dataesr/scientific-paragraphs-categorization huggingface dataset:
[26] , and Hyde et al. [27]  for Pleosporales (127 sequences) and Capnodiales (85 sequences), Wang et al. [28, 29]  and Nekoduka et al. [30]  for Leotiomycetes (71 sequences), and Tang et al. ,  [31]  for Sordariomycetes (165 sequences). The complete dataset is provided in Supporting Information (see S1 Dataset). Alignments were generated using MUSCLE, implemented in MEGA 6. 0 (Molecular Evolutionary Genetics Analysis,  [32] ), and manually refined (number of characters were 733, 776, 782, 814 for Leotiomycetes, Pleosporales, Sordariomycetes, Capnodiales, respectively). Phylogenetic analyses were performed using both Bayesian Inference (BI; MrBayes 3. 2. 2; four incrementally heated simultaneous Monte Carlo Markov Chains (MCMC), run over 10 million generations, under GTR + Γ evolutionary model) and Maximum Likelihood (ML; RAxML v.
Statistical analysis Statistical analyses were performed using PRIMER 7. 0 (Plymouth Routines In Multivariate Ecological Research  [34] ). The biodiversity within sampling sites was estimated by calculating Shannon-Weaver's index (H'), Gini-Simpson's index (1-Lambda) and Pielou's evenness (J') on presence/absence matrix (S3 Table ). The difference between fungal abundance at the different locations or on the isolation media was evaluated with PAST 3. x software  [35]  using F-test (p 0. 05). The Non-Metric Multi Dimensional Scaling (NMDS) analysis was performed in R (Vegan package)  [36].
oceanica  [33] , close to Neoroussoella bambusae (a monotypic genus described by Liu et al. [53] ), and may represent a new species of the same genus; (ii) the other well supported clade included MUT 4884 and another strain isolated from P. oceanica  [33] , both from Mediterranean Sea. Within Biatriosporaceae, a Biatriospora sp. well supported clade was identified and included MUT 4883 and a P. oceanica isolate  [33]. Within Massarinaceae, MUT 4860 and 4863, which grouped closely to MUT 4887 Massarina rubi (a species occurring on at least eight plant families as saprotroph), represent separate entities. Within Sporormiaceae, the strain MUT 4858 (Sporormiaceae sp. ), fell between Westerdykella and Preussia genera. However, the mycelium was sterile and the reference dataset still needs to be improved by more LSU sequences from type species deposited in public collections.
Statistical analysis The proc GLIMMIX procedure of SAS 9. 3 (2002-2010; SAS Institute Inc. , Cary, NC, USA) was used to output lsmeans by treatment and time for daily N 2 O fluxes and soil mineral N concentrations. The terms in the model were treatment, time and the interaction of these two factors. Differences in cumulative N 2 O and fraction of N applied lost as N 2 O (%) between treatments over the study period were determined using the proc GLIMMIX procedure of SAS using the F-protected least significant difference (LSD) test (Table  1 ). Data on N 2 O and the percentage of applied N lost as N 2 O was checked for normality of distribution and log-transformed prior to analysis. The terms in the model were treatment as a fixed effect and block as a random effect. Statistical analysis was performed separately for fertiliser-only treatments and for urine and urine + fertiliser treatments.
Acknowledgements The authors would like to thank the laboratory and field staff at both  Teagasc ,  Johnstown Castle , for their assistance on this project, in particular  Camille Bartolini  and  Victoria Magny  ( Université de Bourgogne, Dijon, France ). This research was financially supported under the National Development Plan, through the  Research Stimulus Fund , administered by the  Department of Agriculture, Food and the Marine  (grant numbers  RSF10/RD/SC/716  and  11S138 ).
Acknowledgments The authors gratefully acknowledge the financial supports by  PRODEP-SEP Networks, Mexico ,  DSA/103. 5/15/14156 ,AIRD, France (JEAI-2011, NANOBIOSA),  PN-CONACYT, Mexico ,  2014-248560 , and  PAICYT-UANL, Mexico. Claudia Janeth Martínez-Rivas  is thankful for CONACyT scholarship, Mexico, no. 280112.
Phylogenetic analysis. The Bayesian analysis 50% majority-rule consensus tree is given in Fig. 3  (and Supplementary 1). We included 51 species whose 23 species represent 21 genera of Icacinaceae and 27 species represent all other groups of the asterid. We used a combined morphological and molecular data with 73 protein-coding genes for a total of 59132 bp and 22 morphological characters (see the material and method for more precisions). As expected, we found a topology similar to the previous phylogenetic study using the same DNA data for the species included here  27. This fossil, when included in the analyses, is placed close to Natsiatum. However the node with Icacinanthium and Natsiatum have very low support (PPB < 0. 95). In this sense, the position of Icacinanthium is considered as unresolved at the base of the group IV sensu Stull et al.
Phylogenetic reconstructions. Preliminary exploratory herbarium studies (P) focusing on small pentamerous hypogynous flower with petals fused at the base and with stamens free from the petals lead to comparison of the flower in amber to those of the family Icacinaceae. We employed the most complete molecular data for the asterid clade focusing on the Icacinaceae  27. Theses data were composed of 73 protein-coding genes for a total of 59132 bp. We retained 51 species among the 112 accessions available  27  of which 23 species represent 21 genera of Icacinaceae. We included at least 2 species from other asterid orders, except for Metteniusales where we used 9 species as this order includes species which were formerly included in genera of Icacinaceae, which are morphologically close to Icacinaceae sensu stricto.
Morphological studies. A morphology matrix was made using Xper 3 47 containing 22 flower and pollen characters coded for 51 taxa including the Le Quesnoy flower (Supplementary 2) The matrix was constructed from direct morphological observation of herbarium specimens (P, see Supplementary 3) and from bibliographic data for flowers  28, 37, [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]  and pollen  [58] [59] [60] [61] [62] [63]. We observed the flower embedded in amber using a light microscope (Nikon Eclipse80i). Numerous pollen grains were found around the flower and between hairs on the adaxial surface of the petals (Fig. 1D, F ); the vicinity and abundance of grains of the same type indicate that they probably belong to the flower. The pollen was also extracted from the amber in order to obtain a better understanding of its type (Fig.
2 ) following a previously published protocol  25  and observed using the same microscope. Before extraction we only observe the imprint left by the pollen in amber. After extraction, we show an exceptional preservation of grains with well-preserved exine wall and remains of cellular content. A darker zone could correspond to the rest of the nucleus (clearly visible on Fig. 1D ). Due to the presence of echinae (spines), pollen grains could not be fully separated from resin and were observed still embedded inside a small resin block. All these features were mapped into the phylogeny using Mesquite software  64  with a parsimony ancestral state reconstruction.
Acknowledgements The fossil was collected during field work of the "amber team" of  MNHN , with the help of Lafarge-Granulat, and we thank the  Langlois-Meurinne  family for giving authorization to work on their property. We thank the staff of the  Paris Herbarium (MNHN P)  for the loan of modern flower samples and access to herbarium sheets. We also thank  Valentin Seizille de Mazancourt  for the help in naming the species. We thank  Martin Pickford  and  Steven Manchester  for improving the English. This work was supported by a grant from  Agence Nationale de la Recherche  under the LabEx  ANR-10-LABX-0003-BCDiv , in the program " Investissements d'avenir "  ANR-11-IDEX-0004-02  and by the  CR2P.
| Animal models In order to estimate additive genetic variances for laying date and the prelaying interval, as well as phenotypic and additive genetic correlations between these traits, we used restricted F I G U R E 1 Two transponder-tagged common terns using a resting platform equipped with an antenna for automated registration at the Banter See breeding colony (photo by S. Bouwhuis) maximum-likelihood mixed models (known as "animal models,"  Kruuk, 2004 ) in a frequentist approach (ASReml software,  Gilmour, Gogel, Cullis, & Thompson, 2009). We first performed a bivariate animal model with prelaying interval and laying date. Age was included as a fixed effect and year, individual identity, and additive genetic variation as random effects. The total phenotypic variance (σ 2 p ) of laying date or prelaying interval in experienced females was partitioned into the following components: where σ 2 pe was the permanent environmental variance, that is, persistent influence of female identity over time with environmental origin, σ 2 a the additive genetic variance, and σ 2 r the residual variance.
of many researchers, students, and field assistants. We greatly appreciated the helpful comments of  F. Bairlein  and A. van Noordwijk on the manuscript. The data collection was supported by the  DFG  ( BE 916 ). C. A. was supported by a PhD stipend from the  AXA Research Fund , A. C. and F. S. D. by the  CNRS in France  and an  Agence Nationale de la Recherche  grant ( ANR-08-JCJC-0041-01 ), and A. C. by the  European Research Council  (Starting grant  ERC-2013-StF-337365-SHE ).
Microarray analysis Gene expression profiles of SEs were analyzed using a whole human genome microarray containing 47,231 probes (HumanHT-12 v4 Expression BeadChip; Illumina Inc. , San Diego, CA, USA). RNA amplification, microarray hybridization, scanning, as well as data normalization and analysis were performed at the ProfileXpert genome facility (Lyon, France) as previously described. 3 enes significantly modulated were selected with a fold change cutoff of 1. 5 and p<0. 05 (one-way analysis of variance [ANOVA]). A Venn diagram was used to visualize relationships between the gene lists thus created.
Histological and immunohistological analysis Harvested SEs were immediately fixed in neutral buffered formalin 4% (Diapath, Martinengo, Italy) for 24 h, embedded in paraffin (for corneodesmosin, cFos, and LCE6 expression analysis) or in OCT compound (for LCE1A expression analysis), and frozen at -20°C. Preparation of SE section and analysis of protein expression by immunohistochemistry were performed exactly as described previously 4 using the primary antibodies cFos monoclonal antibody (sc-8047; Santa Cruz, Dallas, TX, USA) and corneodesmosin polyclonal antibody (13184-1-AP; Proteintech, Rosemont, IL, USA). Images were acquired using an Axioskop 2 Plus optical microscope (Zeiss, Oberkochen, Germany). 4 Six representative images were obtained for each condition. For immunofluorescence, 5 μm air-dried cryosections were incubated with primary antibodies LCE1A polyclonal antibody (PA5-24375; Thermo Fisher Scientific, Waltham, MA, USA) or LCE6 polyclonal antibody (HPA046376; Sigma, St Louis, MO, USA).
Image analysis Image analysis was performed using ImageJ software. The parameters of interest were epidermal thickness for HPSstained sections, cFos nucleus positive cells, and the surface area of corneodesmosin, LCE1A, and LCE6 immunostaining. Stratum corneum thickness was quantified using Visilog software (FEI, Hillboro, OR, USA). The algorithm followed two steps: segmentation and measurement. The epidermis was removed using a semiautomatic method. A K-mean algorithm was used to segment the image into regions with same characteristics. The region corresponding to the stratum corneum was preserved. The stratum corneum cavities were filled and an average thickness was computed. The quantification of cFos-positive epidermal cells was performed exactly as previously described for other nuclear proteins.
The qPCR data perfectly matched the microarray data, except for COL4A1, which qPCR did not find significantly repressed by treatment 2 (Figure  1C ). To decipher the cellular functions and pathways potentially impacted by the climatic changes, the Database for Annotation, Vizualisation and Integrated Discovery (DAVID) functional annotation tool was used. 5 This analysis revealed (Figure  1D ) strong enrichment in genes involved in extracellular matrix maintenance or synthesis for transcripts repressed by treatment 1 (n=22, p=1. 1E-12) and, to a lesser extent, for transcripts repressed by treatment 2 (n=15, p=8. 4E-5). This result was confirmed by annotation of the 87 transcripts modulated after both treatments, which identified extracellular matrix and collagen genes as being significantly enriched (Figure  1D ).
Statistical methods Data were statistically analysed using the GLM procedure SAS version 9. 3 (SAS Institute Inc. , Cary, NC, USA) to evaluate the effect of sampling day (H10, H20, B10, B20). In case of a significant sampling day effect, orthogonal contrasts were performed to test the evolution within each diet (H10 v. H20; B10 v. B20) and the difference between the two diets (H v. B). The CORR procedure of SAS was used to assess the correlation (Pearson's correlation coefficient) between the caecal/colonic and faecal parameters in a two by two comparison. The significance threshold was set at P < 0. 05, and at P < 0. 1 for trends. Principal component analyses (PCA) was used to generate an overall view of the relationship between all caecal and faecal parameters, and between all colonic and faecal parameters.
Acknowledgements The authors acknowledged  Alltech  for their financial support and their revisions of this manuscript, and  Jules Taylor-Pickard  and  Helen Warren  for their support throughout this study. They thank the staff of the  AgroSup Dijon's experimental facilities (Bernard Château and Claire Sivry) and laboratory (Francine Delamarche ,  Emmanuel Jacotot  and  Marie-Claire De Vos Franzin ) who contributed actively to this trial. The authors also acknowledged  Jean-Paul Pais de Barros  ( Lipidomic platform Dijon, INSERM UMR 866 ) for analyses of lipopolysaccharides. They are grateful to  Alain Breuvart  and  Christine Fant  from  Agrosup Dijon  for their help with the statistical analyses. Finally, the  Agrosup Dijon students (Cléo Omphalius ,  Manon Schouller  and  Clothilde Villot ) are thanked for their involvement in the project.
Acknowledgements We acknowledge the  World Climate Research Programme 's Working Group on Coupled Modelling, which is responsible for CMIP, and we thank the climate modeling groups (listed in Supplementary Table 1 of this paper) for producing and making available their model output. We thank also  Gil Compo  for making the 20 th Century Reanalyses available and  Bastien Dieppois  and  Yves Richard  for helpful discussions. Calculations were performed using HPC resources from  DSI-CCUB (université de Bourgogne ).
| Molecular phylogeny We obtained a robust phylogeny of Hygrotini, with good support for most internal nodes except for the monophyly of F I G U R E 1 Best maximum likelihood (ML) phylogram obtained in RAxML with the extended dataset of Hygrotini (including outgroups and multiple terminals per species). Black circles, nodes with bootstrap support in RAxML (BS) >70 and posterior probability (pp) in BEAST >0. 95; when support values were lower: numbers above nodes, BS; numbers below nodes, pp. X, nodes not recovered in the BEAST analyses (Fig. S1 ). See Table  S1  for details on the specimens. For clarity, only the subgenus name is given in Hygrotus s. str. and Coelambus. Habitus photograph: Hygrotus (Coelambus) lagari  (Fery, 1992 ) (from Millán et al. , 2014)  clade B3 and its relationship with Hyphoporus.
ACKNOWLEDGEMENTS We would like to thank all colleagues mentioned in Table S1 for sending valuable material for study, as well as  Ana Izquierdo  (MNCN),  Rocío Alonso  and  Anabela Cardoso  ( IBE ) for laboratory work. M. Manuel is grateful to  Andriamirado T. Ramahandrison  for help during field work in Madagascar, in the context of the RicciaTeam expedition led by  Catherine Reeb. We also thank  Josefa Velasco  and  Susana Pallarés  ( Universidad de Murcia ) and  Paula Arribas  ( Instituto de Productos Naturales y Agrobiología-CSIC ) for comments on the origin and evolution of salinity tolerance, and three anonymous referees for their comments and suggestions. This work was partly funded by an  FPI  grant to A. V. , and projects  CGL2013-48950-C2-1-P  and  CGL2013-48950-C2-2-P  ( AEI/FEDER, UE)  to I.
The mixed-model repeated-measures analysis for photosynthesis was done using data shown in Fig. 1a ), with the time term indicating sampling date across three years. For ANPP, the time term is 'year', the first to third year of the full eCO2 treatment. In both analyses, a mixed-model repeated-measures analysis was done using a fixed treatment (CO2) and a random plot effect, and Type III sums of squares computed using restricted maximum likelihood estimates for F-tests. Foliage and twig production were measured as litterfall, collected monthly in ~0. 2 m 2 circular fine-mesh traps at eight random locations per plot  33. Litter was sorted into leaf, twigs and bark, and other material, dried at 40°C and weighed. A subsample was reweighed when dried at 70°C and a small moisture correction was applied to the leaf component of the whole dataset.
Acknowledgments EucFACE was built as an initiative of the  Australian Government  as part of the  Nationbuilding Economic Stimulus Package , and is supported by the  Australian Commonwealth  in collaboration with  Western Sydney University. A portion of this work was supported by grants from the  Australian Research Council (ARC)   Discovery grants scheme , particularly grants  DP110105102  and  DP160102452. KYC acknowledges  ARC support (DECRA program ), and TEG acknowledges the  CSIRO  and a  Marie S. Curie IEF  Fellowship. We thank the team of people who have assisted with the canopy sampling, and  S. Wohl ,  C. Barton ,  V. Kumar ,  C. McNamara , and  C. Beattie  who provided technical assistance. We thank  C. P. Osborne  for comments on an early version of the manuscript. The data are available as a package from Research Data Australia.
Image processing and features extraction The application of image processing analysis was necessary to extract the droplets geometrical information from the optical micrographs. Fig  2  shows the scheme of the proposed image processing procedure that was previously used in material classification and identification tasks such as wood species  [9]. This procedure provides an alternative way to collect information about relaxation processes in magnetic droplets within polymeric solutions. Image analysis application allows to extract a vector of representative features related to the geometry of the objects in the image such as diameter, area, distance, circularity, rectangularity, position, etc. [9]. ImageJ  [10]  and R software (through biOps library)  [11]  free software programs have been used to implement the enhancement and segmentation tasks (Fig  2 ).
Optimum fittings were obtained by applying the Differential Evolution evolutionary global optimization algorithm (DE), through the DEoptim function of the R DEoptim package  [24, 25]. The KWW parameters (a, b, λ c , β) obtained from fittings corresponding to the 3 geometrical indexes of the droplets are given in Table  1. The good fittings of experimental data are attested by the values of the determination coefficients (R 2 )  [14]. Whatever the geometrical parameter (area, AR or major diameter), it could be observed that the characteristic relaxation time λ c is in the same order of magnitude for the deformation and relaxation of droplets indicating a reversibility of the process. There is only one exception for droplet 3 that could be explained by its smaller size. Moreover in most case the exponent β is close to one corresponding to a process with a single relaxation time  [23].
Bibliographic data This study is based on an extensive literature survey where no boundary dates were fixed; therefore, this review covers literature published about Greece since the beginning of scientific writing and observations. We searched for records of alien molluscan species in the waters of Greece in both indexed and nonindexed journals (often manually), as well as relevant institutional reports and grey literature. However, we particularly focused on recent records of species labelled as aliens in Greek waters, species considered to be alien in the Mediterranean basin and recorded from Greece, and species already included in previous alien-species check-lists. Particular attention was given to the reliability of published records and to the status of species labelled as non-indigenous.
facebook. com/groups/331466433724867/), both mostly contributed to by Greek subscribers. In the case of straightforward identifications, we asked the contributors for the permission to use the data as well as any relevant additional information. These data were augmented by additional information obtained through the Ellenic Network on Aquatic Invasive Species (ELNAIS), a dynamic online information platform aiming to collect and report spatial information on aquatic alien species in Greek waters  (Zenetos et al. 2015a). Records reported to ELNAIS were further validated before being included in this study. Finally, unpublished data for Siphonaria pectinata (Linnaeus, 1758), a species not included in previous reviews, were sought in the Goulandris Natural History Museum (GNHM) to better determine its first detection in Greece.
Database development A database of taxa recently reported from Greece was developed for the present study. In contrast to rejected species, where mostly the rationale for exclusion was explained, detailed information was provided for each included alien taxon, including: i) taxonomic notes; ii) date and literature reference of the first sighting/collection; iii) presence of additional confirmed records; iv) possible misspellings, synonyms, different genus/species combinations or misidentifications published from Greece; v) presence of unpublished records; vi) various notes on accuracy of identification and/or finding data; vii) status as alien or cryptogenic in the Mediterranean Sea as a whole; viii) establishment success in Greece and possible invasiveness; ix) most likely primary or secondary pathway/s in the Mediterranean and in Greece (see detailed explanations in Appendix 2).
Unpublished data The different groups of citizen scientists contacted allowed us to obtain records that spanned three molluscan classes. While amateur shell collectors are mostly interested in shelled molluscs, including microshells that can be only found by the analysis of sediments under a stereo-microscope, underwater photographers are mostly interested in conspicuous and photogenic taxa, such as the large alien sea slugs or cephalopods. We obtained 173 unpublished records, covering 29 taxa (25 aliens and 4 cryptogenics, including one possible intra-Mediterranean transfer) (Appendix 1). To these should be added 4 lots of Siphonaria pectinata (Linnaeus, 1758) from GNHM (Appendix 1), one of which confirmed the presence of this species from Greece as early as 1973. Due to the presence of some earlier reports (e.
g. ,  Zenetos et al. 2008a Zenetos et al. , 2008b Zenetos et al. , 2011b Zenetos et al. , 2013)) , the majority of new unpublished data (138 records) are from 2010 to 2015. However, some researchers/amateurs not contacted previously had older records of some alien taxa in their logbooks or photo archives. Moreover, some shell collectors preserve their specimens with full data and often collect large amounts of biogenic sediment that may remain unsorted for decades. Thus we obtained some older, unreported, data, the three oldest ones (apart those of S. pectinata) dating back to 1994. Records of four gastropods constituted new sightings for Greece, namely Cerithidium perparvulum (Watson, 1886), Cerithiopsis pulvis (A. Issel, 1869), Cerithiopsis tenthrenois (Melvill, 1896), and Pyrunculus fourierii (Audouin, 1826) (Table  2 ; Figure  2 ; Appendix 1-2) (for a previous record of C.