dataesr/scientific-paragraphs-categorization huggingface dataset:
Sampling and in situ measurements Photosynthetically active radiation PAR (~ 400 -700 nm) was measured 1 m above the mesocosms with a 1 s step and averaged each day using a LI-COR quantum sensor and LI-COR Li1400 data logger. Daily rainfall data were measured at proximity of the experimental facilities (< 100 m) and obtained from the local weather forecast service (Météo-France, Nouméa). Water temperature was automatically and continuously monitored with a 1 h step randomly in five tanks using thermo buttons (Proges plus). In 8 tanks (two per treatment D12S + , D12S -, D4S + and D4S -), an automatic system associated with an YSI 6600 probe provided continuous and hourly measurement of different parameters in the water column (salinity, temperature, fluorescence and turbidity). Discrete measurements of salinity, dissolved oxygen (DO) and temperature were also made in each tank every morning (08:00) using a portable conductivity meter (WTW cond330i, Welheim, Germany) and an oxygen meter (WTW oxi330i, Welheim, Germany).
(1985). Flow cytometry. Water column subsamples (1. 5 ml) were preserved with 1% Glutaraldehyde (final concentration) and stored in liquid nitrogen pending flow cytometric analysis  (Vaulot et al. , 1989). Samples were defrosted at ambient temperature and subsequently analysed using a FACSCan flow cytometer (BD-Biosciences, San Jose, CA) equipped with an air-cooled argon laser (488 nm, 15 mW). Methodology and data analysis used in this study are fully described in  Lemonnier et al. (2016). Based on cellular RALS and fluorescence properties, several populations were conventionally distinguished (e. g. Lucas et al. , 2010) : two distinct Synechococcus populations and five eukaryotes groups. The two picocyanobacteria populations (Syn) were pooled in a single group. Spectrofluorimetry. Water samples (0.
Statistical analyses Results are presented as means ± standard deviation (S. D. ). Statistical comparisons of experimental data were carried out using XLStat software 2011 (Addinsoft, Paris, France), at each sampling date by a two-way analysis of variance (ANOVA), with shrimp density (D) (two or three fixed levels -function of the data set) and with or without access to the sediment (S) (2 fixed levels) as major sources of variance  (Scherrer, 1984). Data were first checked for normal distribution and homogeneity of variance using the Shapiro-Wilk and Bartlett's tests, respectively. If data were not normally distributed, they were transformed for normality using log-transformation, square root or arcsine transforms. If data did not meet the test criteria after appropriate transformations, comparisons were made using the nonparametric Kruskal-Wallis test.
Pico-and nanophytoplankton abundance by flow cytometry Mean abundances ranged between 5. 5 x 10 2 and 4. 7 x 10 6 cells ml -1 (Fig. 4a ). S + tanks showed higher abundances than S -tanks from day 11. However, due to the high data variability, differences were significant (p < 0. 05) only at days 8, 39 and 43. Shrimp density effect on picocyanobacteria abundance was observable only for the last sampling date. Among the eukaryotes, the smallest were assigned to picoeukaryotes (Peuk) and the largest to cryptophytes (Cry)  (Courties et al. , 2005; Lucas et al. , 2010). To make the presentation of results easier, the three other eukaryote populations were pooled in a single group named nanophytoplankton (Nan). Mean abundances of Peuk ranged from 0 to 1. 0 x 10 6 cells ml -1. They increased from day 11 in S + tanks (Fig.
4b ) as did picocyanobacteria, but due to the high data variability, the effect of S was not statistically demonstrated. Likewise, no D effect was observed. Nanophytoplankton was amongst the less abundant groups, with abundances ranging between 0. 3 x 10 3 to 3. 0 x 10 5 cells ml -1 (Fig. 4c ). Maximum abundance was recorded in the treatment D12S +. S did not show any significant effect except at day 22 with a positive effect. Abundances were significant with D at days 11, 22 and 39. Cryptophytes occurred in 85% of the samples, but their abundances (data not shown) were always lower than 70 x 10 3 cells ml -1. Factor D showed a significant positive effect at days 4, 15 and factor S a negative and positive effect at days 18 and 39, respectively.
However, the community shift was similar in all treatments characterized by different turbidity levels. Concerning the green algae community blooming mainly during period B, three assemblages were distinguished according to their chl b/chl a chlorophytes ratios. Interestingly, the chl b/chl a chlorophytes ratios calculated for each assemblage (0. 86; 0. 61; 0. 38) from spectrofluorometry data were close to those measured in a shrimp pond from HPLC data using CHEMTAX software, i. e. 0. 81, 0. 65, and 0. 35  (Lemonnier et al. , 2016). According to the authors, the ratio 0. 81 was associated with Prasinophytes type 3 (with prasinoxanthin) and the ratio 0. 65 with Prasinophytes type 1-2 (without prasinoxanthin)  (Latasa et al. , 2004). The ratio 0. 35 identified as Chlorophytes by HPLC was slightly lower than the value found in our study (0.
Acknowledgements This work was supported by a research grant between the Loyalty Islands, Northern Province, Southern Province Government of New Caledonia and Institut Français de Recherche et d'Exploitation de la Mer (IFREMER) (12/1219969/C). The authors thank the anonymous reviewers for their useful comments and suggestions to improve the manuscript. We would like to thank Aline Personne who kindly helped in the analysis. Growth (g j -1 ) 0. 07 ± 0. 02a 0. 16 ± 0. 01b 0. 05 ± 0. 00a 0. 13 ± 0. 01c.
Other data were obtained from samples taken from farms in which snails have been experimentally transplanted. Among the three departments of Limousin, the Haute-Vienne was chosen for this study because of numerous samples of snails collected by our team in this area from the 1970s. The results obtained in several farms or in several wild watercress beds have already been reported  [1] [2] 32, 52]. In contrast, the data on the natural infection of other snail populations have not yet been published.
Statistical analyses The prevalence of F. hepatica infection was calculated using the ratio between the number of infected snails and that of adult snails collected from a farm or a watercress bed. The individual values obtained for the different farms  Different categories for the mean altitude of municipalities, their mean annual rainfall or their mean annual temperature were used according to the data provided by the Carte-de-France website (altitude) or the maps published by Météo France  [40]. These categories have been chosen so that they have identical amplitude. As the altitude of farms and watercress beds ranged from 160 m to 570 m, the individual values noted for the prevalence of natural infection in snails were classified in the following four categories of altitude: < 300 m, 300-400 m, 401-500 m, and > 500 m.
Tropical forests of the Guiana Shield are the most affected by gold-mining in South America, experiencing an exponential increase in deforestation since the early 2000's. Using yearly deforestation data encompassing Guyana, Suriname, French Guiana and the Brazilian State of Amapá, we demonstrated a strong relationship between deforestation due to gold-mining and gold-prices at the regional scale. In order to assess additional drivers of deforestation due to gold-mining, we focused on the national scale and highlighted the heterogeneity of the response to gold-prices under different political contexts. Deforestation due to gold-mining over the Guiana Shield occurs mainly in Guyana and Suriname. On the contrary, past and current repressive policies in Amapá and French Guiana likely contribute to the decorrelation of deforestation and gold prices.
In both cases, the chaotic expansion of small-scale goldmining remains largely uncontrolled  (MacDonald 2016). Since 2002, facing the increasing activity of illegal miners, the French government launched a series of military operations in French Guiana (Colonel Danede 2005, de Rohan et al 2011). In Amapá, stricter regulation imposed in the 1990's by Brazil has limited the local expansion of gold-mining but provoked leakages to neighbouring countries  (Veiga 1997 , WWF Guianas 2012 , Ayala et al 2013 , de Theije 2015). The objective of the present study is thus to assess regional and national drivers of deforestation due to gold-mining in the Guiana Shield. Assessing goldmining related deforestation is challenging; both high spatial and temporal resolution data are needed to cope with its small geographical extent and high temporal variability.
Focusing on the East-West contact area, i. e. the boundary between French Guiana and Suriname (figure  1 ), and based on an extended dataset covering close to 20 years of deforestation derived from existing maps by  Hansen et al (2013)  and maps produced for the purpose of the present study, we estimated deforestation leakages between both countries. Under our model's assumptions, the repressive context in French Guiana and the absence of regional political cooperation for controlling the expansion of gold-mining might have contributed to substantial deforestation leakages from French Guiana to Suriname. We conclude by discussing how gold-mining challenges some corner-stone principles of REDDþ and provide some recommendations for policy makers regarding the efficiency of current national policies against illegal gold-mining activity.
Extending the dataset from 1996 To test the hypothesis of deforestation leakages between Suriname and French Guiana, we extended the deforestation dataset to include the range 1996-2000 for both countries. This allowed us to know more about what was occurring before the beginning of the repressive policy. 67 Landsat 5 scenes were used, covering the extent of gold-mining areas in 2000. Forest cover was classified using Random Forest algorithm  (Breiman 2001) , known for its good accuracy  (Grinand et al 2013). Forest cover maps were built for  1996, 1997, 1998 and 1999, and compared  to create yearly deforestation maps until 2000. More details on the methodology used for forest cover classification and to ensure homogeneity with the Hansen dataset are provided as supplementary materials (SM3).
Bayesian inference The models parameters described above were estimated using Bayesian inference in a MCMC scheme. Compared to frequentist inference, this allowed us to restrict the range and distribution of values of each parameter to realistic intervals. Priors are given in table 1. 50 000 iterations were computed for each model. 10 000 runs were excluded as burning periods. All data processing was accomplished via the free and open-source softwares GRASS GIS (GRASS Development Team 2015), QGIS (QGIS Development Team 2009) and R (R Core Team 2015).
Acknowledgments We thank the handling editor and the anonymous reviewers for their comments on a previous version of this manuscript. This study is part of a PhD project funded by the  French Ministry of Research  and was supported by the REDDþ for the  Guiana Shield  project, itself granted by the  FFEM , the  Région Guyane , the  European Union  and the  Interreg Caraïbes program. It was also part of the  GFclim  project funded by the  PO-Feder Région Guyane  ( FEDER 2014-2020 , Project  GY0006894 ). Finally, this work benefited from an ' Investissement d'Avenir' grant  managed by the  Agence Nationale de la Recherche  ( CEBA , ref  ANR-10-LABX-0025 ).
Acknowledgements. This study used equipment from and data collected for the AgrHyS environmental research observatory (http: //www6. inra. fr/ore_agrhys). We thank  Sen Gu  and technical staff from  INRA  and  Géosciences Rennes  for their assistance during the field sampling. We also thank all of the people involved in the maintenance of the field installations and the creation of the databases. Sara Mullin  carried out English-language editing work on an earlier version of this paper (www. trad8. eu/us/sara-mullin. html). We would also like to express our thanks to the reviewers and associate editor for their constructive suggestions and helpful comments. Edited by:  Marcel  van der Meer Reviewed by:  Peter J. Hernes  and one anonymous referee.
Acknowledgements We thank  Philippe Gaspar ,  Franck Mercier  and  Jacques Stum  from  CLS  for providing sea ice concentrations data, Thomas Lavergne from  Osi-Saf  who provided sea ice extent data,  Stefan Kern  from the  University of Hamburg  for his expertise and his precious help in identifying the coastal polynyas,  Robert Johnson  from the  University of Tasmania  for providing the phytoplankton concentrations. Author contributions A. A. and R. C. designed the study. A. A. , P. F. and P. T. collected the data. A. A. and M. B. wrote the first draft of the paper and all authors contributed to subsequent revisions. A. A. and R. C. prepared the figures.
Pot experiment A pot experiment using various secondary P-fertilizers and TSP as a reference was carried out with two soils (pH 4. 9 and pH 7. 1 in 0. 1 M CaCl 2 ) that had a low total P content. The soils were collected at two sites in Brandenburg, Germany, and included an acidic soil from Thyrow that had a sandy soil texture and a nearly neutral soil pH from Berge that had a loamy sand soil texture. These soils were mixed with equal amounts of quartz sand to lower the P content. The total P in the acidic soil was 114 mg kg -1 , and the extractable calcium acetate lactate P (P CAL ) was 38. 0 mg kg -1. The total P in the nearly neutral soil was 117 mg kg -1 and the P CAL was 17. 0 mg kg -1. To achieve a nearly neutral pH value, lime was added to the latter soil (see Table  S1  for additional data of both soils).
l-XRF and XANES microspectroscopy Micro-XRF maps and XANES spectra were collected on the ID21 X-ray microscopy beamline  (Salomeet al. 2013)  at the European Synchrotron Radiation Facility (ESRF, Grenoble, France). For detailed information of the setup see the supplementary material. The reference substances were prepared as thin films on adhesive tape. The XANES spectra were collected in transmission mode using a Si diode downstream of the sample. Two-dimensional l-XRF elemental maps were collected at 2. 25 keV (above the P K-edge) by raster scanning the sample with respect to the X-ray beam. Maps were collected using 250-500 ms data collection times per 1. 0-5. 0 lm step depending on the P concentration, value of the incident flux, and size of the P spot. To optimize the discrimination of the various XRF line contributions and, specifically, to remove the Si contribution to the P signal that originated from quartz and clay, the XRF spectra were batch fitted at each map pixel using the PyMCA software  (Soleet al.
2007 ). The P K-edge XANES spectra were collected from 2. 13 to 2. 20 keV with 0. 2 eV energy steps in continuous scan mode. Depending on the P concentration and the matrix, 2-50 quick scan spectra of 0. 1 s per energy step were recorded and averaged to optimize the signal-to-noise ratio (SNR). No radiation damage was observed during successive data collections. For each sample, 10-50 l-XANES spectra were collected. The XANES spectra were reduced using the standard normalization procedure of the Athena package in the Demeter 0. 9. 20 system  (Newville 2001; Ravel and Newville 2005). The E 0 edge energy was chosen as the maximum of the first derivative of the data. The spectra were background corrected using a linear regression fit through the pre-edge region [E 0 -18 eV; E 0 -8 eV] and a polynomial regression fit through the post-edge region [E 0 ? 30 (± 2) eV; E 0 ? 47 eV], aiming at a horizontal post-edge signal and so that pre-and postedge lines are parallel.
Acknowledgements Synchrotron analyses were conducted on the ID21 beamline at the European Synchrotron Radiation Facility (Grenoble, France) on in-house research beam time. CV thanks the German Federal Ministry for Food and Agriculture (2811NA022) and the German Research Foundation (VO 1794/4-1) for financial support. VW, AM, and CA thank the European Union for funding within the European Union's Seventh Programme for Research, Technological Development and Demonstration under Grant Agreement No.
MATERIALS AND METHODS In autumn 2013 and 2014, four experimental sites (> 3 km apart) were selected in southern Belgium (Table  1 ). All sites were mixed oak stands dominated by adult trees of Q. robur and/or Q. rubra. Acorns of both species were collected from the ground under fruiting trees and stored at room temperature. Acorns with obvious damages were discarded. Acorns were manipulated with latex. At every site, four pairs of 28-cm diameter plastic dishes (10-20 cm apart) were randomly placed on the ground. One dish per pair contained 20 acorns of Q. robur, the other 20 acorns of Q. rubra. Every week, the acorns remaining in each dish were counted and removed, and the dishes were refilled with 20 acorns. When a dish was accidentally spilled, the data of the considered week were ignored.
For each Quercus species, the number of acorns removed from the dishes was converted to the proportion of acorns removed during one week, i. e. acorn removal rate. For each site, the mean acorn removal rate of the four dishes was calculated according to species and week, and arcsine-transformed. A mixed model with repeated measurements (proc. MIXED) was used to analyze the effects of species (fixed), week (random), site (random), and the interaction site × species on the mean acorn removal rate. Analyses were performed using SAS version 9. 4 (SAS Institute Inc. , USA).
Acknowledgements The authors would like to thank  Thierry Kervyn  for access to Onoz site and  Alain Licoppe  for the loan of camera equipment. This study has been carried out with financial support from the  French National Research Agency (ANR)  in the frame of the  Investments for the future Program  ( ANR-10-IDEX-03-02 ); and from the  University of Liege  in the frame of the " Fonds spéciaux pour la recherche ".
Overall evolutionary conservation of the Smc5/6 complex in primates To trace the evolutionary history of the Smc5/6 complex, we compared the sequence of its six subunits in primates (Figure  1A ). As a comparison, we also analyzed the evolutionary history of all the other primate SMC genes. These include the Smc1 and Smc3 genes, which encode the core cohesin subunits, and the Smc2 and Smc4 genes encoding the condensin core subunits. The sequences of these genes were retrieved from publically available datasets (Table  1 , Dataset S1). To perform more robust phylogenetic and selection analyses, we obtained additional primate species sequences using RT-PCR approaches (Table  1 , Figure  1B ; see Methods). Overall, we included up to 20 simian primate species in our positive selection analyses to span 40 million years of evolution  (25, 26).
We found that the synteny of the genes was conserved during primate evolution, although some subunits had duplicated pseudogenes in a few primate species (Figure  S1 ). Amongst the core SMC proteins, the most conserved are the cohesin Smc1 and Smc3 subunits, which share 100% and 99. 9% pairwise identity at the amino acid level in a simian primate alignment, respectively (Dataset S1). Smc6 was the least conserved SMC protein with 97. 4% pairwise identity in simian primates. Using the Genetic Algorithm for Recombination Detection (GARD) on the complete set of genes  (27) , evidence of recombination (GARD, p<0. 05) was only found for Nsmce3, and therefore subsequent phylogenetic and selection analyses were performed on Filleton, Abdul, et al. both the whole Nsmce3 gene and the two identified Nsmce3 gene fragments (from 1-246 bp and 247-912 bp).
Phylogenetic analysis of the ten genes showed that the gene trees derived from nucleotide alignments were largely in accordance with the accepted species tree from Perelman and colleagues (Figure  1B , and Dataset S1)  (26). To assess whether the Smc5/6 complex and the Smc1-4 genes have experienced diversifying selection during primate evolution, we performed four types of positive selection analyses. Firstly, we used the BUSTED method that tests whether a gene has experienced positive selection on at least one site or one branch during evolution  (28). Of the six Smc5/6 complex subunits and the four SMC genes from the cohesin and condensin complexes, only one, Smc6, showed gene-wide evidence of episodic positive selection (BUSTED, p<0. 05, Figure  1C ). These findings were confirmed using the PARRIS method that also detects evidence of positive selection using a codon alignment  (29) , although the level of significance was not reached for the Smc6 gene (p=0.
19; Figure  1C ). Thirdly, we ran the Codeml program from the PAML package  (30)  on our codon alignments to compare two models: one that allows positive selection at certain sites (M8, alternative hypothesis) and one that disallows positive selection (M7, null hypothesis). We then performed a likelihood ratio test (LRT) to examine which of the two models fitted better our data. Overall, there was no convergence for seven of the ten genes because they were too conserved (see Methods for details) and no evidence of significant positive selection was found for the remaining genes (Figure  1C ). Finally, we used the Bio++ package from Guéguen et al. (31) , which has two main advantages over PAML to similarly test for evidence of positive selection (M7 vs. M8 as implemented in Bio++). First, the DNA substitution models use non-stationary matrices, which allow nucleotide composition to change over time, and therefore improve the fitting to real data  (32).
These "genetic innovations" would be missed in typical methods screening for positive selection. We found some indels in genes encoding for several Smc5/6 complex subunits (Dataset S1). In particular, we found a 5-amino acid (aa) indel in the N-terminal region of Smc6 (Figure  2C ). The five New World monkey species, including the two sequenced in this study, display a TASFT motif at this position. However, this 5-aa motif was not present in any of the retrieved Catarrhini species sequences (n=13) (Figure  2C  Hominoids and Old World Monkeys; Dataset S1). To decipher if this 5-aa indel was specific to simian primates, we extended our analysis to mammals. We found a significant plasticity within this region with both indels and amino acid changes during mammalian evolution. For example, the prosimians' proteins contain a 5-aa motif, but with amino acid differences in the TASFT motif (TVSFT and AVAFT, respectively; Figure  2C ).
Host phylogenetic analyses Sequences of primate or mammalian orthologous genes were retrieved from publically available databases using UCSC Blat and NCBI Blastn with the human sequence as the query. After including sequences obtained from de novo sequencing in this study, the sequences of the orthologues were codon-aligned using Muscle  (65)  with minor adjustments (alignments are in Dataset S1). The name of each sequence has been uniformed: the first three letters of the host genus name followed by the first three letters of the species name (e. g. papAnu for Papio Anubis, or macMul for Macaca mulata). When sequences were retrieved using Blat on the primate full-genome assembly, the name of the genome assembly was used (e. g. panTro4 for Pan troglodytes, or hg38 for human). The synteny of each locus of interest was analyzed in UCSC using Blat and the Genome Browser.