dataesr/scientific-paragraphs-categorization huggingface dataset:
The majority of the Fragilaria sequences are coming from the TCC collection and are not yet published (all photos and related data are available of R-Syst website). In the Bacillariophyceae (Figure  10 ), the most sequenced genera are Nitzschia, Navicula, Gomphonema, Pinnularia, Pseudo-nitzschia, Sellaphora. In particular, Nitzschia palea, an indicator of polluted freshwaters, is the most sequenced species (respectively, 66 and 88 for 18S and rbcL sequences), because it is intensively studied  (47, 65, 66). Similarly, Gomphonema parvulum, which is also an important freshwater quality indicator species, is intensively barcoded (respectively, 51 and 54 for 18S and rbcL   (67). The Sellaphora genus is also a very well-studied genus, in particular the Sellaphora pupula species complex since it was studied as well for its reproduction mode than its phylogeny  (68) (69) (70)  and has been a model for barcode tests  (25).
Conclusion In their article, Zimmermann et al. (82)  highlight the importance of the quality of reference barcoding libraries. In particular, the traceability and availability of the metadata (sampling site, isolation protocols, pherograms, vouchers, slides, DNA, photos, etc. ) and the physical deposit of vouchers (culture, raw material, slides, DNA, etc. ) associated with the barcode are necessary for accurate biodiversity studies. Such requirements were recently integrated into a Moreover, Zimmermann et al. (82)  say that barcodes 'lacking voucher specimens. are of no future use and valuable information is lost to science'. Our position is slightly different: historical data stored in NCBI may not meet the criteria now being established in the pre-standard protocol but are nevertheless precious and are not all 'lost to science'.
Indeed, getting a clonal culture from a natural sample and then growing it until getting enough biomass to extract its DNA, to mount it for permanent slide, to treat it for scanning electron microscopy is a long and risky process (many cultures are lost before getting DNA or permanent slides). Not considering barcodes that are not backed by voucher specimens will in some cases waste valuable data for barcode reference libraries: some such barcodes have been published in peer reviewed journals and are accompanied by photographs and other metadata. These, if carefully evaluated as described in this article, before sequences are integrated into the database, can be valuable, filling gaps in the taxon coverage. Routine molecular identification of diatom taxa in natural communities to a genus level (instead to a species level) with R-Syst::diatom is not a problem  (18, 22, 84)  because taxon coverage of the reference library at a genus level in freshwaters is almost complete.
But, for molecular identification at a species level, even using all possible barcodes and after curating them (as shown in this article) before their integration in R-Syst::diatom, the library still suffers from an underrepresentation of some taxa living in particular habitats. In particular, pristine freshwater habitats and tropical rivers should be sampled more frequently to get cultures and to barcode them. This is a challenge of the next few decades. Another difficulty met in the database is that several sister species-the definition and delimitation of which are classically based on morphological criteria-display an overlap when considering their barcodes proximity. The result is that such species could be paraphyletic. This is currently the case for species in the Fragilaria capucina group (capucina, perminuta, nanoides, gracilis.
) when considering their 18S or rbcL barcodes. This type of problem also occurs, but less often, for generic levels (e. g. Surirella, Campylodiscus). Our curation procedure is not sufficient in these cases and an integrative study based on genetic data (using multiple markers), morphological data (scanning electron microscopy, light microscopy) and also ecological data must be undertaken to adjust taxonomy. A good example of such integrative studies is shown in the sister species Nitzschia soratensis/inconspicua (85, 86). More studies of this kind are required for the development of the database, in order to present well-defined and monophyletic taxa so that the molecular identifications of sequences from NGS can be done easily. Finally, barcode databases have until now linked sequences only to a taxonomic identification, together with sufficient metadata to ensure data traceability and sequence origin (e.
g. Barcoding of Life Data Systems (BOLD), http://www. boldsystems. org/). However, this information is not enough to move forward to a routine biomonitoring with metabarcoding. Ecological functions or requirements (e. g. diatom indices values in our case) of taxa are unfortunately not provided in the existing barcoding databases. Providing such information in R-Syst::diatom should enable a routine use of metabarcoding for next-generation biomonitoring  (87).
Acknowledgements R-Syst database system has been supported by annual grants of Divisions EFPA and  SPE of INRA  given to BioGeCo for collaborative work in the network. VirtualBiodiversityL@b and Declic software have been built with a grant of  Labex CEBA  ( Centre d'Etude de la Biodiversit e Amazonienne ) given to A. F. The following research programs enabled us to isolate and sequence the diatom strains: @speedID, Bibliotheque du vivant (French Barcoding of Life projects),  IperRetro  ( ANR project, France ),  Mayotte  project ( ONEMA France ), Diamed, Modelecotox (FNR projects, Luxembourg),  L. Kermarrec PhD  grant ( Asconit Consultants  and  ANRT, France). The authors thank  Agnes Rimet ,  Sonia Lacroix ,  Isabelle Huguet  for their input in the update of the database. The co-operation with Sweden was possible via funding of the  Swedish Agency for Marine and Water Management (HaV)  and the  Lakes and Watercourses Monitoring Program (FOMA-SLU ).
The multi-dimensional trade-off approach allows links with other multi-dimensional evolutionary theories of plant strategies  (Grime 1977; Southwood 1988). For instance, some outcomes of our models (predicting a decrease in trait ß), produce a syndrome of slowgrowing conservative strategy very similar to stress-tolerant strategies introduced by  Grime (1977). In a context where databases of plant traits are systematically studied to predict the effects of global changes and the variations in ecosystem services  (Lavorel and Garnier 2002) , an important issue remains open. Plant species can be classified along a trade-off between acquisition and conservation of the resource  (Díaz et al. 2004 ). Though this is clear for aboveground traits that define the leaf economic spectrum  (Wright et al.
Data were collected using an IGA-003 system (Hiden Isochema, Warrington, UK) equipped with a turbomolecular pumping system. Acetone exchanged samples were loaded into the system and degassed at 120 °C and 1 × 10 -6 mbar for 20 h to give a dry, desolvated material of typical mass ca. 50 mg. 99. 995+% grade H 2 and CH 4 were purchased from Air Liquide and used as received. High pressure (0-50 bar) gravimetric gas adsorption and desorption data were collected using a Xemis system (Hiden Isochema, Warrington, UK) equipped with a turbomolecular pumping system backed by a diaphragm pump. CH 4 isotherms (0-50 bar) were recorded at 273, 283, 293, 298, and 303 K by a temperature controlled water bath. Neutron Powder Diffraction. Neutron powder diffraction experiments were undertaken at the WISH diffractometer at the ISIS facility.
MFM-300(In) was loaded into a 6 mm diameter vanadium sample can and outgassed at 1 × 10 -7 mbar and 100 °C for 1 day. The sample was loaded into a liquid helium cryostat and cooled to 7 K for data collection. D 2 and CD 4 gas were introduced by warming the samples to 50 and 150 K, respectively, and the gas was dosed volumetrically from a calibrated volume. The gas-loaded sample was then cooled to 7 K over a period of 2 h to ensure good mobility of adsorbed D 2 and CD 4 within the crystalline structure of MFM-300(In). The sample was kept at 7 K for an additional half an hour before date collection to ensure the thermal equilibrium. Inelastic Neutron Scattering. Inelastic neutron scattering (INS) experiments were undertaken using the TOSCA spectrometer at the ISIS facility. MFM-300(In) was loaded into an 11 mm diameter vanadium sample can and outgassed at 1 × 10 -7 mbar and 100 °C for 1 day.
Thus, this study may open new investigations of binding interactions in clathrate materials when strong space confinement is considered. 3 C-H guest •••O host -H. Studies of the Rotational Motion of Adsorbed H 2 and CH 4 Molecules by INS/DFT/MD. The absolute orientation for all of the adsorbed D 2 and CD 4 molecules cannot be unambiguously determined from the NPD data due to the thermal motion of the host-guest system, despite data collection at 7 K. It is widely accepted that both of these adsorbates (H 2 and CH 4 ) act as a "free rotor" in bulk phase,  39, 40  but studies on the rotational motions and dynamics of adsorbed H 2 are still in their infancy and the dynamics of CH 4 molecules in MOFs remain unexplored. To gain insights into these properties, inelastic neutron scattering (INS) spectra were recorded for bare MFM-300(In) as a function of H 2 and CH 4 loading to investigate the rotational and vibrational properties of the host-guest system.
In all other cases, the evaluation area corresponds to the CDTi project area, as defined by APOC. Data for the target population and number of people treated in each evaluation area were obtained from the annual technical reports from each CDTi project to APOC. Treatment coverage was calculated as the percentage of the total population (≥0 years old) in the CDTi project area that was treated in a given year. For project areas where mass drug administration with ivermectin had been undertaken during years before the establishment of the APOC project an attempt was made to collect data on start year of treatment, number of years of treatment and treatment coverage from the Ministry of health and/or a non-governmental organisation that supported those early treatments. However, these data are less complete than those for the APOC period.
Parasitological surveys The parasitological evaluation involved skin snip surveys to estimate the prevalence and intensity of O. volvulus infection. All skin-snip surveys were done 11-12 months after the last ivermectin treatment round (thus just before the next distribution). In each surveyed village, all subjects aged 5 years or above who agreed to participate (or whose parents agree for them to participate in the case of children) and who voluntarily presented themselves at the screening centre for the survey were asked for identification data (name, age, sex, number of years resident). In a few surveys that were undertaken before 2011 children between 1 and 5 years of age were also examined but these results for this age group were excluded from the current analysis. For villages with less than 100 examined subjects, the examination results were combined with those for the nearest village if there existed such a village at less than 5 km distance.
For each surveyed village, the pre-control endemicity level was estimated from the map of the predicted precontrol prevalence of nodules in APOC countries, and converted to the prevalence of mf as described in the statistical classification section below. Secondly, we undertook a detailed statistical analysis to compare the observed prevalence for each surveyed village and each evaluation area with the corresponding model predictions and classify the decline in prevalence in each evaluation area as "faster than predicted", "on track" or "delayed" after taking the statistical uncertainty in the various data sources into account, as explained below.
Analysis of phase 1B evaluation data For each evaluation area we assessed whether the two criteria for stopping treatment were met after taking the statistical uncertainty in the sample data into account. As for the Phase 1a data, this was done again using a combination of Bayesian statistics and Monte Carlo sampling. For each stratum S j in an evaluation area, we define the posterior distribution of the true mf prevalence Pmf j as a beta distribution with parameters α = (m j + 1) and β = (n j m j + 1)  [42]. Here, n j is the number of individuals examined for mf and m j the number of examined individuals who were mf positive in the survey that was undertaken in stratum S j. Next, we generated draws from the posterior distributions of the true mf prevalence Pmf in the evaluation unit and the true maximum stratum prevalence of mf Pmax (i.
All surveys were reportedly undertaken according to the standard procedures as described in the Epidemiological Evaluation Guide of APOC that is based on the OCP guide for epidemiological evaluations of onchocerciasis control that has been in use in Africa for more than four decades  [46]. In almost all surveys there was direct APOC involvement in the actual survey activities in the field especially during the first years by sending technical advisors and/or APOC staff for planning, training and supervision to standardize the quality of the surveys across the countries. All survey results were reviewed by the Technical Consultative Committee of APOC, a group of experts who technically advised the programme. The data was recorded on standard forms and processed at country and APOC level for data cleaning and double data entry before forwarding the data for analysis.
5 % and a CMFL 115. 9 mf/s. That represents an enormous reduction in infection from the extreme levels of the pre-control period, but it is still significantly higher than predicted for 21 years of annual treatment with 72 % coverage at a pre-control CMFL of 70 mf/s, i. e. the local endemicity level estimated from the nodule prevalence map and the maximum endemicity level considered in the ONCHOSIM predictions. We have therefore done some ad hoc ONCHOSIM simulations for a pre-control CMFL of 115 mf/s which indicated that the observed prevalence data for Touboro after 21 years of ivermectin treatment are still broadly consistent with predictions. But it does raise the question of how many years of treatment would be required in such extremely endemic areas and whether annual treatment can ever achieve complete elimination  [50].
This is true for isolated areas where there is usually only one village per river stratum. In other areas locally available entomological data or remote sensing data on location of river rapids were used to identify high risk locations near potential vector breeding sites within each stratum and select the nearest village for the sample. These villages were likely to represent the maximum prevalence for the stratum which is the information we are interested in. For the remaining areas we selected one of the villages closest to the river (previously referred to as 1st line villages  [1] ), but there was no additional information available to guide the selection of sample villages from the set of 1st line villages. The length of river strata, with an average of 8 km and an upper limit of 20 km, falls within the active flight range of Simulium damnosum s.
The aim of this serology testing would be to provide information on exposure to transmission over the preceding 10 years. This differs from the evaluation methodology used by APOC where entomological data are collected to measure transmission but where the epidemiological data measure current infection in the human population. The thresholds also differ. The new guidelines recommend as the threshold for stopping treatment an OV16 prevalence of 0. 1 % in children below the age of 10 years but it does not provide a rationale for this figure. An important priority for further modelling research would be to clarify the relationship between different indicators and the risk of recrudescence after stopping treatment, and how this varies with endemicity levels. This would help improve decision-making on when to stop treatment which is critically important: stopping too early may result in recrudescence but stopping too late may be very costly  [2].
Acknowledgements The work presented in this paper is the result of an effective collaboration between many people and organizations at national and international levels. The Ministries of  Health of the 12 APOC countries (Burundi, Cameroon, Central African Republic, Chad, Congo, Democratic Republic of Congo, Ethiopia, Liberia, Malawi, Nigeria, Tanzania and Uganda ) were responsible for organizing and implementing most of the EPI surveys in close collaboration with APOC. We would like to acknowledge the key role played by the former and current national onchocerciasis coordinators, in particular:  Dr Onésime Ndayishemiye ,  Dr Naomi Pitchouna Awaca Uvon ,  Dr François Missamou ,  Dr Upendo Mwingira ,  Dr Benjamin Didier Biholong ,  Dr Marcelline Ntep ,  Dr Yisa Saka ,  Mr. Chukwu Okoronkwo ,  Mr Kadu Meribo ,  Mr Laston Sitima ,  Mr Tom Lakwo ,  Mr Nadjilar Lokemla ,  Dr Anacleto Sima Nsue ,  Mr Anthony K.
35). The average clutch size is B 6 eggs  35. The fluctuations in population size in this area are strongly influenced by severe winter weather causing large mortality  36. The probability of an adult to be recaptured alive was 40. 8 in this study population  34. Blue tits C. caeruleus were studied at Vlieland, which is an island in the Dutch Waddensea, and consists of mixed pine-deciduous woodland. Here almost all Blue Tits breed in nest boxes, resulting in very precise population counts. When the nestlings were 7-10 days old, the parents were caught on the nest using a spring trap. The number of fledglings was counted and ringed at day 10-15 after hatching. The collared flycatcher F. albicollis is a small migratory hole-nesting passerine  37. Data on collared flycatcher were collected in several study plots at the island of Gotland (57°30 0 N 18°33 0 E), Sweden, during the period 1986-2007 as part of a long-term study of individual-based demography and genetic, and phenotypic variation in several fitness-related traits  [38] [39] [40] [41].
Data on reproduction and survival were obtained through weekly inspection of nest boxes, and banding of chicks and adults with uniquely numbered aluminium rings. The analyses of the population dynamics of tawny owl Strix aluco and ural owl Strix uralensis were based on data collected from birds breeding in nest boxes in two Finnish study sites approximately 150 km apart  56. Females were captured during incubation and ringed if not already banded as a nestling. The tawny owl population was studied in Kirkkonummi (60°13 0 N 24°15 0 E) during the period 1978-2008. The population size was estimated based on the number of inhabited nest boxes in addition to the number birds actively responding to playback in territories where the pair was assumed to breed in natural cavities. Thus, the population estimates were likely to be precise.
Acknowledgements This study would not have been possible without the help from a large number of dedicated field workers, too numerous to thank by name. The study was financed by the  European Research Council  ( ERC-2010-AdG 268562 ) and the  Research Council of Norway  ( SFF-III 223257/F50 ). Jan Visser  managed the Coot population for many years, the data on the Blue Tits on Vlieland were collected under the supervision of Arie van Noordwijk. P. K. was funded by the  Academy of Finland  (Project  252377 ), the  Oskar O ¨flund foundation  and the  Swedish cultural foundation , and would like to thank  Kari Ahola  and  Teuvo Karstinen  for help with organizing the Tawny owl field study. During 1985During -1988During and 2000During -2003 Ural owl research was financed by the  Academy of Finland.
The invasive alien species Ambrosia artemisiifolia (common or short ragweed) is increasing its range in Europe. In the UK and the Netherlands, airborne concentrations of Ambrosia pollen are usually low. However, more than 30 Ambrosia pollen grains per cubic metre of air (above the level capable to trigger allergic symptoms) were recorded in Leicester (UK) and Leiden (NL) on 4 and 5 September 2014. The aims of this study were to determine whether the highly allergenic Ambrosia pollen recorded during the episode could be the result of long distance transport, to identify the potential sources of these pollen grains and to describe the conditions that facilitated this possible long distance transport. Airborne Ambrosia pollen data were collected at 10 sites in Europe. Back trajectory and atmospheric dispersion calculations were performed using HYSPLIT_4.
Meteorological data The overall synoptic weather situation was investigated using analysed weather maps from the UK Met Office, as well as reanalysed meteorological data and meteorological observations obtained from the National Centre for Environmental Prediction (NCEP) using the methodology given by  Stach et al. (2007)  and  Kasprzyk et al. (2011). Synoptic charts were obtained from the website: http://www. wetterzentrale. de/topkarten/tkfaxbraar. htm.
All calculated trajectories examined in this study showed little variation with respect to transport path  (Stach et al. 2007). Input meteorological data for 1-7 September 2014 came from the Global Data Analysis System (GDAS) dataset provided by the NCEP that covers the period 2006 to present in the form of a 1°latitude-longitude grid (https://ready. arl. noaa. gov/gdas1. php).
0156 m/s which corresponds to the settling velocity of Ambrosia artemisiifolia pollen grains  (Raynor et al. 1970 ) and applying the conversion module that deposits each particle rather than reduce their mass. The starting locations for the particles released into the dispersion model were previously identified as being the most important source areas for Ambrosia pollen on the Pannonian Plain  (Skjøth et al. 2010)  and France  (Thibaudon et al. 2014 ) (Fig. 1 ). These source areas had been identified by the use of detailed knowledge of Ambrosia ecology, land cover information and spatial variations in the annual sum of atmospheric Ambrosia pollen concentrations. Simulations of particle deposition using the HYSPLIT_4 were conducted again in order to determine whether Ambrosia pollen travelling at the height of air masses (as described by back trajectories) could settle out from the atmosphere to reach ground level monitoring sites.
Acknowledgments The results presented here address one of the scientific challenges described in the  COST Action SMARTER. CHP is supported by the  Midlands Asthma and Allergy Research Association (MAARA)  and the  National Institute for Health Research Leicester Fig. 6 The output of the HYSPLIT model calculations of the distribution of particles released from 6 to 14 h at the location air masses pass on 5 September 2014, 6 h before arrival to Leicester (a) and  Leiden  (b).
We hope this work will stimulate and provide a benchmark for future experimental studies on systems undergoing a continuous yielding transition, for which detailed data on noise statistics is presently very scarce. JLB, EEF and CL acknowledge financial support from ERC grant ADG20110209. JLB is supported by IUF. KM acknowledges financial support from grant ANR-14-CE32-0005 (project FAPRES). EEF and JLB acknowledge the hospitality of the KITP, supported in part by the National Science Foundation under Grant No. NSF PHY11-25915. Most of the computations were performed using the Froggy platform of the CIMENT infrastructure supported by the Rhône-Alpes region (GRANT CPER07-13 CIRA) and the Equip@Meso project (reference ANR-10-EQPX-29-01). Further we would like to thank Alexandre Nicolas, Elisabeth Agoritsas, Eric Bertin, Jordi Ortín and Stéphane Santucci for fruitful discussions, and Mark Robbins and Matthieu Wyart for a useful correspondence.