dataesr/scientific-paragraphs-categorization huggingface dataset:
As in other climatologies, the meandering, together with the seasonal and interannual variations of the current position, enlarges the width of the jets in the climatological fields compared with the instantaneous characteristics of the currents. At the same time, the geostrophic currents, derived from the MEDTRANS climatology, reveal several features not reproduced by the existing climatologies but in close correspondence to independent observations (e. g. Lozier et al. , 1995; New et al. , 2001)  and theory (Cushman-Rosin, 2010): (i) periodic intensification of the AzC as it turns south in quasistationary meanders; (ii) inflows and outflows in the AzC meanders; (iii) recirculation of the AzC west of the Cruiser-Great Meteor seamounts; and (iv) a cyclonic beta gyre in the Gulf of Cadiz. At 1000 m depth, the geostrophic currents referring to the 1900 m level, derived from the MEDTRANS data set, show two veins of the MUC along the western slope of the Iberian Peninsula: one travels along the slope, while the other separates from the slope around the Gorringe Bank and then merges with the other vein, south of the Galicia Bank.
Acknowledgements. The authors acknowledge the  MEDTRANS scientific project  ( PTDC/MAR/117265/2010 ), sponsored by the  Portuguese Foundation for Science and Technology (FCT)  and the  MARE -Marine and Environmental Sciences Centre of Oceanography of the University of Lisbon  ( CO-Pest-OE/MAR/UI0199/2011 ). I. Bashmachnikov also acknowledges contract  C2008-UL-CO-3  of Ciência 2008 between the  Foundation for Science and Technology (FCT)  and the  University of Lisbon  (UL). Edited by:  D. Stevens.
The morphing approach combines the rural temperature and the monthly average UCM temperature to give an hourly temperature including the urban heat island. This method requires weather forecast data in order to run the meso-scale model by downscaling of the reanalyses. Bueno et al. (2013)  and  Erell and Williamson (2006)  developed two other methods, adapted from an UCM approach, the urban weather generator (UWG) and the canyon air temperature (CAT) model. Both methods just need one point of measurement outside of the city exposed to the same meso-scale climatic conditions, like an operational measure station at an airport for example. The weather data from Typical Meteorological Year 3  (Wilcox and Marion, 2008)  or from the software Meteonorm  (Remund, 2008)  provide appropriate files for these models.
1-A ) and the timescale of this migration was recorded for each experiment. By combining this extensive dataset with in situ oxygen measurements, EPS concentration and surface charge quantification, rheology experiments and microscopic observations, we rule out the influence of gas vesicles on this process and evidence the coupled roles of photosynthetically-produced oxygen accumulation and anionic EPS-mediated cell aggregation following salt addition on blooming. The mechanism of collective upward biomass migration identified here relies on the trapping of oxygen bubbles within cell clusters that provide a buoyant lift to the biomass and can occur within timescales as short as 30 minutes.
In order to quantify the extent and dynamics of this aggregation, we monitored the rheological properties of the cyanobacterial culture over time as a proxy for the evolution of the biomass microstructure. The data shown in Fig. 3-C  indicate that the low-shear viscosity was constant around * 0. 1Pa. s before nutrient addition. Following the sudden addition of BG11, the viscosity increased roughly by an order of magnitude. Fitting the data with a simple exponential yielded a characteristic timescale of 15min for the aggregation dynamic. Given the typical metabolic timescales of M. aeruginosa (doubling time * 50 hours), this timescale is not compatible with the production of significant amounts of extracellular materials. To further establish that irreversible blooming depends on the presence of extracellular components present before BG11 addition, we first separated the cells from the EPS.
Anionic EPS-cations interactions trigger biomass flocculation In order to further pinpoint the mechanisms leading to the aggregation and blooming of the biomass, we individually tested the effect of the various components of the BG11 nutritive medium. It clearly appeared that sodium nitrate could induce bloom formation although at a slightly higher threshold than when NaNO 3 was dispensed with the other components of the BG11 medium. This reveals a synergistic effect between the various salts present in the BG11 medium. To discriminate between sodium and nitrate, we then assayed bloom formation following the addition of various other salts. The data presented in Table  1  show that Na + , as well as other cations, could trigger the aggregation of the biomass. When the cation chelator EDTA was added to the culture with the salts, bloom formation was suppressed.
The genome starting point and the position of a putative Direct Terminal Repeat (DTR) were revealed by a particular distribution of the sequencing reads or by comparison with closely related phages. Multiple alignments were performed using the Geneious 8. 1 software platform (Biomatters Ltd, Auckland, New Zealand) running MAFFT  [41]. Annotation of open reading frames (ORF) was performed with RAST  [42] , using a 0. 1 blastp E-value cut-off, and ARAGORN was applied to localize tRNA genes  [43]. SNPs identification, Minimum spanning tree, and dN/dS analyses were performed in BioNumerics version 7. 5 using the full bacteriophage sequences. Phage genome assemblies have been deposited to EBI/EMBL: Ab02 LN610572, Ab03 LN610573, Ab04 LN610581, Ab05 LN610574, Ab06 LN610582, Ab08 LN610575, Ab10 LN610586, Ab11 LN610583, Ab15 LN610587, Ab17 LN610576, Ab18 LN610577, Ab19 LN610584, Ab20 LN610585, Ab22 LN610578, Ab27 LN610579, Ab28 LN610589, Ab29 LN610588, Ab30 LN610590, 1-15 pyo LN610580.
The water sample origin, the date of isolation and the bacterial strains used to isolate and amplify new phages are summarized in Table  1. Interestingly, phage Ab22 produced both clear and turbid plaques on strain C2-10, in high density zones, and this phenotype was seen even after replating of a clear or a turbid plaque (S1 Fig). A similar phenotype was previously observed with phage p2-10 0r , a LUZ24-like phage isolated in Orsay, France  [26] , and with other phages of this genus  [44]. Phage Ab05 produced clear plaques on PA14 and PA01, and a halo was seen on PA14. Phage 1-15 pyo , a ɸKMV-like phage isolated from Pyo-Phage and used here as a control, made similar plaques with a halo on PAO1  [26]. All phage genomes were digested with different restriction enzymes, showing that the banding pattern were identical or very similar in some phages, whereas others had specific profiles (data not shown).
A region of 827bp, present in JG004 only (position 34,438 to 35,264), encompassed the gene for an endonuclease (PJG4_070), inserted between the genes homologous to Ab02 ORF62 and ORF63. A 21 bp polymorphism in the phages of this group corresponded to the length of a short duplication. It encoded a seven amino acid peptide (VGAPWYS), part of the hypothetical ORF75 of phage Ab02, containing a putative leucine zipper-like domain. Phages Ab02, Ab15, Ab24 and Ab25 had one copy whereas the other phages had two copies, and this polymorphism was confirmed by PCR amplification (data not shown). KPP10-like viruses. Five phages (Ab03, Ab04, Ab06, Ab11, Ab17) isolated in 2010 and 2011 at four different locations in Abidjan, belonged to the KPP10-like virulent phage genus. They were all different, and shared 88-96% sequence identity with the genomes of KPP10 from Japan  [27] , and PAK_P3 from France  [23, 45].
Acknowledgments We are grateful to  Nanga Zinzendorf  ( LNSP, Abidjan ) and  Timothée Ouassa  ( CeDRes, Abidjan ) for their precious help in isolating new bacteriophages. We thank  Jeremy Brunet  and  Adrien Bouchard  for their contribution to the study of lysogeny, and  Maxime Appé  for bioinformatics investigations. The work has benefited from the facilities and expertise of the  Imagif Cell Biology Unit of the Gif campus  (www. imagif. cnrs. fr).
, 2008). At present, GALION consists of eight existing and developing networks (two operative networks operating backscatter systems working on a constant (24/7) basis, and six research networks) in different regions of the globe: Among those networks, EARLINET is the only one operating a majority of advanced Raman systems  (Pappalardo et al. , 2014). EARLINET (www. earlinet. org), established in 2000, is the first coordinated aerosol lidar network whose key goal is the provision of a comprehensive, quantitative, and statistically significant database on the spatial and temporal aerosol distribution on a continental scale  (Bösenberg, et al. , 2001; Pappalardo et al. , 2014). At present, the network includes 27 active stations distributed over Europe  (Pappalardo et al. , 2014). Lidar observations within the network are performed on a regular schedule of one daytime measurement per week around 12 solar time, when the boundary layer is usually well developed, and two night time measurements per week, with low background light, in order to perform Raman extinction measurements.
, 2010; Belegante et al. , 2015; Bravo-Aranda et al. , 2015; Freudenthaler et al. , 2015b)  and error characterization  (Engelmann et al. , 2015; Amodeo et al. , 2015). The SCC is installed on a common server accessible by all EARLINET stations through a web interface which improves the user friendliness of the SCC. All the details of the SCC modules are described in this special issue  (D'Amico at al. , 2015a, b; Mattis et al. , 2015). For the exercise the SCC was configured to provide two kinds of aerosol products: -SCC-1: pre-processed range-square corrected signal (RCS) in netcdf format generated by the ELPP module from the raw netcdf files submitted by each station. These products were generated in a full automatic way and in real time. At the same time the ELPP outputs were stored, an email was automatically sent to the contact point of the originating station.
Statistics of the SCC results during the campaign As summarized in Table  3 , a total of 665 files were sent to the SCC. The ELPP module was successful in pre-processing 650 of them (98 %). For a minor subset (15 files) the signal quality was not sufficient to pass ELPP quality control tests in two procedures: in applying the gluing algorithm and the dead time correction to photon-counting channels. The automatic procedure of gluing between analog and corresponding photon-counting signals consists of enhancing the detected dynamic range using the analog profile in the strong signal region and the photon-counting profile in the weak signal region. The gluing algorithm implemented in ELPP tries to find the optimal region where to combine the two signals performing a set of statistical and consistency tests  (D'Amico et al.
In those cases, ELDA returns the error code "No valid data points for calibration". In particular, it has been verified for the SCC-1 products that 28 (out of 60) cases for which ELDA could not find a calibration interval with the required accuracy contained clouds. The rest of the cases (32) were due mostly to problems in inverting the ultraviolet wavelengths (351 and 355 nm, 28 cases) and only occasionally 1064 nm (4 cases). The inversion at 532 nm was always successful. Among those 32 cases, the impossibility of finding a calibration interval occurred a little more during daytime when applying the elastic algorithm (18 cases) than during nighttime when applying the Raman algorithm (14 cases). All 32 cases occurred at four stations (CL: 1; LA: 10, PO: 8, AT: 13) which means that the SCC could always find a suitable calibration interval at the other six stations (leaving apart the cloud cases).
Finally, in a non-negligible number of cases (21, 17 % of the cases for which ELDA could not successfully perform the optical processing) the reason has a computing origin. We have checked that in 17 cases, the profiles were contaminated by clouds and that in 4 cases (all of them in BA) the computing error was raised during the elastic inversion at 355 nm. In summary, this statistical analysis allows for the identification of the most critical/sensitive products and steps of the optical processing module of the SCC. Throughout the exercise, with the exception of the cloud cases, ELDA is unable to finalize the inversion with the required accuracy in two main steps of the processing: in the search of a calibration interval and in the iterative procedure of the method used to invert the backscatter coefficient from elastic signals only.
Backscatter coefficient profiles at several wavelengths (SCC-2 products) The ELDA module of the SCC provides inversions of the aerosol optical properties. During daytime all elastic wavelengths are inverted by means of the iterative method  (Di Girolamo et al. , 1999; Masci, 1999; Mattis et al. , 2015). Figures 7 and 8 show the temporal evolution of the profiles of the backscatter coefficient at all stations with at least two wavelengths on J10. Figure  7  reports the results at the Iberian stations and Fig. 8  at the central and eastern European stations. All the profiles are reported as a function of height above mean sea level. This is the reason why the different stations present profiles starting at different heights in agreement with their respective altitudes above sea level. Some inversions are missing in the middle of the day in MA, BA,   1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2 1 2  RSCS [a.
The real-time requirement is an important issue because SCC-2 products are needed for the evaluation of operational dust models. The potential operationality of EARLINET, but not only, is also fundamental for the reliability of mineral dust forecasting and early warning system such as the WMO Sand and Dust Storm Warning Advisory and Assessment System (SDS-WAS) which usually relies on the output of several models (see http://sds-was. aemet. es/). The use of aerosol data for assimilation in a numerical weather prediction model is very recent:  Collins et al. (2001)  and  Rasch et al. (2001)  focused on regional studies while  Benedetti et al. (2009)  assimilated aerosol data globally. At the global scale, the first attempt was made with aerosol optical depth from satellite sensors. Again, like in air quality modeling, the information on the vertical distribution of the aerosols is not taken into account.
As far as we know, aerosol lidar data have never been assimilated in a weather prediction model, the main reason being that the development of aerosol modules for weather prediction model is relatively new. So there is a large community that will be interested, most likely in the near future, in using aerosol lidar data for assimilation in weather prediction models. The EARLINET 72 h measurement exercise is a great opportunity for weather modelers to investigate the feasibility of lidar data assimilation in weather forecast modeling at the regional scale in a first approach. For the assimilation to be efficient, a lot of research remains to be done in that field, in particular on the coupling of the aerosol module with the meteorology and generally on the aerosol interactions with the atmospheric system as a whole.
Calibration/validation activities of spaceborne lidars The validation of ongoing and the preparation of future satellite-based lidars has been and still is a continuous activity of EARLINET that started before the launch in 2006 of the Cloud Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) mission. At network level, a measurement plan was developed and optimized. The coordinated efforts permitted to validate at continental scale different CALIPSO products and to foster new improvements in CALIPSO data (e. g. Pappalardo et al. , 2010 , Wandinger et al. , 2011). Collected measurements (The EARLINET publishing group  [2000] [2001] [2002] [2003] [2004] [2005] [2006] [2007] [2008] [2009] [2010] 2014)  were the pillar for investigating the effects of local variability on validation studies (e.
g. Mamouri et al. , 2009; Mona et al. , 2009). Today, EAR-LINET activities in satellite data validation have increased: investigation of climatological CALIPSO products, and participation in design and optimization of lidar measurements for next-to-come lidar-based satellite missions like ADM-Aeolus (and EarthCARE (Earth Clouds, Aerosols and Radiation Explorer). Moreover within the Copernicus programme, other sensors will be launched in space for aerosol monitoring at global and continental scale. EARLINET is already committed by the European Space Agency (ESA) for the validation of ADM-Aeolus and Copernicus Sentinel-5 Precursor missions. All those activities will require important efforts for performing, analyzing using measurements for validation studies. The use of the SCC would represent a valuable help for calibration/validation activities of spaceborne lidars by reducing the efforts of data manipulation.
For the first time, the single calculus chain developed within EARLINET was used in real time for a multitude of different systems: the pre-processing of the data (ELPP module, SCC-1 products) was performed in real time while the optical processing (ELDA module, SCC-2 products) was performed in near-real time. ELPP was configured in such a way that at the same time that the outputs were stored, an email was automatically sent to the contact point of the originating station. This email gave a real-time feedback from the SCC about the pre-processing status and revealed to be extremely useful for real-time fine tuning the SCC configuration of each individual system and of its associated products. Three parameters of the product configuration revealed themselves as being especially critical for ELDA processing: the detection limit parameter and the maximum allowed statistical errors (below and above 2 km).
In order to homogenize and guarantee the same order of magnitude of the overall error associated to the final products, independently of the systems, those parameters were set to the same value for all products. A total of 665 files were sent to the SCC. Out of them the ELPP module pre-processed successfully 650 files (98 %), while the ELDA module processed successfully 527 files (79 %). This percentage is quite large taking into account that no cloud screening was performed on the lidar data. After an a posteriori manual cloud screening this percentage rises to 87 %. At the pre-processing level, the raw data quality was not sufficient to pass ELPP quality control tests in two procedures: in applying the gluing algorithm and the dead time correction to photon-counting channels. At the optical processing level, ELDA was unable to finalize the inversion with the required accuracy in two main steps of the processing: in the search of a calibration interval and in the iterative procedure of the method used to invert the backscatter coefficient from elastic signals only.
Unsuccessful inversions occurred at 355 nm in 94 % of the cases (at 1064 nm in the rest of them). Among the unsuccessful inversions at 355 nm, 78 % of them occurred during the elastic inversion (daytime) and 22 % during the Raman inversion (nighttime). Low signal-to-noise ratios of the 355 nm channels, especially during daytime, emerged as a critical issue common to most of the systems involved in the exercise. Some initiatives are already ongoing to tackle some of the problems encountered during the analysis of the 72 h database: (1) the developers of ELPP are working on the development of a reliable and robust cloud screening  (D'Amico et al. , 2015a)  and (2) in the framework of the ongoing ACTRIS-2 project, EARLINET is working on the setup of a multi-wavelength post-retrieval quality check procedure for both SCC and manual inversions.
More generally, the outputs of the exercise are valuable information in fields such as the monitoring of special events, atmospheric modeling, climate research and calibration/validation activities of spaceborne lidars. The efforts made to define the measurements protocol and to configure properly the SCC makes the operationality exercise repeatable for any of the applications above mentioned. In the meantime, the EARLINET community is working on three aspects that will significantly improve the operationality of the network and the quality of the products delivered in real time by the SCC, at the hardware level, on the capability of daytime Raman measurements and at the software level on cloud screening and on smoothing procedure of daytime data.
Acknowledgements. The financial support for EARLINET in the ACTRIS Research Infrastructure Project by the  European Union 's  Horizon 2020 research and innovation programme  under grant agreement no. 654169  and previously under grant agreement no. 262254  in the 7th  Framework Programme  ( FP7/2007-2013 ) is gratefully acknowledged. Measurements in Barcelona are supported by the  Spanish Ministry of Economy and Competitiveness  (project  TEC2012-34575 ) and of  Science and Innovation  project  UNPC10-4E  and  FEDER  funds, and by the  Department of Economy and Knowledge fo the Catalan autonomous government  (grant  2014 SGR 583 ). Research activities in Granada are supported by the  Spanish Ministry of Economy and Competitiveness  through the project  CGL2013-45410-R  and by the  Andalusia Regional Government  through projects  P10-RNM-6299  and  P12-RNM-2409.
Measurements in Évora were supported by  FCT (Fundação para a Ciência e a Tecnologia)  through the project  PTDC/GEO-MET/4222/2012  and grants  SFRH/BD/47521/2008  and  SFRH/BPD/81132/2011. This project has also received funding from the  European Union 's  Seventh Framework Programme  for research, technological development and demonstration under grant agreement no. 289923 -ITaRS. The authors gratefully acknowledge the  NOAA Air Resources Laboratory (ARL)  for the provision of the HYSPLIT transport and dispersion model and READY website (http://www. arl. noaa. gov/ready. html). Edited by:  A. Ansmann.
HT-TPM setup and procedure HT-TPM on chip assembly and the experimental setup are such as described in  (38). The DNA/particle complexes were visualized in TPM buffer with an ionic strength of 165 mM (1. 06 mM KH 2 PO 4 , 3. 00 mM Na 2 HPO 4 , 154 mM NaCl, 1 mg. mL -1 Pluronic F127, 0. 1mg. mL -  BSA) at 21 ± 1°C using a dark-field microscope (Axiovert 200, Zeiss). Acquisitions of 5 min were performed at a recording rate of 25 Hz with acquisition time of 40ms on a CMOS camera Dalsa Falcon 1. 4M100. The field of observation covers an area of ~ 215 µm x 160 µm. Details can be found in SI text. The software Nanomultiplex co-developed with Magellium Toulouse (request should be addressed at info@magellium. fr) tracks in real time the positions of all the particles using the centroid method, averages these absolute positions on a 5 s window giving access to the anchoring point of the DNA molecule, calculates the 2Dvector positions of the bead ∥ relative to the anchoring point of the DNA which corrects for experimental drift, calculates the asymmetry factor of the particle trajectories  (41) , and the amplitude of motion of the particle defined as √〈 ∥ 〉 and noted Rexp||raw.
Methods Museum acronyms follow Sabaj Pérez (2014). Specimens were examined in the collections of the British Museum of Natural History, UK (BMNH); Muséum national d'Histoire naturelle, France (MNHN); Naturhistorisches Museum Basel, Switzerland (NMB); and National Museum of Sri Lanka (NMSL). Morphometric and meristic data for species comparisons were obtained from examined specimens (see Appendix 1). We checked the external morphology of specimens with a Wild M3Z stereomicroscope and photographed them with a Canon EOS 7D SLR digital camera. The map was constructed based on  Cooray (1967). The conservation status of the species was evaluated using Red List Categories and Criteria in IUCN Standards and Petitions Subcommittee (2013: version 10. 1) to assess their risk of extinction. Sex was determined by ventral tail incision of adult specimens followed by the checking for the presence or absence of hemipenes.