https://www. guidetopharmacology. org/ nciupharPublications. jsp#Database). We also share posters and presentations made by the team at national and international conferences. These are collated on our SlideShare account (www. slideshare. net/GuidetoPHARM). We regularly use Social Media (Twitter (@GuidetoPHARM), Facebook and LinkedIn) to announce database updates, publications of interest and alert followers to upcoming events. Our blog is used to provide detailed descriptions of database releases, technical descriptions of developments and commentaries on hot topics in pharmacology (https: //blog.
FUTURE DIRECTIONS From its origins in 2011, the GtoPdb has become recognized as an authoritative, open resource that provides expert-curated molecular interactions between ligands and targets encoded by the human genome. As described in this update, the unique model of content selection and quality control provided by the GtoPdb has recently been extended to capture data for the priority areas of immunopharmacology and malaria pharmacology. In the immediate future, work will continue on increasing the content of both the GtoImmuPdb and GtoMPdb. For the GtoMPdb, new data curation will continue until June 2020, with a focus on expanding the antimalarial targets family. We will also address the need to provide a hierarchical organization of subcategories for this expanded family. The initial development phase for the GtoMPdb database and web-application is now complete, but it will continue to be supported and maintained through core GtoPdb development resources.
We will be seeking feedback from users and we aim to implement the most useful suggested improvements to the interface. In addition, work is planned to include all data for the GtoMPdb in our web-services output, and to provide advanced search tools specific to the malaria project. For the core database, we are also working with Bioschemas (http://bioschemas. org/) (48) to add schema. org semantic mark-up to GtoPdb, which would make it simpler for search engines to index the website, and make it easier to collate and analyse the data. Our current focus is on implementing mark-up on all ligand summary pages, including properties from the Bioschemas MolcularEntity profile (https: //bioschemas. org/specifications/drafts/MolecularEntity). In the longer term, we are exploring other key areas of pharmacological interest with the intention of providing further expansion of the GtoPdb.
ACKNOWLEDGEMENTS The authors wish to thank all members of  NC-IUPHAR  for their continued support (www. guidetopharmacology. org/nciuphar. jsp#membership). This includes the following members who are not already listed on this manuscript:  A. Christopoulos ,  D. Fabbro ,  J. Cidlowski ,  K. Kaibuchi ,  Y. Kanai ,  F. Levi-Schaffer ,  E. H. Ohlstein ,  J. A. Peters ,  A. Phipps ,  J. Striessnig. We also thank the global network of NC-IUPHAR subcommittees and all CGTP contributors (a full list of all subcommittee members and contributors can be found at www. guidetopharmacology. org/GRAC/ContributorListForward). The authors gratefully acknowledge the contribution made by the  Expert Advisory Committee and Scientific Advisors  for the  GtoMPdb  project (www. guidetomalariapharmacology. org/malaria/gtmpAbout.
FUNDING International Union of Basic and Clinical Pharmacology ; the  British Pharmacological Society  [MED791];  Wellcome Trust  [ 108420/Z/15/Z ];  Medicines for Malaria Venture  [ CT-5535 ];  American Society for Pharmacology and Experimental Therapeutics ; Laboratoires Servier; University D1020 Nucleic Acids Research, 2020, Vol. 48, Database issue of Edinburgh. Funding for open access charge:  Wellcome Trust.
DATA ACCESS GtoPdb, GtoImmuPdb and GtoMPdb are available online at www. guidetopharmacology. org, www. guidetoimmunopharmacology. org and www. guidetomalariapharmacology. org, respectively. All three resources are licensed under the Open Data Commons Open Database License (ODbL) (www. opendatacommons. org/licenses/odbl/) and the contents are licensed under the Creative Commons Attribution ShareAlike 4. 0 International (CC BY-SA 4. 0, https://creativecommons. org/licenses/by-sa/4. 0/). Advice on linking to us and for accessing and downloading data are provided here: https://www. guidetopharmacology. org/linking. jsp. GtoPdb aims to make three to four public database releases per year; the data summaries and statistics reported in this paper are from release 2019. 4 (September 2019). Our downloads page (available from www.
• In Section 2, the principles of coil guns are presented with limitations concerning their modeling; • In Section 3, a mechanic and electromagnetic model is proposed and implemented using finite elements simulation tools for the electromagnetic part of the coil gun, and using Matlab Simulink for the mechanical and electrical aspects; • In Section 4, the simulation results are discussed in order to optimize the parameters of an existing indirect coil gun. The RoboCup is an international competition where robot teams play soccer. One of the objectives of the competition is for one of the robot teams to have won against a professional, human soccer team by 2050. In the Middle Size League (MSL), teams are composed of five robots playing autonomously on a 22 m by 14 m soccer field with a real soccer ball (diameter 22 cm) weighting 450 g.
In order to take these non-linearities into account, a finite-element model-based simulator was used for calculating the force and the inductance values under different conditions  [4]. The open source software used was   -→ B at any place in the system for each plunger and current combination. Numerical computation is performed in a static way, meaning that the kicking system evolution can be considered as a succession of short time independent magneto-static problems. For each of these problems, the following equations link magnetic field intensity B and magnetic excitation H: ∇ • -→ B = 0 (1) ∇ × -→ H = J (2) -→ B and -→ H can be linked together in a linear approach: -→ B = µ -→ H (3) or in a more realistic non-linear approach: - → B = µ( -→ H ) -→ H. (4) FEMM software tries to find a field that satisfies the linear approach and the flux density equation with the magnetic vector potential -→ A defined as -→ B = ∇ × -→ A.
Electrical Model The coil gun inductance L is powered by a pre-loaded high value and voltage (i. e. , 4700 µF, 450 V) capacitor C, switched by an Insulated Gate Bipolar Transistor (IGBT), as shown in Figure  6. Resistor R has to be taken into account considering the high number of loops of the coil, it can be measured or calculated using R = ρL S where ρ is the resistivity of copper, L the length of the coil wire, and S the surface of a wire section. This leads to the differential Equation  (7). d 2 U C dt 2 + R L dU C dt + U C LC = 0 (7) R C L E Figure 6. Electric circuit. This equation can be solved easily when L, C, and R are constants; however, L is not constant in our case. As shown in Figure  7 , simulations on FEMM 4. 2 using a LUA script show that the L inductance value can vary by a factor of 18 in our case study, going from 19 mH to 342 mH for the same coil depending on the plunger position and on the coil current.
Mechanical Model As explained before, force on the plunger cannot be calculated analytically. Simulations using FEMM 4. 2 combined with a LUA script show (Figure  8 ) that force varies in our case study from 0 N to 850 N for the same coil depending on the plunger position and on the coil current. Discrete values of the force are calculated for positions (as shown in Figure  1 ) of the plunger varying from x = 0 mm to 130 mm by increment of 10 mm, and for coil currents varying from 0 A to 100 A by an increment of 10 A, as shown in Table  2. When the plunger is outside the coil, the force is very small. This is due to the importance of the air gap related to the absence of the plunger for looping back the magnetic circuit. When the plunger is exactly in the centre of the coil, force is null for any value of the current because magnetic flux is maximal.
Mixed Electrical and Mechanical Model of the Indirect Coil Gun Inductance and magnetic force values are necessary to build a model of the coil gun for simulating it precisely. Calculated using FEMM 4. 2, they are implemented using look-up tables, taking into account the plunger position and coil current in order to approximate inductance and force for every configuration of the system. For this mechatronic model combining mechanic, electric, and magnetic modeling, the Matlab Simulink tool was used, as shown in Figure  9.
This leads to a plunger speed just after the shock equal to the x f inal , given in Equation (  10 ). ẋFinal = m p m p + m B R 2 2 R 2 1 + J Lever R 2 1 ẋInit (10) • Phase 3: plunger is accelerated in contact with the lever, which one is also in contact with the ball. This means that the lever applies a force on the plunger in subtraction of the magnetic force as shown in Equation (  11 ). This force is inertial due to the acceleration of the ball and the lever, as shown in Equation (12). m p ẍ = F Magneto (x, I) -F Lever (11) where F Lever = J Lever + m B R 2 2 R 1 θ (12) with J Lever = m Lever R 2 2 3. For small θ angles, θ ẍ R 1 , this leads to m p R 2 1 + J Lever + m B R 2 2 R 2 1 ẍ = F Magneto (x, I). (13) This mechanical model is implemented with Matlab Simulink using discrete blocks and switches for simulating the different phases of the movement, as shown in Figure  13.
Indirect Coil Gun Simulation Results The indirect coil gun system presented here and used in the robots at the RoboCup was simulated using Matlab Simulink. Even if the mechanical structure and the electromagnetic properties of the kicking system are completely defined, as in Figure  1 , there are 2 remaining degrees of freedom in order to optimize its power: the initial position x init of the plunger and the length L ext of the non-magnetic extension of the plunger. In order to compare the results with other previous studies, the kicking system simulated is identical to that of the Tech United Team described in  [5]. Parameters of the model are the following:.
Plain Language Summary The Chicxulub crater, Mexico, is widely known for its association with the extinction of the nonavian dinosaurs at the end of the Cretaceous period. The crater was first identified due to its gravitational and magnetic anomalies. Potential impact structures are often identified, in part, on the basis of geophysical anomalies, most commonly including a circular gravity low. Gravity is slightly weaker at craters because the impact cratering process removes mass from the impact site. In this study, we examine the cause of the Chicxulub gravity anomaly by combining observations from recent drilling of the crater, geophysical data measured across the crater, and numerical impact simulations. We demonstrate that porosity in rocks beneath the crater floor is primarily accommodated by fracturing during the impact cratering process, that the orientation of those fractures are consistent with predictions from numerical impact simulations, and that impact-induced porosity is one of the primary causes of gravity anomalies in large impact craters.
Introduction Impact cratering is the dominant surface process on most solid bodies of the solar system. The process of hypervelocity impact causes irreversible changes to the nature and physical properties of rocks  (Melosh, 1989). These changes produce anomalies in geophysical data that make craters conspicuous in comparison to the surrounding rocks. The identification of potential craters, on Earth and, increasingly, across the 10. 1029/2019JE005929 Solar System (e. g. ,  Zuber et al. , 2013)  is primarily achieved by remote geophysical surveying. The most commonly observed geophysical signature of an impact structure is a circular region of negative residual gravity  (Pilkington & Grieve, 1992). Negative residual gravity anomalies at craters are caused by the replacement of high-density intact rocks in the preimpact target with fractured para-autochthonous rocks, porous impact breccias, and/or the relative loss of mass due to excavation and basin infill (whether it is filled by atmosphere, water, post-impact sedimentary rocks, or vacuum).