dataesr/scientific-paragraphs-categorization huggingface dataset:
The polymerase gene encoded a 6,285-nt long ORF (2,095 AA), whereas the glycoprotein gene encoded a 4,002-nt long ORFs  (1, 334). The small segment encoded a 942-nt and a 762-nt long ORF which were translated to a nucleocapsid protein (314AA) and a non-structural protein (254AA), respectively. The complete genome of the CFUV consisted of 6,453nts, 4,329nts, and 1,704nts for the L, M and S segment, respectively (Genbank acc. no KR106177, KR106178, and KR106179). The polymerase gene encoded a 6270-nt long ORF (2,090AA), whereas the glycoprotein gene encoded a 4,077-nt long ORFs (1,359 AA). The small segment encoded a 738-nt and a 780-nt long ORF which were translated to a nucleocapsid protein (246AA) and a non-structural protein (260AA), respectively.
Genotyping the sandflies of virus-positive pools Genotyping was performed for 7 pools. The species composition of the pools and number of reads are shown in Table  2. NGS reads were compared with available sequences in Genbank (Genbank accession numbers: KT634318, KF483675, KR349298, JQ769142, KF137560, KJ481126) by Blastn using the CLC Genomic Workbench 6. 5. The species were determined when the consensus sequences had 98% similarity with the regional reference sequences except Sergentomyia sp. sequences which had 85% similarity with S. dentata from Adana (Genbank accession numbers: KU659595, KU659596, KU659597, KU659598; release date 01 July 2016). Therefore we indicated these sequences as Sergentomyia sp.
There is no doubt that SFSV "historic strains" were causing massive outbreak of debilitation and incapacitating disease  [12, 40, 41]. Moreover, SFCV was also isolated from human cases  [42, 43] , as well as SFTV  [13]. Antibodies against CFUV / SFSV were reported in humans living in mainland Greece and on Corfu Island using the immunofluorescence assay (IFA)  [44]. Viral RNA of Chios virus, closely related to CFUV, was detected in the CSF of a patient presenting with severe encephalitis (Papa and Pavlidou, 2003, Genbank no, AY293623). In contrast, specific antibodies were never described in humans for THEV  [12] , although SFNV a close relative of THEV and subsequently ZERV was undoubtedly the cause of explosive outbreaks in newcomers to endemic areas during summertime  [9]. Importantly, although serological studies have not yet been reported we do have serological data to support the concept that the newly isolated ZERV and TORV can infect vertebrates.
This situation applies for viruses that may belong to (i) the SFNV species such as FERV  [2] , Provincia virus  [48] , Girne1 virus  [18] , and Saddaguia virus  [45] , (ii) the SALV species such as Adria virus  [46, 47]  Olbia virus  [48]  and Edirne virus  [18] , and to (iii) the SFSV / CFUV complex such as Chios virus  (Papa and Pavlidou, 2003 , Genbank no, AY293623), Utique virus  [4] , Girne2 virus  [18] , SFS-like viruses  [4, 42, 43, 49]. Accordingly, although our knowledge of sandfly-borne phleboviruses is more extensive than it was a half-decade ago; efforts to isolate virus strains and determine their complete sequence should continue. Since virus taxonomy for the Phlebovirus genus still relies on neutralisationbased antigenic relationships, virus isolation is also essential. Nevertheless, the criteria for taxonomy appear to be evolving towards full-length genome comparative analysis.
This work was supported in part by (i) by the  European Virus Archive goes Global (EVAg)  project that has received funding from the  European Union  s  Horizon 2020 research and innovation programme  under grant agreement No  653316 , (ii) the EDENext FP7-n°261504  EU  project and this paper is catalogued by the EDENext Steering Committee as EDENext448 (http://www. edenext. eu). The work of RNC was done under the frame of EurNegVec  COST Action   TD1303. The funders had.
Plant Material Broomrape seeds (P. aegyptiaca, O. cernua, O. crenata, O. cumana, O. foetida, O. hederae, O. minor, and P. ramosa) were either obtained from international collections or collected during field sampling by GEVES, Syngenta, Terres Inovia, or University of Nantes. Available data concerning the tested seed lots are summarized in Table  1.
aegyptiaca. To control the identification made by HRM, sequencing of the pseudogenes trnL and rbcL was performed on all the analyzed DNA extracts. Sequences were submitted to GenBank and are available with accession numbers KX539159-KX539172. Comparison of the HRM and sequencing interpretations is presented in Table  1. Concerning the targeted species, results show a 100% match between interpretations obtained using both techniques. Furthermore, all the samples identified as non-target by sequencing are designated as non-identifiable by HRM. It is interesting to note that identifications performed by sequencing are not always consistent with primary identification based on visual criteria. For samples 38 and 39 visually identified as O. purpurea and O. flava, HRM identifications as O. hederae are consistent with sequencing results, suggesting that the HRM identification is correct and that the initial morphological identification failed.
conservationevidence. com/site/page?view=methods), but must be clearly explained and transparent to maintain rigour and replicability. As the two projects selected methodological approaches from adjacent levels of the 4S hierarchy (Fig. 2 ), they articulated together well as a combined work programme. As indicated in Fig. 1 , the systematic search became the main source of literature for the collated synopsis. Step 1: systematic literature search Following the guidelines for environmental systematic reviews (Collaboration for Environmental Evidence 2013), a systematic literature search was undertaken by librarians at l'Institut National de la Recherche Agronomique (INRA, France), using CAB Abstract as the main database, complemented by Web of Science (both searched 1973-July 2012). The search equation comprised strings of relevant terms in English, including a comprehensive list of pest groups (from INRA HYPPZ9; http://www7.
Retained studies were tagged according to the practice(s) they tested, and compiled into a Microsoft Access database. This final database could be considered an unpublished systematic map (a catalogue or database of available evidence, as defined in  Dicks et al. 2014b; James et al. 2016 ), and contained 3947 individual studies (see ''Results'' section). This volume of literature could not be summarised in full with the available resources, so we selected a subset of practices for which to summarise and assess evidence. To prioritize a subset of practices to be summarised, we asked stakeholders from the food production industry, agricultural policy and academia to select practices for which they would most like to see evidence summarised (Fig. 1 , stakeholder interaction 4). A prioritisation exercise was repeated four times with different groups of eight stakeholders (similar methods described in  Sutherland et al.
The evidence for the shortlisted subset of 22 practices is fully summarised in  Wright et al. (2013) , also available as an open access searchable database of practices online (http://www. conservationevidence. com). These practices have between 1 and 19 relevant studies (numbers given in Table  2  for 20 practices assessed at the next stage), with 'Convert to organic farming' (19 studies) and 'Create beetle banks' (18 studies) having the most.
Acknowledgments Elements of this work were funded by the  European Commission  under its 7th framework programme ( BiodiversityKnowledge  project, Grant number:  265299 ), the  Natural Environment Research Council (NERC)'s Knowledge Exchange Programme on Sustainable Food Production  (Grant code:  NE/K001191/1 ) and Waitrose plc. L. V. D is funded by  NERC  under the  Biodiversity and Ecosystem Service Sustainability (BESS) Programme  (Grant code:  NE/K015419/1 ). We are grateful to all policymakers, practitioners and scientists who participated in the consultations. B. L. is very grateful to  Sophie Le Perchec  and  Anne-Sophie Grenier  ( INRA ) for tremendous help with searches in CAB Abstracts.
Secondly, MASC provides a holistic view of the various performances of the cropping system, because it takes into account the conflicting objectives underlying the economic, social and environmental dimensions of sustainability. Thirdly, this model was also chosen because it can handle various sources of knowledge, managing both quantitative and qualitative information, in the assessment of cropping system performances. MASC was implemented within DEXi computer software  (Bohanec, 2014). This software can be used to design qualitative multicriteria models breaking decision problems down into smaller, less complex subproblems formulated in terms of a hierarchy of criteria and aggregation functions. Through this formalism, MASC conceptualises the sustainability assessment problem by breaking it down into the three classical dimensions used to define sustainability  (social, economic and environmental; Ikerd, 1993 , United Nations, 1996).
Twenty indicators are based on quantitative variables obtained by calculation. For this type of indicator, quantitative values are converted into qualitative variables compatible with the DEXi software through the use of locally defined thresholds. For instance, for the criterion "Profitability", results for the semi-net margin are based on threshold values covering the diversity of the margin observed in a region (e. g. : Very low ≤ €200 /ha ≤ Medium to low ≤ €400/ha ≤ Medium to high ≤ €600/ha). The other 13 indicators are classified as "mixed" as they can deal with both qualitative and quantitative data. These indicators are developed in DEXi software by disaggregating a basic criterion in a subtree, the inputs of which are obtained from a qualitative description of the system or by simple calculation, with the use of threshold values for conversion into qualitative inputs.
, 2012b). In this study, we performed assessments with the weights assigned by the designers of the MASC model (Figure  2 ). Using the aggregation devices of the MASC model, it is possible to rank the cropping systems according to their overall sustainability and its three dimensions (i. e. economic, social, and environmental). In DEXi software, an ordinal scale is associated with each qualitative scale (e. g. very low=1, low=2, … , very high=5). The mean and standard deviation of the ordinal scales can therefore be calculated and used to represent the results. Relative to the first version published by  Sadok et al. (2009) , the second version of the model, as used here, presents several improvements that helped to delimit the outline of this assessment. The designers made use of feedback from the initial users  (Craheix et al.
Description of the cropping systems evaluated In this study, 31 cropping systems were selected from both farm-based and experimental station sites, to represent a wide diversity of practices, from ploughed systems with short crop rotations to systems in which the principles of CA were fully applied (Table  3 ). The description of these cropping systems was based on a list of farming practices and the yields obtained for each crop, through a combination of recorded data and expertise. The cropping systems were collected from six different regions of France (i. e. Haute-Normandie, Champagne-Ardenne, Rhône-Alpes, Centre, Aquitaine, Franche-Comté), so as to take into account various pedoclimatic contexts. In terms of economic data, we considered, for all the cropping systems assessed, the same purchase prices for inputs and selling prices for crops, based on the average over the preceding five years  (i.
Acknowlegements The authors would like to thank  Ms N. Landé  (CETIOM),  J. Peigné  (ISARA),  N. Torrès (Vivescia), M. M. F Hirissou (Chambre d'Agriculture de la Dordogne) and B. Omon (Chambre d'Agriculture de l'Eure)  for providing them with data for this analysis. This work was carried out with the financial support of the  ANR-Agence Nationale de la Recherche  (The  French National Research Agency)  under the Programme national de recherches écoSystèmes,  Territoires, Ressources vivantes et agricultures (Systerra)  project  ANR-08-STRA-10 , PEPITES.
Frequency sweeps, strain sweep and stress relaxation measurements were performed. The extent of the linear regime was probed by running strain sweeps typically at a frequency of 1 rad/s. Frequency sweeps and stress relaxation were performed in the linear regime, with amplitude of the applied shear strain typically between 1 and 20%. Some additional tests were performed by loading a freshly prepared sample in the Couette cell of the rheometer and probing regularly the viscoelasticity of the sample over a period of 8 days. The results are shown in Supplementary data and demonstrate that the sample loading does not play any role on the gelation process. Scattering experiments. Details concerning the experimental conditions for the scattering experiments are described in  Dahesh et al. , 2014.
In brief, small-angle scattering experiments were conducted on different instruments using either X-ray or neutron beam. For the very low wave vector range (2. 10 -3 -10 -1 nm -1 ), data were measured using neutrons on the KWS3 instrument operated by FRMII at the Heinz Maier-Leibnitz Zentrum, Garching, Germany. The ID2 beam line of the European Synchrotron radiation facilities (ESRF) at Grenoble, France, was used for the measurement of the intensity scattered in the intermediate q-range (0. 04 -1. 5 nm -1 ). Finally, an X-ray laboratory set-up was used to measure data at large wave vectors. Infrared Spectroscopy. Fourier Transformed InfraRed (FTIR) spectroscopy experiments were performed on an Alpha FTIR Bruker apparatus equipped with the single reflection diamond Attenuated Total Reflection (ATR) module.
Origin of the spontaneous gelation process To get some insight about the physical origin of the slow gelation, we first have measured over ageing time the molecular weight distribution of the proteins using high-performance liquid chromatography (HPLC) in a SDS-buffer (this buffer is expected to disrupt all weak bonds). Data (Fig. 7 ) clearly show a weak but continuous decrease of the peak corresponding to low molecular weight (MW) proteins (gliadin, MW around 30 kDa) and the region corresponding to (short) glutenin polymers (MW in the range 80-300 kDa). By contrast, the excluded peaks related to very large assemblies of proteins increases. New interchain disulfide bonds arising from disulfide /thiol exchange or thiol oxidation, as observed upon heating and/or mixing of gluten  (Morel et al.
Supplementary data Comparison between in-situ ageing and ex-situ ageing Because of the long ageing times, samples usually age in a hermetically closed container (ex-situ gelation). Aliquots of those samples are regularly loaded in the rheometer to probe their viscoelasticity, following a protocol described below in the Method section. To check for the possible role of the sample loading on the aging behavior, some additional tests were performed by loading a freshly prepared sample in the Couette cell of the rheometer and probing regularly the viscoelasticity of the sample over a period of 8 days. We quantitatively compare the viscoelasticity for a sample allowed to age in-situ to that of a sample that has aged ex-situ. We show in figure S1 comparable evolution with ageing time of the zerofrequency elastic plateaus for in-situ and ex-situ gelation of a sample with concentration C= 317 mg/ml.
Acknowledgements We thank  J. Bonicel  ( IATE ) for help in the  SE-HPLC ,  P. Dieudonné  ( L2C ) for the in-house SAXS measurements and  C. Charbonneau  ( L2C ) for help during the neutron scattering measurements. We acknowledge the  European Synchrotron Radiation Facility  for provision of synchrotron radiation facilities. We would like to thank  Pawel Kwasniewski  for assistance in using beamline ID02 at  ESRF  and  Zhendong Fu  for assistance during the neutron scattering experiments. This work was supported by the  Laboratoire of Excellence NUMEV  ( ANR-10-LAB-20 ) and  INRA (CEPIA department). Besides, this research project has been supported by the  European Commission  under the  7th Framework Program  through the " Research Infrastructures" action of the Capacities Program ,  NMI3-II , Grant Agreement number  28388  to perform the neutron scattering measurements at the  Heinz Maier-Leibnitz Zentrum (MLZ), Garching, Germany.
The berries were collected between veraison and maturity, separated in skin and pulp, and their content was analyzed by conventional analytical procedures and untargeted metabolomics. For anthocyanins, the relative quantitation was fairly comparable with both LC-MS determination and HPLC-DAD, which is a fully quantitative technique. The data show complex responses of the metabolite content (sugars, organic acids, amino acids, anthocyanins, flavonols, flavan-3-ols/procyanidins, stilbenes, hydroxycinnamic, and hydroxybenzoic acids) that depend on the rootstock, the scion, the vintage, the nitrogen level, the berry compartment. This opens a wide range of possibilities to adjust the content of these compounds through the choice of the roostock, variety and nitrogen fertilization.
7; eluent B, acetonitrile; eluent C, water). Chromatograms corresponding to excitation at 250 nm and emission at 395 nm were recorded. The compounds were quantified by their peak area with Chromeleon software, version 7. 1 (Thermo Electron SAS, Waltham, MA, USA) using external standards. Chemical standards were purchased from Sigma (St Louis, MO, USA). Twenty amino acids were identified and quantified as described by  Pereira et al. (2006). The results were expressed in nmoles/g DW.
The injection volume was 20 µL for all samples. The Bruker ion trap Esquire 6000 mass spectrometer was equipped with electrospray ionization source (ESI). The analyses were performed both in positive and negative modes, setting the scan among 50-3000 m/z and a target mass of 400 m/z. The ESI values were 50 psi and 350 • C for the nitrogen nebulizing gas and 10 L/min for the drying gas. Mass spectra were recorded using an Averages of 5 spectra and Max Accu Time of 100 ms. The fragmentation was carried out in AutoMS, fragmenting molecules up to three times. Helium was injected to induce molecule fragmentation. MS data were collected with Bruker Daltonics Esquire 5. 2 Control software and processed with Esquire 3. 2 Data Analysis software  (Bruker Daltonik GmbH, Bremen, Germany). MS data files were converted from.
d extension to net. cdf and submitted to mzMine 2. 10 (http://mzmine. sourceforge. net). The resulting data matrix, reporting the samples and the peak areas of the detected signals, was imported in Simca 13 (Umetrix, Sweden) software to perform the statistical analysis. Metabolite identification was performed by comparing the retention times, m/z and fragmentation patterns of a signal with those of authentic commercial standards included in our home-made library. When no match was observed, the m/z and the fragmentation pattern of the putative molecule were compared with those reported in literature or in on-line databases (massbank. jp; hmbd. ca). The absorbances were recorded among 190-600 nm (UV-Vis) in LC-DAD analyses. Molecules identified as anthocyanins and hydroxycinnamic acid derivatives in LC-MS were confirmed by measuring their absorbance at 520 and 320 nm, respectively.
Statistical Analyses The MS data matrix was imported into Simca 13 software (Umetrix, Sweden) and unsupervised Principal Component (PCA) and supervised Orthogonal Partial Least Square Discriminant (OPLS-DA) analyses were performed using centering and pareto scaling. The unsupervised PCA was carried out to observe homogeneous sample clusters that were used as Y classes in the supervised OPLS-DA. As final output, molecules responsible for cluster separation in OPLS-DA were identified by plotting the pq(corr), i. e. the correlation between p (based on the X component, the metabolites) and q (based on the Y component, the classes), against p. The statistical analyses were validated by performing: (a) permutation test (200 permutations); (b) CV-ANOVA (p < 0. 05); (c) t-test (p < 0. 05) for a cluster characterizing molecule.
ACKNOWLEDGMENTS The authors thank the  Conseil InterProfessionnel du Vin de Bordeaux , and  France Agrimer  for supporting the Ph. D. work of AH,  COST Action  FA  1106  for providing a travel grant and the  Conseil Régional d'Aquitaine  for general support. The authors also thank  Bernard Douens  and  Christel Renaud  for technical support, and  ZhanWu Dai  and  Jean-Pascal Goutouly  for scientific interactions.
Bees were captured either in the cage, trying to get out of their nest, or nearby the outside of the cage with a net, when trying to come back into their nest. In the winter 2012, we collected a composite sample of 100 g of soil representative of the soil volume in each square and the granulometric composition of these samples was analyzed using standard methodology (National Soil Analysis Laboratory, INRA Arras). The percentages of clay, silt and sand on a weight basis were used to locate the soil of each square into the discrete categories of a soil texture triangle (U. S. Department of Agriculture 1951). We used R package plotrix to represent the distribution of soil squares in the texture triangle  (Lemon 2006 ; see Supplementary Methods 1).
Data analyses As human-made nesting structures were put in place over 2 years, we conducted diachronic (relating to the changes in the data base that happen over the 2 years) and synchronic (relating to differences between two data base obtained the same year) analyses of the species occurrence and abundance data. First, we analyzed the bees that emerged from the nesting elements of the hotels built in Year 1 in the 2 years that followed their set-up (2012 and 2013; diachronic approach). The same sampling schedule was used for the soil squares set-up in Year 1. This first approach was used to evaluate the colonization pattern over the two seasons in the same structures. Second, we investigated the influence of the age of the nesting materials that was put in place in Year 1 or Year 2 by scoring the emergence that took place over 2013 in all sites (synchronic approach).
2011 ) and nlme  (Pinheiro et al. 2010 ) packages in R version 3. 2. 2 (R Core Team 2015). Post-hoc Tukey tests were computed using multcomp package in R  (Hothorn et al. 2008). For the diachronic and synchronic analyses, we used a threefold Bonferroni correction for all models on the three groups of species  (Rice 1989). For the analyses, we took 14 (87. 5 % of the total number of studied sites) and 15 (93. 75 %) sites into account for soil squares and bee hotels, respectively, because all logs and stems had been stolen from the bee hotels on one site and the square soils of two sites were not built soon enough to take them into account.
Results First of all, we collected bees at all 16 sites of our study on both soil squares and bee hotels. Furthermore, our dataset is a subsample because we only sampled at random 1/4th of each soil square and 1/8th of the total number of cavities of each type of nesting substrate in each compartment at each site. So, by extrapolation we could expect to have four times as many bees that nested in the soil squares (i. e. 232) and eight times as many bees that emerged from the hotels (i. e. 3102), that is about 1,000 and 25,000 bees, respectively.
Acknowledgments We would like to thank  Jean Aptel ,  Quentin Brunet-Dunand ,  Anne Laure Guirao ,  Vincent Letoublon , and  Jean-Paul Vermande  `re for field assistance. We also thank all the specialists who identified our bee specimens:  Holger Dathe  for Hylaeus spp. , Eric Dufrene for Nomada spp. and Sphecodes spp. ,  David Genoud  for.