dataesr/scientific-paragraphs-categorization huggingface dataset:
, 2019; Weigand et al. , 2019). Primers located on the 12S mitochondrial region have been recognized as the best to specifically amplify fishes, unlike COI primers which lack specificity, resulting in low fish detectability  (Valentini et al. , 2016). Unfortunately, we show that the 12S still has a very low species completeness in genetic databases, with strong spatial disparities. With the goal to sequence a maximum of species, it is crucial to reach a consensus in the genetic marker selection to join efforts towards a globally coordinated sampling strategy for this genetic marker. Once species gaps in the 12S sequences will be almost filled, it would pave the way to install eDNA metabarcoding as a robust and standard monitoring and inventory tool, capable of fish identification to the species level in every location.
| Mapping species coverage gaps to improve eDNA monitoring The global diversity of both freshwater and marine fishes is not well covered in public genetic databases. Globally, we show a higher coverage around high latitude in the Northern Hemisphere consistent across the genetic markers and primers while tropical areas, which host more species, have more species gaps in public sequence databases (Figures  2  and 3 ). For freshwater fishes, the genetic species coverage exhibits a clear U-shaped pattern for almost all markers F I G U R E 3 Global and latitudinal distributions of marine fish species richness (a, b), coverage of online genetic database for the Miya primer pair targeting the 12S mitochondrial rDNA region (c, d), the Kocher primer targeting the cytochrome B mitochondrial rDNA region (e, f), the DiBattista primer targeting the 16S rDNA region (g, h) and the Ward f2 primer targeting the COI mitochondrial region (i, j).
The location of the gaps may drive the future sampling efforts required to fill them. Tropical environments are under-represented in public sequence databases and will require a costly, time-consuming and globally coordinated efforts to both describe and sequence the numerous species left to be discovered, as well as sequence the numerous species already described  (Juhel et al. , 2020; Pinheiro, Moreau, Daly, & Rocha, 2019). Environmental DNA is settling as an efficient inventory tool that can overcome hurdles encountered when sampling in tropical ecosystems. In many large water bodies, such as the Mekong or the Amazon, water turbidity prevents visual census leaving the eDNA the only non-invasive monitoring method  (Cilleros et al. , 2019; Yamamoto et al. , 2017). The need to fill species gaps is urgent in these environments as they are experiencing major turnover in species identities with unknown consequences on ecosystem functioning and resilience  (Magurran et al.
Tropical countries are also projected to undergo among the most severe environmental impacts related to human population expansion and climate change  (Barlow et al. , 2018)  metres depth) are still poorly known while they potentially host very different species assemblages that can be also affected by climate change  (Lesser, Slattery, Laverick, Macartney, & Bridge, 2019; Rocha et al. , 2018). Their exploration will require new eDNA-based protocols (fish sampling for reference database and water filtering) that must complement visual surveys that remain limited at this depth. Yet, there is a clear publication bias with the most diverse ecosystems being the least studied in ecology  (Hickisch et al. , 2019). So, the efforts to achieve genetic database completeness are massive but necessary in such highly diverse environments in order to tackle major conservation challenges like the protection of vulnerable but still poorly described biodiversity.
, 2016; Hunter et al. , 2015). Yet, a successful detection of species introduction relies on database completeness for those species. We show that, even among fish species identified as non-indigenous in freshwater ecosystems, up to 30% are currently missing in the best curated 16S database (Figure  4 ). For the genetic marker 12S, a maximum of 55% of non-indigenous species are sequenced per basin, twice as much as native species. It was expected that more non-indigenous species would be genetically referenced compared to native ones since referencing species occurrence outside their native range necessarily assumes their observation and a large proportion of introductions being intentional for recreational fishing  (Leprieur, Beauchard, Blanchet, Oberdorff, & Brosse, 2008) , making tissue for genetic sequencing easily available.
| Sequencing threatened species to support their monitoring Environmental DNA has a great potential in biodiversity conservation, addressing the constraints of detecting elusive or low-abundant species missed by traditional surveys. The proportions of threatened species estimated by the IUCN Red List (11% of freshwater and 3% of marine fishes) are likely underestimated as 48% of fish species are unevaluated while 7 to 9% are Data Deficient (Figure  S2 ). Although the fate of Data Deficient species remains largely unexplored, they form the category with the least coverage in public genetic databases and are estimated to hide a large proportion of already threatened species  (Bland, Collen, Orme, & Bielby, 2015). Even among threatened species, less than 50% have referenced sequences across all genetic markers, and surprisingly, their coverage is lower than Least Concern species for freshwater fishes.
This can be due to the high number of threatened freshwater fishes, mainly located in hard-toexplore tropical regions  (Collen et al. , 2014). Most threatened freshwater fishes live in large tropical basins such as the Congo, the Mekong or the Amazon (Figure  5 ). However, the Mississippi Basin, although located in a well-developed and science-leading country, the United States, where conservation measures and monitoring programs are well established, hosts 72 threatened species that are not sequenced for a 12S primer pair. So, efforts to complement genetic reference databases must be widespread and are not only related to the level of species richness or economic development, as often assumed.
| Interactive online application to support eDNA metabarcoding studies We developed the user-friendly web app interface GAPeDNA to synthetize this large amount of information and make it easily accessible, even without any coding skills. It allows users to select a taxonomic group (at the moment, only freshwater and marine fish are available), the spatial unit or area, the genetic markers of interest and the corresponding primers to evaluate their global spatialized species coverage in public genetic databases, and have access to the corresponding list of species per spatial unit and status (IUCN). This permits the assessment of species remaining to be sequenced for a given spatial zone and sets priorities for sequencing. Although this study is focused on fish as an example, any new taxa can be added to GAPeDNA, providing necessary information is given: 1) primers suited for metabarcoding and 2) global spatialized species checklists.
g. , IncuCyte-Essen BioScience or NanoLive). A real-time bio-imaging cytotoxic assay has been proposed for 96-well microplate  [13]. All these software tools have been conceived to work in 2D settings, with focus on temporal information. Recently, an ingenious 96-well microfluidic platform was developed to perform bio-imaging cytotoxic assay in 3D gels  [14]. Since 3D microfluidic devices allow to keep confined the cells as well as their released soluble factors, they are appropriate to investigate the consequences of each death event on surrounding cells. For this purpose, we focused on analysis strategies to extract not only the temporal information, but also the spatial information of cancer death events. STAMP introduces the new concept of 'potential of death induction', by calculating the induction that each death region (defined as 'object') produces on the surrounding regions, with respect to their mutual distances and to their temporal relationships.
Second, the STAMP code needs to be adapted to different cell morphologies; for example, the cell radius parameter must be revised. Moreover, the STAMP image analysis method might be useful for many other cellular contexts and biological questions, beyond the ToC technology. This adaptability to multiple experimental conditions is possible thanks to the integration within the STAMP software of three modular parameters. First, the T LAG mentioned in step 6-iii and used in Eq (4) (see Materials and Methods). T LAG is the temporal window used to measure the average number of apoptotic events N ap (t, T LAG ) and the average number of living cells N avg (t, T LAG ), allowing to compute the percentage of apoptosis events. T LAG should be set depending on the time frame image acquisition frequency and on the desired time resolution of the investigated phenomenon.
The biological implications Among the various types of cell death  [25] , this work specifically investigates the programmed apoptosis which involves the activation of the cascade of caspase enzymes. Both cytotoxic stimuli we used are known to promote apoptosis of cancer cells. Doxorubicin, which acts by causing irremediable DNA damages in dividing cells, has been shown to induce apoptosis on breast cancer cell lines in vitro  [26] , as well in breast cancer patients in vivo  [27]. The CTL clone (P62) used in this work kills autologous cells (IGR-Pub) at least in part via Apo2L/ TRAIL-dependent pathway  [15]. By using novel mathematical (potential of death) and computational (STAMP software) strategies, we achieved an original spatiotemporal analysis of apoptotic cancer death in the 3D confined environments of ToC cultures.
The STAMP method A STAMP software was developed under MATLAB environment and can be downloaded using the following link: https://cloudstore. bee. uniroma2. it/index. php/s/LEpHYTsPnDj4Ajt (password: STAMP2021). The STAMP method was applied on each video V, with spatial dimensions D 1 (number of row) and D 2 (number of columns) and with a total duration of T frames (from 48 to 72 depending on experiments, with a frame rate of 1 h). Let us consider (x,y,t)2{1,. ,D 1 }×{1,. D 2 }×{1,. T} the tuple indicating the position of the coordinates (x,y) occupied by an arbitrary pixel on the video frame of V acquired at time t, where t = 1,. ,T. Then, V(x,y,t) indicates the video sequence with the specific coordinates (x, y) at time t. We can refer to the video under examination indistinctly with V or V(x,y,t) to vary of (x,y,t)2{1,.
,D 1 }×{1,. D 2 }×{1,. T}. 1. Cell localization and tracking. Tumor cells (stained in red) were located and tracked in the red channel video of V by adapting Cell-Hunter software to the frame rate of 1 h  [7, 35, 36]. Localization was performed by preliminary binarizing the red channel video of V by Otsu approach  [37]. Then, Cell-Hunter was applied. Shortly, in each binarized video frame, the software implements the Circular Hough Transform (CHT)  [38]  which automatically locates tumor cells, assumed as circular-shaped objects of radius imposed, providing an accurate estimate of individual cell radii. Then cell trajectories/tracks were constructed by linking positions between consecutive frames according to an optimized procedure based on the concept of cell proximity and optimal assignment problem  [39].
However, it should be pointed out that our students have no specific IT skills. In fact, if GIS and database training are usually part of an archaeology curriculum, the digital turn in the humanities still requires the implementation of many other skills within their academic training. The active involvement of students in our project was therefore meant, on the one hand, to develop their ability to deal with an archaeological artefact, an archive, or a whole collection in terms of description, analysis, interpretation, and conservation. On the other hand it was also intended to strengthen their digital skills by leading them to seek out solutions to the various technical or documentary issues they faced in the process. To fulfil the requirements linked to the digital teaching and dissemination of our particular heritage to our students and to a wider community, a user-friendly digital architecture was sought.
The idea was to focus on content and methodology, rather than on technology. Very often, the choice of a complex digital solution not only makes us, as scholars in the humanities, dependent on the help of IT specialists, but it also prevents us from understanding the logic and rules of knowledge production. Conversely, I wanted to place my project in a 'win-win' logic: while the university acquires data and enriches its digital archive, the students also develop their skills for the job market. Accordingly, I chose Omeka Classic, a quite simple and modular open access CMS. Eventually, in November 2016, I launched VERGILIUS, the portal dedicated to the heritage of the Department of Art History and Archaeology of Paris 1. Before illustrating the main features of this portal and the way I adapted the structure of Omeka to our pedagogical needs, I will start with an overview of the project, focusing on the main issues and solutions.
Before VERGILIUS: surfing between data and metadata Slides and photos from former professors and researchers One of the most important collections held by our department consists of thousands of slides and photographs for teaching and research. Some are images taken from books, others are original photographs taken by researchers and academics throughout the 20 th century. In the case of images from books, it seemed useless to digitize these slides or photos for which we have no copyright ownership; they can be accessed directly in the original publications they were taken from or in the large iconographic online databases made available by well-known repositories of archaeological iconography, like the Perseus Project, Arachne, the digital LIMC, the Beazley Archive, etc. For this series, we established a global inventory in order to identify the subjects and understand the teaching methods in the department before the advent of new technologies.
During these operations, special attention was given to metadata, which presented a real challenge for students. We chose two open-sourced pieces of software, XnView and Geosetter, which allow users to modify the textual and geographic metadata embedded in image files. These indexing and referencing operations are now necessary to ensure that our resources will not become 'lost in translation' in the world wide web. In the long run, a precise indexation will allow researchers to find them in national and international research platforms (such as Isidore in France), which are based on sophisticated queries of metadata. Working on these old pictures requires a detailed workflow and therefore allows for specific training. Students should deal with scanning and image processing issues: in doing so, they are forced to transform the photograph into an agent of their training, both digital and archaeological.
The pieces are largely Mesopotamian in origin, with a distinct series from Arabia. Chronologically, most of the sherds date to the Neolithic and Bronze Ages. The objective of this study collection is to establish, through the technological study of a wide spectrum of pottery productions, a reference atlas for students and pottery specialists. 10 or the technological processing of each sherd, students worked under the supervision of pottery specialists François Giligny and Sophie Meri, and produced descriptive cards to be filled manually. For the database -that represents the digital translation of these cards -, I chose the FileMaker Pro proprietary solution, which allowed in few weeks to come up with a very user-friendly and powerful tool. Even if the interface has still to be improved, the data entry has already started.
Thanks to a FileMaker Server provided free of charge by the Huma-Num national research infrastructure, the database (named 'TEchSSON') is already accessible online to the project managers and to Paris 1 students. 11 Once completed, it will be open to the general public, which will make it a broadly accessible teaching and a research tool that can demonstrate the potential of a relational database for the analysis and understanding of ancient pottery technologies. A few 3D models of the most interesting sherds were also produced, introducing students to photogrammetry. We chose the proprietary software PhotoScan (now Metashape) for the first steps (point and dense cloud) and the open source software Meshlab and Cloud Compare for further processing. 12 By training students to photogrammetry, we initiated the production of 3D models, which are now used in our pottery courses, while allowing the dissemination of the data beyond our university.
The assemblage of seal impressions from Ancient Iran The last case study presented here is the assemblage of 495 modern impressions of ancient Iranian seals created during the 1950s and the 1960s and related to the work of Jean Deshayes, then a professor at the University of Paris. 14 During this period Deshayes was involved in various projects led by French archaeologist Jean-Claude Gardin -one of the founders of archaeological computing -on the development of automatic data recording in archaeology. 15 The assemblage of seal impressions could be traced back to these years and related to this epistemological framework, which is in turn part of the foundation of modern digital archaeology. In order to inventory and study this assemblage we produced a relational database (CESIA id. Corpus des empreintes des sceaux de l'Iran Ancien), once again using FileMaker Pro.
16 This tool, already available online to the project managers thanks to the FileMaker Server provided by Huma-Num, 17 is aimed at describing all relevant features of a cylinder or stamp seal, including its size, shape and form (material data) and its iconography (immaterial data). It combines scientific needs with patrimonial ones, while introducing our students to the principles of relational databases, as well as allowing us to communicate our university heritage (and scientific production) to a wider audience. 11 https://fm01. db. huma-num. fr/fmi/webd/TEchSSON (last accessed May 27, 2021). 12 Some of these 3D models are already available on the Sketchfab account of the University: https://sketchfab. com/Sorbonne-university-Paris1 (last accessed May 27, 2021). 13 For a first overview, combining 3D and RTI techniques, see Ferrari, Giligny 2019.
VERGILIUS: From data processing to data sharing In 2016, VERGILIUS was launched as a unified access portal, gathering all the department's iconographic and heritage resources. The tool is based on Omeka Classic (version 2. 4. 1), a free and user-friendly CMS developed by the Roy Rosenzweig Center for History and New Media. 18 Operating at the crossroad of web content management systems, archive management systems and museum management systems, it allows users to create or collaborate on a website to display collections and to build virtual exhibitions. It also offers a series of themes and plugins that can extend its functionalities. 19 Omeka uses the Dublin Core metadata standard to manage metadata, 20 as do French national libraries or the national scientific search engine Isidore. 21 Omeka therefore fits the pedagogical and institutional needs of both our department and this particular pedagogical project very well.
It also manages users according to various access privileges: a super-user, who has all privileges of administration and management (members of our IT System department); various administrators (professors and researchers of our Department), who have the right to access and modify documents, collections and tags; and contributors (students), who have the right to add and edit the documents they have created. VERGILIUS is the result of this network operation, moving from the server configuration and the back-office set-up (installation of several plugins and metadata specification) to data entry of university collections. Although the layout is still a work in progress with some technical issues that need to be fixed, large parts of our collections are already available. The core of the portal is the panel 'Images & Archives', which includes all the image libraries already processed: 22 1.
In VERGILIUS metadata can be filled in using free text, but in most cases, we implemented lists of values or codes from a controlled vocabulary. Especially for the archives folder, we decided to add specific metadata in addition to those inherent to Dublin Core, trying to digitally reproduce the archives' materiality. The archives of Bohumil Soudský -a former professor who introduced European Bronze and Iron age archaeology into Paris 1 teaching in the early 1970s 23  -are a good example in this respect. 24 They consist of personal notes, drawings, press clippings, excavation files, and a large number of student homeworks and exams. We followed a precise protocol: from sorting and ranking to inventory, then from scanning to uploading a selection of the more interesting pieces. Through data uploading we created a detailed hierarchical tree, which corresponds accurately to the physical organisation of the archives in the shelves of our department.
In order to further exploit these resources, we used the Neatline plugin 25  to create a virtual exhibition showing the main stages of Soudský's education and scientific career on an interactive map. 26 This is a good example of Omeka's flexibility, which not only allows users to store and manage data, but also to produce new data. In other words, after data collecting and data processing, we finally reach real data visualisation: a completely new resource with a great heuristic potential, produced by students for both students and scholars alike.
The last 5 years of this simulation are averaged to create a monthly varying aerosol field. Soil and snowpack initial conditions were computed in 2 steps. First, the E3SM land model was run from January 1, 1979 through August 1, 2016 at the target resolution forced by observed atmospheric conditions from Version 7 of the Climatic Research Unit-National Centers for Environmental Prediction (CRUN-CEPv7,  Viovy [2018] ) atmospheric forcing data. This simulation couldn't be extended beyond 2016 because of CRUNCEPv7 data availability. The second step was therefore to run from August 1, 2016 to January 20, 2020 using EAMv1 at 1° nudged to ERA5 reanalysis with a 6 hr timescale. Prescribed weekly SST and sea ice from OISSTv2  (Reynolds et al. , 2002)  is used for this simulation. The machinery for this second step came from the Cloud-Associated Parameterizations Testbed  (Ma et al.
, 2013 (Doelling et al. , , 2016)). Cloud fraction and liquid water content are taken from CloudSat  (Austin et al. , 2009; Su et al. , 2011)  and from the CERES-CALIPSO-CloudSat-MODIS merged product  (Kato et al. , 2010, C3M). CloudSat and C3M are not available for the 2020 dates simulated and are instead climatological averages. Where possible, we compute long-term averages using the last 30 days of the simulation (January 30 through February 28); we exclude the first 10 days of the run as spinup (though SCREAM fields stabilize after just one day of spinup, see Figure  5 ). As noted above, some observational data sets are only available as monthly averages. For corresponding variables, we show results using just days in Feb. Finally, the first week or so of the simulation can be treated as a weather forecast, we use all 40 days of the simulation for some analysis of storm behavior.