dataesr/scientific-paragraphs-categorization huggingface dataset:
This study investigates the scientific quality of the GEOV1 Leaf Area Index (LAI), Fraction of Absorbed Photosynthetically Active Radiation (FAPAR) and Fraction of Vegetation Cover (FCover) products based on PROBA-V observations. The procedure follows, as much as possible, the guidelines, protocols and metrics defined by the Land Product Validation (LPV) group of the Committee on Earth Observation Satellite (CEOS) for the validation of satellite-derived land products. This study is focused on the consistency of SPOT/VGT and PROBA-V GEOV1 products developed in the framework of the Copernicus Global Land Services, providing an early validation of PROBA-V GEOV1 products using data from November 2013 to May 2014, during the overlap period (November 2013-May 2014). The first natural year of PROBA-V GEOV1 products (2014) was considered for the rest of the quality assessment including comparisons with MODIS C5.
Several criteria of performance were evaluated including product completeness, spatial consistency, temporal consistency, intra-annual precision and accuracy. Firstly, and inter-comparison with both spatial and temporal consistency were evaluated with reference satellite products (SPOT/VGT GEOV1 and MODIS C5) are presented over a network of sites (BELMANIP2. 1). Secondly, the accuracy of PROBA-V GEOV1 products was evaluated against a number of concomitant agricultural sites is presented. The ground data was collected and up-scaled using high resolution imagery in the context of the FP7 ImagineS project in support of the evolution of Copernicus Land Service. Our results demonstrate that GEOV1 PROBA-V products were found spatially and temporally consistent with similar products (SPOT/VGT, MODISC5), and good agreement with limited ground truth data with an accuracy (RMSE) of 0.
The continuity of the GEOV1 products is based on PROBA-V observations at 1 km. To provide continuity of the variables at 1km, the processing chains are to be updated towards the new PROBA-V mission which started its lifetime in November, 2013. Although the sensor of the latter mission is very compatible with the former mission, a spectral correction is to be performed to continue the 15-year time series at 1km resolution in a consistent manner. Therefore a pre-processing module is developed that performs next to the spectral correction a transformation of the new PROBA-V input data into SPOT-VGT compatible input data. Validation of PROBA-V GEOV1 is thus mandatory before delivering the products to the users. This paper describes the main results of the early scientific quality assessment of PROBA-V GEOV1 LAI, FAPAR, FCover products.
This preliminary validation is focused on the consistency with SPOT/VGT GEOV1 products during the overlap period  (November 2013 -May 2014). MODIS C5 LAI/FPAR products are also considered for the intercomparison The procedure follows the guidelines and metrics defined by the Land Product Validation (LPV) group of the Committee on Earth Observation Satellite (CEOS) for the validation of satellite-derived land products. Several criteria of performance were evaluated including product completeness, spatial consistency, temporal consistency, intra-annual precision and accuracy. The accuracy of PROBA-V GEOV1 products was evaluated against a number of agricultural sites. The ground data was collected in the context of the FP7 ImagineS project (http://fp7imagines. eu) in support of the evolution of Copernicus Land Service  (Camacho et al.
Direct Validation The accuracy assessment was performed against ground truth data processed according to CEOS LPV guidelines for validation of LAI products. The data set used to validate is the ground data collected in the framework of the ImagineS project over agricultural sites for the period under study. Up-scaling of ground data was achieved with high-resolution satellite image using an empirical transfer function  (Camacho et al. , 2014). Eight sites were made available for the accuracy assessment for 2014 coming from FP7 ImagineS (Table  1 ). Due to the limited number of concomitant ground measurements, the number of ground reference maps was increased by using data from a different year from  Camacho et al. , 2013 , and available at CEOS OLIVE Cal/Val portal (http://calvalportal. ceos.
For concomitant data over some croplands sites of 25Mayo (#1), LaReina (#3) and Psenichne (#13) a large overestimation was observed (samples not identified as outliers). These results seems to indicate that the FCover product tend to overestimate the ground references, even if the dataset considered is still very limited. Forest stands for Broadleaf Evergreen, Broadleaf Deciduous and Needle-leaf Forests, Crops stands for Cultivated and Grass refers to Herbaceous, Shrubs, Sparse and Bare Areas. Numbers identify the ground data (Table  1 ). Crosses identify outliers (weight<0. 3).
CONCLUSIONS In this study, an early scientific validation of GEOV1 (LAI, FAPAR and FCover) products based on PROBA-V observation was performed for the overlap period between SPOT/VGT and PROBA-V. The methodology used follows the guidelines proposed by the CEOS LPV group for validation of remote sensing vegetation products. First, an intercomparison with existing global products (SPOT/VGT GEOV1 and MODIS C5) was performed. The BELMANIP2. 1 network of sites was used to perform the global statistical analysis at 3x3 km 2 and at a 10days time step. Second, the uncertainties were quantified by direct comparison with ground-based reference maps. GEOV1 LAI, FAPAR and FCover estimates from PROBA-V data were found consistent with that of GEOV1 based on SPOT/VGT observations. The completeness of PROBA-V GEOV1 products is similar to that of SPOT/VGT GEOV1 products (around 5% lower).
Both PROBA-V and SPOT/VGT shows consistent spatial distribution of retrievals, whereas discrepancies between PROBA-V and MODIS are larger, mainly for the FAPAR product (large discrepancies). The temporal variations of PROBA-V were found also consistent with that of SPOT/VGT GEOV1 products. The overall consistency between SPOT/VGT and PROBA-V evaluated in term of RMSE over BELMANIP-2 is better than the CEOS requirements on accuracy (0. 5 for LAI, 0. 05 for FAPAR), which demonstrates the good consistency between both products. The direct validation shows that the accuracy of PROBA-V GEOV1 LAI product was very close to CEOS requirement on accuracy using limited concomitant data (RMSE=0. 54) or using additional non-concomitant references (RMSE=0. 51). For the FAPAR the accuracy is also quite good (0.
g. connectivity) with regards to forest organisms such as the PPM. The geographical range of the PPM is currently expanding northward in relation to climate change (Roques 2015). During this process, the moth colonizes various non-forest areas where TOF are likely to play a key role by facilitating its dispersal especially in large openfield regions. The data reported here were specifically collected to assess how TOF that are suitable for hosts for the PPM contribute to landscape connectivity for that specie. For that reason, we did not record the tree species identity but only their status as hosts (or not). We used the data set for landscape analyses  (Rossi et al. under review)  and point process analyses  (Rossi and Rousselet 2015). Since tree species were not recorded, we provide here the points locations without any taxonomic taxonomic information.
Data analysis This study incorporated two different sampling locations (BMSM and Boulogne) along the French coastal area. Analysis of the stable isotope data was performed for each of the locations separately since they are characterized by different environmental settings. Primary food sources. Differences in the δ 13 C and δ 15 N isotope values of the primary food sources (SPOM and MPB diatom ) between levels of the fixed factors sampling area (L. conchilega aggregation versus control) and period (spring versus autumn) were tested by a twoway ANOVA (Analysis of Variance). Significant interaction effects (p < 0. 05) were further investigated by means of a TukeyHSD test. Prior to ANOVA, the assumptions of normality and homogeneity of variances were tested on untransformed data with Shapiro-Wilk tests and Levene tests respectively.
[25]  and reformulated in a Bayesian framework by Jackson et al. [26]. Trophic diversity within the community is reflected by the total extent of spacing within δ 13 C-δ 15 N biplot space and measured by the first four metrics: δ 15 N range (NR; representation of the vertical food web structure), δ 13 C range (CR; representation of diversity at the base of the food web), total area of the convex hull encompassing the data (TA; representation of the niche space occupied) and mean distance to centroid (CD; representation of the average trophic diversity within the food web). The extent of trophic redundancy (the relative position of taxa to each other within niche space) is measured by metrics five and six: mean nearest neighbour distance (MNND) and standard deviation of the nearest neighbour distance (SDNND).
Sampling area (L. conchilega aggregation vs. control) and period (spring vs. autumn) were fixed factors. Analyses were performed on untransformed stable isotope data and run separately for the bay of the Mont Saint-Michel (BMSM) and Boulogne-Sur-Mer (Boulogne). Pair-wise Tukey HSD test results were shown for significant sampling area x period interactions. In case of significant differences (p < 0. 05) p values are in bold.
Acknowledgments The authors would like to acknowledge the marine station in Dinard for providing the speedboat Marphysa (CNRS). We thank  Julien Guillaudeau ,  Jezabel Lamoureux  (MNHN),  Niels Viane  and  Bart Beuselinck  for their assistance during the field campaigns in Boulogne and/or the  Bay of the Mont Saint-Michel. Liesbet Colson  is highly acknowledged for the help during sample processing and  Bob Clarke  ( PRIMER-E ) for the inspiring statistical comments. We thank  Tom De Smet  for improving the language of the manuscript.
The consensus structural model was derived from the alignment of the three guide RNAs included in the 3D structures of the full H/ACA RNP assemblies (L7Ae, Nop10, Cbf5 with or without Gar1) determined by X-ray crystallography (PDB IDs: 2HVY  (17) , 3HAX  (18) , 3LWO  (19) ). More recently, the discovery of 'atypical' H/ACA motifs in the Pyrobaculum genus has suggested an alternate way for this machinery to assemble and achieve its function  (16). These non-canonical H/ACA motifs, further designated as H/ACA-like motifs, are detected specifically in this genus of Crenarchaea and differ from the canonical H/ACA motifs in that the lower stem is truncated. They generally include two long free single-stranded regions at both 5' and 3' ends forming a pseudo-internal loop and the generic hairpin with an embedded K-turn motif.
In all the 3D structures of the full H/ACA RNP complexes (L7Ae, Nop10, Cbf5 and Gar1) in presence or not of a target RNA (PDB IDs: 2HVY, 3LWO, 3HAX)  (17) (18) (19) , the GA stem is 10 base-pairs long (Figure  1D ): it orients the K-turn or K-loop motif within the RNP complex so that L7Ae binds the guide RNA and interacts with Nop10. There are striking differences between the structure/function models in Pyrococcus and Pyrobaculum which are representative of the fold diversity of H/ACA guide RNAs in other archaea (Figure  1 ). All the consensus models for natural H/ACA guide RNAs show pretty loose constraints in the length of the lower stem, GA stem and internal loop (Figure  1A-C ) which contrast with the tight constraints for the consensus model derived from crystallized RNAs in H/ACA sRNP (Figure  1D ).
The substitution between K-turn and K-loop motifs is allowed: two descriptors are used for each of the six families of sRNAs. All the descriptors are provided (as text files) in the supplementary material. A series of S-MART scripts  (40)  is used to extract the H/ACA(-like) motifs that lie in the non-coding transcriptome of P. abyssi. A minimum overlap of 50 nucleotides is required to filter out the initial hits. The sequence and motif conservation are verified using the UCSC archaeal genome browser  (41, 42). A combination of two softwares: locaRNA  (51)  and RNAalifold  (52)  are used to identify optimal and sub-optimal 2D structures which are consistent with the H/ACA(-like) fold. The search for associated targets is performed using the RIsearch program (53), using the recommended extension penalty ('-d 30').
Only target sequences with at most two bulge nucleotides are tolerated  The genome is initially screened for the presence of H/ACA-like motifs using a descriptor-based approach (RNAMotif (39)). The number of hits is given at each step of the workflow as an indicative value for the motifs carrying either a K-turn or K-loop submotif. The first filter is the selection of motifs in the non-coding transcriptome (S-MART scripts  (36, 40) ), then the selection of conserved sequences and motifs among other archaea (UCSC archaea genome browser  (41, 42) ) and finally the selection of motifs that have potential target(s) in the genome which are themselves transcribed and conserved among other archaea. but no bulge nucleotide is allowed on the 5' duplex (5' end of the paired target sequence) upstream from the predicted modified position.
The productive folds are classified in the two fold families '10/5/9' and '10/6/9' (Figure  4  and Supplementary Listing 17). The '10/5/9' fold family is consistent with the 3D structure of a chimeral H/ACA RNA from P. furiosus (3D: Figure  4B ; 2D: Supplementary Figure  S4 ) while the '10/6/9' fold family is consistent with the 3D structure of another chimeral H/ACA RNA (3D: Figure  4G ; 2D: Supplementary Figure  S4 ) derived from Archaeoglobus fulgidus (Afu46) which is assembled with the H/ACA ribonucleoproteins from P. furiosus (PDB ID: 3HAX)  (17). In the '10/6/9' fold family, the internal loop is extended by the addition of one nucleotide in the 3' guide sequence which folds with 6 stacked nucleotides (Figure  4G-I ). As a result, Table  1. Functional and structural features from known H/ACA guide RNAs in Pyrococcus targeting 16S and 23S rRNAs a as provided by the UCSC genome browser  (41, 42).
b as determined from RNA-seq data  (36). c as determined from previous work by RT-CMCT analysis and in vitro activity of pseudouridylation (  5 ). d structure-function model as proposed from the 'productive'/'nonproductive' classification (the ± sign indicates whether it is predicted to be productive or not); the listed models also include some additional models that optimize the hybrid and duplex energies: 10/6/8 (Pa40. 2-L1932) and 10/8/7 (Pa35. 1-L2672) which are derived from 10/5/9 and 10/6/9 by opening the lower stem by one or two base-pairs (Supplementary Figure  S7 ), respectively. e as calculated by RNAsnoop (kcal/mol) from the Vienna RNA package  (44). f the duplex energy includes both the 5' and 3' duplex energies with a correction factor (+4. 1 kcal/mol). g the Pab19-S1017 pairing proposed previously is based on a 8/7/9 model (5).
Pae_sR207(-) U U A G G A G A G U C G G G U G G G G G A C U U A G A G C G G C C C G U A G G G C C C C C G U G A A G A A G U C C C C U G C C G C G G G G U U G C A C A 5´U U A G G A G A G U C G G G U G G G G G A C U U A G A G C G G C C C G U A G G G C C C C C G U G A A G A A G U C C C C U G C C G C G G G G U U G C A C A Pyrobaculum sR207-L2597 Y R Y A R G G G G G G G G G Y U Y G A G Y G G C C C R A G G G C C Y C Y G U G A R R A R C C C C C U G C C G C G G G G U U A C A 0-1 nt 12 bp 0-1 nt 0-1 nt 0-1 nt 0-1 nt 0-1 nt ANA box 5´P ae sR207 U G U G C C G C G G G G U U G A C C C C G C G G U U U G guide target 5´C G 5´ E = - c structure-function model as proposed from the 'productive'/'nonproductive' classification; the +/-sign indicates whether it is predicted to be productive or not. d as calculated by RNAsnoop (kcal/mol) from the Vienna RNA package  (44).
Structural compensations in H/ACA(-like) guide RNAs In all the 3D structures of the full H/ACA RNP complexes (L7Ae, Nop10, Cbf5 and Gar1) including an RNA substrate or not, the GA stem is composed of exactly 10 base-pairs. The only exception is the case of the incomplete H/ACA RNP complex reconstituted with a composite guide RNA derived from Pf9 (Pa160 ortholog) which exhibits a 9 base-pairs constraint (PDB ID: 2RFK)  (29). Interestingly, the L7Ae protein is missing in this particu-lar H/ACA RNP complex. This suggests that the length of the GA stem is indeed a critical structural determinant for the function of the H/ACA guide RNA machinery; the productive H/ACA guide RNAs can be folded or refolded to fit into the consensus model (through a series of structural compensations described previously) with a GA stem including 10 base-pairs or 10 stacked layers which preserve the orientation of the K-turn or K-loop motif in the H/ACA sRNP complex.
These findings are consistent with the structure of a functional H/ACA RNP complex (PDB ID: 3HJW and 3HJY)  (31)  including the H/ACA RNA guide assembled from the Pf9 and Pf6 motifs (PDB ID: 3LWO; Figure  4B  and Supplementary Figure  S4 ). The two crystallized H/ACA guide RNAs (PDB IDs: 3LWO and 3HAX; Figure  4B  and Figure  4G ) which are representative from both fold families do exhibit the same relative positions of the internal loop, lower stem and ANA box when superposing the two RNP complexes. In the '10/6/9' family, the additional stacked nucleotide in the 3' end duplex sits at the location of the first base-pair from the lower stem in the '10/5/9' family. This is made possible by a change in the morphology of the lower stem where the RNA helix is more bent in '10/6/9'. This more pronounced bending is associated with a more compact helix (smaller helical rise) by almost 1 Å and less twisted (smaller helical twist) by about 15 degrees (Table  S3 ).
In other closely related species like P. horikoshii, P. yayanossi and T. kodakaraensis, the first base-pair is preserved as a wobble U-G or U-A base-pair. The second minor variation involves a bulge nucleotide in Pa105. 1 (A at position 16: Pa105. 1-L2554a in Supplementary Figure  S5 ) which is assumed to be stacked in the GA stem: this conformation is supported by compensatory changes in the motif from T. kodakaraensis corresponding to the ortholog gene from P. abyssi: the substitution of the bulge nucleotide by a base-pair which is correlated with the substitution of the two additional G-A sheared base-pairs embedded in the GA stem by two canonical base-pairs (Supplementary Figure  S8 ). The presence of both a single bulge nucleotide and two additional sheared G-A base-pairs in the GA stem are expected to allow the adjustment of the helical twist so that the relative position of the K-turn/K-loop motif with respect to the internal loop is preserved (a bulge A nucleotide adopts such a stacked conformation in the 24-mer RNA hairpin coat protein binding site from bacteriophage R17 (PDB ID: 1RHT (60)).
Photolysis reaction and PIF analytical measurements Photolysis reactions were performed by irradiating with UV light 3. 5-ml volumes of the fenvalerate working standard solutions for fixed periods of time at room temperature. Then, the PIF spectra were recorded at a scanning speed of 500 nm/min. Curves of fluorescence intensity versus UV irradiation time were constructed at 1-min intervals, using the fenvalerate photoproduct constant excitation (λ ex ) and emission (λ em ) analytical wavelengths (see the irradiation time, λ ex and λ em values in Table  1 ). The statistical analysis of data was performed with OriginPro 8. 5. 1 software.
Ovaries were taken from five sexually mature amphipods: Gammarus fossarum, Gammarus pulex, Gammarus roeseli, Hyallela azteca and Parhyale hawaiensis. The soluble proteome extracted from individual pair of ovaries from five biological replicates was trypsin digested and the resulting peptides were analyzed by high resolution tandem mass spectrometry. The spectra were assigned with four protein sequence databases with different specificities: a RNAseq-derived G. fossarum database; a RNAseq-derived P. hawaiensis database; both originating from ovaries transcriptome; the Daphnia pulex database derived from whole-genome sequencing and the NCBInr database. The best interpretation was obtained for most animals with the specific RNA-seq protein database previously established by means of RNAseq carried out on G.
fossarum. Proteins identified in the five amphipod species allow defining the core-proteome of female reproductive tissues of the Senticaudata suborder. The data accompanying the manuscript describing the database searches and comparative analysis Trapp  et al. , 2015 [1]  have been deposited to the ProteomeXchange with identifiers PXD002253 (G. fossarum), PXD002254 (G. pulex),.
Amphipod comparative proteomics Type of data MS data, Tables How data was acquired Data-dependent acquisition of tandem mass spectra using a LTQ-Orbitrap-XL mass spectrometer (Thermo). , Data format. raw files,. mgf peak lists,. mzid identified files from MASCOT (Matrix science),. xls output data after validation with IRMA software. Experimental factors For each female, the ovary pair was dissected under stereomicroscope magnification, immediately frozen in liquid nitrogen and stored at À 80 1C until needed. Proteins were extracted and analyzed by shotgun proteomics.
Experimental features The 25 proteomes were briefly run on SDS-PAGE, followed by trypsin proteolysis. Tryptic peptides were analyzed by nanoLC-MS/MS and spectra were assigned with four protein sequence databases. Data source location CEA-Marcoule, DSV-Li2D, Laboratory "Innovative technologies for Detection and Diagnostics", BP 17171, F-30200 Bagnols-sur-Cèze, France Data accessibility Deposited to the ProteomeXchange with identifiers PXD002253 for G. fossarum, PXD002309 for G. pulex, PXD002311 for G. roeseli, PXD002308 for H. Azteca, and PXD002310 for P. hawaiensis (http://proteomecentral. proteomexchange. org).
Value of the data The data are a precious resource about an ovary proteome map comparison of five different amphipods from the Senticaudata suborder for researchers working on emerging model organisms in the field of ecotoxicology or evolutionary ecology. We proposed a new strategy for protein quantification for comparing three species of the Gammarida infraorder and two of the Talitrida infraorder taking advantage of a restricted database including proteins previously identified after the search with four databases. The data have been used to define the core-proteome of five amphipods and elaborate on the most conserved proteins. As described in detail in the accompanying manuscript  [1] , an overall view of ovary proteome map of female sexually mature of five amphipods is presented.
Experimental design and data Fig. 1  shows the schematic flowchart of experiments, data processing and results that were presented in. xls tables. s Amphipods were sampled from rivers in mid-eastern France or from laboratory husbandries. Ovaries were taken and then treated for shotgun mass spectrometry analysis. Five biological replicates per species were analyzed, resulting in 25 proteome samples. The peptides from each sample were analyzed by tandem mass spectrometry with an LTQ-Orbitrap-XL spectrometer (Thermo). A first round of MS/MS spectra search was done with four different databases to assign them to tryptic peptide sequences. Two databases derived from RNASeq were used, GFOSS, described by Trapp et al. [2]  which is G. fossarum specific and PHAWA, P. hawaiensis specific  [3]. These two databases contain the six frame translation of the sequenced transcriptome.