dataesr/scientific-paragraphs-categorization huggingface dataset:
Modularity followed a normal law while centralisation, global efficiency and resilience followed a log-normal law. We then used individual network measures and the function PCA and HCPC of the FactormineR package in R to perform a hierarchical clustering analysis using principal components analysis to assess the presence of intermediary domestics. The HCPC function permitted us to determine whether some domestics acted as intermediaries (i. e. whether certain domestics had higher strength, in-strength, out-strength, degree and betweenness relative to other domestics). We also performed Pearson correlations between the different individual network measures. All tests were conducted on R 3. 6 (R Development Core Team, 2009). The significance level was set at 0. 05. Results are shown as mean ± stdv  [median].
Acknowledgments MQ was funded by the  Ministère Français de l'Enseignement Supérieur et de la Recherche. OB was funded by the  Fonds pour la Recherche dans l'Industrie et dans l'Agriculture and the Van Buuren Fund (Belgium). CS is a junior member of  IUF (Academic Institute of France ) and a fellow of  USIAS (University of Strasbourg Institute for Advanced Studies ).
SDS-PAGE. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of BLG, in the absence or presence of ligands, before and after HP-SANS measurements, was performed under nonreducing conditions  (22) , unless it is otherwise stated. An amount of 12 µg of each protein sample was applied on 4-20% gradient precast gel (BioRad, USA). Gels were stained using Coomassie brilliant blue G-250 (Sigma Aldrich) and band intensities were quantitated using ImageJ software (National Institutes of Health, USA). The intensity of each band was normalized to the total band intensity within sample and results were expressed as %.
The pressure was increased at a speed of 10 MPa/min. Measurements of buffer solutions in the absence or presence of ligands (without protein) were performed at the same above conditions and recorded spectra were subtracted from the spectra of BLG without ligand or BLG/ligand complexes, respectively. The fourth derivative spectra were calculated by OriginPro 8. 5 Software (USA) using Savitzky-Golay smoothing algorithm with 100-point window. The exact position of the maximum absorption bands at ~291 nm (characteristic of Trp residues of BLG) in the fourth derivative spectra was determined and the percentage of protein unfolding was determined using the following equation: % !"# %&'()*+&, = -!. # %&'. -& -!. # %&'. -(!! %&' * 100 Eq. 1 where l0. 1 MPa, l300 MPa, and lP represent the absorption maximum at 0.
4 where NA is the Avogadro number and Dr 3 the contrast. ScÅtter software (http://www. bioisis. net/tutorial/9) was used to determine the intensity at zero angle I(0) and the radius of gyration (Rg). These values are defined at small Q-values (QRg < 0. 8-1. 4) by the Guinier approximation with  (27) : ln(𝐼(𝑄)) = ln(𝐼(0)) - > 6 ? 7 6 @ Eq. 5 The distance distribution function P(r) was calculated with PRIMUS (ATSAS) program  (28). In situ HP-SANS data were fitted using a cylinder model  (27)  in SasView software (https://www. sasview. org), with obtained chi 2 values not exceeding 1. 2. However, the SANS data measured after HP treatment for BLG oligomers were better fitted with a triaxial ellipsoid model  (29)  with chi 2 values given in Table  3. BLG oligomers were also modeled by ab initio rigid body modeling using MASSHA software (ATSAS) (30): oligomers were built using crystal structures from, either BLG monomer (3BLG.
Structural features for native and fully unfolded BLG. We checked that native BLG at pD 7. 2 is dimeric by fitting SANS data with the theoretical curve obtained from the dimeric BLG crystal structure (1GX8. pdb (  18 )) using CRYSON software (ATSAS) (31) (Fig. 2 ). Besides, using the scattering length density of BLG determined by "contrast variation" experiment (Table  1 ), we estimated, using Eq. 4 with d = 1. 35 g/cm 3 and c = 8 mg/mL, that MW of the scattering particles is equal to 37,924 ± 1,129 g/mol, in very good agreement with the theoretical MW of dimeric BLG (37,142 g/mol). The pair-distribution function P(r) analysis, giving a Dmax of ~71 Å, confirms the dimeric conformation of BLG in our study conditions (Fig. 2B ). The presence of deuterated 6 M guanidine (Gdn)-DCl completely unfolds BLG, as shown by the SANS data that fit the Gaussian coil model commonly used for fully unfolded proteins (Fig.
05-0. 06 Å -1 (Fig. S3 , B & D) to ~0. 03 Å -1 (Fig. 6A ). The ab initio envelopes of BLG oligomers simulated by MASSHA and DAMMIF programs (ATSAS) (30)  (34)  show that a higher protein concentration induces larger oligomers, which confirms the increased dimensions of the ellipsoid model that fits the data in SasView program (Figs. 6 and S7, B & D, Table  3 ). MASSHA simulations use BLG crystal structures (monomers or dimers) as building blocks, that are assumed to remain "folded". However, without making any assumption on BLG folding state, DAMMIF  (35)  ab initio simulations confirm MASSHA results (Fig. S7, B  & D ). Effect of ligands on BLG oligomerization. Resveratrol binding does not change significantly HPinduced BLG refolding and oligomerization (Fig. 6A ). In contrast, retinol binding prevents partly, but significantly, both protein irreversible unfolding and oligomerization extent, as observed with the peak shift to a lower Q-value (0.
In retinol-induced stabilization of BLG folding, the protein may spend more time in its native conformation during in situ HP treatment, preventing SH group exposure to the solvent and consequently reducing the extent of aggregation. SANS probes both covalent and noncovalent oligomers, giving access to their MW (Table  3 ) and shapes (Figs. 6  and S7 ) through analytical fitting and ab initio simulations. The MASSHA modeling uses the ellipsoid model parameters from SasView (Fig. 6 ) as constraints to "build" the oligomer shapes, in agreement with the data obtained on BLG oligomerization by gamma irradiation  (52). The overall envelopes are also consistent with those obtained from DAMMIF program without any a priori geometrical assumption (Fig. S7 ). Interestingly, we found for BLG/retinol complex the formation of octamers in the presence of retinol (Table  3 ), as reported in other studies on BLG at pH 4-5  (16).
ACKNOWLEDGMENTS We thank  Mikaela Börjesson  ( LLB, France ) for BLG preparation, as well as  Adrien Lerbret  ( PAM, France ),  Marie-Sousai Appavou  ( JCNS, Germany ), and  Raphael Dos Santos Morais  ( LIBio, France ) for their advice. LLB neutron facility is acknowledged for beamtime on PACE SANS instrument.
Statistical analysis Data are expressed as mean ± standard error and were verified their normality and homogeneity before used for statistical analysis. All statistical analyses were performed using IBM SPSS version 21 (IBM Corp. Armonk, New York, USA). If data did not meet the assumption of normality and homogeneity of variance, data were log transformed. Statistical analysis of the data was performed using one-way ANOVA followed by a Tukey's HSD post hoc comparison test to evaluate daily effect of Hg on serum osmolality, serum ions, hematological parameters and Hg level in gills. Differences were considered statistically significant at p < 0. 05.
MATERIALS AND METHODS Production of amiRNA Lines Displaying Reduced OsHKT1;4 Transcript Levels Two artificial microRNA (amiRNA) sequences targeting OsHKT1;4 transcript (I3amiR and I4amiR) were selected among those proposed by the WMD3 program (web MicroRNA designer; http://wmd3. weigelworld. org/). Their hybridization energy (indicative of their efficiency) was as recommended (i. e. , between -35 and -38 kcal. mol -  ) for I4amiR and slightly higher than that recommended for I3amiR (Table  S1 ). I3amiR and I4amiR sequences displayed at most 68% identity with other transcripts than the OsHKT1;4 target. The hybridization energy of both I3amiR and I4amiR on these off-target mRNA was thus far below the range given by the software for efficiency of the amiRNA, indicating that substantial off-target effect of the two amiRNA in planta was unlikely.
Among these weakly likely offtargets was identified a sequence of OsHKT1;3 mRNA, which showed 66% of identity with the complementary sequence of the I4amiR. Each selected 21 mer amiRNA sequence (Table  S1 ) was then entered to the program "Oligo" tool which generated four oligonucleotide primers for PCR cloning of the amiRNA precursor DNA sequence to introduce in transgenic plants for producing amiRNA (Table  S2 ). The PCR aimed at replacing in a cloned DNA sequence naturally transcribed into a stem-loop precursor of miRNA (osa-MIR528), the sequence corresponding to the active 21 nt miRNA and that corresponding to the complementary miRNA* (not strictly complementary to the active 21 nt miRNA sequence on the precursor stem, and degraded during maturation process) by those corresponding to the I3 or I4 amiRNA and the corresponding amiRNA* designed by the WMD3 program, targeting OsHKT1;4.
Real Time PCR Analyses Total RNA were extracted from pools of root or shoot tissues of hydroponically grown plants (as described above), using the "RNeasy Mini Kit" (Qiagen, France). Each pool constituted one biological replicate, and at least three biological replicates were done per condition. RNA were treated by DNase using the "DNAse I" kit (Invitrogen), then assayed using Ribogreen reagent (from "Quant-iT ™ RiboGreen ® RNA" kit; Molecular Probes, France) and a plate reader (VICTOR3 multilabel Counter 1420, Perkin-Elmer, Wellesley, USA). First strand cDNA synthesis was performed from 3 µg of DNase-treated RNA using the "SuperScript III Reverse transcriptase" kit (Invitrogen). Real-time PCR was performed in 96-well plates using the LightCycler ® 480 Real-Time PCR System (Roche diagnostics) and SYBR Green I probe (Roche) to monitor cDNA amplification.
In each well, the final reaction medium was prepared by mixing 3 µl of cDNA (obtained from 40 ng of DNase-treated RNA), 0. 5 µl of each primer (at 10 µM), 5 µl of LightCycler ® FastStart DNA Master PLUS SYBR Green I mix (Roche diagnostics) and 1 µl of purified water. All samples were analyzed in triplicates. Applied PCR program (software: LightCycler ® 480 1. 5; Roche) consisted of 10 min at 95°C, then 45 amplification cycles composed of 10 s at 95°C, 10 s at 60°C, 15 s at 72°C, then a melting curve building (5 s at 95°C, 1 min at 65°C and 5 min with temperature increase from 65 to 97°C), and finally 30 s cooling at 40°C. The absolute number of HKT cDNA copies was determined in each sample based on standard curves obtained from dilution series of known amounts of corresponding cDNA fragments.
Three housekeeping genes Tip41  (Caldana et al. , 2007) , SMT3 ubiquitin-like protein gene  (Horie et al. , 2007)  and EF1b elongation factor gene were used for rough HKT expression values normalization, using geNORM v. 3. 5 software  (Vandesompele et al. , 2002). Forward and reverse primers used for real-time PCR experiments are given in Table  S3. Na + and K + Assays in Tissues and Xylem Sap The root system was excised, rinsed in deionized water, then briefly dried in-between two layers of towel-type paper and transferred into pre-weighed plastic vials (20 ml "liquid scintillation" type). Sheaths and blades of third leaves were also collected, separately, and transferred into pre-weighed plastic vials. The samples were dried at 60°C for 3 days and the plastic vials were weighed again, allowing to determine sample dry weight (DW).
8 mM CaCl 2 , 1 mM MgCl 2 , 2. 5 mM Na-pyruvate, and 5 mM HEPES-NaOH, pH 7. 4) supplemented with 0. 5 mg. l -1 gentamycin. Whole oocyte currents were recorded using the two-electrode voltage clamp technique 1 to 2 days after cRNA injection, as described by  Mian et al. (2011). The voltage-clamp amplifier was a GeneClamp 500B (Axon Instruments, Foster City, USA). Voltage-pulse protocols, data acquisition, and data analyses were performed using pClamp10 (Axon Instruments) and Sigmaplot10 (Jandel Scientific, Germany) softwares. Both membrane potential and current were recorded. Correction was made for voltage drop through the series resistance of the bath and the reference electrode using, in addition to the reference electrode, a voltage recording electrode in the bath close to the oocyte surface, both external electrodes being connected to a bath probe (V6-2A ×100 virtual ground bath clamp; Axon Instruments).
Production of amiRNA has been reported as a highly effective and sequence specific approach for post transcriptional gene silencing in plants  (Schwab et al. , 2006). The imperfect complementary microRNA to the amiR released from the stem of the precursor (amiR*) is degraded during the maturation process. A dedicated web platform (web MicroRNA designer; http:// wmd3. weigelworld. org/) was used to design amiR sequences targeting OsHKT1;4 transcript (and the "complementary" amiR* sequences), and to assess the quality of the proposed amiR (efficiency, specificity). Two proposed amiRNA, that were named I3amiR and I4amiR, were chosen (Figures  5A, B ; Table  S1 ). Their hybridization position on OsHKT1;4 mRNA was at the very end of the translated region (I4amiR) and within the 3'UTR region (I3amiR) (Figure  5B  top; Table  S1 ).
(2) Leaf area is most easily measured (in the absence of a leaf area meter) by laying out the leaves on a white surface with a scale (typically a bar with 1-mm increments) and taking a photo with a digital camera. The area of the leaves can then be computed with appropriate software, such as Image J  (Rueden et al. 2017). (3) Trichomes can be counted by using a stereomicroscope or binocular microscope linked to a digital camera. If leaves are small, trichomes can be counted on the entire leaf surface. For larger leaves, a disc of a known area is removed by using a cork borer or punch (e. g. trichomes by the leaf area (trichomes mm -2 see Fig. 5 ).
Defining forbs A common definition of a forb is a non-grassy herbaceous plant, although definitions vary greatly. The total woody tissue in an adult plant remains debatable when it comes to defining a forb. For the purpose of this study, we will use a broad definition of forbs, which represents an adapted version of the US Department of Agriculture PLANTS Database definition (USDA, Natural Resources Conservation Service, see https://plants. sc. egov. usda. gov/java/, accessed 4 November 2020), as follows: all non-graminoid vascular plants with a limited degree of aboveground woody tissue and with buds at or below the ground surface. Forbs are widely acknowledged for their significant contribution to overall species richness of savanna ecosystems, and yet their value in addressing ecological questions remains poorly studied.
The presence of knobs may confer some advantage by limiting stripping of the stems. (2) Bark regrowth Greater bark regrowth increases the probability of survival, whereas limited bark regrowth exposes the stem to pathogens, insect feeding and fires  (Moncrieff et al. 2008; Wigley et al. 2019b). Limited unpublished data suggest that resistance to bark stripping and increased bark recovery is highest in firedriven systems, i. e. mesic savannas, where the increased intensity and frequency would select for these traits. measure. Flutedness should be measured on at least 10 individuals per species. Bark-fibrousness index. The bark-fibrousness index should be measured on at least 10 individuals per species. At a height of 1. 5-2 m on the trunk, a strip that is 3 cm wide and 10 cm long (avoiding lateral stems and spines) is cut, but the bottom edge is left attached (Fig.
Software such as ImageJ can then be used to calculate the area of the removed bark section. The bark-fibrousness index (cm 2 N -1 ) can then be calculated by dividing the total area of bark removed (cm 2 ) by the force (N) required to remove the bark section. The removal of a strip of bark usually represents little threat to the tree's survival. Bark regrowth. Bark recovery following stripping is recorded as the proportion of bark recovered following a stripping event after a full growing season. However, it is worth noting whether the tree can continue to recover its bark during subsequent growing seasons. Bark regrowth can be empirically measured by removing a circular section of bark of 5-cm diameter (~20 cm 2 ) with a mallet and a sharpened corer before the growing season. Bark regrowth focuses on the recovery of the living inner bark.
The thin layer of outer bark (i. e. periderm and cork) is removed using a wood chisel and then the entire layer of inner bark (i. e. secondary phloem) is removed, without damaging the underlying wood  (Wigley et al. 2019b). Regrowth can be calculated by measuring the regrowth on two perpendicular axes (see Fig. 13 ) on a regular basis (3-4 months), but should be enumerated after a full growing season. Regrowth can also be measured by taking a photograph with a scale bar included, and calculating percentage recovery by using ImageJ or similar software. The removal of a small disc of bark usually poses little risk to the tree.
Matrix-matching. After an in-house validation of the analytical method for digestion, quantification and evaluation of the Al content in the investigated organs, an ANOVA and PCA analysis based on the different treatment groups were performed (see Methods section for details). This step was conducted to exclude the possibility that animals did not correspond to the variation in the overall population. The results of ANOVA and PCA (see Supplementary Table  S1  and Supplementary Fig. S1 ) showed no significant difference among the animals of the different treatment groups. In order to minimize measurement uncertainties and standard deviation for the quantification, a matrix calibration was carried out for each organ investigated. The calibration points quantified in the different matrices were highly correlated to the data points calculated from the regression curve of each organ (Fig.
(3) in the methods section). Additionally, the recovery of the microwave-assisted digestion was calculated. Considering a factor taking into account these corrections, it was possible to calculate the concentration of Al burden per gram of tissue in a highly robust manner (see Eqs. (4-6) in the methods section). All obtained values were above the LOQ (Fig. 2 ). Assuming that the data are not equally distributed, through median and average comparison (Table  3 ), the Wilcoxon sign test was used for statistical analysis of non-normal distributed dependent groups. For each dose group, the distribution of Al concentrations in the organs was examined. The significance levels were corrected according to Holm-Šidàk and an unspecific pairwise comparison was carried out  31. For almost all comparisons, a significant difference between dose groups and the Al species as well as to the control group at the significance level of 0.
Discussion In the current study we compared the oral bioavailability and distribution of ionic and nanoparticulate Al 0 and Al 2 O 3 in rats following a 3-day oral treatment. ICP-MS was used to quantify the Al concentration in duodenum, colon, blood, liver, kidney and spleen to evaluate the biodistribution patterns of the three Al species. Some challenges were faced for the quantification of Al amounts. First, the ubiquitous presence of Al in the tissues hinders the detection of Al that originates from the treatment. The background levels of Al were shown to vary from organ to organ (see Supplementary Fig. S3 ). For this purpose, a robust calibration methodology was developed where matrix effects were taken into account. Our matrix calibration data clearly indicated the need for matrix correction (see Supplementary Fig.
Acknowledgements The  French-German bilateral project SolNanoTOX  was funded by the  German Research Foundation  (DFG, Project  ID: DFG  ( FKZ LA 3411/1-1  and  LA 1177/9-1 ) and the  French National Research Agency (ANR , Project  ID :  ANR-13-IS10-0005 ). The  BfR  provided intramural support  SFP1322-642  for F. L. K. and A. L.
List of abbreviations The paper is structured as follows: Section 2 introduces the modelling framework and tool used for assessing the economic and environmental impacts of sustainable supply potential of willow; Section 3 describes the case study country, i. e. Poland, as well as the scenarios and assumptions used to test the integration of willow within different crop diversification situations; Section 4 presents results regarding the economic and environmental impacts resulting from willow production. The impacts are declined into Polish FADN (Farm Accountancy Data Network) regions, farming type and economic size classes; Section 5 discusses and compares some of our findings to those found in the literature. Finally, Section 6 presents our conclusions.
The latter is made possible by the upgraded version of the agricultural supply model AROPAj, in which a new module of stylised CAP greening measures is integrated to provide information on the number and combination of eligible crops that can be efficiently cultivated. To be consistent with the EU strategies, for instance with the updated bioeconomy strategy, farmers can consider, through crop diversification options, adopting alternative PEC such as willow SRC to increase their sustainability, ecology and biodiversity performance.
These variables are then called by the linear programming AROPAj model to return the optimal output for each activity at FG level. The modelled crop activities include only arable crops, particularly soft and durum wheat, barley, sugar beet, potatoes, rapeseed, sunflower and soya. Furthermore, a module for computing GHG emissions from agriculture is integrated on the basis of the methodological framework developed within the International Panel for Climate Change (IPCC) guidelines  (Jayet et al. , 2020; De Cara and Jayet, 2011). The emissions are broken down into 20 items, thirteen of which concern CH4 emissions from manure, enteric fermentation and rice cultivation, and seven relate to N2O emissions, i. e direct and indirect emissions from agricultural soils as well as emissions from grazing livestock and manure application.
While CH4 emissions from enteric fermentation and manure are induced by the number of animals and the composition of their feed, N2O emissions from agricultural soils are driven by N-fertiliser application dependent on either input and output prices or optimal crop area mix. One of the most important features of AROPAj model is its capacity to generate spatial outcomes at a fine geographical scale, which can be aggregated at regional level. To spatially locate FG and activities,  Cantelaube et al. (2012)  integrated a spatial distribution module, thereby expanding the micro-economic data by physical information on climate (Monitoring Agriculture from Remote Sensing project database), soils (JRC), land cover (CorineLandCover), land use (LUCAS) and terrain elevation (digital elevation model).
In Simulation scenarios and assumptions -A wide range of perennial dedicated activities are integrated in AROPAj model, ranging from miscanthus, switchgrass, poplar, to willow. In this study, we consider only willow. As regards yields, we suggest to correlate data with those of a control plant, e. g oat, in a similar way to that in  Mola-Yudego and Aronsson (2008). The authors estimated willow yields by combining crop management and climate data with local productivity of oats, based on more than 2000 commercial plantations in Northern Europe. Willow yields are then calculated through applying Eq. (  1 ). 3 ) are also used as benchmark. The estimation reveals an average yield of around 8 tdm ha 1 (Fig. 2 ).