dataesr/scientific-paragraphs-categorization huggingface dataset:
, 2005; Bo et al. , 2011) , but not in scleractinian corals so far, thus it was not surprising that sequences of this clade were absent from our dataset. In contrast, clades A, C, D were the most common. In particular, clade C was dominant in New Caledonia, whereas clades D and A were mainly found in Djibouti. This result was similar to the analysis of the same samples using ITS2  (Brener-Raffalli et al. , 2018). Thus, 18SV1V2 not only had a similar phylogenetic signal to ITS2, but also offered similar community composition for Symbiodinium. Coccidians and Licnophora Were the Two Other Main Taxa Within P. damicornis Although eukaryotic microborers were common in coral colonies  (Tribollet, 2008b; Pica et al. , 2016) , we did not find any of them in our samples. However, even though boring microflora inhabited live and dead corals, they were more abundant in the latter ones  (Le Campion-Alsumard et al.
damicornis sensu lato. Among them, Licnophora and unidentified coccidia genera were common in coral samples from Djibouti and New Caledonia. In particular, coccidian sequences were phylogenetically related to coccidians described in other scleractinian coral species. Furthermore, different distributions were highlighted between Licnophora and coccidians, and between Symbiodinium clades C and A/D. Because the dataset was limited to two geographic regions, we did not know the respective influence of geography, P. damicornis clades or thermal regimes on protist assemblages. Moreover, we could not confirm that Licnophora and coccidians were part of the coral holobiont, and not simply just a part of the larger environmental microbial community. Notably, future studies should decipher if they serve a specific function within the holobiont.
FUNDING CC benefited of post-doctoral fellowships from  CNRS  and  IFREMER. This work was supported by the  French National Research Agency ANR , project  ANR-14-CE19-0023  DECIPHER (coordinator G. Mitta),  Campus France PHC Hubert Curien program Maïmonide-Israel , and by the  DHOF program  of the  UMR5244/IHPE  (http://ihpe. univ-perp. fr/en/ihpe-transversalholobiont/).
A culturomics approach has enabled the isolation of >295 new bacterial species from the human gut  [1]. Here, using culture conditions containing a high salt concentration  [2] , we isolated strain S35 T from an extremely saline soil sample collected from the dry lake of Ank el Djamel in Algeria. This strain could not be identified by our systematic matrix-assisted laser desorptionionization time-of-flight mass spectrometry (MALDI-TOF-MS) screening (http://mediterranee-infection. com/article. php?laref= 256&titre=urms-database) on a Microflex spectrometer (Bruker Daltonics, Bremen, Germany)  [3]. Strain S35 T was isolated after 14 days of incubation at 30°C on International Streptomyces Project 4 medium (ISP4) (Becton Dickinson, Le Pont-de-Claix, France) modified by the addition of 50 g/L of NaCl and with pH adjusted to 8.
Then, the growing colonies were sub-cultured on 5% sheep's blood-enriched Columbia agar (bioMérieux, Marcy l'Etoile, France) for 7 days in an aerobic atmosphere at 37°C. Strain S35 T is a Gram-positive, filamentous-shape, ranging from 0. 4 to 0. 6 μm in diameter. The colonies obtained after 7 days of incubation appear opaque, brown with a wrinkled surface with a mean diameter of 2 mm. Strain S35 T exhibited catalase but not oxidase activity. This strain is mesophilic and strictly aerobic, growing optimally at 37°C and pH 7. 5. Identification based on 16S rDNA demonstrates that strain S35 T exhibits 97. 26% sequence identity with Streptomyces albus ATCC 25426 (GenBank Accession number DQ026669. 1), its most closely related species with standing in nomenclature  [4]  (Fig. 1 ). This value is under the threshold of 98.
It has been estimated that out of 16 500 known antibiotics, 8700 are produced by Actinobacteria, including 6550 by Streptomyces species  [6]. These bacteria actually have a large number of "hidden" or "cryptic" metabolites. If we could induce the production of these metabolites, it would be possible to obtain several new molecules of therapeutic interest. MALDI-TOF spectrum The MALDI-TOF-MS spectrum of "Streptomyces massilialgeriensis" is available in: http://www. mediterranee-infection. com/article. php?laref=256&titre=urmsdatabase. Nucleotide sequences accession numbers The 16S rRNA gene sequence of "Streptomyces massilialgeriensis" was deposited in GenBank under Accession number: LT838406. Deposit in a culture collection The strain S35 T was deposited in the Collection de Souches de l'Unité des Rickettsies (CSUR) under number P3927.
Data and methods The partitioning of the AOD in the BL (from the surface to the top of the boundary layer) and FT (from the boundary layer top to the tropopause) has been computed from the CALIOP aerosol extinction retrievals and the BL height from the ERA-Interim archive. The final output is monthly averaged AOD values over a 2 × 2 • grid from January 2007 to December 2015. Results for the Antarctica region are likely spurious and thus excluded because high aerosol values are reported by CALIOP despite the region being known to be pristine.
, 2013). A comparison of CALIOP data with MODIS retrievals is performed below and with in situ measurements in Sect. 3. 3. In this study, we use 9 years  (2007) (2008) (2009) (2010) (2011) (2012) (2013) (2014) (2015)  of CALIOP Version 4. 10 Level 2 532 nm aerosol extinction data and the Atmospheric Volume Description (AVD) product containing feature classification flags. With the AVD feature flag, an aerosol type is indicated for each aerosol layer and each profile bin. Note that although the solar background illumination decreases the signal-to-noise ratio during daytime, both daytime and nighttime aerosol extinction data are here analyzed in a similar manner. To minimize the uncertainties associated with the aerosol extinction, the data were screened following the recommendation by  Winker et al.
(2013) : only aerosol extinction values with a cloud aerosol discrimination confidence inclusive of -100 to -20, with an extinction quality control flag value of 0, 1, 18, or 16 and cloud-free scenes were considered, and negative aerosol extinction values and "clear air" (meaning air without aerosols) below an aerosol layer base lower than 2. 46 km were removed. The 2. 46 km threshold was chosen not to bias low the aerosol extinction near the surface where the layer detection algorithm sometimes places the aerosol layer base above the surface  (Winker et al. , 2013). Finally, aerosol extinction profiles are averaged only for ten or more profiles per grid box which excludes 1 % of data but leads to more robust statistics. With help of the AVD product, the aerosol type of each aerosol extinction data point is determined before the calculation of the AOD.
Therefore, AODs are computed for each of the seven aerosol types considered by CALIOP, for both the BL and FT as further described in the Sect. 2. 2. This screening procedure leads to the global AOD averages over land and ocean listed in Table  1. Our calculated AOD values are in good agreement with those previously derived using data from CALIOP  (Winker et al. , 2013)  as well as the MODIS-Aqua instrument (Collection 6;  Levy et al. , 2013). The slightly larger values in the present study compared to  Winker et al. (2013)  are most likely due to the use of V4. 10 CALIOP data instead of CALIOP V3. Overall, more than 1. 1 million CALIOP vertical profiles are used per month; 55 % (45 %) of them are retrieved during daytime (nighttime) and 40 % (60 %) of them are retrieved over land (ocean).
ERA-Interim data The European Centre for Medium-range Weather Forecasts Re-Analysis-Interim (ERA-Interim) archive is based on data assimilation of observations, in particular from satellites, and numerical weather prediction modeling  (Berrisford et al. , 2011; Dee et al. , 2011). The boundary layer height product is diagnosed using the parcel lifting method (or bulk Richardson method) proposed by  Troen and Mahrt (1986). The product has been evaluated and showed good agreement with other methods to determine the BL height  (von Engeln and Teixeira, 2013). In this study, the ERA-Interim boundary layer height product was used at a horizontal resolution of 1 • and with a 3 h time step. Since the CALIOP spatial and temporal resolution (5 km and 6 s, respectively) is higher than ERA-Interim, the height of the BL is determined for each CALIOP vertical profile by using the corresponding ERA-Interim grid box and the closest time step.
This value is used to separate the BL and FT AOD before averaging AOD values over a 2 × 2 • grid. The different spatial and temporal resolutions between CALIOP retrievals and ERA-Interim data likely leads to spatial and temporal sampling errors  (Schutgens et al. , 2016) ; however, an increase in the horizontal resolution of ERA-Interim data from 1 to 0. 5 • changed our AOD results by only 0. 3-0. 4 %. Since the spatial sampling error does not vary significantly, we used 1 • horizontal resolution assimilation data for computational efficiency. As expected, the diurnal cycle of the ERA-Interim BL is more pronounced over land than over ocean. The global and annual average of the BL height varies from about 200 m during night to 1400 m during day above land, while it remains around 700 m over ocean both during day and night (Fig.
The annual contribution of aerosol types in the BL and FT are summarized in Table  3. It should be noted that some of the CALIOP aerosol typing will lean toward the BL or FT by design. For instance, an aerosol layer will be classified as clean marine if the layer base is below 2. 5 km, over ocean, strongly scattering and weakly depolarizing. Simi- larly, the dusty marine classification occurs for layers with bases below 2. 5 km over ocean and moderately depolarizing. The elevated smoke classification occurs for layers having tops above 2. 5 km, whereas layers having similar measured optical properties but have tops below 2. 5 km are classified as polluted continental/smoke. In Table  3 , a tiny fraction of particles classified as clean marine are found over land because CALIOP data have been averaged over a 2 × 2 • grid that can be partly land and ocean (see "Data and methods" section).
02. In terms of aerosol extinction,  Winker et al. (2013)  indicated that true aerosol extinction values of 0. 001 km -1 or less are underestimated by CALIOP, while  Sheridan et al. (2012)  showed that 95 % of aerosol extinction values larger than 0. 05 km -1 are detected, 50 % of aerosol extinction values lower than 0. 02 km -1 are undetected and almost none of them are detected below 0. 01 km -1. Although these studies used CALIOP v3 data, our results with CALIOP v4. 1 data do not show a different behavior. Indeed, the study of  Sheridan et al. (2012)  has been repeated with v4. 1 data and we arrived at the same conclusion with regards to extinction at the limits of CALIOP detection (i. e. , an underestimate of the lowest aerosol extinction values). As a consequence, the global statistics of the study are very likely biased low, in particular in the free troposphere, as they are more likely to occur in the FT than in the BL (i.
01-0. 02 km -1 occurring above 3-4 km is slightly underestimated by CALIOP. Considering two different particle types and the 23 flights separately, the fraction of AOD retrieved by LOAC in the FT is between 17 and 31 %. In comparison, the fraction of AOD retrieved by CALIOP in the FT is 30 %. These results show that CALIOP data agree well with LOAC observations even though CALIOP data are often underestimated, in particular in the FT.
Discussion and conclusion This paper examines the vertical distribution of the aerosol optical depth (AOD) through its partitioning between the boundary layer (BL) and free troposphere (FT). For this purpose, the CALIOP aerosol extinction product is combined with estimates of BL height from ERA-Interim over a 9-year period  (2007) (2008) (2009) (2010) (2011) (2012) (2013) (2014) (2015). The BL and FT contribute 69 and 31 %, respectively, of the global AOD during the day. It should be noted that although CALIOP data have often been reported as underestimated, in particular in the FT, in previous studies due to detection limitations, the case study over Aire sur l'Adour shows a good agreement between the LOAC in situ measurements and CALIOP data. The daytime annual average FT contribution ranges from about 10 % at mid-latitudes to 50 % within the tropics, likely indicating a difference in vertical transport efficiency.
Acknowledgements. This work was supported by the  Swedish National Space Board (Rymdstyrelsen). We acknowledge  ECMWF  for providing access to the  ERA-Interim Archive  (http://ecmwf. int/en/research/climate-reanalysis/era-interim, last access: April 2018), and the  ICARE Data Services and Center  (http://icare. univ-lille1. fr,last access: September 2017) for providing access to the CALIOP observations and tools to process them. Edited by: Anne Perring Reviewed by: two anonymous referees.
Code availability. All codes that have contributed to the results reported in this study are available on request. Data availability. CALIOP data have been retrieved through the ICARE Data Services and Center (http://www. icare. univ-lille1. fr, last access: April 2018) and the ERA-Interim Archive is available on the ECMWF website (http://ecmwf. int/en/research/ climate-reanalysis/era-interim, last access: September 2017).
Reorienting the measles and rubella elimination program to increase emphasis on surveillance so that programmatic and strategic deci-sions can be guided by data is critical. Many of the recommendations made in this report are directly aligned with the Global Health Security Agenda's (GHSA's) Action Packages, which are designed to prevent outbreaks, detect threats in real time, and rapidly respond to infectious disease threats. 2  A focus on measles surveillance can help detect populations unreached by immunization systems and, by extension, program weaknesses. Measles serves as the 'canary in the coal mine' for detecting problems with immunization programs, a characteristic whose importance has recently been highlighted in the context of global health security. of five core strategies. Significant gains toward measles elimination have been made.
Re-orienting the measles and rubella elimination program to increase emphasis on surveillance so that programmatic and strategic decisions can be guided by data on disease occurrence is critical. The inextricable linkage between achieving and maintaining measles and rubella elimination and strong immunization systems is repeatedly underlined in the report. Measles incidence is recognized as a marker of the success of immunization systems, and of health systems overall. Because measles is one of the most contagious of the vaccine-preventable diseases (VPDs) and virtually all measles infections are clinically manifest with rash and fever, often measles is the first recognized VPD to infect population clusters of susceptible persons. Thus, a focus on measles surveillance can help detect populations unreached by immunization systems and, by extension, program weaknesses.
Sera collected to investigate cases of rash illness with fever to diagnose measles should be tested for rubella if found to be negative for measles, or tested for both measles and rubella at the same time. The results of laboratory testing should routinely be fed back to the original health care provider and the caregiver. Training materials should be developed based on existing experience for use at global, regional and country levels to design and improve systems to collect surveillance data, as well as to understand the underlying reasons that cases are occurring and disseminate results to all levels of the system. It is critical that there be country and local level ownership and use of surveillance and outbreak data for program improvement and advocacy. Countries need to dedicate resources for surveillance and partners need to supplement resources as needed, including resources for staffing, laboratory support, training, and other operational costs.
Status EUR set the goal of reaching measles and rubella elimination and prevention of CRS by 2015. All 53 countries in the Region have two doses of MRCV in their routine immunization schedules. In 2015, reported regional coverage with MCV1 was 94% with little change in the past four years. District level data are not currently available from all countries. Significant measles outbreaks were reported in 2013 and in 2014 in Azerbaijan, Bosnia and Herzegovina, Georgia, Germany, Italy, Latvia, the Netherlands, Russian Federation, Turkey, Ukraine and the United Kingdom. There is a continuing large outbreak of rubella in Poland, although the number of cases began to decline in 2014. Most recent outbreaks of measles and rubella have occurred among the general population but some have been focused on recognized under-vaccinated groups.
Status WPR set the goal of achieving measles elimination by 2012. Although it has a goal to eliminate rubella and prevent CRS, there is currently no target year associated with this goal. In the region, 34 (92%) of 37 countries, (i. e. , all except the Lao People's Democratic Republic, Solomon Islands and Vanuatu) have two doses of MCV in their routine immunization schedules and, as of 2016, all countries and areas routinely provide at least one dose of RCV. Since 2009, both MCV1 and MCV2 coverage have been over 90% at regional level but variation exists between and within countries for which data are available, with only 33% of countries having both MCV1 >90% nationally and >80% in all districts. However, district-level data are not available in three countries: Fiji, Japan and New Zealand.
Background Surveillance data are critical to guiding measles and rubella control and eradication efforts. Surveillance enables the establishment of burden of disease and mortality, and thus plays an important role in advocacy for and prioritization of activities targeting measles and rubella. Measles cases detected by surveillance identify un-or under-vaccinated populations, highlighting geographic areas or sub-populations in which vaccination programs overall -not only those targeting measles and rubellarequire further support. Surveillance measures the best outcome indicator of disease control and eradication programs: disease incidence. Well-done outbreak investigations are an important aspect of surveillance. Such investigations are invaluable to allow understanding of who is giving disease to whom.
Discussion From 2001-2015, substantial gains were made in measles surveillance. During 2004-2011, the number of countries using case-based surveillance increased from 120 (62%) to 182 (94%); by 2015 this had increased to 189 countries. Expansion in casebased surveillance has been supported by expansion in the GMRLN. The GMRLN is a highly proficient laboratory network with a strong emphasis on quality control. It provides timely and accurate surveillance data to national programs, and has successfully introduced molecular methods for detection of measles and rubella, and genotyping. Laboratory testing has also successfully been integrated with that for other VPDs, such as yellow fever and Japanese encephalitis. The global sequence databases established for measles and rubella provide models for data sharing.
Despite these successes, the global measles and rubella surveillance system now faces four types of challenges. The first is that the system, as it currently exists, has not yet met its full potential. The second is the need to expand the system in order to better inform and guide disease control and eradication efforts as well as advocate for these. The third challenge is to ensure that data are used to the fullest extent possible. The final challenge is to ensure that funding is adequate to meet programmatic needs, particularly in an environment where measles activities supported by GPEI will be reduced. The sensitivity of surveillance is assessed using an indicator of at least two discarded measles cases per 100,000 population annually. This indicator is based upon limited data derived largely from a 2004 study which recommended 1 per 100,000 population as a minimum standard against which to compare the sensitivity of measles surveillance.
Recommendations A top priority for achieving the goals of the Measles and Rubella Strategic Plan is to enhance integrated case-based, laboratorysupported surveillance for measles and rubella. All countries must implement case-based surveillance for measles and rubella, and report case information to the WHO Regional Office on a weekly basis. A working group on surveillance and outbreak investigation and response should be developed at global level; this group should also provide guidance on linking surveillance findings with programmatic changes. Protocols should be updated or, when necessary, developed, to guide: o how to conduct outbreak investigations including: critical data to be collected; criteria for laboratory confirmation, guidelines for analysis, interpretation of analysis results, and presentation of the data (see Strategy 3 below); o setting up and strengthening surveillance systems to detect and investigate cases of rash illness and fever which could be measles or rubella, analyze the data, and interpret and disseminate the results of analysis for action and policy.
The traditional emphasis placed on vaccination coverage as opposed to incidence should be reconsidered. Conceptually, incidence is an outcome indicator, whereas coverage is an intermedi-ate indicator. In addition, administrative coverage is plagued by unreliable denominator data while precisely measuring coverage at the very high levels of coverage required to stop transmission is also technically difficult. Nonetheless, to the extent possible, coverage should be validated, and differences in coverage between MCV1 and MCV2 should be monitored. The most effective way of achieving and maintaining very high dose coverage is through the routine immunization system.
Discussion Since 2012 there has been an increased emphasis on the importance of communications, as evidenced by the creation of a dedicated post in UNICEF and the development of a strategic communications plan. While many activities demonstrate dedication and creativity, the scope of these activities -in terms of numbers reached and breadth of focus -appears limited by resources. The 40 World Health Organization. Framework for verifying elimination of measles and rubella. Weekly Epidemiological Record, 2014, 88(9):89-100. ability to argue for more resources based on the impact of communications activities is limited by a lack of data; the ability to generate such data is, in turn, limited by lack of resources. Communications teams need to have the resources to craft and test messages aimed at particular target audiences, such as politicians, public health leaders and workers, health care providers, and parents.
This report recommends focusing on improving ongoing immunization systems -although this may delay reaching measles and rubella elimination goals -in order to ensure that gains in measles and rubella control can be sustained. Reorienting the measles and rubella elimination program to increase emphasis on surveillance so that programmatic and strategic decisions can be guided by data is critical. The inextricable linkage between achieving and maintaining measles and rubella elimination and strong immunization systems is also repeatedly underlined in this report. Measles incidence is recognized as a marker of the health of immunization systems, and of health systems overall. Because of its ability to detect unreached populations and program weaknesses, measles also serves as an indicator disease, or the 'canary in the coal mine', a characteristic whose importance has recently been highlighted in the context of global health security.