dataesr/scientific-paragraphs-categorization huggingface dataset:
Design of the ADB tool The above listed objectives for the ESPREssO-ADB led to identify a global concept of the database, with the following requirements: -The structure has to be exhaustive enough to describe, characterize, and evaluate an action proposed by a stakeholder; an action being defined as any initiative related to DRR, CCA or cross border management. The action can refer to a process as a whole, be a constitutive element of a larger framework or correspond to a particular effort. The action can be of varying nature: it can relate to a research project, urban or land use planning procedures, the implementation of a new legislative framework, an improved coordination strategy for first aid response, a risk education initiative, etc. -The criteria used in the evaluation need to be general enough to allow comprehensive situations and not too detailed to avoid a large number of cases referring to each of them; the compromise found by the ESPREssO Consortium was to restrict criteria to those describing situations at national and regional level; -Each action needs to be characterized by a set of contextual parameters (metadata) allowing quick searching and filtering (title, date of entry, author that proposes the action, challenge concerned, etc.
); -Each action needs to be described by a number of qualitative criteria to understand the framework it applies to: the typology (legal, scientific, …), the thematic context and respective scale of implementation (prevention, crisis, mitigation, preparedness), the gap it refers to, etc. ; -Each action is evaluated by quantitative indicators referring to different criteria, so that it is easy to rank the actions to identify the best and the worse, as understood by the user that completed the form. The development of the ESPREssO-ADB database thus required several steps. First, a literature review was performed to identify key metadata and a first set of assessment criteria  [13] [14] [15]. Indeed, during the first phase of the project, a preliminary draft of the database was sketched thanks to an extensive analysis of existing knowledge from the bibliography.
This literature review led to the first version of the ESPREssO-ADB that has been refined with feedback from ESPREssO project partners following the project meeting in Copenhagen in January 2017, and was tested a first time by BRGM teams in the spring of 2017. Furthermore, the ESPREssO-ADB has featured an operational web service since the Stakeholder Forum meeting organized by the ESPREssO project in Bonn on  May 4, 2017. This first draft was refined again in late 2017 early 2018 with the drafting of the final products of the project. Taking into account testers, partners and stakeholders' feedback, the ESPREssO-ADB has evolved toward a 2nd prototype which was finally validated as the definitive tool  [16]. During and following the Forum, and Think Tank meetings, new statements of stakeholders were entered into the database.
Structure and operating The ESPREssO-ADB website and database have been developed using the Drupal open-source content management system. Its technical solution to implement the ADB was chosen following close exchanges between the project management and BRGM's IT services, responsible for implementing the project's technical tools. Indeed, Drupal is an open-source content management software that is very flexible and modular. It allowed easy modification to the structure of the ADB to adapt the needs of the ESPREssO project all along its duration. This aspect is important because the database was and is still intended to be used during different kinds of activity (forum, scenario study, think tank discussions …). In addition, Drupal benefits from a performant search module, which is useful to navigate within the ADB entries.
The Drupal content (text fields) is then supported by a database that manages the structure of the information system. To ensure accessibility and to avoid simultaneous multiple versions, the ESPREssO-ADB has been implemented as a web service  [19]  and can be accessed using its specific URL (http://adb-espresso. brgm. fr) or via the official ESPREssO website (http://www. espressoproject. eu/wp/wp 4. html). The portal is now available in 4 different languages: English, German, French, and Italian  [20]. Access to the website is open but submitting new entries require a password identification. Thereby to contribute, a user account is necessary but it can be created by self-registration to ensure a good dissemination. The main interface of the ESPREssO-ADB portal is structured into six main blocks (Fig.
This page is introduced by a few lines providing background information on the ESPREssO project and a short description of what actions are interesting for this project. The questionnaire was design to collect stakeholders' experience, enabling them to describe and evaluate an "action" in term of its impact at its respective scale of implementation. This form takes about 15-20 min to complete. It includes 50 questions divided into 7 sections: -Secion 1 "Participant's information" collects basic data about the person filling in the questionnaire, such as its host institution, the area of expertise, the level of involvement in the action or project, etc. -Section 2 collects basic information about the action. It includes title and acronym of the action as well as its thematic context, a short description, countries involved, spatial scale, etc.
Data management and analysis By the end of the ESPREssO project, the ADB has been filled with 110 actions meanly coming from projects report or deliverables (31%), ESPREssO Think tanks (29%) and professional experiences (20%) of Stakeholders (Fig. 5 ). Actions coming from literature review and scientific publications represent 11% and 7%, respectively. The Think Tanks represent more than a quarter of the actions. Indeed, actions discussed in the Stakeholder forum and during the three Think Tanks are detailed in the database and associated with at least one of the three ESPREssO challenges, and different criteria. The ADB provides the opportunity to formalize discussions during workshops and to store their content in a synthetic format. Once this information is classified using different criteria, including some meta-data like the date of the entry, it enables to know about the impacts of each action and their evolution in time.
Version tracking of the database has also be considered in the implementation of the database in order to track stakeholders' opinion about these actions during the life of the ESPREssO project and associated activities (forum, think tanks, etc. ). Let's remember that the first version of the ADB has been elaborated thanks to literature reviews performed in the dedicated project workpackage (WP) and other WP's inputs that were taken into account as soon as useable inputs were available. In addition, the ADB structure has been adapted to fit the Vision Paper  [23]  and Guidelines purposes  [18]. Among those 110 actions, most of them are related to a single challenge (Fig. 6 ). It is to highlight that actions mainly concerned Table  3  Percentage of actions meeting each range of quotation (rows) and for each criteria of the 2 multi-criteria analysis (columns): the Extended Sendai Framework (ESF 1 to 5) and the SHIELD model (SM 1 to 7).
Indicators: definition and analysis To assess the actions hosted in the database, a multi-criteria analysis was developed using the criteria previously presented (see Table  2 ). Table  2 : Detail of questions meeting each criteria of the Extended Sendai Framework (ESF 1 to 5) and the SHIELD model (SM 1 to 7). The first level of multicriteria analysis, structured according to the Sendai Framework priorities, is composed by 32 criteria/questions split over 5 categories: "Risk evaluation and understanding", "Optimizing governance", "Investment for increasing resilience", "Improvement of response", "Potential for transformative change" (see Table  2 ). The second level of multi-criteria analysis, developed around the SHIELD model  [18] ; Albris et al. , in this issue), is composed by the 7 categories related to the ESPREssO guidelines structure (Table  2 ): "From disaster risk management to disaster risk governance", "Sharing knowledge", "Harmonizing capacities", "Institutionalizing coordination", "Engaging stakeholders", "Leveraging political commitment", "Developing communication".
Diagrams also help to define different "profiles" between the actions mainly focused on one or the other of the challenges of the ESPREssO project, or according to the notation of the Extended Sendai Framework or the SHIELD model. For example in Fig. 8  the examples 2 and 3 perform better than example 1 on the "improvement of response" category and the 3 examples perform differently regarding "Chapter 3: Harmonizing Capacity" category. As results, the ADB actions performances regarding the 12 categories have been analyzed and summarized in Table  3. They highlight a first an interesting point: most of the actions of the database are not very efficient for the "Investment for increasing resilience" (EFS3), "Improvement of response" (EFS4), "Leveraging Political Commitment" (SM6) and, in less extent, for "Harmonizing Capacities" (SM3).
-DISCOVER: Some solution to DRR or CCA challenges may have already been implemented elsewhere. The tool offer information about new or unknown initiatives, how they achieved their goals and created lasting change. -TRANSPOSE: Build a DRR or CCA action that works for each region by transposing effective solutions for each social, cultural and geographical context. -HARMONIZE: Help in work towards a European Union without boundaries for DRR and CCA by participating in the discussion about how to reduce incoherencies and build a common approach for coordinated action. Rich in lessons on the numerous actions brought to knowledge, the ADB keeps to this day some limitations inherent to its format and its management. Despite the efforts made to feed the online database, both from project members and other users, it is not excluded that the ADB is not fully exhaustive (related to the youth of the project).
However, this remains a living tool that will continue after the project. The already noticeable number of actions, at the writing of this article, is probably (and already) led to evolve over new future additions. This raises the question of the accessibility of the questionnaire and its dissemination. Indeed, the duration and the constraints of the project initially limited the role of author to the members and partners of the project, and then opened to the circle of professional acquaintances and project related actions, etc. Further larger opening to specialists related to the three main challenges of ESPREssO could later enrich the completeness of the ADB. Based on the voluntarism and the expertise of the authors who have entered actions in the database, questions may arise as to the reliability of the actions considered.
Are these actions necessarily the most representative? Have the initiatives further from the project circle been explored? The quality control and the validation of the submitted actions for integration in the database was assumed by the members of the ESPREssO project. But it has sometimes proved difficult to evaluate the total relevance of the targeted actions, or even the accuracy of the criteria evaluated for the actions by each of the authors. Actually, two contributors (Authors 1 and 2) entered more than half of the actions, suggesting a quite unbalanced repartition of contributions (a maximum of 46 actions entered for 1 author, a minimum of 1). For the rest, the main contributors that will be considered are those who entered at least three actions in the ADB. Seven authors entered at least three actions into the ESPREssO database.
The systematic correction of action notation does not seem appropriate. Strong recommendations to authors, provided in advance, could help in more consistency for scoring criteria. The analysis of the ADB content identified 68 possible solutions and 30 good cases to overcome at least one of the three ESPREssO challenges  [24]. The possible solutions identified to overcome Challenge 1 (integrating CCA and DRR) are particularly in line with recommendation formulated in Birkmann and von Teichman  [13]  (see Table  4 ). The ESPREssO Action Database strives to be a database of good examples and good ideas for DRR and CCA. Not reliving the wheel, but gathering stakeholder experience in a centralized way everyone can learn from what has worked in the past, why it worked and how to find ways to adapt those solutions to other contexts and/or scales.
Conclusion The ESPREssO project was dedicated to identify a new strategic vision on DRR and CCA in Europe. This strategic vision was analyzed through three challenges: how to integrate CCA and DRR to foster resilience? How to integrate Science and Legal/Policy issues in DRR and CCA? How to improve national regulations to prepare for trans-boundary crises? To overcome these issues, stakeholders working with CCA and/or DRR in Europe were consulted to identify measures boosting adaptation or societies' resilience. To compile, manage and analyze such information, an Action Data Base (ADB) was developed. This database was filled by the measured proposed during Stakeholder Forums, Think Tanks events and serious games organized during the project. Each idea, measure or comment raised during these events were stored and ranked in the ADB using qualitative and quantitative criteria based on the Sendai Priorities and the SHIELD model proposed by the ESPREssO Team.
Although these actions are presently relatively rare, they hold great potential for transferable lessons learned. Coherent monitoring of implemented schemes: coherent and coordinated monitoring of the effectiveness of implemented CCA-DRR schemes would allow for comparisons to be made and lessons to be learned. " Nevertheless, the ADB was also conceived to be extensively used beyond the ESPRESSO project. Indeed, the platform allow volunteers to contribute to the database by entering additional information about past or current actions so that the system can be enriched gradually in time. In addition to be an interesting valuable media to see what is the state of the art in the domain, our ADB could be used in future research/ governance activities to evaluate decisions related to disaster risk reduction planning or policies.
In addition, we performed different osmotic treatments and always observed a sharp decrease in stiffness values, demonstrating that AFM measurements are responsive to osmotic changes (S2E-S2G Fig). Finally, it is known that follicles are surrounded by a stiff BM  [31, 51]. To determine the importance of the BM in NC pressure, we also performed AFM measurements on collagenasetreated follicles. In such follicles, the A/P pressure gradient is still detected, although the absolute values of pressure are lower than in untreated follicles, possibly because of NC expansion (S2H Fig). Overall, the data are in favor of the presence of a cytoplasmic pressure gradient within the NC compartment at LS9 and at S10. Since curvature of a soft interface is physically ascribed to differences in hydrodynamic pressure between the two sides of this interface  [34, 35] , we predicted from the gradient in pressure that the interfaces between NC should be curved toward the posterior in normal conditions.
To assess this, we examined NC membrane shape and quantified the curvatures of NC membranes in fixed tissues throughout S9 (Figs 2E, 2F, S3A and S3B). This analysis shows that NC membranes bulge toward the posterior at the same time as StC are flattening and that a gradient of curvature is observed from anterior to posterior NC (those abutting the oocyte), with the anterior NC being the most curved. We also analyzed membrane curvature in follicles treated with the ROCK inhibitor and found that most of the membranes still bulge toward the posterior. This does not support a role for cortical tension in generating this gradient of curvature (S3C and S3D Fig). Finally, to obtain more precise data on membrane curvature, we generated 3D reconstructions of live follicles (S1 Movie). To this end, we used the MARS pipeline (Multi-Angle image acquisition, three-dimensional Reconstruction and cell Segmentation)  [52]   We observed that posterior NC membranes become progressively convex during S8 and S9, with no significant influence of the position of the membrane along the A/P axis (Figs 2G, 2H, S4B, S4C and S4E).
High NC cytoplasmic pressure and TGFβ signaling lead to enhanced anterior follicle expansion Our data show that anterior NCs are more pressurized than posterior NCs and the oocyte when follicles elongate. We reasoned that this might force the growing follicle to expand more anteriorly than posteriorly. To test this, we first used fluorescent beads that adhere to the BM (K), and (L) can be found in the S1 Data file. A/P, antero-posterior; dic, dicephalic; Ecad, Ecadherin; ES9, early S9; Eya, eye-absent expression; kel, kelch; NC, nurse cell; S, stage; StC, stretched cell; WT, wild type. https://doi. org/10. 1371/journal. pbio. 3000940. g003 and analyzed their movement during follicle growth (S7A and S7B Fig). From S8 to S10, we observed that beads at the anterior display a greater shift toward the anterior than posterior beads do toward the posterior (n = 12) (Figs 5A, 5B, S7C and S7D).
Cell curvature measurements The 2D measurements are performed on fixed ovaries by manually applying circles fitting the curvatures between adjacent NC at a focal plane allowing border cell visualization. The 3D measurements are performed from segmented NC generated by the MARS method using a custom-made Image macro, called "Find-Curve. " The Find-Curve macro for the Ima-geJ program  [102]  automatically processes all cell stacks contained in a root folder indicated by the user. As the third dimension of the stacks, created by the MARS 3D reconstructions, corresponds to the z axis, the program generates (X and Y) complementary orthogonal views. The three different views are then independently analyzed. Using the "Default" threshold, derived from the Iso-Data algorithm  [103] , the macro identifies the slice with the largest area.
Acknowledgments We thank DSHB and  Bloomington Stock Center  for flies and reagents. We thank  Lyon Multiscale Imaging Center (LyMiC)  and  Arthrotools of the SFR Bioscience  ( UMS3444/US8 ). We are very grateful to  A. Guichet ,  D. Bilder ,  Anne Ephrussi ,  J. R. Huynh ,  B. Loppin , and  Sally Horne-Badovinac  for flies;  V. Van de Bor  for flies and discussions; and  F. Schweisguth  for discussions. We acknowledge  X. Wang  for critical comments on the manuscript.
Results LCOs are produced by a wide range of fungi in the Kingdom Fungi. We tested 59 species of fungi belonging to most phyla within the kingdom for the presence of LCOs exuded into their culture media (Fig. 1  and Supplementary Data 1, 2, and 3). These exudates were assayed for LCO activity using the highly sensitive root hair deformation response triggered by LCOs in barrel medic (Medicago truncatula) and common vetch (Vicia sativa)  1, 2. As some of these root hair deformations, such as waving or bulb formation, are not specific responses to LCOs, our assay was scored strictly on root hair branching. In control experiments, as expected from their known Nod factor specificities, M. truncatula responded only to sulfated (s) LCOs, whereas V. sativa responded only to non-sulfated (ns) LCOs 2 (Supplementary Fig.
To confirm our findings with the root hair branching assay for LCOs and to determine the structure of LCOs produced by the various fungi, we used mass spectrometry (MS). The culture media were fractionated by butanol:water phase separation. The water phases were analyzed directly for COs and the butanol phases, in which LCOs were expected to fractionate, were either analyzed directly or were further purified by chromatography to minimize matrix effects on the MS analyses. Taking advantage of an in-house database (Supplementary Data 5) listing all possible mass-to-charge ratios (precursors/products ions) calculated from known Nod factors, and by using the very sensitive Multiple Reaction Monitoring (MRM) MS approach, we found mass signals of LCOs in 16 of the 20 fungal exudates we analyzed (Fig.
fumigatus. We found 91 differentially expressed genes (DEGs) between control and LCO-treated cultures after only 30 min of treatment and 152 DEGs after 120 min (Fig. 3j , Supplementary Fig. 12 , and Supplementary Data 6). Gene Ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses revealed that several DEGs encoding proteins associated with the cell membrane activities and cell wall processes were regulated at 30 min after treatment with LCOs. A much more diverse set of functions was represented at 120 min with a large number of proteins associated with responses to chemical stimuli and enzymes related to the tricarboxylic acid cycle (Supplementary Data 7 and 8). The vast majority of regulated genes in response to LCOs increased in expression and there was a significant overlap in these upregulated genes at 30 and 120 min, suggesting that some of these genes could be good reporters for the response to LCOs in A.
A QTRAP 4500 mass spectrometer (Applied Biosystems, Foster City, USA) equipped with an electrospray ionization source in the positive ion mode was used to analyze samples in the MRM mode or in the EMS-EPI mode (see below). For the MRM mode analyses, from the known substitutions and chitin lengths already described for Nod factor structures, we created a database of all possible combinations of structures, including new ones never described before, with their corresponding precursor proton adduct [M + H] + and product B ions: in total, 76,386 precursor ions, 2,598,159 theoretical combined structures, and 358,473 MRM transitions (Supplementary Data 5). Given that the number of MRM transitions to be selected for each analysis must be reasonably low to ensure proper sensitivity, we have selected the most commonly described Nod-LCOs (corresponding to 990 MRM transitions).
This highly sensitive, targeted, analytical approach was suitable for samples containing low concentrations of molecules. For samples with higher concentrations of molecules, full scan EMS-EPI analyses were performed. During EMS analysis, major precursor ions are selected automatically, and, after the collision, EPI analysis accumulates their product ions in the trapping module. From this data set, we selected only the precursor ions containing 3 to 6 GlcNAc. This more comprehensive mode could only be used with P. adelphus, P. involutus, and G. rosea LCO-rich samples. Short COs were separated and analyzed using the same LC-MS system, equipped with an hypercarb column (5 μm, 2 × 100 mm; Hypercarb, Thermo). Samples of 10 µl were injected. The elution was done at a constant flow rate of 400 µl min -1 using solvent A, water : acetic acid (1000 : 1, v-v) and solvent B, ACN, as follows: 100% A for 1 min, then 100-50% A in 30 min then 50-0% A in 3 min.
COs were identified in the MRM mode by monitoring the transitions from precursor proton adduct ion [M + H] + m/z 628 (CO3), 831 (CO4), 1034 (CO5), or 1237 (CO6) generating after collision-induced dissociation (CID) the common product B ion m/z 204, comparatively to standard solutions  (10 -7  M in water). The capillary voltage was fixed at 4500 V and the source temperature at 400 °C. Fragmentation was performed by CID with nitrogen at a collision energy of 22-54 V; declustering potential was 90-130 V, optimized for each synthetic molecule available. Data processing was performed using Analyst 1. 6. 1 software (AB Sciex). Experiments with A. fumigatus. A. fumigatus strain Af293 was grown in standard 90 mm Petri dishes on solid glucose minimal medium (GMM) and placed in the dark at 37 °C for 48 h  52.