dataesr/scientific-paragraphs-categorization huggingface dataset:
Errors associated with remaining environmental effects are estimated and provided at the pixel level in the form of a credible interval, the 95% HPDI, which reveals potentially large errors locally when the environmental conditions contrast drastically with the average conditions of each area. Two validation approaches, namely one cross-validation with the in situ dataset and a validation with a LiDAR AGB dataset, reveal a good accuracy of our dataset, with an RMSD between 8 and 17 Mg•ha -1. Finally, the dataset has been used to provide estimates of the total national carbon stocks of most African countries, which have been compared to other estimates from FAO and existing AGB maps. The approach developed in this study can be applied to similar Lband mosaics produced at later epochs, for example the ALOS-2 PALSAR-2 mosaics that are being produced on a yearly basis since 2015, or on the open forests of other continents.
To do so, the model developed in Africa in 2010 in this study would require minor  adjustments to account for systematic radiometric differences occurring in the production of the mosaics. In the case of other continents, these adjustments would ideally require another set of high quality in situ AGB estimates. In the absence of such high quality in situ datasets, other approaches that do not rely on in situ measurements, as described in previous studies over temperate or boreal forests  (Cartus et al. , 2012) , can be considered. The potential of such methods in tropical woodlands and savannahs should therefore be investigated, e. g. in comparison with the results produced in this study. In the future, the L-band time-series that will be provided by NISAR will provide a good opportunity to correct for errors linked to local variations of the environmental conditions, and therefore to overcome the major limitation of our approach based on mono-temporal mosaic datasets only.
Acknowledgements The authors would like to thank  Edward Mitchard  from  University of Edinburgh  for providing some in situ data and  Masanobu Shimada  and his team from  JAXA  for providing the global 25 m resolution PALSAR Mosaics. This data is owned by  JAXA. The  CCI Land Cover (CCI-LC ) database has been processed by the  CCI-LC consortium  led by  UCL-Geomatics (Belgium) , and is made available to the public by  ESA  and the consortium. ©  ESA Climate Change Initiative -Land Cover  project  2014. The authors gratefully acknowledge financial support from  CNES (TOSCA program , purchase order  BCT_71SC ), from  ESA  ( DUE   GlobBiomass  project,  ESA  Contract No. 4000113100/14/I-NB ) and from the  European Union 's  Horizon 2020 Research and Innovation Programme  under grant agreement No.
Second-line pembrolizumab Pembrolizumab's clinical activity and safety were evaluated in the international multicenter Phase I KEYNOTE-001 trial (NCT01295827) of 495 untreated (101 first-line therapy) or previously treated (394 second-line or more) patients. 28 All patients received pembrolizumab intravenously (IV): 2 or 10 mg/kg every 3 weeks (Q3W) or 10 mg/kg Q2W. Primary end points were safety and efficacy: objective response rate (ORR), OS, progression-free survival (PFS), and duration of response (DOR). 28 Observation during the trial of an association between tumor-cell PDL1 expression and pembrolizumab effectiveness led to a protocol amendment, with the adjunction of another principal outcome criterion: efficacy in patients with high PDL1-expressing tumors. 29 n that study, the safety profile of pembrolizumab was acceptable.
First-line pembrolizumab Several clinical trials have evaluated first-line pembrolizumab. An analysis of 101 treatment-naïve patients included in the Phase-1 (KEYNOTE-001) trial was published in 2017. 30 ORR (51. 9%), 12-month PFS (54%), and 12-month OS (84%) for patients with PDL1 $50% NSCLC were better than for the entire population (26. 7%, 35%, and 71%, respectively). Those findings led to Phase I-III trials testing the molecule as first-line therapy. The Phase III randomized KEYNOTE-024 trial (NCT02142738) compared pembrolizumab (200 mg IV, 3QW) until disease progression or unacceptable toxicity for a maximum of 2 years vs standard platinum-based doublet chemotherapy (four to six cycles with maintenance therapy possible) as first-line therapy for advanced NSCLC without EGFR mutation or ALK rearrangement, but with PDL1 $50% determined by immunohistochemistry (IHC).
BubbleGUM analysis displaying enrichment of gene sets on the pairwise comparisons of R, VdR, and VR tumors (NES, normalized enrichment score). The gene sets were downloaded from MSigDB (Broad Institute). The bubble area is proportional to the normalized enrichments score (NES) calculated by GSEA. The intensity of the color corresponds to the statistical significance of the enrichment. (F, G) Typing of the differentiation grade of J2A tumors by in situ collagen (Masson trichrome) versus hematoxylin staining (F) or qRT-PCR analysis of collagen 1 and caveolin 1 transcripts (n = 5, unpaired t test, *P < 0. 05; **P < 0. 01) (G). Lac, lactate; Glc, glucose; GSH, glutathione; Tau, taurine; GPC, glycerophocholine; FA, fatty acids; and UFA, unsaturated FA. accumulate in the fast-growing R cell lines that rather rely on glucose for energy  (Fig 2)  and which also showed lowered CoA levels  (Fig 4).
LC-MS and NMR-based metabolomics For both analyses, technical details for metabolite extraction are provided in supplementary information. Annotation was performed by matching exact mass to publicly available databases and from plausible biological context. The resulting matrix was curated from unannotated peaks and used for further statistical analysis. Metabolites identified by LC-MS analysis were grouped into metabolic function performed on the ground of literature data (Tables  S2  and S3 ).
1 mm × 5 μm, 2A) with a gradient elution of ACN containing 0. 1% formic acid and water containing 16 mM ammonium formate at 250 μl/min flow rate and a column temperature of 25°C. The injection volume was 5 μl. The LC conditions were as follows: solvent A-16 mM ammonium formate in water, solvent B-0. 1% formic acid in ACN, solvent B 97% for 2 min, then B to 70% in 8 min, then B to 10% in 5 min, held 2 min, then back to B 97% in 1 min, and held 4 min, vials tray 4°C. For the MS settings, the capillary voltage was set at 3,500 V (positive mode), and the nebulizing parameters were set as follows: nebulizing gas (N 2 ) pressure at 50. 8 psi, drying gas (N 2 ) flow at 12 liters/min, and drying temperature at 200°C. Mass spectra were recorded from m/z 50 to 1,200. After acquisition, raw data files were converted into mzXML before or to XCMS processing to generate a data matrix of deconvoluted ions with their intensity, m/z, and retention times  (Martin et al, 2015).
For each spectrum, 128 free induction decays of 16,384 data points were collected using 8,000 Hz of spectral window. The free induction decays were multiplied by an exponential weighting function corresponding to a line broadening of 0. 3 Hz and zerofilled before Fourier transformation. The calibration on the alanine doublet (δ = 1. 47 ppm) and the phase and baseline corrections and the alignment of shifted signals were performed using NMRprocflow online software  (Jacob et al, 2017). The identification of the NMR signals was carried out using 1 H-1 H TOCSY, 1 H-13 C HSQC NMR experiments, online databases (Human Metabolome Database  [Wishart et al, 2013] ) and literature  (Nicholson et al, 1995). Each spectrum was divided into 0. 005-ppm-width integrated buckets and normalized to total spectrum intensity after removing the pre-saturated water signal region (4.
Biological resources are structured by the clinical departments in various databases Conticabase tumor bank (conticabase. org) for soft tissue and visceral sarcoma includes n = 15,808 samples with clinical annotations and follow-up (https://conticabase. sarcomabcb. org/). The analysis of gene expression was conducted on selected samples of this database; data and methods are accessible online on atg-sarc. sarcomabcb. org.
Statistical analysis Analysis was performed on the GraphPad Prism 7. 03 software. Values are represented with standard deviations or minimum to maximum plots. We used ANOVA, and t and log rank tests for tumor size evaluation and survival curves, respectively. For metabolomics analysis, partial least squares-discriminant analysis, a supervised statistical method that attempts to separate the three groups of samples by regressing on a so-called dummy y-vector consisting of the class codes, was used for classification purposes. All experiments performed are recapitulated in Table  S4.
008). (E) Transcriptomic analysis of J2A tumors (n = 5). BubbleGUM analysis displaying enrichment of gene sets on the pairwise comparisons of R, VdR, and VR tumors (NES, normalized enrichment score). The gene sets were downloaded from MSigDB (Broad Institute). The bubble area is proportional to the normalized enrichments score (NES) calculated by GSEA. The intensity of the color corresponds to the statistical significance of the enrichment. (F, G) Typing of the differentiation grade of J2A tumors by in situ collagen (Masson trichrome) versus hematoxylin staining (F) or qRT-PCR analysis of collagen 1 and caveolin 1 transcripts (n = 5, unpaired t test, *P < 0. 05; **P < 0. 01) (G). Lac, lactate; Glc, glucose; GSH, glutathione; Tau, taurine; GPC, glycerophocholine; FA, fatty acids; and UFA, unsaturated FA.
Metabolites with positive intensities are in higher concentrations in R samples, whereas metabolites with negative intensities are in higher concentrations in VR samples (P value of 0. 008). (E) Transcriptomic analysis of J2A tumors (n = 5). BubbleGUM analysis displaying enrichment of gene sets on the pairwise comparisons of R, VdR, and VR tumors (NES, normalized enrichment score). The gene sets were downloaded from MSigDB (Broad Institute). The bubble area is proportional to the normalized enrichments score (NES) calculated by GSEA. The intensity of the color corresponds to the statistical significance of the enrichment. (F, G) Typing of the differentiation grade of J2A tumors by in situ collagen (Masson trichrome) versus hematoxylin staining (F) or qRT-PCR analysis of collagen 1 and caveolin 1 transcripts (n = 5, unpaired t test, *P < 0.
Benchmark Graphs The graphs that we will use in our tests are three benchmark graphs of different sizes and come from different domains. These graphs are available in the Gephi standard dataset accessible in the following link: https://github. com/medialab/benchmarkForceAtlas2/blob/master/dataset. zip (last checked: December 21 th , 2017). The 4 graphs are: a. facebook_ego_686 (168 nodes and 1656 links) b. yeast (2361 nodes and 7182 links) c. arxiv_general_relativity (5242 nodes and 28980 links) d. oregon2_010331 (10900 nodes and 31180 links) Table  1  displays the layouts of the 4 benchmark graphs.
The PBM transforms pollen proportions from each site into a number of land cover classes (LCCs  12, 13  ). Fyfe et al. 12  applied the PBM to data taken from the European Pollen Database  23  at 200-year time steps, producing three closed forest type LCCs, and a fourth semi-open forest LCC, i. e. a mix of open and forest vegetation. Two different PBM values are provided here, firstly, the closed forest sum (= PBM score, abbreviated as PBM sc ); secondly, percentage of samples assigned to forested Land Cover Classes (= LCC assigned, abbreviated as PBM lcc )(see methods). The PFT approach groups pollen taxa into plant functional types and changes in landscape openness are assessed by calculating the arboreal pollen PFT percentage. Davis et al. 16  applied this method to data from the EPD in 500-cal.
In this study we have undertaken a systematic comparison of past forest cover using REVEALS, PBM and PFT approaches in order to assess when and where Europe's primaeval wildwood was transformed into today's semi-natural landscapes and habitats. We divided the study region into mid-latitude and northern Europe. The boundary between the two sub-regions was drawn between the temperate and hemi-boreal vegetation zones as defined by Ahti et al. 26  for northern Europe (except for Scotland where the Lowland-Highland divide was used). Because of limited pollen data coverage, we do not attempt to make forest cover reconstructions for the area east of 32° E. This region includes the major share of land that was never occupied by woodland because of low precipitation. Similarly, because of the lack of REVEALS reconstructions for Mediterranean Europe, no comparison has been attempted here for this southern region of Europe.
A second means of testing the different forest reconstructions is to examine how well they match modern forest cover for the same grid cells. While remotely sensed estimates of forest might be expected to offer the clearest results and the most rigorous test, in fact the Corine and Forest Map 2006 data have strongly different outcomes; i. e. 45% and 29% modern forest cover, respectively. This inconsistency partly reflects the ontological question of "what is a forest?" Corine uses distinct land-cover classes, and land classified as forest may include some open areas as the minimum required crown cover for a forested class is only 30%. The Forest Map 2006 is based on a minimum 50% tree crown cover with 5 m used as a minimum height of trees  28. It also highlights the epistemological problem that differences in spatial resolution of measurement can fundamentally alter results  30  , in this case between 25 m and 100 m measured spatial resolution.
An alternative data source for modern forest cover derives from surface pollen samples. We have transformed the surface pollen data set for Europe 27 using both variants of the PBM, which leads to modern forest cover estimates of 49% (PBM sc ) and 54% (PBM lcc ). Overall, most estimates of modern forest cover for the grid cells used by Trondman et al. 10  are between 45% and 49%; that is, close to that reconstructed for the 100 to -65 BP REVEALS time window. A test of the different semi-quantitative reconstruction methods (i. e. PBM, PFT) is provided by comparison with the REVEALS forest estimates for the five different time windows. We use here standardized major axis regression as standard correlation methods and assume a dependent relationship between the variables under consideration. The statistical comparison shows an r value from standardized major axis regression of 0.
10. In order to compare them statistically (Fig. 3 ), data were averaged for each of the 230 1 × 1 degree grid cells, used in  10  , and re-sampled on a common time interval. As well as this data set for inter-comparison of the different methods, our PBM and PFT reconstructions also include a second, larger data set that incorporates pollen sites and grid cells not covered by the REVEALS reconstructions. The data used for this inter-comparison derive from, and can be accessed via, the European Pollen Database (EPD)  23  , supplemented in the case of REVEALS and PFT by some additional data as described in  10, 16  , respectively. All the pollen records used have calibrated  14  C-based chronologies  12, 23  and meet the minimum dating standard set out by  51. For the REVEALS and PFT-based estimates, we use the sum of arboreal taxa as a proxy for forest cover.
Acknowledgements We are grateful to the funding bodies and institutions that have supported the different research groups that datasets used in this study draw upon. This includes the  Leverhulme Trust and Plymouth University  ( Roberts, Fyfe and Woodbridge ), The  Swedish Research Council (VR)  and  Faculty of Health and Life Science, Linnaeus University , the  Swedish Research Area MERGE  (ModElling the Regional and Global Earth system) (Gaillard), and the  European Research Council  ( COEVOLVE 313797 ) (Kaplan and Davis). Thanks are also given to contributors to the European Pollen Database. This paper is a contribution to the  PAGES LANDCOVER6K  working group, which in turn received funding support from the  US National Science Foundation  and from the  Swiss Academy of Sciences.
Data availability. The primary datasets analysed during the current study are available via the European Pollen Database repository, http://www. europeanpollendatabase. net/ and the European surface pollen database at http://www. europeanpollendatabase. net/wiki/doku. php?id=empd_download_database. The transformed results using the PBM are available in PANGAEA at https://doi. pangaea. de/10. 1594/PANGAEA. 853947. The REVEALS data are in the process of being archived in PANGAEA.
Assessment of the phylogenetic relationship of the species using average nucleotide identity (ANI) values (7; see also http://enve-omics. ce. gatech. edu/ani) determined that the closest species whose genome is available is Streptomyces sp. strain 4F with an ANIb value of 94% (GenBank accession number CP013142). Despite its first assignment (1), the ANIb value (ϳ81%) was too low to support its assignment to the species S. ambofaciens; it does, however, support the organism being renamed Streptomyces sp. The isolates Streptomyces sp. strain ETH9427, Streptomyces sp. strain 4F, and S. ambofaciens strain ATCC 23877 (8) constitute, however, a group of related strains, since the divergence of their 16S rRNA genes does not exceed 1%. A preliminary analysis of the Streptomyces sp. strain ETH9427 sequence using.
ACKNOWLEDGMENTS This work was funded by the  French National Research Agency  through  two programs (ANR Streptoflux   ANR-07-BLAN-0096  and  ANR MiGenIs)  and by the  French National Institute for Agricultural Research (INRA) ,  Région Lorraine  and the  Laboratory of Excellence ARBRE  ( ANR-11-LABX-0002-01 ). C. M. Vicente was also supported by the  AgreenSkillsPlus Program  ( FP7-609398. 0000 ). We acknowledge support of DynAMic by the " Impact Biomolecules" project of the Lorraine Université d'Excellence (Investissements d'avenir-ANR ).
Aims. We show how the XXL multiwavelength survey can be used to shed light on radio galaxies and their environment. Methods. Two prominent radio galaxies were identified in a visual examination of the mosaic of XXL-North obtained with the Giant Metrewave Radio Telescope at 610 MHz. Counterparts were searched for in other bands. Spectroscopic redshifts from the GAMA database were used to identify clusters and/or groups of galaxies, estimate their masses with the caustic method, and quantify anisotropies in the surrounding galaxy distribution via a Fourier analysis. Results. Both radio galaxies are of FR i type and are hosted by early-type galaxies at a redshift of 0. 138. The first radio source, named the Exemplar, has a physical extent of ∼ 400 kpc; it is located in the cluster XLSSC 112, which has a temperature of ∼ 2 keV, a total mass of ∼ 10 14 M , and resides in an XXL supercluster with eight known members.
Multiwavelength We used data from the following surveys: -The X-ray measurements with XMM-Newton and the XXL project are described in XXL Paper I. (SDSS DR14 7 ) contains optical and near-infrared images of our fields and spectra of some of the sources. -The Galaxy and Mass Assembly (GAMA) database 8 contains spectra, spectroscopic redshifts, and information on the detected spectral lines for the host galaxies of our two radio sources and other galaxies in the field  (Baldry et al. 2018 ). -The Wide-field Infrared Survey Explorer (WISE;  Wright et al. 2010 ) has detected the host galaxies of our two radio sources in several bands. Notes. (1) X-ray and optical characteristics from XXL Paper II. N galaxies is the number of galaxies on which the mean redshift, z cluster , was based. (2) X-ray-derived quantities from XXL Paper III.
A closer inspection of the X-ray image (Fig. 5 ) does not reveal any clear extended emission. The noise varies across the image and the quality of the data does not allow us to say anything about the presence or absence of gas interaction with the radio lobes. -Optical. A search in the GAMA database led to the identification of 32 galaxies with spectroscopic redshifts in the 0. 13 ≤ z ≤ 0. 15 range and within a radius of 6. 3 (0. 92 Mpc) of the core of the Double Irony. This radius was chosen as it corresponds to r 200 (which is approximately the virial radius) of the Exemplar galaxy cluster. The actual virial radius of the Double Irony galaxy might be different, but this shows that the radio galaxy is surrounded by a large number of galaxies. In Fig. 9  we show the GMRT 610 MHz image of the Double Irony radio galaxy in red, superimposed on an optical i-band image from the CFHT in blue.
0-041358, XXL-GMRT J020357. 6-041244, XXL-GMRT J020359. 1-041303, XXL-GMRT J020348. 5-041416, XXL-GMRT J020356. 1-041216, and XXL-GMRT J020344. 7-041505. lower surface brightness are found (e. g. ,  Lara et al. 2001a; Saripalli et al. 2005). In Tables  6  and 7  we list the values for the flux densities and the spectral indices measured in different regions displayed in Fig. 6. The spectral indices measured between 150 MHz and 1. 4 GHz are systematically steeper than the low-frequency spectral indices measured between 150 MHz and 610 MHz, an indication of spectral aging of the cosmic-ray electrons. The Elbow and the central region both have a relatively flat spectral index, but no systematic pattern is seen. We intend to model the evolution of cosmic-ray electrons in the Double Irony and in the Exemplar and to derive spectral age estimates by analyzing more sensitive low-frequency data (pending GMRT observations below 500 MHz).
Gravitational interaction with the second brightest galaxy A second galaxy is clearly visible to the NE of the host of the Double Irony. It is the next brightest galaxy within a radius of 1 Mpc and is listed in SDSS (SDSS J020357. 62-041321. 5). With a spectroscopic redshift (from BOSS) of 0. 13433, the line-ofsight velocity difference with the host of the Double Irony is 840 km s -1. It is at a distance on the sky of 59 , or a projected distance of 146 kpc. An analysis of the spectrum in the GAMA database (GAMA J20357. 62-041321. 5) yields a stellar mass of about 0. 9 × 10 11 M , which is about one-third of the stellar mass of the host of the Double Irony (Table  5 ). There is no sign of tidal perturbations in the optical surface brightness distribution of this galaxy, which is an argument against a prograde encounter with the host of the Double Irony.
Brightest cluster galaxies The host galaxy of the Double Irony is somewhat brighter than that of the Exemplar in all bands except the WISE W1 and W2 bands (the difference is largest in the u band, Tables A. 2 and A. 1). The two host galaxies have very similar optical spectra (Fig. A. 1) characteristic of old stellar populations. Detection of  Hα, Hβ, and [Oii]  is reported in the GAMA database for both galaxies. However, there is no detection of high-excitation emission lines such as  [Oiii]  that is seen in the host galaxies of highexcitation radio galaxies (HERGs). It has been shown that the most luminous radio galaxies (FR ii) are predominantly HERGs, while the hosts of the less powerful FR i radio galaxies do not exhibit such spectral lines. Low-excitation radio galaxies (LERGs) are in general hosted by galaxies that have a lower star formation rate, are located in clusters, and are more massive than the host galaxies of HERGs.