dataesr/scientific-paragraphs-categorization huggingface dataset:
- , https://doi. org/10. 5194/bg-2019-73 Manuscript under review for journal Biogeosciences Discussion started: 27 March 2019 c Author(s) 2019. CC BY 4. 0 License. Table 2. Growth chamber experiment 2a and 2b. Experimental set-up, phytolith content and triple oxygen isotope data obtained for phytoliths (Phyto), leaf water (LW) and irrigation water (IW). Isotope fractionation (and l) between leaf water and irrigation water (LW-IW) and phytoliths and irrigation water (Phyto-IW) are presented. Samples are named according to the climate chamber # they were collected in (e. g. F4), the date of sampling (dd/mm/yy) and the sampling after day or night (Day vs Night in experiment 2a) or after constant climate conditions or day/night alternation (Cst vs DN in experiment 2b). n : number of replicates ; SD : standard deviation calculated on the replicates; Phyto Conc.
However, metagenomic approaches through NGS have opened new opportunities, and 17 additional phytoplasma genome draft sequences have been deposited in GenBank (NCBI). Such genome-wide sequence analyses have provided easy access to genetic markers, allowed unbiased definitions of species boundaries in the genus "Candidatus Phytoplasma," and have revealed the horizontal transfer of potential mobile units and effectors  (14, 15). MLST schemes have been developed for many Mollicutes, almost exclusively Mycoplasma and Ureaplasma, because of their impacts on humans and animals  (16) (17) (18). For phytoplasmas, most of the MLST schemes that have been developed for "Candidatus Phytoplasma" species or 16S taxonomic groups target rRNAs, housekeeping genes, protein coding genes, and also positively selected genes involved in the interaction with the host  (19, 20).
Two  types of sequences were identified. Seventeen samples corresponding to ST5 to ST8 originating from Nigeria and Mozambique were all identical to the 16S rRNA sequence of the LDN strain from Nigeria (accession number Y14175)  (44, 45)  and were therefore classified as members of subgroup 16SrXXII-A. Twenty-four samples of ST1 to ST4 from Ghana were all identical to the 16S rRNA of CSPW-dna19 and were therefore assigned to subgroup 16SrXXII-B (accession number KF364359)  (37). Sequences from subgroups 16SrXXII-A and -B differed by six single-nucleotide polymorphisms (SNPs) over 1,505 bp (99. 6% homology). Geographic distribution of the "Ca. Phytoplasma palmicola" sequence types. All the DNA samples were spatially referenced, allowing the mapping of the distribution of their corresponding STs.
MATERIALS AND METHODS Housekeeping gene selection and primer design. Highly fragmented preliminary genome drafts obtained for one Mozambican isolate of the "Ca. Phytoplasma palmicola" subgroup 16SrXXII-A and one Ghanaian isolate of the "Ca. Phytoplasma palmicola" subgroup 16SrXXII-B (unpublished data) were used to select housekeeping genes and to design the corresponding PCR primers. Housekeeping genes were selected for their availabilities on both drafts and their locations on different contigs to avoid contiguity. The two sequences of each selected gene from the two "Ca. Phytoplasma palmicola" genome drafts were aligned with BioEdit 7. 0 software (http://www. mbio. ncsu. edu/BioEdit/bioedit. html) to produce a consensus sequence. Consensus sequences served as the templates to define specific PCR primers with predicted product sizes of 450 to 850 bp using Primer-BLAST (https://www.
The MLST scheme was applied to the 132 "Ca. Phytoplasma palmicola" DNA samples (Table  4 ; Data Set S1 in the supplemental material). The DNA samples were extracted from stem sawdust or inflorescences of LYD-infected coconuts collected between 2004 and 2013 in Ghana (96 samples), Nigeria (4 samples), and Mozambique (32 samples). DNA was extracted using a modified CTAB protocol  (39)  or the DNeasy plant mini kit (Qiagen, Hilden, Germany). Housekeeping genes and 16S rRNA gene amplification and sequencing. PCR amplification was performed for each of the seven selected housekeeping genes (i. e. , genes encoding DNA recombinase A [recA], DNA gyrase subunit B [gyrB], leucyl-tRNA synthetase [leuS], dihydrolipoyl dehydrogenase [lpd], DNA replication protein [dnaC], protein translocase subunit [secA], and rRNA small subunit methyltransferase I [rsmI]) plus the rplV gene for the 132 isolates.
14  (93) , and recombination was tested for each gene and for the concatenated sequences by performing the pairwise homoplasy index (phi) test  (94). Recombination was also estimated for concatenated sequences by RDP4  (95). Interspecific analysis. To conduct interspecific analysis, a total of 23 full and incomplete phytoplasma chromosomes available in GenBank were screened for the availability of all eight MLST-selected housekeeping genes and the 16SrRNA operon. Since some of the drafts lack complete recA sequences, the analysis was restricted to the seven other housekeeping genes (i. e. , dnaC, gyrB, leuS, lpd, secA, rsmI, and rplV). The data set included "Ca. Phytoplasma asteris" strain onion yellows OY-M (NC_005303. 2), wheat blue dwarf (AVAO00000000. 1), chrysanthemum yellows strain CYP (JSWH00000000.
The seven housekeeping gene sequences were aligned using Muscle (Codon) implemented in MEGA version 7. 0. 26 and then concatenated. The maximum likelihood (ML) phylogenetic tree was constructed by using the best-fitting model option of RDP4  (95) , with recombinant regions removed when detected by more than three methods. Bootstrap values were calculated from 1,000 replications. The analysis was repeated with one of the two 16Sr RNA gene sequences of each genome. The congruence of the phylogenetic trees from the two sets of sequences (MLSA and 16S) were calculated by using the congruency index I cong  (46)  (http://max2. ese. u-psud. fr/icong/index. help. html). Accession number(s). The 1,056 sequences obtained are available in the European Nucleotide Archive (ENA) (https://www. ebi. ac. uk/ena/) under project no.
ACKNOWLEDGMENTS We thank  O. Pruvost  for helpful discussions during manuscript preparation and  C. Boyer ,  K. Boyer ,  S. Javegny , and  S. Sisteron  at the  Plant Protection Platform  ( 3P , IBISA) as well as  N. Munguambe  for technical support. We thank  S. Hogenhout ,  M. Kube ,  C. Siewert ,  D. Severac , and  S. Carrere  for their contributions toward obtaining the first LY phytoplasma genome drafts under the  Phytoplasma Sequencing Initiative  of the European COST action FA0807. This work was cofunded by the  European Union  under the  European Regional Development Fund  (grant  ERDF GURDT I2016-1731-0006632 ), the  Conseil Régional de La Réunion , and the  Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD).
Chemical abundance dating methods open new paths for temporal evolution studies of the Milky Way stellar populations. In this paper, we use a high spectral resolution database of turn-off stars in the solar neighbourhood to study the age dependence of the [Y/Mg] chemical abundance ratio. Our analysis reveals a clear correlation between [Y/Mg] and age for thin disc stars of different metallicities, in synergy with previous studies of solar-type stars. In addition, no metallicity dependence with stellar age is detected, allowing us to use the [Y/Mg] ratio as a reliable age proxy. Finally, the [Y/Mg]-age relation presents a discontinuity between thin and thick disc stars around 9-10 Gyr. For thick disc stars, the correlation has a different zero point and probably a steeper trend with age, reflecting the different chemical evolution histories of the two disc components.
In this paper, a chemical definition of the thin/thick disc populations has been followed. As revealed by several studies inside and outside the solar neighbourhood, thick and thin disc stars seem to separate in two sequences in the [α/Fe] versus metallicity plane (e. g. Adibekyan et al. 2012; Recio-Blanco et al. 2014). Thick disc stars have higher [α/Fe] abundances than thin disc stars of the same metallicity, showing also a faster evolution of their [α/Fe] abundance with time  (Haywood et al. 2013; Hayden et al. 2018). The aim of our work is to analyse the age dependence of the [Y/Mg] ratio for turn-off stars in a wide range of metallicities, using a homogeneous and high-resolution spectroscopic sample from the AMBRE project  (de Laverny et al. 2012 (de Laverny et al. , 2013)). To this purpose, isochrone fitting ages using astrometric Gaia data from the first data release (Gaia Collaboration 2016a) are used.
The AMBRE-TGAS data The Archeologie avec Matisse Basée sur les aRchives de l'ESO (AMBRE) project, established by ESO and l'Observatoire de la  Côte d'Azur in 2009 (de Laverny et al. 2013) , concerns the parameterisation of the stellar high-resolution spectra of the ESO archives. Stellar spectra collected by three high-resolution spectrographs have already been analysed (FEROS, HARPS, UVES). In this paper, we concentrate on the 4355 parametrised HARPS spectra for which the best stellar T eff , log(g), [Fe/H], and radial velocity are available  (De Pascale et al. 2014). Within the AMBRE database, the HARPS spectra have the highest spectral resolution and contain an important number of stars at the turnoff stage for which isochrone ages can be reliably derived. The robust identification of the AMBRE/HARPS targets was carefully addressed to overcome the challenges of a catalogue that is build up from archival data.
The 2MASS catalogue was chosen as a reference because it offered the advantage of providing photometric information for the targets. The crossmatch between the AMBRE/HARPS and 2MASS coordinates was performed using the xcross program (ESO client). In the case of multiple matches within the radius of search (5 arcsec for AMBRE/HARPS), a comparison of the spectroscopic and the photometric effective temperatures was performed. For each match from the 2MASS catalogue, the photometric effective temperature was calculated using the relations of  Alonso et al. (1996)  and constants from González  Hernández & Bonifacio (2009). When there were multiple matches, the objects with the minimal values of |T phot -T AMBRE | were selected. A total of 2416 different stars along the Hertzprung-Russell diagram were found.
The identified stars were then searched in the Tycho-Gaia Astrometric Solution (TGAS) catalogue. Ages were determined using Bayesian analysis by comparing derived stellar parameters from AMBRE/HARPS data (T eff , [Fe/H], [Mg/Fe], M K ) with theoretical isochrones from the Dartmouth group 1   (Dotter et al. 2008) , using a method similar to that described by  Jørgensen & Lindegren (2005). A complete description of the methods employed in this paper to determine ages are provided by the AMBRE-Gaia DR1 catalogue  (Hayden et al. 2018). The isochrones are spaced in age from 0 to 15 Gyr, with steps of 100 Myr, in [Fe/H] from -2. 0 to +0. 6 dex in steps of 0. 1 dex, and from 0. 0 to +0. 4 dex in [Mg/Fe] in steps of 0. 2 dex. The median variance of the age probability distribution function is about 1.
2006; De Pascale et al. 2014)  for the AMBRE project. The GAUGUIN code includes a local normalisation step around the selected spectral lines. It is worth noting that GAUGUIN is part of the GSPspec module of the APSIS pipeline (Bailer-Jones et al. 2013) implemented within the Gaia Data Processing and Analysis Consortium. In particular, GSPspec is in charge of deriving parameters and abundances from Gaia RVS spectra  (Recio-Blanco et al. 2016). The reference theoretical spectra grid used by GAUGUIN for the magnesium abundance estimation was the GES synthetic grid of non-rotating FGKM-type spectra, provided by the GES consortium. It is a high-resolution optical synthetic spectra grid in the 4200-6900 Å wavelength range calculated from the MARCS stellar atmosphere models  (Gustafsson et al. 2008 ) and the GES/Linelist_V5 atomic and molecular line-lists, provided by GES/LineList Group.
Differences between the thin and the thick disc. The dependence of [Y/Mg] on stellar age is based on the chemical evolution of the analysed population, which means that different galactic components could present different trends with age depending, among other things, on their star formation history. In the previous sections, we focus the analysis on thin disc stars, which represent the majority of the AMBRE/HARPS turnoff data. However, in Sect. 5 we point out the shift that thick disc stars seem to present with respect to the thin disc, causing a discontinuity in the [Y/Mg] correlation with age. Figure  8  shows the high-precision thin disc data set together with the thick disc set, but relaxing the errors to 0. 1 dex in [Mg/Fe] and 0. 20 dex in [Y/H]. This allows us to include more metal-poor stars in the sample.
Acknowledgements. The spectra calculations were performed with the highperformance computing facility MESOCENTRE, hosted by  OCA. This work has made use of data from the  European Space Agency (ESA) mission Gaia  (https://www. cosmos. esa. int/gaia),processed by the Gaia Data Processing and Analysis Consortium (DPAC; https://www. cosmos. esa. int/web/gaia/dpac/consortium). We acknowledge financial support form the  ANR   14-CE33-014-01. Funding for the DPAC has been provided by national institutions, in particular the institutions participating in the Gaia Multilateral Agreement.
Several articles have addressed the conditions of acceleration and survival of nuclei in high-luminosity  [129, [168] [169] [170] [171] , and low-luminosity GRBs  [129, 169, 172, 173]  and find regimes in which GRBs could power all the observed UHECRs and be consistent with the UHECR composition measurements. Though standard supernovae are not expected to be able to accelerate cosmic rays to ultrahigh energies, the ejecta of trans-relativistic and engine-driven supernovae which typically reach mildly relativistic speeds may also be able to accelerate UHECRs  [174] [175] [176] [177] [178]. A feature of GRB and engine-drive SN models is that the composition resulting from stellar evolution models can explain the UHECR composition data observed by Auger. In 2017 the detection of gravitational waves from the merger of a neutron star binary, followed by a short GRB and electromagnetic emission from the remnant marked the discovery of this, long-sought-for, class of events  [146, 179].
Nonetheless, attempts at full-sky coverage by combining data from the largest Northern and Southern observatories have been performed by the Pierre Auger and Telescope Array Collaborations. Such an approach is limited by the mismatch in energy scale between the two experiments, which could cause spurious anisotropies due to an improper contrast between the flux inferred from each dataset. The collaborations have designed a method to match the flux in the declination band covered from both sites, providing a common view on the UHECR sky beyond the ankle and above the flux suppression  [246] [247] [248]. Future tests against catalogs with such a dataset could prove informative regarding correlations with extragalactic sources. Moreover, the ongoing upgrade of the Telescope Array, aimed at increasing the effective area of the observatory by a factor of 4  [249] , will significantly reduce the contrast between the Northern and Southern exposures.
Open Questions in Cosmic-Ray Research at Ultrahigh Energies Most current anisotropy studies exploit the arrival directions of UHECR events above a given (or scanned) energy threshold. This information could be supplemented by spectral and composition data to perform tomography of the UHECR production rate. Propagation of nuclei of different species affects the expected composition and spectrum as detected on Earth. Combined fits of the spectral and composition data show constraining power on the evolution of the density of sources at a fixed a luminosity (see, e. g. ,  [142] ). Constraints on composition are mostly inferred from fluorescence data, limited in statistics beyond few tens of EeV. With the upgrade of the Pierre Auger Observatory, the joint detection of showers with scintillators and water tanks will provide a composition-dependent observable with nearly 100% duty cycle  [250].
None of these simulations provides an acceptable description of the Auger and TA data. This is most obvious for the expected and observed compositions but also the simulated and observed all-particle spectra differ: in the Auger data sets, the suppression is below the GZK cut-off and in the TA datesets, all data points are above the GZK cut-off. The results question the interpretation of the flux suppression as caused solely by the GZK effect. While the energy spectra of Auger and TA could be made to agree with the GZK effect if the uncertainties of the energy scales are accounted for -14% in Auger and 21% in TA -the mass compositions of data and simulations for each experiment are totally different. On the other hand, a simple astrophysical model of identical UHECR sources that accelerate nuclei through a rigidity-dependent mechanism provides a perfect description of the energy spectrum and mass composition above the ankle if the maximum rigidity is at about 10 18.
The lower bound, however, has been subject to much controversy (see, e. g. ,  [273, 274] ). In cosmic filaments, magnetic fields are B ∼ nG, and in the centre of galaxy clusters, B ∼ µG; for reviews, see, e. g. ,  [275, 276]. J(E) [eV 3 E 2 ≤ A ≤ 1 6 ≤ A ≤ 3 19 ≤ A ≤ 7 39 ≤ A ≤ 20 56 ≤ A ≤ 40 Auger 2017 f(1) = 1. 0e+00 (56)= 1. 0e+00 gal f 2. 1e+45 J(E) [eV 3 E 2 ≤ A ≤ 1 6 ≤ A ≤ 3 19 ≤ A ≤ 7 39 ≤ A ≤ 20 56 ≤ A ≤ 40 TA 9 year f(1) = 1. 0e+00 (56)= 1. 0e+00 gal f 2. 3e+45 V(ln A)  The sources follow an SFR evolution and their spectra are pure power-law distributions up to 10 22 eV. For each of the primary beams, the index is chosen such as to provide the best fit to the data from Auger (top) and TA (bottom). K. -H. Kampert and M. Unger for this review. ] -1 yr -1 sr -2 km 2 J(E) [eV 3 E 2 ≤ A ≤ 1 6 ≤ A ≤ 3 19 ≤ A ≤ 7 39 ≤ A ≤ 20 56 ≤ A ≤ 40 The Galactic magnetic field (GMF) is understood better than EGMFs.
g. ,  [142] ). Therefore, it is of prime interest to figure out whether this apparent tension is not an artifact of inaccurate expectations for the mean X max. Moreover, the comparison of the electromagnetic and muonic shower components at surface level offers an even larger composition sensitivity than that provided by the depth of shower maximum. Currently, this sensitivity cannot be fully exploited. Muon-based mass measurements systematically lead to heavier mass compositions than X max -based analyses  [54]. Over the last decades, a rich dataset on proton-proton and proton-antiproton interactions at high energy has been accumulated in various collider experiments. In an air shower, most of the interactions are initiated by pions and kaons, except the first one. There is a severe lack of pion-proton and kaon-proton data that are needed for improving our understanding of hadronic interactions and for tuning interaction models.
Also, K-EUSO data will allow for a full-sky search for UHECR anisotropy to independently confirm or rule out the presence of hotspots in the Northern and Southern hemispheres. The project concept of OWL, based on the simultaneous detection of UHECRs by UV telescopes placed on two satellites, was recently developed in the POEMMA project  [404]. This project, based on the use of Schmidt optics with 45 • FOV and a large photodetector camera, can become a space instrument of record characteristics and surpass in terms of exposure the ground-based Auger and TA installations (see Figure  16 ).
ACKNOWLEDGEMENTS We acknowledge the support of the  Munich Institute for Astro-and Particle Physics (MIAPP)  of the DFG cluster of excellence " Origin and Structure of the Universe ", where this work was initiated. We thank the organisers of the "The  High-Energy Universe: Gamma-Ray, Neutrino , and cosmic-ray astronomy"  MIAPP Program ,  Francis Halzen ,  Angela Olinto ,  Elisa Resconi , and  Paolo Padovani , for the very fruitful workshop.
Shell δ 18 O values Both short and long sequences obtained from sub-fossil samples demonstrate a sinusoidal pattern along the shell growth axis, covering a variable time span between ca. six months and more than three years in the case of some of the long sequences (see Supplementary Material). The maximum and minimum δ 18 O values obtained for all shells studied were 2. 85 and -0. 79‰, respectively. Nevertheless, the maxima and minima, and therefore also the intra-annual δ 18 O range resulting from the datasets, were different between individuals and stratigraphic units (Table  3 ). The maxima and minima values obtained for each level fluctuate between 2. 85 and 2. 37‰ and -0. 09 and -0. 79‰, respectively. Thus, intraannual ranges for each stratigraphic unit vary between 3. 18 and 2. 94‰.
Discussion The exploitation of topshells during Mesolithic in the Cantabrian region Stable oxygen isotope data demonstrates that P. lineatus was collected preferentially in winter and, also, in late autumn. The results from the El Mazo shell midden are very similar to those previously obtained during the 1980s from other three Mesolithic shell midden sites (El Penicial, Mazaculos II and La Riera), also located in the western Cantabrian region  (Bailey et al. 1983; Deith 1983; Deith and Shackleton 1986). This marked seasonal exploitation pattern has also been documented in other places along the Atlantic façade of Europe. This includes the Mesolithic site of Culverwell (UK), where season(s) of death information indicated a predominance of autumn and winter collection  (Mannino et al. 2003; Mannino and Thomas 2007).
Stable isotope analyses performed on another Phorcus species report similar conclusions. The dataset obtained from Phorcus turbinatus (Born, 1778) in different parts of the Mediterranean area (especially in southern Italy but also in Libya) has shown that this species was harvested preferentially during colder months  (Colonese et al. 2009; Mannino et al. 2007 Mannino et al. , 2011 Mannino et al. , 2014;; Prendergast et al. 2016) , although, in some cases, minimal summer exploitation was also observed during the Mesolithic  (Mannino et al. 2007; Prendergast et al. 2016 ). As a result, Mesolithic huntergatherers demonstrated a remarkably consistent focus on the autumn and winter collection of key molluscan resources across space and across time in Atlantic and Mediterranean Europe.
Bailey and Craighead (2003)  proposed that decreased shell sizes were instead induced by changes in climatic and environmental conditions. Nevertheless, Gutiérrez-Zugasti (2011a) addressed this topic by studying size and age distributions of marine gastropods (limpets and topshells) from Upper Palaeolithic and Mesolithic sites in northern Iberia. Results revealed a decrease in the mean size and age of these species. Although these data demonstrated that molluscs were exploited with high intensity at least from the Azilian (c. 12. 5 kys cal BP), information on changes (if any) in intensification processes throughout the Mesolithic is still very limited. Stable oxygen isotope analyses conducted in this investigation have shown that the topshell P. lineatus was collected in late autumn, winter, and, to some extent, early spring.
Conclusions Combining (a) a stable oxygen isotope analyses in order to determine the seasonality of P. lineatus collection during the Mesolithic and (b) an experimental programme to decipher relative molluscan meat yield throughout the year has been crucial to better understand not only littoral exploitation patterns in the past but also human behaviour. Our isotopic results demonstrate that P. lineatus was exclusively gathered during colder months. Collection patterns are in agreement with previous data obtained for this species in the Cantabrian region and, also, in other coastal areas of Atlantic Europe. The arguments previously published to explain the P. lineatus exploitation pattern (limited human settlement in coastal areas during the warmer season, scarcity of food supply during colder months, feasting, etc.