dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical Analysis The classification of the parameters analyzed on liquid fractions of digestates from 29 codigestion plants and 1 WAS plant was performed via Principal component analysis (PCA), hierarchical cluster analysis (HCA) and correlation matrix using R version 3. 3. 2 (31 December 2016)  [45]. PCA was carried out in center-scaled variables using function 'FactoMineR' package version 1. 35  [46]  with PCA plots package 'factoextra' version 1. 0. 4. For HCA, 'stats' package version 3. 3. 2 ('hclust' function) was applied to center-scaled variables and Euclidean distances. The clustering algorithm was referring to Ward  [47]  and the resulting dendrogram was plotted using function 'dendextend' package version 1. 4. 0. Meanwhile, correlation matrices were constructed using 'rcorr' function with the Pearson's correlation method ('rcorr' is a function of the 'Hmisc' package (version 4.
This may possibly be explained by the origins of the easily biodegradable substrates, resulting in lower residual organic matters in the liquid fractions of digestates. The loading scores of measured parameters of Dimension 1 of the PCA is shown in Figure  3. Positive values were correlated to high efficiency separation, which is correlated to dissolved inorganic, alkalinity, ions with significant parameters of conductivity, TKN dissolved, TKN total, IC, NH4 + , dissolved organic nitrogen and alkalinity with value >0. 8. On the contrary, negative values were correlated to low efficiency which is correlated to organic matter and solids. The significant parameters observed were dissolved C/N, turbidity, COD suspended, VS liquid and CST with values <-0. 6. A meta-analysis study on digestate quality with a database containing about 150 raw digestates, solid and liquid fractions resulted in a very similar observation  [8].
Acknowledgments: The authors would like to express their deepest gratitude to  INRAE Bio2E Facility  ( Bio2E ,  INRAE ,  2018. Environmental Biotechnology and Biorefinery Facility  (https://doi. org/10. 15454/1. 557234103446854E12)where all experiments were conducted. The authors would also like to thank  Majlis Amanah Rakyat Malaysia  and  AAIBE Chair of Renewable Energy , Grant No. 201801  KETTHA for the financial assistance obtained for the execution of this research. The authors are also indebted to  Emilie Gout  and  Phillipe Sousbie  for their kind support in the laboratory.
1a ) and we therefore tested this enzyme with candidate DNA and RNA ligands. Remarkably, we observed that T. castaneum XP_969398. 1 is activated to synthesize a nucleotide product in response to recognition of double-stranded RNA (dsRNA) (Fig. 1c ). Despite exhibiting a clear difference in ligand-specificity, analysis of all related structures in the Protein Data Bank confirms that T. castaneum XP_969398. 1 is a close homolog of mammalian cGAS and is distinct from previously characterized RNA sensors including oligoadenylate synthase 1 (Extended Data Fig. 1f )  18, 19. Together, these results establish the existence of cGAS-like Receptors (cGLRs) in animals and demonstrate that remodeling of a primary ligand-binding surface enables the recognition of divergent molecular patterns. To identify additional cGLRs that respond to dsRNA, we used the T.
3b ). We verified these findings with comparative high performance liquid chromatography and tandem mass-spectrometry profiling against a chemically synthesized standard and confirmed that the shared Diptera cGLR product is the novel isomer 3′2′-cGAMP (cG[3′-5′]pA[2′-5′]p) (Figs. 3a, b ; Extended Data Figs. 6a, b ). Dm-cGLR1 synthesizes 3′2′-cGAMP in a two-step reaction through production of the linear intermediate pppA[2′-5′]pG and uses an opposite nucleobase reaction order compared to human cGAS (Extended Data Fig. 7a )  2, 3, 26. We next used mass-spectrometry to further analyze each lysate sample from our screen of recombinant dipteran cGLR proteins. 3′2′-cGAMP was detected as a main reaction product from 15 Diptera cGLRs including active enzymes from each sub-group within Clade 5 of the insect cGLR phylogeny (Fig.
Bioinformatics and Dipteran cGLR sequence analysis Building on previous analyses  [6] [7] [8] [9] [10] [11] [12]  , animal cGAS homologs suitable for crystallography were identified using the amino acid sequences of human cGAS and D. melanogaster CG7194 to seed a position-specific iterative BLAST (PSI-BLAST) search of the NCBI non-redundant protein database. The PSI-BLAST search was performed with an E value cutoff 0. 005 for inclusion into the next search round, BLOSUM62 scoring matrix, gap costs settings existence 11 and extension 1, and using conditional compositional score matrix adjustment. Candidate homologs identified from this search included the uncharacterized human protein MB21D2 and the Tribolium castaneum sequence XP_969398. 1. Pairwise structural comparison between human MB21D2, Tc-cGLR, and protein structures in the Protein Data Bank was performed using DALI 37 and Zscores for homologs less than 90% identical to one another (PDB90) were plotted in GraphPad Prism.
X-ray diffraction data were collected at the Advanced Photon Source beamlines 24-ID-C and 24-ID-E and at the Advanced Light Source beamlines 5. 0. 1 and 8. 2. 2. Data were processed with XDS and Aimless 43 using the SSRL autoxds script (A. Gonzales). Experimental phase information for all proteins was determined using data collected from selenomethionine-substituted crystals. Anomalous sites were identified, and an initial map generated with AutoSol within PHENIX 44. Structural modeling was completed in Coot 45 and refined with PHENIX. Refinement statistics are described in Supplementary Table  1 , and all structure figures were generated with PyMOL 2. 3. 0.
Nucleotide product synthesis analysis cGLR nucleotide synthesis activity was analyzed by thin-layer chromatography as previously described  11. For the Diptera cGLR screen, recombinant protein preparations were incubated in 10 μL reactions containing 0. 5 μL α- Diptera screen reactions, samples were not diluted in sodium acetate prior to spotting on PEIcellulose TLC plates. TLC images were adjusted for contrast using FIJI  46  and quantified using ImageQuant (8. 2. 0). Nucleotide product formation was measured according to the ratio of product to total signal for each reaction. For Figs. 1c, 2d , 2g and Extended Data Figs. 3e, 4b, 5d relative activity was calculated as percent conversion for each reaction relative to maximal conversion observed by wildtype enzyme or in the presence of 40 bp dsRNA for insect cGLRs and 45 bp dsRNA for cGAS.
1% acetic acid (solvent A) and methanol (solvent B). The analytes were eluted at a flow rate of 0. 6 mL min -1. The eluting program was as follows: 0 to 4 min: 0% B, 4 to 7. 3 min: 0 to 10% B. This composition of 10% B was held for 1 min, then the organic content was increased to 30% within 2. 7 min. The column was then re-equilibrated to 0% B for 2 min. Total analysis run time was 13 min. High resolution MS-Data were collected on a Vion IMS-QTOF mass spectrometer equipped with an electrospray ionization source, operating in positive ionization mode. The capillary voltage was set at 2. 5 kV and the cone voltage at 40 V. The source temperature and desolvation gas temperature was 150°C and 600°C, respectively. Analyte fragmentation was achieved using argon as the collision gas. Collision energy of 10 V was used to obtain a low collision energy spectrum.
2′3′-cGAMP was used as positive control as previously characterized  31, 34. Synthetic nucleotide was injected into the body cavity of wildtype (w 1118 ) flies and gene expression was measured after 24 h. RNA levels were measured relative to the housekeeping gene RpL32, and nucleotide concentrations are displayed in μg μL -1. Note that for srg2 measurement after injection of 9E-7 μg μL -1 3′2′-cGAMP there was one outlier replicate with a value of 0. 5977 (data not shown, included in mean analysis). e-k, As in Fig. 5a , RNA expression analysis of STING-regulated genes 24 h after injection with synthetic 3′2′-cGAMP or 3′3′-c-di-GMP. RNA levels are shown as fold induction compared to buffer control in wildtype, dSTING, or Relish mutant flies respectively. dSTINGMut = RXN mutant; RelishMut = Relish E20 mutant, as previously characterized  31, 34.
controlled by a conformational rearrangement. d, e, TLC analysis of in vitro tests for potential activating ligands of hMB21D2. No nucleotide products were identified upon stimulation with 40 nt or bp nucleic acid ligands (d) or ligands known to activate mammalian Toll-like receptors (e) f, Z-score structural similarity plot showing homology between human MB21D2 and Tc-cGLR with representative structures in the Protein Data Bank (PDB90). Increasing Z-score indicates greater homology confirming the close relationship between animal cGLR enzymes and more distantly related similarity with cGAS/DncV-like Nucleotidyltransferases (CD-NTases) in bacterial antiphage defense systems 11,50. Z-scores cutoffs are 13 and 15 for hMB21D2 and Tc-cGLR respectively. Forward biochemical screen of predicted cGLRs in Diptera.
Acknowledgements: The authors are grateful to  P. M. Devant ,  K. Chat ,  A. Holleufer ,  R. Hartmann , T. IV. L. , and members of the  Kranzusch lab  for helpful comments and discussion,  C. de Oliveira Mann  for assistance developing mass spectrometry analysis of insect cGLRs, and  M. Burroughs  and  A. Iyer  for bioinformatics analysis of cGAS-like enzymes. The work was funded by grants to P. J. K. from the  Pew Biomedical Scholars program , the  Burroughs Wellcome Fund PATH program , The  Richard and Susan Smith Family Foundation ,  The Mathers Foundation ,  The Mark Foundation for Cancer Research , a  Cancer Research Institute   CLIP grant , a  V Foundation   V Scholar Award , and the  Parker Institute for Cancer Immunotherapy ; grants to J. L. I and H. C. from the  Agence Nationale de la Recherche  ( ANR-17-CE15-0014 ), the  Investissement d'Avenir Programme  ( ANR-10-LABX-0036  and  ANR-11-EQPX-0022 ), the  Institut Universitaire de France ,.
Data Availability Statement: Coordinates and structure factors of human MB21D2, T. castaneum cGLR, Drosophila STING, and the Drosophila STING-3′2′-cGAMP complex have been deposited in PDB under the accession codes 7LT1, 7LT2, 7MWY, and 7MWZ. All other data are available in the manuscript or the supplementary materials.
Extended Data Figure 2 |Extended Data Figure 6 | 26 controlled by a conformational rearrangement. d, e, TLC analysis of in vitro tests for potential activating ligands of hMB21D2. No nucleotide products were identified upon stimulation with 40 nt or bp nucleic acid ligands (d) or ligands known to activate mammalian Toll-like receptors (e) f, Z-score structural similarity plot showing homology between human MB21D2 and Tc-cGLR with representative structures in the Protein Data Bank (PDB90). Increasing Z-score indicates greater homology confirming the close relationship between animal cGLR enzymes and more distantly related similarity with cGAS/DncV-like Nucleotidyltransferases (CD-NTases) in bacterial antiphage defense systems 11,50. Z-scores cutoffs are 13 and 15 for hMB21D2 and Tc-cGLR respectively.
13) mm 3 in size by waterjet technology to facilitate the GLARE ® mounting on the top of the dynamometer. The acquisition of cutting forces was carried out using a four-component Kistler dynamometer and Dynoware software (see Fig. 1(c)  and (d) ). Coated and uncoated cemented carbide (grade K20) twist drills with 6 mm diameter were used when drilling GLARE ® 2B 11/10-0. 4 without coolant. This diameter is chosen according to the requirements of the aircraft industry  [39] , and the two types of coating are diamond-like carbon (DLC) and Cristall (diamond coating) (see Fig. 1(b) ). All tools are manufactured by GUHRING ®. DLC and Cristall possesses an outstanding hardness in excess of 8000 HV. These coatings are qualified for highly abrasive applications such as for example the machining of GFRP and CFRP, aluminium-alloys, ceramics and graphite.
Within the device, all particles are deposited on a PTFE filter of 47 mm diameter and can be used for gravimetric testing and further study. Within an optical measurement unit, every particle in the aerosol is measured independently through reflected light photometry. The dispersed light impulse of every individual particle is measured according to the intensity of the dispersed light signal corresponding to particle size. The aerosol spectrometer measures the distribution of the particle scale of solid airborne particles in several levels of size. The device is calibrated using polystyrene spheres latex (PSL)  [38]. During dust investigation, the number of particles has been read directly from the software (GRIMM). This software estimates the particle masses by considering only the density of air as a value of 1000 kg/m3.
Acknowledgments This project was realized in  Clément Ader Institute (Paul Sabatier University of Toulouse 3 ) and  MAI laboratory  ( University of Tunis El Manar, ENIT, Tunis, Tunisia ). The authors wish to thank  Xavier Sourd ,  Abdellah Bouzid  and  Akshay Hejjejy  from  Clément Ader Institute  for their technical support. The authors would also like to thank the  Fiber Metal Laminate center in the Netherlands  and  Prof. Jos Sinke  for the provision of GLARE ® sample. The authors would also like to thank Guhring ® cutting tools company and  Mr. Ian Goffey  for the kind support of providing the cutting tools.
Two antibodies, anti-PFR2 (L8C4) and anti-FAZ1 (L3B2), were chosen to mark the whole flagellum and the FAZ, respectively  (Gadelha et al. , 2005; Kohl et al. , 1999). Our immunofluorescence data showed that TbE-Syt overlapped with PFR2 along the flagellum, but the signal did not reach the flagellar tip (Figure  2B ). TbE-Syt overlapped with FAZ1 along the entire FAZ, however (Figure  2C ). This is consistent with the FAZ localization of TbE-Syt reported in a high-throughput screening database where the majority of C-terminally mNeonGreen-tagged TbE-Syt was observed in the FAZ area, with some weak signals forming reticulated patches in the cytoplasm  (Dean et al. , 2017)  (Figure  S3 ). To further verify its association with the ER, we checked TbE-Syt localization at the ultrastructural level by immuno-gold labeling.
identified by the protein structure homology-modeling program SWISS-MODEL Workspace  (Waterhouse et al. , 2018)  was the crystal structure of the SMP domain of HsE-Syt2, which was solved to 2. 4 A ˚resolution with bound phospholipids (PDB: 4P42)  (Schauder et al. , 2014). We chose this crystal structure, which shares 20. 45% identity with TbE-Syt-SMP, as the template for our homology modeling (Figures  3A  and S4A ). The resulting homodimeric model was of high quality based on the confidence evaluation and local similarity to the template (Figures  S4B  and S4C ). Superimposing the TbE-Syt-SMP model onto the template structure of HsE-Syt2-SMP showed an excellent agreement (Figure  3B ). The homodimeric TbE-Syt-SMP model, which was generated using the quaternary structure prediction option of SWISS-MODEL  (Bertoni et al.
(D) Hydrogen bonds between the Ca 2+ ions and coordinating residues in TbE-Syt-C2B. The plot was generated using LigPlot+  (Laskowski and Swindells, 2011). See also Figure  S5. TbE-Syt-C2A lacks the Ca 2+ -binding site but retains the PI(4,5)P 2 -binding patch Previous studies have shown that the C2A domain in all mammalian E-Syts binds Ca 2+ and is involved in lipid interaction  (Min et al. , 2007; Xu et al. , 2014). We wondered whether TbE-Syt-C2A functions similarly. We tried to express recombinant TbE-Syt-C2A, either alone or together with C2B, SMP, or both, but did not succeed in obtaining soluble proteins. We thus tried to understand its structure and function by homology modeling. One of the top hits recognized by SWISS-MODEL  (Waterhouse et al. , 2018)  was the crystal structure of HsE-Syt2-C2A (PDB: 4NPK)  (Xu et al.
TbE-Syt-C2A and C2B are connected by a long flexible loop Previous structural studies revealed that the first two C2 domains, i. e. , C2A and C2B, of HsE-Syt2 shares high structural similarities with each other  (Xu et al. , 2014). A high-resolution NMR structure of the last C2 domain of HsE-Syt2, i. e. , C2C, has also been determined (PDB: 2DMG). We therefore compared the structure of TbE-Syt-C2B with that of the three C2 domains of HsE-Syt2. TbE-Syt-C2B adopts the same topology as HsE-Syt2-C2A and C2B, i. e. , type II, whereas HsE-Syt2-C2C has a distinct type I topology (Figure  S7A ). Superimposing TbE-Syt-C2B onto each of the three C2 domains of HsE-Syt2 showed that it is very similar to HsE-Syt2-C2A and C2B, with average RMSDs of 1. 05 A ˚and 0. 75 A ˚, respectively, but substantially deviated from C2C, with an RMSD of 3.
Consistently, homology modeling based on the crystal structure of HsE-Syt-SMP-C2A (PDB: 4NPK) generated a compact structure of TbE-Syt-SMP-C2A (Figure  S8B ). To generate MCSs between the ER and the plasma membrane, the dimeric TbE-Syt is first anchored on the ER membrane via the N-terminal TM domains. The two C2B domains at the distal end of the structure would make initial contact with the plasma membrane both via the acidic patch in a Ca 2+ -dependent manner and via the basic patch to interact with PI(4,5)P 2. It is noteworthy that the basic residues (K502, K511) in the PI(4,5)P 2 -binding site on TbE-Syt-C2B are not as conserved as those acidic residues in the Ca 2+ -binding site in other trypanosome species (Figure  1B ), suggesting that the Ca 2+ -binding site is the major and universal element for TbE-Syt-C2B to interact with the plasma membrane.
ACKNOWLEDGMENTS We thank  Drs. K. Ersfeld ,  J. Bangs ,  K. Gull , and  P. Bastin  for the antibodies of anti-myc, anti -BiP ,  L8C4 , and  L3B2 , respectively. We also thank  Dr. J. Sunter  for sharing the raw imaging data of TbE-Syt that initially appeared on the TrypTag. orgwebsite. We are grateful to the staff at the beamline of ID23-2 at the  European Synchrotron Radiation Facility (ESRF)  for their help with X-ray diffraction, to  Y. Zhang  for generating the.
Data analyses and graphic representations Experiments were carried on a randomized block design, with three repetitions for each treatment. All statistical analyses were performed using the software package INFOSTAT® (University of Cordoba, Argentina). The data were subjected to analysis of variance (ANOVA). Mean comparisons were performed using Fisher's least significant difference (LSD) test and significance was set at P ≤0. 05 (*), P ≤0. 01 (**) and P ≤0. 001 (***). Principal component analysis (PCA) was performed to identify the overall behavior of the experiment.
For GAPs, no specific variations were observed for each family of aroma precursors studied, which showed a similar behavior to the total GAPs in the different years (Table  S4 ). With 77 % of the total GAPs in average, glycosylated alcohols were the more abundant GAPs, with other groups being less than 10 %. We observed a high correlation between the quantities of each aroma precursor's family and the total GAPs expressed either in concentrations in the fruits or in quantities per plant (Table  3 ). Therefore, to simplify the representation of the GAPs data set, only total GAPs were considered and further discussed in this manuscript. Fruit GAPs concentration depended on the variety and the environment, with a significant effect of the genotype and GxE interactions (Table  2 ). This was also true when GAPs were expressed in quantity per fruit or per plant, suggesting a higher dependence of this parameter to environmental fluctuations.
(2018)  performed a multi-objective calibration using NSE for streamflow and total water storage from GRACE satellite data;  Milzow et al. (2011)  combined several satellite datasets -surface soil moisture, radar altimetry and total water storage -to calibrate a semi-distributed model in a catchment with few streamflow measurements through a composite of nine criteria;  Demirel et al. (2019)  explored the use of dif-ferent combinations of objective functions, computed based on several satellite products measuring soil moisture and water storage, to calibrate a conceptual model, and achieved little gain in streamflow simulation performance; and  Dembélé et al. (2020)  performed a composite calibration of a distributed model with four datasets -measured streamflow and satellite evaporation, soil moisture and water storage -and improved the model's representation of processes at the expense of a small degradation of the streamflow simulation performance.
, 2011)  to make it simulate groundwater table levels. Since no element of the existing model structure was designed to explicitly simulate the groundwater level, and because of the huge scale gap between point piezometric measurements and aquifer-scale storage volumes, we could not propose a physically explicit solution; thus, we investigated an empirical adaptation of the model structure. Section 2 recounts the process that led to designing this adaptation and the calibration and evaluation schemes of the new model. Section 3 presents the hydroclimatic dataset of 107 catchments across mainland France that was used to evaluate the new calibration with respect to the original one performed only on streamflow. Section 4 summarises the results and proposes recommendations for model calibration in various contexts.
As highlighted in the "Introduction", even small alluvial aquifers outside plains can have an influence on rivers: for example, several small leftbank tributaries of the Rhone are mostly fed by the Bièvre moraine aquifer, with visible consequences for water quality  (Bel et al. , 1999). Regions in which geological formations are composed of metamorphic or igneous rocks, such as Brittany or the Ardennes, can host fractured bedrock aquifers linked to surface rivers. The wide monitoring network of rivers and groundwater in France, described below, allowed us to select a test dataset of catchments that is representative of this diversity.
Data sources Climatic data -daily cumulative precipitation, average temperature and fraction of solid precipitation -were taken from the SAFRAN (Système d'Analyse Fournissant des Renseignements Adaptés à la Nivologie) re-analysis  (Vidal et al. , 2009)  by Météo France; they are available for daily time steps for the 1958-2018 period. Daily potential evaporation was computed using the formula of  Oudin et al. (2005). Streamflow data were retrieved from the French national database, Banque Hydro  (Leleu et al. , 2014; SCHAPI, 2021). These hydroclimatic data are aggregated at the catchment scale and for daily time steps for mainland France in the HydroSafran database  (Delaigue et al. , 2021)  maintained by INRAE (Institut national de recherche pour l'agriculture, l'alimentation et l'environnement).
Groundwater level data are from the French national database ADES, (BRGM, 2021) (Accès aux données sur les eaux souterraines), which gathers piezometric data from many providers in the French territory. Selected piezometers were taken from two reference networks to ensure the quality of data: RNESOUPMOBRGM (the national quantitative monitoring network managed by BRGM, the French national geological survey) and RNESP (the heritage national network for groundwater monitoring).
Dataset selection Catchments were selected on the basis of data availability criteria, shown below, and an analysis of the hydrogeological context through the French national reference cartography of hydrogeological formations, BDLISA  (Brugeron et al. , 2018)  (Base de données des limites des systèmes aquifères). For each catchment, one or several piezometers were chosen to assess the connections of the monitored aquifers with surface water bodies. First, using the provided metadata, each piezometer extracted from the ADES database was associated with a hydrogeological entity in BDLISA representing an aquifer. Catchments in which anthropogenic activitiesdams, major direct withdrawals or inflows -are known to have a significant influence on streamflow and catchments in which more than 10 % of the precipitation falls as snow were discarded.