dataesr/scientific-paragraphs-categorization huggingface dataset:
Results We produced a database of 937 symptoms standardized image recto-verso pairs from a diversity of varieties and sampling times across 2019, 2020 and 2021. The annotation step distinguished between contrasted situations of expertise ranging from simple consensual cases to disagreement or lack of identification confirming the difficulty of visual and photographic diagnostic. The 6 experts agreed on sets of distinctive criteria for each of the 6 species frequently encountered on oilseed rape in France (Fig. 2 ; FigS1 higher quality pictures). For each of these 6 species, the 6 experts selected subsets of pictures on the one hand with typical symptoms (respecting most of the distinctive criteria); on the other hand with atypical symptoms (variants not respecting all criteria). Figures were produces for.
Discussion We confirmed that along the growth of oilseed rape several fungal diseases co-occur on leaves. This might not be the case in all regions, but the oceanic climate of Brittany allowed observing all the major diseases. The experts were not able to identify distinctive criteria that would be respected by all the symptoms of a given species and not frequently or occasionally shared with other species. However, combining several criteria for selection or exclusion allows to produce guidelines for typical symptoms. For the atypical symptoms (variations respecting only some of the distinctive criteria, the availability of standardized pictures will be of great help for the reader. In addition to the current illustrative figures, the availability of our picture database will enable developing computer applications to train experts.
Acknowledgements We thank  UE La Motte  and surrounding farmers for the cultivation of oilseed rape fields as well as the  INRAe experimental unit in Grignon (Christophe Montagnier ). We thank  Yannick Lucas  for technical assistance. This work benefited from the financial support of  INRAe -the French National Institute for Agronomical Research , and from  CASDAR  project  C2018 -11  (Atipical). The "Effectors and Pathogenesis of L. maculans" group benefits from the support of  Saclay Plant Sciences-SPS  ( ANR-17-EUR-0007 ).
Delineation of Information Gathered from a Review of the Literature and Scope of the Review A literature search using "Staphylococcus aureus", "Biofilm" and "Cystic Fibrosis" in the PubMed database found 152 publications and a similar search for "Pseudomonas aeruginosa" found 1200 results and a combined search for "Staphylococcus aureus" and "Pseudomonas aeruginosa" gave 108 publications (8 October 2022) (Figure  1 ). This highlighted the fact that studies on S. aureus biofilm formation in CF frequently included the two major pathogens, studied either independently or considered through the prism of interactions in dualspecies biofilms, a situation closer to the conditions of the CF lung compared to mono-species biofilms. The proportion of patients co-infected by S. aureus and P. aeruginosa is indeed estimated to be around 30%  [18].
Observational Studies The studies reviewed in this part of the manuscript are summarized in Table  1  and complementary data are given in Supplementary Table  S1. When detailed, strains forming biofilm are usually classified into different categories: non biofilm-producers, weak/minor, moderate/medium/intermediate and strong biofilm-producers. However, different criteria for biofilm production classification may be used according to the study. Unless otherwise specified, the studies investigated biofilm biomass formed by CF S. aureus strains through indirect measurement via CV staining.
Nevertheless, among all these studies, we noted that (i) most studies on the P. aeruginosa-S. aureus combination focused on P. aeruginosa with few or no results on S. aureus  [101]  and (ii) P. aeruginosa co-studied strains were mostly reference strains, i. e. , PA14, originating from a wound on a burns patient  [102, 103] , PAO1, a moderately virulent strain isolated from a wound over 50 years ago  [22, 39]  and strain ATCC 27,853 from blood culture  [96]. As in other parts of this review, we voluntarily focus hereafter on data obtained from CF S. aureus and P. aeruginosa clinical strains, with the aim of reporting results as close as possible to the specific clinical context of CF. A single exception was made for the publication by Barraza & Whiteley that studied laboratory strains of P.
Acknowledgments: The authors gratefully acknowledge  Teresa Sawyers , English medical writer at  Nîmes University Hospital , for editing this paper. We also thank  Nîmes University Hospital  for its structural, human, and financial support through the award obtained by our team during the internal call for tenders " Thématiques phares" (Flagship topics ). All authors except Q. M. are members of the  FHU InCh (Fédération Hospitalo-Universitaire Infections Chroniques, Aviesan ).
Such oligomerized-related strategies have exhibited more efficient results, compared to previous systems generations. Fortunately, some of the newly proposed strategies appear to give encouraging preclinical results and so far, only one of these is currently in clinical trials. APG101 is the best prototype of future therapeutic approaches involving the CD95 system. It is an 84 kDa CD95Lneutralizing CD95 trimer fusion protein, able to pass the bloodbrain barrier. Asunercept, the trade name for APG101, is now the subject of a controlled phase II clinical trial in patients with relapsed glioblastoma multiforme (GBM) (NCT01071837). The glioblastoma model was chosen in accordance with several in vivo and in vitro non-clinical studies, which extensively described the involvement of CD95L in the growth, invasiveness and migration of glioblastoma cells  [152, 324].
European Commission decisions on approval and non-approval are published in the Official Journal of the European Union; information being also available on two websites ("EU pesticides database" and "information on biocides" on the European commission and ECHA -European Chemicals Agency -websites, respectively). Regarding PPP, it is therefore possible to know if an active substance has uses allowed in the different Member States (MS -even if it is recommended to check the national databases) and to access the information regarding environmental risk and notably risk of transport into groundwater. In May 2021, at EU level in the context of PPP, 469 active substances are approved and 61 pending (i. e. waiting for a decision). It should be noted that active substances of PPP are classified in 21 categories and correspond to organic and inorganic compounds as well as fungi and/or viruses.
The ECHA database for biocides contains a list of 366 active substances (corresponding to 21 product-types -May 2021)) of which 169 are approved at EU level as biocides. It should be noted that an active substance can show properties for being both a PPP and a biocide but can be authorised for only one of the cases (e. g. diuron, clothianidine or warfarin not yet approved as PPP but approved as biocide). A cross comparison between the 2 databases is not trivial making difficult to identify which compounds are both an active substance of PPP and a biocide. Although EU regulation encourages the use of less harmful active substances, pesticides are still intensively used and therefore may pose human health or environmental risks. The presence of pesticides or their metabolites in groundwater throughout the world is regularly highlighted either in regional  (Fisher et al.
, 2013). Major environmental directives (Water Framework Directive 2000/60/EC, WFD -and associated Groundwater Directive 2006/118/EC -GWD, and Drinking Water Directive 98/83/EC, recently revised EU 2020/2184, DWD) and the European Regulation (EC) No. 1107/2009 concerning the placing of PPP on the market require the implementation of groundwater monitoring. However, the heterogeneity of datasets through Europe regarding groundwater and the lack of knowledge to support the risk assessment were highlighted by European Environment Agency (EEA) as key obstacles to improve regulation and management of groundwater resources  (Mohaupt et al. , 2020). Very recently, a European wide collection and analysis of existing monitoring data on non-relevant pesticide metabolites (nrM) has been carried out in the frame of the WFD CIS task "Voluntary Groundwater Watch List" (cf.
Up to now three data collections on Pharmaceuticals (Amec Foster  Wheeler, 2016) , PFAS (WFD CIS 2020) and nrM (WFD CIS 2021) have been carried out. The WFD (article 18) also requires the MS to report data on pesticides to the EU Commission (performed every 6 years -A midterm review of the implementation of the Programmes of Measures is also carried out). Within this framework, the Commission must publish a report to the European Parliament and to the Council on the implementation of this Directive after each update of the River Basin Management Plans (see https://ec. europa. eu/environment/water/ water-framework/impl_reports. htm). Within the DWD, to ensure a comparable reporting, countries report to European Environment Agency every three years for a limited number of compounds (actually ten active substances namely atrazine, bentazone, bromacil, diuron, isoproturon, MCPA, mecoprop, simazine, S-metolachlor and terbuthylazine, one metabolite (atrazine-desethyl), and total pesticides concentrations including also other national monitored pesticide beside the short list)  (Mohaupt et al.
It is likely that UK legislation will continue to adhere to EU principles despite leaving the EU. However, how this will be implemented in the long term is a matter at the national level and there is potential for deviation from EU regulations in the medium and long term. For example, in the UK this may affect how groundwater pesticide quality data is collected and on what substances it is collected for in England, Scotland, Wales and Northern Ireland in the future. In Switzerland, these issues are considered by the specific Swiss legislations (e. g. Environment and water protection legislation; Food safety and drinking water legislation), which are updated regularly. In addition, regulation (EC) No 1107/2009 concerning the placing of PPP on the market, which came into force on 14 June 2011 includes groundwater monitoring as the highest tier option (Tier 4) in the regulatory groundwater assessment of PPP in EU (See  Gimsing et al.
Results and discussion 4. 1. Implementation of groundwater monitoring and data collection 4. 1. 1. National scale 4. 1. 1. 1. France. In France, the water law of  December 16, 1964 December 16, (law n°64-1245) )  organizes water management at the basin level with the creation of six water agencies in mainland and four offices in overseas territories, and basin committees. As early as the middle of the 90's, the will to structure a national database appeared (see supplementary material S1 for details). Thus, ADES a national open-access database on groundwater, was created. This base contains data from 314 networks (i. e. wells and/or springs), mainly sanitary and environmental monitoring networks, covering both quantitative (groundwater levels) and qualitative aspects. To date, it contains over 102 million water analyses from about 77,000 quality observation points (vs.
In addition, drinking water producers carry out self-controls; unfortunately, these data are not necessarily shared and are generally poorly stored. Each producer of data uploaded in ADES is responsible of its quality. 4. 1. 1. 2. Denmark. In Denmark, the national groundwater monitoring programme (GRUMO), was initiated in 1988 (see Supporting material S1 for more historic information). GRUMO's aim was to monitor the effect of the Danish Environmental legislation launched in 1987 on general agricultural regulations in relation to the nutrient load (the phosphorus and nitrate load) of the aquatic environment wastewater plants and secondly to ensure the supply of good quality drinking water to the population. GRUMO was hence designed to provide information on the quality of the groundwater in selected catchments estimated to be representative for Denmark.
, 2015). This knowledge is applied in the yearly selection of compounds to be monitored in PLAP. If a metabolite or a pesticide appears in high concentrations in groundwater collected from underneath the PLAP-fields, this knowledge is included when updating the list of compounds to be monitored in GRUMO and the result of the national monitoring will finally appear in the Jupiter database (see Supplementary material). 4. 1. 1. 3. England. Overall, around 30 % of drinking water in England is from groundwater, this figure is much higher for parts of southern England where it is closer to 100 %. In the United Kingdom, a number of pieces of legislation and associated regulatory tools have sought to directly or indirectly protect groundwater from pesticide (and other) pollution (see supplementary material Table  S1 ).
England's groundwater quality data visibility has greatly improved in recent years, and groundwater quality monitoring data is regularly uploaded to the NGWQM database and there is web access to water quality data including pesticides and metabolites in waters (https://environment. data. gov. uk/water-quality/view/landing). Water company data can also be obtained, but this requires a separate application, and is not publicly available in the same way due to issues of confidentiality/security. Devolved nations publish status reports on a regular basis, which includes information on pesticide occurrence in groundwater. 4. 1. 1. 4. Switzerland. Since 2002 the Swiss NAQUA National Groundwater Monitoring provides a nation-wide picture of the situation and evolution of the groundwater resources in terms of both quality and quantity (FOEN/BAFU, 2019).
The results including those for pesticides and their metabolites are summarised and made available annually on the website of the Federal Office for the Environment FOEN (Link: Pesticides in groundwater (admin. ch)) and regularly published in national reports  (FOEN/ BAFU, 2019). The data of the Swiss surface water and groundwater monitoring are stored and managed in a centralised water database at FOEN. The joint federal-cantonal monitoring programme NAQUA records the state of and changes in the groundwater resources at >600 monitoring sites in Switzerland. The natural conditions and the impact of human activity on the typical aquifers of Switzerland are monitored. The purpose of the National Groundwater Monitoring is to: • document the situation and development of groundwater quality and quantity at national level; • detect the occurrence of problematic substances at an early stage and to systematically follow up any undesirable developments; • check the effectiveness of protective measures already adopted and identify the need for further measures; • characterise and classify the most important groundwater resources in Switzerland.
NAQUA forms the basis for nationally coordinated protection of groundwater as a natural resource in Switzerland and ultimately helps to protect the public from harmful substances. As Switzerland collaborates closely with the EU on environmental matters, the collected data are reported to different organisms as the European Environment Agency as a member or on a voluntary base (e. g. IGRAC, IAEA). The Swiss legislation requires the federal government to collect data on environmental pollution (Constitution Art. 65, Environmental Protection Act, Art. 44), water quality and hydrologic conditions in Switzerland (Water Protection Act (WPA) Art. 57) and to inform the public of the results (Environmental Protection Act Art. 10e, WPA Art. 50 & Art. 57). The NAQUA National Groundwater Monitoring carries out these federal functions in relation to groundwater.
Comparison across the four countries and European scale For these four countries, databases, generally created long years ago, ensure storage of raw groundwater quality monitoring data mainly collected in the framework of GWD and DWD. National portals provide access to data from other networks. In contrast, data provided by products applicants is typically restricted to national regulatory agencies. Here Denmark via the presence of PLAP are less sensitive to this lack of access regarding the national regulation of PPPs with its links to the GWD and DWD. Data accessibility via national portals is free or via request, depending on the country. The information are provided in relation with other metadata: information on the geological context, the aquifer and/or the groundwater body, characteristics of the well tapping the sampled water etc.
At European scale, IPCheM Portal (https://ipchem. jrc. ec. europa. eu/) is the European Commission's reference access point for chemical monitoring in various media (environmental, human bio-monitoring, food and feed, products and indoor air) allowing searching, accessing and retrieving chemical occurrence data collected and managed in the EU. The platform has been developed to fill the knowledge gap on chemical exposure and its burdens on health and the environment. Several types of database exist including e. g. Waterbase, which is the generic name given to the EEA's databases on the status and quality of Europe's rivers, lakes, groundwater bodies and transitional, coastal and marine waters, on the quantity of Europe's water resources, and on the emissions to surface waters from point and diffuse sources of pollution.
Its creation is based on the INSPIRE Directive 2007/2/EC which aims to create a European Union spatial data infrastructure for the purposes of EU environmental policies and policies or activities which may have an impact on the environment. According to the data type (notably raw data versus aggregated data), data access could be restricted, public or limited to the owner. In some cases, it is therefore possible to find raw and more detailed information at national level than in the European database. 4. 2. Monitored pesticide substances and occurrence in groundwater 4. 2. 1. National scale 4. 2. 1. 1. France. In France, a national regulatory decree (under revision) sets the guidelines (minimum required) for groundwater monitoring in terms of frequency of measurements, number of points per km 2 and lists of parameters to be measured, a "core list" (Act 2015 published in JORF, 2015 and its modified version of 2018, JORF 2018).
g. crops with limited geographical extension). While this more comprehensive research is important to get a more complete picture of groundwater quality, it makes analysis of the data at the national level more challenging. With respect to drinking water, the minimum frequency of sampling and analyses is determined by the volume of water distributed or produced each day within a supply zone (~32,000 wells tapping groundwater). Among the 54 parameters, the generic term "pesticides and (relevant) metabolites" is used, and it is recommended that monitoring should be adapted to regional context (Direction Générale de la santé, 2020b). The Ministry of Health states given the number of authorised (or formerly authorised) pesticides, it is necessary to target the analysis for pesticides, according to their potential occurrence in water and the risks for human health and adapted based on local use.
3  supplementary material Table  2 ). A dedicated suite of pesticide compounds (n = 42) were used historically as part of WFD reporting. Accredited data collected by the 6 pesticide suites is supplemented by broad screening scan methods (GCMS and LCMS) which also contain pesticide and metabolites. Presently around 40 % of the GWQMN sites are sampled and analysed on an annual basis for the dedicated pesticide suites (1-5). Repeat sampling is undertaken to different extents (typically annual or quarterly) depending on the vulnerability of the particular groundwater body, its current status in terms of pesticide pollution and the pesticide occurrence trends. In 2019 of the 271 groundwater drinking water protection areas (DWPA) in England, 7 (in the Thames and Anglian river basin districts) were classified as of poor chemical status due to pesticide pollution.
European scale The Waterbase -Water quality database includes a large volume of concentration measurement data reported by countries to the European Environment Agency. Data include observations on sampling dates (so called 'disaggregated'), data and aggregated data (including yearly mean, minimum, maximum and Limit of Quantification of pesticide concentrations). Therefore, there are many data sources for pesticides, but the availability of comparable data across Europe is rather limited and except for triazine metabolites, monitoring of metabolites is scarce  (Mohaupt et al. , 2020). Within the WFD, the data on 184 distinct pesticides were extracted from Waterbase  (Mohaupt et al. , 2020 (Mohaupt et al. , data 2007 (Mohaupt et al. , -2017)) , covering a total of 16,886 groundwater monitoring sites in 26 countries.
MS and AC were asked to provide available monitoring data on 53 selected nrM in groundwater across Europe. 29 MS/AC responded and 17 countries provided groundwater data on the nrM compounds in the related questionnaire. nrM were widely detected in European groundwater above limits of quantification. The percentage of detections in groundwater were highest for DPC (31. 7 %), Metolachlor ESA (30. 0 %), N,N-DMS (24. 4 %), MDPC (23. 7 %), Metazachlor ESA (21. 0 %) and Dimethachlor CGA 369873 (20. 7 %). Regarding drinking water, in 2015 a draft list with 21 DWD pesticides and metabolites of concern has been established by compiling voluntary contributions from nine MS sent to European Commission DG Environment. From one contribution including around 700 compounds, only the 25 highest ranked compounds with over 50,000 analyses have been considered.
, 2018). GC x GC TOF-MS methods are also being developed which extend detection limits and the range of compounds compared to conventional GCMS methods (e. g. Mohler et al. , 2020)  and these techniques are also being considered for surveillance monitoring in England. There has been a growing reliance on multi-residue screening techniques, which are semi-quantitative, to undertake surveillance monitoring and the large database of results going back as far as 2009 provides a significant resource for groundwater pesticide and metabolite occurrence data for England. These screening techniques are a flexible and versatile tools and when standards become available for new compounds these can be rapidly added to the existing extensive database of pesticide compounds and they will continue to be an important surveillance tool in the future.
In the three studied EU/recent EU countries, the implementation of European directives (WFD, GWD and DWD) is managed at different scales (regional or national) by one or several stakeholders. Each country has its own dissemination strategies with freely accessible databases including raw data as opposed to the European database including sometimes only aggregate data. In addition, the above-mentioned directives have different objectives, leading to different monitoring strategies. For instance, DWD determines the list of compounds to be monitored in the context of drinking water production considering that "only pesticides which are likely to be present in a given supply need to be monitored". On the other hand, importantly, drinking water is not the only issue of GWD. Indeed, there are other groundwater dependant water bodies and ecosystems for which the presence of pesticides and their metabolites is significant.
Acknowledgements This work was carried out with funds from each of the institutions to which the authors belong. DL was funded by  BGS  national capability funding under the ECAR challenge area. From France , we would like to thank  Dominique Darmendrail  from  BRGM  for her comments and fruitful exchanges. From Denmark , we would like to thanks  Signe Bonde Rasmussen  from the  Danish EPA  for providing material for a list of PESTcompounds included in the GW-monitoring of Denmark excluding screening and verification and  Laerke Thorling  from the  GEUS  providing information and reviewing the text in regard to GRUMO.