dataesr/scientific-paragraphs-categorization huggingface dataset:
Briefly, the amplified fragments were sequenced using BigDye Terminator cycle sequencing ready reaction version 3. 1 and ABI Prism DNA analyzer 3730 (Applied Biosystems)  (18)  at the Genomic Platform/PDTIS/Fiocruz. Polymorphisms in the PfK13 gene were analyzed by direct DNA sequencing of amplicons, and the obtained sequences (from codon 443 to 666, i. e. , 720 bp) were aligned with the PfK13-propeller region (GenBank accession no. NC_004331. 3) of the 3D7 reference sequence (PF3D7_1343700), using the free software BioEdit sequence alignment editor version 7. 2. 5. A total of 69 patients (aged 19 to 55 years) were diagnosed with falciparum malaria by microscopic and molecular tests. The parasitemia ranged from 2,340 to 288,000 parasites/l (x ϭ 88,040). All patients with malaria presented with clinical signs or symptoms of uncomplicated malaria, such as fever, headache, and chills, and the baseline characteristics were similar.
ACKNOWLEDGMENTS C. T. D. R. and M. F. F. C. are recipients of a  Research Productivity Fellowship  from the  National Brazilian Council for Scientific and Technological Development (CNPq)  and from the  Foundation for Research Support in the State of Rio de Janeiro (FAPERJ) as Cientistas do Nosso Estado. L. R. G. received a doctoral fellowship from  FAPERJ. The work was supported by the  POM (Fiocruz)  and the  PNCM, Secretary for Health Surveillance, Brazilian Ministry of Health. Sponsors had no role in the collection, analysis, or interpretation of data; writing of the manuscript, or decision to submit the manuscript for publication.
However, two features of NS2 proteolytic mode of action remain intriguing. On the one hand, the crystal structure of HCV NS2 C-terminal catalytic domain revealed an unexpected dimeric protease with two composite functional active sites, highlighting a unique mode of action of this protease  [48]. On the other hand, although HCV NS2 C-terminal domain contains the cysteine-based catalytic triad, NS2 was reported to exhibit very low intrinsic protease activity and to require NS3 N-terminal domain for efficient processing at the NS2/NS3 junction  [41, 42, 49]. To gain insight into the properties of hepacivirus NS2 proteases, we carried out a comparative study of the proteolytic modes of action and regulatory mechanisms of NS2 from a selection of genetically divergent hepaciviruses. Following our recent work showing that GBV-B NS2 is a cysteine protease that shares common topological organization with HCV NS2  [22] , we report here that NS2 from equine, bat, rodent and Old World primate hepaciviruses are aligned with the T-coffee multiple sequence alignment program  [74]  (A) A phylogenetic tree was constructed using the neighbor joining method under the Jones-Thornton-Taylor model of amino acid substitution implemented in the MEGA6 program  [75].
Accession numbers Viral strains considered in this study and the respective GenBenk accession numbers (in parentheses) are as follows: bat hepacivirus (BHV) PDB-112 (KC796077), BHV PDB-445 (KC796091), BHV PDB-452 (KC796090), BHV PDB-829 (KC796074), GBV-B (AY243572), Guereza hepacivirus (GHV) GHV-1 BWC08 (KC551800), GHV-2 BWC04 (KC551802), HCV 1a-H77 (NC_004102), HCV 1b-Con1 (AJ238799), HCV 2a-JFH1 (AB047639), HCV 2a-J6 (AF177036), HCV 2b-MD2b-1 (AF238486), HCV 3a-CB (AF046866), HCV 3b-TrKj (D49374), HCV 4a-ED43 (NC_009825), HCV 5a-SA13 (AF064490), HCV 6a-EUHK (Y12083), HCV 6b-Th580 (NC_009827), HCV 7a-QC69 (EF108306), nonprimate/equine hepacivirus (NPHV) B10-022 (JQ434004), NPHV G1-073 (JQ434002), NPHV H3-011 (JQ434008), NPHV NZP-1 (JQ434001), rodent hepacivirus (RHV) RHV-339 (KC815310), RHV NLR07-oct70 (KC411784), RHV RMU10-3382 (KC411777), and RHV SAR-46 (KC411807).
org/spdbv/) by using the crystal structures of HCV NS2 protease domain and NS3 as templates (PDB entries: 2HD0  [48]  and 1CU1  [55] , respectively). Figures were generated from structure coordinates by using VMD  [77]  (http://www. ks. uiuc. edu/Research/vmd/) and rendered with POV-Ray (http://www. povray. org/).
Following incubation for 1 h at RT with peroxidase-conjugated (chemiluminescence, GE Healthcare) or Dylight 680 or 800nm-conjugated (fluorescence, Thermo Scientific) anti-mouse or anti-rabbit antibodies, proteins were visualized using ECL Prime Western Blotting Detection Reagent followed by exposure to Hyperfilm MP (GE Healthcare) or an infrared scanner imager (Odyssey CLx, Li-Cor), respectively. Quantifications were performed on images acquired with the latter system using Image Studio Lite software.
Acknowledgments The authors gratefully acknowledge  Sylvie van der Werf  for continuous support,  Nicolas Escriou  for helpful discussions,  Florent Le Parc ,  Florian Bakoa  and  Emeline Simon  for excellent technical assistance and the following colleagues for sharing valuable biological material:  Takaji Wakita  ( JFH1  cDNA),  Ralf Bartenschlager  ( JFH1-2EI3 -adapt plasmid, anti-NS2 JFH1 antibodies),  Charles M. Rice  (Huh-7. 5 cells,  FL-J6/JFH-5'C19Rluc2AUbi  plasmid), and  Darius Moradpour  (pCMVNS2-GFP and pCMV-KEB-GFP plasmids).
Genotyping and SNP quality control Genotyping of the discovery phase studies was performed on the Illumina HumanExome BeadChip 12V. 1. 0 containing 2,44,883 single nucleotide polymorphisms (SNPs) plus additional ~17,000 custom-typed SNPs from the Danish Exome Sequencing Project as described previously  13. The total number of SNPs was 263,894 of which most were exome based (non-synonymous/coding) gene variants (~90%). Thus, we refer to the present association study as an exome-wide association study (Ex-WAS). Genotyping methods and quality control (QC) based inclusions and exclusions in the discovery and replication (20,759 EUR and 2,605 GL) cohorts have been described in Supp. table S1. 2. Albeit a total of 54,606 SNPs remained for a total of 13,226 individuals with complete phenotype and genotype data in the discovery set.
01) and in the combined discovery meta Ex-WAS (λ discovery =1. 0). A chi-square test for heterogeneity was implemented to estimate the heterogeneity in effect sizes across the participating studies. The METAL software (http://csg. sph. umich. edu/abecasis/metal/) was used for meta-analyses and the R meta package (https://github. com/guido-s/meta) for constructing meta forrest plots (discovery set). Ancestry specific linkage disequilibrium (LD) between variants was extracted using the NIH based LDlink database (https://analysistools. nci. nih. gov/LDlink/) or through the SNAP (SNP Annotation and Proxy Search) (http://archive. broadinstitute. org/mpg/snap/index. php) database.
Combined (EUR/EUR-GL) Meta analyses The combined meta-analyses was firstly performed with all individuals of European ancestry (Combined EUR) followed by pooling of Greenlandic data (Combined EUR-GL). Any SNP with a) p replication < 0. 05 and b) p meta_EUR/EUR-GL < 5. 0 × 10 -8 was considered overall significant while those with 5. 0 × 10 -5 > p meta_EUR/EUR-GL > 5. 0 × 10 -8 were considered suggestive.
Gene Aggregate Tests Gene-based multi-marker association testing for rare and common (MAF > 0. 0001) variants was performed using the Meta Analyses for SNP-Set (Sequence) Kernel Association Test (MetaSKAT) R package (https://cran. r-project. org/web/packages/MetaSKAT/index. html). At the study-specific level, the gene-based analyses were performed against the null model accounting for gender and ten principal components, (using the previously described SKAT-O method)  14  generating SKAT objects individually for each cohort with complete ExomeWAS data (discovery studies + MDCS study, n studies = 6)) which were then meta-analyzed. The meta-analyses of the summary-level score statistics were run using the Hom-Meta-SKAT-O "optimal" method (optimal linear combination of burden and SKAT statistics) which assumes that different studies share the same causal variant, weighing them equally.
Phenome Scanning: SNP-trait associations from publicly available data (GWAS, eQTL based gene expression, and SNP-Metabolite associations) The Pheno Scanner database (http://www. phenoscanner. medschl. cam. ac. uk/phenoscanner) comprising publicly available results for SNP-trait associations (GWAS, eQTL and metabolomics data) for the European ancestry  15  was used to mine known SNP-Trait associations of the current SNP findings.
SNP Functionality Prediction: SIFT We used the SIFT (Sorting Intolerant from Tolerant) database (web version) to check whether any top coding variant was associated with functional by nature (http://sift. bii. a-star. edu. sg/). CUBN missense rare SNP rs141640975 was described as functionally deleterious with a SIFT median value of 3. 44 (Supp. Table  S1. 6).
Moreover, a recent exome sequencing study revealed a homozygous frameshift mutation in CUBN associated with the only cause of proteinuria in affected family members  21. Despite being a disease gene, recent exome sequencing studies and related reference databases (ExAC  20  ) have shown that damaging variants of CUBN are rather frequent in "non-diseased" populations and are thus well tolerated by humans  19, 20. On this basis, it was recently hypothesized that the tubular proteinuria caused by cubilin deficiency could actually be protective against tubular overload, seen, for example, in nephrotic syndrome or even diabetic kidney disease  19. As CUBN rs141640975 has been shown to be associated with lower serum creatinine (p: 0. 014, Supp. table  S1. 5c) in a recent meta-GWAS of circulating metabolites  22  and causes albuminuria also in the general population group, our study supports the idea that functional variations in CUBN might not be damaging and instead protective.
The SIFT database testing functionality of the nonsynonymous SNPs resulting in amino acid changes (based on sequence homology and the physical properties of amino acids), suggests CUBN rs141640975 to be a functional (Supp. table  S1. 6). The suggestive common SNP rs10947789 in the KCNK5 locus previously a known locus for CAD  24, 25  (Supp. table  S1. 5a) encodes the potassium two pore domain channel subfamily K member 5 protein which is mainly expressed in the cortical distal tubules and collecting ducts of the kidney. This protein is highly sensitive to pH  26  , and its functional inactivation may lead to renal acidosis  27  , dysregulated membrane potential of pulmonary artery myocytes  28  , and apoptotic volume decrease  29  , as suggested by animal and in vitro studies. Pheno Scanner data mining resource, revealed rs10947789 minor allele (C) associated with increased albuminuria (pooled and diabetes subset)  7  , visual refractive error  30  , and birthweight 31 in Europeans, while lumbar spine bone mineral density  32  in European and East Asian ancestries (Supp.
Safety effect score The annual reduction in fatalities following implementation of the different measures was estimated using criterion 4 (Table  1 ), giving a preliminary indication of the effectiveness of measures. The effects were estimated at a European Union (EU) level by a researcher from the core group, taking the annual numbers of railway suicides and trespassing accidents in EU countries as a starting point (2,854 suicides and 782 trespassing fatalities, using data from the European Railway Agency Database of Interoperability and Safety -ERADIS database, and the International Union of Railways -UIC safety database of incidents,  Silla et al. 2012,). This estimate considered the following factors:  the size of the target groupthis could be influenced by the location of the incidents, the context in which the measure is implemented (such as lighting conditions in daytime or night time) or the type of target groups of people;  the expected level of implementationthis was the assumed proportion of target incidents it was considered possible and realistic to cover by the measure, within a reasonable time period;  the expected percentage reduction in target incidentsthis was estimated and later discussed and adjusted by consensus of the wider group of experts (section 3.
Experimental Results The data set used in the experiments is the HSI captured by the ROSIS during a flight campaign over Pavia University, Northern Italy. The ROSIS owns 103 spectral bands and 610 × 340 pixels with the geometric resolution being 1. 3 m. In this paper, only a part of 250 × 250 pixels of this image is used. Hence, it is modeled as a 250 × 250 × 103 tensor in the experiments. The SD photon noise P and the SI thermal noise T are both taken into account. In order to reproduce different noise scenarios, the SNR ranged from 20 dB to 40 dB with a step of 5 dB. As the power of the SD photon noise and that of the SI thermal noise are of the same level, in this paper, only the case E[ X X T P 2 ] = E[ T 2 ] is taken into account. The random noise is generated with a variance depending on the value of the useful signal according to Equation (  8 ) and added into the signal X as Equation (3) to create the noisy HSI data R.
In Figure  6a , it can be seen that the trend of the mean noise variances in the lower bands is similar to that in Figure  3  thus implying that the noise in the lower bands (from 1 to 20) is not well whitened. On the other hand, in the bands from 20 to 100, the noise variances are relatively constant, the mean noise variance value is not 1. In Figure  6b , the noise whitening results by SDNW-MLR and SDNW-MWF are worse than that in Figure  6a. Hence, the whitening results in Figure  6  are strongly in favor of the proposed method SDNW-MWPT-MWF. The normal probability plot is usually used to visually ascertain whether or not a dataset is approximately normally distributed, which means that the values in the dataset have the same noise variance. Hence, we supply the normal probability plots of the noise before and after whitening in Figure  7.
A proportion of 10% of the reference data of each class is randomly selected as the training samples. The numbers of training and testing samples are shown in Table  1. The SVM classifier is employed to do the classification and its kernel function is RBF with γ = 1 and the penalty parameter C = 100. The second one, referred to as HYDICE HSI, was acquired by the HYperspectral Digital Imagery Collection Experiment (HYDICE) and has 148 spectral bands (from 435 to 2326 nm), 310 rows, and 220 columns. The scene is shown in Figure  13a. This HSI is modeled as a tensor R ∈ R 310×220×148 and its ground truth is shown in Figure  13b. According to the ground truth, there are seven land cover classes in HYDICE HSI: field, trees, road, shadow and three different targets. A proportion of 30% of the reference data of each class is randomly selected as the training samples.
In contrast, SDNW-MWF performs well in preserving the signal though it cannot remove the noise well from the images. However, the proposed SDNW-MWPT-MWF is able to obtain high SNR OUTPUT as well as the high OA, thus implying that it is able to remove noise well while still preserving the signal. These promising results encourage us to extend our experiments on other hyperspectral data such as Indian Pines and Salinas HSIs. In this study, we employed the HYNPE algorithm to estimate the noise parameters, and then filtered noise by the proposed method SDNW-MWPT-MWF. Nonetheless, SDNW-MWPT-MWF converts SD noise to additive white Gaussian noise by a pre-whitening procedure and then applied MWPT-MWF. Due to the parameter estimate errors, the whitened noise is only approximately white, therefore the performance of filters developed for the white noise might degrade.
Sequencing and Bioinformatics Analysis Five µl samples (∼50 ng) from each plant's DNA in triplicates were sent for sequencing to FASTERIS (Switzerland) using the MiSeq illumina technology, comprising fractions representative of light-, heavy-, and root-DNA in triplicates for each plant. The V3-V4 domain of the 16S rRNA gene was amplified with the primers 16S rRNA Fwd primer 3 -CCTACGGGNGGCWGCAG-5 and 16S rRNA Rev primer 3 -GACTACHVGGGTATCTAATCC-5. The tagged primers and barcodes were trimmed off by FASTERIS. We analyzed data using the FROGS software  (Escudie et al. , 2015). Corrected 16S rRNA gene sequences were clustered into operational taxonomic units (OTUs) using the swarm method  (Mahé et al. , 2014) , in which the distance aggregate was set at d = 3. Potential chimeric formations were removed using the VSEARCH tool.
Network Inference and Graph Display To study bacteria inhabiting the RAS, OTUs from the RAS found in more than 25% of the samples were selected ; the same procedure was performed for root-colonizing bacteria. Microbial networks were constructed using the R package phyloseq (version1. 19. 1). The pairwise co-occurrence of OTUs over the different samples was assessed using a Bray-Curtis distance  (Williams et al. , 2014). A proportion table was used instead of an abundance table, so that only the patterns of repartition would be compared and the absolute abundance of any one given OTU would not have an effect. A threshold of 0. 12 was used to select significant associations. Every node, and thus every OTU, was positioned on a graph using Cytoscape (version 3. 5. 1). The horizontal position of every node was calculated according to the preference of the bacteria toward exploitative or conservative plants as follows: x = %exploitative -%conservative %exploitative +%conservative where %exploitative and %conservative represent the proportion of reads detected in the exploitative and conservative samples, respectively.
For each plant and DNA fraction, the triplicates for OTUs abundance were regrouped. Then, the table of OTU abundance for each fraction from the studied plants and BS samples was treated with the phyloseq package in R, according to  McMurdie and Holmes (2013). The core microbiota were identified using QIIME  (Caporaso et al. , 2010)  and were determined by plotting OTU abundance in the core at 5% intervals (from 50 to 100% of samples). To remove sample heterogeneity, we performed rarefaction on the number of sequences. The approach of rarefaction is to randomly sample the same number of sequences from each sample, and use this data to compare the communities at a given level of sampling effort. We defined the core microbiota of each plant as the OTUs present in 100% of the samples. To determine core microbiota, all samples from each plant were compared across all compartments (light-, heavy-, and root-DNA fractions).
Compound 2 was isolated as a white solid and had a C 35 H 62 O 3 molecular formula determined by the [M + Na] + peak at m/z 553. 4592 from its (+)HRESIMS data. The analysis of 1 H-NMR and Jmod, along with HSQC data (Table  2 ), indicated the presence of two aromatic protons, 19 methylene groups (one of them oxygenated), seven methyl groups (six of them as singlets), four aromatic quaternary carbons, and one carbonyl carbon. The presence of two aromatic protons at δ H 6. 99 (2H, s, H-3 /H-5 ) pointed to the existence of a 1,2,4,6-tetrasubstituted phenyl moiety (Figure  4 ). Four spin systems could be revealed via analysis of COSY correlations, corresponding to the C-1 to C-2, C-1 to C-2 , C-3 to C-17 , and C-17 to C-18 fragments. The HMBC correlations from an exchangeable proton (δ H 5. 07, 1H, bs) to C-1 demonstrated that C-1 might be substituted by a hydroxyl group, and it was confirmed by the 13 C shift of C-1 at δ C 152.
Supplementation Assays The structure of Compound 1 was determined to be closely related to that of butylated hydroxyanisole (BHA) which is approved as an antioxidant ingredient added to polymers, foods, and food-related products  [14] [15] [16]. To respond to this issue, a supplementation of the culture of P. odorifer was carried out with standard BHA, put either in a culture flask (a kind of plastic vessel) or in an Erlenmeyer (a kind of glass vessel). Furthermore, the controls were based on the medium incubated in a culture flask and the culture of P. odorifer in an Erlenmeyer flask. The results from the LC-MS data are shown in Figure  5 , and they highlighted that both extracts from the cultures supplemented with BHA in the culture flask and Erlenmeyer flask provided [M -H] -ions at m/z 357 with a retention time of 35.
General Experimental Procedures One-dimensional (1D) and two-dimensional (2D) NMR spectroscopic data were recorded in MeOH-d 4 and CDCl 3 on a Bruker DMX 300 spectrometer (300 MHz ( 1 H) and 75 MHz ( 13 C), Bruker BioSpin, Billerica, MA, USA). NMR spectroscopic data were processed using the MestRenoVa version 10. 0 software (Mestrelab Research, S. L. , Santiago de Compostela, Spain). HRMS measurements for exact mass determination were performed with a Q-Extractive Focus at the Centre Regional de Mesure Physique de l'Ouest (CRMPO), Rennes, France. Analytical HPLC and semi-preparative HPLC were performed on a 5-µm Prevail C 18 column (250 mm × 4. 6 mm for the former, and 250 mm × 10 mm for the later), GRACE, Columbia, MD, USA.
Collection and Phylogenetic Analysis of PC-GYM-TO Strain The PC-GYM-TO strain was isolated from the crustose lichen, Rhizocarpon geographicum, collected in Brittany, France in February 2015. The strain was identified at Banyuls/mer Platform (L. Intertaglia) as Paenibacillus odorifer based on 16S ribosomal RNA (rRNA) gene sequence analysis (GenBank accession number AJ223990). A comparative BLAST similarities search of the 16S rRNA gene sequence gave a 98. 46% similarity to that of P. odorifer (Gene bank entry PODO_RS03805). After culture in GYM Streptomyces medium (containing 4 g of glucose (Sigma-Aldrich, St Louis, MO, USA), 4 g of yeast extract (Sigma-Aldrich, St Louis, MO, USA), 10 g of malt extract (Sigma-Aldrich, St Louis, MO, USA), 2 g of CaCO 3 (Merck KGaA, St Frankfurter, Darmstadt, Germany), and 12 g of agar (Sigma-Aldrich, St Louis, MO, USA) in 1 L), the bacterium was stored in a mixture of 47.
Molecular Models and Dynamic Simulations The structures of Compound 1 and Santonox were built using the Yasara program and were parameterized for the Yamber3 force field following the automated AutoSMILE procedure  [20]. Both geometries were optimized through the standardized minimization protocol of Yasara. Finally, to enhance the conformational space exploration available to the structures, molecular models were used as an initial point for molecular dynamics (MD) simulations. Each isomer was placed in an explicit chloroform solvent box and simulated under periodic boundary conditions at a constant temperature of 300 K. Structures were relaxed during a 2-ns MD simulation and trajectories were collected at 1-ps intervals. Analyses of the MD trajectories (root-mean-square deviation (RMSD) and clustering) was performed using Gromacs tools  [21].
DNA Damage Assays U2OS cells were cultivated in Dulbecco's Modified Eagle's medium DMEM supplemented with 10% fetal calf serum and antibiotics in an atmosphere of 5% CO 2 at 37 • C. The γH2AX staining was performed as previously described  [22]. Images were acquired on an ArrayScan VTI high-content screening reader with a 320 lens (Thermo Scientific, Villebon sur Yvette, France). The images were analyzed using the Cell Profiler software (http://www. cellprofiler. org, Broad Institute). For all analyses, raw data files were obtained with the total amount of Hoechst fluorescence and the total amount of γH2AX fluorescence. The number of γH2AX foci per nucleus is indicated for each condition in Table  4  with more than 3000 cells counted except for the 1 µM concentration because of the high cytotoxicity.
Acknowledgments: We sincerely thank  D. Delmail  for his help in the isolation of the strain P. odorifer from R. geographicum;  P. Jehan ,  F. Lambert , and  T. Delhaye  for the mass spectrometer measurements; L. Intertaglia from Banyuls/mer  Platform Bio2Mar  for the identification of the strain;  E. Poupon  ( Biocis, Paris Saclay ) and  J-P. Hurvois  for a critical discussion about biosynthesis;  P. Uriac  for a discussion about NMR data; and  J. Boustie  for his recommendations in the writing. The Vietnamese government is gratefully acknowledged for the PhD grant of  Thi-Bach-Le Nguyen.