dataesr/scientific-paragraphs-categorization huggingface dataset:
Ethics Both the ECR and BNA databases and their utilisation for the purpose of this study were approved by Paris VI Institutional Review Board and the Commission Nationale de l'Informatique et des Libertés ('National commission for informatics and liberty') responsible in France for data protection and use concerning human identity and human rights. French Legislation allows the use of anonymised clinical data if patients did not specifically object to it during consultation. Hence, every patient included in this study did not oppose to the use of his/her clinical data. However, no written consent was obtained either for the ECR or for the BNA database.
Open access neuropsychological tests The MMSE  13  and the FCSRT  20  were collected in the ECR database. 2] [23] [24] [25]  It is recommended in the diagnosis of AD by the IWG guidelines. 4 5 This test is now implemented to screen patients in disease-modifying drug trials (eg, Clinicaltrials. org: NCT02760602). In our study, we included patients with a free recall score <20 or a total recall score <42. 21 The mild or prodromal stages were ascertained by an MMSE score >20. In the BNA, only the MMSE was available. Cerebrospinal fluid biomarkers of Ad CSF was acquired following standard procedures. The CSF was obtained by LP between the L3/L4 or L4/L5 intervertebral space, using a 22-gauge atraumatic needle. Five hundred microlitres of CSF were used to perform standardised commercially available INNOTEST sandwich ELISA according to the manufacturer's instructions (Fujirebio Europe NV, formerly Innogenetics NV).
statistical analysis First, we studied the descriptive statistics of the population of interest derived from the analysis performed in the 11 CMRR. To assess the external validity of our results, we compared the BNA data from these 11 CMRR to those of the remaining 18 CMRR. To compare sociodemographic and medical characteristics between the 11 CMRR that volunteered to participate in this study and the other 18 CMRR (using data that were available for these CMRR in the BNA), we performed Student's t-tests for quantitative variables describing means and SD and Χ 2 tests for qualitative variables after an assessment of the Gaussian distribution of the continuous variables using the Kolmogorov-Smirnov test. All reported p values are two-sided. Statistical analyses and description of the cohort characteristics were performed with SAS software V.
The BNA includes data from only about 90 private specialists, providing data on 2. 2% of the AD and 2. 5% of the MCI patients in the BNA. As there are about 800 French private neuro specialists, although not all so active in the field of neurodegenerative disorders, one could assume that private specialists consult a large additional number of patients for cognitive problems. However, thanks to a systematically organised medical system with hierarchised and personalised care plan and management (figure  2 ), our results can be generalised to the French AD medical community. 30. Patients do not consult a specialist when they have MCI or mild dementia. One should note that the databases analysed in our study only represent the patients diagnosed by memory specialists. Our analyses do not account for patients who did not consult any physi- Open access cian nor for those who consulted their general practitioner and were not referred to a specialist.
Moreover, general practitioners do not often refer their patients to a neuro specialist as only 41% of them consider that the specific treatments of AD are efficient. 39 These two first points are important to consider as a selection bias. Of course, our data are not representative of the overall French incidence of early stages AD in 2014 and 2015 but only of diagnosed cases, that is, individuals who either by themselves or due to a caregiver or physician came to have a neurological evaluation. No data exist yet in France to address the discrepancy between the total number of early stages AD and the diagnosed cases. The French cohort CON-STANCES, aiming to recruit 200 000 individuals randomly selected from a population and to follow them for 5 years with a yearly cognitive assessment for elderly participants and AD diagnosis recording will allow researchers to address this critical point.
Open access Interestingly, the 195 patients identified with prodromal or mild AD in the 11 CMRRs, which are part of the third-line healthcare organisation, had been most often referred by their general practitioners, whereas one would expect they would be referred mainly by neuro specialists in the second line. This lack of 'specialised referral' is also supported by the small geographical distance (40. 1±6. 7 km) separating these patients from the CMRR. This study has limitations including its retrospective design for the electronic record file database that does not allow us to draw definitive epidemiological conclusions, but still raises the level of awareness concerning the relatively low diagnostic rate of AD at its early clinical stage. Another limitation is that our study, so far and to our knowledge, cannot be generalised to other countries because we lack recent epidemiological data on AD on the same scale as our study.
COnClusiOns Our study is the first and largest to address the critical question of the frequency of a specific AD diagnosis at its early stages in clinical routine. Our estimations of the incidence of clinically diagnosed prodromal or mild AD are only a fraction of previous incidence estimations of AD in the general population. 29 This finding, which is based on two different database analyses, is generalisable on a national scale due to the large number of included participants and the 5-year period of evaluation. Similar findings will have to be evidenced in other countries to be able to generalise these results on a global scale. This topic is important to consider since new disease-modifying drugs, specifically designed to target this population of patients, may become available in the coming years.
17. 1. 14 Illumina). The quality of the sequencing reads was assessed with FASTX-toolkit (v0. 0. 13) and no pre-processing was needed. The alignment of the reads was done with STAR v2. 5  42  against the reference genome of Mus musculus (GRCm38. 90). To assess its expression, the human transgene hCDX2 (ENSG00000165556) was added to the reference murine genome as an additional gene and processed as the canonical ones. The aligner STAR was used with default parameters and the alignment was refined with a second pass. The read counting was done with HTSeq v0. 6. 1  43  in union mode and at gene level. The normalization of gene expression as well as the consistency among biological replicates were both assessed with the R package DESeq2 1. 10. 1  44. Differential expression analysis was also done with DESeq2.
Prior to the Wald test, the values of log2(Fold Change) were not shrunk. The significantly differentially-expressed genes were identified based on the p-value, corrected with the False Discovery Rate (FDR) multiple testing method, and the log2(Fold Change). Genes with an absolute log2(Fold Change) ≥ 0. 4 and an adjusted p-value < 0. 05 were considered as differentially expressed. All the downstream analyses were done with R and with DAVID  45  ; Gene Ontology enrichment was done with the one-tailed exact Fisher test and the pvalues were corrected with FDR multiple testing method. The transcription factor binding motifs in the promoters (from 2000-bp upstream to 50-bp downstream of the transcription starting site) of the differentially expressed genes were analyzed with the software HOMER v4.
, 2018; Mirtl et al. , 2018). This site-based research network measures a broad variety of abiotic and biotic environmental variables, which may feed into other global initiatives. LTER national networks have mainly been developed from the bottom-up and LTER sites were established for different research and monitoring purposes. The ILTER community has produced tools to harmonize and compare measurements and methods, allowing for data integration workflows and analyses between and within individual LTER sites, to ensure the highest quality interoperable services in close interaction with related regional and global research infrastructures and networks  (Haase et al. , 2018; Mirtl et al. , 2018). Long Term Socioeconomic and Ecosystem Research (LTSER) platforms emerged as initiatives aimed at enhancing the capacity of ecological knowledge combined with social science to produce useful knowledge for facing global environmental challenges  (Mauz et al.
, 2012). This emphasis in the ILTER network reflects the desire to produce knowledge particularly useful for addressing complex environmental challenges emerging from nature-society interactions  (Dick et al. , 2018). One of the goals of ILTER is to improve the comparability of site metadata and of long-term ecological data, facilitating their exchange and preservation around the world. ILTER member networks are committed to free and open data sharing  (Vanderbilt et al. , 2010; Vanderbilt and Gaiser, 2017) , in agreement with the F. A. I. R (Findable, Accessible, Interoperable, and Reusable) principles for data management and Open Science  (European Commission, 2016 'FAIR'; Mirtl et al. , 2018; Tanhua et al. , 2019). The Dynamic Ecological Information Management System Site and Dataset Registry (DEIMS-SDR 4  ) provides a common and standardized metadata catalog for the distinct identification of observation facilities (e.
g. , sites, stations, sensors, datasets, persons) used by ILTER members. DEIMS-SDR also provides a web-based service to document and share scientific datasets, implements the ILTER community profile  (Kliment and Oggioni, 2011) , and allows the export to different XML formats (e. g. , EML 2. 1. 1, BDP, ISO19115, INSPIRE). ILTER identified DataONE as the main facility to share and distribute ILTER data, but it also shares data through the GEOSS (Group on Earth Observation System of Systems 5  ) Data Portal. ILTER agrees with the open data principles at the global scale in principle, but putting them into practice is still a challenging issue in most member networks and at the site level.
THE COASTAL AND MARINE ILTER SITES (ILTER-CMS) There are 63 coastal and 52 marine sites in the ILTER (Figure  1  and Supplementary Table  S1 ). Based on classifications in the ILTER's DEIMS-SDR, coastal sites include sand dunes and beaches, lagoons, estuaries, river deltas, fjords, salt marshes and mangroves, while marine sites are located on continental shelves and oceanic islands (Figure  2 ). Nearly half of the CMS include data records that precede the formal establishment of the ILTER (Figure  3 ). For example, the "Dutch Wadden Sea Area" in the Netherlands has records dating to 1872. Observations began in the Western Gulf of Finland in 1902; the Mar Piccolo of Taranto, Italy in 1914; and Shirahama, Japan in 1922. The length of these observations enhances the opportunities for ILTER-CMS to contribute to documenting global change.
Opportunities • ILTER-CMS has the governance structure to coordinate with management and policy programs, interact and link with other large-scale initiatives, create interfaces between the different approaches from the various communities, and establish a co-located network of sites within similar ecosystem typologies, with shared research and monitoring tasks for multi-purpose uses  (Haase et al. , 2018). The ILTER-CMS can contribute substantially to merging frameworks that are behind different global research and monitoring initiatives, producing guidelines for future site-based longterm research and monitoring. The site network could generate connected ecosystem monitoring methodologies and datasets, supporting, as well, synergies in the use of costly infrastructures, through cross-initiative collaborative research.
CS can (i) improve the frequency and geographical coverage of observations, and (ii) improve pedagogy and communication at the science/society/policy interface by involving citizens, managers or different stakeholders in a research program. Hands-on involvement of people in research and monitoring activities is more effective than communicating about science and its benefits. Increasingly apps can be used to assist the citizen scientists to report data in a standardized manner (e. g. , the Secchi disk project 6  or beach observer). CS programs can yield significant results (see, e. g. ,  Abbott et al. , 2018)  and could be applied, for example, in programs with divers, sailors, and beach-goers looking at biodiversity in coastal zones and collecting data of great interest to ILTER and contributing to GOOS.
Threats • Long-term initiatives are difficult to maintain, and they need to be cost-effective and sustainable at the country level. Reduction of ILTER-CMS activities at some sites could produce temporal and spatial gaps that would hamper the functionality and relevance of the network. • A failure in engaging users and stakeholders could limit the full exploitation of ILTER-CMS services and products. The lack of transfer of knowledge and understanding to policy makers and society would prevent informed decision making regarding the long-term safeguarding and effective management of marine ecosystem services. • ILTER Network has historically been more oriented toward "terrestrial, " inland ecosystems: conceptual frameworks, harmonization, and data models not well-suited for the marine component may discourage future ocean initiatives.
, 2013; Muller-Karger et al. , 2018). ILTER-CMS sites are located in 20 of the 66 Large Marine Ecosystem (LME,  Sherman, 1991)  around the world and can contribute to identify areas of the oceans for conservation purposes and enable ecosystem-based management to provide a collaborative approach to management of resources within ecologicallybounded transnational areas. Data collected at ILTER-CMS could be streamed into the OBIS and contribute to increasingly free and open access biodiversity and biogeographic data and information on marine life. ILTER can harbor and link with many other long-term coastal and ocean ecosystem monitoring programs, which may be explicitly reported also on DEIMS -SDR, in each site description. Furthermore, there is a well-established bottom-up procedure from the request of a site to become an LTER site, to the assessment of its suitability, i.
NEW TECHNOLOGIES FOR ILTER One aspect determining the future success of the ILTER will be its ability to adopt and leverage emerging technologies at all levels of organization. Many of these technological developments represent opportunities to catalyze education of and collaboration between young scientists across LTER sites, strengthening the network and thus mitigate identified threats in the SWOT-analysis (Table  1 ). Mature technologies that are economic to implement can directly contribute to counteract currently identified weaknesses by better geographical coverage and harmonized data quality. This spans innovative in situ technologies developed at individual sites to global data networks that enable novel syntheses via increasingly powerful computational technologies or leverage citizen science.
Researcher Level International Long-Term Ecological Research Network sites are ideal incubators for the development and/or deployment of emerging technologies. As noted in the introduction, the general sampling rate of eco/bio/geo/chemical phenomena has long lagged behind the rapid data collection possible by physical oceanographers. In the last two decades, however, there has been a rapid development of novel high-throughput technologies. These include chemical, imaging, acoustic and molecular sensor systems that have enabled continuous and long-term measurement of new parameters that are of great interest  (Johnson et al. , 2007). Examples include nitrate  (Johnson and Coletti, 2002) , ammonium  (Plant et al. , 2009) , and pH  (Seidel et al. , 2008; Martz et al. , 2010)  sensors. Similarly, advances in rapid image collection and processing have enabled cataloging and enumeration of phytoplankton and zooplankton biodiversity at tidal to interannual scales  (Olson and Sosik, 2007; Sosik and Olson, 2007; Faillettaz et al.
S. Shelf (NES) LTER site and other time series locations in the U. S. , and has a growing user base around the world. Continued advances along this trajectory will enable novel biological and ecological studies. For example, embedded sensors within organisms have enabled metabolic and physiological studies  (McGaw et al. , 2018) ; underwater tracking technology has revealed ecological interactions between predator, prey and the environment  (Osterback et al. , 2013). The rich contextual data at the ILTER sites provide an ideal framework to develop this new technology and interpret the data it produces. In addition to developments of in situ technologies, ILTER sites are also promoting advances in remote sensing technologies that are critical for characterizing ecosystems at large scales. For example, in coastal dune systems the use of high-resolution remote sensed imagery (LiDAR -Light Detection and Ranging -and orthophotos) is helping to explain the invasion success of some alien species and the roles of propagule pressure, abiotic, and biotic factors in coastal landscapes  (Bazzichetto et al.
, 2015). Machine learning will enable the deployment of technologies that have heretofore been too data-rich to make significant impacts to understanding biology and ecology within LTER sites. We give two examples: passive acoustics and flow cytometers. The use of passive acoustics across a broad sound spectrum has not been feasible due to limitations in memory, battery power, and processing capabilities. With the advances mentioned above and the maturation of machine learning techniques in parallel with increasingly powerful computers (at both the personal and cloud/cluster level), tackling the processing requirements of such large datasets in now feasible  (Mooney et al. , 2017). We envision that monitoring the soundscape within ILTER-CMS will become one of the most widely adopted technologies in the coming decade.
• The ILTER-CMS need to harmonize and coordinate longterm environmental (both biotic and abiotic) observations in line with the EOVs to the extent possible, to allow comparisons within and across networks, sites and scales. These efforts should consider socio-ecological aspects, as well. • Launch or improve coordination and integration of observations across scales (e. g. , from coast to open sea) in concert with other international observing networks. • Develop standard operating procedures, adopt guidelines for measurement program design, and establish routines for recurrent intercalibration exercises for all subject fields in line with the OceanBestPractices (OBP 7  ). Such activities may include increasing the use of shared infrastructure, protocols and data platforms; and developing metadata and dataset harmonization/interoperability necessary to foster and facilitate sharing and open access.
ILTER coastal and marine sites are uniquely poised to contribute to biological and ecosystem EOVs by virtue of the existing ILTER governance, infrastructure, and research resources (both human and technological). • The long time span of many ILTER-CMS members enables the identification of global trends (e. g. , warming) and local pressures (e. g. , nutrient loads) against the background of natural variation. Recent evidence of global changes and impacts from marine organisms and ecosystems are mainly derived from global databases of in situ observations (Poloczanska et al. , 2016), stressing the value of global networks such as ILTER-CMS. • A marked diversity and wide range of partners and institutions across the globe characterize ILTER-CMS, guaranteeing multi-disciplinary data acquisition, analysis, integration and synthesis, and cost-effective sustainable observations.
• ILTER coastal and marine sites are uniquely poised to contribute to biological and ecosystem EOVs by virtue of the existing ILTER governance, infrastructure, and research resources (both human and technological). • The long time span of many ILTER-CMS members enables the identification of global trends (e. g. , warming) and local pressures (e. g. , nutrient loads) against the background of natural variation. Recent evidence of global changes and impacts from marine organisms and ecosystems are mainly derived from global databases of in situ observations (Poloczanska et al. , 2016), stressing the value of global networks such as ILTER-CMS. • A marked diversity and wide range of partners and institutions across the globe characterize ILTER-CMS, guaranteeing multi-disciplinary data acquisition, analysis, integration and synthesis, and cost-effective sustainable observations.
Methods Records of ill travelers attending a MG between August 17, 2015, and April 30, 2019, were collected by GeoSentinel, a global clinicianbased surveillance network that monitors travel-related illnesses among international travelers and migrants  [3]. GeoSentinel was established in 1995 as a collaboration between the Centers for Disease Control and Prevention and the International Society of Travel Medicine. It consists of 68 clinical sites in 28 countries. GeoSentinel records ill persons' visits to network sites; well travelers are not captured. Attendance at a MG is routinely recorded. During the study period, investigators were directed to enter supplemental details on the nature and location of the MG and to evaluate whether the diagnosis was likely associated with MG attendance. Records were excluded if the mass gathering was likely to have < 25,000 attendees or if data were missing regarding the type of MG.
Section 2 presents the instruments and datasets involved in the study. Passive and active remote sensing measurements are mainly used, completed by meteorological model outputs and the dataset of the Airparif air quality measuring network. We highlight the most polluted winter days of the past decade in Section 3 from archived ground-based PM10 measurements and analyse the associated weather situations. In Section 4 we analyse in depth the measurements performed during winter 2016/2017, which included those of the N2-Raman ground-based lidar. This period was associated with two exceptional APEs whose characteristics are described in Section 5: we take advantage of the entire lidar dataset of these APEs. It covers a wide range of aerosol load, from pollution free days to severely polluted days.
The Ångström exponent is derived from the AErosol RObotic NETwork database (AERONET, http://aeronet. gsfc. nasa. gov/) for the Paris site. This assumption is consistent as all aerosols are concentrated in the shallow PBL with low horizontal advection of aerosol plumes. During daytime, the lidar-derived AOT is checked against the one measured by the sun-photometer of the AERONET Paris site at concomitant times. The AOTs, combined with the elastic channel, lead to the retrieval of the aerosol extinction and backscatter coefficient profiles (AEC and ABC, respectively), and to their ratio, also called LR. The LR may vary in the atmospheric column since different types of aerosols can be present. However, in the particular case of this work, with most of the particles trapped close to ground level in a winter PBL, the assumption of an equivalent LR for the entire column is justified.
Relationship between aerosol optical properties and PM 2. 5 5 The parameter legally used to gage an APE is PM10 (n° 2008/50/CE and 2004/107/CE), however,  Randriamiarisoa et al. (2006)  demonstrate that the accumulation mode (PM2. 5) contributes the most to optical properties of an aerosol population in the Paris area. Thus, in search of a correlation between Figure  6  and Figure  10 , we chose PM2. 5 over PM10. We consider the dataset combining the two events displayed in Figure  6 , Figure  7  and Figure  10. It ranges from pollution free days to severely polluted days and thus covers a wide range of AEC,  AOT and PM2. 5 values. 10  Figure  11  shows the scatterplot between the PM2. 5 measured at ground level and the total AOTlid. The linear regression conducted on all the data of Figure  11  (dashed grey line), i.