dataesr/scientific-paragraphs-categorization huggingface dataset:
Flow cytometry HMDMs were seeded at 0. 5 x 10 6 cells/mL and treated with or without OA (178 ng/mL) for 16 hours. The next day, heat-killed pHrodoTM Green E. coli BioParticlesTM Conjugate (#P35366, ThermoFisher Scientific) was added to the well (50 g/well) for 90 minutes. Cytochalasin D (BioMol, Plymouth Meeting, PA) (10 M, 30 minutes pre-treatment) was used as positive control to block phagocytosis (ThermoFisher Scientific). Cells were then harvested in ice-cold PBS containing 0. 1% sodium azide and 25 mM EDTA. Flow cytometric analysis was performed using a GALLIOS Flow Cytometer (Beckman Coulter) and data were analyzed using Kaluza Analysis 1. 3. software.
A555 was acquired with a band pass excitation filter 531/40 nm, dichromatic mirror reflection 499-555 and transmission 659-730 nm and a band pass emission filter (593/40 nm). A647 was acquired with excitation band pass filter 628/40 nm, dichromatic mirror reflection 549-651 nm and transmission 699-726 nm and a band pass emission filter (692/40 nm). Images were collected using the LAS X Navigator software. High-resolution images of liver areas were captured using the Tile Scan acquisition mode. For quantitation of LD-bacteria proximity, images were taken with 63x objective lens using a Zeiss Axiovert 200 Upright Microscope Stand with LSM 710 Meta Confocal Scanner, with spectral detection and Airyscan super resolution detector. 2-photon imaging with a fully tunable Mai Tai eHP DeepSee 760-intensity was quantified from each cell to differentiate expressing PLIN5 cells.
After incubation with primary antibodies, membranes were washed and incubated with peroxidase-conjugated secondary antibodies (1:3000): goat anti-rabbit IgG (H + L)-HRP conjugate (1706515, BioRad), goat anti-mouse IgG (H + L)-HRP conjugate (1706516, BioRad) and peroxidase affinitypure donkey anti-goat IgG (H+L) (705-035-147, Jackson ImmunoResearch, Ely, UK). HRPconjugated secondary antibodies were detected with ECL (Biological Industries) and visualized using ImageQuant LAS4000 (GE Healthcare, Chicago, IL, US). Immunoblotting quantification was performed using the Fiji-ImageJ software (NIH).
1% formic acid; B=90% acetonitrile, 0. 1% formic acid; flow rate of 200 nL/minutes) for analysis in an Orbitrap Fusion mass spectrometer (ThermoFisher Scientific). MS/MS spectra from the Nth most intense parent ions were analyzed along the chromatographic run. For peptide identification, all spectra were analyzed with Proteome Discoverer (v. 2. 1. 0. 81) using SEQUEST-HT (ThermoFisher Scientific) and queried onto the Uniprot database with the following search parameters: 2 maximum missed tryptic sites; precursor and fragment mass tolerances of 2 Da and 0. 02 Da, respectively; carbamidomethyl cysteine and TMT modifications at N-terminal and Lys residues as fixed modifications, and methionine oxidation as dynamic modification. Peptide identification was performed using the probability ratio method  (47) , and false discovery rate (FDR) was calculated using inverted databases.
Biological invasions can cause substantial economic losses and expenses for management, as well as harm biodiversity, ecosystem services and human well-being. A comprehensive assessment of the economic costs of invasions is a challenging but essential prerequisite for efficient and sustainable management of invasive alien species. Indeed, these costs were shown to be inherently heterogeneous and complex to determine, and substantial knowledge gaps prevent a full understanding of their nature and distribution. Hence, the development of a still-missing global, standard framework for assessing and deciphering invasion costs is essential to identify effective management approaches and optimise legislation. The recent advent of the InvaCost database -the first comprehensive and harmonised compilation of the economic costs associated with biological invasions worldwide -offers unique opportunities to investigate these complex and diverse costs at different scales.
Insights provided by such a dataset are likely to be greatest when a diverse range of experience and expertise are combined. For this purpose, an international and multidisciplinary workshop was held from 12 th to 15 th November 2019 near Paris (France) to launch several project papers based on the data available in InvaCost. Here, we highlight how the innovative research arising from this workshop offers a major step forward in invasion science. We collectively identified five core research opportunities that InvaCost can help to address: (i) decipher how existing costs of invasions are actually distributed in human.
2016; Faulkner et al. 2020). Consequently, a synthesis of the costs of invasions worldwide is topical and crucial for understanding the complex and context-specific nature of invasion costs. Unfortunately, studies that provided such a global-scale approach to the costs of invasions are so far either recognised as methodologically flawed, incomplete or outdated (e. g. ,  Pimentel et al. 2005) , or restricted to a single taxonomic group (e. g. , insects; Bradshaw et al. 2016) or a particular economic sector (e. g. , agriculture;  Paini et al. 2016). The new InvaCost database  (Diagne et al. 2020 ) helps to meet this need by providing the first comprehensive compilation of the documented economic costs of invasive alien species globally. This updatable catalogue of 2419 cost estimates (extracted from 849 primary sources) and 46 variables, covering most taxa, geographical regions and activity sectors worldwide provides great opportunities to comprehensively assess and understand the economic impacts of invasions at different scales.
The advent of the In-vaCost database therefore provides unique opportunities to get a detailed picture of the economic impacts of invaders through integrative and novel approaches. Nonetheless, deciphering the complex nature of the economic costs of invasions through this unique dataset requires resources, skills and expertise from a range of disciplines (e. g. , ecology, economics) and sectors (e. g. , management, politics). To efficiently analyse these rich but complex data stored in the InvaCost database, an international and multidisciplinary workshop was held from 12 th to 15 th November 2019 near Paris, France. The main objective of the workshop was to initiate studies from several research questions, share common approaches and tools for data investigation, and structure further work on each started project in a sustainable and high-quality science context.
Outcomes and insights During the workshop, we identified five core research opportunities that InvaCost can help to address (Table  1 ). First, InvaCost offers unprecedented opportunities to provide the first global overview of the recorded economic costs. All attendees agree that a much-needed objective is to decipher how costs of invasions are actually distributed over space, taxa, society sectors and types of impacts. In that way, the global coverage (90 countries distributed across all continents) and the high taxonomic diversity (plants, vertebrates, invertebrates from both aquatic and terrestrial environments) of the database allowed us to initiate several draft manuscripts. Moreover, there was consensus among attendees that a crucial, yet unexplored topic is the identification of the ecological and socioenvironmental drivers of invasion costs at different scales.
Hence, specific projects were launched to analyse the relationships between invasion impacts and (i) management expenditure (e. g. , investigating the damage costs of spreading aliens in relation with the spending on measures to prevent, control or eradicate them), (ii) activity sectors (e. g. , describing how economic losses are distributed across the main production sectors such as fisheries, agriculture and forestry), and (iii) invader and recipient area traits (e. g. , parameterising generalisable explanatory models that could be used to guide future management efforts). Second, common gaps and biases in invasion research  (Pyšek et al. 2008)  were also detected in the cost data available, given they are spatially and taxonomically biased  (Diagne et al. 2020). About two thirds of the cost entries belonged to North American and Oceanian regions, and 343 species were recorded while 869 species are actually registered in the Global Invasive Species Database (GISD, http://www.
iucngisd. org/ gisd/). To bridge these gaps, one-third of the attendees undertook extensive complementary data searches to expand the content of the database. The most illustrative example of this work package is the collection of cost information available in about 15 languages other than English. A preliminary data search has already suggested that the current number of cost entries in InvaCost could double. The diverse origin of the attendees represents a key asset to establish relevant local collaborations, and thus access to a large amount of information largely inaccessible to the international community as a whole. Further, we started to apply different methods to infer the fragmented cost information available at different scales (e. g. , spatial, taxonomic, activity sector). The aim is to take into account societal and environmental features as well as research effort for accurately estimating the actual distribution and extent of costs.
Novel statistical and mathematical methods (e. g. , 'multidimensional extrapolation') -some based on existing approaches (e. g. , Bayesian spatiotemporal risk models  (Aukema et al. 2011 )) -are therefore under development by the modelling specialists who attended the workshop. Third, the content of InvaCost highlighted even more the complexity and heterogeneity of the economic costs of invasions. This situation is made worse by the lack of reporting consistency  (Robertson et al. 2020 ) that may hamper consistent data categorisation. For instance, the database evidenced that the term 'control' is often dubiously used in reports and articles to represent different types of management actions. Ultimately, this lack of framework could lead to misconceptions and limited understanding in scientific and non-scientific communities.
Hence, the group attendees recognised the strong need to harmonise terminology and concepts for both research and management purposes. A study was therefore initiated to build a robust and consensual framework at the interface of the different disciplines devoted to study these economic costs of invasions. The objective is not to create an unrealistic, universal framework that should apply to all approaches and thoughts. Our ambition is rather to develop a dynamic framework integrating a holistic, but standardised set of definitions underlying the 'economic costs of invasions'. Fourth, analysing the content of the database in the most relevant way requires a cautious approach  (Diagne et al. 2020 ). Indeed, cost information were not categorised Table  1. Examples of topics raised during the workshop, which are associated with research questions and ideas of project papers initiated during the workshop.
Issues raised from the database Primary research questions Examples of project papers Cost estimates are multiple and depicted by numerous taxonomic, geographic, temporal, methodological, and habitatrelated variables What is the current distribution of the costs of invasions worldwide? Which ecological and societal variables are currently driving the distribution patterns of these costs? Descriptive and inferential (e. g. , metaanalysis, GLMMs) approach considering specific descriptors of the InvaCost database Knowledge of cost information is fragmented as well as spatially and taxonomically biased Which information and data are missing from the InvaCost database? What insights could they provide? Synthesis of costs published in local, non-English reports globally; development of multidimensional extrapolation-based approaches Relevant analysis of the cost data requires strong caution and several steps of data processing How should the cost data be analysed to take into account the time lag between cost occurrences and cost reporting as well as the temporal dynamics of invasions? Development of a R package that provides all basic functions and processing steps for fully analysing the costs of invasions The economic costs of invasions are more complex and diverse than expected How may invasion costs be harmonised to be unambiguously understood in the same way by different audiences? A global conceptual, interdisciplinary framework for the economic costs of invasive alien species Cost information is not stand-alone to assess the whole impact of invaders for prioritisation and management actions How can cost data help to ensure a standardised assessment of alien species impacts across regions and to track potential changes over time? Context-based insights for invader management from linking cost estimates to established indicators of alien impacts worldwide (e.
g. , GRIIS, SEICAT) in InvaCost within a working framework directly implementable for all types of studies. For instance, while obvious duplicate cost estimates (i. e. , same cost figures from different sources) were removed when building the database, some overlaps may still occur in the dataset. This could be the case for some taxa when recent cost entries incorporate older ones, or when cost entries cover a large spatial scale that could include some costs provided at smaller scales. To help future users in appropriately investigating the data available, we started to create a dedicated R package (called 'invacost';  Leroy et al. in prep). This package aimed to implement (i) all basic instructions to fully understand the global database and its statistic requirements, (ii) necessary processing steps for getting the most relevant subsets, and (iii) a range of diverse approaches and methods (e.
The original database is intended to be regularly updated with new cost information  (Diagne et al. 2020). Having an international community around InvaCost would thus be highly beneficial for both the scientific community and stakeholders. Therefore, further translating InvaCost to an official cost register for information delivery to decision makers would allow the sustainability of the global project (see  Pagad et al. 2018  for a similar initiative) while ensuring information relevance and transparency as the database is expanded and used. Indeed, we envision that this database will be ultimately hosted on a stable personal website, which would allow crossing information with other relevant information sources on invasive species (e. g. GISD, http://www. iucngisd. org/gisd/). This website could rely on existing well-recognised international systems (e.
Interestingly, most of these features can be applied even for remote events, which are increasingly considered as a sustainable alternative to conventional meetings  (Porpiglia et al. 2020 ). Typically, it should be exciting to recreate a similar experience for other existing or developing databases (e. g. Dyer et al. 2017; Pagad et al. 2018; van Kleunen et al. 2019 ) investigating different facets of invasions.
Acknowledgements We are extremely grateful to  Marion Cordonnier  for her active involvement in organising this event. We also thank  Elsa Bonnaud ,  Céline Bellard  and  Camille Bernery  for their valuable contributions during the workshop. We express our gratitude to  Liliana Ballesteros-Mejia  for her help with a graphical item. We appreciate the helpful comments and feedback from  Moritz von der Lippe ,  Benjamin Hoffmann  and an anonymous reviewer.
Funding This workshop was funded through generous support by the  ECOMOB programme  (funded by the  French Centre National de la Recherche Scientifique) , the  Université Paris Saclay  ( Department of Biology ) and the  AXA Research Fund  through the  Invasion Biology Chair. We acknowledge the  French National Research Agency  ( ANR-14-CE02-0021 ) and the  BNP-Paribas Foundation  for providing funds to the  InvaCost  project that led to the construction of the database. The organisers and FE appreciate funding by the  AlienScenarios  project ( FWF  project no I  4011-B32 ).
1 ). Surface files are available on the online repository Morphosource (https://www. morphosource. org/MyProjects/Dashboard/dashboard/select_project_id/798). Tomographical data of Centrochelys sulcata, Gallus gallus and Crocodylus niloticus embryos were obtained from the ESRF database (http://paleo. esrf. eu; acquisition parameters provided in Table  S2 ). Each sampled developmental percentage in that dataset (i. e. , approximately x% through the incubation period, depending on taxon and specimen availability) was reconstructed for each taxon. Data for Pogona vitticeps was obtained from literature  23  that used µCT scans. It is important to note that this taxon was analysed using the illustrations provided to test our method on published data, that it does not include all developmental percentages in the incubation period, and therefore that it needs to be considered with caution.
1 ). They can, however, clearly be seen on the specimen and we have coded them in our ossification level scheme with the aid of visual inspections under a microscope (in this case, as a level 2). As an additional sensitivity analysis, we also coded them as a level 3 and present the results in the supplement (see Table  S4 ). A matrix was created with each row representing a different relative developmental percentage (days in incubation) of each taxon during incubation (i. e. , between the start and end of embryonic ossification, see Table  S3 ) and each column representing a different cranial bone. A dissimilarity distance matrix containing all pairwise comparisons of developmental percentages across all comparable bones using the "Gower" method was computed using R Studio Max v1. 1. 453  50 and the package vegan  51.
The "Gower" method was selected as it corrects for missing data (in this case bones which are not present across all taxa) as NAs are not considered when calculating distances  52. The matrix was used to quantitatively compare dissimilarity between individual stages in extant saurian ontogenetic sequences and the ossification pattern observed in the Massospondylus carinatus embryos (see Tables  1  and S5  for distance matrix results using S3, and see S6 for sensitivity analysis distance matrix results using S4). The distance matrix (Table  S5 ) was then subjected to a principal coordinate analysis (PCoA) using the R package ape  53  (see Table  S7  and Fig. S8 ). As an additional sensitivity analysis, the stage-code matrix (Table  S5 ) was replaced by a simple presence|absence matrix (binary 0 and 1 stage-codes, see Table  S9 ), and a dissimilarity matrix using the same parameters as above was generated (see Table  S10 ).
A strong, highly conserved pattern of cranial ossification is seen in saurians. Both this pattern and the level of ossification at the different developmental percentages are enough to correlate and approximate the Massospondylus carinatus embryos. However, several complicating factors need to be taken into account with regards to the comparative extant embryonic datasets. Because X-ray µCT imaging of extant embryos can involve sacrificing the specimens, the series we present for these taxa do not track the ossification sequence of one single individual, but rather of several individuals (one for each developmental percentage represented). Previous research has found that there is slight inter-individual variations in the timing of ossification  11. However, given the strength of the overall pattern, we do not consider the variance introduced by these minor differences to compromise our overarching result.
Acknowledgements We acknowledge the  European Synchrotron Radiation Facility  for provision of synchrotron radiation facilities and we would like to thank  Paul Tafforeau  for assistance in using beamline ID19. We thank  Céline  for her kind hospitality during data collection. We thank  Josef Stiegler  for interesting input. Funding for this research was provided by the  DST-NRF African Origins Platform  grants (98800 and  118794  to JNC), the  DST-NRF Centre of Excellence in Palaeosciences (KEJC)  and the  Palaeontological Scientific Trust (KEJC).
Data availability Tomographical data of Centrochelys sulcata, Gallus gallus and Crocodylus niloticus embryos are available on the ESRF database (http://paleo. esrf. eu). Surface files of the embryos presented in Fig. 2  have been uploaded to Morphosource (https://www. morphosource. org/MyProjects/Dashboard/dashboard/select_project_id/798). Tomographical data of the Massospondylus carinatus embryos (BP/1/5347a) are property of the University of the Witwatersrand. Surface files are available on the online repository Morphosource (https://www. morphosource. org/MyProjects/Dashboard/dashboard/select_project_id/798).
Statistics Due to low p-values values of Shapiro-Wilk tests of normality, all dependent variables were subjected to Mann-Whitney U group independent tests in the anterior-posterior and medio-lateral plane separately. The effect size statistic for the Mann-Whitney test is r is the Z value from the test divided by the total number of observations. : small 0. 1-< 0. 3, medium 0. 3-< 0. 5, large > = 05. Statistical evidence of significance was set at p < 0. 05. All tests were conducted with free and open software JAMOVI, Version 1. 2 (retrieved from https://www. jamovi. org) and in R with rcompanion  [21].
We provide a stand-alone software, the BioAFMviewer, which transforms biomolecular structures into the graphical representation corresponding to the outcome of atomic force microscopy (AFM) experiments. The AFM graphics is obtained by performing simulated scanning over the molecular structure encoded in the corresponding PDB file. A versatile molecular viewer integrates the visualization of PDB structures and control over their orientation, while synchronized simulated scanning with variable spatial resolution and tip-shape geometry produces the corresponding AFM graphics. We demonstrate the applicability of the BioAFMviewer by comparing simulated AFM graphics to high-speed AFM observations of proteins. The software can furthermore process molecular movies of conformational motions, e. g. those obtained from servers which model functional transitions within a protein, and produce the corresponding simulated AFM movie.
By improving technological aspects of hs-AFM, those drawbacks can be overcome only up to a certain extent. A promising strategy to help in the interpretation and understanding of measurement results may consist in a complementary approach, taking into account the plethora of available structural data and computational modelling of biomolecular systems. The static structures of many biological macromolecules are known. This data is deposited in the Protein Data Bank (PDB)  [15, 16]  in a well-defined format, providing the spatial coordinates of atomic positions in a PDB file. On the other side, functional conformational dynamics in proteins, such as the motions underlying e. g. ligand-induced transitions, can often be obtained from modelling servers, e. g. [17] [18] [19]. A comparison of the wealth of both static and dynamical protein data to AFM experiments is therefore possible.
This, however, requires the development of suitable computational tools. We provide a stand-alone software which makes an important step in that direction. The BioAFMviewer transforms the molecular representation of any structure given in the PDB file format into the corresponding AFM graphics by performing simulated scanning. The software implements a high degree of usability. A versatile molecular viewer allows the visualization of molecular structures and control over their orientation, while synchronized scanning with variable spatial resolution and tip-shape geometry generates the corresponding AFM graphics. Obtained results can be conveniently exported as images and movies. We demonstrate the applicability of the BioAFMviewer by comparing simulated AFM images with snapshots of selected hs-AFM experiments of proteins.